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
SORCS1	114815	broad.mit.edu	37	10	108371774	108371774	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:108371774G>T	uc001kyl.2	-	c.2928C>A	c.(2926-2928)TTC>TTA	p.F976L	SORCS1_uc001kym.2_Missense_Mutation_p.F976L|SORCS1_uc009xxs.2_Missense_Mutation_p.F976L|SORCS1_uc001kyn.1_Missense_Mutation_p.F976L|SORCS1_uc001kyo.2_Missense_Mutation_p.F976L	NM_001013031	NP_001013049	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform b	976	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)	1		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)										0.173333	22.225671	29.787285	13	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108371774	108371774	15430	10	G	T	T	T	529	41	SORCS1	2	2
PNLIPRP1	5407	broad.mit.edu	37	10	118355764	118355764	+	Silent	SNP	T	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:118355764T>A	uc001lco.1	+	c.504T>A	c.(502-504)ATT>ATA	p.I168I	PNLIPRP1_uc001lcp.2_Silent_p.I168I|PNLIPRP1_uc009xys.1_Non-coding_Transcript	NM_006229	NP_006220	P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1 precursor	168					lipid metabolic process		calcium ion binding|triglyceride lipase activity			ovary(1)|breast(1)	2				all cancers(201;0.0161)										0.438878	655.95458	657.592678	219	280	KEEP	---	---	---	---	capture		Silent	SNP	118355764	118355764	12576	10	T	A	A	A	809	63	PNLIPRP1	3	3
KNDC1	85442	broad.mit.edu	37	10	135011939	135011939	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:135011939G>T	uc001llz.1	+	c.2005G>T	c.(2005-2007)GCG>TCG	p.A669S	KNDC1_uc001lma.1_Missense_Mutation_p.A604S|KNDC1_uc001lmb.1_Missense_Mutation_p.A81S	NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)	669					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					ovary(1)	1		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)										0.304348	17.414395	18.201141	7	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135011939	135011939	8740	10	G	T	T	T	442	34	KNDC1	2	2
FAM171A1	221061	broad.mit.edu	37	10	15326063	15326063	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:15326063G>T	uc001iob.2	-	c.139C>A	c.(139-141)CAG>AAG	p.Q47K		NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061 precursor	47	Extracellular (Potential).					integral to membrane				ovary(2)|breast(1)	3														0.214286	53.79686	62.200474	24	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15326063	15326063	5695	10	G	T	T	T	611	47	FAM171A1	2	2
ITGA8	8516	broad.mit.edu	37	10	15573137	15573137	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:15573137G>A	uc001ioc.1	-	c.2894C>T	c.(2893-2895)CCC>CTC	p.P965L	ITGA8_uc010qcb.1_Missense_Mutation_p.P950L	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor	965	Extracellular (Potential).				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6														0.268657	104.966673	111.422662	36	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15573137	15573137	8186	10	G	A	A	A	559	43	ITGA8	2	2
GPR158	57512	broad.mit.edu	37	10	25886829	25886829	+	Silent	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:25886829T>C	uc001isj.2	+	c.2274T>C	c.(2272-2274)ATT>ATC	p.I758I	GPR158_uc001isk.2_Silent_p.I133I	NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	758	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)	7														0.184211	73.251644	87.436751	28	124	KEEP	---	---	---	---	capture		Silent	SNP	25886829	25886829	6938	10	T	C	C	C	783	61	GPR158	4	4
ZNF248	57209	broad.mit.edu	37	10	38120804	38120804	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:38120804T>C	uc001izd.1	-	c.1479A>G	c.(1477-1479)ATA>ATG	p.I493M	ZNF248_uc009xmc.2_Intron|ZNF248_uc001izb.2_Intron|ZNF248_uc001izc.2_Intron|ZNF248_uc010qeu.1_Missense_Mutation_p.I493M	NM_021045	NP_066383	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	493	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.27	86.088585	90.855492	27	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38120804	38120804	18384	10	T	C	C	C	628	49	ZNF248	4	4
SLC18A3	6572	broad.mit.edu	37	10	50818982	50818983	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:50818982_50818983GG>TT	uc001jhw.2	+	c.196_197GG>TT	c.(196-198)GGG>TTG	p.G66L	CHAT_uc001jhv.1_Intron|CHAT_uc001jhx.1_5'Flank|CHAT_uc001jhy.1_5'Flank	NM_003055	NP_003046	Q16572	VACHT_HUMAN	vesicular acetylcholine transporter	66	Lumenal, vesicle (Potential).				neurotransmitter secretion	clathrin sculpted acetylcholine transport vesicle membrane|integral to plasma membrane|membrane fraction	acetylcholine transmembrane transporter activity			ovary(1)	1														0.217391	13.364688	15.05662	5	18	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	50818982	50818983	14923	10	GG	TT	TT	TT	507	39	SLC18A3	1	1
DDX50	79009	broad.mit.edu	37	10	70666761	70666761	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:70666761G>T	uc001jou.2	+	c.382G>T	c.(382-384)GAG>TAG	p.E128*	DDX50_uc001jot.2_Nonsense_Mutation_p.E128*|DDX50_uc010qjc.1_Nonsense_Mutation_p.E128*	NM_024045	NP_076950	Q9BQ39	DDX50_HUMAN	nucleolar protein GU2	128						nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1														0.20202	41.03935	49.211133	20	79	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	70666761	70666761	4539	10	G	T	T	T	533	41	DDX50	5	2
PRF1	5551	broad.mit.edu	37	10	72360447	72360447	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:72360447C>A	uc009xqg.2	-	c.212G>T	c.(211-213)GGC>GTC	p.G71V	PRF1_uc001jrf.3_Missense_Mutation_p.G71V	NM_001083116	NP_001076585	P14222	PERF_HUMAN	perforin 1 precursor	71	MACPF.				apoptosis|cellular defense response|cytolysis|defense response to tumor cell|defense response to virus|immune response to tumor cell|protein homooligomerization	cytolytic granule|endosome lumen|extracellular region|integral to membrane|plasma membrane	calcium ion binding|protein binding|wide pore channel activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3														0.337349	75.2083	77.133943	28	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72360447	72360447	12921	10	C	A	A	A	338	26	PRF1	2	2
CDHR1	92211	broad.mit.edu	37	10	85961589	85961589	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:85961589C>A	uc001kcv.2	+	c.552C>A	c.(550-552)GAC>GAA	p.D184E	CDHR1_uc001kcw.2_Missense_Mutation_p.D184E|CDHR1_uc009xst.2_5'UTR	NM_033100	NP_149091	Q96JP9	CDHR1_HUMAN	protocadherin 21 precursor	184	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion		calcium ion binding|receptor activity			ovary(1)	1														0.267857	39.998851	42.724502	15	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85961589	85961589	3247	10	C	A	A	A	233	18	CDHR1	2	2
BTAF1	9044	broad.mit.edu	37	10	93695424	93695424	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:93695424C>T	uc001khr.2	+	c.25C>T	c.(25-27)CTT>TTT	p.L9F	BTAF1_uc009xua.1_Non-coding_Transcript	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription	9					negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0846)												0.254545	39.722307	42.729945	14	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93695424	93695424	1568	10	C	T	T	T	312	24	BTAF1	2	2
MUC2	4583	broad.mit.edu	37	11	1080962	1080962	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1080962T>A	uc001lsx.1	+	c.1346T>A	c.(1345-1347)CTG>CAG	p.L449Q		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	449	VWFD 2.					inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)									0.430233	113.163881	113.528363	37	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1080962	1080962	10369	11	T	A	A	A	715	55	MUC2	3	3
ROBO3	64221	broad.mit.edu	37	11	124744018	124744018	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:124744018A>G	uc001qbc.2	+	c.1837A>G	c.(1837-1839)ACA>GCA	p.T613A	ROBO3_uc010saq.1_5'Flank|ROBO3_uc001qbd.2_5'Flank|ROBO3_uc010sar.1_5'Flank|ROBO3_uc001qbe.2_5'Flank	NM_022370	NP_071765	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3	613	Fibronectin type-III 1.|Extracellular (Potential).				axon midline choice point recognition	integral to membrane	receptor activity			breast(1)|central_nervous_system(1)	2	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)										0.189922	125.056825	148.226576	49	209	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124744018	124744018	13994	11	A	G	G	G	130	10	ROBO3	4	4
KIF18A	81930	broad.mit.edu	37	11	28106288	28106288	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:28106288C>A	uc001msc.2	-	c.965G>T	c.(964-966)GGA>GTA	p.G322V		NM_031217	NP_112494	Q8NI77	KI18A_HUMAN	kinesin family member 18A	322					blood coagulation|microtubule depolymerization|microtubule-based movement|mitotic metaphase plate congression|mitotic prometaphase|protein transport	caveola|cytosol|kinetochore microtubule|microtubule organizing center|nucleus|ruffle	actin binding|ATP binding|microtubule plus-end binding|plus-end-directed microtubule motor activity|tubulin-dependent ATPase activity|ubiquitin binding			ovary(2)	2														0.202532	30.548719	37.049365	16	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28106288	28106288	8591	11	C	A	A	A	390	30	KIF18A	2	2
ELP4	26610	broad.mit.edu	37	11	31669325	31669325	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:31669325G>T	uc001mtb.2	+	c.964G>T	c.(964-966)GAT>TAT	p.D322Y	ELP4_uc001mta.1_Non-coding_Transcript|ELP4_uc001mtc.2_Missense_Mutation_p.D322Y|ELP4_uc010rdz.1_Missense_Mutation_p.D323Y	NM_019040	NP_061913	Q96EB1	ELP4_HUMAN	elongation protein 4 homolog	322					histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			ovary(1)	1	Lung SC(675;0.225)													0.233333	32.915713	36.823892	14	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31669325	31669325	5274	11	G	T	T	T	429	33	ELP4	2	2
CSTF3	1479	broad.mit.edu	37	11	33112197	33112197	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:33112197G>T	uc001muh.2	-	c.1522C>A	c.(1522-1524)CGG>AGG	p.R508R	TCP11L1_uc001muf.1_Intron	NM_001326	NP_001317	Q12996	CSTF3_HUMAN	cleavage stimulation factor subunit 3 isoform 1	508					mRNA cleavage|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	protein binding|RNA binding				0														0.161765	23.380686	30.7798	11	57	KEEP	---	---	---	---	capture		Silent	SNP	33112197	33112197	4127	11	G	T	T	T	519	40	CSTF3	1	1
PGAP2	27315	broad.mit.edu	37	11	3845193	3845193	+	Silent	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:3845193C>T	uc010qxw.1	+	c.600C>T	c.(598-600)GGC>GGT	p.G200G	PGAP2_uc001lyl.2_Silent_p.G100G|PGAP2_uc010qxx.1_Missense_Mutation_p.P124S|PGAP2_uc001lyp.3_Intron|PGAP2_uc010qxy.1_Silent_p.G139G|PGAP2_uc010qxz.1_Silent_p.G139G|PGAP2_uc001lyn.3_Missense_Mutation_p.P36S|PGAP2_uc010qya.1_Non-coding_Transcript|PGAP2_uc001lyr.2_Silent_p.G82G|PGAP2_uc010qyb.1_Missense_Mutation_p.P86S|PGAP2_uc001lys.2_Silent_p.G143G|PGAP2_uc001lyt.2_5'UTR	NM_014489	NP_055304	Q9UHJ9	PGAP2_HUMAN	FGF receptor activating protein 1 isoform 1	143					GPI anchor biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein transporter activity				0														0.116438	15.448045	36.659865	17	129	KEEP	---	---	---	---	capture		Silent	SNP	3845193	3845193	12201	11	C	T	T	T	338	26	PGAP2	2	2
OR51D1	390038	broad.mit.edu	37	11	4661687	4661687	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4661687G>T	uc010qyk.1	+	c.667G>T	c.(667-669)GAC>TAC	p.D223Y		NM_001004751	NP_001004751	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D,	223	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.204082	57.557667	69.517412	30	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4661687	4661687	11503	11	G	T	T	T	533	41	OR51D1	2	2
OR5I1	10798	broad.mit.edu	37	11	55703060	55703060	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55703060C>T	uc010ris.1	-	c.817G>A	c.(817-819)GAT>AAT	p.D273N		NM_006637	NP_006628	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I,	273	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.217391	11.361508	13.056081	5	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55703060	55703060	11574	11	C	T	T	T	377	29	OR5I1	2	2
OR8J3	81168	broad.mit.edu	37	11	55904471	55904471	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55904471C>T	uc010riz.1	-	c.724G>A	c.(724-726)GCT>ACT	p.A242T		NM_001004064	NP_001004064	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J,	242	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(21;0.00693)													0.21875	31.714134	36.380642	14	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55904471	55904471	11653	11	C	T	T	T	351	27	OR8J3	1	1
MS4A2	2206	broad.mit.edu	37	11	59857910	59857910	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59857910T>G	uc001nop.2	+	c.288T>G	c.(286-288)TTT>TTG	p.F96L	MS4A2_uc009ymu.2_Missense_Mutation_p.F96L	NM_000139	NP_000130	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member	96	Extracellular (Potential).				cell proliferation|humoral immune response	integral to plasma membrane	calcium channel activity			ovary(1)	1		all_epithelial(135;0.245)			Omalizumab(DB00043)									0.267327	76.191267	81.131679	27	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59857910	59857910	10253	11	T	G	G	G	790	61	MS4A2	4	4
STIP1	10963	broad.mit.edu	37	11	63964764	63964764	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:63964764G>A	uc001nyk.1	+	c.694G>A	c.(694-696)GGG>AGG	p.G232R	STIP1_uc010rnb.1_Missense_Mutation_p.G208R	NM_006819	NP_006810	P31948	STIP1_HUMAN	stress-induced-phosphoprotein 1	232	Bipartite nuclear localization signal (Potential).|TPR 4.				axon guidance|response to stress	Golgi apparatus|nucleus				ovary(2)|liver(1)	3														0.283333	48.148721	50.678898	17	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63964764	63964764	15805	11	G	A	A	A	559	43	STIP1	2	2
NRXN2	9379	broad.mit.edu	37	11	64402833	64402833	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64402833C>A	uc001oar.2	-	c.3495G>T	c.(3493-3495)CTG>CTT	p.L1165L	NRXN2_uc001oas.2_Silent_p.L1125L|NRXN2_uc001oap.2_Silent_p.L119L|NRXN2_uc001oaq.2_Silent_p.L832L	NM_015080	NP_055895	P58401	NRX2B_HUMAN	neurexin 2 isoform alpha-1 precursor	119	Extracellular (Potential).|Laminin G-like.				cell adhesion	integral to membrane				ovary(2)|pancreas(1)|kidney(1)|central_nervous_system(1)|skin(1)	6														0.268657	42.210213	45.455059	18	49	KEEP	---	---	---	---	capture		Silent	SNP	64402833	64402833	11071	11	C	A	A	A	262	21	NRXN2	2	2
ZNHIT2	741	broad.mit.edu	37	11	64884413	64884413	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64884413G>A	uc001ocw.2	-	c.713C>T	c.(712-714)TCT>TTT	p.S238F		NM_014205	NP_055020	Q9UHR6	ZNHI2_HUMAN	zinc finger, HIT domain containing 2	238							metal ion binding			breast(1)	1														0.24	15.837007	17.379762	6	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64884413	64884413	18811	11	G	A	A	A	429	33	ZNHIT2	2	2
ARFIP2	23647	broad.mit.edu	37	11	6500372	6500372	+	Nonsense_Mutation	SNP	T	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6500372T>A	uc010ran.1	-	c.412A>T	c.(412-414)AAG>TAG	p.K138*	ARFIP2_uc001mdk.2_Nonsense_Mutation_p.K105*|ARFIP2_uc001mdl.2_Nonsense_Mutation_p.K105*|ARFIP2_uc010ral.1_Nonsense_Mutation_p.K67*|ARFIP2_uc010ram.1_Intron|ARFIP2_uc001mdm.2_Non-coding_Transcript|ARFIP2_uc009yfe.1_3'UTR|FXC1_uc001mdn.3_5'Flank|FXC1_uc001mdo.3_5'Flank	NM_012402	NP_036534	P53365	ARFP2_HUMAN	ADP-ribosylation factor interacting protein 2	105					actin cytoskeleton organization|cellular component movement|lamellipodium assembly|ruffle organization|small GTPase mediated signal transduction	cell cortex|plasma membrane|ruffle	GTP binding|GTP-dependent protein binding|Rac GTPase binding				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;3.41e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		Melanoma(119;796 1674 9049 20480 24794)								0.2	45.559332	55.188684	23	92	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	6500372	6500372	866	11	T	A	A	A	793	61	ARFIP2	5	3
GAL	51083	broad.mit.edu	37	11	68455487	68455487	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:68455487G>A	uc001oob.2	+	c.142G>A	c.(142-144)GTT>ATT	p.V48I		NM_015973	NP_057057	P22466	GALA_HUMAN	galanin preproprotein	48					growth hormone secretion|insulin secretion|neuropeptide signaling pathway|smooth muscle contraction	extracellular region	neuropeptide hormone activity				0	Esophageal squamous(3;7.33e-10)	Melanoma(852;0.0749)	LUAD - Lung adenocarcinoma(13;0.0514)	Kidney(183;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.000152)|LUSC - Lung squamous cell carcinoma(976;0.00154)										0.265625	43.649264	46.824028	17	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68455487	68455487	6460	11	G	A	A	A	520	40	GAL	1	1
PPFIA1	8500	broad.mit.edu	37	11	70221071	70221071	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:70221071A>C	uc001opo.2	+	c.3187A>C	c.(3187-3189)ATT>CTT	p.I1063L	PPFIA1_uc001opn.1_Missense_Mutation_p.I1063L|PPFIA1_uc001opp.2_Non-coding_Transcript|PPFIA1_uc001opr.2_Missense_Mutation_p.I202L|PPFIA1_uc001ops.2_Missense_Mutation_p.I102L	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	PTPRF interacting protein alpha 1 isoform b	1063	SAM 3.				cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			lung(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)											0.16129	51.72075	65.252233	20	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70221071	70221071	12739	11	A	C	C	C	52	4	PPFIA1	4	4
CLPB	81570	broad.mit.edu	37	11	72028186	72028186	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:72028186T>C	uc001osj.2	-	c.1042A>G	c.(1042-1044)ATT>GTT	p.I348V	CLPB_uc010rqx.1_Missense_Mutation_p.I303V|CLPB_uc010rqy.1_Missense_Mutation_p.I289V|CLPB_uc001osk.2_Missense_Mutation_p.I318V|CLPB_uc009ytg.2_Non-coding_Transcript|CLPB_uc010rqz.1_Missense_Mutation_p.I147V	NM_030813	NP_110440	Q9H078	CLPB_HUMAN	caseinolytic peptidase B	348					cellular response to heat		ATP binding|nucleoside-triphosphatase activity|protein binding			pancreas(1)	1														0.277778	151.643953	160.439527	55	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72028186	72028186	3689	11	T	C	C	C	663	51	CLPB	4	4
RIC3	79608	broad.mit.edu	37	11	8161742	8161742	+	Splice_Site_SNP	SNP	T	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:8161742T>A	uc010rbm.1	-	c.125_splice	c.e2-1	p.G42_splice	RIC3_uc001mgb.2_5'Flank|RIC3_uc001mgc.2_Splice_Site_SNP_p.G42_splice|RIC3_uc001mge.2_Intron|RIC3_uc010rbl.1_Splice_Site_SNP|RIC3_uc001mgd.2_Splice_Site_SNP_p.G42_splice|RIC3_uc009yfm.2_Splice_Site_SNP_p.G42_splice|RIC3_uc009yfn.2_Intron|RIC3_uc001mgf.3_Intron	NM_024557	NP_078833			resistance to inhibitors of cholinesterase 3							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				large_intestine(1)|ovary(1)|pancreas(1)	3				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)										0.142857	10.722775	15.883789	6	36	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	8161742	8161742	13829	11	T	A	A	A	715	55	RIC3	5	3
SVOP	55530	broad.mit.edu	37	12	109332689	109332689	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:109332689G>T	uc010sxh.1	-	c.811C>A	c.(811-813)CAG>AAG	p.Q271K		NM_018711	NP_061181	Q8N4V2	SVOP_HUMAN	SV2 related protein	271	Cytoplasmic (Potential).					cell junction|integral to membrane|synaptic vesicle membrane	ion transmembrane transporter activity				0														0.479401	383.660207	383.759692	128	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109332689	109332689	15943	12	G	T	T	T	611	47	SVOP	2	2
C12orf51	283450	broad.mit.edu	37	12	112654685	112654685	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:112654685C>A	uc009zwc.2	-	c.6011G>T	c.(6010-6012)GGA>GTA	p.G2004V	C12orf51_uc001ttr.1_Missense_Mutation_p.G179V	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)	1														0.187919	52.202734	65.799166	28	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112654685	112654685	1740	12	C	A	A	A	390	30	C12orf51	2	2
GCN1L1	10985	broad.mit.edu	37	12	120613618	120613618	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:120613618G>C	uc001txo.2	-	c.973C>G	c.(973-975)CTG>GTG	p.L325V		NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis	325	HEAT 2.				regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(3)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.403846	62.953346	63.376431	21	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120613618	120613618	6565	12	G	C	C	C	451	35	GCN1L1	3	3
ZNF664	144348	broad.mit.edu	37	12	124496938	124496938	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:124496938G>T	uc001ufz.2	+	c.247G>T	c.(247-249)GTG>TTG	p.V83L	ZNF664_uc001uga.2_Missense_Mutation_p.V83L|ZNF664_uc001ugb.2_Missense_Mutation_p.V83L	NM_152437	NP_689650	Q8N3J9	ZN664_HUMAN	zinc finger protein 664	83					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.000239)|OV - Ovarian serous cystadenocarcinoma(86;0.000247)|all cancers(50;0.00155)|BRCA - Breast invasive adenocarcinoma(302;0.249)										0.443038	216.724765	217.172236	70	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124496938	124496938	18667	12	G	T	T	T	468	36	ZNF664	2	2
TMEM132B	114795	broad.mit.edu	37	12	125834059	125834059	+	Silent	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:125834059C>T	uc001uhe.1	+	c.114C>T	c.(112-114)CTC>CTT	p.L38L		NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	38	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)										0.145455	64.959203	98.174844	40	235	KEEP	---	---	---	---	capture		Silent	SNP	125834059	125834059	16577	12	C	T	T	T	379	30	TMEM132B	2	2
TMEM132D	121256	broad.mit.edu	37	12	129559341	129559341	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:129559341G>T	uc009zyl.1	-	c.2379C>A	c.(2377-2379)ATC>ATA	p.I793I	TMEM132D_uc001uia.2_Silent_p.I331I	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	793	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)	12	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)										0.394958	260.59869	262.896056	94	144	KEEP	---	---	---	---	capture		Silent	SNP	129559341	129559341	16579	12	G	T	T	T	577	45	TMEM132D	2	2
GPR133	283383	broad.mit.edu	37	12	131590398	131590398	+	Silent	SNP	C	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:131590398C>G	uc010tbm.1	+	c.1971C>G	c.(1969-1971)CTC>CTG	p.L657L	GPR133_uc001uit.3_Silent_p.L625L|GPR133_uc009zyo.2_Intron|GPR133_uc001uiv.1_Silent_p.L144L|GPR133_uc009zyp.2_Non-coding_Transcript	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor	625	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)										0.333333	28.097234	28.685034	8	16	KEEP	---	---	---	---	capture		Silent	SNP	131590398	131590398	6917	12	C	G	G	G	392	31	GPR133	3	3
GRIN2B	2904	broad.mit.edu	37	12	13715944	13715944	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:13715944T>G	uc001rbt.2	-	c.4228A>C	c.(4228-4230)ACG>CCG	p.T1410P		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	1410	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|lung(2)|skin(1)	10					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)					371				0.435484	96.522129	96.745938	27	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13715944	13715944	7059	12	T	G	G	G	767	59	GRIN2B	4	4
SLCO1A2	6579	broad.mit.edu	37	12	21457403	21457403	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:21457403T>C	uc001rer.2	-	c.547A>G	c.(547-549)ATA>GTA	p.I183V	SLCO1A2_uc001res.2_Missense_Mutation_p.I183V|SLCO1A2_uc010siq.1_Missense_Mutation_p.I51V|SLCO1A2_uc010sio.1_Missense_Mutation_p.I51V|SLCO1A2_uc010sip.1_Missense_Mutation_p.I51V|SLCO1A2_uc001ret.2_Missense_Mutation_p.I181V|SLCO1A2_uc001reu.2_Missense_Mutation_p.I163V	NM_021094	NP_066580	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A	183	Helical; Name=4; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|ovary(1)|pancreas(1)	3														0.434211	119.170163	119.455786	33	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21457403	21457403	15219	12	T	C	C	C	637	49	SLCO1A2	4	4
KRAS	3845	broad.mit.edu	37	12	25398285	25398285	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:25398285C>A	uc001rgp.1	-	c.34G>T	c.(34-36)GGT>TGT	p.G12C	KRAS_uc001rgq.1_Missense_Mutation_p.G12C|KRAS_uc001rgr.2_Non-coding_Transcript	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	12	GTP.		G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation).|G -> R (in lung cancer and bladder cancer; somatic mutation).|G -> S (in lung carcinoma and GASC; somatic mutation).|G -> A (in a colorectal cancer sample; somatic mutation).|G -> C (in lung carcinoma; somatic mutation).|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.G12C(2374)|p.G12S(1078)|p.G12R(674)|p.G12?(50)|p.G12F(33)|p.G12D(15)|p.G12N(6)|p.G12V(6)|p.G12L(5)|p.G12I(3)|p.G12W(3)|p.G12A(2)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12_G13insG(1)		large_intestine(11742)|pancreas(3256)|lung(2694)|biliary_tract(514)|ovary(437)|endometrium(339)|haematopoietic_and_lymphoid_tissue(303)|stomach(179)|thyroid(145)|prostate(85)|soft_tissue(75)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|breast(27)|liver(21)|testis(17)|oesophagus(15)|central_nervous_system(8)|peritoneum(5)|kidney(5)|salivary_gland(5)|thymus(5)|eye(4)|gastrointestinal_tract_(site_indeterminate)(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	20148	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12C(CALU1_LUNG)|G12C(NCIH2030_LUNG)|G12C(LU99_LUNG)|G12C(NCIH1792_LUNG)|G12R(KP2_PANCREAS)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(NCIH2122_LUNG)|G12C(NCIH358_LUNG)|G12R(PSN1_PANCREAS)|G12C(KYSE410_OESOPHAGUS)|G12S(A549_LUNG)|G12R(HUPT3_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12C(HCC44_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(SW1463_LARGE_INTESTINE)|G12C(NCIH23_LUNG)|G12C(LU65_LUNG)|G12C(NCIH1373_LUNG)|G12C(MIAPACA2_PANCREAS)|G12R(HS274T_BREAST)|G12S(LS123_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(OV56_OVARY)|G12C(IALM_LUNG)	119	p.G12R(PSN1-Tumor)|p.G12C(NCIH1373-Tumor)|p.G12C(NCIH1792-Tumor)|p.G12S(KMS20-Tumor)|p.G12C(HCC44-Tumor)|p.G12C(HCC1171-Tumor)|p.G12C(SW837-Tumor)|p.G12C(LU65-Tumor)|p.G12R(HUPT3-Tumor)|p.G12S(A549-Tumor)|p.G12C(NCIH2122-Tumor)|p.G12R(KP2-Tumor)|p.G12C(OV56-Tumor)|p.G12C(IALM-Tumor)|p.G12C(SW1463-Tumor)|p.G12C(SW1573-Tumor)|p.G12R(NCIH1339-Tumor)|p.G12C(NCIH23-Tumor)|p.G12C(MIAPACA2-Tumor)|p.G12C(CALU1-Tumor)|p.G12C(NCIH2030-Tumor)|p.G12S(LS123-Tumor)|p.G12C(KYSE410-Tumor)|p.G12C(UMUC3-Tumor)|p.G12C(NCIH2291-Tumor)|p.G12R(TCCPAN2-Tumor)|p.G12C(KHM1B-Tumor)|p.G12C(LU99-Tumor)|p.G12C(NCIH358-Tumor)|p.G12C(NCIH1385-Tumor)|p.G12R(CAL62-Tumor)	262	TSP Lung(1;<1E-8)|Multiple Myeloma(2;<1E-6)			0.333333	11.79876	12.092589	4	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25398285	25398285	8753	12	C	A	A	A	273	21	KRAS	2	2
ANO6	196527	broad.mit.edu	37	12	45795743	45795743	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:45795743A>G	uc010slf.1	+	c.1615A>G	c.(1615-1617)ATA>GTA	p.I539V	ANO6_uc001roo.2_Missense_Mutation_p.I518V|ANO6_uc010sld.1_Missense_Mutation_p.I518V|ANO6_uc010sle.1_Missense_Mutation_p.I518V|ANO6_uc010slg.1_Missense_Mutation_p.I500V	NM_001142678	NP_001136150	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform b	518	Helical; (Potential).				activation of blood coagulation via clotting cascade	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2														0.130719	41.804728	62.081982	20	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45795743	45795743	709	12	A	G	G	G	208	16	ANO6	4	4
SP7	121340	broad.mit.edu	37	12	53722173	53722173	+	Silent	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:53722173C>T	uc001sct.2	-	c.1053G>A	c.(1051-1053)GAG>GAA	p.E351E	SP7_uc001scu.2_Silent_p.E333E|SP7_uc001scv.2_Silent_p.E351E	NM_152860	NP_690599	Q8TDD2	SP7_HUMAN	osterix	351					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0												OREG0021867	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.4	132.140829	133.141615	46	69	KEEP	---	---	---	---	capture		Silent	SNP	53722173	53722173	15469	12	C	T	T	T	415	32	SP7	2	2
MAP3K12	7786	broad.mit.edu	37	12	53875772	53875772	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:53875772C>T	uc001sdn.1	-	c.2533G>A	c.(2533-2535)GAA>AAA	p.E845K	MAP3K12_uc001sdm.1_Missense_Mutation_p.E812K	NM_006301	NP_006292	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase	812					histone phosphorylation|JNK cascade|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation	cytosol|membrane fraction|plasma membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			lung(2)|ovary(1)|breast(1)	4										178		OREG0021873	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.383784	193.231791	195.437557	71	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53875772	53875772	9629	12	C	T	T	T	377	29	MAP3K12	2	2
MAP3K12	7786	broad.mit.edu	37	12	53876414	53876414	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:53876414G>T	uc001sdn.1	-	c.2173C>A	c.(2173-2175)CGG>AGG	p.R725R	MAP3K12_uc001sdm.1_Silent_p.R692R	NM_006301	NP_006292	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase	692					histone phosphorylation|JNK cascade|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation	cytosol|membrane fraction|plasma membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			lung(2)|ovary(1)|breast(1)	4										178				0.388715	368.300756	371.734266	124	195	KEEP	---	---	---	---	capture		Silent	SNP	53876414	53876414	9629	12	G	T	T	T	506	39	MAP3K12	1	1
PPM1H	57460	broad.mit.edu	37	12	63042381	63042381	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:63042381G>T	uc001srk.3	-	c.1433C>A	c.(1432-1434)GCC>GAC	p.A478D		NM_020700	NP_065751	Q9ULR3	PPM1H_HUMAN	protein phosphatase 1H (PP2C domain containing)	478	PP2C-like.						phosphoprotein phosphatase activity			ovary(1)	1			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)										0.2125	34.936372	40.973859	17	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63042381	63042381	12776	12	G	T	T	T	546	42	PPM1H	2	2
GRIP1	23426	broad.mit.edu	37	12	66786504	66786504	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:66786504T>G	uc001stk.2	-	c.2066A>C	c.(2065-2067)CAG>CCG	p.Q689P	GRIP1_uc010sta.1_Missense_Mutation_p.Q633P|GRIP1_uc001stj.2_Missense_Mutation_p.Q471P|GRIP1_uc001stl.1_Missense_Mutation_p.Q581P|GRIP1_uc001stm.2_Missense_Mutation_p.Q689P	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	741	PDZ 6.				androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)										0.142132	54.181187	78.491533	28	169	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66786504	66786504	7066	12	T	G	G	G	715	55	GRIP1	4	4
LGR5	8549	broad.mit.edu	37	12	71978097	71978097	+	Silent	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:71978097C>T	uc001swl.2	+	c.2307C>T	c.(2305-2307)GCC>GCT	p.A769A	LGR5_uc001swm.2_Silent_p.A745A|LGR5_uc001swn.1_Intron	NM_003667	NP_003658	O75473	LGR5_HUMAN	leucine-rich repeat-containing G protein-coupled	769	Helical; Name=6; (Potential).					integral to plasma membrane	protein-hormone receptor activity			ovary(1)|pancreas(1)	2										516				0.421053	330.956822	332.300766	104	143	KEEP	---	---	---	---	capture		Silent	SNP	71978097	71978097	9083	12	C	T	T	T	275	22	LGR5	2	2
USP44	84101	broad.mit.edu	37	12	95927916	95927916	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:95927916C>A	uc001teg.2	-	c.117G>T	c.(115-117)TGG>TGT	p.W39C	USP44_uc001teh.2_Missense_Mutation_p.W39C|USP44_uc009zte.2_Missense_Mutation_p.W36C	NM_001042403	NP_001035862	Q9H0E7	UBP44_HUMAN	ubiquitin thiolesterase 44	39	UBP-type.				anaphase|cell division|mitosis|negative regulation of mitotic anaphase-promoting complex activity|protein deubiquitination|regulation of spindle checkpoint|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1												OREG0022039	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.183007	57.205095	71.642554	28	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95927916	95927916	17639	12	C	A	A	A	286	22	USP44	2	2
C13orf26	122046	broad.mit.edu	37	13	31513891	31513891	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:31513891C>T	uc001uti.2	+	c.122C>T	c.(121-123)ACA>ATA	p.T41I		NM_152325	NP_689538	Q8N6G2	CM026_HUMAN	hypothetical protein LOC122046	41										ovary(2)	2		Lung SC(185;0.0281)		all cancers(112;0.0176)|Epithelial(112;0.0768)|OV - Ovarian serous cystadenocarcinoma(117;0.0852)										0.191489	16.242388	20.429105	9	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31513891	31513891	1769	13	C	T	T	T	221	17	C13orf26	2	2
PDS5B	23047	broad.mit.edu	37	13	33344830	33344830	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:33344830A>T	uc010abf.2	+	c.4103A>T	c.(4102-4104)CAG>CTG	p.Q1368L	PDS5B_uc010abg.2_Non-coding_Transcript	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog	1368					cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)										0.166667	7.384119	9.913333	4	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33344830	33344830	12113	13	A	T	T	T	91	7	PDS5B	3	3
FREM2	341640	broad.mit.edu	37	13	39261752	39261752	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:39261752C>T	uc001uwv.2	+	c.271C>T	c.(271-273)CCC>TCC	p.P91S		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	91	Extracellular (Potential).				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)	10		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)										0.484848	42.914286	42.919282	16	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39261752	39261752	6292	13	C	T	T	T	390	30	FREM2	2	2
MYCBP2	23077	broad.mit.edu	37	13	77656020	77656020	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:77656020T>G	uc001vkf.2	-	c.11031A>C	c.(11029-11031)GAA>GAC	p.E3677D	MYCBP2_uc010aev.2_Missense_Mutation_p.E3081D|MYCBP2_uc001vke.2_Missense_Mutation_p.E297D	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	3677					regulation of mitotic metaphase/anaphase transition|regulation of transcription, DNA-dependent|transcription, DNA-dependent	anaphase-promoting complex	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|lung(2)|pancreas(1)	11		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)										0.280899	72.441384	76.278943	25	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77656020	77656020	10413	13	T	G	G	G	725	56	MYCBP2	4	4
DIO3	1735	broad.mit.edu	37	14	102028496	102028497	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:102028496_102028497CC>AA	uc010txq.1	+	c.585_586CC>AA	c.(583-588)AGCCTG>AGAATG	p.195_196SL>RM	DIO3OS_uc001ykd.1_5'Flank|MIR1247_hsa-mir-1247|MI0006382_5'Flank	NM_001362	NP_001353	P55073	IOD3_HUMAN	deiodinase, iodothyronine, type III	195_196	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|oxidation-reduction process	endosome membrane|integral to membrane|plasma membrane	thyroxine 5'-deiodinase activity|thyroxine 5-deiodinase activity			ovary(1)|central_nervous_system(1)	2		all_neural(303;0.185)												0.187215	85.543276	105.61252	41	178	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	102028496	102028497	4705	14	CC	AA	AA	AA	337	26	DIO3	2	2
OR4Q3	441669	broad.mit.edu	37	14	20216428	20216428	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20216428C>A	uc010tkt.1	+	c.842C>A	c.(841-843)CCT>CAT	p.P281H		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	281	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)										0.098113	14.95158	57.791976	26	239	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20216428	20216428	11491	14	C	A	A	A	312	24	OR4Q3	2	2
OR4N5	390437	broad.mit.edu	37	14	20612554	20612554	+	Silent	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20612554C>T	uc010tla.1	+	c.660C>T	c.(658-660)GTC>GTT	p.V220V		NM_001004724	NP_001004724	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N,	220	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)										0.23913	76.909147	85.48295	33	105	KEEP	---	---	---	---	capture		Silent	SNP	20612554	20612554	11489	14	C	T	T	T	366	29	OR4N5	2	2
HOMEZ	57594	broad.mit.edu	37	14	23746238	23746238	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23746238T>A	uc001wjb.2	-	c.205A>T	c.(205-207)AAT>TAT	p.N69Y	HOMEZ_uc001wja.2_Missense_Mutation_p.N67Y	NM_020834	NP_065885	Q8IX15	HOMEZ_HUMAN	homeodomain leucine zipper protein	67	Homeobox 1.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)										0.2	51.159324	60.787731	23	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23746238	23746238	7573	14	T	A	A	A	819	63	HOMEZ	3	3
RNF31	55072	broad.mit.edu	37	14	24620512	24620512	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:24620512C>G	uc001wmn.1	+	c.1661C>G	c.(1660-1662)GCC>GGC	p.A554G	RNF31_uc001wml.1_Missense_Mutation_p.A403G|RNF31_uc001wmm.1_Intron|RNF31_uc010alg.1_Missense_Mutation_p.A313G|RNF31_uc001wmo.1_Missense_Mutation_p.A21G|RNF31_uc001wmp.2_Non-coding_Transcript	NM_017999	NP_060469	Q96EP0	RNF31_HUMAN	ring finger protein 31	554					CD40 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein linear polyubiquitination|T cell receptor signaling pathway	CD40 receptor complex|internal side of plasma membrane|LUBAC complex	ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(265;0.00861)										0.258824	62.240286	66.700448	22	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24620512	24620512	13966	14	C	G	G	G	338	26	RNF31	3	3
RNF31	55072	broad.mit.edu	37	14	24620762	24620762	+	Silent	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:24620762A>T	uc001wmn.1	+	c.1806A>T	c.(1804-1806)GGA>GGT	p.G602G	RNF31_uc001wml.1_Silent_p.G451G|RNF31_uc001wmm.1_Intron|RNF31_uc010alg.1_Silent_p.G361G|RNF31_uc001wmo.1_Silent_p.G69G|RNF31_uc001wmp.2_Non-coding_Transcript	NM_017999	NP_060469	Q96EP0	RNF31_HUMAN	ring finger protein 31	602	Interaction with RBCK1.|UBA.				CD40 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein linear polyubiquitination|T cell receptor signaling pathway	CD40 receptor complex|internal side of plasma membrane|LUBAC complex	ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(1)|ovary(1)	2				GBM - Glioblastoma multiforme(265;0.00861)										0.226667	36.904815	42.086095	17	58	KEEP	---	---	---	---	capture		Silent	SNP	24620762	24620762	13966	14	A	T	T	T	132	11	RNF31	3	3
INSM2	84684	broad.mit.edu	37	14	36004201	36004201	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:36004201C>A	uc001wth.1	+	c.743C>A	c.(742-744)GCG>GAG	p.A248E		NM_032594	NP_115983	Q96T92	INSM2_HUMAN	insulinoma-associated protein IA-6	248					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)|skin(1)	2	Breast(36;0.122)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(9;2.16e-07)|Lung(238;2.63e-07)|Epithelial(34;0.00145)|all cancers(34;0.00452)	GBM - Glioblastoma multiforme(112;0.0223)										0.294118	36.016146	37.94554	15	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36004201	36004201	8073	14	C	A	A	A	351	27	INSM2	1	1
SOS2	6655	broad.mit.edu	37	14	50649236	50649236	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:50649236G>A	uc001wxs.3	-	c.803C>T	c.(802-804)ACT>ATT	p.T268I	SOS2_uc010tql.1_Missense_Mutation_p.T268I|SOS2_uc001wxt.2_5'Flank	NM_006939	NP_008870	Q07890	SOS2_HUMAN	son of sevenless homolog 2	268	DH.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)													0.259259	34.416532	37.258339	14	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50649236	50649236	15437	14	G	A	A	A	468	36	SOS2	2	2
FRMD6	122786	broad.mit.edu	37	14	52186866	52186866	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:52186866C>T	uc001wzd.2	+	c.1118C>T	c.(1117-1119)GCG>GTG	p.A373V	FRMD6_uc001wzb.2_Missense_Mutation_p.A365V|FRMD6_uc001wzc.2_Missense_Mutation_p.A365V|FRMD6_uc001wze.2_Missense_Mutation_p.A296V|FRMD6_uc001wzf.2_Missense_Mutation_p.A66V|FRMD6_uc001wzg.2_Missense_Mutation_p.A15V	NM_152330	NP_689543	Q96NE9	FRMD6_HUMAN	FERM domain containing 6	373						cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(31;0.0163)|Breast(41;0.089)													0.206897	24.668285	29.287502	12	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52186866	52186866	6304	14	C	T	T	T	351	27	FRMD6	1	1
C14orf37	145407	broad.mit.edu	37	14	58471506	58471506	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:58471506C>T	uc010tro.1	-	c.2387G>A	c.(2386-2388)AGC>AAC	p.S796N	C14orf37_uc001xdc.2_Missense_Mutation_p.S758N|C14orf37_uc001xdd.2_Missense_Mutation_p.S757N	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor	758	Cytoplasmic (Potential).					integral to membrane	binding				0														0.2	71.386777	83.527636	29	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58471506	58471506	1820	14	C	T	T	T	364	28	C14orf37	2	2
ZFYVE26	23503	broad.mit.edu	37	14	68272236	68272236	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:68272236C>A	uc001xka.2	-	c.1117G>T	c.(1117-1119)GGC>TGC	p.G373C	ZFYVE26_uc010tsz.1_Non-coding_Transcript|ZFYVE26_uc001xkc.3_Missense_Mutation_p.G373C|ZFYVE26_uc010tta.1_Missense_Mutation_p.G373C	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	373					cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	phosphatidylinositol-3-phosphate binding|protein binding|zinc ion binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)										0.295918	73.891037	77.511948	29	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68272236	68272236	18258	14	C	A	A	A	286	22	ZFYVE26	2	2
DPF3	8110	broad.mit.edu	37	14	73220047	73220047	+	Missense_Mutation	SNP	C	G	G	rs34110101		TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:73220047C>G	uc001xnc.2	-	c.226G>C	c.(226-228)GCC>CCC	p.A76P	DPF3_uc001xnf.2_Non-coding_Transcript|DPF3_uc010ari.1_Missense_Mutation_p.A76P|DPF3_uc010ttq.1_Missense_Mutation_p.A86P	NM_012074	NP_036206	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	76					chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)										0.148148	9.780985	12.989879	4	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73220047	73220047	4902	14	C	G	G	G	325	25	DPF3	3	3
NRXN3	9369	broad.mit.edu	37	14	79175581	79175581	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:79175581A>T	uc001xun.2	+	c.124A>T	c.(124-126)ATC>TTC	p.I42F	NRXN3_uc001xum.1_Non-coding_Transcript|NRXN3_uc010asv.1_Missense_Mutation_p.I176F	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	415	Laminin G-like 2.|Extracellular (Potential).				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)										0.219178	42.562479	47.863994	16	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79175581	79175581	11072	14	A	T	T	T	104	8	NRXN3	3	3
KCNK10	54207	broad.mit.edu	37	14	88729728	88729728	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:88729728A>G	uc001xwm.2	-	c.220T>C	c.(220-222)TGG>CGG	p.W74R	KCNK10_uc001xwn.2_Missense_Mutation_p.W74R|KCNK10_uc001xwo.2_Missense_Mutation_p.W69R	NM_138318	NP_612191	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	69	Cytoplasmic (Potential).				signal transduction	integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|pancreas(1)	3														0.185185	41.759894	51.778272	20	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88729728	88729728	8364	14	A	G	G	G	78	6	KCNK10	4	4
BCL11B	64919	broad.mit.edu	37	14	99724120	99724120	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:99724120C>T	uc001yga.2	-	c.115G>A	c.(115-117)GAG>AAG	p.E39K	BCL11B_uc001ygb.2_Missense_Mutation_p.E39K	NM_138576	NP_612808	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B isoform 1	39						nucleus	zinc ion binding			central_nervous_system(8)|large_intestine(1)	9		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)						98				0.307692	44.279211	45.994276	16	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99724120	99724120	1385	14	C	T	T	T	416	32	BCL11B	2	2
GABRA5	2558	broad.mit.edu	37	15	27185181	27185181	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:27185181C>A	uc001zbd.1	+	c.834C>A	c.(832-834)TCC>TCA	p.S278S	GABRB3_uc001zbb.2_5'Flank	NM_000810	NP_000801	P31644	GBRA5_HUMAN	gamma-aminobutyric acid A receptor, alpha 5	278	Helical; (Potential).				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			ovary(1)	1		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)									0.217391	20.221702	23.612793	10	36	KEEP	---	---	---	---	capture		Silent	SNP	27185181	27185181	6415	15	C	A	A	A	301	24	GABRA5	2	2
OCA2	4948	broad.mit.edu	37	15	28096577	28096577	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:28096577C>A	uc001zbh.3	-	c.2289G>T	c.(2287-2289)CTG>CTT	p.L763L	OCA2_uc010ayv.2_Silent_p.L739L	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II	763	Helical; (Potential).				eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)										0.268293	25.497795	27.493691	11	30	KEEP	---	---	---	---	capture		Silent	SNP	28096577	28096577	11220	15	C	A	A	A	314	25	OCA2	2	2
MGA	23269	broad.mit.edu	37	15	42041781	42041781	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:42041781G>T	uc010ucy.1	+	c.5976G>T	c.(5974-5976)AAG>AAT	p.K1992N	MGA_uc010ucz.1_Missense_Mutation_p.K1783N|MGA_uc010uda.1_Missense_Mutation_p.K608N|MGA_uc001zoi.2_Missense_Mutation_p.K206N	NM_001164273	NP_001157745	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 1	1953	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				0.310811	60.593298	62.954908	23	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42041781	42041781	9930	15	G	T	T	T	451	35	MGA	2	2
DUOX2	50506	broad.mit.edu	37	15	45391598	45391598	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:45391598G>T	uc010bea.2	-	c.3498C>A	c.(3496-3498)AAC>AAA	p.N1166K	DUOX2_uc001zun.2_Missense_Mutation_p.N1166K	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	1166	Interaction with TXNDC11 (By similarity).|Helical; (Potential).|Ferric oxidoreductase.				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|oxidation-reduction process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|pancreas(1)	3		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)										0.290909	44.978	47.132033	16	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45391598	45391598	4986	15	G	T	T	T	516	40	DUOX2	1	1
SEMA6D	80031	broad.mit.edu	37	15	48063266	48063266	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:48063266G>T	uc010bek.2	+	c.2506G>T	c.(2506-2508)GAC>TAC	p.D836Y	SEMA6D_uc001zvw.2_Missense_Mutation_p.D774Y|SEMA6D_uc001zvy.2_Missense_Mutation_p.D836Y|SEMA6D_uc001zvz.2_Missense_Mutation_p.D780Y|SEMA6D_uc001zwa.2_3'UTR|SEMA6D_uc001zwb.2_Missense_Mutation_p.D774Y|SEMA6D_uc001zwc.2_Missense_Mutation_p.D761Y	NM_153618	NP_705871	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 4 precursor	836	Cytoplasmic (Potential).				axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			breast(1)	1		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)										0.300752	102.038658	106.761017	40	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48063266	48063266	14528	15	G	T	T	T	585	45	SEMA6D	2	2
CEP152	22995	broad.mit.edu	37	15	49030736	49030736	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:49030736C>A	uc001zwz.2	-	c.4843G>T	c.(4843-4845)GGT>TGT	p.G1615C	CEP152_uc001zwy.2_Missense_Mutation_p.G1559C	NM_014985	NP_055800	O94986	CE152_HUMAN	centrosomal protein 152kDa	1559					G2/M transition of mitotic cell cycle	cytosol|microtubule organizing center				lung(2)	2		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)										0.231884	40.66438	45.207696	16	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49030736	49030736	3381	15	C	A	A	A	299	23	CEP152	1	1
MYO9A	4649	broad.mit.edu	37	15	72146723	72146723	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:72146723T>C	uc002atl.3	-	c.6341A>G	c.(6340-6342)GAT>GGT	p.D2114G	MYO9A_uc002atj.2_Missense_Mutation_p.D27G|MYO9A_uc002atk.2_Missense_Mutation_p.D909G	NM_006901	NP_008832	B2RTY4	MYO9A_HUMAN	myosin IXA	2114	Phorbol-ester/DAG-type 2.|Tail.|Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3														0.2657	168.840735	179.101419	55	152	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72146723	72146723	10479	15	T	C	C	C	650	50	MYO9A	4	4
MAN2C1	4123	broad.mit.edu	37	15	75652055	75652055	+	Silent	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:75652055C>T	uc002baf.2	-	c.1854G>A	c.(1852-1854)GAG>GAA	p.E618E	MAN2C1_uc002bag.2_Silent_p.E618E|MAN2C1_uc002bah.2_Silent_p.E618E|MAN2C1_uc010bkk.2_Silent_p.E519E|MAN2C1_uc010umi.1_Silent_p.E400E	NM_006715	NP_006706	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	618					mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0														0.234375	33.888665	38.024005	15	49	KEEP	---	---	---	---	capture		Silent	SNP	75652055	75652055	9601	15	C	T	T	T	363	28	MAN2C1	2	2
CSPG4	1464	broad.mit.edu	37	15	75975009	75975009	+	Silent	SNP	C	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:75975009C>G	uc002baw.2	-	c.4722G>C	c.(4720-4722)GTG>GTC	p.V1574V		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4 precursor	1574	Extracellular (Potential).|Gly/Ser-rich (glycosaminoglycan attachment domain).				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3										549				0.25	79.672452	85.807912	27	81	KEEP	---	---	---	---	capture		Silent	SNP	75975009	75975009	4101	15	C	G	G	G	366	29	CSPG4	3	3
DET1	55070	broad.mit.edu	37	15	89070888	89070888	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:89070888C>T	uc002bmq.2	-	c.1246G>A	c.(1246-1248)GAA>AAA	p.E416K	DET1_uc002bmp.3_Non-coding_Transcript|DET1_uc010bnk.2_Intron|DET1_uc002bmr.2_Missense_Mutation_p.E405K	NM_017996	NP_060466	Q7L5Y6	DET1_HUMAN	de-etiolated 1 isoform 1	405						nucleus				lung(1)|pancreas(1)	2	Lung NSC(78;0.105)|all_lung(78;0.182)		BRCA - Breast invasive adenocarcinoma(143;0.188)											0.298246	45.450244	47.525672	17	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89070888	89070888	4629	15	C	T	T	T	377	29	DET1	2	2
TNRC6A	27327	broad.mit.edu	37	16	24802953	24802953	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:24802953G>T	uc002dmm.2	+	c.2990G>T	c.(2989-2991)CGC>CTC	p.R997L	TNRC6A_uc010bxs.2_Missense_Mutation_p.R744L|TNRC6A_uc010vcc.1_Missense_Mutation_p.R744L|TNRC6A_uc002dmn.2_Missense_Mutation_p.R744L|TNRC6A_uc002dmo.2_Missense_Mutation_p.R744L	NM_014494	NP_055309	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	997	Sufficient for interaction with EIF2C1 and EIF2C4.				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)										0.151163	24.622998	34.643659	13	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24802953	24802953	16881	16	G	T	T	T	494	38	TNRC6A	1	1
KIAA0556	23247	broad.mit.edu	37	16	27772805	27772805	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:27772805G>T	uc002dow.2	+	c.3703G>T	c.(3703-3705)GGC>TGC	p.G1235C		NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	1235										ovary(4)|large_intestine(2)	6														0.166667	19.541992	26.449962	11	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27772805	27772805	8490	16	G	T	T	T	559	43	KIAA0556	2	2
SETD1A	9739	broad.mit.edu	37	16	30991099	30991099	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30991099C>T	uc002ead.1	+	c.3992C>T	c.(3991-3993)CCA>CTA	p.P1331L		NM_014712	NP_055527	O15047	SET1A_HUMAN	SET domain containing 1A	1331					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)	2														0.363636	11.896579	12.076727	4	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30991099	30991099	14618	16	C	T	T	T	273	21	SETD1A	2	2
ITGAX	3687	broad.mit.edu	37	16	31374568	31374568	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31374568T>A	uc002ebt.2	+	c.1583T>A	c.(1582-1584)CTG>CAG	p.L528Q	ITGAX_uc002ebu.1_Missense_Mutation_p.L528Q|ITGAX_uc010vfk.1_Missense_Mutation_p.L178Q	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	528	Extracellular (Potential).|FG-GAP 6.				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.233962	145.697511	162.886165	62	203	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31374568	31374568	8193	16	T	A	A	A	715	55	ITGAX	3	3
TGFB1I1	7041	broad.mit.edu	37	16	31484820	31484820	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31484820C>A	uc002ecd.1	+	c.72C>A	c.(70-72)CCC>CCA	p.P24P	TGFB1I1_uc002ece.1_Silent_p.P7P|TGFB1I1_uc010caq.1_5'UTR	NM_001042454	NP_001035919	O43294	TGFI1_HUMAN	transforming growth factor beta 1 induced	24	Transcription activation (By similarity).|Interaction with PTK2B.				androgen receptor signaling pathway|cell adhesion|negative regulation of cell proliferation|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|positive regulation of transforming growth factor beta receptor signaling pathway|transcription from RNA polymerase II promoter|ubiquitin-dependent SMAD protein catabolic process|Wnt receptor signaling pathway	cytoplasm|cytoskeleton|focal adhesion|nuclear matrix	androgen receptor binding|I-SMAD binding|Roundabout binding|transcription coactivator activity|zinc ion binding				0														0.15625	16.8123	24.031025	10	54	KEEP	---	---	---	---	capture		Silent	SNP	31484820	31484820	16345	16	C	A	A	A	262	21	TGFB1I1	2	2
GPT2	84706	broad.mit.edu	37	16	46962902	46962902	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:46962902A>G	uc002eel.2	+	c.1565A>G	c.(1564-1566)TAC>TGC	p.Y522C	GPT2_uc002eem.2_Missense_Mutation_p.Y422C|GPT2_uc002een.2_Missense_Mutation_p.Y165C	NM_133443	NP_597700	Q8TD30	ALAT2_HUMAN	glutamic pyruvate transaminase 2 isoform 1	522					2-oxoglutarate metabolic process|cellular amino acid biosynthetic process|L-alanine metabolic process	mitochondrial matrix	L-alanine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)	1		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)									0.258621	44.599382	47.660222	15	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46962902	46962902	7014	16	A	G	G	G	182	14	GPT2	4	4
ZFHX3	463	broad.mit.edu	37	16	72830619	72830619	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:72830619A>T	uc002fck.2	-	c.5962T>A	c.(5962-5964)TGC>AGC	p.C1988S	ZFHX3_uc002fcl.2_Missense_Mutation_p.C1074S	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	1988	C2H2-type 17.				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription repressor activity|transcription repressor activity|zinc ion binding			ovary(2)	2		Ovarian(137;0.13)												0.228972	121.468439	135.883372	49	165	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72830619	72830619	18222	16	A	T	T	T	91	7	ZFHX3	3	3
PKD1L2	114780	broad.mit.edu	37	16	81181802	81181802	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:81181802C>A	uc002fgh.1	-	c.4914G>T	c.(4912-4914)CTG>CTT	p.L1638L	PKD1L2_uc002fgg.1_Non-coding_Transcript	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	1638	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														0.105263	2.869344	8.758094	4	34	KEEP	---	---	---	---	capture		Silent	SNP	81181802	81181802	12389	16	C	A	A	A	366	29	PKD1L2	2	2
MSLNL	401827	broad.mit.edu	37	16	823017	823017	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:823017T>G	uc002cjz.1	-	c.2168A>C	c.(2167-2169)CAG>CCG	p.Q723P		NM_001025190	NP_001020361	Q96KJ4	MSLNL_HUMAN	mesothelin-like	372	Extracellular (Potential).				cell adhesion	integral to membrane				breast(3)|ovary(1)	4														0.08589	8.131171	36.453835	14	149	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	823017	823017	10275	16	T	G	G	G	715	55	MSLNL	4	4
IRF8	3394	broad.mit.edu	37	16	85945192	85945192	+	Silent	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:85945192A>T	uc002fjh.2	+	c.375A>T	c.(373-375)GCA>GCT	p.A125A	IRF8_uc010chp.2_Non-coding_Transcript	NM_002163	NP_002154	Q02556	IRF8_HUMAN	interferon regulatory factor 8	125					interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(2)|ovary(1)	3		Prostate(104;0.0771)												0.111111	7.379105	16.799713	7	56	KEEP	---	---	---	---	capture		Silent	SNP	85945192	85945192	8139	16	A	T	T	T	54	5	IRF8	3	3
MYH13	8735	broad.mit.edu	37	17	10210316	10210316	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10210316C>A	uc002gmk.1	-	c.5235G>T	c.(5233-5235)GTG>GTT	p.V1745V		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1745	Potential.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)	4														0.247191	53.707617	58.883768	22	67	KEEP	---	---	---	---	capture		Silent	SNP	10210316	10210316	10427	17	C	A	A	A	262	21	MYH13	2	2
MYH8	4626	broad.mit.edu	37	17	10314198	10314198	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10314198G>T	uc002gmm.2	-	c.1483C>A	c.(1483-1485)CAC>AAC	p.H495N		NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	495	Myosin head-like.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(3)|breast(2)	5														0.252525	125.040755	136.065046	50	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10314198	10314198	10436	17	G	T	T	T	611	47	MYH8	2	2
MYO15A	51168	broad.mit.edu	37	17	18058480	18058480	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:18058480G>A	uc010vxh.1	+	c.8281G>A	c.(8281-8283)GTG>ATG	p.V2761M	MYO15A_uc010vxi.1_Missense_Mutation_p.V25M|MYO15A_uc010vxj.1_De_novo_Start_InFrame|MYO15A_uc010vxk.1_Intron|MYO15A_uc010vxl.1_5'Flank	NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	2761	Tail.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)|skin(1)	6	all_neural(463;0.228)													0.320755	46.063192	47.572278	17	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18058480	18058480	10458	17	G	A	A	A	520	40	MYO15A	1	1
NOS2	4843	broad.mit.edu	37	17	26114745	26114745	+	Silent	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:26114745T>C	uc002gzu.2	-	c.426A>G	c.(424-426)CAA>CAG	p.Q142Q	NOS2_uc010crh.1_Silent_p.Q142Q|NOS2_uc010wab.1_Silent_p.Q142Q	NM_000625	NP_000616	P35228	NOS2_HUMAN	nitric oxide synthase 2A	142					arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|oxidation-reduction process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding			ovary(1)|breast(1)	2					Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)					578				0.234043	204.209305	222.456322	66	216	KEEP	---	---	---	---	capture		Silent	SNP	26114745	26114745	10946	17	T	C	C	C	725	56	NOS2	4	4
NOS2	4843	broad.mit.edu	37	17	26114747	26114747	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:26114747G>C	uc002gzu.2	-	c.424C>G	c.(424-426)CAA>GAA	p.Q142E	NOS2_uc010crh.1_Missense_Mutation_p.Q142E|NOS2_uc010wab.1_Missense_Mutation_p.Q142E	NM_000625	NP_000616	P35228	NOS2_HUMAN	nitric oxide synthase 2A	142					arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|oxidation-reduction process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding			ovary(1)|breast(1)	2					Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)					578				0.236111	210.552744	228.885875	68	220	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26114747	26114747	10946	17	G	C	C	C	585	45	NOS2	3	3
CPD	1362	broad.mit.edu	37	17	28791816	28791816	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:28791816A>G	uc002hfb.1	+	c.4127A>G	c.(4126-4128)TAT>TGT	p.Y1376C	CPD_uc010wbo.1_Missense_Mutation_p.Y1129C|CPD_uc010wbp.1_Non-coding_Transcript	NM_001304	NP_001295	O75976	CBPD_HUMAN	carboxypeptidase D precursor	1376	Cytoplasmic (Potential).				proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			liver(1)	1														0.232877	50.741326	55.506726	17	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28791816	28791816	3936	17	A	G	G	G	208	16	CPD	4	4
TNS4	84951	broad.mit.edu	37	17	38636951	38636951	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38636951C>A	uc010cxb.2	-	c.1741_splice	c.e9+1	p.G581_splice	TNS4_uc002huu.3_Intron	NM_032865	NP_116254			tensin 4 precursor						apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)											0.142857	18.604732	27.206075	10	60	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	38636951	38636951	16886	17	C	A	A	A	234	18	TNS4	5	2
KRTAP4-2	85291	broad.mit.edu	37	17	39334304	39334304	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39334304G>A	uc002hwd.2	-	c.113C>T	c.(112-114)CCC>CTC	p.P38L		NM_033062	NP_149051	Q9BYR5	KRA42_HUMAN	keratin associated protein 4-2	38	5.|20 X 5 AA repeats OF C-C-[GRQVS]-[SPT]- [VSTQ].					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)											0.224719	41.750491	47.952746	20	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39334304	39334304	8873	17	G	A	A	A	559	43	KRTAP4-2	2	2
CRHR1	1394	broad.mit.edu	37	17	43907550	43907550	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:43907550C>A	uc010dap.2	+	c.612C>A	c.(610-612)ACC>ACA	p.T204T	CRHR1_uc010wjx.1_5'UTR|CRHR1_uc002ijp.2_Silent_p.T74T|CRHR1_uc002ijm.2_Silent_p.T175T|CRHR1_uc002ijn.2_Silent_p.T135T|CRHR1_uc010dar.2_Silent_p.T175T|CRHR1_uc010dao.2_Silent_p.T74T|CRHR1_uc010daq.2_5'UTR|CRHR1_uc010das.1_Non-coding_Transcript|CRHR1_uc002ijo.1_Non-coding_Transcript	NM_001145146	NP_001138618	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	204	Extracellular (Potential).				female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity				0	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		Ovarian(110;57 1568 10207 38216 49865)								0.327103	95.1835	98.022924	35	72	KEEP	---	---	---	---	capture		Silent	SNP	43907550	43907550	4010	17	C	A	A	A	262	21	CRHR1	2	2
VPS53	55275	broad.mit.edu	37	17	600720	600720	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:600720G>T	uc010cjo.1	-	c.223C>A	c.(223-225)CTG>ATG	p.L75M	VPS53_uc002frl.2_Non-coding_Transcript|VPS53_uc002frm.2_Missense_Mutation_p.L75M|VPS53_uc002frn.2_Missense_Mutation_p.L75M|VPS53_uc002fro.2_De_novo_Start_OutOfFrame|VPS53_uc010cjp.1_Missense_Mutation_p.L75M	NM_001128159	NP_001121631	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 isoform 1	75	Potential.				protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)										0.291139	132.098086	138.265352	46	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	600720	600720	17782	17	G	T	T	T	464	36	VPS53	2	2
VPS53	55275	broad.mit.edu	37	17	600722	600722	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:600722C>T	uc010cjo.1	-	c.221G>A	c.(220-222)AGA>AAA	p.R74K	VPS53_uc002frl.2_Non-coding_Transcript|VPS53_uc002frm.2_Missense_Mutation_p.R74K|VPS53_uc002frn.2_Missense_Mutation_p.R74K|VPS53_uc002fro.2_5'UTR|VPS53_uc010cjp.1_Missense_Mutation_p.R74K	NM_001128159	NP_001121631	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 isoform 1	74	Potential.				protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)										0.283871	126.641535	133.139106	44	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	600722	600722	17782	17	C	T	T	T	416	32	VPS53	2	2
AXIN2	8313	broad.mit.edu	37	17	63534419	63534419	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:63534419C>G	uc002jfi.2	-	c.1102G>C	c.(1102-1104)GCC>CCC	p.A368P	AXIN2_uc010den.1_Missense_Mutation_p.A368P|AXIN2_uc002jfh.2_Missense_Mutation_p.A368P	NM_004655	NP_004646	Q9Y2T1	AXIN2_HUMAN	axin 2	368	Interaction with GSK3B (By similarity).				cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity			central_nervous_system(1)|skin(1)	2										240				0.192771	39.196092	46.477436	16	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63534419	63534419	1258	17	C	G	G	G	351	27	AXIN2	3	3
PRKCA	5578	broad.mit.edu	37	17	64770156	64770156	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:64770156G>A	uc002jfp.1	+	c.1576G>A	c.(1576-1578)GTC>ATC	p.V526I	PRKCA_uc002jfo.1_Missense_Mutation_p.V397I	NM_002737	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	526	Protein kinase.				activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|ovary(1)	7			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)					554				0.069124	-12.254011	29.393829	15	202	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64770156	64770156	12950	17	G	A	A	A	520	40	PRKCA	1	1
POLR2A	5430	broad.mit.edu	37	17	7405880	7405880	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7405880G>A	uc002ghf.3	+	c.2616G>A	c.(2614-2616)ATG>ATA	p.M872I		NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA-directed RNA polymerase II A	872					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)												0.231707	46.881199	52.289391	19	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7405880	7405880	12642	17	G	A	A	A	611	47	POLR2A	2	2
POLR2A	5430	broad.mit.edu	37	17	7405883	7405883	+	Silent	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7405883G>A	uc002ghf.3	+	c.2619G>A	c.(2617-2619)GTG>GTA	p.V873V		NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA-directed RNA polymerase II A	873					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)												0.232558	46.750489	52.387779	20	66	KEEP	---	---	---	---	capture		Silent	SNP	7405883	7405883	12642	17	G	A	A	A	574	45	POLR2A	2	2
AZI1	22994	broad.mit.edu	37	17	79182788	79182788	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:79182788T>C	uc002jzp.1	-	c.212A>G	c.(211-213)AAC>AGC	p.N71S	AZI1_uc002jzn.1_Missense_Mutation_p.N71S|AZI1_uc002jzo.1_Missense_Mutation_p.N71S|AZI1_uc010wum.1_Missense_Mutation_p.N71S	NM_014984	NP_055799	Q9UPN4	AZI1_HUMAN	5-azacytidine induced 1 isoform a	71					cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centrosome|cytosol|intracellular membrane-bounded organelle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)											0.266667	51.974499	54.923823	16	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79182788	79182788	1261	17	T	C	C	C	780	60	AZI1	4	4
HEXDC	284004	broad.mit.edu	37	17	80394589	80394589	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:80394589G>T	uc002kev.3	+	c.678G>T	c.(676-678)ACG>ACT	p.T226T	HEXDC_uc010diq.2_Silent_p.T226T|HEXDC_uc002kew.2_Silent_p.T226T|HEXDC_uc010wvm.1_Non-coding_Transcript|HEXDC_uc010wvn.1_5'Flank	NM_173620	NP_775891	Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20,	226					carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)	1	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)											0.151515	9.761972	13.592547	5	28	KEEP	---	---	---	---	capture		Silent	SNP	80394589	80394589	7358	17	G	T	T	T	496	39	HEXDC	1	1
GAS7	8522	broad.mit.edu	37	17	9820602	9820602	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:9820602C>G	uc002gmg.1	-	c.1374G>C	c.(1372-1374)GAG>GAC	p.E458D	GAS7_uc010vvc.1_Missense_Mutation_p.E272D|GAS7_uc002gmh.1_Missense_Mutation_p.E318D|GAS7_uc010vvd.1_Missense_Mutation_p.E410D|GAS7_uc002gmi.2_Missense_Mutation_p.E394D|GAS7_uc002gmj.1_Missense_Mutation_p.E398D|GAS7_uc010coh.1_Missense_Mutation_p.E398D	NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c	458					cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			pancreas(1)	1										523				0.274809	108.651277	114.63001	36	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9820602	9820602	6514	17	C	G	G	G	363	28	GAS7	3	3
SOCS6	9306	broad.mit.edu	37	18	67993064	67993064	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:67993064G>A	uc002lkr.1	+	c.1160G>A	c.(1159-1161)GGA>GAA	p.G387E	SOCS6_uc010dqq.2_Missense_Mutation_p.G387E	NM_004232	NP_004223	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	387	SH2.				defense response|JAK-STAT cascade|negative regulation of signal transduction|regulation of growth	cytoplasm				large_intestine(1)	1		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				Melanoma(84;1024 1361 24382 36583 42651)								0.252336	65.540034	71.532592	27	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67993064	67993064	15418	18	G	A	A	A	533	41	SOCS6	2	2
YES1	7525	broad.mit.edu	37	18	724522	724522	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:724522C>A	uc002kky.2	-	c.1534G>T	c.(1534-1536)GAC>TAC	p.D512Y	YES1_uc002kkz.2_Missense_Mutation_p.D512Y	NM_005433	NP_005424	P07947	YES_HUMAN	viral oncogene yes-1 homolog 1	512	Protein kinase.				blood coagulation|leukocyte migration|protein phosphorylation|regulation of vascular permeability|T cell costimulation	cytosol|plasma membrane	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|ovary(1)	3					Dasatinib(DB01254)					156				0.259259	46.329343	50.589467	21	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	724522	724522	18057	18	C	A	A	A	390	30	YES1	2	2
KEAP1	9817	broad.mit.edu	37	19	10600477	10600477	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10600477T>C	uc002moq.1	-	c.1378A>G	c.(1378-1380)AGG>GGG	p.R460G	KEAP1_uc002mop.1_Missense_Mutation_p.R178G|KEAP1_uc002mor.1_Missense_Mutation_p.R460G	NM_012289	NP_036421	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	460	Kelch 3.				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)											0.368421	49.549586	50.124028	14	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10600477	10600477	8447	19	T	C	C	C	726	56	KEAP1	4	4
ZNF676	163223	broad.mit.edu	37	19	22363270	22363270	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22363270C>A	uc002nqs.1	-	c.1249G>T	c.(1249-1251)GGA>TGA	p.G417*		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	417					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)												0.364865	77.501889	78.691855	27	47	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	22363270	22363270	18678	19	C	A	A	A	273	21	ZNF676	5	2
ZNF536	9745	broad.mit.edu	37	19	30934586	30934586	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:30934586C>A	uc002nsu.1	+	c.117C>A	c.(115-117)ATC>ATA	p.I39I	ZNF536_uc010edd.1_Silent_p.I39I	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	39					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)	9	Esophageal squamous(110;0.0834)													0.225	76.017041	87.137286	36	124	KEEP	---	---	---	---	capture		Silent	SNP	30934586	30934586	18568	19	C	A	A	A	369	29	ZNF536	2	2
UBA2	10054	broad.mit.edu	37	19	34922808	34922808	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:34922808A>G	uc002nvk.2	+	c.265A>G	c.(265-267)ATC>GTC	p.I89V	UBA2_uc010xrx.1_Intron|UBA2_uc002nvl.2_De_novo_Start_OutOfFrame	NM_005499	NP_005490	Q9UBT2	SAE2_HUMAN	SUMO-1 activating enzyme subunit 2	89					protein sumoylation	nucleus	ATP binding|enzyme activator activity|ligase activity|metal ion binding|protein heterodimerization activity|SUMO activating enzyme activity			ovary(1)	1	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)											0.252874	210.753936	225.20552	66	195	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34922808	34922808	17385	19	A	G	G	G	208	16	UBA2	4	4
PIP5K1C	23396	broad.mit.edu	37	19	3664855	3664855	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:3664855C>A	uc010xhr.1	-	c.184G>T	c.(184-186)GGT>TGT	p.G62C	PIP5K1C_uc002lyj.1_Missense_Mutation_p.G62C|PIP5K1C_uc010xhq.1_Missense_Mutation_p.G62C	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type	62					axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		Esophageal Squamous(135;99 1744 12852 27186 39851)				246				0.358779	129.884934	132.186982	47	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3664855	3664855	12365	19	C	A	A	A	312	24	PIP5K1C	2	2
SPTBN4	57731	broad.mit.edu	37	19	41081361	41081361	+	Silent	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:41081361G>A	uc002ony.2	+	c.7581G>A	c.(7579-7581)GCG>GCA	p.A2527A	SPTBN4_uc002onz.2_Silent_p.A2527A|SPTBN4_uc010egx.2_Silent_p.A1270A|SHKBP1_uc002oob.2_5'Flank|SHKBP1_uc002ooc.2_5'Flank|SHKBP1_uc002ood.2_5'Flank|SHKBP1_uc010xvl.1_5'Flank|SHKBP1_uc002ooe.2_5'Flank|SHKBP1_uc002oof.2_5'Flank	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	2527	PH.				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)	4			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)											0.363636	22.694859	23.054383	8	14	KEEP	---	---	---	---	capture		Silent	SNP	41081361	41081361	15635	19	G	A	A	A	496	39	SPTBN4	1	1
CCDC94	55702	broad.mit.edu	37	19	4267771	4267771	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:4267771G>T	uc002lzv.3	+	c.859G>T	c.(859-861)GGA>TGA	p.G287*		NM_018074	NP_060544	Q9BW85	CCD94_HUMAN	coiled-coil domain containing 94	287											0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0348)|STAD - Stomach adenocarcinoma(1328;0.183)								OREG0025164	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.368421	18.518776	18.808371	7	12	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	4267771	4267771	2998	19	G	T	T	T	455	35	CCDC94	5	2
ZNF221	7638	broad.mit.edu	37	19	44470819	44470819	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44470819A>T	uc002oxx.2	+	c.1165A>T	c.(1165-1167)ACA>TCA	p.T389S	ZNF221_uc010ejb.1_Missense_Mutation_p.T389S|ZNF221_uc010xws.1_Missense_Mutation_p.T389S	NM_013359	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	389					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)												0.27451	114.287789	121.292508	42	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44470819	44470819	18366	19	A	T	T	T	78	6	ZNF221	3	3
MARK4	57787	broad.mit.edu	37	19	45762388	45762388	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:45762388A>T	uc002pba.1	+	c.193A>T	c.(193-195)ATT>TTT	p.I65F	MARK4_uc002paz.1_Intron|MARK4_uc002pbb.1_Missense_Mutation_p.I65F	NM_031417	NP_113605	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	65	ATP (By similarity).|Protein kinase.				microtubule bundle formation|nervous system development|positive regulation of programmed cell death|protein phosphorylation	centrosome|neuron projection	ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding			central_nervous_system(2)|large_intestine(1)	3		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)						167				0.271186	45.886742	48.6642	16	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45762388	45762388	9698	19	A	T	T	T	104	8	MARK4	3	3
DPP9	91039	broad.mit.edu	37	19	4685763	4685763	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:4685763G>A	uc002mba.2	-	c.1906C>T	c.(1906-1908)CCT>TCT	p.P636S		NM_139159	NP_631898	Q86TI2	DPP9_HUMAN	dipeptidylpeptidase 9	607					proteolysis	cytosol|membrane	aminopeptidase activity|serine-type peptidase activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)										0.30303	26.536484	27.679898	10	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4685763	4685763	4917	19	G	A	A	A	533	41	DPP9	2	2
KLK7	5650	broad.mit.edu	37	19	51483646	51483646	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51483646G>T	uc002puo.2	-	c.319C>A	c.(319-321)CAG>AAG	p.Q107K	KLK7_uc002pup.2_Missense_Mutation_p.Q107K|KLK7_uc010yco.1_5'UTR|KLK7_uc010eok.2_Missense_Mutation_p.Q35K	NM_139277	NP_644806	P49862	KLK7_HUMAN	stratum corneum chymotryptic enzyme	107	Peptidase S1.				epidermis development|proteolysis	extracellular region	serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00382)|GBM - Glioblastoma multiforme(134;0.00895)						155				0.277778	65.507725	69.52988	25	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51483646	51483646	8723	19	G	T	T	T	624	48	KLK7	2	2
VN1R2	317701	broad.mit.edu	37	19	53762540	53762540	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53762540C>A	uc002qbi.2	+	c.912C>A	c.(910-912)TAC>TAA	p.Y304*		NM_173856	NP_776255	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	304	Cytoplasmic (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0				GBM - Glioblastoma multiforme(134;0.00301)										0.27027	158.00262	168.572116	60	162	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	53762540	53762540	17746	19	C	A	A	A	233	18	VN1R2	5	2
ZNF761	388561	broad.mit.edu	37	19	53952872	53952872	+	Silent	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53952872T>C	uc010eqp.2	+	c.123T>C	c.(121-123)TAT>TAC	p.Y41Y	ZNF761_uc002qbr.2_Non-coding_Transcript|ZNF761_uc010ydy.1_5'UTR|ZNF761_uc002qbs.2_Non-coding_Transcript|ZNF761_uc002qbt.1_5'Flank	NM_001008401	NP_001008401	Q86XN6	ZN761_HUMAN	zinc finger protein 761	41	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(134;0.00786)										0.322034	63.508235	65.16556	19	40	KEEP	---	---	---	---	capture		Silent	SNP	53952872	53952872	18734	19	T	C	C	C	634	49	ZNF761	4	4
ZNF813	126017	broad.mit.edu	37	19	53989993	53989993	+	Silent	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53989993T>C	uc002qbu.2	+	c.123T>C	c.(121-123)TAT>TAC	p.Y41Y	ZNF813_uc010eqq.1_Non-coding_Transcript	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	41	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)										0.063291	-6.339943	24.990891	10	148	KEEP	---	---	---	---	capture		Silent	SNP	53989993	53989993	18773	19	T	C	C	C	634	49	ZNF813	4	4
KIR3DL1	3811	broad.mit.edu	37	19	55340905	55340905	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:55340905T>A	uc002qhk.3	+	c.1090T>A	c.(1090-1092)TGC>AGC	p.C364S	KIR2DS4_uc010yfj.1_Intron|KIR2DS4_uc010yfk.1_Intron|KIR3DL1_uc010yfn.1_Missense_Mutation_p.C289S|KIR3DL1_uc010esf.2_Missense_Mutation_p.C269S|KIR3DL1_uc010yfo.1_Missense_Mutation_p.C306S|KIR3DL1_uc002qhl.3_Intron	NM_013289	NP_037421	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three	364	Cytoplasmic (Potential).				immune response|regulation of immune response	integral to plasma membrane	HLA-B specific inhibitory MHC class I receptor activity			ovary(2)|kidney(1)	3				GBM - Glioblastoma multiforme(193;0.0192)										0.506494	131.328199	131.331068	39	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55340905	55340905	8632	19	T	A	A	A	767	59	KIR3DL1	3	3
ZNF135	7694	broad.mit.edu	37	19	58579319	58579319	+	Silent	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:58579319A>G	uc010yhq.1	+	c.1503A>G	c.(1501-1503)ACA>ACG	p.T501T	ZNF135_uc002qre.2_Silent_p.T489T|ZNF135_uc002qrd.1_Intron|ZNF135_uc002qrf.2_Silent_p.T447T|ZNF135_uc002qrg.2_Silent_p.T459T|ZNF135_uc010yhr.1_Silent_p.T310T	NM_003436	NP_003427	B4DHH9	B4DHH9_HUMAN	zinc finger protein 135 isoform 2	501					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)										0.16129	30.164345	40.317784	15	78	KEEP	---	---	---	---	capture		Silent	SNP	58579319	58579319	18316	19	A	G	G	G	80	7	ZNF135	4	4
ZNF135	7694	broad.mit.edu	37	19	58579321	58579321	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:58579321G>T	uc010yhq.1	+	c.1505G>T	c.(1504-1506)GGG>GTG	p.G502V	ZNF135_uc002qre.2_Missense_Mutation_p.G490V|ZNF135_uc002qrd.1_Intron|ZNF135_uc002qrf.2_Missense_Mutation_p.G448V|ZNF135_uc002qrg.2_Missense_Mutation_p.G460V|ZNF135_uc010yhr.1_Missense_Mutation_p.G311V	NM_003436	NP_003427	B4DHH9	B4DHH9_HUMAN	zinc finger protein 135 isoform 2	502					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)										0.16129	25.086969	35.225011	15	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58579321	58579321	18316	19	G	T	T	T	559	43	ZNF135	2	2
MUC16	94025	broad.mit.edu	37	19	9077163	9077163	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9077163G>T	uc002mkp.2	-	c.10283C>A	c.(10282-10284)TCT>TAT	p.S3428Y		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	3429	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														0.393035	221.56884	223.58617	79	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9077163	9077163	10367	19	G	T	T	T	429	33	MUC16	2	2
UBE4B	10277	broad.mit.edu	37	1	10155625	10155625	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:10155625G>A	uc001aqs.3	+	c.318G>A	c.(316-318)ATG>ATA	p.M106I	UBE4B_uc001aqr.3_Missense_Mutation_p.M106I|UBE4B_uc010oai.1_Non-coding_Transcript|UBE4B_uc010oaj.1_5'UTR	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1	106					apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(1)	3		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)										0.297297	89.525081	93.606934	33	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10155625	10155625	17441	1	G	A	A	A	611	47	UBE4B	2	2
KIF1B	23095	broad.mit.edu	37	1	10407885	10407886	+	Splice_Site_DNP	DNP	GG	AT	AT			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:10407885_10407886GG>AT	uc001aqz.2	+	c.3864_splice	c.e35+1	p.Q1288_splice	KIF1B_uc001aqw.3_Splice_Site_DNP_p.Q1242_splice|KIF1B_uc001aqx.3_Splice_Site_DNP_p.Q1288_splice|KIF1B_uc001aqy.2_Splice_Site_DNP_p.Q1262_splice|KIF1B_uc001ara.2_Splice_Site_DNP_p.Q1248_splice|KIF1B_uc001arb.2_Splice_Site_DNP_p.Q1274_splice	NM_015074	NP_055889			kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|nerve-nerve synaptic transmission|neuromuscular synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)	2	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)										0.243902	47.857675	52.760158	20	62	KEEP	---	---	---	---	capture		Splice_Site_DNP	DNP	10407885	10407886	8595	1	GG	AT	AT	AT	451	35	KIF1B	5	2
PRPF38B	55119	broad.mit.edu	37	1	109241810	109241810	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:109241810G>C	uc001dvv.3	+	c.809G>C	c.(808-810)CGG>CCG	p.R270P	PRPF38B_uc001dvw.3_Missense_Mutation_p.R159P|PRPF38B_uc010ouz.1_Missense_Mutation_p.R73P	NM_018061	NP_060531	Q5VTL8	PR38B_HUMAN	PRP38 pre-mRNA processing factor 38 (yeast)	270	Arg-rich.				mRNA processing|RNA splicing	spliceosomal complex					0		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161)										0.344828	92.821138	94.672283	30	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109241810	109241810	13011	1	G	C	C	C	507	39	PRPF38B	3	3
C1orf127	148345	broad.mit.edu	37	1	11008316	11008316	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:11008316G>A	uc010oao.1	-	c.1429C>T	c.(1429-1431)CGC>TGC	p.R477C	C1orf127_uc001arr.1_Missense_Mutation_p.R459C|C1orf127_uc001ars.1_Missense_Mutation_p.R451C	NM_173507	NP_775778	B7ZLG7	B7ZLG7_HUMAN	hypothetical protein LOC148345	477										ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)										0.146341	32.987837	52.737773	24	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11008316	11008316	2061	1	G	A	A	A	520	40	C1orf127	1	1
TTLL10	254173	broad.mit.edu	37	1	1118337	1118337	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:1118337C>T	uc001acy.2	+	c.998C>T	c.(997-999)GCC>GTC	p.A333V	TTLL10_uc010nyg.1_Missense_Mutation_p.A333V|TTLL10_uc001acz.1_Missense_Mutation_p.A260V	NM_001130045	NP_001123517	Q6ZVT0	TTL10_HUMAN	tubulin tyrosine ligase-like family, member 10	333	TTL.				protein modification process		ATP binding|tubulin-tyrosine ligase activity			large_intestine(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;4.75e-36)|OV - Ovarian serous cystadenocarcinoma(86;5.82e-22)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)										0.157895	4.91895	7.034793	3	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1118337	1118337	17278	1	C	T	T	T	338	26	TTLL10	2	2
SEMA6C	10500	broad.mit.edu	37	1	151110269	151110269	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:151110269T>A	uc001ewv.2	-	c.674A>T	c.(673-675)CAC>CTC	p.H225L	SEMA6C_uc001ewu.2_Missense_Mutation_p.H225L|SEMA6C_uc001eww.2_Missense_Mutation_p.H185L|SEMA6C_uc010pcq.1_Missense_Mutation_p.H225L|SEMA6C_uc009wml.1_Non-coding_Transcript	NM_030913	NP_112175	Q9H3T2	SEM6C_HUMAN	semaphorin Y precursor	225	Extracellular (Potential).|Sema.					integral to membrane	receptor activity			ovary(1)	1	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)											0.212644	93.401008	106.661943	37	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151110269	151110269	14527	1	T	A	A	A	767	59	SEMA6C	3	3
HRNR	388697	broad.mit.edu	37	1	152191540	152191540	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152191540G>T	uc001ezt.1	-	c.2565C>A	c.(2563-2565)GGC>GGA	p.G855G		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	855	9.				keratinization		calcium ion binding|protein binding			ovary(1)	1	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.413793	201.430883	202.54158	72	102	KEEP	---	---	---	---	capture		Silent	SNP	152191540	152191540	7653	1	G	T	T	T	535	42	HRNR	2	2
IVL	3713	broad.mit.edu	37	1	152882670	152882670	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152882670C>A	uc001fau.2	+	c.397C>A	c.(397-399)CAA>AAA	p.Q133K		NM_005547	NP_005538	P07476	INVO_HUMAN	involucrin	133					isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine|keratinization|response to UV-B	cornified envelope|cytoplasm	protein binding, bridging|structural molecule activity			ovary(3)	3	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)											0.224138	30.640944	34.700366	13	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152882670	152882670	8233	1	C	A	A	A	325	25	IVL	2	2
GBA	2629	broad.mit.edu	37	1	155207330	155207330	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155207330C>A	uc001fjh.2	-	c.801G>T	c.(799-801)TGG>TGT	p.W267C	RAG1AP1_uc010pey.1_Intron|GBA_uc010pfw.1_Missense_Mutation_p.W154C|GBA_uc010pfx.1_Missense_Mutation_p.W218C|GBA_uc001fji.2_Missense_Mutation_p.W267C|GBA_uc001fjj.2_Missense_Mutation_p.W267C|GBA_uc001fjk.2_Missense_Mutation_p.W267C|GBA_uc001fjl.2_Missense_Mutation_p.W267C|GBA_uc010pfy.1_Missense_Mutation_p.W180C|GBA_uc009wqk.1_Missense_Mutation_p.W180C	NM_000157	NP_000148	P04062	GLCM_HUMAN	glucocerebrosidase precursor	267					carbohydrate metabolic process|cell death|lysosome organization|sphingolipid metabolic process	lysosomal membrane	cation binding|glucosylceramidase activity|protein binding			ovary(1)	1	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		Alglucerase(DB00088)|Imiglucerase(DB00053)									0.137255	10.192178	16.685306	7	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155207330	155207330	6532	1	C	A	A	A	286	22	GBA	2	2
ARHGEF11	9826	broad.mit.edu	37	1	156914841	156914841	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156914841C>A	uc001fqn.2	-	c.2961G>T	c.(2959-2961)AGG>AGT	p.R987S	ARHGEF11_uc010phu.1_Missense_Mutation_p.R363S|ARHGEF11_uc001fqo.2_Missense_Mutation_p.R947S	NM_198236	NP_937879	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	947					actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|pancreas(1)|lung(1)|kidney(1)|pleura(1)	7	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)													0.264535	209.740428	227.006866	91	253	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156914841	156914841	910	1	C	A	A	A	285	22	ARHGEF11	2	2
IGSF8	93185	broad.mit.edu	37	1	160063683	160063683	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:160063683C>T	uc001fva.2	-	c.721G>A	c.(721-723)GGG>AGG	p.G241R	IGSF8_uc001fuz.2_Missense_Mutation_p.G241R|IGSF8_uc009wtf.2_Missense_Mutation_p.G241R	NM_052868	NP_443100	Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	241	Extracellular (Potential).|Ig-like C2-type 2.				cell proliferation|cellular component movement|nervous system development|single fertilization|skeletal muscle tissue development	integral to membrane	protein binding				0	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)											0.363636	59.185197	60.084921	20	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160063683	160063683	7905	1	C	T	T	T	312	24	IGSF8	2	2
OLFML2B	25903	broad.mit.edu	37	1	161970075	161970075	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:161970075G>T	uc010pkq.1	-	c.780C>A	c.(778-780)ATC>ATA	p.I260I	OLFML2B_uc001gbu.2_Silent_p.I259I	NM_015441	NP_056256	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B precursor	259											0	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)											0.303797	56.501153	59.260356	24	55	KEEP	---	---	---	---	capture		Silent	SNP	161970075	161970075	11263	1	G	T	T	T	473	37	OLFML2B	1	1
PRG4	10216	broad.mit.edu	37	1	186278009	186278009	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:186278009G>T	uc001gru.3	+	c.3158G>T	c.(3157-3159)CGC>CTC	p.R1053L	PRG4_uc001grt.3_Missense_Mutation_p.R1012L|PRG4_uc009wyl.2_Missense_Mutation_p.R960L|PRG4_uc009wym.2_Missense_Mutation_p.R919L|PRG4_uc010poo.1_Non-coding_Transcript	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	1053					cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity				0														0.2	66.662851	79.221663	30	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	186278009	186278009	12924	1	G	T	T	T	494	38	PRG4	1	1
UBR4	23352	broad.mit.edu	37	1	19433433	19433433	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:19433433C>A	uc001bbi.2	-	c.12133G>T	c.(12133-12135)GTG>TTG	p.V4045L	UBR4_uc001bbg.2_5'Flank|UBR4_uc001bbh.2_5'Flank	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	4045					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)	23		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)										0.181818	11.148237	14.276317	6	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19433433	19433433	17462	1	C	A	A	A	234	18	UBR4	2	2
UBR4	23352	broad.mit.edu	37	1	19443790	19443790	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:19443790C>A	uc001bbi.2	-	c.10748G>T	c.(10747-10749)CGG>CTG	p.R3583L	UBR4_uc001bbj.1_5'UTR	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	3583					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)	23		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)										0.348718	195.443273	199.380453	68	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19443790	19443790	17462	1	C	A	A	A	299	23	UBR4	1	1
CRB1	23418	broad.mit.edu	37	1	197390532	197390532	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197390532T>C	uc001gtz.2	+	c.1574T>C	c.(1573-1575)TTC>TCC	p.F525S	CRB1_uc010poz.1_Missense_Mutation_p.F456S|CRB1_uc010ppa.1_Non-coding_Transcript|CRB1_uc009wza.2_Missense_Mutation_p.F413S|CRB1_uc010ppb.1_Missense_Mutation_p.F525S|CRB1_uc010ppc.1_Non-coding_Transcript|CRB1_uc010ppd.1_Missense_Mutation_p.F6S|CRB1_uc001gub.1_Missense_Mutation_p.F174S	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	525	Extracellular (Potential).|Laminin G-like 1.				cell-cell signaling|establishment or maintenance of cell polarity|response to stimulus|visual perception	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|large_intestine(1)	6														0.353535	115.399034	117.270034	35	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197390532	197390532	3987	1	T	C	C	C	806	62	CRB1	4	4
CACNA1S	779	broad.mit.edu	37	1	201044702	201044702	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:201044702C>A	uc001gvv.2	-	c.1869G>T	c.(1867-1869)GGG>GGT	p.G623G		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	623	II.|Extracellular (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)	4					Magnesium Sulfate(DB00653)|Verapamil(DB00661)									0.298561	203.401176	213.493873	83	195	KEEP	---	---	---	---	capture		Silent	SNP	201044702	201044702	2663	1	C	A	A	A	379	30	CACNA1S	2	2
LRRN2	10446	broad.mit.edu	37	1	204587527	204587527	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:204587527G>T	uc001hbe.1	-	c.1594C>A	c.(1594-1596)CGG>AGG	p.R532R	MDM4_uc001hbd.1_Intron|LRRN2_uc001hbf.1_Silent_p.R532R|LRRN2_uc009xbf.1_Silent_p.R532R|MDM4_uc001hbc.2_Intron	NM_006338	NP_006329	O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2 precursor	532	Extracellular (Potential).				cell adhesion	integral to membrane	receptor activity			central_nervous_system(2)	2	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)											0.345794	98.144685	100.390156	37	70	KEEP	---	---	---	---	capture		Silent	SNP	204587527	204587527	9411	1	G	T	T	T	506	39	LRRN2	1	1
LAMB3	3914	broad.mit.edu	37	1	209801421	209801421	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:209801421C>A	uc001hhg.2	-	c.1247G>T	c.(1246-1248)GGC>GTC	p.G416V	LAMB3_uc009xco.2_Missense_Mutation_p.G416V|LAMB3_uc001hhh.2_Missense_Mutation_p.G416V|LAMB3_uc010psl.1_Non-coding_Transcript	NM_001017402	NP_001017402	Q13751	LAMB3_HUMAN	laminin, beta 3 precursor	416	Laminin EGF-like 3.				cell adhesion|epidermis development|hemidesmosome assembly		structural molecule activity			central_nervous_system(2)|large_intestine(1)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(81;0.0519)								OREG0014217	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.2	5.216347	6.473714	3	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	209801421	209801421	8935	1	C	A	A	A	338	26	LAMB3	2	2
CENPF	1063	broad.mit.edu	37	1	214818476	214818476	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:214818476G>T	uc001hkm.2	+	c.5563G>T	c.(5563-5565)GAG>TAG	p.E1855*		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	1951	Potential.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)	12				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		Colon(80;575 1284 11000 14801 43496)								0.102041	3.135412	10.876446	5	44	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	214818476	214818476	3364	1	G	T	T	T	533	41	CENPF	5	2
NUP133	55746	broad.mit.edu	37	1	229588306	229588306	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:229588306G>A	uc001htn.2	-	c.3065C>T	c.(3064-3066)GCG>GTG	p.A1022V		NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	1022					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|ovary(1)	5	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)							p.A1022V(SNU175-Tumor)	578				0.2	31.982832	38.2619	15	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	229588306	229588306	11159	1	G	A	A	A	494	38	NUP133	1	1
RYR2	6262	broad.mit.edu	37	1	237656365	237656365	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237656365C>A	uc001hyl.1	+	c.1939C>A	c.(1939-1941)CGT>AGT	p.R647S		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	647	Cytoplasmic (By similarity).|B30.2/SPRY 1.				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)											0.222222	15.339963	17.253295	6	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237656365	237656365	14249	1	C	A	A	A	247	19	RYR2	1	1
ZP4	57829	broad.mit.edu	37	1	238048738	238048738	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:238048738G>T	uc001hym.2	-	c.1113C>A	c.(1111-1113)CCC>CCA	p.P371P	LOC100130331_uc010pyc.1_Intron	NM_021186	NP_067009	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4 preproprotein	371	ZP.|Extracellular (Potential).				acrosomal vesicle exocytosis|negative regulation of binding of sperm to zona pellucida|positive regulation of acrosome reaction|positive regulation of humoral immune response|positive regulation of protein kinase activity|positive regulation of T cell proliferation|protein kinase A signaling cascade|protein kinase C signaling cascade	integral to membrane|plasma membrane|proteinaceous extracellular matrix	acrosin binding|receptor activity			ovary(1)	1	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			NSCLC(166;160 2029 11600 18754 19936)								0.185185	41.63954	51.672916	20	88	KEEP	---	---	---	---	capture		Silent	SNP	238048738	238048738	18822	1	G	T	T	T	600	47	ZP4	2	2
OR2L13	284521	broad.mit.edu	37	1	248263535	248263535	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248263535C>A	uc001ids.2	+	c.858C>A	c.(856-858)CCC>CCA	p.P286P		NM_175911	NP_787107	Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L,	286	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)							85				0.089552	1.793306	13.194572	6	61	KEEP	---	---	---	---	capture		Silent	SNP	248263535	248263535	11412	1	C	A	A	A	262	21	OR2L13	2	2
OR2M5	127059	broad.mit.edu	37	1	248308920	248308920	+	Silent	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248308920C>T	uc010pze.1	+	c.471C>T	c.(469-471)ATC>ATT	p.I157I		NM_001004690	NP_001004690	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M,	157	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|kidney(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)											0.197619	169.015486	204.760887	83	337	KEEP	---	---	---	---	capture		Silent	SNP	248308920	248308920	11419	1	C	T	T	T	369	29	OR2M5	2	2
OR2T12	127064	broad.mit.edu	37	1	248457981	248457981	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248457981T>A	uc010pzj.1	-	c.900A>T	c.(898-900)AAA>AAT	p.K300N		NM_001004692	NP_001004692	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T,	300	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	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;0.0201)											0.07173	-9.711793	35.068306	17	220	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248457981	248457981	11425	1	T	A	A	A	777	60	OR2T12	3	3
LDLRAP1	26119	broad.mit.edu	37	1	25880433	25880433	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:25880433G>T	uc001bkl.3	+	c.109G>T	c.(109-111)GAC>TAC	p.D37Y		NM_015627	NP_056442	Q5SW96	ARH_HUMAN	low density lipoprotein receptor adaptor protein	37					amyloid precursor protein metabolic process|cholesterol homeostasis|cholesterol metabolic process|positive regulation of cholesterol metabolic process|positive regulation of receptor-mediated endocytosis|receptor internalization|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport|regulation of establishment of protein localization in plasma membrane|regulation of protein binding	basal plasma membrane|cytosol|early endosome|internal side of plasma membrane|neurofilament|recycling endosome	beta-amyloid binding|clathrin binding|low-density lipoprotein particle receptor binding|phosphatidylinositol-4,5-bisphosphate binding|phosphotyrosine binding|protein binding, bridging|protein complex binding|receptor signaling complex scaffold activity|signaling adaptor activity			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.63e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|GBM - Glioblastoma multiforme(114;0.00914)|READ - Rectum adenocarcinoma(331;0.0649)										0.2	20.118804	24.307035	10	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25880433	25880433	9032	1	G	T	T	T	429	33	LDLRAP1	2	2
PPCS	79717	broad.mit.edu	37	1	42922700	42922700	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:42922700A>G	uc001chl.2	+	c.464A>G	c.(463-465)TAT>TGT	p.Y155C	ZMYND12_uc001chj.2_5'Flank|ZMYND12_uc010ojt.1_5'Flank|PPCS_uc001chk.2_Intron	NM_024664	NP_078940	Q9HAB8	PPCS_HUMAN	phosphopantothenoylcysteine synthetase isoform	155					coenzyme biosynthetic process|pantothenate metabolic process	cytosol	phosphopantothenate--cysteine ligase activity				0	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)												0.28	67.164672	70.414794	21	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42922700	42922700	12735	1	A	G	G	G	208	16	PPCS	4	4
SLC6A9	6536	broad.mit.edu	37	1	44474186	44474186	+	Silent	SNP	G	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:44474186G>C	uc001cll.2	-	c.648C>G	c.(646-648)CCC>CCG	p.P216P	SLC6A9_uc009vxe.2_Silent_p.P72P|SLC6A9_uc010okm.1_Silent_p.P143P|SLC6A9_uc001clm.2_Silent_p.P162P|SLC6A9_uc009vxd.2_Non-coding_Transcript|SLC6A9_uc010okn.1_Silent_p.P147P|SLC6A9_uc001cln.2_Silent_p.P143P|SLC6A9_uc010oko.1_Silent_p.P32P|SLC6A9_uc010okp.1_Non-coding_Transcript	NM_201649	NP_964012	P48067	SC6A9_HUMAN	solute carrier family 6 member 9 isoform 2	216	Extracellular (Potential).					integral to plasma membrane|membrane fraction	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity				0	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)									0.219858	72.542609	82.739507	31	110	KEEP	---	---	---	---	capture		Silent	SNP	44474186	44474186	15188	1	G	C	C	C	444	35	SLC6A9	3	3
MKNK1	8569	broad.mit.edu	37	1	47030775	47030775	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:47030775C>T	uc001cqb.2	-	c.706G>A	c.(706-708)GGC>AGC	p.G236S	MKNK1_uc010omd.1_Missense_Mutation_p.G100S|MKNK1_uc001cqc.2_Missense_Mutation_p.G195S|MKNK1_uc009vyi.2_Missense_Mutation_p.G195S|MKNK1_uc010ome.1_Missense_Mutation_p.G100S|MKNK1_uc009vyj.2_Missense_Mutation_p.G140S	NM_003684	NP_003675	Q9BUB5	MKNK1_HUMAN	MAP kinase-interacting serine/threonine kinase 1	236	Protein kinase.				intracellular protein kinase cascade|peptidyl-serine phosphorylation|regulation of translation	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2	Acute lymphoblastic leukemia(166;0.155)									255				0.160305	81.078176	109.864759	42	220	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47030775	47030775	9994	1	C	T	T	T	286	22	MKNK1	2	2
KANK4	163782	broad.mit.edu	37	1	62740193	62740193	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:62740193C>A	uc001dah.3	-	c.583G>T	c.(583-585)GGT>TGT	p.G195C	KANK4_uc001dai.3_Intron|KANK4_uc001dag.3_5'Flank	NM_181712	NP_859063	Q5T7N3	KANK4_HUMAN	ankyrin repeat domain 38	195	Pro-rich.									ovary(3)|lung(1)	4														0.234375	34.592755	38.724571	15	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62740193	62740193	8283	1	C	A	A	A	286	22	KANK4	2	2
C1orf173	127254	broad.mit.edu	37	1	75037769	75037769	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:75037769G>T	uc001dgg.2	-	c.3625C>A	c.(3625-3627)CGC>AGC	p.R1209S		NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	1209	Glu-rich.									ovary(3)|central_nervous_system(1)	4														0.350515	204.511556	208.304835	68	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75037769	75037769	2081	1	G	T	T	T	507	39	C1orf173	1	1
LHX8	431707	broad.mit.edu	37	1	75608973	75608973	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:75608973G>A	uc001dgo.2	+	c.560G>A	c.(559-561)AGA>AAA	p.R187K	LHX8_uc001dgq.2_Missense_Mutation_p.R126K	NM_001001933	NP_001001933	Q68G74	LHX8_HUMAN	LIM homeobox 8	187	LIM zinc-binding 2.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(3)	3														0.1875	18.843502	23.23562	9	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75608973	75608973	9102	1	G	A	A	A	429	33	LHX8	2	2
IFI44L	10964	broad.mit.edu	37	1	79107250	79107250	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:79107250G>C	uc010oro.1	+	c.1280G>C	c.(1279-1281)CGG>CCG	p.R427P	IFI44L_uc010orp.1_Missense_Mutation_p.R164P|IFI44L_uc010orq.1_Missense_Mutation_p.R164P	NM_006820	NP_006811	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	427						cytoplasm					0														0.140187	28.053211	41.426975	15	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79107250	79107250	7819	1	G	C	C	C	507	39	IFI44L	3	3
LPHN2	23266	broad.mit.edu	37	1	82408764	82408764	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:82408764T>C	uc001dit.3	+	c.509T>C	c.(508-510)ATT>ACT	p.I170T	LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Missense_Mutation_p.I170T|LPHN2_uc001div.2_Missense_Mutation_p.I170T|LPHN2_uc009wcd.2_Missense_Mutation_p.I170T	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor	170	Extracellular (Potential).|Olfactomedin-like.				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(2)|central_nervous_system(1)	3				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)										0.129032	16.060063	24.36465	8	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82408764	82408764	9289	1	T	C	C	C	676	52	LPHN2	4	4
SYDE2	84144	broad.mit.edu	37	1	85648290	85648290	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:85648290A>G	uc009wcm.2	-	c.2035T>C	c.(2035-2037)TCT>CCT	p.S679P	SYDE2_uc001dku.3_Missense_Mutation_p.S679P	NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	679					activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)										0.418605	62.243082	62.491529	18	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85648290	85648290	15957	1	A	G	G	G	156	12	SYDE2	4	4
CLCA2	9635	broad.mit.edu	37	1	86900337	86900337	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:86900337C>A	uc001dlr.3	+	c.881C>A	c.(880-882)ACT>AAT	p.T294N		NM_006536	NP_006527	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2 precursor	294	Extracellular (Potential).				cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity			ovary(1)|breast(1)	2		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)								0.110169	11.880927	29.635199	13	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86900337	86900337	3594	1	C	A	A	A	260	20	CLCA2	2	2
LRRC8C	84230	broad.mit.edu	37	1	90179493	90179493	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:90179493A>T	uc001dnl.3	+	c.1364A>T	c.(1363-1365)AAG>ATG	p.K455M		NM_032270	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member	455	LRR 3.					endoplasmic reticulum membrane|integral to membrane				ovary(3)|central_nervous_system(1)|pancreas(1)	5		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)										0.264706	85.431093	92.243335	36	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90179493	90179493	9399	1	A	T	T	T	39	3	LRRC8C	3	3
C20orf46	55321	broad.mit.edu	37	20	1161882	1161882	+	Silent	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:1161882G>A	uc010gaa.1	-	c.381C>T	c.(379-381)CTC>CTT	p.L127L	C20orf46_uc002weq.1_Silent_p.L127L	NM_018354	NP_060824	Q9NUR3	CT046_HUMAN	hypothetical protein LOC55321	127	Helical; (Potential).					integral to membrane	protein binding			ovary(1)	1														0.317073	106.490472	110.145172	39	84	KEEP	---	---	---	---	capture		Silent	SNP	1161882	1161882	2193	20	G	A	A	A	470	37	C20orf46	1	1
CST9	128822	broad.mit.edu	37	20	23586393	23586393	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:23586393C>A	uc002wtl.2	-	c.109G>T	c.(109-111)GGT>TGT	p.G37C		NM_001008693	NP_001008693	Q5W186	CST9_HUMAN	cystatin 9 precursor	37						extracellular region	cysteine-type endopeptidase inhibitor activity			ovary(1)	1	Colorectal(13;0.0993)													0.18638	106.420951	132.147818	52	227	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23586393	23586393	4120	20	C	A	A	A	273	21	CST9	2	2
VPS16	64601	broad.mit.edu	37	20	2846896	2846898	+	Nonsense_Mutation	TNP	CGA	ATT	ATT			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:2846896_2846898CGA>ATT	uc002whe.2	+	c.2310_2312CGA>ATT	c.(2308-2313)TACGAA>TAATTA	p.770_771YE>*L	VPS16_uc002whh.2_Intron|PTPRA_uc002whj.2_Intron|VPS16_uc002whf.2_Nonsense_Mutation_p.626_627YE>*L|VPS16_uc002whd.2_Non-coding_Transcript|VPS16_uc002whg.2_Nonsense_Mutation_p.456_457YE>*L|VPS16_uc002whi.2_Nonsense_Mutation_p.254_255YE>*L	NM_022575	NP_072097	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 isoform 1	770_771					intracellular protein transport	early endosome|HOPS complex|late endosome membrane|lysosomal membrane|recycling endosome				ovary(2)|pancreas(1)	3														0.173333	24.025732	31.591193	13	62	KEEP	---	---	---	---	capture		Nonsense_Mutation	TNP	2846896	2846898	17760	20	CGA	ATT	ATT	ATT	246	19	VPS16	5	1
SUN5	140732	broad.mit.edu	37	20	31587901	31587901	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:31587901T>C	uc002wyi.2	-	c.319A>G	c.(319-321)ATT>GTT	p.I107V		NM_080675	NP_542406	Q8TC36	SUN5_HUMAN	sperm associated antigen 4-like	107					spermatogenesis						0														0.3	22.653816	23.732367	9	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31587901	31587901	15914	20	T	C	C	C	663	51	SUN5	4	4
PHACTR3	116154	broad.mit.edu	37	20	58322818	58322818	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:58322818G>C	uc002yau.2	+	c.286G>C	c.(286-288)GAG>CAG	p.E96Q	PHACTR3_uc002yat.2_Missense_Mutation_p.E93Q|PHACTR3_uc010zzw.1_Missense_Mutation_p.E55Q|PHACTR3_uc002yav.2_Missense_Mutation_p.E55Q|PHACTR3_uc002yaw.2_Missense_Mutation_p.E55Q|PHACTR3_uc002yax.2_Missense_Mutation_p.E55Q	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1	96	RPEL 1.					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)											0.204255	129.883566	148.946567	48	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58322818	58322818	12234	20	G	C	C	C	533	41	PHACTR3	3	3
DIDO1	11083	broad.mit.edu	37	20	61542643	61542643	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:61542643C>A	uc002ydr.1	-	c.322G>T	c.(322-324)GAG>TAG	p.E108*	DIDO1_uc002yds.1_Nonsense_Mutation_p.E108*|DIDO1_uc002ydt.1_Nonsense_Mutation_p.E108*|DIDO1_uc002ydu.1_Nonsense_Mutation_p.E108*|DIDO1_uc002ydv.1_Nonsense_Mutation_p.E108*|DIDO1_uc002ydw.1_Nonsense_Mutation_p.E108*|DIDO1_uc002ydx.1_Nonsense_Mutation_p.E108*|DIDO1_uc011aao.1_Nonsense_Mutation_p.E108*	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	108					apoptosis	cytoplasm|nucleus	zinc ion binding			ovary(3)	3	Breast(26;5.68e-08)					Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)								0.25641	19.280074	21.428192	10	29	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	61542643	61542643	4701	20	C	A	A	A	403	31	DIDO1	5	1
KCNQ2	3785	broad.mit.edu	37	20	62038665	62038665	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62038665G>A	uc002yey.1	-	c.1951C>T	c.(1951-1953)CCC>TCC	p.P651S	KCNQ2_uc002yez.1_Missense_Mutation_p.P620S|KCNQ2_uc002yfa.1_Missense_Mutation_p.P633S|KCNQ2_uc002yfb.1_Missense_Mutation_p.P623S	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein	651	Cytoplasmic (Potential).				axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)									0.226667	33.67719	38.891266	17	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62038665	62038665	8388	20	G	A	A	A	559	43	KCNQ2	2	2
ADAMTS5	11096	broad.mit.edu	37	21	28296423	28296423	+	Silent	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:28296423A>T	uc002ymg.2	-	c.2742T>A	c.(2740-2742)CCT>CCA	p.P914P		NM_007038	NP_008969	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1	914	TSP type-1 2.				proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3						Esophageal Squamous(53;683 1080 10100 14424 45938)								0.220588	32.293641	37.178541	15	53	KEEP	---	---	---	---	capture		Silent	SNP	28296423	28296423	270	21	A	T	T	T	132	11	ADAMTS5	3	3
RIPK4	54101	broad.mit.edu	37	21	43161537	43161537	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:43161537T>C	uc002yzn.1	-	c.1816A>G	c.(1816-1818)ACG>GCG	p.T606A		NM_020639	NP_065690	Q9H4D1	Q9H4D1_HUMAN	ankyrin repeat domain 3	606					protein phosphorylation	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7										268				0.246988	112.656929	122.302895	41	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43161537	43161537	13860	21	T	C	C	C	754	58	RIPK4	4	4
EFCAB6	64800	broad.mit.edu	37	22	43936185	43936185	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:43936185T>G	uc003bdy.1	-	c.3701A>C	c.(3700-3702)TAC>TCC	p.Y1234S	EFCAB6_uc003bdz.1_Missense_Mutation_p.Y1082S|EFCAB6_uc010gzi.1_Missense_Mutation_p.Y1082S|EFCAB6_uc010gzj.1_3'UTR	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	1234	EF-hand 14.				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)												0.315068	71.206272	73.423134	23	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43936185	43936185	5126	22	T	G	G	G	741	57	EFCAB6	4	4
GRAMD4	23151	broad.mit.edu	37	22	47058939	47058939	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:47058939C>T	uc003bhx.2	+	c.469C>T	c.(469-471)CGC>TGC	p.R157C	GRAMD4_uc010had.2_Missense_Mutation_p.R96C	NM_015124	NP_055939	Q6IC98	GRAM4_HUMAN	death-inducing-protein	157					apoptosis	integral to membrane|mitochondrial membrane				ovary(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)										0.361111	67.122768	68.348107	26	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47058939	47058939	7028	22	C	T	T	T	351	27	GRAMD4	1	1
RANBP2	5903	broad.mit.edu	37	2	109399221	109399221	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:109399221G>T	uc002tem.3	+	c.9272G>T	c.(9271-9273)CGG>CTG	p.R3091L		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	3091	PPIase cyclophilin-type.				carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(14)	soft_tissue(14)|pancreas(1)	15														0.239583	178.527306	196.362116	69	219	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109399221	109399221	13488	2	G	T	T	T	507	39	RANBP2	1	1
ACOXL	55289	broad.mit.edu	37	2	111556667	111556667	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:111556667G>A	uc010yxk.1	+	c.537G>A	c.(535-537)ATG>ATA	p.M179I	ACOXL_uc010fkc.2_Missense_Mutation_p.M179I|ACOXL_uc002tgr.3_Missense_Mutation_p.M179I	NM_001142807	NP_001136279	Q9NUZ1	ACOXL_HUMAN	acyl-Coenzyme A oxidase-like 1	179					fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0										368				0.326241	121.404256	125.179446	46	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111556667	111556667	162	2	G	A	A	A	624	48	ACOXL	2	2
SNTG2	54221	broad.mit.edu	37	2	1271214	1271214	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:1271214G>T	uc002qwq.2	+	c.1155G>T	c.(1153-1155)AGG>AGT	p.R385S	SNTG2_uc010ewi.2_Missense_Mutation_p.R258S	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	385	PH.				central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)										0.285714	19.986821	21.141637	8	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1271214	1271214	15375	2	G	T	T	T	542	42	SNTG2	2	2
MYO7B	4648	broad.mit.edu	37	2	128389269	128389269	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:128389269G>T	uc002top.2	+	c.5112G>T	c.(5110-5112)CCG>CCT	p.P1704P	MYO7B_uc002tos.1_5'Flank|MYO7B_uc002tot.2_5'Flank	NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	1704	MyTH4 2.					apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)										0.135135	7.367182	12.126568	5	32	KEEP	---	---	---	---	capture		Silent	SNP	128389269	128389269	10478	2	G	T	T	T	496	39	MYO7B	1	1
LRP1B	53353	broad.mit.edu	37	2	142004803	142004803	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:142004803G>A	uc002tvj.1	-	c.584C>T	c.(583-585)GCT>GTT	p.A195V	LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	195	Extracellular (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.230769	39.890726	44.208343	15	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142004803	142004803	9328	2	G	A	A	A	442	34	LRP1B	2	2
PXDN	7837	broad.mit.edu	37	2	1667444	1667444	+	Silent	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:1667444G>A	uc002qxa.2	-	c.1500C>T	c.(1498-1500)TAC>TAT	p.Y500Y	PXDN_uc002qxb.1_Silent_p.Y500Y	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	500	Ig-like C2-type 3.				extracellular matrix organization|hydrogen peroxide catabolic process|immune response|oxidation-reduction process	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)						2093				0.069364	-9.641723	23.510631	12	161	KEEP	---	---	---	---	capture		Silent	SNP	1667444	1667444	13305	2	G	A	A	A	516	40	PXDN	1	1
UBR3	130507	broad.mit.edu	37	2	170871812	170871812	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:170871812G>T	uc010zdi.1	+	c.4389G>T	c.(4387-4389)TTG>TTT	p.L1463F	UBR3_uc002ufr.3_Non-coding_Transcript|UBR3_uc010fqa.2_Missense_Mutation_p.L284F|UBR3_uc002uft.3_Missense_Mutation_p.L320F|UBR3_uc010zdj.1_Missense_Mutation_p.L125F|UBR3_uc002ufu.3_5'UTR	NM_172070	NP_742067	Q6ZT12	UBR3_HUMAN	E3 ubiquitin-protein ligase UBR3	1463					sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0														0.310345	23.862582	24.792713	9	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170871812	170871812	17461	2	G	T	T	T	581	45	UBR3	2	2
ITGA6	3655	broad.mit.edu	37	2	173340413	173340413	+	Silent	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:173340413G>A	uc002uhp.1	+	c.1269G>A	c.(1267-1269)CAG>CAA	p.Q423Q	ITGA6_uc010zdy.1_Silent_p.Q304Q|ITGA6_uc002uho.1_Silent_p.Q423Q|ITGA6_uc010fqm.1_Silent_p.Q69Q	NM_001079818	NP_001073286	P23229	ITA6_HUMAN	integrin alpha chain, alpha 6 isoform a	462	Extracellular (Potential).|FG-GAP 7.				blood coagulation|cell adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|leukocyte migration|positive regulation of apoptosis	integrin complex	protein binding|receptor activity			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0979)											0.281481	112.792333	118.585017	38	97	KEEP	---	---	---	---	capture		Silent	SNP	173340413	173340413	8184	2	G	A	A	A	451	35	ITGA6	2	2
TTN	7273	broad.mit.edu	37	2	179421984	179421984	+	Silent	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179421984A>T	uc010zfg.1	-	c.80301T>A	c.(80299-80301)GCT>GCA	p.A26767A	TTN_uc010zfh.1_Silent_p.A20462A|TTN_uc010zfi.1_Silent_p.A20395A|TTN_uc010zfj.1_Silent_p.A20270A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3158										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.3	40.104316	41.891912	15	35	KEEP	---	---	---	---	capture		Silent	SNP	179421984	179421984	17290	2	A	T	T	T	28	3	TTN	3	3
FASTKD2	22868	broad.mit.edu	37	2	207631989	207631989	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:207631989T>C	uc002vbu.2	+	c.572T>C	c.(571-573)ATT>ACT	p.I191T	MDH1B_uc010ziw.1_5'Flank|MDH1B_uc002vbs.2_5'Flank|MDH1B_uc010fui.2_5'Flank|MDH1B_uc010fuj.2_5'Flank|MDH1B_uc002vbt.2_5'Flank|FASTKD2_uc002vbv.2_Missense_Mutation_p.I191T|FASTKD2_uc002vbx.2_Missense_Mutation_p.I191T|FASTKD2_uc002vbw.1_Missense_Mutation_p.I191T	NM_001136193	NP_001129665	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	191					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(2)	2				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)										0.293023	207.447496	215.687775	63	152	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	207631989	207631989	5922	2	T	C	C	C	676	52	FASTKD2	4	4
APOB	338	broad.mit.edu	37	2	21230206	21230206	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:21230206C>G	uc002red.2	-	c.9534G>C	c.(9532-9534)AAG>AAC	p.K3178N		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	3178	Heparin-binding.|Basic (possible receptor binding region).				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.268041	82.904381	87.617451	26	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21230206	21230206	796	2	C	G	G	G	415	32	APOB	3	3
APOB	338	broad.mit.edu	37	2	21246397	21246397	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:21246397G>T	uc002red.2	-	c.2604C>A	c.(2602-2604)AAC>AAA	p.N868K		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	868					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.240741	70.293826	76.920568	26	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21246397	21246397	796	2	G	T	T	T	516	40	APOB	1	1
APOB	338	broad.mit.edu	37	2	21260849	21260849	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:21260849G>T	uc002red.2	-	c.518C>A	c.(517-519)GCC>GAC	p.A173D		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	173	Vitellogenin.				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.229412	90.751088	102.157468	39	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21260849	21260849	796	2	G	T	T	T	546	42	APOB	2	2
VIL1	7429	broad.mit.edu	37	2	219295487	219295487	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:219295487G>T	uc002via.2	+	c.988G>T	c.(988-990)GTG>TTG	p.V330L	VIL1_uc010zke.1_Missense_Mutation_p.V19L|VIL1_uc002vib.2_Missense_Mutation_p.V330L|VIL1_uc002vic.1_Missense_Mutation_p.V330L	NM_007127	NP_009058	P09327	VILI_HUMAN	villin 1	330	Core.				actin filament capping|actin filament depolymerization|actin filament polymerization|actin filament severing|apoptosis|cellular response to epidermal growth factor stimulus|cytoplasmic actin-based contraction involved in cell motility|epidermal growth factor receptor signaling pathway|positive regulation of actin filament bundle assembly|positive regulation of epithelial cell migration|regulation of actin nucleation|regulation of cell shape|regulation of lamellipodium morphogenesis|regulation of wound healing|response to bacterium	actin filament bundle|cytoplasm|filopodium tip|intracellular membrane-bounded organelle|lamellipodium|microvillus|ruffle	actin filament binding|calcium ion binding|caspase inhibitor activity|lysophosphatidic acid binding|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.198529	56.447417	67.95804	27	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	219295487	219295487	17731	2	G	T	T	T	572	44	VIL1	2	2
CHRND	1144	broad.mit.edu	37	2	233398943	233398943	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:233398943C>A	uc002vsw.2	+	c.1262C>A	c.(1261-1263)CCA>CAA	p.P421Q	CHRND_uc010zmg.1_Missense_Mutation_p.P406Q|CHRND_uc010fyc.2_Missense_Mutation_p.P294Q|CHRND_uc010zmh.1_Missense_Mutation_p.P227Q	NM_000751	NP_000742	Q07001	ACHD_HUMAN	nicotinic acetylcholine receptor delta	421	Cytoplasmic (Potential).				muscle contraction|musculoskeletal movement|neuromuscular process|skeletal muscle tissue growth|synaptic transmission	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	nicotinic acetylcholine-activated cation-selective channel activity|receptor activity			ovary(1)|breast(1)	2		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)										0.282051	54.004118	57.342757	22	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	233398943	233398943	3528	2	C	A	A	A	273	21	CHRND	2	2
OTOF	9381	broad.mit.edu	37	2	26691312	26691312	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:26691312C>A	uc002rhk.2	-	c.4054G>T	c.(4054-4056)GAC>TAC	p.D1352Y	OTOF_uc010yla.1_Missense_Mutation_p.D82Y|OTOF_uc002rhh.2_Missense_Mutation_p.D585Y|OTOF_uc002rhi.2_Missense_Mutation_p.D662Y|OTOF_uc002rhj.2_Missense_Mutation_p.D585Y	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	1352	Cytoplasmic (Potential).				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GBM(102;732 1451 20652 24062 31372)								0.266667	100.424083	107.806613	40	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26691312	26691312	11715	2	C	A	A	A	377	29	OTOF	2	2
GCKR	2646	broad.mit.edu	37	2	27731038	27731039	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27731038_27731039CC>AA	uc002rky.2	+	c.1342_1343CC>AA	c.(1342-1344)CCT>AAT	p.P448N	GCKR_uc010ezd.2_Missense_Mutation_p.P446N|GCKR_uc010ylu.1_Missense_Mutation_p.P258N	NM_001486	NP_001477	Q14397	GCKR_HUMAN	glucokinase regulatory protein	448	SIS 2.				carbohydrate metabolic process|glucose transport|negative regulation of glucokinase activity|positive regulation of gene expression|protein import into nucleus, translocation|regulation of glucose transport|response to fructose stimulus|transmembrane transport|triglyceride homeostasis|urate metabolic process	cytosol|nucleoplasm	fructose-6-phosphate binding|protein binding			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)													0.181818	36.987371	46.405924	18	81	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	27731038	27731039	6560	2	CC	AA	AA	AA	286	22	GCKR	2	2
SPAST	6683	broad.mit.edu	37	2	32289089	32289089	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:32289089G>T	uc002roc.2	+	c.189G>T	c.(187-189)CTG>CTT	p.L63L	SPAST_uc002rod.2_Silent_p.L63L	NM_014946	NP_055761	Q9UBP0	SPAST_HUMAN	spastin isoform 1	63	Required for interaction with SSNA1 and microtubules.|Required for interaction with RTN1.|Nuclear export signal.|Required for interaction with ATL1.|Helical; (Potential).|Required for midbody localization.				cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)													0.25	32.047684	35.00361	13	39	KEEP	---	---	---	---	capture		Silent	SNP	32289089	32289089	15505	2	G	T	T	T	587	46	SPAST	2	2
ABCG5	64240	broad.mit.edu	37	2	44051409	44051409	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:44051409A>G	uc002rtn.2	-	c.1067T>C	c.(1066-1068)TTC>TCC	p.F356S	ABCG5_uc002rtm.2_Intron|ABCG5_uc002rto.2_Missense_Mutation_p.F185S|ABCG5_uc002rtp.2_Intron	NM_022436	NP_071881	Q9H222	ABCG5_HUMAN	ATP-binding cassette sub-family G member 5	356	Cytoplasmic (Potential).				cholesterol efflux|cholesterol homeostasis|excretion|intestinal cholesterol absorption|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)												0.21875	136.159731	152.481773	49	175	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44051409	44051409	72	2	A	G	G	G	117	9	ABCG5	4	4
MSH6	2956	broad.mit.edu	37	2	48027856	48027856	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:48027856T>C	uc002rwd.3	+	c.2734T>C	c.(2734-2736)TGG>CGG	p.W912R	MSH6_uc002rwc.2_Missense_Mutation_p.W912R|MSH6_uc010fbj.2_Missense_Mutation_p.W610R|MSH6_uc010yoi.1_Missense_Mutation_p.W782R|MSH6_uc010yoj.1_Missense_Mutation_p.W610R	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6	912					determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|endometrium(28)|central_nervous_system(27)|stomach(21)|haematopoietic_and_lymphoid_tissue(9)|skin(6)|urinary_tract(5)|lung(5)|ovary(3)|breast(2)|thyroid(1)	160		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)							517				0.288235	127.325758	134.221951	49	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48027856	48027856	10267	2	T	C	C	C	663	51	MSH6	4	4
GKN1	56287	broad.mit.edu	37	2	69204898	69204898	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:69204898T>A	uc002sfc.2	+	c.238T>A	c.(238-240)TAT>AAT	p.Y80N		NM_019617	NP_062563	Q9NS71	GKN1_HUMAN	18 kDa antrum mucosa protein precursor	80	BRICHOS.				digestion|positive regulation of cell division	extracellular region				breast(1)	1														0.333333	73.096863	75.090089	27	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69204898	69204898	6692	2	T	A	A	A	793	61	GKN1	3	3
GNLY	10578	broad.mit.edu	37	2	85924772	85924772	+	Silent	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:85924772G>A	uc010ysx.1	+	c.480G>A	c.(478-480)GAG>GAA	p.E160E	GNLY_uc010fgp.2_Silent_p.E118E|GNLY_uc002sql.3_Silent_p.E133E	NM_012483	NP_036615	P22749	GNLY_HUMAN	granulysin isoform 519	133	Saposin B-type.				cellular defense response|defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular space					0														0.329545	87.045279	89.311596	29	59	KEEP	---	---	---	---	capture		Silent	SNP	85924772	85924772	6808	2	G	A	A	A	451	35	GNLY	2	2
GUCA1C	9626	broad.mit.edu	37	3	108634993	108634993	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:108634993C>G	uc003dxj.2	-	c.423G>C	c.(421-423)AAG>AAC	p.K141N	GUCA1C_uc003dxk.2_Missense_Mutation_p.K141N	NM_005459	NP_005450	O95843	GUC1C_HUMAN	guanylate cyclase activator 1C	141	EF-hand 4.				signal transduction|visual perception		calcium ion binding|calcium sensitive guanylate cyclase activator activity				0						NSCLC(157;1360 1999 30631 40189 44208)								0.205128	66.530242	75.969327	24	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108634993	108634993	7170	3	C	G	G	G	415	32	GUCA1C	3	3
SLC6A1	6529	broad.mit.edu	37	3	11060301	11060301	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:11060301G>C	uc010hdq.2	+	c.388G>C	c.(388-390)GCT>CCT	p.A130P		NM_003042	NP_003033	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter	130	Helical; Name=3; (Potential).				neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(1)	1		Ovarian(110;0.0392)		OV - Ovarian serous cystadenocarcinoma(96;0.00099)	Cocaine(DB00907)|Tiagabine(DB00906)									0.317073	40.859611	42.079849	13	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11060301	11060301	15170	3	G	C	C	C	598	46	SLC6A1	3	3
TRIM42	287015	broad.mit.edu	37	3	140409919	140409919	+	Missense_Mutation	SNP	G	T	T	rs115301879	by1000genomes	TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:140409919G>T	uc003eto.1	+	c.1970G>T	c.(1969-1971)CGG>CTG	p.R657L		NM_152616	NP_689829	Q8IWZ5	TRI42_HUMAN	tripartite motif-containing 42	657	Fibronectin type-III.					intracellular	zinc ion binding			lung(2)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)|skin(1)	6										261				0.3	126.015264	131.376635	45	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140409919	140409919	17061	3	G	T	T	T	507	39	TRIM42	1	1
MME	4311	broad.mit.edu	37	3	154884701	154884701	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:154884701C>A	uc010hvr.1	+	c.1671C>A	c.(1669-1671)GCC>GCA	p.A557A	MME_uc003fab.1_Silent_p.A557A|MME_uc003fac.1_Silent_p.A557A|MME_uc003fad.1_Silent_p.A557A|MME_uc003fae.1_Silent_p.A557A	NM_007289	NP_009220	P08473	NEP_HUMAN	membrane metallo-endopeptidase	557	Extracellular (Potential).				cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)									0.2375	98.039531	108.065133	38	122	KEEP	---	---	---	---	capture		Silent	SNP	154884701	154884701	10035	3	C	A	A	A	288	23	MME	1	1
SI	6476	broad.mit.edu	37	3	164767647	164767647	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:164767647G>T	uc003fei.2	-	c.1529C>A	c.(1528-1530)TCC>TAC	p.S510Y		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	510	Lumenal.|Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|pancreas(1)	8		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)									0.142857	5.8792	9.322849	4	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	164767647	164767647	14792	3	G	T	T	T	533	41	SI	2	2
IGF2BP2	10644	broad.mit.edu	37	3	185363402	185363402	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:185363402G>A	uc003fpq.2	-	c.1732C>T	c.(1732-1734)CGC>TGC	p.R578C	IGF2BP2_uc010hyi.2_Missense_Mutation_p.R516C|IGF2BP2_uc010hyj.2_Missense_Mutation_p.R510C|IGF2BP2_uc010hyk.2_Missense_Mutation_p.R437C|IGF2BP2_uc010hyl.2_Missense_Mutation_p.R467C|IGF2BP2_uc003fpo.2_Missense_Mutation_p.R573C|IGF2BP2_uc003fpp.2_Missense_Mutation_p.R530C	NM_006548	NP_006539	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding	573	KH 4.				anatomical structure morphogenesis|negative regulation of translation|regulation of cytokine biosynthetic process	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)											0.094017	2.629575	22.024181	11	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185363402	185363402	7875	3	G	A	A	A	494	38	IGF2BP2	1	1
TRIM71	131405	broad.mit.edu	37	3	32860298	32860298	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:32860298G>T	uc003cff.2	+	c.726G>T	c.(724-726)CCG>CCT	p.P242P		NM_001039111	NP_001034200	Q2Q1W2	LIN41_HUMAN	tripartite motif-containing 71	242					multicellular organismal development	cytoplasm	zinc ion binding			ovary(2)|large_intestine(1)	3														0.358974	40.9388	41.621956	14	25	KEEP	---	---	---	---	capture		Silent	SNP	32860298	32860298	17093	3	G	T	T	T	483	38	TRIM71	1	1
CHL1	10752	broad.mit.edu	37	3	424293	424293	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:424293G>T	uc003bot.2	+	c.2115G>T	c.(2113-2115)GTG>GTT	p.V705V	CHL1_uc003bou.2_Silent_p.V689V|CHL1_uc003bow.1_Silent_p.V689V|CHL1_uc011asi.1_Silent_p.V705V	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM	689	Fibronectin type-III 1.|Extracellular (Potential).				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				central_nervous_system(4)|large_intestine(2)|ovary(1)	7		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)						659				0.196078	20.317691	24.711029	10	41	KEEP	---	---	---	---	capture		Silent	SNP	424293	424293	3483	3	G	T	T	T	574	45	CHL1	2	2
CCBP2	1238	broad.mit.edu	37	3	42906917	42906917	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:42906917C>T	uc003cme.2	+	c.923C>T	c.(922-924)TCC>TTC	p.S308F	CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmf.2_Missense_Mutation_p.S308F|CCBP2_uc003cmg.2_Intron|CYP8B1_uc010hif.2_Intron	NM_001296	NP_001287	O00590	CCBP2_HUMAN	chemokine binding protein 2	308	Helical; Name=7; (Potential).				chemotaxis|immune response|multicellular organismal development	integral to plasma membrane	C-X-C chemokine receptor activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.241)										0.159836	60.842872	87.806792	39	205	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42906917	42906917	2854	3	C	T	T	T	390	30	CCBP2	2	2
TGM4	7047	broad.mit.edu	37	3	44916184	44916184	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:44916184C>T	uc003coc.3	+	c.14C>T	c.(13-15)TCA>TTA	p.S5L	TGM4_uc003coa.2_Missense_Mutation_p.S5L|TGM4_uc003cob.2_Non-coding_Transcript	NM_003241	NP_003232	P49221	TGM4_HUMAN	transglutaminase 4 (prostate)	5					peptide cross-linking|protein polyamination		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)									0.208955	28.007227	33.268391	14	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44916184	44916184	16360	3	C	T	T	T	377	29	TGM4	2	2
PRSS50	29122	broad.mit.edu	37	3	46758935	46758935	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:46758935G>T	uc003cqe.1	-	c.299C>A	c.(298-300)CCA>CAA	p.P100Q	PRSS50_uc003cqf.1_Missense_Mutation_p.P14Q	NM_013270	NP_037402	Q9UI38	TSP50_HUMAN	testes-specific protease 50 precursor	100	Peptidase S1.				proteolysis	endoplasmic reticulum	serine-type endopeptidase activity|threonine-type endopeptidase activity				0						Pancreas(41;915 1239 11561 17469)								0.27451	71.854684	76.527126	28	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46758935	46758935	13082	3	G	T	T	T	611	47	PRSS50	2	2
LAMB2	3913	broad.mit.edu	37	3	49165960	49165961	+	Missense_Mutation	DNP	GC	CA	CA			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49165960_49165961GC>CA	uc003cwe.2	-	c.1948_1949GC>TG	c.(1948-1950)GCC>TGC	p.A650C	LAMB2_uc003cwf.1_Missense_Mutation_p.A650C	NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	650	Laminin IV type B.				cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)										0.153846	19.905216	27.357289	10	55	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	49165960	49165961	8934	3	GC	CA	CA	CA	546	42	LAMB2	3	3
SLC38A3	10991	broad.mit.edu	37	3	50256083	50256083	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:50256083G>T	uc003cyn.3	+	c.1095G>T	c.(1093-1095)CTG>CTT	p.L365L		NM_006841	NP_006832	Q99624	S38A3_HUMAN	solute carrier family 38, member 3	365					cellular nitrogen compound metabolic process|sodium ion transport	integral to plasma membrane	antiporter activity|L-alanine transmembrane transporter activity|L-asparagine transmembrane transporter activity|L-glutamine transmembrane transporter activity|L-histidine transmembrane transporter activity|symporter activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615)	L-Asparagine(DB00174)|L-Glutamine(DB00130)|L-Histidine(DB00117)									0.166667	18.609021	24.933021	10	50	KEEP	---	---	---	---	capture		Silent	SNP	50256083	50256083	15102	3	G	T	T	T	574	45	SLC38A3	2	2
GRM2	2912	broad.mit.edu	37	3	51743114	51743114	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:51743114C>T	uc010hlv.2	+	c.115C>T	c.(115-117)CCA>TCA	p.P39S	GRM2_uc003dbo.3_Intron|GRM2_uc010hlu.2_Non-coding_Transcript	NM_000839	NP_000830	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2 isoform a	39	Extracellular (Potential).				synaptic transmission	integral to plasma membrane					0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acamprosate(DB00659)|Nicotine(DB00184)									0.289157	63.963666	67.272994	24	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51743114	51743114	7076	3	C	T	T	T	286	22	GRM2	2	2
C3orf32	51066	broad.mit.edu	37	3	8667996	8667996	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:8667996C>A	uc011atg.1	-	c.686G>T	c.(685-687)TGC>TTC	p.C229F	C3orf32_uc003bqz.2_Missense_Mutation_p.C207F|C3orf32_uc003bqt.2_Missense_Mutation_p.C156F|C3orf32_uc003bqu.2_Missense_Mutation_p.C207F|C3orf32_uc003bqv.2_Missense_Mutation_p.C156F|C3orf32_uc003bqw.2_Non-coding_Transcript|C3orf32_uc003bqx.2_Non-coding_Transcript|C3orf32_uc003bqy.2_Missense_Mutation_p.C207F	NM_015931	NP_057015	Q9Y2M2	CC032_HUMAN	hypothetical protein LOC51066	207	Cys-rich.										0														0.291892	142.064718	149.247787	54	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8667996	8667996	2315	3	C	A	A	A	325	25	C3orf32	2	2
EPHA6	285220	broad.mit.edu	37	3	97124023	97124023	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:97124023G>T	uc010how.1	+	c.1636G>T	c.(1636-1638)GAC>TAC	p.D546Y		NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	451	Fibronectin type-III 2.|Extracellular (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(3)|lung(3)|stomach(2)|breast(1)|skin(1)|ovary(1)|kidney(1)	12										480				0.5	11.599142	11.599142	4	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97124023	97124023	5364	3	G	T	T	T	533	41	EPHA6	2	2
SEC24D	9871	broad.mit.edu	37	4	119745843	119745843	+	Silent	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:119745843A>G	uc003icj.3	-	c.180T>C	c.(178-180)GGT>GGC	p.G60G	SEC24D_uc003ici.3_Silent_p.G60G|SEC24D_uc003icl.2_Non-coding_Transcript|SEC24D_uc010imz.1_Non-coding_Transcript|SEC24D_uc011cgg.1_Non-coding_Transcript	NM_014822	NP_055637	O94855	SC24D_HUMAN	Sec24-related protein D	60	Pro-rich.				COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0														0.253456	146.280205	158.3084	55	162	KEEP	---	---	---	---	capture		Silent	SNP	119745843	119745843	14483	4	A	G	G	G	119	10	SEC24D	4	4
TRPC3	7222	broad.mit.edu	37	4	122853479	122853479	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:122853479G>T	uc003ieg.2	-	c.934C>A	c.(934-936)CTA>ATA	p.L312I	TRPC3_uc010inr.2_Missense_Mutation_p.L239I|TRPC3_uc003ief.2_Missense_Mutation_p.L239I|TRPC3_uc011cgl.1_5'UTR	NM_001130698	NP_001124170	Q13507	TRPC3_HUMAN	transient receptor potential cation channel,	227	Cytoplasmic (Potential).				axon guidance|phototransduction|platelet activation	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2														0.189189	13.500203	16.847533	7	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122853479	122853479	17130	4	G	T	T	T	451	35	TRPC3	2	2
PLK4	10733	broad.mit.edu	37	4	128814717	128814717	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:128814717G>A	uc003ifo.2	+	c.2372G>A	c.(2371-2373)AGG>AAG	p.R791K	PLK4_uc011cgs.1_Missense_Mutation_p.R759K|PLK4_uc011cgt.1_Missense_Mutation_p.R750K	NM_014264	NP_055079	O00444	PLK4_HUMAN	polo-like kinase 4	791					G2/M transition of mitotic cell cycle|positive regulation of centriole replication|protein phosphorylation|trophoblast giant cell differentiation	centriole|cleavage furrow|cytosol|nucleolus	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0						Colon(135;508 1718 19061 31832 42879)				258				0.263158	42.897519	45.789943	15	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128814717	128814717	12524	4	G	A	A	A	455	35	PLK4	2	2
DCHS2	54798	broad.mit.edu	37	4	155278377	155278377	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:155278377T>G	uc003inw.2	-	c.794A>C	c.(793-795)CAC>CCC	p.H265P	DCHS2_uc003inx.2_Intron	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	265	Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)										0.270833	164.996487	174.10727	52	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155278377	155278377	4459	4	T	G	G	G	767	59	DCHS2	4	4
ZNF718	255403	broad.mit.edu	37	4	155375	155375	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:155375A>T	uc003fzt.3	+	c.900A>T	c.(898-900)GAA>GAT	p.E300D	ZNF595_uc003fzu.1_Intron|ZNF718_uc010iaz.2_Non-coding_Transcript|ZNF718_uc003fzw.3_Missense_Mutation_p.N80I	NM_001039127	NP_001034216	Q3SXZ3	ZN718_HUMAN	zinc finger protein 718	300	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0681)|Epithelial(2;0.0838)|all cancers(2;0.135)|LUSC - Lung squamous cell carcinoma(95;0.18)										0.193548	13.132474	15.849118	6	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155375	155375	18717	4	A	T	T	T	24	2	ZNF718	3	3
FSTL5	56884	broad.mit.edu	37	4	162376242	162376242	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:162376242C>A	uc003iqh.2	-	c.1755G>T	c.(1753-1755)ACG>ACT	p.T585T	FSTL5_uc003iqi.2_Silent_p.T584T|FSTL5_uc010iqv.2_Silent_p.T575T	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a	585						extracellular region	calcium ion binding			ovary(2)|pancreas(2)|large_intestine(1)|central_nervous_system(1)	6	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)										0.173913	7.585122	9.894599	4	19	KEEP	---	---	---	---	capture		Silent	SNP	162376242	162376242	6331	4	C	A	A	A	392	31	FSTL5	1	1
TXK	7294	broad.mit.edu	37	4	48106930	48106930	+	Silent	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:48106930T>C	uc003gxx.3	-	c.489A>G	c.(487-489)CTA>CTG	p.L163L	TXK_uc003gxy.1_Silent_p.L163L	NM_003328	NP_003319	P42681	TXK_HUMAN	TXK tyrosine kinase	163	SH2.				protein phosphorylation	cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity				0										451				0.181818	29.319255	34.547105	10	45	KEEP	---	---	---	---	capture		Silent	SNP	48106930	48106930	17342	4	T	C	C	C	626	49	TXK	4	4
FRYL	285527	broad.mit.edu	37	4	48536685	48536685	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:48536685C>A	uc003gyh.1	-	c.6582G>T	c.(6580-6582)TTG>TTT	p.L2194F	FRYL_uc003gyg.1_Missense_Mutation_p.L890F|FRYL_uc003gyi.1_Missense_Mutation_p.L1082F|FRYL_uc003gyj.1_Missense_Mutation_p.L489F	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	2194					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1														0.125	4.675352	9.074429	4	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48536685	48536685	6314	4	C	A	A	A	220	17	FRYL	2	2
KIAA1211	57482	broad.mit.edu	37	4	57179457	57179457	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:57179457C>T	uc003hbk.2	+	c.449C>T	c.(448-450)GCT>GTT	p.A150V	KIAA1211_uc010iha.2_Missense_Mutation_p.A143V|KIAA1211_uc011bzz.1_Missense_Mutation_p.A60V|KIAA1211_uc003hbm.1_Missense_Mutation_p.A36V	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	150										ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)													0.285068	179.447873	188.602463	63	158	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57179457	57179457	8523	4	C	T	T	T	364	28	KIAA1211	2	2
AMTN	401138	broad.mit.edu	37	4	71390668	71390668	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:71390668T>G	uc003hfk.1	+	c.284T>G	c.(283-285)CTG>CGG	p.L95R	AMTN_uc010ihy.1_Missense_Mutation_p.L94R	NM_212557	NP_997722	Q6UX39	AMTN_HUMAN	amelotin precursor	95					biomineral tissue development|cell adhesion|odontogenesis of dentine-containing tooth	basal lamina|cell-cell junction				large_intestine(1)|central_nervous_system(1)	2			Lung(101;0.235)											0.375	55.938182	56.596604	18	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71390668	71390668	593	4	T	G	G	G	715	55	AMTN	4	4
ANXA3	306	broad.mit.edu	37	4	79522696	79522696	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:79522696G>A	uc003hld.2	+	c.763G>A	c.(763-765)GCC>ACC	p.A255T	ANXA3_uc003hle.2_Missense_Mutation_p.A216T|ANXA3_uc010ijk.2_Missense_Mutation_p.A216T	NM_005139	NP_005130	P12429	ANXA3_HUMAN	annexin A3	255					defense response to bacterium|neutrophil degranulation|phagocytosis|positive regulation of angiogenesis|positive regulation of endothelial cell migration|positive regulation of sequence-specific DNA binding transcription factor activity	phagocytic vesicle membrane|plasma membrane|specific granule	calcium ion binding|calcium-dependent phospholipid binding|phospholipase A2 inhibitor activity				0						GBM(2;126 157 27790 28920 42492)								0.373832	121.391079	122.879651	40	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79522696	79522696	727	4	G	A	A	A	442	34	ANXA3	2	2
SLCO6A1	133482	broad.mit.edu	37	5	101748746	101748746	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:101748746A>T	uc003knn.2	-	c.1574T>A	c.(1573-1575)TTT>TAT	p.F525Y	SLCO6A1_uc003kno.2_Missense_Mutation_p.F272Y|SLCO6A1_uc003knp.2_Missense_Mutation_p.F525Y|SLCO6A1_uc003knq.2_Missense_Mutation_p.F463Y	NM_173488	NP_775759	Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family,	525	Extracellular (Potential).|Kazal-like.					integral to membrane|plasma membrane	transporter activity			ovary(3)|central_nervous_system(1)	4		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)										0.26087	15.039344	16.22996	6	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101748746	101748746	15229	5	A	T	T	T	13	1	SLCO6A1	3	3
ACSL6	23305	broad.mit.edu	37	5	131308464	131308464	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:131308464T>C	uc003kvx.1	-	c.1291A>G	c.(1291-1293)ATC>GTC	p.I431V	ACSL6_uc003kvv.1_Non-coding_Transcript|ACSL6_uc003kvy.1_Missense_Mutation_p.I431V|ACSL6_uc003kwb.2_Missense_Mutation_p.I396V|ACSL6_uc010jdo.1_Missense_Mutation_p.I406V|ACSL6_uc003kvz.1_Missense_Mutation_p.I331V|ACSL6_uc003kwa.1_Missense_Mutation_p.I417V|ACSL6_uc003kvw.1_Missense_Mutation_p.I52V|ACSL6_uc010jdn.1_Missense_Mutation_p.I421V	NM_015256	NP_056071	Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	406	Cytoplasmic (Potential).				fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane|plasma membrane	ATP binding|long-chain fatty acid-CoA ligase activity			ovary(1)	1		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)							264				0.283465	105.649426	110.995255	36	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131308464	131308464	182	5	T	C	C	C	663	51	ACSL6	4	4
LOC153328	153328	broad.mit.edu	37	5	135188390	135188390	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:135188390C>A	uc003lba.2	+	c.301C>A	c.(301-303)CGC>AGC	p.R101S	LOC153328_uc003laz.1_Missense_Mutation_p.R101S	NM_145282	NP_660325	Q6ZT89	S2548_HUMAN	mitochondrial carrier protein-like	101	Solcar 2.				transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)											0.18018	37.7013	48.332764	20	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135188390	135188390	9210	5	C	A	A	A	299	23	LOC153328	1	1
HNRNPA0	10949	broad.mit.edu	37	5	137089549	137089549	+	Silent	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:137089549G>A	uc003lbt.2	-	c.207C>T	c.(205-207)CCC>CCT	p.P69P	MYOT_uc011cye.1_Intron|HNRNPA0_uc010jeo.2_Intron	NM_006805	NP_006796	Q13151	ROA0_HUMAN	heterogeneous nuclear ribonucleoprotein A0	69	RRM 1.				nuclear mRNA splicing, via spliceosome	heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|RNA binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)											0.240385	56.674882	63.044224	25	79	KEEP	---	---	---	---	capture		Silent	SNP	137089549	137089549	7548	5	G	A	A	A	548	43	HNRNPA0	2	2
PCDHA6	56142	broad.mit.edu	37	5	140207895	140207895	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140207895C>A	uc003lho.2	+	c.219C>A	c.(217-219)GAC>GAA	p.D73E	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Missense_Mutation_p.D73E|PCDHA6_uc011dab.1_Missense_Mutation_p.D73E	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	73	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.254958	236.3998	255.62058	90	263	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140207895	140207895	11948	5	C	A	A	A	233	18	PCDHA6	2	2
PCDHA12	56137	broad.mit.edu	37	5	140255747	140255747	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140255747A>G	uc003lic.2	+	c.690A>G	c.(688-690)ATA>ATG	p.I230M	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc011daf.1_Missense_Mutation_p.I230M	NM_018903	NP_061726	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12 isoform 1 precursor	230	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			Pancreas(113;759 1672 13322 24104 50104)								0.319672	131.99499	135.513041	39	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140255747	140255747	11942	5	A	G	G	G	163	13	PCDHA12	4	4
PCDHB4	56131	broad.mit.edu	37	5	140502904	140502904	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140502904G>T	uc003lip.1	+	c.1324G>T	c.(1324-1326)GAC>TAC	p.D442Y		NM_018938	NP_061761	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4 precursor	442	Cadherin 4.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	cytoplasm|integral to plasma membrane|intermediate filament cytoskeleton	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.181818	74.905054	93.721214	36	162	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140502904	140502904	11964	5	G	T	T	T	481	37	PCDHB4	1	1
PCDHB5	26167	broad.mit.edu	37	5	140517152	140517152	+	Silent	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140517152G>A	uc003liq.2	+	c.2136G>A	c.(2134-2136)CTG>CTA	p.L712L		NM_015669	NP_056484	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5 precursor	712	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.20339	92.283934	111.556172	48	188	KEEP	---	---	---	---	capture		Silent	SNP	140517152	140517152	11965	5	G	A	A	A	613	48	PCDHB5	2	2
PCDHB7	56129	broad.mit.edu	37	5	140553013	140553013	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140553013G>T	uc003lit.2	+	c.597G>T	c.(595-597)GTG>GTT	p.V199V		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	199	Extracellular (Potential).|Cadherin 2.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.213483	40.46457	47.227968	19	70	KEEP	---	---	---	---	capture		Silent	SNP	140553013	140553013	11967	5	G	T	T	T	587	46	PCDHB7	2	2
PCDHGA4	56111	broad.mit.edu	37	5	140736243	140736243	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140736243C>A	uc003ljq.1	+	c.1476C>A	c.(1474-1476)GCC>GCA	p.A492A	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljp.1_Silent_p.A492A	NM_018917	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4 isoform 1	492	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.225941	133.227281	149.710934	54	185	KEEP	---	---	---	---	capture		Silent	SNP	140736243	140736243	11976	5	C	A	A	A	288	23	PCDHGA4	1	1
PCDHGA9	56107	broad.mit.edu	37	5	140784669	140784669	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140784669G>A	uc003lkh.1	+	c.2150G>A	c.(2149-2151)AGG>AAG	p.R717K	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc011dax.1_Missense_Mutation_p.R717K	NM_018921	NP_061744	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9 isoform 1	717	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.171875	45.409943	58.403329	22	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140784669	140784669	11981	5	G	A	A	A	455	35	PCDHGA9	2	2
PCDH12	51294	broad.mit.edu	37	5	141335023	141335023	+	Silent	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:141335023C>T	uc003llx.2	-	c.2394G>A	c.(2392-2394)GTG>GTA	p.V798V		NM_016580	NP_057664	Q9NPG4	PCD12_HUMAN	protocadherin 12 precursor	798	Cytoplasmic (Potential).				neuron recognition	integral to plasma membrane	calcium ion binding			ovary(3)	3		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.381818	61.560135	62.234456	21	34	KEEP	---	---	---	---	capture		Silent	SNP	141335023	141335023	11930	5	C	T	T	T	262	21	PCDH12	2	2
GPX3	2878	broad.mit.edu	37	5	150407000	150407000	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:150407000C>G	uc011dcm.1	+	c.367C>G	c.(367-369)CGA>GGA	p.R123G	GPX3_uc003ltc.2_Non-coding_Transcript|GPX3_uc003ltd.2_Non-coding_Transcript	NM_002084	NP_002075	P22352	GPX3_HUMAN	glutathione peroxidase 3 precursor	123					hydrogen peroxide catabolic process|oxidation-reduction process|protein homotetramerization|response to lipid hydroperoxide	extracellular space	glutathione peroxidase activity|selenium binding|transcription factor binding				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Glutathione(DB00143)									0.255034	98.481263	106.592251	38	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150407000	150407000	7017	5	C	G	G	G	295	23	GPX3	3	3
SOX30	11063	broad.mit.edu	37	5	157078599	157078599	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:157078599G>A	uc003lxb.1	-	c.488C>T	c.(487-489)TCC>TTC	p.S163F	SOX30_uc003lxc.1_Missense_Mutation_p.S163F|SOX30_uc011dds.1_Intron	NM_178424	NP_848511	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30 isoform a	163					regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|response to corticosteroid stimulus|transcription, DNA-dependent	nucleus|nucleus	sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)|central_nervous_system(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			Esophageal Squamous(31;525 799 19355 21125 41744)								0.4	119.511553	120.434277	42	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157078599	157078599	15452	5	G	A	A	A	533	41	SOX30	2	2
LSM11	134353	broad.mit.edu	37	5	157181018	157181018	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:157181018A>G	uc003lxe.1	+	c.595A>G	c.(595-597)ACT>GCT	p.T199A	LSM11_uc003lxf.1_5'Flank	NM_173491	NP_775762	P83369	LSM11_HUMAN	LSM11, U7 small nuclear RNA associated	199	SM 1.				histone mRNA 3'-end processing|S phase of mitotic cell cycle|termination of RNA polymerase II transcription	histone pre-mRNA 3'end processing complex|nucleoplasm|U7 snRNP	protein binding|U7 snRNA binding				0	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)											0.293478	93.697169	97.204102	27	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157181018	157181018	9428	5	A	G	G	G	182	14	LSM11	4	4
FBXL7	23194	broad.mit.edu	37	5	15936997	15936997	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:15936997G>T	uc003jfn.1	+	c.1178G>T	c.(1177-1179)GGT>GTT	p.G393V		NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	393	LRR 9.				ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3														0.24	13.943435	15.482196	6	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15936997	15936997	5961	5	G	T	T	T	572	44	FBXL7	2	2
GABRA1	2554	broad.mit.edu	37	5	161324188	161324188	+	Silent	SNP	T	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:161324188T>C	uc010jiw.2	+	c.1131T>C	c.(1129-1131)CCT>CCC	p.P377P	GABRA1_uc010jix.2_Silent_p.P377P|GABRA1_uc010jiy.2_Silent_p.P377P|GABRA1_uc003lyx.3_Silent_p.P377P|GABRA1_uc010jiz.2_Silent_p.P377P|GABRA1_uc010jja.2_Silent_p.P377P|GABRA1_uc010jjb.2_Silent_p.P377P	NM_000806	NP_000797	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha	377	Cytoplasmic (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			ovary(2)|pancreas(1)	3	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Alprazolam(DB00404)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Halazepam(DB00801)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Metharbital(DB00463)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Picrotoxin(DB00466)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Zaleplon(DB00962)|Zolpidem(DB00425)									0.239437	98.309435	107.094293	34	108	KEEP	---	---	---	---	capture		Silent	SNP	161324188	161324188	6411	5	T	C	C	C	678	53	GABRA1	4	4
BASP1	10409	broad.mit.edu	37	5	17275921	17275921	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:17275921C>T	uc003jfx.2	+	c.596C>T	c.(595-597)GCC>GTC	p.A199V		NM_006317	NP_006308	P80723	BASP1_HUMAN	brain abundant, membrane attached signal protein	199					glomerular visceral epithelial cell differentiation|negative regulation of gene-specific transcription	cytoplasm|cytoskeleton|growth cone|nuclear speck|plasma membrane	promoter binding|protein domain specific binding|specific transcriptional repressor activity|transcription corepressor activity				0														0.170213	13.222156	18.022985	8	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17275921	17275921	1338	5	C	T	T	T	338	26	BASP1	2	2
HK3	3101	broad.mit.edu	37	5	176308305	176308305	+	Silent	SNP	C	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176308305C>G	uc003mfa.2	-	c.2625G>C	c.(2623-2625)CCG>CCC	p.P875P	HK3_uc003mez.2_Silent_p.P431P	NM_002115	NP_002106	P52790	HXK3_HUMAN	hexokinase 3	875	Catalytic.				glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity			ovary(3)|large_intestine(1)|breast(1)	5	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.230769	105.743132	116.967358	39	130	KEEP	---	---	---	---	capture		Silent	SNP	176308305	176308305	7483	5	C	G	G	G	340	27	HK3	3	3
MAPK9	5601	broad.mit.edu	37	5	179666965	179666965	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:179666965G>A	uc003mls.3	-	c.1019C>T	c.(1018-1020)GCC>GTC	p.A340V	MAPK9_uc003mlt.3_Missense_Mutation_p.A340V|MAPK9_uc010jlc.2_Missense_Mutation_p.A340V|MAPK9_uc003mlv.3_Missense_Mutation_p.A340V	NM_002752	NP_002743	P45984	MK09_HUMAN	mitogen-activated protein kinase 9 isoform JNK2	340					innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|protein binding|protein binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)	4	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)							167				0.247525	61.627775	67.485253	25	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179666965	179666965	9670	5	G	A	A	A	546	42	MAPK9	2	2
CDH6	1004	broad.mit.edu	37	5	31323229	31323229	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:31323229C>A	uc003jhe.1	+	c.2187C>A	c.(2185-2187)GCC>GCA	p.A729A		NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein	729	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|large_intestine(1)	5														0.255319	29.186717	31.733675	12	35	KEEP	---	---	---	---	capture		Silent	SNP	31323229	31323229	3243	5	C	A	A	A	275	22	CDH6	2	2
SPEF2	79925	broad.mit.edu	37	5	35700681	35700681	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:35700681C>T	uc003jjo.2	+	c.2225C>T	c.(2224-2226)ACA>ATA	p.T742I	SPEF2_uc003jjq.3_Missense_Mutation_p.T737I|SPEF2_uc003jjp.1_Missense_Mutation_p.T228I	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	742	Potential.				nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			ovary(1)|central_nervous_system(1)	2	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)											0.257732	59.224156	64.388153	25	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35700681	35700681	15547	5	C	T	T	T	221	17	SPEF2	2	2
UGT3A1	133688	broad.mit.edu	37	5	35968187	35968187	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:35968187G>C	uc003jjv.1	-	c.245C>G	c.(244-246)CCT>CGT	p.P82R	UGT3A1_uc003jjw.1_Non-coding_Transcript|UGT3A1_uc011coq.1_Missense_Mutation_p.P82R|UGT3A1_uc011cor.1_Missense_Mutation_p.P48R|UGT3A1_uc003jjy.1_Missense_Mutation_p.P28R	NM_152404	NP_689617	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	82	Extracellular (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(2)|central_nervous_system(1)	3	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)											0.195122	19.480654	23.03066	8	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35968187	35968187	17521	5	G	C	C	C	455	35	UGT3A1	3	3
NNT	23530	broad.mit.edu	37	5	43656049	43656049	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:43656049A>G	uc003joe.2	+	c.2167A>G	c.(2167-2169)ATT>GTT	p.I723V	NNT_uc003jof.2_Missense_Mutation_p.I723V	NM_012343	NP_036475	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	723	Cytoplasmic.				tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)									0.253968	44.874009	48.332215	16	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43656049	43656049	10913	5	A	G	G	G	104	8	NNT	4	4
SKIV2L2	23517	broad.mit.edu	37	5	54618257	54618257	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:54618257G>T	uc003jpy.3	+	c.237G>T	c.(235-237)AAG>AAT	p.K79N	SKIV2L2_uc011cqi.1_Intron	NM_015360	NP_056175	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2	79					maturation of 5.8S rRNA|nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(1)	1		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				Melanoma(2;92 134 23744 29976 33782)								0.204082	43.735122	51.710176	20	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54618257	54618257	14855	5	G	T	T	T	438	34	SKIV2L2	2	2
GPBP1	65056	broad.mit.edu	37	5	56527069	56527069	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:56527069A>T	uc010iwg.2	+	c.332A>T	c.(331-333)CAT>CTT	p.H111L	GPBP1_uc003jrh.3_Missense_Mutation_p.H111L|GPBP1_uc003jri.3_5'UTR|GPBP1_uc003jrj.3_Missense_Mutation_p.H118L|GPBP1_uc003jrk.3_Missense_Mutation_p.H118L|GPBP1_uc003jrl.3_Non-coding_Transcript	NM_001127235	NP_001120707	Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1 isoform 2	111					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			large_intestine(1)|central_nervous_system(1)	2		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)										0.255814	61.63805	66.269783	22	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56527069	56527069	6869	5	A	T	T	T	104	8	GPBP1	3	3
SV2C	22987	broad.mit.edu	37	5	75505590	75505590	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:75505590C>A	uc003kei.1	+	c.791C>A	c.(790-792)TCG>TAG	p.S264*		NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	264	Helical; (Potential).				neurotransmitter transport|transmembrane transport	cell junction|integral to membrane|synaptic vesicle membrane	transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)										0.261905	58.612103	62.920523	22	62	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	75505590	75505590	15939	5	C	A	A	A	403	31	SV2C	5	1
RASGRF2	5924	broad.mit.edu	37	5	80376481	80376481	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:80376481A>G	uc003kha.1	+	c.1034A>G	c.(1033-1035)TAC>TGC	p.Y345C	RASGRF2_uc011ctn.1_Non-coding_Transcript|RASGRF2_uc003khb.1_Missense_Mutation_p.Y173C	NM_006909	NP_008840	O14827	RGRF2_HUMAN	Ras protein-specific guanine	345	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(3)|ovary(2)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)						847				0.235897	143.678785	156.093334	46	149	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80376481	80376481	13534	5	A	G	G	G	182	14	RASGRF2	4	4
ATP6AP1L	92270	broad.mit.edu	37	5	81608494	81608494	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:81608494A>G	uc003khv.2	+	c.196A>G	c.(196-198)ATC>GTC	p.I66V	ATP6AP1L_uc003khw.2_Missense_Mutation_p.I66V	NM_001017971	NP_001017971	Q52LC2	VAS1L_HUMAN	ATPase, H+ transporting, lysosomal accessory	66					ATP hydrolysis coupled proton transport	integral to membrane|proton-transporting V-type ATPase, V1 domain	hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism				0												OREG0016689	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.27931	253.858554	266.555391	81	209	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81608494	81608494	1185	5	A	G	G	G	156	12	ATP6AP1L	4	4
FOXO3	2309	broad.mit.edu	37	6	108985039	108985039	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:108985039G>A	uc003psk.2	+	c.1003G>A	c.(1003-1005)GAA>AAA	p.E335K	FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_Missense_Mutation_p.E335K|FOXO3_uc011ean.1_Missense_Mutation_p.E115K|FOXO3_uc010kdj.1_Missense_Mutation_p.E115K	NM_201559	NP_963853	O43524	FOXO3_HUMAN	forkhead box O3A	335					antral ovarian follicle growth|apoptosis|embryo development|glucose homeostasis|induction of apoptosis|initiation of primordial ovarian follicle growth|insulin receptor signaling pathway|negative regulation of gene-specific transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|oocyte maturation|ovulation from ovarian follicle|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			central_nervous_system(4)|lung(2)	6		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)						42				0.408451	81.257841	81.778633	29	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108985039	108985039	6270	6	G	A	A	A	585	45	FOXO3	2	2
AMD1	262	broad.mit.edu	37	6	111214177	111214177	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:111214177A>T	uc003puk.1	+	c.773A>T	c.(772-774)AAC>ATC	p.N258I	AMD1_uc011eay.1_Missense_Mutation_p.N189I|AMD1_uc011eaz.1_Missense_Mutation_p.N229I|AMD1_uc011eba.1_Missense_Mutation_p.N138I|AMD1_uc003pul.1_Missense_Mutation_p.N110I	NM_001634	NP_001625	P17707	DCAM_HUMAN	adenosylmethionine decarboxylase 1 isoform 1	258					spermidine biosynthetic process|spermine biosynthetic process	cytosol	adenosylmethionine decarboxylase activity				0		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)									0.507042	222.399266	222.40539	72	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111214177	111214177	569	6	A	T	T	T	26	2	AMD1	3	3
GPRC6A	222545	broad.mit.edu	37	6	117121759	117121759	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:117121759G>T	uc003pxj.1	-	c.1536C>A	c.(1534-1536)TTC>TTA	p.F512L	GPRC6A_uc003pxk.1_Missense_Mutation_p.F337L|GPRC6A_uc003pxl.1_Intron	NM_148963	NP_683766	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, family C, group 6,	512	Extracellular (Potential).				response to amino acid stimulus		G-protein coupled receptor activity			ovary(4)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)										0.517241	141.273749	141.296004	45	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117121759	117121759	7004	6	G	T	T	T	581	45	GPRC6A	2	2
THEMIS	387357	broad.mit.edu	37	6	128134393	128134393	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:128134393C>A	uc011ebt.1	-	c.1393G>T	c.(1393-1395)GAT>TAT	p.D465Y	THEMIS_uc010kfa.2_Missense_Mutation_p.D368Y|THEMIS_uc003qbi.2_Missense_Mutation_p.D465Y|THEMIS_uc010kfb.2_Missense_Mutation_p.D430Y	NM_001010923	NP_001010923	Q8N1K5	THMS1_HUMAN	thymocyte selection pathway associated isoform	465	CABIT 2.				negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)	2														0.348315	79.79952	81.60598	31	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128134393	128134393	16388	6	C	A	A	A	390	30	THEMIS	2	2
FHL5	9457	broad.mit.edu	37	6	97053871	97053871	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:97053871T>A	uc003pos.1	+	c.428T>A	c.(427-429)ATC>AAC	p.I143N	FHL5_uc003pot.1_Missense_Mutation_p.I143N	NM_020482	NP_065228	Q5TD97	FHL5_HUMAN	activator of cAMP-responsive element modulator	143	LIM zinc-binding 2.					nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)										0.072289	-1.815284	13.812445	6	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97053871	97053871	6119	6	T	A	A	A	650	50	FHL5	3	3
MYL10	93408	broad.mit.edu	37	7	101267507	101267507	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:101267507G>T	uc003uyr.2	-	c.116C>A	c.(115-117)GCC>GAC	p.A39D		NM_138403	NP_612412	Q9BUA6	MYL10_HUMAN	myosin, light chain 10, regulatory	39						mitochondrion	calcium ion binding			ovary(1)|breast(1)	2						Esophageal Squamous(24;575 709 17516 40384 51639)								0.299145	91.274562	95.4959	35	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101267507	101267507	10439	7	G	T	T	T	546	42	MYL10	2	2
NAMPT	10135	broad.mit.edu	37	7	105903983	105903983	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:105903983G>T	uc003vdq.2	-	c.824C>A	c.(823-825)TCT>TAT	p.S275Y	NAMPT_uc003vdr.1_Missense_Mutation_p.S275Y|NAMPT_uc011klu.1_Missense_Mutation_p.S188Y	NM_005746	NP_005737	P43490	NAMPT_HUMAN	nicotinamide phosphoribosyltransferase	275					cell-cell signaling|NAD biosynthetic process|nicotinamide metabolic process|positive regulation of cell proliferation|positive regulation of nitric-oxide synthase biosynthetic process|signal transduction	cytosol	cytokine activity|nicotinamide phosphoribosyltransferase activity|nicotinate phosphoribosyltransferase activity|nicotinate-nucleotide diphosphorylase (carboxylating) activity			large_intestine(1)	1														0.193878	37.347265	45.945102	19	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105903983	105903983	10545	7	G	T	T	T	429	33	NAMPT	2	2
CTTNBP2	83992	broad.mit.edu	37	7	117417645	117417645	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:117417645C>A	uc003vjf.2	-	c.2698G>T	c.(2698-2700)GTT>TTT	p.V900F		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	900										ovary(4)	4	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)										0.220779	41.937354	47.460929	17	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117417645	117417645	4204	7	C	A	A	A	221	17	CTTNBP2	2	2
PDIA4	9601	broad.mit.edu	37	7	148709033	148709033	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:148709033T>A	uc003wff.2	-	c.884A>T	c.(883-885)CAG>CTG	p.Q295L		NM_004911	NP_004902	P13667	PDIA4_HUMAN	protein disulfide isomerase A4 precursor	295	Thioredoxin 2.				cell redox homeostasis|glycerol ether metabolic process|protein secretion	endoplasmic reticulum lumen|melanosome	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)											0.221239	61.517326	69.596836	25	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148709033	148709033	12091	7	T	A	A	A	715	55	PDIA4	3	3
SSPO	23145	broad.mit.edu	37	7	149522402	149522402	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:149522402G>T	uc010lpk.2	+	c.14029G>T	c.(14029-14031)GAC>TAC	p.D4677Y	SSPO_uc010lpm.1_Non-coding_Transcript|SSPO_uc003wgg.2_Non-coding_Transcript|SSPO_uc003wgh.2_Non-coding_Transcript|SSPO_uc003wgi.1_Non-coding_Transcript	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	4677	TIL 6.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)											0.16185	42.367334	61.277438	28	145	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149522402	149522402	15705	7	G	T	T	T	533	41	SSPO	2	2
DPP6	1804	broad.mit.edu	37	7	154172027	154172027	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:154172027A>C	uc003wlk.2	+	c.362A>C	c.(361-363)GAA>GCA	p.E121A	DPP6_uc003wli.2_Missense_Mutation_p.E57A|DPP6_uc003wlj.2_Missense_Mutation_p.E121A|DPP6_uc010lqh.1_Missense_Mutation_p.E59A|DPP6_uc003wlm.2_Missense_Mutation_p.E59A|DPP6_uc011kvq.1_Missense_Mutation_p.E59A	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1	121	Extracellular (Potential).				cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			NSCLC(125;1384 1783 2490 7422 34254)								0.285714	51.478168	53.784853	16	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154172027	154172027	4914	7	A	C	C	C	117	9	DPP6	4	4
LMBR1	64327	broad.mit.edu	37	7	156518480	156518480	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:156518480C>G	uc010lqn.2	-	c.1168G>C	c.(1168-1170)GCG>CCG	p.A390P	LMBR1_uc003wmv.3_Missense_Mutation_p.A197P|LMBR1_uc003wmw.3_Missense_Mutation_p.A349P|LMBR1_uc003wmx.3_Missense_Mutation_p.A197P|LMBR1_uc011kvx.1_Missense_Mutation_p.A328P	NM_022458	NP_071903	Q8WVP7	LMBR1_HUMAN	limb region 1 protein	349	Helical; (Potential).			A -> V (in Ref. 1; AAK94061).		integral to membrane	receptor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)										0.185185	26.817125	31.835189	10	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156518480	156518480	9169	7	C	G	G	G	325	25	LMBR1	3	3
CBX3	11335	broad.mit.edu	37	7	26248069	26248069	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:26248069C>T	uc003sxt.2	+	c.224C>T	c.(223-225)GCG>GTG	p.A75V	CBX3_uc003sxu.2_Missense_Mutation_p.A75V|CBX3_uc003sxv.2_Intron	NM_007276	NP_009207	Q13185	CBX3_HUMAN	chromobox homolog 3	75	Chromo 1.				chromatin assembly or disassembly|chromatin remodeling|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome, centromeric region|nuclear centromeric heterochromatin|nuclear euchromatin|nuclear inner membrane|spindle	chromatin binding|enzyme binding|general transcriptional repressor activity|protein domain specific binding			ovary(1)	1														0.197917	42.067269	50.226775	19	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26248069	26248069	2838	7	C	T	T	T	351	27	CBX3	1	1
INHBA	3624	broad.mit.edu	37	7	41730009	41730009	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:41730009G>T	uc003thq.2	-	c.520C>A	c.(520-522)CGC>AGC	p.R174S	INHBA_uc003thr.2_Missense_Mutation_p.R174S	NM_002192	NP_002183	P08476	INHBA_HUMAN	inhibin beta A precursor	174					cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway|regulation of gene-specific transcription from RNA polymerase II promoter	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity|transcription activator activity			lung(5)|ovary(1)	6										102	TSP Lung(11;0.080)			0.273381	102.610633	109.029777	38	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41730009	41730009	8042	7	G	T	T	T	507	39	INHBA	1	1
SLC29A4	222962	broad.mit.edu	37	7	5327485	5327485	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:5327485G>T	uc003sod.2	+	c.38G>T	c.(37-39)AGC>ATC	p.S13I	SLC29A4_uc011jwg.1_Non-coding_Transcript|SLC29A4_uc003soc.2_Missense_Mutation_p.S13I|SLC29A4_uc003soe.2_Missense_Mutation_p.S13I	NM_153247	NP_694979	Q7RTT9	S29A4_HUMAN	solute carrier family 29 (nucleoside	13	Extracellular (Potential).				nucleobase, nucleoside and nucleotide metabolic process	apical plasma membrane|integral to membrane	nucleoside transmembrane transporter activity			liver(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)										0.27451	34.825329	37.163084	14	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5327485	5327485	15034	7	G	T	T	T	442	34	SLC29A4	2	2
ZNF479	90827	broad.mit.edu	37	7	57188666	57188666	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:57188666G>T	uc010kzo.2	-	c.456C>A	c.(454-456)ACC>ACA	p.T152T		NM_033273	NP_150376	Q96JC4	ZN479_HUMAN	zinc finger protein 479	152					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3			GBM - Glioblastoma multiforme(1;9.18e-12)											0.166667	20.18004	27.136738	11	55	KEEP	---	---	---	---	capture		Silent	SNP	57188666	57188666	18527	7	G	T	T	T	548	43	ZNF479	2	2
SEMA3A	10371	broad.mit.edu	37	7	83610721	83610721	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:83610721G>C	uc003uhz.2	-	c.1568C>G	c.(1567-1569)GCG>GGG	p.A523G		NM_006080	NP_006071	Q14563	SEM3A_HUMAN	semaphorin 3A precursor	523					axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4														0.354839	36.716497	37.292049	11	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83610721	83610721	14510	7	G	C	C	C	494	38	SEMA3A	3	3
VPS13B	157680	broad.mit.edu	37	8	100454673	100454673	+	Silent	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:100454673G>T	uc003yiv.2	+	c.3255G>T	c.(3253-3255)CTG>CTT	p.L1085L	VPS13B_uc003yiw.2_Silent_p.L1085L|VPS13B_uc003yiu.1_Silent_p.L1085L|VPS13B_uc003yix.1_Silent_p.L555L	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	1085					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			Colon(161;2205 2542 7338 31318)				1116				0.333333	80.392288	82.620361	30	60	KEEP	---	---	---	---	capture		Silent	SNP	100454673	100454673	17757	8	G	T	T	T	587	46	VPS13B	2	2
FAM135B	51059	broad.mit.edu	37	8	139164306	139164306	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139164306C>G	uc003yuy.2	-	c.2412G>C	c.(2410-2412)AAG>AAC	p.K804N	FAM135B_uc003yux.2_Missense_Mutation_p.K705N|FAM135B_uc003yuz.2_Non-coding_Transcript|FAM135B_uc003yva.2_Missense_Mutation_p.K366N|FAM135B_uc003yvb.2_Missense_Mutation_p.K366N	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	804										ovary(7)	7	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)											0.225	77.29636	85.709959	27	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139164306	139164306	5646	8	C	G	G	G	415	32	FAM135B	3	3
COL22A1	169044	broad.mit.edu	37	8	139890410	139890410	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139890410G>A	uc003yvd.2	-	c.241C>T	c.(241-243)CGC>TGC	p.R81C		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	81	VWFA.				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)											0.333333	15.743154	16.186388	6	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139890410	139890410	3819	8	G	A	A	A	494	38	COL22A1	1	1
GPIHBP1	338328	broad.mit.edu	37	8	144297309	144297309	+	Silent	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144297309C>T	uc003yxu.1	+	c.471C>T	c.(469-471)CCC>CCT	p.P157P		NM_178172	NP_835466	Q8IV16	HDBP1_HUMAN	glycosylphosphatidylinositol anchored high	157					cholesterol homeostasis|positive regulation of chylomicron remnant clearance|positive regulation of lipoprotein lipase activity|protein stabilization|response to heparin|triglyceride homeostasis	anchored to external side of plasma membrane|high-density lipoprotein particle|integral to membrane	apolipoprotein binding|chylomicron binding|lipase binding|lipid binding				0	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)													0.364706	85.07055	86.451002	31	54	KEEP	---	---	---	---	capture		Silent	SNP	144297309	144297309	6886	8	C	T	T	T	275	22	GPIHBP1	2	2
WRN	7486	broad.mit.edu	37	8	30999102	30999102	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:30999102G>C	uc003xio.3	+	c.3124G>C	c.(3124-3126)GCC>CCC	p.A1042P	WRN_uc010lvk.2_Missense_Mutation_p.A509P	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein	1042					base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)	5		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		Ovarian(18;161 598 2706 14834 27543)				832				0.276923	54.629679	57.536516	18	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30999102	30999102	17976	8	G	C	C	C	494	38	WRN	3	3
CSMD1	64478	broad.mit.edu	37	8	3889486	3889486	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:3889486G>A	uc011kwk.1	-	c.551C>T	c.(550-552)ACC>ATC	p.T184I		NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	184	Extracellular (Potential).|Sushi 1.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)										0.175	13.611491	17.588363	7	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3889486	3889486	4085	8	G	A	A	A	572	44	CSMD1	2	2
ANK1	286	broad.mit.edu	37	8	41554022	41554022	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:41554022G>T	uc003xom.2	-	c.2942C>A	c.(2941-2943)CCA>CAA	p.P981Q	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Missense_Mutation_p.P256Q|ANK1_uc003xoi.2_Missense_Mutation_p.P940Q|ANK1_uc003xoj.2_Missense_Mutation_p.P940Q|ANK1_uc003xok.2_Missense_Mutation_p.P940Q|ANK1_uc003xol.2_Missense_Mutation_p.P940Q	NM_001142446	NP_001135918	P16157	ANK1_HUMAN	ankyrin 1 isoform 9	940	ZU5.				axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)|breast(1)	8	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)											0.333333	61.532295	63.386596	25	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41554022	41554022	623	8	G	T	T	T	611	47	ANK1	2	2
ST18	9705	broad.mit.edu	37	8	53079434	53079434	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:53079434G>T	uc003xqz.2	-	c.1182C>A	c.(1180-1182)CAC>CAA	p.H394Q	ST18_uc011ldq.1_Missense_Mutation_p.H41Q|ST18_uc011ldr.1_Missense_Mutation_p.H359Q|ST18_uc011lds.1_Missense_Mutation_p.H299Q|ST18_uc003xra.2_Missense_Mutation_p.H394Q|ST18_uc003xrb.2_Missense_Mutation_p.H394Q	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	394	C2HC-type 1.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)												0.224242	87.870204	99.420724	37	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53079434	53079434	15730	8	G	T	T	T	620	48	ST18	2	2
PRDM14	63978	broad.mit.edu	37	8	70982089	70982089	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:70982089G>T	uc003xym.2	-	c.7C>A	c.(7-9)CTA>ATA	p.L3I		NM_024504	NP_078780	Q9GZV8	PRD14_HUMAN	PR domain containing 14	3					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			NSCLC(129;99 1813 5906 40656 46114)								0.375	15.14326	15.363697	6	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70982089	70982089	12897	8	G	T	T	T	425	33	PRDM14	2	2
OR1J1	347168	broad.mit.edu	37	9	125239348	125239348	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125239348G>T	uc011lyu.1	-	c.858C>A	c.(856-858)AAC>AAA	p.N286K	OR1J2_uc004bmj.1_Intron	NM_001004451	NP_001004451	Q8NGS3	OR1J1_HUMAN	olfactory receptor, family 1, subfamily J,	286	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1														0.32	133.640892	137.962242	48	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125239348	125239348	11365	9	G	T	T	T	568	44	OR1J1	2	2
COL5A1	1289	broad.mit.edu	37	9	137704349	137704349	+	Splice_Site_SNP	SNP	G	C	C			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:137704349G>C	uc004cfe.2	+	c.3744_splice	c.e47+1	p.M1248_splice		NM_000093	NP_000084			alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)|skin(1)	8		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)										0.412698	92.548129	92.964871	26	37	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	137704349	137704349	3834	9	G	C	C	C	572	44	COL5A1	5	3
AUH	549	broad.mit.edu	37	9	94060310	94060310	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:94060310C>A	uc004arf.3	-	c.554G>T	c.(553-555)GGT>GTT	p.G185V	AUH_uc004arg.3_Missense_Mutation_p.G156V|AUH_uc011ltu.1_Missense_Mutation_p.G185V	NM_001698	NP_001689	Q13825	AUHM_HUMAN	AU RNA binding protein/enoyl-Coenzyme A	185					branched chain family amino acid catabolic process|mRNA catabolic process	mitochondrial matrix	enoyl-CoA hydratase activity|methylglutaconyl-CoA hydratase activity|mRNA 3'-UTR binding				0														0.325	75.324447	77.497434	26	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94060310	94060310	1240	9	C	A	A	A	234	18	AUH	2	2
PTPDC1	138639	broad.mit.edu	37	9	96860223	96860223	+	Silent	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:96860223C>T	uc010mrj.1	+	c.1375C>T	c.(1375-1377)CTG>TTG	p.L459L	PTPDC1_uc004auf.1_Silent_p.L405L|PTPDC1_uc004aug.1_Silent_p.L405L|PTPDC1_uc004auh.1_Silent_p.L457L|PTPDC1_uc010mri.1_Silent_p.L457L	NM_177995	NP_818931	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1	405							protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1														0.333333	60.579438	62.055756	20	40	KEEP	---	---	---	---	capture		Silent	SNP	96860223	96860223	13228	9	C	T	T	T	311	24	PTPDC1	2	2
ARHGAP6	395	broad.mit.edu	37	X	11162223	11162223	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:11162223G>T	uc004cup.1	-	c.2053C>A	c.(2053-2055)CAA>AAA	p.Q685K	ARHGAP6_uc004cuo.1_Non-coding_Transcript|ARHGAP6_uc004cur.1_Missense_Mutation_p.Q685K|ARHGAP6_uc004cum.1_Missense_Mutation_p.Q482K|ARHGAP6_uc004cun.1_Missense_Mutation_p.Q505K|ARHGAP6_uc010neb.1_Missense_Mutation_p.Q507K|ARHGAP6_uc011mif.1_3'UTR	NM_013427	NP_038286	O43182	RHG06_HUMAN	Rho GTPase activating protein 6 isoform 1	685					actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity			urinary_tract(1)|lung(1)	2												OREG0019666	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.45283	143.684198	143.890117	48	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11162223	11162223	901	23	G	T	T	T	598	46	ARHGAP6	2	2
HTATSF1	27336	broad.mit.edu	37	X	135592243	135592243	+	Silent	SNP	G	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135592243G>A	uc004ezw.2	+	c.927G>A	c.(925-927)AGG>AGA	p.R309R	HTATSF1_uc004ezx.2_Silent_p.R309R	NM_001163280	NP_001156752	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	309	RRM 2.				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|viral genome replication	nucleus	nucleotide binding|protein binding|RNA binding|RNA polymerase II transcription factor activity|transcription elongation regulator activity			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)													0.141509	22.955343	36.095563	15	91	KEEP	---	---	---	---	capture		Silent	SNP	135592243	135592243	7733	23	G	A	A	A	542	42	HTATSF1	2	2
GLRA2	2742	broad.mit.edu	37	X	14550471	14550471	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:14550471C>G	uc010nep.2	+	c.179C>G	c.(178-180)GCA>GGA	p.A60G	GLRA2_uc010neq.2_Missense_Mutation_p.A60G|GLRA2_uc004cwe.3_Missense_Mutation_p.A60G|GLRA2_uc011mio.1_5'UTR|GLRA2_uc011mip.1_Missense_Mutation_p.A38G	NM_001118885	NP_001112357	P23416	GLRA2_HUMAN	glycine receptor, alpha 2 isoform A	60	Extracellular (Probable).				neuropeptide signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity			ovary(1)|lung(1)	2	Hepatocellular(33;0.128)				Ethanol(DB00898)|Glycine(DB00145)									0.571429	77.406089	77.561789	20	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14550471	14550471	6723	23	C	G	G	G	325	25	GLRA2	3	3
AFF2	2334	broad.mit.edu	37	X	148037652	148037652	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:148037652G>T	uc004fcp.2	+	c.2077G>T	c.(2077-2079)GAG>TAG	p.E693*	AFF2_uc004fcq.2_Nonsense_Mutation_p.E683*|AFF2_uc004fcr.2_Nonsense_Mutation_p.E654*|AFF2_uc011mxb.1_Nonsense_Mutation_p.E658*|AFF2_uc004fcs.2_Nonsense_Mutation_p.E660*|AFF2_uc011mxc.1_Nonsense_Mutation_p.E334*	NM_002025	NP_002016	P51816	AFF2_HUMAN	fragile X mental retardation 2	693					brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)													0.519084	207.496364	207.537523	68	63	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	148037652	148037652	358	23	G	T	T	T	481	37	AFF2	5	1
TREX2	11219	broad.mit.edu	37	X	152710691	152710691	+	Silent	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:152710691C>A	uc010nue.1	-	c.324G>T	c.(322-324)CCG>CCT	p.P108P	TREX2_uc010nud.1_Silent_p.P66P|TREX2_uc011myp.1_Silent_p.P66P|HAUS7_uc004fhl.2_Non-coding_Transcript|HAUS7_uc004fhm.2_Non-coding_Transcript	NM_080701	NP_542432	Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2	109					DNA repair	nucleus	3'-5'-exodeoxyribonuclease activity|exodeoxyribonuclease III activity|nucleic acid binding			large_intestine(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.583333	66.079235	66.297617	21	15	KEEP	---	---	---	---	capture		Silent	SNP	152710691	152710691	17021	23	C	A	A	A	288	23	TREX2	1	1
ATP2B3	492	broad.mit.edu	37	X	152826288	152826288	+	Silent	SNP	C	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:152826288C>T	uc004fht.1	+	c.2994C>T	c.(2992-2994)GAC>GAT	p.D998D	ATP2B3_uc004fhs.1_Silent_p.D998D|ATP2B3_uc010nuf.1_Silent_p.D21D|ATP2B3_uc004fhu.1_5'Flank	NM_001001344	NP_001001344	Q16720	AT2B3_HUMAN	plasma membrane calcium ATPase 3 isoform 3b	998	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.586957	167.651796	168.257908	54	38	KEEP	---	---	---	---	capture		Silent	SNP	152826288	152826288	1160	23	C	T	T	T	246	19	ATP2B3	1	1
SH3KBP1	30011	broad.mit.edu	37	X	19650023	19650023	+	Silent	SNP	A	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:19650023A>G	uc004czm.2	-	c.856T>C	c.(856-858)TTG>CTG	p.L286L	SH3KBP1_uc011mje.1_Silent_p.L25L|SH3KBP1_uc011mjf.1_Silent_p.L48L|SH3KBP1_uc004czl.2_Silent_p.L249L	NM_031892	NP_114098	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1 isoform a	286	SH3 3.				apoptosis|cell-cell signaling|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	cytoplasmic vesicle membrane|cytoskeleton|cytosol|focal adhesion|nucleus|synapse|synaptosome	SH3 domain binding				0														0.57971	151.413728	151.796662	40	29	KEEP	---	---	---	---	capture		Silent	SNP	19650023	19650023	14747	23	A	G	G	G	50	4	SH3KBP1	4	4
MAGEB16	139604	broad.mit.edu	37	X	35820818	35820818	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:35820818G>T	uc010ngt.1	+	c.505G>T	c.(505-507)GAT>TAT	p.D169Y		NM_001099921	NP_001093391	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	169	MAGE.									lung(3)|ovary(2)|breast(1)	6										43				0.494253	127.61606	127.618659	43	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35820818	35820818	9555	23	G	T	T	T	585	45	MAGEB16	2	2
RBM10	8241	broad.mit.edu	37	X	47041247	47041247	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:47041247G>T	uc004dhi.2	+	c.1870G>T	c.(1870-1872)GAA>TAA	p.E624*	RBM10_uc004dhf.2_Nonsense_Mutation_p.E559*|RBM10_uc004dhg.2_Nonsense_Mutation_p.E481*|RBM10_uc004dhh.2_Nonsense_Mutation_p.E558*|RBM10_uc010nhq.2_Nonsense_Mutation_p.E482*	NM_005676	NP_005667	P98175	RBM10_HUMAN	RNA binding motif protein 10 isoform 1	559					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)								0.5	32.99635	32.99635	12	12	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	47041247	47041247	13572	23	G	T	T	T	533	41	RBM10	5	2
NAP1L2	4674	broad.mit.edu	37	X	72434120	72434120	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:72434120C>A	uc004ebi.2	-	c.209G>T	c.(208-210)GGG>GTG	p.G70V	NAP1L2_uc011mqj.1_Intron	NM_021963	NP_068798	Q9ULW6	NP1L2_HUMAN	nucleosome assembly protein 1-like 2	70					nucleosome assembly	chromatin assembly complex				lung(1)	1	Renal(35;0.156)													0.604938	146.079856	146.858461	49	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72434120	72434120	10553	23	C	A	A	A	286	22	NAP1L2	2	2
SHROOM2	357	broad.mit.edu	37	X	9862711	9862711	+	Missense_Mutation	SNP	G	T	T	rs111899727		TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:9862711G>T	uc004csu.1	+	c.763G>T	c.(763-765)GCA>TCA	p.A255S		NM_001649	NP_001640	Q13796	SHRM2_HUMAN	apical protein of Xenopus-like	255					apical protein localization|brain development|cell migration|cell morphogenesis|cellular pigment accumulation|ear development|establishment of melanosome localization|eye pigment granule organization|lens morphogenesis in camera-type eye|melanosome organization	apical plasma membrane|cell-cell adherens junction|microtubule|tight junction	actin filament binding|beta-catenin binding|ligand-gated sodium channel activity			ovary(3)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	6		Hepatocellular(5;0.000888)												0.666667	64.608048	65.345672	20	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9862711	9862711	14789	23	G	T	T	T	494	38	SHROOM2	1	1
IRS2	8660	broad.mit.edu	37	13	110435612	110435613	+	Frame_Shift_Ins	INS	-	G	G			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:110435612_110435613insG	uc001vqv.2	-	c.2788_2789insC	c.(2788-2790)CGCfs	p.R930fs		NM_003749	NP_003740	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	930					fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus	cytosol|plasma membrane	insulin receptor binding|signal transducer activity			large_intestine(2)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	5	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			Melanoma(100;613 2409 40847)				156				0.38			3	5		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	110435612	110435613	8145	13	-	G	G	G	351	27	IRS2	5	5
RRP7A	27341	broad.mit.edu	37	22	42910685	42910686	+	Splice_Site_Ins	INS	-	A	A			TCGA-05-4418-01	TCGA-05-4418-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:42910685_42910686insA	uc003bcp.2	-	c.627_splice	c.e3+1	p.E209_splice	SERHL_uc011apm.1_Intron|RRP7A_uc003bcq.2_Splice_Site_Ins_p.E186_splice	NM_015703	NP_056518			ribosomal RNA processing 7 homolog A								nucleotide binding|RNA binding			central_nervous_system(1)	1														0.31			5	11		---	---	---	---	capture_indel		Splice_Site_Ins	INS	42910685	42910686	14169	22	-	A	A	A	677	53	RRP7A	5	5
