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
ANKRD30A	91074	broad.mit.edu	37	10	37430990	37430990	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:37430990G>T	uc001iza.1	+	c.997G>T	c.(997-999)GAA>TAA	p.E333*		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	389					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)	8														0.297872	36.53432	38.24949	14	33	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	37430990	37430990	663	10	G	T	T	T	429	33	ANKRD30A	5	2
GRID1	2894	broad.mit.edu	37	10	87487669	87487669	+	Silent	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:87487669G>A	uc001kdl.1	-	c.1476C>T	c.(1474-1476)TAC>TAT	p.Y492Y	GRID1_uc009xsu.1_Non-coding_Transcript|GRID1_uc010qmf.1_Silent_p.Y63Y	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	492	Extracellular (Potential).					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|large_intestine(2)	7					L-Glutamic Acid(DB00142)						Multiple Myeloma(13;0.14)			0.302632	58.6872	61.337032	23	53	KEEP	---	---	---	---	capture		Silent	SNP	87487669	87487669	7049	10	G	A	A	A	516	40	GRID1	1	1
GRID1	2894	broad.mit.edu	37	10	87487760	87487760	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:87487760C>T	uc001kdl.1	-	c.1385G>A	c.(1384-1386)CGC>CAC	p.R462H	GRID1_uc009xsu.1_Non-coding_Transcript|GRID1_uc010qmf.1_Missense_Mutation_p.R33H	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	462	Extracellular (Potential).					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|large_intestine(2)	7					L-Glutamic Acid(DB00142)						Multiple Myeloma(13;0.14)			0.099099	8.071992	25.882485	11	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87487760	87487760	7049	10	C	T	T	T	351	27	GRID1	1	1
NAT10	55226	broad.mit.edu	37	11	34153690	34153690	+	Silent	SNP	T	C	C			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:34153690T>C	uc001mvk.2	+	c.1539T>C	c.(1537-1539)GAT>GAC	p.D513D	NAT10_uc010ren.1_Silent_p.D441D	NM_024662	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 isoform a	513						nucleolus	ATP binding|N-acetyltransferase activity|protein binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)												0.148571	99.070376	140.481288	52	298	KEEP	---	---	---	---	capture		Silent	SNP	34153690	34153690	10570	11	T	C	C	C	634	49	NAT10	4	4
EHF	26298	broad.mit.edu	37	11	34668230	34668230	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:34668230C>G	uc009ykf.1	+	c.351C>G	c.(349-351)AAC>AAG	p.N117K	EHF_uc001mvr.1_Missense_Mutation_p.N114K|EHF_uc009yke.1_Missense_Mutation_p.N114K	NM_012153	NP_036285	Q9NZC4	EHF_HUMAN	ets homologous factor	114	PNT.				cell proliferation|epithelial cell differentiation|multicellular organismal development|positive regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)											0.195489	54.825596	66.325767	26	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34668230	34668230	5170	11	C	G	G	G	246	19	EHF	3	3
ALX4	60529	broad.mit.edu	37	11	44297153	44297153	+	Silent	SNP	C	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:44297153C>A	uc001myb.2	-	c.522G>T	c.(520-522)GGG>GGT	p.G174G		NM_021926	NP_068745	Q9H161	ALX4_HUMAN	aristaless-like homeobox 4	174					hair follicle development		transcription regulator activity				0														0.395349	85.403074	86.234626	34	52	KEEP	---	---	---	---	capture		Silent	SNP	44297153	44297153	561	11	C	A	A	A	379	30	ALX4	2	2
TMX2	51075	broad.mit.edu	37	11	57480103	57480103	+	Missense_Mutation	SNP	G	C	C			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57480103G>C	uc001nlc.1	+	c.13G>C	c.(13-15)GCA>CCA	p.A5P	CTNND1_uc001nlf.1_5'UTR|MED19_uc001nla.1_5'Flank|MED19_uc001nlb.2_5'Flank|TMX2_uc001nld.1_5'UTR|TMX2_uc001nle.1_Missense_Mutation_p.A5P	NM_015959	NP_057043	Q9Y320	TMX2_HUMAN	thioredoxin domain containing 14 isoform 1	5					cell redox homeostasis	integral to membrane					0														0.25	13.365063	14.501589	5	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57480103	57480103	16808	11	G	C	C	C	546	42	TMX2	3	3
C12orf48	55010	broad.mit.edu	37	12	102569349	102569349	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:102569349G>A	uc010swa.1	+	c.1141G>A	c.(1141-1143)GAA>AAA	p.E381K	C12orf48_uc001tjg.2_Missense_Mutation_p.E223K|C12orf48_uc001tjf.2_Missense_Mutation_p.E304K|C12orf48_uc001tjh.2_Missense_Mutation_p.E223K|C12orf48_uc010swb.1_Intron|C12orf48_uc009zuc.2_Intron|C12orf48_uc001tjj.2_Missense_Mutation_p.E19K|C12orf48_uc001tjk.2_Intron|C12orf48_uc009zud.2_Intron	NM_017915	NP_060385	Q9NWS1	PR1BP_HUMAN	hypothetical protein LOC55010	304					response to DNA damage stimulus	cytoplasm|nucleus	DNA binding				0														0.383333	69.610009	70.326343	23	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102569349	102569349	1736	12	G	A	A	A	533	41	C12orf48	2	2
NCOR2	9612	broad.mit.edu	37	12	124840077	124840077	+	Silent	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:124840077G>A	uc010tay.1	-	c.3303C>T	c.(3301-3303)CCC>CCT	p.P1101P	NCOR2_uc010taz.1_Silent_p.P1085P|NCOR2_uc010tba.1_Silent_p.P1102P|NCOR2_uc010tbb.1_Silent_p.P1094P|NCOR2_uc010tbc.1_Silent_p.P1084P|NCOR2_uc001ugj.1_Silent_p.P1102P	NM_006312	NP_006303	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 1	1102					cellular lipid metabolic process|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity|transcription repressor activity			ovary(1)|skin(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)										0.387097	36.328567	36.661938	12	19	KEEP	---	---	---	---	capture		Silent	SNP	124840077	124840077	10635	12	G	A	A	A	496	39	NCOR2	1	1
KRT7	3855	broad.mit.edu	37	12	52639248	52639248	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52639248C>T	uc001saa.1	+	c.1037C>T	c.(1036-1038)GCG>GTG	p.A346V	KRT7_uc009zmf.1_Intron	NM_005556	NP_005547	P08729	K2C7_HUMAN	keratin 7	346	Rod.|Coil 2.				cytoskeleton organization|DNA replication|interphase|interspecies interaction between organisms|regulation of translation	Golgi apparatus|keratin filament|nucleus	protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.105)										0.206897	10.530409	12.844647	6	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52639248	52639248	8798	12	C	T	T	T	351	27	KRT7	1	1
CD163L1	283316	broad.mit.edu	37	12	7526177	7526177	+	Missense_Mutation	SNP	C	G	G			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:7526177C>G	uc010sge.1	-	c.3499G>C	c.(3499-3501)GAA>CAA	p.E1167Q	CD163L1_uc001qsy.2_Missense_Mutation_p.E1157Q	NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	1157	SRCR 11.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|central_nervous_system(1)	9														0.129032	34.804826	55.563879	20	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7526177	7526177	3095	12	C	G	G	G	390	30	CD163L1	3	3
C14orf49	161176	broad.mit.edu	37	14	95932465	95932465	+	Silent	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:95932465G>A	uc001yei.3	-	c.430C>T	c.(430-432)CTG>TTG	p.L144L	C14orf49_uc010avi.2_Silent_p.L144L|C14orf49_uc001yej.1_Silent_p.L144L	NM_152592	NP_689805	Q6ZMZ3	SYNE3_HUMAN	nesprin-3	144	Cytoplasmic (Potential).				cytoskeletal anchoring at nuclear membrane	integral to membrane|nuclear outer membrane|SUN-KASH complex	actin binding			central_nervous_system(1)	1		all_cancers(154;0.0937)		COAD - Colon adenocarcinoma(157;0.245)										0.438356	93.482099	93.724654	32	41	KEEP	---	---	---	---	capture		Silent	SNP	95932465	95932465	1826	14	G	A	A	A	438	34	C14orf49	2	2
PHKB	5257	broad.mit.edu	37	16	47549445	47549445	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:47549445C>T	uc002eev.3	+	c.527C>T	c.(526-528)TCA>TTA	p.S176L	PHKB_uc010vgi.1_Missense_Mutation_p.S169L|PHKB_uc002eeu.3_Missense_Mutation_p.S169L	NM_000293	NP_000284	Q93100	KPBB_HUMAN	phosphorylase kinase, beta isoform a	176					glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)												0.257143	23.65981	25.530197	9	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47549445	47549445	12269	16	C	T	T	T	377	29	PHKB	2	2
MGAT5B	146664	broad.mit.edu	37	17	74921106	74921106	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:74921106G>A	uc002jti.2	+	c.1117G>A	c.(1117-1119)GAC>AAC	p.D373N	MGAT5B_uc002jth.2_Missense_Mutation_p.D362N	NM_198955	NP_945193	Q3V5L5	MGT5B_HUMAN	N-acetylglucosaminyltranferase VB isoform 2	362	Lumenal (Potential).					Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(2)	2														0.194805	31.609703	38.277894	15	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74921106	74921106	9939	17	G	A	A	A	481	37	MGAT5B	1	1
SLC25A10	1468	broad.mit.edu	37	17	79687107	79687107	+	Nonstop_Mutation	SNP	A	C	C			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:79687107A>C	uc010wut.1	+	c.1329A>C	c.(1327-1329)TGA>TGC	p.*443C	SLC25A10_uc002kbi.2_Nonstop_Mutation_p.*288C|SLC25A10_uc010dif.2_Nonstop_Mutation_p.*297C|SLC25A10_uc010wuu.1_Nonstop_Mutation_p.*242C	NM_012140	NP_036272	Q9UBX3	DIC_HUMAN	solute carrier family 25 (mitochondrial carrier;	443					gluconeogenesis|mitochondrial transport	integral to membrane|mitochondrial inner membrane|nucleus	protein binding				0	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Succinic acid(DB00139)									0.205882	3.827129	6.682025	7	27	KEEP	---	---	---	---	capture		Nonstop_Mutation	SNP	79687107	79687107	14969	17	A	C	C	C	130	10	SLC25A10	5	4
SMAD4	4089	broad.mit.edu	37	18	48604655	48604655	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:48604655G>A	uc010xdp.1	+	c.1477G>A	c.(1477-1479)GAT>AAT	p.D493N	SMAD4_uc002lfb.3_Missense_Mutation_p.D338N	NM_005359	NP_005350	Q13485	SMAD4_HUMAN	mothers against decapentaplegic homolog 4	493	MH2.				BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|promoter binding|protein homodimerization activity|R-SMAD binding|transcription activator activity|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity	p.0?(35)|p.D493H(1)|p.D493N(1)		pancreas(169)|large_intestine(108)|thyroid(19)|lung(10)|small_intestine(9)|biliary_tract(8)|upper_aerodigestive_tract(7)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	364		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)						233				0.366667	30.818137	31.286549	11	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48604655	48604655	15258	18	G	A	A	A	585	45	SMAD4	2	2
CIRBP	1153	broad.mit.edu	37	19	1270962	1270962	+	Silent	SNP	T	G	G			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:1270962T>G	uc002lrt.2	+	c.30T>G	c.(28-30)GTT>GTG	p.V10V	C19orf23_uc010xgk.1_5'Flank|CIRBP_uc010dsg.1_5'UTR|CIRBP_uc002lrr.3_Silent_p.V10V|CIRBP_uc010xgl.1_Silent_p.V10V|CIRBP_uc002lrv.3_Silent_p.V10V|CIRBP_uc002lru.2_Non-coding_Transcript	NM_001280	NP_001271	Q14011	CIRBP_HUMAN	cold inducible RNA binding protein	10	RRM.				mRNA stabilization|positive regulation of translation|response to cold|response to UV|stress granule assembly	nucleoplasm|stress granule	mRNA 3'-UTR binding|nucleotide binding|protein binding|SSU rRNA binding|translation repressor activity				0		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.084967	4.961889	31.69238	13	140	KEEP	---	---	---	---	capture		Silent	SNP	1270962	1270962	3567	19	T	G	G	G	808	63	CIRBP	4	4
RYR1	6261	broad.mit.edu	37	19	38951104	38951104	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:38951104G>A	uc002oit.2	+	c.2450G>A	c.(2449-2451)CGA>CAA	p.R817Q	RYR1_uc002oiu.2_Missense_Mutation_p.R817Q	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	817	Cytoplasmic.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)	10	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)									0.241758	56.517905	62.043936	22	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38951104	38951104	14248	19	G	A	A	A	481	37	RYR1	1	1
FPR1	2357	broad.mit.edu	37	19	52249869	52249869	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52249869C>T	uc002pxq.2	-	c.379G>A	c.(379-381)GTC>ATC	p.V127I		NM_002029	NP_002020	P21462	FPR1_HUMAN	formyl peptide receptor 1	127	Cytoplasmic (Potential).				activation of MAPK activity|cellular component movement|chemotaxis|G-protein signaling, coupled to cAMP nucleotide second messenger|nitric oxide mediated signal transduction	endosome|integral to membrane|plasma membrane	N-formyl peptide receptor activity			ovary(1)	1		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)									0.3	40.142797	41.908641	15	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52249869	52249869	6284	19	C	T	T	T	247	19	FPR1	1	1
CFH	3075	broad.mit.edu	37	1	196706690	196706690	+	Silent	SNP	G	C	C			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:196706690G>C	uc001gtj.3	+	c.2682G>C	c.(2680-2682)GGG>GGC	p.G894G		NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	894	Sushi 15.				complement activation, alternative pathway	extracellular space				ovary(1)|breast(1)|skin(1)	3														0.4375	45.942115	46.051547	14	18	KEEP	---	---	---	---	capture		Silent	SNP	196706690	196706690	3416	1	G	C	C	C	522	41	CFH	3	3
TRIM58	25893	broad.mit.edu	37	1	248039632	248039632	+	Nonsense_Mutation	SNP	C	G	G			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248039632C>G	uc001ido.2	+	c.1302C>G	c.(1300-1302)TAC>TAG	p.Y434*	OR2W3_uc001idp.1_Intron	NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	tripartite motif-containing 58	434	B30.2/SPRY.					intracellular	zinc ion binding			ovary(1)|lung(1)|central_nervous_system(1)|pancreas(1)	4	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)											0.416268	295.694514	296.971818	87	122	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	248039632	248039632	17077	1	C	G	G	G	220	17	TRIM58	5	3
CSF3R	1441	broad.mit.edu	37	1	36932904	36932904	+	Missense_Mutation	SNP	T	C	C			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:36932904T>C	uc001cax.1	-	c.1967A>G	c.(1966-1968)AAT>AGT	p.N656S	MRPS15_uc001cas.2_5'Flank|CSF3R_uc001cat.1_Missense_Mutation_p.N218S|CSF3R_uc009vvc.1_Missense_Mutation_p.N185S|CSF3R_uc001cau.1_Missense_Mutation_p.N56S|CSF3R_uc001cav.1_Missense_Mutation_p.N656S|CSF3R_uc001caw.1_Missense_Mutation_p.N656S|CSF3R_uc001cay.1_Missense_Mutation_p.I625V	NM_156039	NP_724781	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor isoform c	656	Cytoplasmic (Potential).				cell adhesion|defense response	extracellular region|integral to plasma membrane	cytokine receptor activity			central_nervous_system(2)|ovary(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)					322				0.446281	177.724046	178.011816	54	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36932904	36932904	4078	1	T	C	C	C	676	52	CSF3R	4	4
RLF	6018	broad.mit.edu	37	1	40627199	40627199	+	Missense_Mutation	SNP	C	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:40627199C>A	uc001cfc.3	+	c.128C>A	c.(127-129)GCG>GAG	p.A43E		NM_012421	NP_036553	Q13129	RLF_HUMAN	rearranged L-myc fusion	43					chromosome organization|DNA integration|DNA mediated transformation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|protein binding|transcription activator activity|zinc ion binding			ovary(2)|pancreas(1)	3	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)											0.071429	-1.557075	6.345087	3	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40627199	40627199	13866	1	C	A	A	A	351	27	RLF	1	1
TTLL9	164395	broad.mit.edu	37	20	30522516	30522516	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:30522516C>T	uc010gdx.1	+	c.829C>T	c.(829-831)CGC>TGC	p.R277C	TTLL9_uc002wwy.1_Non-coding_Transcript|TTLL9_uc002wwz.1_Intron|TTLL9_uc002wxa.1_Non-coding_Transcript|TTLL9_uc002wxb.1_Non-coding_Transcript|TTLL9_uc010zto.1_Non-coding_Transcript|TTLL9_uc002wxc.2_Missense_Mutation_p.R179C|TTLL9_uc010ztp.1_Non-coding_Transcript|TTLL9_uc010ztq.1_Non-coding_Transcript	NM_001008409	NP_001008409	Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	277	TTL.				protein modification process	cilium|microtubule|microtubule basal body	ATP binding|tubulin-tyrosine ligase activity			ovary(2)	2			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)											0.210526	7.888495	9.362697	4	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30522516	30522516	17289	20	C	T	T	T	351	27	TTLL9	1	1
PROKR2	128674	broad.mit.edu	37	20	5283319	5283319	+	Silent	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:5283319G>A	uc010zqw.1	-	c.522C>T	c.(520-522)ATC>ATT	p.I174I	PROKR2_uc010zqx.1_Silent_p.I174I|PROKR2_uc010zqy.1_Silent_p.I174I	NM_144773	NP_658986	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	174	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5														0.061728	-6.670953	9.546283	5	76	KEEP	---	---	---	---	capture		Silent	SNP	5283319	5283319	12996	20	G	A	A	A	473	37	PROKR2	1	1
LAMA5	3911	broad.mit.edu	37	20	60889674	60889674	+	Silent	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:60889674G>A	uc002ycq.2	-	c.8304C>T	c.(8302-8304)GGC>GGT	p.G2768G		NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor	2768	Laminin G-like 1.				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding|receptor activity|structural molecule activity			pancreas(1)	1	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)									0.175439	19.821336	25.479141	10	47	KEEP	---	---	---	---	capture		Silent	SNP	60889674	60889674	8932	20	G	A	A	A	535	42	LAMA5	2	2
SFRS15	57466	broad.mit.edu	37	21	33073368	33073368	+	Silent	SNP	T	C	C			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:33073368T>C	uc002ypd.2	-	c.717A>G	c.(715-717)ACA>ACG	p.T239T	SFRS15_uc002ype.2_Silent_p.T239T|SFRS15_uc010glu.2_Silent_p.T224T|SFRS15_uc002ypf.1_5'UTR|SFRS15_uc002ypg.2_Silent_p.T239T	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform	239						nucleus	nucleotide binding|RNA binding				0														0.210526	18.578818	21.524941	8	30	KEEP	---	---	---	---	capture		Silent	SNP	33073368	33073368	14661	21	T	C	C	C	756	59	SFRS15	4	4
DSCAM	1826	broad.mit.edu	37	21	41384970	41384970	+	Silent	SNP	G	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:41384970G>T	uc002yyq.1	-	c.6030C>A	c.(6028-6030)ACC>ACA	p.T2010T	DSCAM_uc002yyr.1_Non-coding_Transcript	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	2010	Cytoplasmic (Potential).			HRPGDLIHLPPYLRMDFLLNRGGPGTSRDLSLGQACLEPQK SRTLKRPTVLEPIPMEAASSASSTREGQSWQPGAVATLPQR EGAELGQAAKMSSSQESLLDSRGHLKGNNPYAKSYTLV -> IGQVTSYICLHTLEWTFC (in Ref. 1; AAC17966).	cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)	6		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				Melanoma(134;970 1778 1785 21664 32388)								0.285714	22.628559	24.075836	10	25	KEEP	---	---	---	---	capture		Silent	SNP	41384970	41384970	4952	21	G	T	T	T	548	43	DSCAM	2	2
SEPT3	55964	broad.mit.edu	37	22	42377837	42377837	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:42377837G>A	uc003bbr.3	+	c.199G>A	c.(199-201)GTT>ATT	p.V67I	WBP2NL_uc011ape.1_Intron|SEPT3_uc003bbs.3_Missense_Mutation_p.V67I|SEPT3_uc010gyr.2_Intron|SEPT3_uc011apj.1_Intron|SEPT3_uc010gys.2_5'UTR	NM_145733	NP_663786	Q9UH03	SEPT3_HUMAN	septin 3 isoform A	67					cell cycle|cytokinesis	cell junction|septin complex	GTP binding				0										112				0.142857	3.81054	6.394745	3	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42377837	42377837	14551	22	G	A	A	A	520	40	SEPT3	1	1
MARCO	8685	broad.mit.edu	37	2	119752091	119752091	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:119752091G>A	uc002tln.1	+	c.1558G>A	c.(1558-1560)GTC>ATC	p.V520I	MARCO_uc010yyf.1_Missense_Mutation_p.V442I	NM_006770	NP_006761	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	520	Extracellular (Potential).				cell surface receptor linked signaling pathway|innate immune response	collagen|integral to plasma membrane	pattern recognition receptor activity|scavenger receptor activity			ovary(3)|central_nervous_system(1)	4						GBM(8;18 374 7467 11269 32796)								0.22807	30.350477	34.214241	13	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119752091	119752091	9694	2	G	A	A	A	520	40	MARCO	1	1
PXDN	7837	broad.mit.edu	37	2	1653369	1653369	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:1653369C>T	uc002qxa.2	-	c.2183G>A	c.(2182-2184)CGC>CAC	p.R728H		NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	728					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				0.061538	-4.641511	8.387837	4	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1653369	1653369	13305	2	C	T	T	T	351	27	PXDN	1	1
STAT1	6772	broad.mit.edu	37	2	191873763	191873763	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:191873763G>A	uc002usj.2	-	c.199C>T	c.(199-201)CAA>TAA	p.Q67*	STAT1_uc010fse.1_Nonsense_Mutation_p.Q67*|STAT1_uc002usk.2_Nonsense_Mutation_p.Q67*|STAT1_uc002usl.2_Nonsense_Mutation_p.Q69*|STAT1_uc010fsf.1_5'UTR	NM_007315	NP_009330	P42224	STAT1_HUMAN	signal transducer and activator of transcription	67					activation of caspase activity|I-kappaB kinase/NF-kappaB cascade|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of interferon-gamma-mediated signaling pathway|regulation of transcription, DNA-dependent|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway|tyrosine phosphorylation of STAT protein	cytosol|nucleolus|nucleoplasm	calcium ion binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(2)|central_nervous_system(2)|ovary(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)		Fludarabine(DB01073)					350				0.285714	21.086482	22.241634	8	20	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	191873763	191873763	15784	2	G	A	A	A	585	45	STAT1	5	2
COL6A3	1293	broad.mit.edu	37	2	238280738	238280738	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:238280738G>A	uc002vwl.2	-	c.3922C>T	c.(3922-3924)CGG>TGG	p.R1308W	COL6A3_uc002vwo.2_Missense_Mutation_p.R1102W|COL6A3_uc010znj.1_Missense_Mutation_p.R701W|COL6A3_uc002vwq.2_Missense_Mutation_p.R1102W|COL6A3_uc002vwr.2_Missense_Mutation_p.R901W	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1308	VWFA 7.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)										0.086957	0.673671	8.611532	4	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	238280738	238280738	3839	2	G	A	A	A	493	38	COL6A3	1	1
GKN2	200504	broad.mit.edu	37	2	69173459	69173459	+	Missense_Mutation	SNP	T	G	G			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:69173459T>G	uc002sfa.2	-	c.449A>C	c.(448-450)AAG>ACG	p.K150T	GKN2_uc002sfb.3_Missense_Mutation_p.K150T	NM_182536	NP_872342	Q86XP6	GKN2_HUMAN	trefoil factor interactions(z) 1 precursor	150	BRICHOS.					extracellular region					0														0.3	62.546593	65.791793	27	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69173459	69173459	6693	2	T	G	G	G	728	56	GKN2	4	4
ARHGEF3	50650	broad.mit.edu	37	3	56807778	56807778	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:56807778C>T	uc003dih.2	-	c.259G>A	c.(259-261)GTG>ATG	p.V87M	ARHGEF3_uc011bew.1_Missense_Mutation_p.V55M|ARHGEF3_uc011bev.1_Missense_Mutation_p.V26M|ARHGEF3_uc003dif.2_Missense_Mutation_p.V61M|ARHGEF3_uc003dig.2_Missense_Mutation_p.V55M|ARHGEF3_uc010hmy.1_De_novo_Start_OutOfFrame|ARHGEF3_uc003dii.2_Missense_Mutation_p.V55M	NM_001128615	NP_001122087	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor 3 isoform	55					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)										0.2	6.216057	7.472429	3	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56807778	56807778	918	3	C	T	T	T	247	19	ARHGEF3	1	1
EGF	1950	broad.mit.edu	37	4	110914495	110914495	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:110914495C>T	uc003hzy.3	+	c.2827C>T	c.(2827-2829)CGC>TGC	p.R943C	EGF_uc011cfu.1_Missense_Mutation_p.R901C|EGF_uc011cfv.1_Intron|EGF_uc010imk.2_Missense_Mutation_p.R91C	NM_001963	NP_001954	P01133	EGF_HUMAN	epidermal growth factor precursor	943	EGF-like 8; calcium-binding (Potential).|Extracellular (Potential).				angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			central_nervous_system(1)	1		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)					724				0.209877	37.072492	43.353623	17	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110914495	110914495	5151	4	C	T	T	T	247	19	EGF	1	1
FAM190A	401145	broad.mit.edu	37	4	91549259	91549259	+	Missense_Mutation	SNP	C	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:91549259C>A	uc003hsv.3	+	c.1808C>A	c.(1807-1809)GCG>GAG	p.A603E	FAM190A_uc010ikv.2_Non-coding_Transcript|FAM190A_uc003hsw.2_Missense_Mutation_p.A603E	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1	603										large_intestine(1)|ovary(1)	2														0.075	-0.698029	6.707444	3	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91549259	91549259	5732	4	C	A	A	A	351	27	FAM190A	1	1
SLC4A9	83697	broad.mit.edu	37	5	139751848	139751848	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:139751848C>T	uc003lfm.2	+	c.2764C>T	c.(2764-2766)CGA>TGA	p.R922*	SLC4A9_uc003lfj.2_Nonsense_Mutation_p.R898*|SLC4A9_uc011czg.1_Nonsense_Mutation_p.R835*|SLC4A9_uc003lfl.2_Nonsense_Mutation_p.R898*|SLC4A9_uc003lfk.2_Nonsense_Mutation_p.R884*	NM_031467	NP_113655	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate	922	Membrane (anion exchange).					integral to membrane|plasma membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			large_intestine(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.4	18.647399	18.778401	6	9	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	139751848	139751848	15157	5	C	T	T	T	295	23	SLC4A9	5	1
PCDHB4	56131	broad.mit.edu	37	5	140503027	140503027	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140503027G>A	uc003lip.1	+	c.1447G>A	c.(1447-1449)GCC>ACC	p.A483T		NM_018938	NP_061761	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4 precursor	483	Cadherin 5.|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)											0.207792	32.283957	38.364509	16	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140503027	140503027	11964	5	G	A	A	A	494	38	PCDHB4	1	1
PCDHGA3	56112	broad.mit.edu	37	5	140723793	140723793	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140723793C>T	uc003ljm.1	+	c.193C>T	c.(193-195)CGC>TGC	p.R65C	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_5'UTR|PCDHGA3_uc011dap.1_Missense_Mutation_p.R65C	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	65	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)									OREG0016855	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.058333	-10.423297	14.065132	7	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140723793	140723793	11975	5	C	T	T	T	299	23	PCDHGA3	1	1
FOXP2	93986	broad.mit.edu	37	7	114282647	114282647	+	Missense_Mutation	SNP	C	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:114282647C>A	uc003vgz.2	+	c.1033C>A	c.(1033-1035)CAG>AAG	p.Q345K	FOXP2_uc003vgu.2_Non-coding_Transcript|FOXP2_uc003vha.2_Missense_Mutation_p.Q228K|FOXP2_uc003vhb.2_Missense_Mutation_p.Q320K|FOXP2_uc011kmu.1_Missense_Mutation_p.Q337K|FOXP2_uc011kmv.1_Missense_Mutation_p.Q319K|FOXP2_uc010ljz.1_Missense_Mutation_p.Q228K|FOXP2_uc003vgx.2_Missense_Mutation_p.Q320K|FOXP2_uc003vhd.2_Missense_Mutation_p.Q320K|FOXP2_uc003vhc.2_Missense_Mutation_p.Q345K	NM_148898	NP_683696	O15409	FOXP2_HUMAN	forkhead box P2 isoform II	320					camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|lung(1)|breast(1)|pancreas(1)	7														0.097561	6.742638	20.03708	8	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114282647	114282647	6273	7	C	A	A	A	221	17	FOXP2	2	2
PTPRZ1	5803	broad.mit.edu	37	7	121651781	121651781	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:121651781G>A	uc003vjy.2	+	c.2681G>A	c.(2680-2682)AGT>AAT	p.S894N	PTPRZ1_uc003vjz.2_Intron|PTPRZ1_uc011knt.1_Intron	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	894	Extracellular (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9														0.347826	45.468102	46.416282	16	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121651781	121651781	13272	7	G	A	A	A	468	36	PTPRZ1	2	2
SPAM1	6677	broad.mit.edu	37	7	123594255	123594255	+	Missense_Mutation	SNP	C	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:123594255C>T	uc003vle.2	+	c.631C>T	c.(631-633)CGG>TGG	p.R211W	SPAM1_uc011koa.1_5'Flank|SPAM1_uc003vld.2_Missense_Mutation_p.R211W|SPAM1_uc003vlf.3_Missense_Mutation_p.R211W|SPAM1_uc010lku.2_Missense_Mutation_p.R211W	NM_003117	NP_003108	P38567	HYALP_HUMAN	sperm adhesion molecule 1 isoform 1	211				R->G: Reduces activity by over 90%.	binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)									0.103896	5.132279	17.198072	8	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123594255	123594255	15489	7	C	T	T	T	399	31	SPAM1	1	1
GARNL3	84253	broad.mit.edu	37	9	130027251	130027251	+	Missense_Mutation	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:130027251G>A	uc011mae.1	+	c.95G>A	c.(94-96)GGC>GAC	p.G32D	GARNL3_uc011mad.1_Missense_Mutation_p.G10D	NM_032293	NP_115669	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	32					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			central_nervous_system(1)|skin(1)	2														0.140845	31.030056	48.689869	20	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130027251	130027251	6505	9	G	A	A	A	546	42	GARNL3	2	2
CBWD6	644019	broad.mit.edu	37	9	69247529	69247529	+	Silent	SNP	G	A	A			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:69247529G>A	uc004afj.3	-	c.483C>T	c.(481-483)TAC>TAT	p.Y161Y	CBWD6_uc004afk.3_Intron|CBWD6_uc011lrf.1_Intron	NM_001085457	NP_001078926	Q4V339	CBWD6_HUMAN	COBW domain containing 6	161							ATP binding				0														0.142857	4.7149	7.292819	3	18	KEEP	---	---	---	---	capture		Silent	SNP	69247529	69247529	2835	9	G	A	A	A	568	44	CBWD6	2	2
BMP15	9210	broad.mit.edu	37	X	50659038	50659038	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:50659038C>T	uc011mnw.1	+	c.610C>T	c.(610-612)CGA>TGA	p.R204*		NM_005448	NP_005439	O95972	BMP15_HUMAN	bone morphogenetic protein 15 precursor	204					female gamete generation|granulosa cell development|ovarian follicle development	extracellular space	cytokine activity|growth factor activity			ovary(2)	2	Ovarian(276;0.236)													0.390244	45.286826	45.720353	16	25	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	50659038	50659038	1483	23	C	T	T	T	243	19	BMP15	5	1
ZDHHC14	79683	broad.mit.edu	37	6	157803062	157803064	+	In_Frame_Del	DEL	CGG	-	-			TCGA-05-5429-01	TCGA-05-5429-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:157803062_157803064delCGG	uc003qqt.2	+	c.9_11delCGG	c.(7-12)CCCGGC>CCC	p.G7del	ZDHHC14_uc003qqs.2_In_Frame_Del_p.G7del	NM_024630	NP_078906	Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14 isoform 1	7						integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)|skin(1)	2		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)										0.33			2	4		---	---	---	---	capture_indel		In_Frame_Del	DEL	157803062	157803064	18192	6	CGG	-	-	-	288	23	ZDHHC14	5	5
