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
HPS1	3257	broad.mit.edu	37	10	100182214	100182214	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:100182214C>A	uc001kpi.1	-	c.1658G>T	c.(1657-1659)GGG>GTG	p.G553V	HPS1_uc010qpf.1_Missense_Mutation_p.G552V|HPS1_uc001kpj.1_Missense_Mutation_p.G460V|HPS1_uc001kpk.1_Missense_Mutation_p.G377V	NM_000195	NP_000186	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1 protein isoform a	552					lysosome organization|response to stimulus|visual perception	cytoplasmic membrane-bounded vesicle|integral to plasma membrane|lysosome|membrane fraction|soluble fraction	protein dimerization activity				0		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)										0.229437	119.816445	135.28344	53	178	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100182214	100182214	7631	10	C	A	A	A	286	22	HPS1	2	2
PAX2	5076	broad.mit.edu	37	10	102541090	102541090	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:102541090G>T	uc001krk.3	+	c.584G>T	c.(583-585)CGC>CTC	p.R195L	PAX2_uc001krl.3_Missense_Mutation_p.R195L|PAX2_uc001krm.3_Missense_Mutation_p.R195L|PAX2_uc001kro.3_Missense_Mutation_p.R195L|PAX2_uc001krn.3_Missense_Mutation_p.R195L|PAX2_uc010qps.1_Missense_Mutation_p.R194L|PAX2_uc001krp.1_Missense_Mutation_p.R199L	NM_003990	NP_003981	Q02962	PAX2_HUMAN	paired box protein 2 isoform e	195					anti-apoptosis|axonogenesis|brain morphogenesis|branching involved in ureteric bud morphogenesis|cell fate determination|cellular response to glucose stimulus|cellular response to hydrogen peroxide|cellular response to retinoic acid|cochlea development|glial cell differentiation|inner ear morphogenesis|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesodermal cell fate specification|mesonephros development|metanephric collecting duct development|metanephric distal convoluted tubule development|metanephric mesenchymal cell differentiation|metanephric nephron tubule formation|negative regulation of caspase activity|negative regulation of cytolysis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|negative regulation of reactive oxygen species metabolic process|negative regulation of transcription, DNA-dependent|nephric duct formation|neural tube closure|optic chiasma development|optic cup morphogenesis involved in camera-type eye development|optic nerve formation|optic nerve structural organization|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|pronephric field specification|protein kinase B signaling cascade|reactive oxygen species metabolic process|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of metanephros size|retinal pigment epithelium development|stem cell differentiation|transcription from RNA polymerase II promoter|ureter development|vestibulocochlear nerve formation|visual perception	centriolar satellite|nucleus|protein complex|protein-DNA complex	core promoter proximal region sequence-specific DNA binding|promoter binding|superoxide-generating NADPH oxidase activity|transcription activator activity|transcription repressor activity				0		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)										0.194737	80.483807	96.984123	37	153	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102541090	102541090	11899	10	G	T	T	T	494	38	PAX2	1	1
PPRC1	23082	broad.mit.edu	37	10	103899654	103899654	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:103899654G>T	uc001kum.2	+	c.1389G>T	c.(1387-1389)AAG>AAT	p.K463N	PPRC1_uc001kun.2_Missense_Mutation_p.K343N|PPRC1_uc010qqj.1_Missense_Mutation_p.K463N|PPRC1_uc009xxa.2_Non-coding_Transcript	NM_015062	NP_055877	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor	463	Necessary for interaction with CREB1 and NRF1 and for transcriptional coactivation.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)										0.181102	40.244577	52.391754	23	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103899654	103899654	12846	10	G	T	T	T	425	33	PPRC1	2	2
NFKB2	4791	broad.mit.edu	37	10	104160161	104160161	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:104160161G>T	uc001kvb.2	+	c.1711G>T	c.(1711-1713)GGC>TGC	p.G571C	NFKB2_uc001kva.2_Missense_Mutation_p.G571C|NFKB2_uc001kvd.2_Missense_Mutation_p.G571C|NFKB2_uc009xxc.2_Missense_Mutation_p.G571C	NM_001077494	NP_001070962	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene	571	ANK 3.				innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|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	Bcl3/NF-kappaB2 complex|cytosol|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)						140				0.246575	40.893075	45.182469	18	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104160161	104160161	10776	10	G	T	T	T	455	35	NFKB2	2	2
PDCD11	22984	broad.mit.edu	37	10	105162908	105162908	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:105162908G>T	uc001kwy.1	+	c.268G>T	c.(268-270)GTG>TTG	p.V90L		NM_014976	NP_055791	Q14690	RRP5_HUMAN	programmed cell death 11	90	S1 motif 1.				mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)						545				0.239394	213.561609	234.022861	79	251	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105162908	105162908	12038	10	G	T	T	T	520	40	PDCD11	1	1
CCDC147	159686	broad.mit.edu	37	10	106118310	106118310	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:106118310A>T	uc001kyh.2	+	c.221A>T	c.(220-222)AAT>ATT	p.N74I		NM_001008723	NP_001008723	Q5T655	CC147_HUMAN	coiled-coil domain containing 147	74										ovary(2)|central_nervous_system(1)	3		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)										0.241379	48.716495	54.041346	21	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106118310	106118310	2901	10	A	T	T	T	52	4	CCDC147	3	3
SORCS1	114815	broad.mit.edu	37	10	108447959	108447959	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:108447959G>C	uc001kyl.2	-	c.1551C>G	c.(1549-1551)CAC>CAG	p.H517Q	SORCS1_uc001kym.2_Missense_Mutation_p.H517Q|SORCS1_uc009xxs.2_Missense_Mutation_p.H517Q|SORCS1_uc001kyn.1_Missense_Mutation_p.H517Q|SORCS1_uc001kyo.2_Missense_Mutation_p.H517Q	NM_001013031	NP_001013049	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform b	517	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)										0.198529	71.666539	83.15482	27	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108447959	108447959	15430	10	G	C	C	C	464	36	SORCS1	3	3
C10orf81	79949	broad.mit.edu	37	10	115526214	115526214	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:115526214G>A	uc001lat.1	+	c.55G>A	c.(55-57)GAT>AAT	p.D19N	C10orf81_uc001lar.1_Missense_Mutation_p.D25N|C10orf81_uc009xyc.1_5'UTR|C10orf81_uc001las.1_Intron	NM_024889	NP_079165	Q5SXH7	CJ081_HUMAN	hypothetical protein LOC79949	19	PH.									central_nervous_system(1)	1		Colorectal(252;0.175)		Epithelial(162;0.0181)|all cancers(201;0.0204)										0.083333	1.483096	20.548377	9	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115526214	115526214	1656	10	G	A	A	A	429	33	C10orf81	2	2
WDR37	22884	broad.mit.edu	37	10	1170222	1170222	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:1170222G>T	uc009xhm.1	+	c.1171G>T	c.(1171-1173)GTG>TTG	p.V391L	WDR37_uc001igf.1_Missense_Mutation_p.V390L|WDR37_uc009xhn.1_Non-coding_Transcript|WDR37_uc001igg.1_Non-coding_Transcript	NM_014023	NP_054742	Q9Y2I8	WDR37_HUMAN	WD repeat domain 37	390	WD 5.										0		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)										0.156716	38.983895	54.057401	21	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1170222	1170222	17864	10	G	T	T	T	572	44	WDR37	2	2
PNLIPRP3	119548	broad.mit.edu	37	10	118196348	118196348	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:118196348T>C	uc001lcl.3	+	c.175T>C	c.(175-177)TAC>CAC	p.Y59H		NM_001011709	NP_001011709	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3 precursor	59					lipid catabolic process	extracellular region	triglyceride lipase activity			ovary(1)	1				all cancers(201;0.0131)										0.125	33.712929	52.365001	17	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118196348	118196348	12578	10	T	C	C	C	689	53	PNLIPRP3	4	4
PDZD8	118987	broad.mit.edu	37	10	119043130	119043130	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:119043130G>A	uc001lde.1	-	c.3114C>T	c.(3112-3114)TTC>TTT	p.F1038F		NM_173791	NP_776152	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	1038	Potential.				intracellular signal transduction		metal ion binding				0		Colorectal(252;0.19)		all cancers(201;0.0121)										0.169697	48.079437	65.139299	28	137	KEEP	---	---	---	---	capture		Silent	SNP	119043130	119043130	12126	10	G	A	A	A	581	45	PDZD8	2	2
C10orf120	399814	broad.mit.edu	37	10	124457441	124457441	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:124457441C>A	uc001lgn.2	-	c.816G>T	c.(814-816)CCG>CCT	p.P272P		NM_001010912	NP_001010912	Q5SQS8	CJ120_HUMAN	hypothetical protein LOC399814	272										kidney(1)	1		all_neural(114;0.169)|Glioma(114;0.222)												0.07113	-10.753074	34.782574	17	222	KEEP	---	---	---	---	capture		Silent	SNP	124457441	124457441	1625	10	C	A	A	A	288	23	C10orf120	1	1
MKI67	4288	broad.mit.edu	37	10	129901357	129901357	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:129901357T>A	uc001lke.2	-	c.8747A>T	c.(8746-8748)GAA>GTA	p.E2916V	MKI67_uc001lkf.2_Missense_Mutation_p.E2556V|MKI67_uc009yav.1_Missense_Mutation_p.E2491V|MKI67_uc009yaw.1_Missense_Mutation_p.E2066V	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	2916	16 X 122 AA approximate repeats.|16.				cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(1)	5		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)												0.074627	-11.601938	38.180195	20	248	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129901357	129901357	9988	10	T	A	A	A	806	62	MKI67	3	3
EBF3	253738	broad.mit.edu	37	10	131755543	131755543	+	Nonsense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:131755543G>C	uc001lki.1	-	c.533C>G	c.(532-534)TCA>TGA	p.S178*		NM_001005463	NP_001005463	Q9H4W6	COE3_HUMAN	early B-cell factor 3	178					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|protein binding|transcription regulator activity			central_nervous_system(1)|pancreas(1)	2		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)										0.211454	136.167897	153.648858	48	179	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	131755543	131755543	5068	10	G	C	C	C	585	45	EBF3	5	3
ADAM8	101	broad.mit.edu	37	10	135080912	135080912	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:135080912T>G	uc010quz.1	-	c.2263A>C	c.(2263-2265)ACT>CCT	p.T755P	ADAM8_uc009ybi.2_Missense_Mutation_p.H699P|ADAM8_uc010qva.1_Missense_Mutation_p.T690P	NM_001109	NP_001100	Q14C66	Q14C66_HUMAN	ADAM metallopeptidase domain 8 isoform 1	755					integrin-mediated signaling pathway|proteolysis		metalloendopeptidase activity|zinc ion binding			large_intestine(2)	2		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)										0.102564	5.274216	11.408892	4	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135080912	135080912	253	10	T	G	G	G	767	59	ADAM8	4	4
SLC39A12	221074	broad.mit.edu	37	10	18250693	18250693	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:18250693A>T	uc001ipo.2	+	c.445A>T	c.(445-447)AGC>TGC	p.S149C	SLC39A12_uc001ipn.2_Missense_Mutation_p.S149C|SLC39A12_uc001ipp.2_Missense_Mutation_p.S149C|SLC39A12_uc010qck.1_Missense_Mutation_p.S15C	NM_001145195	NP_001138667	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter),	149	Extracellular (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)|breast(1)	2														0.190476	48.523879	59.812101	24	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18250693	18250693	15112	10	A	T	T	T	143	11	SLC39A12	3	3
PLXDC2	84898	broad.mit.edu	37	10	20432250	20432250	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:20432250C>T	uc001iqg.1	+	c.568C>T	c.(568-570)CAT>TAT	p.H190Y	PLXDC2_uc001iqh.1_Missense_Mutation_p.H141Y|PLXDC2_uc009xkc.1_Non-coding_Transcript	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor	190	Extracellular (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)	3														0.12	11.32301	25.501576	12	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20432250	20432250	12544	10	C	T	T	T	221	17	PLXDC2	2	2
C10orf114	399726	broad.mit.edu	37	10	21784772	21784772	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:21784772C>A	uc001iqn.3	-	c.168G>T	c.(166-168)CCG>CCT	p.P56P		NM_001010911	NP_001010911	Q5T4H9	CJ114_HUMAN	hypothetical protein LOC399726	56											0												OREG0020066	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.363636	11.498186	11.677639	4	7	KEEP	---	---	---	---	capture		Silent	SNP	21784772	21784772	1620	10	C	A	A	A	288	23	C10orf114	1	1
MSRB2	22921	broad.mit.edu	37	10	23399200	23399200	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:23399200G>T	uc001iro.2	+	c.249G>T	c.(247-249)AAG>AAT	p.K83N		NM_012228	NP_036360	Q9Y3D2	MSRB2_HUMAN	methionine sulfoxide reductase B2 precursor	83					oxidation-reduction process|protein repair	mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding				0					L-Methionine(DB00134)	Esophageal Squamous(89;1240 1363 4973 30188 42299)								0.098214	6.632835	24.734458	11	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23399200	23399200	10281	10	G	T	T	T	451	35	MSRB2	2	2
ARHGAP21	57584	broad.mit.edu	37	10	24959289	24959289	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:24959289G>T	uc001isb.2	-	c.101C>A	c.(100-102)ACT>AAT	p.T34N	ARHGAP21_uc009xkl.1_Missense_Mutation_p.T34N|ARHGAP21_uc001isc.1_Missense_Mutation_p.T34N|ARHGAP21_uc001isd.1_Missense_Mutation_p.T34N	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	33					signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8														0.133333	16.294854	26.083468	10	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24959289	24959289	882	10	G	T	T	T	468	36	ARHGAP21	2	2
GPR158	57512	broad.mit.edu	37	10	25840010	25840010	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:25840010C>T	uc001isj.2	+	c.1510C>T	c.(1510-1512)CAC>TAC	p.H504Y		NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	504	Helical; Name=3; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)	7														0.075269	-7.211928	27.227819	14	172	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25840010	25840010	6938	10	C	T	T	T	377	29	GPR158	2	2
SVIL	6840	broad.mit.edu	37	10	29775094	29775094	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:29775094G>A	uc001iut.1	-	c.4699C>T	c.(4699-4701)CGT>TGT	p.R1567C	LOC387647_uc001iuq.1_Intron|SVIL_uc010qdw.1_Missense_Mutation_p.R481C|SVIL_uc001iuu.1_Missense_Mutation_p.R1141C|SVIL_uc009xlc.2_Missense_Mutation_p.R359C	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	1567	Gelsolin-like 2.|Interaction with NEB.				cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)	5		Breast(68;0.103)												0.16129	40.62919	54.15694	20	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29775094	29775094	15941	10	G	A	A	A	507	39	SVIL	1	1
SVIL	6840	broad.mit.edu	37	10	29812654	29812654	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:29812654C>A	uc001iut.1	-	c.2889G>T	c.(2887-2889)ATG>ATT	p.M963I	SVIL_uc010qdw.1_5'Flank|SVIL_uc001iuu.1_Missense_Mutation_p.M537I	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	963					cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)	5		Breast(68;0.103)												0.187234	92.797258	114.299599	44	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29812654	29812654	15941	10	C	A	A	A	273	21	SVIL	2	2
MTPAP	55149	broad.mit.edu	37	10	30602883	30602883	+	Silent	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:30602883T>C	uc001ivb.3	-	c.1794A>G	c.(1792-1794)AAA>AAG	p.K598K	MTPAP_uc001iva.3_Silent_p.K468K	NM_018109	NP_060579	Q9NVV4	PAPD1_HUMAN	PAP associated domain containing 1 precursor	468	PAP-associated.				cell death|histone mRNA catabolic process|mRNA polyadenylation|transcription, DNA-dependent	mitochondrion	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|protein homodimerization activity|RNA binding|UTP binding			ovary(1)	1														0.132353	17.528787	26.453908	9	59	KEEP	---	---	---	---	capture		Silent	SNP	30602883	30602883	10349	10	T	C	C	C	777	60	MTPAP	4	4
PARD3	56288	broad.mit.edu	37	10	34690798	34690798	+	Silent	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:34690798T>C	uc010qej.1	-	c.762A>G	c.(760-762)GGA>GGG	p.G254G	PARD3_uc010qek.1_Silent_p.G254G|PARD3_uc010qel.1_Silent_p.G254G|PARD3_uc010qem.1_Silent_p.G254G|PARD3_uc010qen.1_Silent_p.G254G|PARD3_uc010qeo.1_Silent_p.G254G|PARD3_uc010qep.1_Silent_p.G210G|PARD3_uc010qeq.1_Silent_p.G210G|PARD3_uc001ixo.1_5'UTR|PARD3_uc001ixp.1_Silent_p.G119G|PARD3_uc001ixq.1_Silent_p.G254G|PARD3_uc001ixr.1_Silent_p.G254G|PARD3_uc001ixt.1_Silent_p.G75G|PARD3_uc001ixu.1_Silent_p.G210G	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog	254					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)												0.191083	79.762848	93.76089	30	127	KEEP	---	---	---	---	capture		Silent	SNP	34690798	34690798	11860	10	T	C	C	C	743	58	PARD3	4	4
ANKRD30A	91074	broad.mit.edu	37	10	37508094	37508094	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:37508094C>A	uc001iza.1	+	c.3286C>A	c.(3286-3288)CTG>ATG	p.L1096M		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1152	Potential.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)	8														0.136842	41.410198	65.673486	26	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37508094	37508094	663	10	C	A	A	A	259	20	ANKRD30A	2	2
ZNF33A	7581	broad.mit.edu	37	10	38345076	38345076	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:38345076G>T	uc010qev.1	+	c.2042G>T	c.(2041-2043)TGT>TTT	p.C681F	ZNF33A_uc001izg.2_Missense_Mutation_p.C675F|ZNF33A_uc001izh.2_Missense_Mutation_p.C674F|ZNF33A_uc001izi.1_Intron	NM_006974	NP_008905	Q06730	ZN33A_HUMAN	zinc finger protein 33A isoform b	674	C2H2-type 13.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(1)	3														0.113333	19.958785	42.093546	17	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38345076	38345076	18446	10	G	T	T	T	624	48	ZNF33A	2	2
BMS1	9790	broad.mit.edu	37	10	43288497	43288497	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:43288497G>T	uc001jaj.2	+	c.994G>T	c.(994-996)GAG>TAG	p.E332*		NM_014753	NP_055568	Q14692	BMS1_HUMAN	BMS1-like, ribosome assembly protein	332					ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)	2														0.066298	-15.042329	20.300077	12	169	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	43288497	43288497	1497	10	G	T	T	T	533	41	BMS1	5	2
TMEM72	643236	broad.mit.edu	37	10	45430239	45430239	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:45430239C>T	uc001jbn.2	+	c.485C>T	c.(484-486)TCT>TTT	p.S162F	TMEM72_uc009xmm.1_Missense_Mutation_p.S44F	NM_001123376	NP_001116848	A0PK05	TMM72_HUMAN	transmembrane protein 72	162						integral to membrane					0														0.058011	-31.842565	42.339396	21	341	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45430239	45430239	16740	10	C	T	T	T	416	32	TMEM72	2	2
FAM21C	253725	broad.mit.edu	37	10	46222982	46222982	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:46222982G>C	uc001jcu.2	+	c.121G>C	c.(121-123)GCG>CCG	p.A41P	FAM21C_uc001jcs.1_Missense_Mutation_p.A41P|FAM21C_uc001jct.2_Missense_Mutation_p.A41P|FAM21C_uc010qfi.1_Missense_Mutation_p.A41P	NM_015262	NP_056077	A8K5W5	A8K5W5_HUMAN	hypothetical protein LOC253725	41										ovary(1)	1														0.272727	7.51963	8.03211	3	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46222982	46222982	5757	10	G	C	C	C	494	38	FAM21C	3	3
GPRIN2	9721	broad.mit.edu	37	10	47000059	47000059	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:47000059G>T	uc001jec.2	+	c.1179G>T	c.(1177-1179)GTG>GTT	p.V393V	GPRIN2_uc010qfq.1_Silent_p.V156V	NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth	393											0														0.073529	-4.154127	21.270598	10	126	KEEP	---	---	---	---	capture		Silent	SNP	47000059	47000059	7006	10	G	T	T	T	613	48	GPRIN2	2	2
C10orf71	118461	broad.mit.edu	37	10	50532407	50532407	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:50532407G>T	uc010qgp.1	+	c.1817G>T	c.(1816-1818)GGG>GTG	p.G606V		NM_199459	NP_955629	Q711Q0	CJ071_HUMAN	hypothetical protein LOC118461 isoform 2	606											0														0.37931	31.016785	31.387803	11	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50532407	50532407	1651	10	G	T	T	T	559	43	C10orf71	2	2
ERCC6	2074	broad.mit.edu	37	10	50736571	50736571	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:50736571C>A	uc001jhs.3	-	c.544G>T	c.(544-546)GAA>TAA	p.E182*	PGBD3_uc009xoe.2_Nonsense_Mutation_p.E182*|PGBD3_uc001jhu.2_Nonsense_Mutation_p.E182*	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent	182					base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding|transcription elongation regulator activity			breast(5)|ovary(2)|large_intestine(2)|lung(1)	10										738				0.206349	27.640776	32.676837	13	50	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	50736571	50736571	5410	10	C	A	A	A	390	30	ERCC6	5	2
SLC18A3	6572	broad.mit.edu	37	10	50818978	50818978	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:50818978G>C	uc001jhw.2	+	c.192G>C	c.(190-192)ATG>ATC	p.M64I	CHAT_uc001jhv.1_Intron|CHAT_uc001jhx.1_5'Flank|CHAT_uc001jhy.1_5'Flank	NM_003055	NP_003046	Q16572	VACHT_HUMAN	vesicular acetylcholine transporter	64	Lumenal, vesicle (Potential).				neurotransmitter secretion	clathrin sculpted acetylcholine transport vesicle membrane|integral to plasma membrane|membrane fraction	acetylcholine transmembrane transporter activity			ovary(1)	1														0.242424	18.117305	20.183851	8	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50818978	50818978	14923	10	G	C	C	C	598	46	SLC18A3	3	3
A1CF	29974	broad.mit.edu	37	10	52566492	52566492	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:52566492G>T	uc010qho.1	-	c.1806C>A	c.(1804-1806)TTC>TTA	p.F602L	A1CF_uc010qhn.1_Missense_Mutation_p.F594L|A1CF_uc001jji.2_Missense_Mutation_p.F586L|A1CF_uc001jjj.2_Missense_Mutation_p.F594L|A1CF_uc001jjh.2_Missense_Mutation_p.F594L|A1CF_uc009xov.2_Missense_Mutation_p.F586L	NM_138933	NP_620311	Q9NQ94	A1CF_HUMAN	apobec-1 complementation factor isoform 3	594					cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			central_nervous_system(1)	1														0.231707	42.877366	48.288684	19	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52566492	52566492	2	10	G	T	T	T	425	33	A1CF	2	2
PCDH15	65217	broad.mit.edu	37	10	55626410	55626410	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:55626410C>A	uc010qhy.1	-	c.3724G>T	c.(3724-3726)GAT>TAT	p.D1242Y	PCDH15_uc010qhq.1_Missense_Mutation_p.D1242Y|PCDH15_uc010qhr.1_Missense_Mutation_p.D1237Y|PCDH15_uc010qhs.1_Missense_Mutation_p.D1249Y|PCDH15_uc010qht.1_Missense_Mutation_p.D1244Y|PCDH15_uc010qhu.1_Missense_Mutation_p.D1237Y|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.D1237Y|PCDH15_uc010qhw.1_Missense_Mutation_p.D1200Y|PCDH15_uc010qhx.1_Missense_Mutation_p.D1166Y|PCDH15_uc010qhz.1_Missense_Mutation_p.D1237Y|PCDH15_uc010qia.1_Missense_Mutation_p.D1215Y|PCDH15_uc001jju.1_Missense_Mutation_p.D1237Y|PCDH15_uc010qib.1_Missense_Mutation_p.D1215Y	NM_001142763	NP_001136235	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-1 precursor	1237	Cadherin 11.|Extracellular (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)	9		Melanoma(3;0.117)|Lung SC(717;0.238)								1612				0.272727	29.879956	31.929107	12	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55626410	55626410	11931	10	C	A	A	A	403	31	PCDH15	1	1
KIAA1274	27143	broad.mit.edu	37	10	72285877	72285878	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:72285877_72285878CC>AA	uc001jrd.3	+	c.170_171CC>AA	c.(169-171)GCC>GAA	p.A57E		NM_014431	NP_055246	Q9ULE6	PALD_HUMAN	KIAA1274	57										ovary(2)|central_nervous_system(1)	3														0.107692	6.174172	16.098894	7	58	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	72285877	72285878	8529	10	CC	AA	AA	AA	338	26	KIAA1274	2	2
ADAMTS14	140766	broad.mit.edu	37	10	72493775	72493775	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:72493775G>T	uc001jrg.2	+	c.1352G>T	c.(1351-1353)CGC>CTC	p.R451L	ADAMTS14_uc001jrh.2_Missense_Mutation_p.R448L|ADAMTS14_uc001jri.1_5'UTR	NM_139155	NP_631894	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1	448	Peptidase M12B.				collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)	5														0.090909	3.250449	18.082493	8	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72493775	72493775	260	10	G	T	T	T	494	38	ADAMTS14	1	1
UNC5B	219699	broad.mit.edu	37	10	73051452	73051452	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:73051452C>A	uc001jro.2	+	c.1558C>A	c.(1558-1560)CAC>AAC	p.H520N	UNC5B_uc001jrp.2_Missense_Mutation_p.H509N	NM_170744	NP_734465	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B precursor	520	Cytoplasmic (Potential).				apoptosis|axon guidance|regulation of apoptosis	integral to membrane				ovary(2)|lung(1)	3														0.240506	42.283863	47.14254	19	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73051452	73051452	17550	10	C	A	A	A	273	21	UNC5B	2	2
ITIH2	3698	broad.mit.edu	37	10	7786920	7786920	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:7786920C>T	uc001ijs.2	+	c.2575C>T	c.(2575-2577)CTA>TTA	p.L859L		NM_002216	NP_002207	P19823	ITIH2_HUMAN	inter-alpha globulin inhibitor H2 polypeptide	859					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)|pancreas(1)	2														0.109489	17.21644	37.908463	15	122	KEEP	---	---	---	---	capture		Silent	SNP	7786920	7786920	8208	10	C	T	T	T	259	20	ITIH2	2	2
KCNMA1	3778	broad.mit.edu	37	10	78850213	78850214	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:78850213_78850214CC>AA	uc001jxn.2	-	c.1278_1279GG>TT	c.(1276-1281)AAGGAC>AATTAC	p.426_427KD>NY	KCNMA1_uc001jxj.2_Missense_Mutation_p.426_427KD>NY|KCNMA1_uc001jxk.1_Missense_Mutation_p.41_42KD>NY|KCNMA1_uc009xrt.1_Missense_Mutation_p.246_247KD>NY|KCNMA1_uc001jxl.1_Missense_Mutation_p.80_81KD>NY|KCNMA1_uc001jxo.2_Missense_Mutation_p.426_427KD>NY|KCNMA1_uc001jxm.2_Missense_Mutation_p.426_427KD>NY|KCNMA1_uc001jxq.2_Missense_Mutation_p.426_427KD>NY	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium	426_427	RCK N-terminal.|Cytoplasmic (Potential).				cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|catalytic activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)									0.242424	74.938351	82.921937	32	100	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	78850213	78850214	8378	10	CC	AA	AA	AA	390	30	KCNMA1	2	2
NRG3	10718	broad.mit.edu	37	10	84733612	84733612	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:84733612C>A	uc001kco.2	+	c.1353C>A	c.(1351-1353)CCC>CCA	p.P451P	NRG3_uc010qlz.1_Silent_p.P450P|NRG3_uc001kcp.2_Silent_p.P230P|NRG3_uc001kcq.2_Silent_p.P101P|NRG3_uc001kcr.2_Silent_p.P101P	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1	451	Cytoplasmic (Potential).				regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity				0				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)										0.280702	39.271914	41.738766	16	41	KEEP	---	---	---	---	capture		Silent	SNP	84733612	84733612	11054	10	C	A	A	A	275	22	NRG3	2	2
LRIT2	340745	broad.mit.edu	37	10	85985202	85985202	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:85985202C>A	uc010qmc.1	-	c.75G>T	c.(73-75)CTG>CTT	p.L25L	LRIT2_uc001kcy.2_Silent_p.L25L	NM_001017924	NP_001017924	A6NDA9	LRIT2_HUMAN	leucine rich repeat containing 22 precursor	25	LRRNT.					integral to membrane				ovary(2)	2														0.219512	20.951531	23.923768	9	32	KEEP	---	---	---	---	capture		Silent	SNP	85985202	85985202	9321	10	C	A	A	A	314	25	LRIT2	2	2
GRID1	2894	broad.mit.edu	37	10	87628918	87628918	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:87628918A>G	uc001kdl.1	-	c.800T>C	c.(799-801)ATC>ACC	p.I267T	GRID1_uc009xsu.1_Non-coding_Transcript	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	267	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)			0.141509	28.560877	41.69415	15	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87628918	87628918	7049	10	A	G	G	G	156	12	GRID1	4	4
IFIT1B	439996	broad.mit.edu	37	10	91144107	91144107	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:91144107T>A	uc001kgh.2	+	c.1037T>A	c.(1036-1038)CTG>CAG	p.L346Q	LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron	NM_001010987	NP_001010987	Q5T764	IFT1B_HUMAN	interferon-induced protein with	346	TPR 6.						binding				0														0.259259	73.25567	78.921146	28	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91144107	91144107	7823	10	T	A	A	A	715	55	IFIT1B	3	3
BTAF1	9044	broad.mit.edu	37	10	93716298	93716298	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:93716298G>T	uc001khr.2	+	c.715G>T	c.(715-717)GAT>TAT	p.D239Y	BTAF1_uc009xua.1_Non-coding_Transcript|BTAF1_uc001khs.1_5'UTR	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription	239					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)												0.2	8.287136	9.962585	4	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93716298	93716298	1568	10	G	T	T	T	585	45	BTAF1	2	2
PLCE1	51196	broad.mit.edu	37	10	96081748	96081748	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:96081748T>A	uc001kjk.2	+	c.6433T>A	c.(6433-6435)TCT>ACT	p.S2145T	PLCE1_uc010qnx.1_Missense_Mutation_p.S2129T|PLCE1_uc001kjm.2_Missense_Mutation_p.S1837T|PLCE1_uc001kjp.2_Missense_Mutation_p.S503T	NM_016341	NP_057425	Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1 isoform 1	2145	Ras-associating 2.				activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|phospholipid metabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)												0.255814	47.847	52.558427	22	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	96081748	96081748	12460	10	T	A	A	A	806	62	PLCE1	3	3
TLL2	7093	broad.mit.edu	37	10	98165037	98165037	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:98165037C>A	uc001kml.1	-	c.1219G>T	c.(1219-1221)GAT>TAT	p.D407Y	TLL2_uc009xvf.1_Missense_Mutation_p.D385Y	NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2 precursor	407	CUB 1.				cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)										0.064356	-14.598409	25.275163	13	189	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98165037	98165037	16476	10	C	A	A	A	377	29	TLL2	2	2
SLIT1	6585	broad.mit.edu	37	10	98820417	98820417	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:98820417C>A	uc001kmw.2	-	c.921G>T	c.(919-921)CTG>CTT	p.L307L	SLIT1_uc009xvh.1_Silent_p.L307L	NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor	307	LRRNT 2.				axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)										0.197531	31.947551	38.855564	16	65	KEEP	---	---	---	---	capture		Silent	SNP	98820417	98820417	15237	10	C	A	A	A	314	25	SLIT1	2	2
C10orf28	27291	broad.mit.edu	37	10	99968101	99968101	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:99968101G>T	uc001kox.3	+	c.230G>T	c.(229-231)AGA>ATA	p.R77I	C10orf28_uc001kow.3_Missense_Mutation_p.R77I|C10orf28_uc001koy.3_Missense_Mutation_p.R77I|C10orf28_uc009xvx.2_Missense_Mutation_p.R77I|C10orf28_uc009xvy.2_Intron|C10orf28_uc001koz.3_Intron	NM_014472	NP_055287	Q4KMY3	Q4KMY3_HUMAN	growth inhibition and differentiation related	77							nucleotide binding			large_intestine(1)	1		Colorectal(252;0.234)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)										0.216867	39.502335	45.641308	18	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99968101	99968101	1638	10	G	T	T	T	429	33	C10orf28	2	2
TRPC6	7225	broad.mit.edu	37	11	101353888	101353888	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:101353888C>A	uc001pgk.3	-	c.1302G>T	c.(1300-1302)AAG>AAT	p.K434N	TRPC6_uc009ywy.2_Missense_Mutation_p.K318N|TRPC6_uc009ywz.1_Missense_Mutation_p.K379N	NM_004621	NP_004612	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel,	434	Cytoplasmic (Potential).				axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		Colon(166;1315 1927 11094 12848 34731)								0.111111	3.206094	11.290477	6	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101353888	101353888	17134	11	C	A	A	A	415	32	TRPC6	2	2
TRPC6	7225	broad.mit.edu	37	11	101374853	101374853	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:101374853G>T	uc001pgk.3	-	c.847C>A	c.(847-849)CCG>ACG	p.P283T	TRPC6_uc009ywy.2_Missense_Mutation_p.P283T|TRPC6_uc009ywz.1_Missense_Mutation_p.P283T	NM_004621	NP_004612	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel,	283	Cytoplasmic (Potential).				axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		Colon(166;1315 1927 11094 12848 34731)								0.185328	87.760714	111.802979	48	211	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101374853	101374853	17134	11	G	T	T	T	533	41	TRPC6	2	2
DYNC2H1	79659	broad.mit.edu	37	11	102992159	102992159	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:102992159A>T	uc001phn.1	+	c.1419A>T	c.(1417-1419)CCA>CCT	p.P473P	DYNC2H1_uc001pho.2_Silent_p.P473P|DYNC2H1_uc009yxe.1_Silent_p.P473P	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	473	Stem (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)										0.115942	11.151535	21.168823	8	61	KEEP	---	---	---	---	capture		Silent	SNP	102992159	102992159	5032	11	A	T	T	T	67	6	DYNC2H1	3	3
DYNC2H1	79659	broad.mit.edu	37	11	102992199	102992199	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:102992199G>T	uc001phn.1	+	c.1459G>T	c.(1459-1461)GTT>TTT	p.V487F	DYNC2H1_uc001pho.2_Missense_Mutation_p.V487F|DYNC2H1_uc009yxe.1_Missense_Mutation_p.V487F	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	487	Stem (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)										0.103448	7.904582	21.531477	9	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102992199	102992199	5032	11	G	T	T	T	468	36	DYNC2H1	2	2
DYNC2H1	79659	broad.mit.edu	37	11	103270430	103270430	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:103270430G>T	uc001phn.1	+	c.12217G>T	c.(12217-12219)GAT>TAT	p.D4073Y	DYNC2H1_uc001pho.2_Missense_Mutation_p.D4066Y|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	4066					cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)										0.166667	12.328564	16.120065	6	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103270430	103270430	5032	11	G	T	T	T	481	37	DYNC2H1	1	1
DDI1	414301	broad.mit.edu	37	11	103908038	103908038	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:103908038G>T	uc001phr.2	+	c.488G>T	c.(487-489)CGC>CTC	p.R163L	PDGFD_uc001php.2_Intron|PDGFD_uc001phq.2_Intron	NM_001001711	NP_001001711	Q8WTU0	DDI1_HUMAN	DDI1, DNA-damage inducible 1, homolog 1	163					proteolysis		aspartic-type endopeptidase activity			large_intestine(3)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)										0.13986	32.420933	50.324919	20	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103908038	103908038	4499	11	G	T	T	T	494	38	DDI1	1	1
CASP4	837	broad.mit.edu	37	11	104821732	104821732	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:104821732C>A	uc001pid.1	-	c.466G>T	c.(466-468)GAC>TAC	p.D156Y	CASP4_uc001pib.1_Missense_Mutation_p.D100Y|CASP4_uc009yxg.1_Missense_Mutation_p.D65Y|CASP4_uc010rux.1_Missense_Mutation_p.D156Y	NM_001225	NP_001216	P49662	CASP4_HUMAN	caspase 4 isoform alpha precursor	156					apoptosis|induction of apoptosis|proteolysis	intracellular	cysteine-type endopeptidase activity|protein binding			lung(2)|ovary(1)|skin(1)	4		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)						204				0.177778	45.711326	58.917603	24	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104821732	104821732	2792	11	C	A	A	A	377	29	CASP4	2	2
NPAT	4863	broad.mit.edu	37	11	108044227	108044227	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:108044227G>C	uc001pjz.3	-	c.1484C>G	c.(1483-1485)CCG>CGG	p.P495R	NPAT_uc001pka.2_Missense_Mutation_p.P290R	NM_002519	NP_002510	Q14207	NPAT_HUMAN	nuclear protein,  ataxia-telangiectasia locus	495					regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)						345				0.072816	0.162428	38.826319	15	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108044227	108044227	10970	11	G	C	C	C	507	39	NPAT	3	3
ATM	472	broad.mit.edu	37	11	108153533	108153533	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:108153533C>T	uc001pkb.1	+	c.3673C>T	c.(3673-3675)CAA>TAA	p.Q1225*	ATM_uc009yxr.1_Nonsense_Mutation_p.Q1225*	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	1225					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(24)|breast(14)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	238		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)						1073	TSP Lung(14;0.12)			0.074074	-3.320981	11.781873	6	75	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	108153533	108153533	1128	11	C	T	T	T	377	29	ATM	5	2
EXPH5	23086	broad.mit.edu	37	11	108383973	108383973	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:108383973T>C	uc001pkk.2	-	c.2261A>G	c.(2260-2262)AAC>AGC	p.N754S	EXPH5_uc010rvy.1_Missense_Mutation_p.N566S|EXPH5_uc010rvz.1_Missense_Mutation_p.N598S|EXPH5_uc010rwa.1_Missense_Mutation_p.N678S	NM_015065	NP_055880	Q149M6	Q149M6_HUMAN	exophilin 5 isoform a	754					intracellular protein transport		Rab GTPase binding			ovary(2)	2		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)										0.254658	130.803379	139.592261	41	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108383973	108383973	5516	11	T	C	C	C	780	60	EXPH5	4	4
RDX	5962	broad.mit.edu	37	11	110128497	110128497	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:110128497G>T	uc009yxy.2	-	c.693C>A	c.(691-693)GAC>GAA	p.D231E	RDX_uc009yxx.1_Non-coding_Transcript|RDX_uc009yxz.2_Intron|RDX_uc009yya.2_Intron|RDX_uc001pku.2_Missense_Mutation_p.D231E|RDX_uc010rwe.1_Missense_Mutation_p.D95E	NM_002906	NP_002897	P35241	RADI_HUMAN	radixin	231	FERM.				actin filament capping	cleavage furrow|cytoskeleton|extrinsic to membrane|Golgi apparatus|nucleolus|plasma membrane	actin binding				0		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		Esophageal Squamous(55;25 1062 11040 28755 44273)								0.09434	8.331424	25.797222	10	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110128497	110128497	13667	11	G	T	T	T	516	40	RDX	1	1
DRD2	1813	broad.mit.edu	37	11	113287585	113287585	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:113287585C>A	uc001pnz.2	-	c.532G>T	c.(532-534)GAC>TAC	p.D178Y	DRD2_uc010rwv.1_Missense_Mutation_p.D177Y|DRD2_uc001poa.3_Missense_Mutation_p.D178Y|DRD2_uc001pob.3_Missense_Mutation_p.D178Y|DRD2_uc009yyr.1_Missense_Mutation_p.D178Y	NM_000795	NP_000786	P14416	DRD2_HUMAN	dopamine receptor D2 isoform long	178	Extracellular (By similarity).				activation of phospholipase C activity by dopamine receptor signaling pathway|adenohypophysis development|adult walking behavior|arachidonic acid secretion|axonogenesis|behavioral response to cocaine|behavioral response to ethanol|branching morphogenesis of a nerve|cerebral cortex GABAergic interneuron migration|circadian regulation of gene expression|diuresis|dopamine metabolic process|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|intracellular protein kinase cascade|natriuresis|negative regulation of blood pressure|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of dopamine receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|negative regulation of synaptic transmission, glutamatergic|neurological system process involved in regulation of systemic arterial blood pressure|peristalsis|phosphatidylinositol metabolic process|positive regulation of dopamine uptake|positive regulation of growth hormone secretion|positive regulation of neuroblast proliferation|prepulse inhibition|protein localization|regulation of heart rate|regulation of long-term neuronal synaptic plasticity|regulation of potassium ion transport|regulation of sodium ion transport|regulation of synaptic transmission, GABAergic|release of sequestered calcium ion into cytosol|response to amphetamine|response to drug|response to histamine|response to morphine|sensory perception of smell|synapse assembly|temperature homeostasis|visual learning	integral to plasma membrane|integral to plasma membrane	dopamine D2 receptor activity|dopamine receptor activity, coupled via Gi/Go|drug binding|potassium channel regulator activity|protein binding			pancreas(1)	1		all_cancers(61;3.91e-16)|all_epithelial(67;2.95e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000977)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0494)		BRCA - Breast invasive adenocarcinoma(274;5.77e-06)|Epithelial(105;6.66e-05)|all cancers(92;0.000307)|OV - Ovarian serous cystadenocarcinoma(223;0.216)	Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Carphenazine(DB01038)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Domperidone(DB01184)|Droperidol(DB00450)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Mesoridazine(DB00933)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Pimozide(DB01100)|Pramipexole(DB00413)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Sulpiride(DB00391)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Ziprasidone(DB00246)|Zuclopenthixol(DB01624)					215				0.166667	10.424794	14.220197	6	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113287585	113287585	4941	11	C	A	A	A	312	24	DRD2	2	2
HTR3A	3359	broad.mit.edu	37	11	113860404	113860404	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:113860404G>T	uc010rxb.1	+	c.1470G>T	c.(1468-1470)CTG>CTT	p.L490L	HTR3A_uc010rxa.1_Silent_p.L458L|HTR3A_uc009yyx.2_Non-coding_Transcript|HTR3A_uc010rxc.1_Silent_p.L437L	NM_213621	NP_998786	P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A	452	Cytoplasmic (Potential).				digestion|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	serotonin binding|serotonin receptor activity|serotonin-activated cation-selective channel activity				0		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Dolasetron(DB00757)|Granisetron(DB00889)|Mirtazapine(DB00370)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Tubocurarine(DB01199)									0.131579	25.608558	45.65204	20	132	KEEP	---	---	---	---	capture		Silent	SNP	113860404	113860404	7744	11	G	T	T	T	587	46	HTR3A	2	2
CEP164	22897	broad.mit.edu	37	11	117261501	117261501	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:117261501G>T	uc001prc.2	+	c.1943G>T	c.(1942-1944)AGG>ATG	p.R648M	CEP164_uc001prb.2_Missense_Mutation_p.R651M|CEP164_uc010rxk.1_Missense_Mutation_p.R622M|CEP164_uc001prf.2_Non-coding_Transcript|CEP164_uc009yzp.1_Non-coding_Transcript|CEP164_uc001prg.1_Missense_Mutation_p.R81M	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	648	Glu-rich.				cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)										0.193548	110.37602	134.842635	54	225	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117261501	117261501	3382	11	G	T	T	T	455	35	CEP164	2	2
CCDC153	283152	broad.mit.edu	37	11	119063892	119063892	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:119063892C>A	uc010rze.1	-	c.318G>T	c.(316-318)GAG>GAT	p.E106D		NM_001145018	NP_001138490	Q494R4	CC153_HUMAN	coiled-coil domain containing 153	106	Potential.										0														0.098592	8.037759	30.933474	14	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119063892	119063892	2908	11	C	A	A	A	311	24	CCDC153	2	2
USP47	55031	broad.mit.edu	37	11	11957904	11957904	+	Missense_Mutation	SNP	G	T	T	rs36096029	byFrequency	TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:11957904G>T	uc001mjs.2	+	c.1924G>T	c.(1924-1926)GAT>TAT	p.D642Y	USP47_uc001mjq.1_Missense_Mutation_p.D662Y|USP47_uc001mjr.2_Missense_Mutation_p.D574Y|USP47_uc001mjt.1_5'Flank	NM_017944	NP_060414	Q96K76	UBP47_HUMAN	ubiquitin specific protease 47	662					base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of gene-specific transcription|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	specific transcriptional repressor activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)										0.078125	-1.080106	10.570015	5	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11957904	11957904	17642	11	G	T	T	T	585	45	USP47	2	2
OAF	220323	broad.mit.edu	37	11	120097704	120097704	+	Silent	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:120097704A>G	uc001pxb.2	+	c.546A>G	c.(544-546)CAA>CAG	p.Q182Q		NM_178507	NP_848602	Q86UD1	OAF_HUMAN	OAF homolog precursor	182											0		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)										0.134615	11.788461	18.519963	7	45	KEEP	---	---	---	---	capture		Silent	SNP	120097704	120097704	11203	11	A	G	G	G	37	3	OAF	4	4
BLID	414899	broad.mit.edu	37	11	121986441	121986441	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:121986441C>A	uc001pyf.2	-	c.190G>T	c.(190-192)GTG>TTG	p.V64L	LOC399959_uc009zba.2_Intron	NM_001001786	NP_001001786	Q8IZY5	BLID_HUMAN	BRCC2 protein	64					apoptosis	mitochondrion					0		Breast(109;0.0164)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;2.08e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.101)								OREG0021435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.162304	59.792538	80.512455	31	160	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121986441	121986441	1468	11	C	A	A	A	260	20	BLID	2	2
OR6X1	390260	broad.mit.edu	37	11	123625061	123625061	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123625061G>C	uc010rzy.1	-	c.166C>G	c.(166-168)CCA>GCA	p.P56A		NM_001005188	NP_001005188	Q8NH79	OR6X1_HUMAN	olfactory receptor, family 6, subfamily X,	56	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)										0.086207	8.056984	28.179332	10	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123625061	123625061	11623	11	G	C	C	C	533	41	OR6X1	3	3
OR10G4	390264	broad.mit.edu	37	11	123886909	123886909	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123886909T>A	uc010sac.1	+	c.628T>A	c.(628-630)TTT>ATT	p.F210I		NM_001004462	NP_001004462	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G,	210	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)										0.122905	22.118547	47.042634	22	157	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123886909	123886909	11307	11	T	A	A	A	728	56	OR10G4	3	3
OR10G4	390264	broad.mit.edu	37	11	123886968	123886968	+	Silent	SNP	C	A	A	rs116021926	by1000genomes	TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123886968C>A	uc010sac.1	+	c.687C>A	c.(685-687)ACC>ACA	p.T229T		NM_001004462	NP_001004462	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G,	229	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)										0.235849	54.009256	60.783841	25	81	KEEP	---	---	---	---	capture		Silent	SNP	123886968	123886968	11307	11	C	A	A	A	301	24	OR10G4	2	2
OR10G8	219869	broad.mit.edu	37	11	123901162	123901162	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123901162T>C	uc001pzp.1	+	c.833T>C	c.(832-834)CTG>CCG	p.L278P		NM_001004464	NP_001004464	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G,	278	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)										0.176923	47.2553	60.033596	23	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123901162	123901162	11309	11	T	C	C	C	715	55	OR10G8	4	4
OR8G2	26492	broad.mit.edu	37	11	124095877	124095877	+	Silent	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:124095877A>G	uc010saf.1	+	c.480A>G	c.(478-480)GGA>GGG	p.G160G		NM_001007249	NP_001007250	Q8N0Y1	Q8N0Y1_HUMAN	olfactory receptor, family 8, subfamily G,	160						integral to membrane	olfactory receptor activity				0		Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.91e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)										0.100478	48.14255	114.843675	42	376	KEEP	---	---	---	---	capture		Silent	SNP	124095877	124095877	11646	11	A	G	G	G	132	11	OR8G2	4	4
OR8B12	219858	broad.mit.edu	37	11	124413356	124413356	+	Silent	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:124413356G>C	uc010sam.1	-	c.195C>G	c.(193-195)CTC>CTG	p.L65L		NM_001005195	NP_001005195	Q8NGG6	OR8BC_HUMAN	olfactory receptor, family 8, subfamily B,	65	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.L65L(1)		ovary(1)|breast(1)	2		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0213)										0.126437	19.05949	30.911593	11	76	KEEP	---	---	---	---	capture		Silent	SNP	124413356	124413356	11637	11	G	C	C	C	418	33	OR8B12	3	3
KCNJ1	3758	broad.mit.edu	37	11	128709558	128709558	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:128709558A>G	uc001qeo.1	-	c.638T>C	c.(637-639)GTG>GCG	p.V213A	KCNJ1_uc001qep.1_Missense_Mutation_p.V194A|KCNJ1_uc001qeq.1_Missense_Mutation_p.V194A|KCNJ1_uc001qer.1_Missense_Mutation_p.V194A|KCNJ1_uc001qes.1_Missense_Mutation_p.V194A	NM_000220	NP_000211	P48048	IRK1_HUMAN	potassium inwardly-rectifying channel J1 isoform	213	Cytoplasmic (By similarity).				excretion	voltage-gated potassium channel complex	ATP binding|inward rectifier potassium channel activity			ovary(3)|breast(1)	4	all_hematologic(175;0.0641)	all_lung(97;4.89e-06)|Lung NSC(97;9.34e-06)|Breast(109;0.00123)|all_hematologic(192;0.00793)|Renal(330;0.0112)|all_neural(223;0.0189)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;4.05e-06)|LUSC - Lung squamous cell carcinoma(976;0.008)|Lung(977;0.00942)	Acetohexamide(DB00414)|Chlorpropamide(DB00672)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolazamide(DB00839)|Tolbutamide(DB01124)									0.117647	23.710981	43.246666	16	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128709558	128709558	8348	11	A	G	G	G	78	6	KCNJ1	4	4
ARHGAP32	9743	broad.mit.edu	37	11	128839671	128839671	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:128839671C>A	uc009zcp.2	-	c.5395G>T	c.(5395-5397)GGG>TGG	p.G1799W	ARHGAP32_uc009zcq.1_3'UTR|ARHGAP32_uc009zco.2_Missense_Mutation_p.G758W|ARHGAP32_uc001qez.2_Missense_Mutation_p.G1450W	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1	1799	Interaction with FYN.				cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5														0.184524	60.512865	76.208861	31	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128839671	128839671	893	11	C	A	A	A	273	21	ARHGAP32	2	2
SPON1	10418	broad.mit.edu	37	11	14282211	14282211	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:14282211C>A	uc001mle.2	+	c.1909C>A	c.(1909-1911)CGA>AGA	p.R637R		NM_006108	NP_006099	Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein	637	TSP type-1 4.				cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding				0				Epithelial(150;0.00898)										0.09	3.706261	20.662026	9	91	KEEP	---	---	---	---	capture		Silent	SNP	14282211	14282211	15595	11	C	A	A	A	295	23	SPON1	1	1
SOX6	55553	broad.mit.edu	37	11	16340125	16340125	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:16340125T>G	uc001mme.2	-	c.351A>C	c.(349-351)GAA>GAC	p.E117D	SOX6_uc001mmd.2_Missense_Mutation_p.E107D|SOX6_uc001mmf.2_Missense_Mutation_p.E104D|SOX6_uc001mmg.2_Missense_Mutation_p.E104D|SOX6_uc001mmh.1_Non-coding_Transcript|SOX6_uc009ygs.2_Non-coding_Transcript|SOX6_uc001mmi.3_Missense_Mutation_p.E104D|SOX6_uc001mmj.2_Missense_Mutation_p.E104D	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4	104					muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3														0.103825	19.984825	48.576645	19	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16340125	16340125	15455	11	T	G	G	G	725	56	SOX6	4	4
PIK3C2A	5286	broad.mit.edu	37	11	17172116	17172116	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:17172116C>A	uc001mmq.3	-	c.1256G>T	c.(1255-1257)GGA>GTA	p.G419V	PIK3C2A_uc009ygu.1_5'UTR|PIK3C2A_uc010rcw.1_Missense_Mutation_p.G39V|PIK3C2A_uc001mmr.3_Non-coding_Transcript|PIK3C2A_uc010rcx.1_Missense_Mutation_p.G419V|PIK3C2A_uc009ygv.1_Missense_Mutation_p.G419V	NM_002645	NP_002636	O00443	P3C2A_HUMAN	phosphoinositide-3-kinase, class 2 alpha	419					cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling	clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			central_nervous_system(4)|lung(2)|ovary(1)	7					Phosphatidylserine(DB00144)					733				0.093458	3.582845	21.354708	10	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17172116	17172116	12333	11	C	A	A	A	390	30	PIK3C2A	2	2
ABCC8	6833	broad.mit.edu	37	11	17428936	17428936	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:17428936C>A	uc001mnc.2	-	c.2885G>T	c.(2884-2886)AGG>ATG	p.R962M		NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8	962	Cytoplasmic (By similarity).				carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)									0.126829	31.89191	59.770842	26	179	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17428936	17428936	59	11	C	A	A	A	312	24	ABCC8	2	2
TPH1	7166	broad.mit.edu	37	11	18048061	18048061	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:18048061G>A	uc001mnp.2	-	c.779C>T	c.(778-780)TCA>TTA	p.S260L	TPH1_uc009yhe.2_Non-coding_Transcript	NM_004179	NP_004170	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	260					aromatic amino acid family metabolic process|hormone biosynthetic process|oxidation-reduction process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity				0					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)					206				0.066667	-6.667504	13.78121	7	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18048061	18048061	16945	11	G	A	A	A	585	45	TPH1	2	2
GTF2H1	2965	broad.mit.edu	37	11	18369250	18369250	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:18369250G>C	uc001moi.2	+	c.953G>C	c.(952-954)GGA>GCA	p.G318A	GTF2H1_uc001moh.2_Missense_Mutation_p.G318A|GTF2H1_uc009yhm.2_Missense_Mutation_p.G202A|GTF2H1_uc001moj.2_Missense_Mutation_p.G6A	NM_001142307	NP_001135779	P32780	TF2H1_HUMAN	general transcription factor IIH, polypeptide 1,	318					mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|regulation of cyclin-dependent protein kinase activity|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	general RNA polymerase II transcription factor activity|protein binding				0														0.131313	25.910874	38.987301	13	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18369250	18369250	7140	11	G	C	C	C	533	41	GTF2H1	3	3
LDHC	3948	broad.mit.edu	37	11	18436751	18436751	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:18436751C>G	uc001mon.3	+	c.147C>G	c.(145-147)GCC>GCG	p.A49A	LDHC_uc001mom.3_Silent_p.A49A|LDHC_uc009yhp.2_Silent_p.A49A|LDHC_uc001moo.3_Intron|LDHC_uc009yhq.2_Intron|LDHC_uc009yhr.2_Intron	NM_017448	NP_059144	P07864	LDHC_HUMAN	L-lactate dehydrogenase C	49	NAD (By similarity).				glycolysis|oxidation-reduction process	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)									0.10989	12.37861	26.088977	10	81	KEEP	---	---	---	---	capture		Silent	SNP	18436751	18436751	9026	11	C	G	G	G	275	22	LDHC	3	3
PRMT3	10196	broad.mit.edu	37	11	20429516	20429516	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:20429516G>T	uc001mqb.2	+	c.831G>T	c.(829-831)GGG>GGT	p.G277G	PRMT3_uc001mqc.2_Silent_p.G200G|PRMT3_uc010rdn.1_Silent_p.G215G	NM_005788	NP_005779	O60678	ANM3_HUMAN	protein arginine methyltransferase 3 isoform 1	277							zinc ion binding				0														0.111111	11.833133	27.971971	12	96	KEEP	---	---	---	---	capture		Silent	SNP	20429516	20429516	12981	11	G	T	T	T	548	43	PRMT3	2	2
SLC6A5	9152	broad.mit.edu	37	11	20673895	20673896	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:20673895_20673896CC>AA	uc001mqd.2	+	c.2131_2132CC>AA	c.(2131-2133)CCT>AAT	p.P711N	SLC6A5_uc009yic.2_Missense_Mutation_p.P476N	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	711					synaptic transmission	integral to plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)	3					Glycine(DB00145)									0.129353	26.791745	53.739111	26	175	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	20673895	20673896	15184	11	CC	AA	AA	AA	390	30	SLC6A5	2	2
ANO5	203859	broad.mit.edu	37	11	22296138	22296138	+	Silent	SNP	A	T	T	rs61746201	byFrequency;by1000genomes	TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:22296138A>T	uc001mqi.2	+	c.2259A>T	c.(2257-2259)TCA>TCT	p.S753S	ANO5_uc001mqj.2_Silent_p.S752S	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	753	Helical; (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4														0.113208	14.525897	30.172388	12	94	KEEP	---	---	---	---	capture		Silent	SNP	22296138	22296138	708	11	A	T	T	T	80	7	ANO5	3	3
SLC17A6	57084	broad.mit.edu	37	11	22397614	22397614	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:22397614G>T	uc001mqk.2	+	c.1261G>T	c.(1261-1263)GGA>TGA	p.G421*		NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent	421	Helical; (Potential).				sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4														0.101911	13.877395	38.690693	16	141	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	22397614	22397614	14917	11	G	T	T	T	559	43	SLC17A6	5	2
ANO3	63982	broad.mit.edu	37	11	26463539	26463539	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:26463539G>T	uc001mqt.3	+	c.121G>T	c.(121-123)GCC>TCC	p.A41S	ANO3_uc010rdr.1_Missense_Mutation_p.A25S	NM_031418	NP_113606	Q9BYT9	ANO3_HUMAN	transmembrane protein 16C	41	Cytoplasmic (Potential).					chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.236364	167.343911	184.810439	65	210	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26463539	26463539	706	11	G	T	T	T	494	38	ANO3	1	1
ANO3	63982	broad.mit.edu	37	11	26552826	26552826	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:26552826C>G	uc001mqt.3	+	c.812C>G	c.(811-813)CCA>CGA	p.P271R	ANO3_uc010rdr.1_Missense_Mutation_p.P255R|ANO3_uc010rds.1_Missense_Mutation_p.P110R|ANO3_uc010rdt.1_Missense_Mutation_p.P125R	NM_031418	NP_113606	Q9BYT9	ANO3_HUMAN	transmembrane protein 16C	271	Cytoplasmic (Potential).					chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.108108	18.688566	41.224712	16	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26552826	26552826	706	11	C	G	G	G	273	21	ANO3	3	3
ANO3	63982	broad.mit.edu	37	11	26669343	26669343	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:26669343C>A	uc001mqt.3	+	c.2516C>A	c.(2515-2517)CCA>CAA	p.P839Q	ANO3_uc010rdr.1_Missense_Mutation_p.P823Q|ANO3_uc010rds.1_Missense_Mutation_p.P678Q|ANO3_uc010rdt.1_Missense_Mutation_p.P693Q	NM_031418	NP_113606	Q9BYT9	ANO3_HUMAN	transmembrane protein 16C	839	Extracellular (Potential).					chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.119403	7.549592	17.082865	8	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26669343	26669343	706	11	C	A	A	A	273	21	ANO3	2	2
KIF18A	81930	broad.mit.edu	37	11	28058003	28058003	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:28058003T>A	uc001msc.2	-	c.2157A>T	c.(2155-2157)ACA>ACT	p.T719T		NM_031217	NP_112494	Q8NI77	KI18A_HUMAN	kinesin family member 18A	719					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														0.084906	2.791061	21.321954	9	97	KEEP	---	---	---	---	capture		Silent	SNP	28058003	28058003	8591	11	T	A	A	A	704	55	KIF18A	3	3
DCDC1	341019	broad.mit.edu	37	11	31327816	31327816	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:31327816G>A	uc001msv.2	-	c.554C>T	c.(553-555)ACA>ATA	p.T185I	DCDC1_uc001msu.1_5'UTR	NM_181807	NP_861523	P59894	DCDC1_HUMAN	doublecortin domain containing 1	185	Doublecortin.				intracellular signal transduction						0	Lung SC(675;0.225)													0.096774	3.198933	13.305854	6	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31327816	31327816	4455	11	G	A	A	A	624	48	DCDC1	2	2
PAX6	5080	broad.mit.edu	37	11	31812322	31812322	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:31812322G>T	uc001mtg.3	-	c.1161C>A	c.(1159-1161)ACC>ACA	p.T387T	PAX6_uc001mtd.3_Silent_p.T373T|PAX6_uc001mte.3_Silent_p.T373T|PAX6_uc001mtf.3_Silent_p.T373T|PAX6_uc001mth.3_Silent_p.T373T|PAX6_uc009yjr.2_Silent_p.T373T	NM_001604	NP_001595	P26367	PAX6_HUMAN	paired box gene 6 isoform b	373	Pro/Ser/Thr-rich.				central nervous system development|eye development|gene-specific transcription from RNA polymerase II promoter|negative regulation of neurogenesis|neuron fate commitment|organ morphogenesis|pancreatic A cell development|positive regulation of gene expression|regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|transcription activator activity|ubiquitin-protein ligase activity			ovary(2)|pancreas(1)	3	Lung SC(675;0.225)													0.106796	7.846906	23.661806	11	92	KEEP	---	---	---	---	capture		Silent	SNP	31812322	31812322	11903	11	G	T	T	T	548	43	PAX6	2	2
PAX6	5080	broad.mit.edu	37	11	31822341	31822341	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:31822341C>T	uc001mtg.3	-	c.463G>A	c.(463-465)GGC>AGC	p.G155S	PAX6_uc001mtd.3_Missense_Mutation_p.G141S|PAX6_uc001mte.3_Missense_Mutation_p.G141S|PAX6_uc001mtf.3_Missense_Mutation_p.G141S|PAX6_uc001mth.3_Missense_Mutation_p.G141S|PAX6_uc009yjr.2_Missense_Mutation_p.G141S	NM_001604	NP_001595	P26367	PAX6_HUMAN	paired box gene 6 isoform b	141	Gln/Gly-rich.				central nervous system development|eye development|gene-specific transcription from RNA polymerase II promoter|negative regulation of neurogenesis|neuron fate commitment|organ morphogenesis|pancreatic A cell development|positive regulation of gene expression|regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|transcription activator activity|ubiquitin-protein ligase activity			ovary(2)|pancreas(1)	3	Lung SC(675;0.225)													0.128378	24.937722	44.84491	19	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31822341	31822341	11903	11	C	T	T	T	299	23	PAX6	1	1
WT1	7490	broad.mit.edu	37	11	32413568	32413568	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:32413568G>A	uc001mtn.1	-	c.1382C>T	c.(1381-1383)TCC>TTC	p.S461F	WT1_uc001mtl.1_Missense_Mutation_p.S249F|WT1_uc001mtm.1_Missense_Mutation_p.S232F|WT1_uc001mto.1_Missense_Mutation_p.S461F|WT1_uc001mtp.1_Missense_Mutation_p.S444F|WT1_uc001mtq.1_Missense_Mutation_p.S444F|WT1_uc009yjs.1_Non-coding_Transcript	NM_024426	NP_077744	P19544	WT1_HUMAN	Wilms tumor 1 isoform D	393	C2H2-type 3.|Important for interaction with target DNA.				adrenal gland development|branching involved in ureteric bud morphogenesis|glomerular basement membrane development|glomerular visceral epithelial cell differentiation|induction of apoptosis|male gonad development|metanephric S-shaped body morphogenesis|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription|negative regulation of transcription from RNA polymerase II promoter|negative regulation of translation|positive regulation of gene-specific transcription|sex determination|visceral serous pericardium development	cytoplasm|nuclear speck|nucleoplasm	C2H2 zinc finger domain binding|promoter binding|RNA binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription repressor activity|zinc ion binding	p.V380_S410del(1)	EWSR1/WT1(231)	haematopoietic_and_lymphoid_tissue(302)|soft_tissue(231)|kidney(132)|pleura(2)|peritoneum(1)|lung(1)	669	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)							684				0.124122	67.328628	126.269856	53	374	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32413568	32413568	17982	11	G	A	A	A	533	41	WT1	2	2
FBXO3	26273	broad.mit.edu	37	11	33792333	33792333	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:33792333C>A	uc001muz.2	-	c.148G>T	c.(148-150)GAT>TAT	p.D50Y	FBXO3_uc001muy.2_5'UTR|FBXO3_uc009ykb.2_Non-coding_Transcript|FBXO3_uc001mva.1_Missense_Mutation_p.D50Y|FBXO3_uc001mvb.1_Missense_Mutation_p.D45Y|FBXO3_uc010rek.1_Non-coding_Transcript	NM_012175	NP_036307	Q9UK99	FBX3_HUMAN	F-box only protein 3 isoform 1	50	F-box.				proteolysis	nucleus	ubiquitin-protein ligase activity			pancreas(1)	1		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)										0.099359	19.585156	69.654672	31	281	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33792333	33792333	5976	11	C	A	A	A	377	29	FBXO3	2	2
LMO2	4005	broad.mit.edu	37	11	33881003	33881003	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:33881003G>C	uc010rem.1	-	c.583C>G	c.(583-585)CAG>GAG	p.Q195E	LMO2_uc001mvc.2_Missense_Mutation_p.Q119E|LMO2_uc001mvd.2_Missense_Mutation_p.Q119E|LMO2_uc001mve.2_Missense_Mutation_p.Q126E|LMO2_uc010rel.1_Missense_Mutation_p.Q126E	NM_005574	NP_005565	P25791	RBTN2_HUMAN	LIM domain only 2 isoform 1	126	LIM zinc-binding 2.				multicellular organismal development	nucleus	protein binding|zinc ion binding				0										60				0.084211	6.32055	22.997683	8	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33881003	33881003	9181	11	G	C	C	C	585	45	LMO2	3	3
RAG2	5897	broad.mit.edu	37	11	36614951	36614951	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:36614951G>T	uc001mwv.3	-	c.768C>A	c.(766-768)ATC>ATA	p.I256I	C11orf74_uc010rfd.1_5'Flank|C11orf74_uc001mww.1_5'Flank|C11orf74_uc001mwx.1_5'Flank|C11orf74_uc001mwy.1_5'Flank|C11orf74_uc001mwz.1_5'Flank|C11orf74_uc010rfe.1_5'Flank	NM_000536	NP_000527	P55895	RAG2_HUMAN	recombination activating gene 2	256					chromatin modification|pre-B cell allelic exclusion|somatic diversification of immunoglobulins|T cell differentiation in thymus|V(D)J recombination	nucleus	chromatin binding|DNA binding|endonuclease activity|methylated histone residue binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-4,5-bisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)	2	all_lung(20;0.226)	all_hematologic(20;0.00756)												0.194805	28.777942	35.470632	15	62	KEEP	---	---	---	---	capture		Silent	SNP	36614951	36614951	13465	11	G	T	T	T	421	33	RAG2	2	2
ART1	417	broad.mit.edu	37	11	3682645	3682645	+	Splice_Site_SNP	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:3682645T>A	uc001lye.1	+	c.886_splice	c.e4+2	p.A296_splice		NM_004314	NP_004305			ADP-ribosyltransferase 1 precursor						protein ADP-ribosylation	anchored to membrane|integral to plasma membrane|sarcoplasmic reticulum membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity				0		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0351)|LUSC - Lung squamous cell carcinoma(625;0.195)	Becaplermin(DB00102)									0.086538	1.703969	19.703231	9	95	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	3682645	3682645	1015	11	T	A	A	A	741	57	ART1	5	3
OR52K1	390036	broad.mit.edu	37	11	4510987	4510987	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4510987C>A	uc001lza.1	+	c.857C>A	c.(856-858)CCA>CAA	p.P286Q		NM_001005171	NP_001005171	Q8NGK4	O52K1_HUMAN	olfactory receptor, family 52, subfamily K,	286	Helical; Name=7; (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;1.76e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0836)|LUSC - Lung squamous cell carcinoma(625;0.192)										0.138686	54.048134	88.656249	38	236	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4510987	4510987	11533	11	C	A	A	A	273	21	OR52K1	2	2
CHST1	8534	broad.mit.edu	37	11	45671848	45671848	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:45671848C>A	uc001mys.1	-	c.626G>T	c.(625-627)CGC>CTC	p.R209L		NM_003654	NP_003645	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6)	209	Lumenal (Potential).				galactose metabolic process|inflammatory response|keratan sulfate metabolic process	Golgi membrane|integral to membrane	keratan sulfotransferase activity			pancreas(1)	1				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)										0.148649	18.308394	27.048822	11	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45671848	45671848	3531	11	C	A	A	A	351	27	CHST1	1	1
DGKZ	8525	broad.mit.edu	37	11	46393118	46393118	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:46393118C>A	uc001ncn.1	+	c.1288C>A	c.(1288-1290)CCG>ACG	p.P430T	DGKZ_uc001nch.1_Missense_Mutation_p.P258T|DGKZ_uc010rgq.1_Missense_Mutation_p.P185T|DGKZ_uc001ncj.1_Missense_Mutation_p.P208T|DGKZ_uc010rgr.1_Missense_Mutation_p.P207T|DGKZ_uc001nck.1_Missense_Mutation_p.P20T|DGKZ_uc001ncl.2_Missense_Mutation_p.P242T|DGKZ_uc001ncm.2_Missense_Mutation_p.P241T|DGKZ_uc009yky.1_Missense_Mutation_p.P242T|DGKZ_uc010rgs.1_Missense_Mutation_p.P219T	NM_001105540	NP_001099010	Q13574	DGKZ_HUMAN	diacylglycerol kinase zeta isoform 4	430					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell migration|intracellular signal transduction|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of mitotic cell cycle|platelet activation	cytoplasm|lamellipodium|nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|diacylglycerol kinase activity|lipid kinase activity|metal ion binding|protein binding|protein C-terminus binding			pancreas(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)										0.121212	4.076337	8.718236	4	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46393118	46393118	4653	11	C	A	A	A	286	22	DGKZ	2	2
LRP4	4038	broad.mit.edu	37	11	46921855	46921855	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:46921855C>T	uc001ndn.3	-	c.274G>A	c.(274-276)GGG>AGG	p.G92R	LRP4_uc009ylh.1_Missense_Mutation_p.G43R	NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein	92	Extracellular (Potential).|LDL-receptor class A 2.				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			ovary(1)	1				Lung(87;0.159)										0.121429	21.361279	41.064891	17	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46921855	46921855	9332	11	C	T	T	T	299	23	LRP4	1	1
OR4X1	390113	broad.mit.edu	37	11	48285915	48285915	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:48285915G>T	uc010rht.1	+	c.503G>T	c.(502-504)GGC>GTC	p.G168V		NM_001004726	NP_001004726	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X,	168	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2														0.098361	3.200984	13.051029	6	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48285915	48285915	11494	11	G	T	T	T	546	42	OR4X1	2	2
OR51S1	119692	broad.mit.edu	37	11	4869790	4869790	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4869790C>A	uc010qyo.1	-	c.649G>T	c.(649-651)GAC>TAC	p.D217Y		NM_001004758	NP_001004758	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S,	217	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.139394	28.51306	49.250705	23	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4869790	4869790	11515	11	C	A	A	A	390	30	OR51S1	2	2
OR51A7	119687	broad.mit.edu	37	11	4928835	4928835	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4928835C>A	uc010qyq.1	+	c.236C>A	c.(235-237)CCT>CAT	p.P79H		NM_001004749	NP_001004749	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A,	79	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.120567	19.766468	39.680863	17	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4928835	4928835	11498	11	C	A	A	A	312	24	OR51A7	2	2
MMP26	56547	broad.mit.edu	37	11	5013214	5013214	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5013214G>A	uc001lzv.2	+	c.616G>A	c.(616-618)GCA>ACA	p.A206T		NM_021801	NP_068573	Q9NRE1	MMP26_HUMAN	matrix metalloproteinase 26 preproprotein	206					collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227)		Epithelial(150;1.33e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0287)|LUSC - Lung squamous cell carcinoma(625;0.191)										0.113208	4.30755	12.139822	6	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5013214	5013214	10054	11	G	A	A	A	598	46	MMP26	2	2
OR4A16	81327	broad.mit.edu	37	11	55110916	55110916	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55110916G>T	uc010rie.1	+	c.240G>T	c.(238-240)ATG>ATT	p.M80I		NM_001005274	NP_001005274	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A,	80	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(2)|pancreas(1)	3														0.19214	86.25204	106.539513	44	185	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55110916	55110916	11447	11	G	T	T	T	585	45	OR4A16	2	2
OR4A15	81328	broad.mit.edu	37	11	55136382	55136382	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55136382G>A	uc010rif.1	+	c.1023G>A	c.(1021-1023)CTG>CTA	p.L341L		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	341	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.208333	52.302575	61.762698	25	95	KEEP	---	---	---	---	capture		Silent	SNP	55136382	55136382	11446	11	G	A	A	A	613	48	OR4A15	2	2
OR4C16	219428	broad.mit.edu	37	11	55339919	55339919	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55339919G>T	uc010rih.1	+	c.316G>T	c.(316-318)GGC>TGC	p.G106C		NM_001004701	NP_001004701	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C,	106	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		all_epithelial(135;0.0748)												0.162264	76.940672	105.697869	43	222	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55339919	55339919	11455	11	G	T	T	T	611	47	OR4C16	2	2
OR4P4	81300	broad.mit.edu	37	11	55405850	55405850	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55405850A>G	uc010rij.1	+	c.17A>G	c.(16-18)AAT>AGT	p.N6S		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	6	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.102151	28.788067	58.129469	19	167	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55405850	55405850	11490	11	A	G	G	G	52	4	OR4P4	4	4
OR4P4	81300	broad.mit.edu	37	11	55406188	55406188	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55406188G>T	uc010rij.1	+	c.355G>T	c.(355-357)GAC>TAC	p.D119Y		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	119	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.22449	66.786292	77.053123	33	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55406188	55406188	11490	11	G	T	T	T	585	45	OR4P4	2	2
OR4P4	81300	broad.mit.edu	37	11	55406302	55406302	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55406302C>G	uc010rij.1	+	c.469C>G	c.(469-471)CAG>GAG	p.Q157E		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	157	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.122222	21.757272	34.335459	11	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55406302	55406302	11490	11	C	G	G	G	377	29	OR4P4	3	3
OR4C6	219432	broad.mit.edu	37	11	55433201	55433202	+	Missense_Mutation	DNP	TG	CT	CT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55433201_55433202TG>CT	uc001nht.3	+	c.559_560TG>CT	c.(559-561)TGC>CTC	p.C187L	OR4C6_uc010rik.1_Missense_Mutation_p.C187L	NM_001004704	NP_001004704	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C,	187	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.194118	90.881309	105.715291	33	137	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	55433201	55433202	11459	11	TG	CT	CT	CT	715	55	OR4C6	4	4
OR5D13	390142	broad.mit.edu	37	11	55541279	55541279	+	Silent	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55541279T>C	uc010ril.1	+	c.366T>C	c.(364-366)TAT>TAC	p.Y122Y		NM_001001967	NP_001001967	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D,	122	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2		all_epithelial(135;0.196)												0.095041	15.948177	55.783371	23	219	KEEP	---	---	---	---	capture		Silent	SNP	55541279	55541279	11564	11	T	C	C	C	660	51	OR5D13	4	4
OR5D14	219436	broad.mit.edu	37	11	55563543	55563543	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55563543C>A	uc010rim.1	+	c.512C>A	c.(511-513)TCT>TAT	p.S171Y		NM_001004735	NP_001004735	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D,	171	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3		all_epithelial(135;0.196)												0.166023	74.139733	101.569477	43	216	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55563543	55563543	11565	11	C	A	A	A	416	32	OR5D14	2	2
OR5D16	390144	broad.mit.edu	37	11	55606961	55606961	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55606961C>A	uc010rio.1	+	c.734C>A	c.(733-735)TCC>TAC	p.S245Y		NM_001005496	NP_001005496	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D,	245	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3		all_epithelial(135;0.208)												0.100775	4.176047	24.728478	13	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55606961	55606961	11566	11	C	A	A	A	390	30	OR5D16	2	2
OR5W2	390148	broad.mit.edu	37	11	55681905	55681905	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55681905C>A	uc010rir.1	-	c.154G>T	c.(154-156)GAT>TAT	p.D52Y		NM_001001960	NP_001001960	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W,	52	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						Melanoma(48;171 1190 15239 43886 49348)								0.2	20.017616	24.206758	10	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55681905	55681905	11595	11	C	A	A	A	390	30	OR5W2	2	2
C11orf35	256329	broad.mit.edu	37	11	557581	557581	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:557581G>A	uc001lpx.2	-	c.615C>T	c.(613-615)CCC>CCT	p.P205P	RASSF7_uc001lqa.2_5'Flank	NM_173573	NP_775844	Q8IXW0	CK035_HUMAN	hypothetical protein LOC256329	205										pancreas(1)	1		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)										0.133333	13.098825	22.887507	10	65	KEEP	---	---	---	---	capture		Silent	SNP	557581	557581	1677	11	G	A	A	A	600	47	C11orf35	2	2
OR5AS1	219447	broad.mit.edu	37	11	55798241	55798241	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55798241C>A	uc010riw.1	+	c.347C>A	c.(346-348)GCA>GAA	p.A116E		NM_001001921	NP_001001921	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS,	116	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|liver(1)	4	Esophageal squamous(21;0.00693)													0.108108	6.642002	17.914033	8	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55798241	55798241	11556	11	C	A	A	A	325	25	OR5AS1	2	2
OR8J3	81168	broad.mit.edu	37	11	55904794	55904794	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55904794A>G	uc010riz.1	-	c.401T>C	c.(400-402)GTG>GCG	p.V134A		NM_001004064	NP_001004064	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J,	134	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(21;0.00693)													0.086614	4.834183	26.804903	11	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55904794	55904794	11653	11	A	G	G	G	78	6	OR8J3	4	4
OR8K5	219453	broad.mit.edu	37	11	55926935	55926935	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55926935G>T	uc010rja.1	-	c.859C>A	c.(859-861)CCT>ACT	p.P287T		NM_001004058	NP_001004058	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K,	287	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)	3	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)												0.127907	13.261429	24.872587	11	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55926935	55926935	11656	11	G	T	T	T	559	43	OR8K5	2	2
OR5J2	282775	broad.mit.edu	37	11	55944330	55944330	+	Silent	SNP	C	A	A	rs35777813		TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55944330C>A	uc010rjb.1	+	c.237C>A	c.(235-237)CCC>CCA	p.P79P		NM_001005492	NP_001005492	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J,	79	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)													0.094828	10.166576	48.422411	22	210	KEEP	---	---	---	---	capture		Silent	SNP	55944330	55944330	11575	11	C	A	A	A	262	21	OR5J2	2	2
OR5J2	282775	broad.mit.edu	37	11	55944912	55944912	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55944912G>T	uc010rjb.1	+	c.819G>T	c.(817-819)GTG>GTT	p.V273V		NM_001005492	NP_001005492	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J,	273	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)													0.263158	76.896433	82.68103	30	84	KEEP	---	---	---	---	capture		Silent	SNP	55944912	55944912	11575	11	G	T	T	T	600	47	OR5J2	2	2
TRIM6-TRIM34	445372	broad.mit.edu	37	11	5653697	5653697	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5653697G>A	uc001mbf.2	+	c.1198G>A	c.(1198-1200)GCA>ACA	p.A400T	HBG2_uc001mak.1_Intron|TRIM34_uc001mbh.2_Missense_Mutation_p.A46T|TRIM34_uc009yeq.2_5'UTR|TRIM34_uc001mbi.2_Missense_Mutation_p.A46T|TRIM34_uc001mbj.2_Missense_Mutation_p.A46T	NM_001003819	NP_001003819	B2RNG4	B2RNG4_HUMAN	tripartite motif-containing 6 and tripartite	400						intracellular	zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;1.01e-08)|BRCA - Breast invasive adenocarcinoma(625;0.145)										0.112245	8.950786	23.51053	11	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5653697	5653697	17080	11	G	A	A	A	546	42	TRIM6-TRIM34	2	2
OR9I1	219954	broad.mit.edu	37	11	57886814	57886814	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57886814A>G	uc001nml.1	-	c.103T>C	c.(103-105)TAC>CAC	p.Y35H	OR9Q1_uc001nmj.2_Intron	NM_001005211	NP_001005211	Q8NGQ6	OR9I1_HUMAN	olfactory receptor, family 9, subfamily I,	35	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1		Breast(21;0.0589)												0.134021	27.413391	40.009314	13	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57886814	57886814	11664	11	A	G	G	G	195	15	OR9I1	4	4
OR1S2	219958	broad.mit.edu	37	11	57970994	57970994	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57970994G>C	uc010rkb.1	-	c.660C>G	c.(658-660)ATC>ATG	p.I220M		NM_001004459	NP_001004459	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S,	220	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.0589)												0.184211	36.402363	43.513103	14	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57970994	57970994	11379	11	G	C	C	C	577	45	OR1S2	3	3
OR1S2	219958	broad.mit.edu	37	11	57971380	57971380	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57971380G>T	uc010rkb.1	-	c.274C>A	c.(274-276)CCC>ACC	p.P92T		NM_001004459	NP_001004459	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S,	92	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.0589)												0.172973	56.280973	74.977123	32	153	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57971380	57971380	11379	11	G	T	T	T	559	43	OR1S2	2	2
OR52N5	390075	broad.mit.edu	37	11	5799384	5799384	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5799384C>T	uc010qzn.1	-	c.481G>A	c.(481-483)GGT>AGT	p.G161S	TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Intron	NM_001001922	NP_001001922	Q8NH56	O52N5_HUMAN	olfactory receptor, family 52, subfamily N,	161	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)										0.142857	10.489642	16.515328	7	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5799384	5799384	11540	11	C	T	T	T	286	22	OR52N5	2	2
OR5B12	390191	broad.mit.edu	37	11	58207340	58207340	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:58207340A>C	uc010rkh.1	-	c.285T>G	c.(283-285)TGT>TGG	p.C95W		NM_001004733	NP_001004733	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B,	95	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(5;0.0027)	Breast(21;0.0778)												0.252427	74.815617	80.540514	26	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58207340	58207340	11558	11	A	C	C	C	76	6	OR5B12	4	4
OR52E4	390081	broad.mit.edu	37	11	5906024	5906024	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5906024C>A	uc010qzs.1	+	c.502C>A	c.(502-504)CTG>ATG	p.L168M	TRIM5_uc001mbq.1_Intron	NM_001005165	NP_001005165	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E,	168	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.107784	12.330291	37.811063	18	149	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5906024	5906024	11526	11	C	A	A	A	415	32	OR52E4	2	2
OR56A4	120793	broad.mit.edu	37	11	6023680	6023680	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6023680G>C	uc010qzv.1	-	c.699C>G	c.(697-699)ATC>ATG	p.I233M		NM_001005179	NP_001005179	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A,	181	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.119048	7.743479	13.728747	5	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6023680	6023680	11545	11	G	C	C	C	421	33	OR56A4	3	3
PHRF1	57661	broad.mit.edu	37	11	607913	607913	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:607913C>G	uc001lqe.2	+	c.2457C>G	c.(2455-2457)ATC>ATG	p.I819M	PHRF1_uc010qwc.1_Missense_Mutation_p.I818M|PHRF1_uc010qwd.1_Missense_Mutation_p.I817M|PHRF1_uc010qwe.1_Missense_Mutation_p.I815M|PHRF1_uc009ybz.1_Missense_Mutation_p.I609M|PHRF1_uc009yca.1_Non-coding_Transcript	NM_020901	NP_065952	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	819							RNA polymerase binding|zinc ion binding				0														0.147436	50.519069	69.142021	23	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	607913	607913	12285	11	C	G	G	G	369	29	PHRF1	3	3
CD5	921	broad.mit.edu	37	11	60885946	60885946	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:60885946T>A	uc009ynk.2	+	c.394T>A	c.(394-396)TGC>AGC	p.C132S		NM_014207	NP_055022	P06127	CD5_HUMAN	CD5 molecule precursor	132	Extracellular (Potential).|SRCR 1.				cell proliferation|cell recognition	integral to plasma membrane	scavenger receptor activity			ovary(1)	1		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)										0.205607	49.003538	57.59429	22	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60885946	60885946	3149	11	T	A	A	A	715	55	CD5	3	3
ARL2	402	broad.mit.edu	37	11	64789247	64789247	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64789247G>A	uc001och.3	+	c.475G>A	c.(475-477)GCC>ACC	p.A159T	SNX15_uc001oci.3_Intron	NM_001667	NP_001658	P36404	ARL2_HUMAN	ADP-ribosylation factor-like 2	159					cell cycle|centrosome organization|maintenance of protein location in nucleus|negative regulation of GTPase activity|positive regulation of cell-substrate adhesion|positive regulation of microtubule polymerization|small GTPase mediated signal transduction|tight junction assembly|tubulin complex assembly	centrosome|lateral plasma membrane|mitochondrial intermembrane space|nucleus	GTP binding|GTPase activity|GTPase inhibitor activity|protein binding				0														0.117647	4.749928	14.541962	8	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64789247	64789247	950	11	G	A	A	A	494	38	ARL2	1	1
OVOL1	5017	broad.mit.edu	37	11	65554911	65554911	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:65554911C>A	uc001ofp.2	+	c.67C>A	c.(67-69)CCC>ACC	p.P23T		NM_004561	NP_004552	O14753	OVOL1_HUMAN	OVO-like 1 binding protein	23					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1				READ - Rectum adenocarcinoma(159;0.17)										0.333333	7.621283	7.843047	3	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65554911	65554911	11739	11	C	A	A	A	286	22	OVOL1	2	2
CATSPER1	117144	broad.mit.edu	37	11	65793261	65793261	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:65793261G>T	uc001ogt.2	-	c.590C>A	c.(589-591)TCC>TAC	p.S197Y		NM_053054	NP_444282	Q8NEC5	CTSR1_HUMAN	sperm-associated cation channel 1	197	His-rich.|Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	protein binding			ovary(2)	2														0.236559	45.730579	51.613962	22	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65793261	65793261	2806	11	G	T	T	T	533	41	CATSPER1	2	2
NPAS4	266743	broad.mit.edu	37	11	66190662	66190662	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:66190662C>A	uc001ohx.1	+	c.767C>A	c.(766-768)CCC>CAC	p.P256H	NPAS4_uc010rpc.1_Intron	NM_178864	NP_849195	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	256	PAS 2.				transcription, DNA-dependent		DNA binding|signal transducer activity				0														0.212121	14.411015	16.936818	7	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66190662	66190662	10969	11	C	A	A	A	286	22	NPAS4	2	2
DCHS1	8642	broad.mit.edu	37	11	6662548	6662548	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6662548C>A	uc001mem.1	-	c.297G>T	c.(295-297)GGG>GGT	p.G99G		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	99	Cadherin 1.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.148649	16.782788	25.546239	11	63	KEEP	---	---	---	---	capture		Silent	SNP	6662548	6662548	4458	11	C	A	A	A	275	22	DCHS1	2	2
KDM2A	22992	broad.mit.edu	37	11	66947681	66947681	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:66947681A>C	uc001ojw.2	+	c.174A>C	c.(172-174)GAA>GAC	p.E58D	KDM2A_uc001ojx.2_Non-coding_Transcript	NM_012308	NP_036440	Q9Y2K7	KDM2A_HUMAN	F-box and leucine-rich repeat protein 11	58					oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			ovary(3)|skin(1)	4														0.105263	4.171112	10.056899	4	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66947681	66947681	8430	11	A	C	C	C	37	3	KDM2A	4	4
TBX10	347853	broad.mit.edu	37	11	67402363	67402363	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:67402363T>C	uc001omp.2	-	c.301A>G	c.(301-303)AAG>GAG	p.K101E		NM_005995	NP_005986	O75333	TBX10_HUMAN	T-box 10	101	T-box.				anatomical structure morphogenesis|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity				0														0.076923	-2.158288	16.948099	8	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67402363	67402363	16177	11	T	C	C	C	806	62	TBX10	4	4
OR10A4	283297	broad.mit.edu	37	11	6898191	6898191	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6898191T>G	uc010rat.1	+	c.313T>G	c.(313-315)TTC>GTC	p.F105V		NM_207186	NP_997069	Q9H209	O10A4_HUMAN	olfactory receptor, family 10, subfamily A,	105	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)										0.070064	-3.890494	26.061808	11	146	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6898191	6898191	11298	11	T	G	G	G	728	56	OR10A4	4	4
OR2D3	120775	broad.mit.edu	37	11	6942258	6942258	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6942258C>A	uc010rav.1	+	c.26C>A	c.(25-27)ACA>AAA	p.T9K		NM_001004684	NP_001004684	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D,	9	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)										0.151515	18.402006	26.083695	10	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6942258	6942258	11401	11	C	A	A	A	221	17	OR2D3	2	2
TMEM80	283232	broad.mit.edu	37	11	702964	702964	+	Silent	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:702964A>G	uc010qwi.1	+	c.321A>G	c.(319-321)ACA>ACG	p.T107T	TMEM80_uc001lqr.2_Silent_p.T107T|TMEM80_uc001lqs.2_Silent_p.T99T	NM_001042463	NP_001035928	Q96HE8	TMM80_HUMAN	transmembrane protein 80 isoform 2	107						integral to membrane					0		all_cancers(49;5.11e-06)|all_epithelial(84;0.00143)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.44e-27)|Epithelial(43;2.29e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.19e-20)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)										0.242424	38.867759	42.860337	16	50	KEEP	---	---	---	---	capture		Silent	SNP	702964	702964	16743	11	A	G	G	G	80	7	TMEM80	4	4
NLRP14	338323	broad.mit.edu	37	11	7064401	7064401	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7064401C>A	uc001mfb.1	+	c.1144C>A	c.(1144-1146)CAA>AAA	p.Q382K		NM_176822	NP_789792	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	382	NACHT.				cell differentiation|multicellular organismal development|spermatogenesis		ATP binding			ovary(3)|breast(2)|lung(1)|pancreas(1)	7				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)										0.106742	15.401014	42.723154	19	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7064401	7064401	10879	11	C	A	A	A	325	25	NLRP14	2	2
DHCR7	1717	broad.mit.edu	37	11	71150017	71150017	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:71150017C>G	uc001oqk.2	-	c.739G>C	c.(739-741)GCC>CCC	p.A247P	DHCR7_uc001oql.2_Missense_Mutation_p.A247P	NM_001163817	NP_001157289	Q9UBM7	DHCR7_HUMAN	7-dehydrocholesterol reductase	247			A -> V (in SLOS).		cholesterol biosynthetic process|oxidation-reduction process	endoplasmic reticulum membrane|integral to membrane|nuclear outer membrane	7-dehydrocholesterol reductase activity|protein binding			ovary(1)|liver(1)	2					NADH(DB00157)									0.108911	16.270317	31.553944	11	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71150017	71150017	4656	11	C	G	G	G	351	27	DHCR7	3	3
C2CD3	26005	broad.mit.edu	37	11	73814209	73814209	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:73814209C>G	uc001ouu.2	-	c.2547G>C	c.(2545-2547)TGG>TGC	p.W849C		NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	849										ovary(3)|pancreas(2)	5	Breast(11;4.16e-06)													0.193966	111.842387	132.113957	45	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73814209	73814209	2237	11	C	G	G	G	286	22	C2CD3	3	3
OR2AT4	341152	broad.mit.edu	37	11	74799863	74799863	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:74799863T>A	uc010rro.1	-	c.896A>T	c.(895-897)AAC>ATC	p.N299I		NM_001005285	NP_001005285	A6NND4	O2AT4_HUMAN	olfactory receptor, family 2, subfamily AT,	299	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.221429	67.253031	77.251404	31	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74799863	74799863	11393	11	T	A	A	A	780	60	OR2AT4	3	3
INTS4	92105	broad.mit.edu	37	11	77671418	77671419	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:77671418_77671419CC>AA	uc001oys.2	-	c.676_677GG>TT	c.(676-678)GGA>TTA	p.G226L	INTS4_uc001oyt.2_Non-coding_Transcript|INTS4_uc001oyu.1_Missense_Mutation_p.G226L	NM_033547	NP_291025	Q96HW7	INT4_HUMAN	integrator complex subunit 4	226	HEAT 3.				snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)											0.084211	-0.269081	16.405748	8	87	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	77671418	77671419	8081	11	CC	AA	AA	AA	390	30	INTS4	2	2
ODZ4	26011	broad.mit.edu	37	11	78413441	78413441	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:78413441A>T	uc001ozl.3	-	c.4217T>A	c.(4216-4218)CTG>CAG	p.L1406Q	ODZ4_uc009yvb.1_5'UTR	NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	1406	Extracellular (Potential).|NHL 4.				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4														0.094241	8.91982	40.511462	18	173	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78413441	78413441	11242	11	A	T	T	T	91	7	ODZ4	3	3
ODZ4	26011	broad.mit.edu	37	11	78437147	78437147	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:78437147T>A	uc001ozl.3	-	c.3527A>T	c.(3526-3528)CAT>CTT	p.H1176L		NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	1176	Extracellular (Potential).				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4														0.226069	285.43791	319.320719	111	380	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78437147	78437147	11242	11	T	A	A	A	663	51	ODZ4	3	3
NLRP10	338322	broad.mit.edu	37	11	7982364	7982364	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7982364C>A	uc001mfv.1	-	c.795G>T	c.(793-795)AGG>AGT	p.R265S		NM_176821	NP_789791	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	265	NACHT.						ATP binding			lung(4)|ovary(2)|kidney(1)|pancreas(1)	8				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)						109				0.107345	10.801257	37.885192	19	158	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7982364	7982364	10875	11	C	A	A	A	285	22	NLRP10	2	2
NLRP10	338322	broad.mit.edu	37	11	7982526	7982526	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7982526C>A	uc001mfv.1	-	c.633G>T	c.(631-633)GTG>GTT	p.V211V		NM_176821	NP_789791	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	211	NACHT.						ATP binding			lung(4)|ovary(2)|kidney(1)|pancreas(1)	8				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)						109				0.095238	3.308283	13.662613	6	57	KEEP	---	---	---	---	capture		Silent	SNP	7982526	7982526	10875	11	C	A	A	A	262	21	NLRP10	2	2
LRDD	55367	broad.mit.edu	37	11	799386	799386	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:799386C>A	uc001lro.1	-	c.2654G>T	c.(2653-2655)CGA>CTA	p.R885L	SLC25A22_uc009yci.2_5'Flank|SLC25A22_uc001lrj.2_5'Flank|LRDD_uc009yck.1_Non-coding_Transcript|LRDD_uc001lrk.1_Missense_Mutation_p.R868L|LRDD_uc001lrl.1_Missense_Mutation_p.R728L|LRDD_uc001lrm.1_Missense_Mutation_p.R572L|LRDD_uc001lrn.1_Missense_Mutation_p.R728L|LRDD_uc001lrp.1_3'UTR	NM_145886	NP_665893	Q9HB75	PIDD_HUMAN	leucine rich repeat and death domain containing	885					apoptosis|signal transduction	cytoplasm|nucleus	death receptor binding				0		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)										0.123711	15.269175	28.670831	12	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	799386	799386	9309	11	C	A	A	A	403	31	LRDD	1	1
RIC3	79608	broad.mit.edu	37	11	8132302	8132302	+	Silent	SNP	G	A	A	rs17852022		TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:8132302G>A	uc010rbm.1	-	c.1137C>T	c.(1135-1137)ACC>ACT	p.T379T	RIC3_uc001mgb.2_Silent_p.T189T|RIC3_uc001mgc.2_Silent_p.T350T|RIC3_uc001mge.2_Silent_p.T169T|RIC3_uc010rbl.1_Silent_p.T301T|RIC3_uc001mgd.2_Silent_p.T351T|RIC3_uc009yfm.2_Silent_p.T270T|RIC3_uc009yfn.2_Silent_p.T154T	NM_024557	NP_078833	Q7Z5B4	RIC3_HUMAN	resistance to inhibitors of cholinesterase 3	351	Cytoplasmic (Potential).					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)										0.110465	21.107736	46.918345	19	153	KEEP	---	---	---	---	capture		Silent	SNP	8132302	8132302	13829	11	G	A	A	A	496	39	RIC3	1	1
TMEM135	65084	broad.mit.edu	37	11	86802403	86802403	+	Splice_Site_SNP	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:86802403G>T	uc001pch.2	+	c.363_splice	c.e4-1	p.R121_splice	TMEM135_uc010rtt.1_Intron|TMEM135_uc001pci.2_Splice_Site_SNP_p.R121_splice|TMEM135_uc001pcg.1_Splice_Site_SNP_p.R121_splice	NM_022918	NP_075069			transmembrane protein 135							integral to membrane					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)												0.139535	9.318059	14.717706	6	37	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	86802403	86802403	16583	11	G	T	T	T	455	35	TMEM135	5	2
GRM5	2915	broad.mit.edu	37	11	88330421	88330421	+	Silent	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:88330421T>C	uc001pcq.2	-	c.1494A>G	c.(1492-1494)GAA>GAG	p.E498E	GRM5_uc009yvm.2_Silent_p.E498E	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a	498	Extracellular (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(1)	5		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)									0.225	56.211222	61.766077	18	62	KEEP	---	---	---	---	capture		Silent	SNP	88330421	88330421	7079	11	T	C	C	C	725	56	GRM5	4	4
FOLH1B	219595	broad.mit.edu	37	11	89403612	89403612	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:89403612G>A	uc001pda.2	+	c.150G>A	c.(148-150)GTG>GTA	p.V50V		NM_153696	NP_710163	Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B	50					proteolysis	cytoplasm	dipeptidase activity|metal ion binding|metallopeptidase activity			ovary(3)|central_nervous_system(1)	4														0.103093	4.96809	20.225372	10	87	KEEP	---	---	---	---	capture		Silent	SNP	89403612	89403612	6222	11	G	A	A	A	574	45	FOLH1B	2	2
FOLH1B	219595	broad.mit.edu	37	11	89424067	89424067	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:89424067C>A	uc001pda.2	+	c.717C>A	c.(715-717)AGC>AGA	p.S239R		NM_153696	NP_710163	Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B	239					proteolysis	cytoplasm	dipeptidase activity|metal ion binding|metallopeptidase activity			ovary(3)|central_nervous_system(1)	4														0.16	14.666773	20.172225	8	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89424067	89424067	6222	11	C	A	A	A	350	27	FOLH1B	1	1
ASCL3	56676	broad.mit.edu	37	11	8959435	8959435	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:8959435G>T	uc001mhd.1	-	c.274C>A	c.(274-276)CCA>ACA	p.P92T		NM_020646	NP_065697	Q9NQ33	ASCL3_HUMAN	ASCL3	91					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleolus	DNA binding|transcription regulator activity				0				Epithelial(150;1.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0228)										0.109091	8.917524	25.577996	12	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8959435	8959435	1054	11	G	T	T	T	546	42	ASCL3	2	2
NAALAD2	10003	broad.mit.edu	37	11	89882210	89882210	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:89882210G>T	uc001pdf.3	+	c.418G>T	c.(418-420)GGC>TGC	p.G140C	NAALAD2_uc009yvx.2_Missense_Mutation_p.G140C|NAALAD2_uc009yvy.2_Missense_Mutation_p.G140C|NAALAD2_uc001pdd.2_Missense_Mutation_p.G140C|NAALAD2_uc001pde.2_Missense_Mutation_p.G140C	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	140	Extracellular (Potential).				proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)												0.138728	38.1728	60.005296	24	149	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89882210	89882210	10523	11	G	T	T	T	611	47	NAALAD2	2	2
NAALAD2	10003	broad.mit.edu	37	11	89907012	89907012	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:89907012G>T	uc001pdf.3	+	c.1431G>T	c.(1429-1431)GGG>GGT	p.G477G	NAALAD2_uc009yvx.2_Silent_p.G444G|NAALAD2_uc009yvy.2_Intron	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	477	Extracellular (Potential).|NAALADase.				proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)												0.201681	49.326954	59.175705	24	95	KEEP	---	---	---	---	capture		Silent	SNP	89907012	89907012	10523	11	G	T	T	T	561	44	NAALAD2	2	2
GPR83	10888	broad.mit.edu	37	11	94129655	94129655	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:94129655C>A	uc001pet.2	-	c.423G>T	c.(421-423)AAG>AAT	p.K141N		NM_016540	NP_057624	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83 precursor	141	Extracellular (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			central_nervous_system(2)|ovary(1)	3		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)												0.223301	53.366374	60.620584	23	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94129655	94129655	6988	11	C	A	A	A	311	24	GPR83	2	2
KDM4D	55693	broad.mit.edu	37	11	94731346	94731346	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:94731346G>T	uc001pfe.2	+	c.810G>T	c.(808-810)GAG>GAT	p.E270D		NM_018039	NP_060509	Q6B0I6	KDM4D_HUMAN	jumonji domain containing 2D	270	JmjC.				chromatin modification|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0														0.097744	7.430205	29.120018	13	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94731346	94731346	8437	11	G	T	T	T	464	36	KDM4D	2	2
KDM4D	55693	broad.mit.edu	37	11	94731482	94731482	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:94731482A>T	uc001pfe.2	+	c.946A>T	c.(946-948)AGG>TGG	p.R316W		NM_018039	NP_060509	Q6B0I6	KDM4D_HUMAN	jumonji domain containing 2D	316					chromatin modification|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0														0.124088	21.006628	39.912417	17	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94731482	94731482	8437	11	A	T	T	T	36	3	KDM4D	3	3
CNTN5	53942	broad.mit.edu	37	11	99715818	99715818	+	Splice_Site_SNP	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:99715818G>T	uc001pga.2	+	c.402_splice	c.e6-1	p.R134_splice	CNTN5_uc009ywv.1_Splice_Site_SNP_p.R134_splice|CNTN5_uc001pfz.2_Splice_Site_SNP_p.R134_splice|CNTN5_uc001pgb.2_Splice_Site_SNP_p.R60_splice	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)						1117				0.139535	15.836105	26.638646	12	74	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	99715818	99715818	3782	11	G	T	T	T	429	33	CNTN5	5	2
UHRF1BP1L	23074	broad.mit.edu	37	12	100444090	100444090	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:100444090C>T	uc001tgq.2	-	c.3574G>A	c.(3574-3576)GTT>ATT	p.V1192I	UHRF1BP1L_uc001tgp.2_Missense_Mutation_p.V842I	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a	1192										ovary(1)	1														0.114286	3.973228	9.108754	4	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100444090	100444090	17527	12	C	T	T	T	247	19	UHRF1BP1L	1	1
ANO4	121601	broad.mit.edu	37	12	101336246	101336246	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:101336246C>A	uc010svm.1	+	c.389C>A	c.(388-390)CCC>CAC	p.P130H	ANO4_uc010svl.1_Non-coding_Transcript|ANO4_uc001thw.2_Missense_Mutation_p.P95H|ANO4_uc001thx.2_Missense_Mutation_p.P130H	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4	130	Extracellular (Potential).					chloride channel complex	chloride channel activity			ovary(4)	4														0.077922	-5.51365	36.561375	18	213	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101336246	101336246	707	12	C	A	A	A	286	22	ANO4	2	2
CLEC1A	51267	broad.mit.edu	37	12	10226012	10226012	+	Splice_Site_SNP	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:10226012T>A	uc001qxb.2	-	c.544_splice	c.e5-1	p.E182_splice	CLEC1A_uc009zhf.2_Splice_Site_SNP_p.E94_splice|CLEC1A_uc001qxc.2_Splice_Site_SNP_p.E94_splice|CLEC1A_uc001qxd.2_Splice_Site_SNP_p.E139_splice|CLEC1A_uc010sgx.1_Splice_Site_SNP_p.E80_splice	NM_016511	NP_057595			C-type lectin-like receptor-1						cell surface receptor linked signaling pathway|defense response	integral to plasma membrane|intracellular	sugar binding|transmembrane receptor activity			ovary(1)|central_nervous_system(1)	2														0.138889	23.844114	37.472758	15	93	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	10226012	10226012	3642	12	T	A	A	A	715	55	CLEC1A	5	3
OLR1	4973	broad.mit.edu	37	12	10321772	10321772	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:10321772G>T	uc001qxo.1	-	c.79C>A	c.(79-81)CTT>ATT	p.L27I	OLR1_uc010sgz.1_5'Flank|OLR1_uc010sha.1_Missense_Mutation_p.L27I	NM_002543	NP_002534	P78380	OLR1_HUMAN	oxidized low density lipoprotein (lectin-like)	27	Cytoplasmic (Potential).				blood circulation|blood coagulation|inflammatory response|leukocyte migration|proteolysis	extracellular region|integral to plasma membrane|membrane fraction	sugar binding			ovary(1)	1														0.212121	28.00863	33.070046	14	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10321772	10321772	11268	12	G	T	T	T	429	33	OLR1	2	2
PAH	5053	broad.mit.edu	37	12	103271254	103271254	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:103271254C>A	uc001tjq.1	-	c.427G>T	c.(427-429)GAT>TAT	p.D143Y	PAH_uc010swc.1_Missense_Mutation_p.D143Y	NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase	143			D -> G (in PKU; haplotype 11).		catecholamine biosynthetic process|L-phenylalanine catabolic process|neurotransmitter biosynthetic process|oxidation-reduction process	cytosol	phenylalanine 4-monooxygenase activity			ovary(4)	4					Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Levodopa(DB01235)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)									0.091667	1.737369	21.896705	11	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103271254	103271254	11810	12	C	A	A	A	390	30	PAH	2	2
C12orf59	120939	broad.mit.edu	37	12	10342590	10342590	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:10342590C>T	uc001qxq.2	+	c.343C>T	c.(343-345)CTC>TTC	p.L115F	C12orf59_uc001qxr.2_Missense_Mutation_p.L135F	NM_153022	NP_694567	Q4KMG9	CL059_HUMAN	hypothetical protein LOC120939	135						integral to membrane				ovary(1)	1														0.177215	30.711139	38.457492	14	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10342590	10342590	1746	12	C	T	T	T	312	24	C12orf59	2	2
ALDH1L2	160428	broad.mit.edu	37	12	105467714	105467714	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:105467714G>T	uc001tlc.2	-	c.118C>A	c.(118-120)CAC>AAC	p.H40N	ALDH1L2_uc009zup.2_Non-coding_Transcript	NM_001034173	NP_001029345	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	40	GART.				10-formyltetrahydrofolate catabolic process|biosynthetic process|oxidation-reduction process	mitochondrion	acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity|phosphopantetheine binding				0														0.141104	34.304191	54.57667	23	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105467714	105467714	498	12	G	T	T	T	611	47	ALDH1L2	2	2
NUAK1	9891	broad.mit.edu	37	12	106480519	106480519	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:106480519C>A	uc001tlj.1	-	c.506G>T	c.(505-507)TGT>TTT	p.C169F		NM_014840	NP_055655	O60285	NUAK1_HUMAN	AMPK-related protein kinase 5	169	Protein kinase.				protein phosphorylation		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|central_nervous_system(1)	2										125				0.189189	30.004263	36.694535	14	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106480519	106480519	11117	12	C	A	A	A	221	17	NUAK1	2	2
POLR3B	55703	broad.mit.edu	37	12	106763069	106763069	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:106763069G>T	uc001tlp.2	+	c.244G>T	c.(244-246)GTT>TTT	p.V82F	POLR3B_uc001tlq.2_Missense_Mutation_p.V24F	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	DNA-directed RNA polymerase III B isoform 1	82					innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2														0.143939	32.628412	48.74818	19	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106763069	106763069	12657	12	G	T	T	T	624	48	POLR3B	2	2
RFX4	5992	broad.mit.edu	37	12	107113822	107113822	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:107113822G>T	uc001tlt.2	+	c.1250G>T	c.(1249-1251)TGT>TTT	p.C417F	RFX4_uc001tlr.2_Missense_Mutation_p.C408F|RFX4_uc001tls.2_Missense_Mutation_p.C417F|RFX4_uc001tlv.2_Missense_Mutation_p.C314F	NM_213594	NP_998759	Q33E94	RFX4_HUMAN	regulatory factor X4 isoform c	408	Necessary for dimerization.				transcription, DNA-dependent	nucleus	DNA binding				0														0.075269	-1.153088	16.060717	7	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107113822	107113822	13737	12	G	T	T	T	624	48	RFX4	2	2
WSCD2	9671	broad.mit.edu	37	12	108589794	108589794	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:108589794C>T	uc001tms.2	+	c.185C>T	c.(184-186)GCT>GTT	p.A62V	WSCD2_uc001tmt.2_Missense_Mutation_p.A62V	NM_014653	NP_055468	Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	62						integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3														0.105714	28.374033	82.311616	37	313	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108589794	108589794	17981	12	C	T	T	T	364	28	WSCD2	2	2
WSCD2	9671	broad.mit.edu	37	12	108641840	108641840	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:108641840A>C	uc001tms.2	+	c.1418A>C	c.(1417-1419)AAG>ACG	p.K473T	WSCD2_uc001tmt.2_Missense_Mutation_p.K473T|WSCD2_uc001tmu.2_Missense_Mutation_p.K241T	NM_014653	NP_055468	Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	473						integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3														0.165138	33.675511	45.284845	18	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108641840	108641840	17981	12	A	C	C	C	39	3	WSCD2	4	4
PPTC7	160760	broad.mit.edu	37	12	110976020	110976020	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:110976020T>C	uc001trh.1	-	c.785A>G	c.(784-786)GAG>GGG	p.E262G		NM_139283	NP_644812	Q8NI37	PPTC7_HUMAN	T-cell activation protein phosphatase 2C	262	PP2C-like.						metal ion binding|phosphoprotein phosphatase activity				0														0.173913	30.958467	37.88145	12	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110976020	110976020	12849	12	T	C	C	C	702	54	PPTC7	4	4
OAS3	4940	broad.mit.edu	37	12	113384680	113384680	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:113384680G>T	uc001tug.2	+	c.769G>T	c.(769-771)GGC>TGC	p.G257C		NM_006187	NP_006178	Q9Y6K5	OAS3_HUMAN	2'-5'oligoadenylate synthetase 3	257	OAS domain 1.				interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	microsome	ATP binding|nucleotidyltransferase activity|RNA binding			central_nervous_system(1)	1														0.140351	10.763978	17.881758	8	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113384680	113384680	11206	12	G	T	T	T	559	43	OAS3	2	2
PLBD2	196463	broad.mit.edu	37	12	113822701	113822701	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:113822701G>T	uc001tve.2	+	c.1164G>T	c.(1162-1164)CCG>CCT	p.P388P	PLBD2_uc001tvf.2_Intron	NM_173542	NP_775813	Q8NHP8	PLBL2_HUMAN	phospholipase B domain containing 2 isoform 1	388					lipid catabolic process	lysosomal lumen	hydrolase activity				0														0.123077	8.490924	17.501096	8	57	KEEP	---	---	---	---	capture		Silent	SNP	113822701	113822701	12452	12	G	T	T	T	496	39	PLBD2	1	1
MED13L	23389	broad.mit.edu	37	12	116428865	116428865	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:116428865C>A	uc001tvw.2	-	c.3894G>T	c.(3892-3894)CTG>CTT	p.L1298L		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1298					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		RNA polymerase II transcription mediator activity			skin(3)|ovary(1)|lung(1)	5	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)						497				0.174312	38.455834	49.367798	19	90	KEEP	---	---	---	---	capture		Silent	SNP	116428865	116428865	9820	12	C	A	A	A	262	21	MED13L	2	2
CIT	11113	broad.mit.edu	37	12	120146113	120146113	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:120146113C>A	uc001txj.1	-	c.5082G>T	c.(5080-5082)CGG>CGT	p.R1694R	CIT_uc001txh.1_Silent_p.R1171R|CIT_uc001txi.1_Silent_p.R1652R	NM_007174	NP_009105	O14578	CTRO_HUMAN	citron	1652	CNH.				intracellular signal transduction|protein phosphorylation		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)						1263				0.184211	24.499359	31.621063	14	62	KEEP	---	---	---	---	capture		Silent	SNP	120146113	120146113	3573	12	C	A	A	A	275	22	CIT	2	2
CIT	11113	broad.mit.edu	37	12	120221783	120221783	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:120221783C>A	uc001txj.1	-	c.1474G>T	c.(1474-1476)GAG>TAG	p.E492*	CIT_uc001txh.1_Nonsense_Mutation_p.E26*|CIT_uc001txi.1_Nonsense_Mutation_p.E492*	NM_007174	NP_009105	O14578	CTRO_HUMAN	citron	492	Potential.				intracellular signal transduction|protein phosphorylation		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)						1263				0.112272	26.336544	83.264664	43	340	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	120221783	120221783	3573	12	C	A	A	A	390	30	CIT	5	2
RNF10	9921	broad.mit.edu	37	12	121004691	121004691	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:121004691G>C	uc001typ.3	+	c.1949G>C	c.(1948-1950)TGC>TCC	p.C650S	RNF10_uc010szk.1_Non-coding_Transcript|RNF10_uc001tyq.3_Missense_Mutation_p.C561S	NM_014868	NP_055683	Q8N5U6	RNF10_HUMAN	ring finger protein 10	650					negative regulation of Schwann cell proliferation|positive regulation of myelination|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	promoter binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.15311	69.042244	93.147075	32	177	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121004691	121004691	13899	12	G	C	C	C	598	46	RNF10	3	3
RHOF	54509	broad.mit.edu	37	12	122217461	122217461	+	Silent	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:122217461G>C	uc001ubb.2	-	c.579C>G	c.(577-579)CTC>CTG	p.L193L	TMEM120B_uc001ubc.3_3'UTR|TMEM120B_uc009zxh.2_3'UTR|TMEM120B_uc001uba.1_Non-coding_Transcript	NM_019034	NP_061907	Q9HBH0	RHOF_HUMAN	ras homolog gene family, member F precursor	193					actin filament organization|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|plasma membrane	GTP binding|GTPase activity			ovary(1)	1	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;4.38e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.223)										0.150442	35.795207	49.035233	17	96	KEEP	---	---	---	---	capture		Silent	SNP	122217461	122217461	13813	12	G	C	C	C	574	45	RHOF	3	3
KNTC1	9735	broad.mit.edu	37	12	123105090	123105090	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:123105090C>T	uc001ucv.2	+	c.6214C>T	c.(6214-6216)CCG>TCG	p.P2072S	KNTC1_uc010taf.1_Missense_Mutation_p.P997S|GPR81_uc001ucw.1_Non-coding_Transcript	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore	2072					cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)										0.12	6.922158	13.999365	6	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123105090	123105090	8742	12	C	T	T	T	390	30	KNTC1	2	2
SBNO1	55206	broad.mit.edu	37	12	123815810	123815810	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:123815810A>C	uc010tap.1	-	c.1022T>G	c.(1021-1023)TTG>TGG	p.L341W	SBNO1_uc010tao.1_Missense_Mutation_p.L340W|SBNO1_uc010taq.1_Intron|SBNO1_uc001uet.2_Missense_Mutation_p.L341W|SBNO1_uc001ueu.2_Missense_Mutation_p.L340W|SBNO1_uc001uev.2_Missense_Mutation_p.L339W|SBNO1_uc009zxy.1_Missense_Mutation_p.L306W	NM_018183	NP_060653	A3KN83	SBNO1_HUMAN	sno, strawberry notch homolog 1	341							ATP binding|DNA binding|hydrolase activity			breast(5)|ovary(1)|kidney(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)										0.060606	-5.382967	27.891039	10	155	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123815810	123815810	14343	12	A	C	C	C	65	5	SBNO1	4	4
ZNF664	144348	broad.mit.edu	37	12	124497156	124497156	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:124497156C>T	uc001ufz.2	+	c.465C>T	c.(463-465)ACC>ACT	p.T155T	ZNF664_uc001uga.2_Silent_p.T155T|ZNF664_uc001ugb.2_Silent_p.T155T	NM_152437	NP_689650	Q8N3J9	ZN664_HUMAN	zinc finger protein 664	155	C2H2-type 6.				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)										0.134021	38.91508	64.125898	26	168	KEEP	---	---	---	---	capture		Silent	SNP	124497156	124497156	18667	12	C	T	T	T	301	24	ZNF664	2	2
TMEM132B	114795	broad.mit.edu	37	12	125834246	125834246	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:125834246C>A	uc001uhe.1	+	c.301C>A	c.(301-303)CTC>ATC	p.L101I		NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	101	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)										0.155779	54.788409	77.312149	31	168	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125834246	125834246	16577	12	C	A	A	A	364	28	TMEM132B	2	2
TMEM132B	114795	broad.mit.edu	37	12	126135350	126135350	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:126135350G>T	uc001uhe.1	+	c.1750G>T	c.(1750-1752)GGG>TGG	p.G584W	TMEM132B_uc001uhf.1_Missense_Mutation_p.G96W	NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	584	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)										0.080808	-0.382532	17.353494	8	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126135350	126135350	16577	12	G	T	T	T	455	35	TMEM132B	2	2
TMEM132B	114795	broad.mit.edu	37	12	126139132	126139132	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:126139132G>T	uc001uhe.1	+	c.3113G>T	c.(3112-3114)GGC>GTC	p.G1038V	TMEM132B_uc001uhf.1_Missense_Mutation_p.G550V	NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	1038	Cytoplasmic (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)										0.12037	11.936533	27.192399	13	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126139132	126139132	16577	12	G	T	T	T	546	42	TMEM132B	2	2
GSG1	83445	broad.mit.edu	37	12	13243462	13243462	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:13243462G>A	uc001rbn.2	-	c.339C>T	c.(337-339)TCC>TCT	p.S113S	GSG1_uc001rbj.2_Silent_p.S100S|GSG1_uc001rbk.2_Silent_p.S100S|GSG1_uc001rbl.2_Silent_p.S100S|GSG1_uc001rbm.2_Silent_p.S100S|GSG1_uc001rbo.2_Silent_p.S113S|GSG1_uc001rbp.2_Silent_p.S113S|GSG1_uc001rbq.1_Silent_p.S113S	NM_001080555	NP_001074024	Q2KHT4	GSG1_HUMAN	germ cell associated 1 isoform 4	100						endoplasmic reticulum membrane|integral to membrane					0		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)										0.132743	22.242165	37.047484	15	98	KEEP	---	---	---	---	capture		Silent	SNP	13243462	13243462	7100	12	G	A	A	A	444	35	GSG1	2	2
GRIN2B	2904	broad.mit.edu	37	12	13719974	13719974	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:13719974G>T	uc001rbt.2	-	c.2583C>A	c.(2581-2583)GTC>GTA	p.V861V		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	861	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				0.083333	-0.84396	13.984703	7	77	KEEP	---	---	---	---	capture		Silent	SNP	13719974	13719974	7059	12	G	T	T	T	418	33	GRIN2B	2	2
GUCY2C	2984	broad.mit.edu	37	12	14778850	14778850	+	Splice_Site_SNP	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:14778850C>T	uc001rcd.2	-	c.2250_splice	c.e21-1	p.G750_splice		NM_004963	NP_004954			guanylate cyclase 2C precursor						intracellular signal transduction|protein phosphorylation|receptor guanylyl cyclase signaling pathway	integral to membrane	ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity			ovary(4)|skin(1)	5										889				0.176471	27.155688	33.864896	12	56	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	14778850	14778850	7176	12	C	T	T	T	416	32	GUCY2C	5	2
DERA	51071	broad.mit.edu	37	12	16189280	16189280	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:16189280G>A	uc001rde.2	+	c.865G>A	c.(865-867)GGT>AGT	p.G289S		NM_015954	NP_057038	Q9Y315	DEOC_HUMAN	deoxyribose-phosphate aldolase-like	289					deoxyribonucleoside catabolic process|deoxyribonucleotide catabolic process	cytoplasm	deoxyribose-phosphate aldolase activity|protein binding				0		Hepatocellular(102;0.121)												0.153846	16.580073	22.52546	8	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16189280	16189280	4624	12	G	A	A	A	455	35	DERA	2	2
PDE3A	5139	broad.mit.edu	37	12	20766631	20766631	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:20766631A>T	uc001reh.1	+	c.1266A>T	c.(1264-1266)CCA>CCT	p.P422P		NM_000921	NP_000912	Q14432	PDE3A_HUMAN	phosphodiesterase 3A	422					lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(3)	3	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)									0.192308	41.639384	50.835856	20	84	KEEP	---	---	---	---	capture		Silent	SNP	20766631	20766631	12058	12	A	T	T	T	54	5	PDE3A	3	3
SLCO1B1	10599	broad.mit.edu	37	12	21391984	21391984	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:21391984C>A	uc001req.3	+	c.1937C>A	c.(1936-1938)GCC>GAC	p.A646D		NM_006446	NP_006437	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family,	646	Helical; Name=12; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	bile acid transmembrane transporter activity|sodium-independent organic anion transmembrane transporter activity|thyroid hormone transmembrane transporter activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					Digoxin(DB00390)|Gemfibrozil(DB01241)|Pravastatin(DB00175)									0.186047	14.473099	18.448013	8	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21391984	21391984	15220	12	C	A	A	A	338	26	SLCO1B1	2	2
KIAA0528	9847	broad.mit.edu	37	12	22624354	22624354	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:22624354C>A	uc010sit.1	-	c.2343G>T	c.(2341-2343)CTG>CTT	p.L781L	KIAA0528_uc010sir.1_Silent_p.L594L|KIAA0528_uc010sis.1_Silent_p.L779L|KIAA0528_uc001rfq.2_Silent_p.L779L|KIAA0528_uc010siu.1_Silent_p.L779L|KIAA0528_uc001rfr.2_Silent_p.L770L	NM_014802	NP_055617	Q86YS7	K0528_HUMAN	hypothetical protein LOC9847	779							protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4														0.169492	18.909475	25.012711	10	49	KEEP	---	---	---	---	capture		Silent	SNP	22624354	22624354	8489	12	C	A	A	A	314	25	KIAA0528	2	2
IQSEC3	440073	broad.mit.edu	37	12	247571	247571	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:247571C>A	uc001qhw.1	+	c.133C>A	c.(133-135)CCA>ACA	p.P45T	IQSEC3_uc001qhu.1_Missense_Mutation_p.P45T|IQSEC3_uc001qht.1_Missense_Mutation_p.P130T	NM_015232	NP_056047	Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	348					regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)	3	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)										0.321429	22.991378	23.770831	9	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247571	247571	8122	12	C	A	A	A	338	26	IQSEC3	2	2
C12orf71	728858	broad.mit.edu	37	12	27234183	27234183	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:27234183G>T	uc001rhq.2	-	c.734C>A	c.(733-735)GCA>GAA	p.A245E		NM_001080406	NP_001073875	A8MTZ7	CL071_HUMAN	hypothetical protein LOC728858	245											0														0.171233	47.476549	62.403628	25	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27234183	27234183	1757	12	G	T	T	T	598	46	C12orf71	2	2
OVCH1	341350	broad.mit.edu	37	12	29624839	29624839	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:29624839G>T	uc001rix.1	-	c.1752C>A	c.(1750-1752)CAC>CAA	p.H584Q		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	584	Peptidase S1 2.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)													0.181818	8.186005	10.279054	4	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29624839	29624839	11736	12	G	T	T	T	464	36	OVCH1	2	2
OVCH1	341350	broad.mit.edu	37	12	29629149	29629149	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:29629149C>G	uc001rix.1	-	c.1461G>C	c.(1459-1461)AAG>AAC	p.K487N		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	487	CUB 2.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)													0.110048	31.353816	62.847634	23	186	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29629149	29629149	11736	12	C	G	G	G	363	28	OVCH1	3	3
OVCH1	341350	broad.mit.edu	37	12	29640733	29640733	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:29640733C>A	uc001rix.1	-	c.785G>T	c.(784-786)TGT>TTT	p.C262F		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	262	Peptidase S1 1.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)													0.3125	15.168945	15.669798	5	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29640733	29640733	11736	12	C	A	A	A	221	17	OVCH1	2	2
DENND5B	160518	broad.mit.edu	37	12	31566471	31566471	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:31566471C>T	uc001rkh.1	-	c.2685G>A	c.(2683-2685)AAG>AAA	p.K895K	DENND5B_uc001rki.1_Silent_p.K860K|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	860	RUN 1.					integral to membrane				ovary(1)|central_nervous_system(1)	2														0.094595	4.465002	16.683175	7	67	KEEP	---	---	---	---	capture		Silent	SNP	31566471	31566471	4616	12	C	T	T	T	415	32	DENND5B	2	2
PKP2	5318	broad.mit.edu	37	12	33030954	33030954	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:33030954C>A	uc001rlj.3	-	c.860G>T	c.(859-861)AGG>ATG	p.R287M	PKP2_uc001rlk.3_Missense_Mutation_p.R287M|PKP2_uc010skj.1_Missense_Mutation_p.R287M	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b	287					cell-cell adhesion	desmosome|integral to membrane|nucleus	binding			ovary(1)|pancreas(1)	2	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)													0.086022	-0.270227	15.886879	8	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33030954	33030954	12410	12	C	A	A	A	312	24	PKP2	2	2
SLC6A13	6540	broad.mit.edu	37	12	333247	333247	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:333247G>T	uc001qic.1	-	c.1222C>A	c.(1222-1224)CAC>AAC	p.H408N	SLC6A13_uc009zdj.1_Missense_Mutation_p.H398N|SLC6A13_uc010sdl.1_Missense_Mutation_p.H316N	NM_016615	NP_057699	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter	408					neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)											0.107143	6.407276	19.279485	9	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	333247	333247	15173	12	G	T	T	T	585	45	SLC6A13	2	2
KIF21A	55605	broad.mit.edu	37	12	39751055	39751055	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:39751055C>A	uc001rly.2	-	c.1400G>T	c.(1399-1401)AGA>ATA	p.R467I	KIF21A_uc001rlx.2_Missense_Mutation_p.R467I|KIF21A_uc001rlz.2_Missense_Mutation_p.R467I|KIF21A_uc010skl.1_Missense_Mutation_p.R467I|KIF21A_uc001rma.1_Missense_Mutation_p.R475I	NM_017641	NP_060111	Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	467	Potential.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|lung(1)|pancreas(1)	6		Lung NSC(34;0.179)|all_lung(34;0.213)												0.211538	69.876563	81.891674	33	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39751055	39751055	8599	12	C	A	A	A	416	32	KIF21A	2	2
CNTN1	1272	broad.mit.edu	37	12	41316138	41316138	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:41316138C>A	uc001rmm.1	+	c.308C>A	c.(307-309)CCT>CAT	p.P103H	CNTN1_uc009zjy.1_Missense_Mutation_p.P103H|CNTN1_uc001rmn.1_Missense_Mutation_p.P92H|CNTN1_uc001rmo.2_Missense_Mutation_p.P103H	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor	103	Ig-like C2-type 1.				axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				ovary(3)|lung(2)|large_intestine(1)	6	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)								952				0.203252	51.793126	61.863822	25	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41316138	41316138	3778	12	C	A	A	A	312	24	CNTN1	2	2
PRICKLE1	144165	broad.mit.edu	37	12	42860072	42860072	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:42860072C>A	uc010skv.1	-	c.699G>T	c.(697-699)AAG>AAT	p.K233N	PRICKLE1_uc001rnl.2_Missense_Mutation_p.K233N|PRICKLE1_uc010skw.1_Missense_Mutation_p.K233N|PRICKLE1_uc001rnm.2_Missense_Mutation_p.K233N	NM_001144881	NP_001138353	Q96MT3	PRIC1_HUMAN	prickle homolog 1	233	LIM zinc-binding 2.				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination	cytosol|nuclear membrane	zinc ion binding			ovary(3)	3	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)										0.134146	12.681618	23.324588	11	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42860072	42860072	12929	12	C	A	A	A	311	24	PRICKLE1	2	2
ANO6	196527	broad.mit.edu	37	12	45771878	45771878	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:45771878G>T	uc010slf.1	+	c.1210G>T	c.(1210-1212)GTA>TTA	p.V404L	ANO6_uc001roo.2_Missense_Mutation_p.V383L|ANO6_uc010sld.1_Missense_Mutation_p.V383L|ANO6_uc010sle.1_Missense_Mutation_p.V383L|ANO6_uc010slg.1_Missense_Mutation_p.V365L	NM_001142678	NP_001136150	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform b	383	Helical; (Potential).				activation of blood coagulation via clotting cascade	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2														0.169935	52.692645	68.433975	26	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45771878	45771878	709	12	G	T	T	T	468	36	ANO6	2	2
ANO6	196527	broad.mit.edu	37	12	45771893	45771893	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:45771893T>A	uc010slf.1	+	c.1225T>A	c.(1225-1227)TGG>AGG	p.W409R	ANO6_uc001roo.2_Missense_Mutation_p.W388R|ANO6_uc010sld.1_Missense_Mutation_p.W388R|ANO6_uc010sle.1_Missense_Mutation_p.W388R|ANO6_uc010slg.1_Missense_Mutation_p.W370R	NM_001142678	NP_001136150	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform b	388	Helical; (Potential).				activation of blood coagulation via clotting cascade	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2														0.157895	41.162591	55.945177	21	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45771893	45771893	709	12	T	A	A	A	663	51	ANO6	3	3
RAPGEF3	10411	broad.mit.edu	37	12	48134466	48134466	+	Silent	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:48134466G>C	uc001rpz.3	-	c.2190C>G	c.(2188-2190)CCC>CCG	p.P730P	RAPGEF3_uc001rpw.2_Silent_p.P23P|RAPGEF3_uc001rpx.2_Silent_p.P145P|RAPGEF3_uc010sln.1_Silent_p.P203P|RAPGEF3_uc001rpy.2_Intron|RAPGEF3_uc009zkp.2_Silent_p.P688P|RAPGEF3_uc009zkq.2_Silent_p.P688P	NM_001098531	NP_001092001	A8K2G5	A8K2G5_HUMAN	Rap guanine nucleotide exchange factor 3 isoform	688					regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex	cAMP-dependent protein kinase regulator activity|guanyl-nucleotide exchange factor activity				0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)										0.132353	12.4258	21.359919	9	59	KEEP	---	---	---	---	capture		Silent	SNP	48134466	48134466	13505	12	G	C	C	C	548	43	RAPGEF3	3	3
DDX23	9416	broad.mit.edu	37	12	49239371	49239371	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:49239371G>A	uc001rsm.2	-	c.195C>T	c.(193-195)TCC>TCT	p.S65S		NM_004818	NP_004809	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	65	Arg-rich.				cis assembly of pre-catalytic spliceosome	catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent RNA helicase activity|nucleic acid binding|protein binding			kidney(3)|ovary(1)|lung(1)	5														0.168224	68.553358	90.877533	36	178	KEEP	---	---	---	---	capture		Silent	SNP	49239371	49239371	4521	12	G	A	A	A	600	47	DDX23	2	2
LMBR1L	55716	broad.mit.edu	37	12	49491726	49491726	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:49491726C>A	uc001rth.3	-	c.1402_splice	c.e16+1	p.G468_splice	LMBR1L_uc001rtg.3_Splice_Site_SNP_p.G463_splice|LMBR1L_uc001rti.3_Splice_Site_SNP_p.G448_splice	NM_018113	NP_060583			lipocalin-interacting membrane receptor						endocytosis	integral to membrane|plasma membrane	receptor activity			pancreas(1)	1												OREG0021783	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.137168	51.168607	79.961075	31	195	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	49491726	49491726	9170	12	C	A	A	A	234	18	LMBR1L	5	2
TUBA1B	10376	broad.mit.edu	37	12	49521755	49521755	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:49521755C>A	uc001rtm.2	-	c.1342G>T	c.(1342-1344)GGA>TGA	p.G448*	TUBA1B_uc001rto.2_Nonsense_Mutation_p.G413*|TUBA1B_uc001rtk.2_Nonsense_Mutation_p.G413*|TUBA1B_uc001rtl.2_Nonsense_Mutation_p.G413*|TUBA1B_uc001rtn.2_Nonsense_Mutation_p.G295*	NM_006082	NP_006073	P68363	TBA1B_HUMAN	tubulin, alpha, ubiquitous	448					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding				0														0.164234	78.803383	108.143755	45	229	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	49521755	49521755	17299	12	C	A	A	A	312	24	TUBA1B	5	2
KCNH3	23416	broad.mit.edu	37	12	49951180	49951180	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:49951180T>G	uc001ruh.1	+	c.2696T>G	c.(2695-2697)CTG>CGG	p.L899R	KCNH3_uc010smj.1_Missense_Mutation_p.L839R	NM_012284	NP_036416	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H	899	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity|voltage-gated potassium channel activity				0														0.180328	21.260364	27.17157	11	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49951180	49951180	8338	12	T	G	G	G	715	55	KCNH3	4	4
KCNH3	23416	broad.mit.edu	37	12	49951281	49951281	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:49951281G>A	uc001ruh.1	+	c.2797G>A	c.(2797-2799)GGG>AGG	p.G933R	KCNH3_uc010smj.1_Missense_Mutation_p.G873R	NM_012284	NP_036416	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H	933	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity|voltage-gated potassium channel activity				0														0.162791	10.895087	15.556259	7	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49951281	49951281	8338	12	G	A	A	A	507	39	KCNH3	1	1
KCNA1	3736	broad.mit.edu	37	12	5021978	5021978	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5021978C>A	uc001qnh.2	+	c.1434C>A	c.(1432-1434)TGC>TGA	p.C478*		NM_000217	NP_000208	Q09470	KCNA1_HUMAN	potassium voltage-gated channel subfamily A	478					synaptic transmission	juxtaparanode region of axon|voltage-gated potassium channel complex	delayed rectifier potassium channel activity|potassium ion transmembrane transporter activity			ovary(1)	1					Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)									0.133047	44.153063	74.622202	31	202	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	5021978	5021978	8306	12	C	A	A	A	324	25	KCNA1	5	2
KCNA1	3736	broad.mit.edu	37	12	5022022	5022022	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5022022C>A	uc001qnh.2	+	c.1478C>A	c.(1477-1479)ACC>AAC	p.T493N		NM_000217	NP_000208	Q09470	KCNA1_HUMAN	potassium voltage-gated channel subfamily A	493	PDZ-binding (By similarity).				synaptic transmission	juxtaparanode region of axon|voltage-gated potassium channel complex	delayed rectifier potassium channel activity|potassium ion transmembrane transporter activity			ovary(1)	1					Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)									0.223602	82.663262	93.937811	36	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5022022	5022022	8306	12	C	A	A	A	234	18	KCNA1	2	2
LASS5	91012	broad.mit.edu	37	12	50529760	50529760	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:50529760G>A	uc001rwd.3	-	c.729C>T	c.(727-729)ATC>ATT	p.I243I	LASS5_uc001rwc.2_Silent_p.I162I|LASS5_uc001rwe.3_Silent_p.I184I|LASS5_uc001rwf.3_Non-coding_Transcript|LASS5_uc010smq.1_Silent_p.I99I	NM_147190	NP_671723	Q8N5B7	LASS5_HUMAN	LAG1 homolog, ceramide synthase 5	243	Lumenal (Potential).|TLC.				ceramide biosynthetic process|regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity				0														0.09205	6.861608	46.924449	22	217	KEEP	---	---	---	---	capture		Silent	SNP	50529760	50529760	8965	12	G	A	A	A	577	45	LASS5	2	2
SLC11A2	4891	broad.mit.edu	37	12	51390650	51390650	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:51390650C>A	uc001rxk.1	-	c.868G>T	c.(868-870)GGA>TGA	p.G290*	SLC11A2_uc001rxe.3_Nonsense_Mutation_p.G261*|SLC11A2_uc001rxd.3_Nonsense_Mutation_p.G110*|SLC11A2_uc001rxc.3_Nonsense_Mutation_p.G261*|SLC11A2_uc001rxf.2_Non-coding_Transcript|SLC11A2_uc001rxg.1_5'Flank|SLC11A2_uc010smx.1_Nonsense_Mutation_p.G257*|SLC11A2_uc001rxh.1_Nonsense_Mutation_p.G261*|SLC11A2_uc001rxj.1_Nonsense_Mutation_p.G261*|SLC11A2_uc001rxi.2_Nonsense_Mutation_p.G261*|SLC11A2_uc010smy.1_Nonsense_Mutation_p.G224*	NM_000617	NP_000608	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled	261	Helical; (Potential).				activation of caspase activity|cellular iron ion homeostasis|cellular response to oxidative stress|detection of oxygen|ferrous iron import|multicellular organismal iron ion homeostasis|response to hypoxia|response to iron ion	apical plasma membrane|basal part of cell|cell surface|cytoplasmic vesicle|early endosome|late endosome|late endosome membrane|lysosomal membrane|lysosome|nucleus|paraferritin complex|perinuclear region of cytoplasm|perinuclear region of cytoplasm|plasma membrane|recycling endosome|trans-Golgi network	cadmium ion transmembrane transporter activity|cadmium ion transmembrane transporter activity|cobalt ion transmembrane transporter activity|copper ion transmembrane transporter activity|ferrous iron transmembrane transporter activity|ferrous iron transmembrane transporter activity|lead ion transmembrane transporter activity|lead ion transmembrane transporter activity|manganese ion transmembrane transporter activity|manganese ion transmembrane transporter activity|nickel ion transmembrane transporter activity|protein binding|solute:hydrogen symporter activity|vanadium ion transmembrane transporter activity|zinc ion transmembrane transporter activity			large_intestine(1)	1														0.116505	12.542228	27.439442	12	91	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	51390650	51390650	14876	12	C	A	A	A	286	22	SLC11A2	5	2
KCNA5	3741	broad.mit.edu	37	12	5153695	5153695	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5153695G>T	uc001qni.2	+	c.382G>T	c.(382-384)GGG>TGG	p.G128W		NM_002234	NP_002225	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related	128						Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(2)|breast(2)	4														0.133333	10.717683	18.51064	8	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5153695	5153695	8311	12	G	T	T	T	507	39	KCNA5	1	1
SCN8A	6334	broad.mit.edu	37	12	52168053	52168053	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52168053C>G	uc001ryw.2	+	c.3726C>G	c.(3724-3726)ATC>ATG	p.I1242M	SCN8A_uc010snl.1_Missense_Mutation_p.I1107M|SCN8A_uc001rza.1_Non-coding_Transcript	NM_014191	NP_055006	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha	1242	Helical; Name=S2 of repeat III; (Potential).|III.				axon guidance|myelination|peripheral nervous system development	cytoplasmic membrane-bounded vesicle|node of Ranvier|voltage-gated sodium channel complex	ATP binding|voltage-gated sodium channel activity			ovary(7)	7				BRCA - Breast invasive adenocarcinoma(357;0.181)	Lamotrigine(DB00555)									0.06383	-3.763038	33.44768	12	176	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52168053	52168053	14406	12	C	G	G	G	408	32	SCN8A	3	3
KRT5	3852	broad.mit.edu	37	12	52911461	52911461	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52911461C>A	uc001san.2	-	c.1005G>T	c.(1003-1005)CTG>CTT	p.L335L	KRT5_uc009zmh.2_Silent_p.L335L	NM_000424	NP_000415	P13647	K2C5_HUMAN	keratin 5	335	Linker 12.|Rod.				epidermis development|hemidesmosome assembly	cytosol|keratin filament	protein binding|structural constituent of cytoskeleton				0				BRCA - Breast invasive adenocarcinoma(357;0.189)										0.176056	46.076276	60.138533	25	117	KEEP	---	---	---	---	capture		Silent	SNP	52911461	52911461	8794	12	C	A	A	A	262	21	KRT5	2	2
KRT71	112802	broad.mit.edu	37	12	52943891	52943891	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52943891T>C	uc001sao.2	-	c.578A>G	c.(577-579)GAG>GGG	p.E193G		NM_033448	NP_258259	Q3SY84	K2C71_HUMAN	keratin 71	193	Coil 1B.|Rod.						structural molecule activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(357;0.194)										0.097166	26.540143	66.679855	24	223	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52943891	52943891	8799	12	T	C	C	C	702	54	KRT71	4	4
KRT72	140807	broad.mit.edu	37	12	52992867	52992867	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52992867C>A	uc001sar.2	-	c.456G>T	c.(454-456)GTG>GTT	p.V152V	KRT72_uc001saq.2_Silent_p.V152V|KRT72_uc010sns.1_Silent_p.V152V|KRT72_uc010snt.1_5'UTR	NM_001146225	NP_001139697	Q14CN4	K2C72_HUMAN	keratin 72 isoform 1	152	Coil 1A.|Rod.					keratin filament	structural molecule activity			ovary(5)|pancreas(1)	6				BRCA - Breast invasive adenocarcinoma(357;0.195)										0.144928	29.79459	46.556189	20	118	KEEP	---	---	---	---	capture		Silent	SNP	52992867	52992867	8800	12	C	A	A	A	314	25	KRT72	2	2
HOXC12	3228	broad.mit.edu	37	12	54350313	54350313	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:54350313G>C	uc010soq.1	+	c.812G>C	c.(811-813)AGA>ACA	p.R271T		NM_173860	NP_776272	P31275	HXC12_HUMAN	homeobox C12	271	Homeobox.				multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0														0.071429	-3.721419	44.25675	18	234	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54350313	54350313	7603	12	G	C	C	C	429	33	HOXC12	3	3
PDE1B	5153	broad.mit.edu	37	12	54963069	54963070	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:54963069_54963070GG>TT	uc001sgd.1	+	c.329_330GG>TT	c.(328-330)CGG>CTT	p.R110L	PDE1B_uc010soz.1_5'UTR|PDE1B_uc010spa.1_Missense_Mutation_p.R69L|PDE1B_uc001sgf.2_5'UTR|PDE1B_uc001sge.2_Missense_Mutation_p.R90L|PDE1B_uc009znq.2_Intron	NM_000924	NP_000915	Q01064	PDE1B_HUMAN	phosphodiesterase 1B isoform 1	110					activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation	cytosol|nucleus	3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(1)	1														0.094737	5.516443	21.17331	9	86	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	54963069	54963070	12055	12	GG	TT	TT	TT	507	39	PDE1B	1	1
NACA	4666	broad.mit.edu	37	12	57106635	57106635	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57106635C>G	uc009zoy.1	-	c.6157G>C	c.(6157-6159)GTG>CTG	p.V2053L	NACA_uc001slz.2_Missense_Mutation_p.V190L|NACA_uc001sly.2_Missense_Mutation_p.V190L|NACA_uc001smc.2_Missense_Mutation_p.V190L|NACA_uc001sma.2_Missense_Mutation_p.V900L|NACA_uc001smb.2_Missense_Mutation_p.V190L|NACA_uc010squ.1_Non-coding_Transcript	NM_001113203	NP_001106674	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha	190	UBA.				interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1										449				0.065327	-3.297408	35.745662	13	186	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57106635	57106635	10528	12	C	G	G	G	221	17	NACA	3	3
ANO2	57101	broad.mit.edu	37	12	5724381	5724381	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5724381G>T	uc001qnm.2	-	c.1899C>A	c.(1897-1899)CCC>CCA	p.P633P		NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2	638	Helical; (Potential).					chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7														0.288889	33.7543	35.553709	13	32	KEEP	---	---	---	---	capture		Silent	SNP	5724381	5724381	705	12	G	T	T	T	600	47	ANO2	2	2
SDR9C7	121214	broad.mit.edu	37	12	57317743	57317743	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57317743G>T	uc010sqw.1	-	c.816C>A	c.(814-816)AGC>AGA	p.S272R		NM_148897	NP_683695	Q8NEX9	DR9C7_HUMAN	short chain dehydrogenase/reductase family 9C,	272					oxidation-reduction process	cytoplasm	binding|oxidoreductase activity			central_nervous_system(1)	1														0.091743	0.666822	18.990961	10	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57317743	57317743	14460	12	G	T	T	T	542	42	SDR9C7	2	2
MYO1A	4640	broad.mit.edu	37	12	57431662	57431662	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57431662C>A	uc001smw.3	-	c.1952G>T	c.(1951-1953)GGG>GTG	p.G651V	MYO1A_uc010sqz.1_Missense_Mutation_p.G489V|MYO1A_uc009zpd.2_Missense_Mutation_p.G651V	NM_005379	NP_005370	Q9UBC5	MYO1A_HUMAN	myosin IA	651	Myosin head-like.				sensory perception of sound|vesicle localization	brush border|cortical actin cytoskeleton|filamentous actin|lateral plasma membrane|microvillus|myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|urinary_tract(1)|skin(1)	4														0.175439	19.416924	25.078142	10	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57431662	57431662	10463	12	C	A	A	A	286	22	MYO1A	2	2
STAT6	6778	broad.mit.edu	37	12	57496082	57496082	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57496082C>A	uc009zpg.2	-	c.1650G>T	c.(1648-1650)CAG>CAT	p.Q550H	STAT6_uc009zpe.2_Missense_Mutation_p.Q501H|STAT6_uc009zpf.2_Missense_Mutation_p.Q501H|STAT6_uc001sna.2_Missense_Mutation_p.Q501H|STAT6_uc010srb.1_Missense_Mutation_p.Q391H|STAT6_uc010src.1_Missense_Mutation_p.Q391H|STAT6_uc010srd.1_Missense_Mutation_p.Q391H	NM_003153	NP_003144	P42226	STAT6_HUMAN	signal transducer and activator of transcription	501					regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(2)|lung(1)	3										241				0.164634	101.046466	136.242638	54	274	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57496082	57496082	15790	12	C	A	A	A	259	20	STAT6	2	2
LRP1	4035	broad.mit.edu	37	12	57559898	57559898	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57559898G>T	uc001snd.2	+	c.2703G>T	c.(2701-2703)AAG>AAT	p.K901N	LRP1_uc009zph.1_5'Flank|LRP1_uc009zpi.1_5'Flank	NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	901	Extracellular (Potential).|LDL-receptor class A 4.				apoptotic cell clearance|multicellular organismal development|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein particle receptor binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(7)|large_intestine(2)|pancreas(2)|skin(1)|central_nervous_system(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)					1456				0.128205	12.265514	22.853747	10	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57559898	57559898	9324	12	G	T	T	T	464	36	LRP1	2	2
KIF5A	3798	broad.mit.edu	37	12	57965898	57965898	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57965898C>A	uc001sor.1	+	c.1417C>A	c.(1417-1419)CTG>ATG	p.L473M	KIF5A_uc010srr.1_Missense_Mutation_p.L384M	NM_004984	NP_004975	Q12840	KIF5A_HUMAN	kinesin family member 5A	473					blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)	2														0.125	9.952461	18.748795	8	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57965898	57965898	8616	12	C	A	A	A	311	24	KIF5A	2	2
PIP4K2C	79837	broad.mit.edu	37	12	57987870	57987870	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57987870C>A	uc001sou.2	+	c.237C>A	c.(235-237)AGC>AGA	p.S79R	PIP4K2C_uc001sot.2_Missense_Mutation_p.S79R|PIP4K2C_uc010srs.1_Missense_Mutation_p.S79R|PIP4K2C_uc010srt.1_Missense_Mutation_p.S79R	NM_001146258	NP_001139730	Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	79	PIPK.					cytoplasm|membrane	1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|identical protein binding			central_nervous_system(2)|lung(1)	3	Melanoma(17;0.122)									258				0.147541	13.630054	20.913992	9	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57987870	57987870	12362	12	C	A	A	A	363	28	PIP4K2C	2	2
VWF	7450	broad.mit.edu	37	12	6125812	6125812	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:6125812G>A	uc001qnn.1	-	c.5181C>T	c.(5179-5181)CTC>CTT	p.L1727L	VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	1727	VWFA 3; main binding site for collagens type I and III.				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7					Antihemophilic Factor(DB00025)									0.207407	59.316407	70.032772	28	107	KEEP	---	---	---	---	capture		Silent	SNP	6125812	6125812	17818	12	G	A	A	A	574	45	VWF	2	2
AVPR1A	552	broad.mit.edu	37	12	63543865	63543865	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:63543865G>T	uc001sro.1	-	c.752C>A	c.(751-753)ACG>AAG	p.T251K		NM_000706	NP_000697	P37288	V1AR_HUMAN	arginine vasopressin receptor 1A	251	Cytoplasmic (Potential).				activation of phospholipase C activity|elevation of cytosolic calcium ion concentration|generation of precursor metabolites and energy	endosome|integral to plasma membrane	protein kinase C binding|vasopressin receptor activity				0			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Vasopressin(DB00067)									0.151163	44.544498	64.597499	26	146	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63543865	63543865	1252	12	G	T	T	T	520	40	AVPR1A	1	1
CHD4	1108	broad.mit.edu	37	12	6710533	6710533	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:6710533C>A	uc001qpp.2	-	c.712G>T	c.(712-714)GTG>TTG	p.V238L	CHD4_uc001qpn.2_Missense_Mutation_p.V234L|CHD4_uc001qpo.2_Missense_Mutation_p.V241L	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	241					chromatin assembly or disassembly|chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	chromatin|microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|chromatin binding|DNA binding|zinc ion binding			central_nervous_system(2)	2						Colon(32;586 792 4568 16848 45314)								0.140541	37.142438	60.207628	26	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6710533	6710533	3461	12	C	A	A	A	234	18	CHD4	2	2
GNB3	2784	broad.mit.edu	37	12	6952808	6952808	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:6952808G>T	uc001qrd.2	+	c.443G>T	c.(442-444)TGC>TTC	p.C148F	GNB3_uc001qrc.2_Missense_Mutation_p.C104F|GNB3_uc009zfe.2_Missense_Mutation_p.C148F	NM_002075	NP_002066	P16520	GBB3_HUMAN	guanine nucleotide-binding protein, beta-3	148	WD 3.				cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of blood pressure|synaptic transmission	plasma membrane	GTPase activity|signal transducer activity				0														0.241071	64.686977	71.526126	27	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6952808	6952808	6788	12	G	T	T	T	598	46	GNB3	2	2
CPSF6	11052	broad.mit.edu	37	12	69656269	69656269	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:69656269A>G	uc001suu.3	+	c.1697A>G	c.(1696-1698)GAG>GGG	p.E566G	CPSF6_uc001sut.3_Missense_Mutation_p.E529G|CPSF6_uc010stk.1_Missense_Mutation_p.E161G	NM_007007	NP_008938	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6,	529	Sufficient for nuclear targeting.|Arg-rich.				mRNA polyadenylation|protein tetramerization	mRNA cleavage factor complex|paraspeckles|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding				0	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)											0.074074	1.313363	21.436033	8	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69656269	69656269	3968	12	A	G	G	G	143	11	CPSF6	4	4
CPSF6	11052	broad.mit.edu	37	12	69656271	69656271	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:69656271A>G	uc001suu.3	+	c.1699A>G	c.(1699-1701)AGG>GGG	p.R567G	CPSF6_uc001sut.3_Missense_Mutation_p.R530G|CPSF6_uc010stk.1_Missense_Mutation_p.R162G	NM_007007	NP_008938	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6,	530	Sufficient for nuclear targeting.|Arg-rich.				mRNA polyadenylation|protein tetramerization	mRNA cleavage factor complex|paraspeckles|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding				0	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)											0.07619	2.841143	22.138205	8	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69656271	69656271	3968	12	A	G	G	G	140	11	CPSF6	4	4
USP5	8078	broad.mit.edu	37	12	6969609	6969609	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:6969609A>T	uc001qri.3	+	c.1298A>T	c.(1297-1299)CAG>CTG	p.Q433L	USP5_uc001qrh.3_Missense_Mutation_p.Q433L	NM_001098536	NP_001092006	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 isoform 1	433					positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process	lysosome	cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|zinc ion binding				0														0.064516	-11.039899	25.614952	12	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6969609	6969609	17645	12	A	T	T	T	91	7	USP5	3	3
CNOT2	4848	broad.mit.edu	37	12	70713103	70713103	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70713103G>T	uc001svv.2	+	c.197G>T	c.(196-198)GGT>GTT	p.G66V	CNOT2_uc009zro.2_Missense_Mutation_p.G66V|CNOT2_uc009zrp.2_Missense_Mutation_p.G46V|CNOT2_uc009zrq.2_Missense_Mutation_p.G66V	NM_014515	NP_055330	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	66					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription from RNA polymerase II promoter, global|transcription, DNA-dependent	cytosol|nucleus	protein binding|RNA polymerase II transcription mediator activity				0	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)											0.108911	11.055418	26.355976	11	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70713103	70713103	3757	12	G	T	T	T	572	44	CNOT2	2	2
CNOT2	4848	broad.mit.edu	37	12	70713110	70713110	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70713110G>T	uc001svv.2	+	c.204G>T	c.(202-204)CTG>CTT	p.L68L	CNOT2_uc009zro.2_Silent_p.L68L|CNOT2_uc009zrp.2_Silent_p.L48L|CNOT2_uc009zrq.2_Silent_p.L68L	NM_014515	NP_055330	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	68					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription from RNA polymerase II promoter, global|transcription, DNA-dependent	cytosol|nucleus	protein binding|RNA polymerase II transcription mediator activity				0	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)											0.201923	50.712518	59.300125	21	83	KEEP	---	---	---	---	capture		Silent	SNP	70713110	70713110	3757	12	G	T	T	T	613	48	CNOT2	2	2
TSPAN8	7103	broad.mit.edu	37	12	71531812	71531812	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:71531812T>C	uc009zrt.1	-	c.365A>G	c.(364-366)TAT>TGT	p.Y122C	TSPAN8_uc001swk.1_Missense_Mutation_p.Y122C|TSPAN8_uc001swj.1_Missense_Mutation_p.Y122C	NM_004616	NP_004607	P19075	TSN8_HUMAN	transmembrane 4 superfamily member 3	122	Extracellular (Potential).				protein glycosylation	integral to membrane|lysosome	signal transducer activity			lung(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)							6				0.131944	42.134816	61.075005	19	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71531812	71531812	17204	12	T	C	C	C	637	49	TSPAN8	4	4
TRHDE	29953	broad.mit.edu	37	12	72680634	72680634	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:72680634C>T	uc001sxa.2	+	c.953C>T	c.(952-954)ACG>ATG	p.T318M		NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	318	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)	2														0.115607	20.701392	45.854223	20	153	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72680634	72680634	17023	12	C	T	T	T	247	19	TRHDE	1	1
CLSTN3	9746	broad.mit.edu	37	12	7290632	7290632	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:7290632G>A	uc001qss.2	+	c.1328G>A	c.(1327-1329)CGC>CAC	p.R443H	CLSTN3_uc001qsr.2_Missense_Mutation_p.R431H	NM_014718	NP_055533	Q9BQT9	CSTN3_HUMAN	calsyntenin 3 precursor	431	Extracellular (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(1)	1														0.1	4.636756	17.428822	8	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7290632	7290632	3701	12	G	A	A	A	494	38	CLSTN3	1	1
CD163	9332	broad.mit.edu	37	12	7649500	7649500	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:7649500C>G	uc001qsz.3	-	c.1008G>C	c.(1006-1008)CAG>CAC	p.Q336H	CD163_uc001qta.3_Missense_Mutation_p.Q336H|CD163_uc009zfw.2_Missense_Mutation_p.Q336H	NM_004244	NP_004235	Q86VB7	C163A_HUMAN	CD163 antigen isoform a	336	SRCR 3.|Extracellular (Potential).				acute-phase response	extracellular region|integral to plasma membrane	protein binding|scavenger receptor activity			ovary(6)|pancreas(1)|skin(1)	8														0.245902	37.992501	41.580898	15	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7649500	7649500	3094	12	C	G	G	G	311	24	CD163	3	3
NAV3	89795	broad.mit.edu	37	12	78400265	78400265	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:78400265G>T	uc001syp.2	+	c.947G>T	c.(946-948)GGG>GTG	p.G316V	NAV3_uc001syo.2_Missense_Mutation_p.G316V	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	316						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|kidney(1)|pancreas(1)	16										1091				0.189189	26.610091	33.296865	14	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78400265	78400265	10581	12	G	T	T	T	559	43	NAV3	2	2
NAV3	89795	broad.mit.edu	37	12	78510671	78510671	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:78510671G>T	uc001syp.2	+	c.2756G>T	c.(2755-2757)AGG>ATG	p.R919M	NAV3_uc001syo.2_Missense_Mutation_p.R919M|NAV3_uc010sub.1_Missense_Mutation_p.R419M|NAV3_uc009zsf.2_5'Flank	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	919						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|kidney(1)|pancreas(1)	16									p.R919K(MEWO-Tumor)	1091				0.101695	8.504375	27.183247	12	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78510671	78510671	10581	12	G	T	T	T	455	35	NAV3	2	2
NAV3	89795	broad.mit.edu	37	12	78513204	78513204	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:78513204T>A	uc001syp.2	+	c.3228T>A	c.(3226-3228)TCT>TCA	p.S1076S	NAV3_uc001syo.2_Silent_p.S1076S|NAV3_uc010sub.1_Silent_p.S576S|NAV3_uc009zsf.2_Silent_p.S84S	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	1076	Ser-rich.					nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|kidney(1)|pancreas(1)	16										1091				0.139535	19.042091	29.836157	12	74	KEEP	---	---	---	---	capture		Silent	SNP	78513204	78513204	10581	12	T	A	A	A	704	55	NAV3	3	3
NAV3	89795	broad.mit.edu	37	12	78542637	78542637	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:78542637C>G	uc001syp.2	+	c.4723C>G	c.(4723-4725)CGG>GGG	p.R1575G	NAV3_uc001syo.2_Missense_Mutation_p.R1575G|NAV3_uc010sub.1_Missense_Mutation_p.R1061G|NAV3_uc009zsf.2_Missense_Mutation_p.R406G	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	1575	Potential.					nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|kidney(1)|pancreas(1)	16									p.R1575W(HT115-Tumor)	1091				0.1	5.96906	12.361759	4	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78542637	78542637	10581	12	C	G	G	G	347	27	NAV3	3	3
PPFIA2	8499	broad.mit.edu	37	12	81747008	81747008	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:81747008T>A	uc001szo.1	-	c.1884A>T	c.(1882-1884)AGA>AGT	p.R628S	PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Non-coding_Transcript|PPFIA2_uc010suh.1_Non-coding_Transcript|PPFIA2_uc010sui.1_Non-coding_Transcript|PPFIA2_uc010suj.1_Non-coding_Transcript|PPFIA2_uc009zsi.1_Non-coding_Transcript|PPFIA2_uc010suf.1_Non-coding_Transcript|PPFIA2_uc009zsh.2_Non-coding_Transcript	NM_003625	NP_003616	O75334	LIPA2_HUMAN	PTPRF interacting protein alpha 2	628					cell-matrix adhesion	cell surface|cytoplasm	protein binding			ovary(3)|lung(2)|pancreas(1)	6														0.183099	23.932403	30.629228	13	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81747008	81747008	12740	12	T	A	A	A	699	54	PPFIA2	3	3
ALX1	8092	broad.mit.edu	37	12	85677430	85677430	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:85677430C>A	uc001tae.3	+	c.307C>A	c.(307-309)CGA>AGA	p.R103R		NM_006982	NP_008913	Q15699	ALX1_HUMAN	cartilage paired-class homeoprotein 1	103					brain development|cartilage condensation|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription corepressor activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(134;0.134)										0.104167	9.175315	24.14557	10	86	KEEP	---	---	---	---	capture		Silent	SNP	85677430	85677430	559	12	C	A	A	A	295	23	ALX1	1	1
PLXNC1	10154	broad.mit.edu	37	12	94618082	94618082	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:94618082C>T	uc001tdc.2	+	c.1781C>T	c.(1780-1782)TCA>TTA	p.S594L		NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor	594	Extracellular (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3														0.130952	24.513447	46.796624	22	146	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94618082	94618082	12552	12	C	T	T	T	377	29	PLXNC1	2	2
PLXNC1	10154	broad.mit.edu	37	12	94654449	94654449	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:94654449C>A	uc001tdc.2	+	c.3283C>A	c.(3283-3285)CTG>ATG	p.L1095M	PLXNC1_uc010sut.1_Missense_Mutation_p.L142M|PLXNC1_uc009zsv.2_5'Flank	NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor	1095	Cytoplasmic (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3														0.115942	10.455828	20.469873	8	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94654449	94654449	12552	12	C	A	A	A	259	20	PLXNC1	2	2
WNK1	65125	broad.mit.edu	37	12	994341	994341	+	Silent	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:994341A>C	uc001qio.3	+	c.4371A>C	c.(4369-4371)TCA>TCC	p.S1457S	WNK1_uc001qip.3_Silent_p.S1210S|WNK1_uc001qir.3_Silent_p.S630S	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1457					intracellular protein kinase cascade|ion transport|neuron development|protein phosphorylation	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			ovary(5)|breast(4)|large_intestine(1)|lung(1)|central_nervous_system(1)	12	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			Colon(19;451 567 6672 12618 28860)				913				0.102439	17.121157	49.417291	21	184	KEEP	---	---	---	---	capture		Silent	SNP	994341	994341	17951	12	A	C	C	C	80	7	WNK1	4	4
CLYBL	171425	broad.mit.edu	37	13	100543590	100543590	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:100543590G>A	uc001vok.2	+	c.946G>A	c.(946-948)GGG>AGG	p.G316R		NM_206808	NP_996531	Q8N0X4	CLYBL_HUMAN	citrate lyase beta like precursor	316					cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)													0.232	70.513845	78.736029	29	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100543590	100543590	3711	13	G	A	A	A	455	35	CLYBL	2	2
NALCN	259232	broad.mit.edu	37	13	101763040	101763040	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:101763040C>A	uc001vox.1	-	c.2295_splice	c.e20-1	p.R765_splice		NM_052867	NP_443099			voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.206186	40.245542	48.011933	20	77	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	101763040	101763040	10544	13	C	A	A	A	312	24	NALCN	5	2
NALCN	259232	broad.mit.edu	37	13	101944674	101944674	+	Silent	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:101944674G>C	uc001vox.1	-	c.843C>G	c.(841-843)GGC>GGG	p.G281G	NALCN_uc001voy.2_5'UTR|NALCN_uc001voz.2_Silent_p.G281G|NALCN_uc001vpa.2_Silent_p.G281G	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	281	Extracellular (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.087719	3.448785	13.231969	5	52	KEEP	---	---	---	---	capture		Silent	SNP	101944674	101944674	10544	13	G	C	C	C	431	34	NALCN	3	3
NALCN	259232	broad.mit.edu	37	13	102029341	102029341	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:102029341G>T	uc001vox.1	-	c.442C>A	c.(442-444)CTG>ATG	p.L148M	NALCN_uc001voy.2_De_novo_Start_OutOfFrame|NALCN_uc001voz.2_Missense_Mutation_p.L148M|NALCN_uc001vpa.2_Missense_Mutation_p.L148M	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	148	Helical; Voltage-sensor; Name=S4 of repeat I; (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.116667	6.885429	15.558602	7	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102029341	102029341	10544	13	G	T	T	T	464	36	NALCN	2	2
ITGBL1	9358	broad.mit.edu	37	13	102344976	102344976	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:102344976G>T	uc001vpb.2	+	c.1057G>T	c.(1057-1059)GAT>TAT	p.D353Y	ITGBL1_uc010agb.2_Missense_Mutation_p.D304Y|ITGBL1_uc001vpc.3_Missense_Mutation_p.D212Y	NM_004791	NP_004782	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat	353	VII.|Cysteine-rich tandem repeats.				cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)	1	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.271739	121.858222	130.509844	50	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102344976	102344976	8206	13	G	T	T	T	429	33	ITGBL1	2	2
FGF14	2259	broad.mit.edu	37	13	102375185	102375185	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:102375185G>C	uc001vpf.2	-	c.755C>G	c.(754-756)ACA>AGA	p.T252R	FGF14_uc001vpe.2_Missense_Mutation_p.T247R|FGF14_uc001vpd.1_5'Flank	NM_175929	NP_787125	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1B	247					cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			large_intestine(1)|ovary(1)	2	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.121212	15.351237	24.631577	8	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102375185	102375185	6080	13	G	C	C	C	624	48	FGF14	3	3
C13orf39	196541	broad.mit.edu	37	13	103338686	103338686	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:103338686G>A	uc001vpj.2	-	c.490C>T	c.(490-492)CTG>TTG	p.L164L	C13orf39_uc001vpk.2_Silent_p.L164L	NM_001010977	NP_001010977	Q5VZV1	MT21C_HUMAN	hypothetical protein LOC196541	164							methyltransferase activity				0														0.411765	146.346762	147.157511	49	70	KEEP	---	---	---	---	capture		Silent	SNP	103338686	103338686	1780	13	G	A	A	A	425	33	C13orf39	2	2
ERCC5	2073	broad.mit.edu	37	13	103514736	103514736	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:103514736G>T	uc001vpu.1	+	c.2599G>T	c.(2599-2601)GGG>TGG	p.G867W	ERCC5_uc010tjb.1_Missense_Mutation_p.G413W|ERCC5_uc001vpw.2_Missense_Mutation_p.G413W|ERCC5_uc010tjc.1_Non-coding_Transcript|ERCC5_uc010tjd.1_Missense_Mutation_p.G245W	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	413					negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|central_nervous_system(1)	5	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)									463				0.416667	113.652944	114.241279	40	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103514736	103514736	5409	13	G	T	T	T	455	35	ERCC5	2	2
LIG4	3981	broad.mit.edu	37	13	108863343	108863343	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:108863343G>C	uc001vqn.2	-	c.274C>G	c.(274-276)CTT>GTT	p.L92V	LIG4_uc001vqo.2_Missense_Mutation_p.L92V|LIG4_uc010agg.1_Missense_Mutation_p.L25V|LIG4_uc010agf.2_Missense_Mutation_p.L92V|LIG4_uc001vqp.2_Missense_Mutation_p.L92V	NM_002312	NP_002303	P49917	DNLI4_HUMAN	DNA ligase IV	92					cell cycle|cell division|cell proliferation|central nervous system development|chromosome organization|DNA ligation involved in DNA recombination|DNA ligation involved in DNA repair|DNA replication|double-strand break repair via nonhomologous end joining|in utero embryonic development|initiation of viral infection|isotype switching|negative regulation of neuron apoptosis|neuron apoptosis|nucleotide-excision repair, DNA gap filling|positive regulation of fibroblast proliferation|positive regulation of neurogenesis|pro-B cell differentiation|provirus integration|response to gamma radiation|response to X-ray|single strand break repair|somatic stem cell maintenance|T cell differentiation in thymus|T cell receptor V(D)J recombination	condensed chromosome|cytoplasm|DNA ligase IV complex|DNA-dependent protein kinase-DNA ligase 4 complex|focal adhesion|nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding|protein C-terminus binding				0	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)													0.173184	77.10799	95.170078	31	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108863343	108863343	9109	13	G	C	C	C	442	34	LIG4	3	3
COL4A2	1284	broad.mit.edu	37	13	111121563	111121563	+	Splice_Site_SNP	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:111121563G>T	uc001vqx.2	+	c.2096_splice	c.e28-1	p.G699_splice		NM_001846	NP_001837			alpha 2 type IV collagen preproprotein						angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			central_nervous_system(2)|ovary(1)	3	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)											0.333333	21.790849	22.381839	8	16	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	111121563	111121563	3828	13	G	T	T	T	455	35	COL4A2	5	2
TUBA3C	7278	broad.mit.edu	37	13	19753702	19753702	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:19753702C>A	uc009zzj.2	-	c.5G>T	c.(4-6)CGT>CTT	p.R2L		NM_006001	NP_005992	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	2					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(3)	3		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)										0.148148	30.037637	42.864237	16	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19753702	19753702	17301	13	C	A	A	A	247	19	TUBA3C	1	1
TPTE2	93492	broad.mit.edu	37	13	20039416	20039416	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:20039416G>T	uc001umd.2	-	c.655C>A	c.(655-657)CTA>ATA	p.L219I	TPTE2_uc009zzk.2_Non-coding_Transcript|TPTE2_uc009zzl.2_Missense_Mutation_p.L108I|TPTE2_uc001ume.2_Missense_Mutation_p.L142I|TPTE2_uc009zzm.2_5'UTR|TPTE2_uc010tcm.1_Non-coding_Transcript	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	219	Phosphatase tensin-type.					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)										0.089744	3.294813	43.068489	21	213	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20039416	20039416	16975	13	G	T	T	T	451	35	TPTE2	2	2
SACS	26278	broad.mit.edu	37	13	23915735	23915735	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:23915735C>A	uc001uon.2	-	c.2280G>T	c.(2278-2280)TTG>TTT	p.L760F	SACS_uc001uoo.2_Missense_Mutation_p.L613F|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Missense_Mutation_p.L613F	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	760					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)|skin(1)	11		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)						738				0.094891	4.56528	27.151952	13	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23915735	23915735	14284	13	C	A	A	A	376	29	SACS	2	2
MIPEP	4285	broad.mit.edu	37	13	24380111	24380112	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:24380111_24380112CC>AA	uc001uox.3	-	c.1825_1826GG>TT	c.(1825-1827)GGC>TTC	p.G609F		NM_005932	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase precursor	609					protein processing involved in protein targeting to mitochondrion|proteolysis	mitochondrial matrix	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)										0.165094	62.523555	85.069763	35	177	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	24380111	24380112	9982	13	CC	AA	AA	AA	338	26	MIPEP	2	2
ATP12A	479	broad.mit.edu	37	13	25266991	25266991	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25266991G>T	uc010aaa.2	+	c.1352G>T	c.(1351-1353)CGA>CTA	p.R451L	ATP12A_uc001upp.2_Missense_Mutation_p.R445L	NM_001676	NP_001667	P54707	AT12A_HUMAN	hydrogen/potassium-exchanging ATPase 12A	445	Cytoplasmic (Potential).				ATP biosynthetic process	hydrogen:potassium-exchanging ATPase complex	ATP binding|hydrogen:potassium-exchanging ATPase activity|metal ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|breast(1)	6		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)	Esomeprazole(DB00736)|Pantoprazole(DB00213)	Pancreas(156;1582 1935 18898 22665 26498)								0.154242	80.181521	124.796593	60	329	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25266991	25266991	1141	13	G	T	T	T	481	37	ATP12A	1	1
RNF17	56163	broad.mit.edu	37	13	25348978	25348978	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25348978C>A	uc001upr.2	+	c.253C>A	c.(253-255)CGC>AGC	p.R85S	RNF17_uc010tdd.1_Intron|RNF17_uc010aab.2_Non-coding_Transcript|RNF17_uc010tde.1_Missense_Mutation_p.R85S|RNF17_uc001ups.2_Missense_Mutation_p.R24S|RNF17_uc001upq.1_Missense_Mutation_p.R85S	NM_031277	NP_112567	Q9BXT8	RNF17_HUMAN	ring finger protein 17	85					multicellular organismal development	cytoplasm|nucleus	hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding			ovary(1)	1		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)										0.088608	2.962861	16.475988	7	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25348978	25348978	13938	13	C	A	A	A	247	19	RNF17	1	1
RASL11A	387496	broad.mit.edu	37	13	27847369	27847369	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:27847369A>T	uc001urd.1	+	c.467A>T	c.(466-468)CAG>CTG	p.Q156L		NM_206827	NP_996563	Q6T310	RSLBA_HUMAN	RAS-like, family 11, member A	156	Small GTPase-like.				positive regulation of transcription from RNA polymerase I promoter|small GTPase mediated signal transduction|transcription, DNA-dependent	membrane|nucleolus	GTP binding|GTPase activity				0		Lung SC(185;0.0161)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0173)|GBM - Glioblastoma multiforme(144;0.0557)|OV - Ovarian serous cystadenocarcinoma(117;0.152)|Epithelial(112;0.164)										0.288889	32.452772	34.25377	13	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27847369	27847369	13542	13	A	T	T	T	91	7	RASL11A	3	3
FLT1	2321	broad.mit.edu	37	13	28959104	28959104	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:28959104G>T	uc001usb.3	-	c.2034C>A	c.(2032-2034)ACC>ACA	p.T678T	FLT1_uc010aar.1_Silent_p.T678T	NM_002019	NP_002010	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1 isoform 1	678	Ig-like C2-type 7.|Extracellular (Potential).				cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(6)|central_nervous_system(5)|ovary(2)|urinary_tract(1)|breast(1)	15	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)					738				0.238372	95.372557	106.143729	41	131	KEEP	---	---	---	---	capture		Silent	SNP	28959104	28959104	6183	13	G	T	T	T	600	47	FLT1	2	2
SLC7A1	6541	broad.mit.edu	37	13	30110070	30110070	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:30110070C>A	uc001uso.2	-	c.256G>T	c.(256-258)GAG>TAG	p.E86*		NM_003045	NP_003036	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid	86	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|ion transport	integral to plasma membrane	receptor activity				0		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)									0.210526	24.465249	28.88762	12	45	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	30110070	30110070	15189	13	C	A	A	A	403	31	SLC7A1	5	1
B3GALTL	145173	broad.mit.edu	37	13	31903674	31903674	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:31903674C>T	uc010aaz.2	+	c.1366C>T	c.(1366-1368)CAT>TAT	p.H456Y	B3GALTL_uc001utn.3_Non-coding_Transcript|B3GALTL_uc001uto.3_Missense_Mutation_p.H61Y	NM_194318	NP_919299	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	456	Lumenal (Potential).				fucose metabolic process	endoplasmic reticulum membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(1)	1		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)										0.283465	84.529968	89.889934	36	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31903674	31903674	1273	13	C	T	T	T	377	29	B3GALTL	2	2
RXFP2	122042	broad.mit.edu	37	13	32360555	32360555	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:32360555C>T	uc001utt.2	+	c.965C>T	c.(964-966)CCT>CTT	p.P322L	RXFP2_uc010aba.2_Missense_Mutation_p.P281L	NM_130806	NP_570718	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	322	Extracellular (Potential).|LRR 8.					integral to membrane|plasma membrane					0		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)										0.193548	43.592533	51.74522	18	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32360555	32360555	14240	13	C	T	T	T	312	24	RXFP2	2	2
FRY	10129	broad.mit.edu	37	13	32783213	32783213	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:32783213G>T	uc001utx.2	+	c.4242G>T	c.(4240-4242)CTG>CTT	p.L1414L	FRY_uc010tdw.1_Non-coding_Transcript	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	1414					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)	6		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)										0.106383	10.147734	31.878966	15	126	KEEP	---	---	---	---	capture		Silent	SNP	32783213	32783213	6313	13	G	T	T	T	600	47	FRY	2	2
FRY	10129	broad.mit.edu	37	13	32805373	32805373	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:32805373G>T	uc001utx.2	+	c.5463G>T	c.(5461-5463)AAG>AAT	p.K1821N	FRY_uc010tdw.1_Non-coding_Transcript	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	1821					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)	6		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)										0.329897	81.055321	83.54914	32	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32805373	32805373	6313	13	G	T	T	T	425	33	FRY	2	2
BRCA2	675	broad.mit.edu	37	13	32913803	32913803	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:32913803G>T	uc001uub.1	+	c.5311G>T	c.(5311-5313)GGT>TGT	p.G1771C		NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	1771			G -> D (in BC; unknown pathological significance).		cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding|transcription activator activity			ovary(19)|endometrium(8)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|lung(3)|pancreas(3)|cervix(1)|salivary_gland(1)|liver(1)|skin(1)|kidney(1)	57		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)				677	TCGA Ovarian(8;0.087)			0.15	14.531153	21.582636	9	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32913803	32913803	1530	13	G	T	T	T	611	47	BRCA2	2	2
SPG20	23111	broad.mit.edu	37	13	36888510	36888510	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:36888510C>A	uc001uvn.2	-	c.1337G>T	c.(1336-1338)GGT>GTT	p.G446V	SPG20_uc010ten.1_Missense_Mutation_p.G436V|SPG20_uc001uvm.2_Missense_Mutation_p.G446V|SPG20_uc001uvo.2_Missense_Mutation_p.G446V|SPG20_uc001uvq.2_Missense_Mutation_p.G446V	NM_001142296	NP_001135768	Q8N0X7	SPG20_HUMAN	spartin	446					cell death	cytoplasm	ubiquitin protein ligase binding				0		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)										0.061224	-12.972708	26.430661	12	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36888510	36888510	15554	13	C	A	A	A	234	18	SPG20	2	2
FREM2	341640	broad.mit.edu	37	13	39435606	39435606	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:39435606G>T	uc001uwv.2	+	c.7558G>T	c.(7558-7560)GAG>TAG	p.E2520*	FREM2_uc001uww.2_Nonsense_Mutation_p.E606*	NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	2520	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)										0.230769	53.739442	60.653389	24	80	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	39435606	39435606	6292	13	G	T	T	T	429	33	FREM2	5	2
AKAP11	11215	broad.mit.edu	37	13	42876961	42876961	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:42876961G>A	uc001uys.1	+	c.4079G>A	c.(4078-4080)AGT>AAT	p.S1360N		NM_016248	NP_057332	Q9UKA4	AKA11_HUMAN	A-kinase anchor protein 11	1360					intracellular protein kinase cascade	microtubule organizing center	protein kinase A binding|protein phosphatase 1 binding			ovary(1)|central_nervous_system(1)	2		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)										0.202899	62.317595	73.633744	28	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42876961	42876961	450	13	G	A	A	A	468	36	AKAP11	2	2
EPSTI1	94240	broad.mit.edu	37	13	43462494	43462494	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:43462494G>T	uc001uyw.1	-	c.1125C>A	c.(1123-1125)GTC>GTA	p.V375V	EPSTI1_uc001uyx.1_3'UTR	NM_001002264	NP_001002264	Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 isoform 1	Error:Variant_position_missing_in_Q96J88_after_alignment										ovary(1)	1		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)										0.160494	22.417939	31.311075	13	68	KEEP	---	---	---	---	capture		Silent	SNP	43462494	43462494	5391	13	G	T	T	T	574	45	EPSTI1	2	2
ENOX1	55068	broad.mit.edu	37	13	43930241	43930241	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:43930241G>T	uc001uza.3	-	c.637C>A	c.(637-639)CGC>AGC	p.R213S	ENOX1_uc001uzb.3_Missense_Mutation_p.R213S|ENOX1_uc001uzc.3_Missense_Mutation_p.R213S|ENOX1_uc001uyz.3_5'UTR|ENOX1_uc010tfm.1_Missense_Mutation_p.R26S	NM_001127615	NP_001121087	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	213	RRM.				electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)	1		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)										0.271028	73.450624	78.496468	29	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43930241	43930241	5319	13	G	T	T	T	507	39	ENOX1	1	1
RCBTB2	1102	broad.mit.edu	37	13	49086998	49086998	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:49086998T>C	uc010tgg.1	-	c.398A>G	c.(397-399)TAT>TGT	p.Y133C	RCBTB2_uc001vch.2_Missense_Mutation_p.Y128C|RCBTB2_uc001vci.2_Missense_Mutation_p.Y104C|RCBTB2_uc010tgh.1_Intron|RCBTB2_uc001vcj.2_Missense_Mutation_p.Y132C|RCBTB2_uc010acv.1_Non-coding_Transcript|RCBTB2_uc010tgi.1_Missense_Mutation_p.Y104C	NM_001268	NP_001259	O95199	RCBT2_HUMAN	regulator of chromosome condensation and BTB	128	RCC1 2.						Ran guanyl-nucleotide exchange factor activity			ovary(2)|lung(2)	4		all_cancers(8;4.86e-71)|all_epithelial(8;2.11e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;2.3e-10)|Lung NSC(96;1.07e-07)|Breast(56;1.53e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.00826)|Myeloproliferative disorder(33;0.0179)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(99;1.8e-09)|LUSC - Lung squamous cell carcinoma(3;0.116)						264				0.327869	136.958126	140.163847	40	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49086998	49086998	13641	13	T	C	C	C	637	49	RCBTB2	4	4
CKAP2	26586	broad.mit.edu	37	13	53030734	53030734	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:53030734G>T	uc001vgv.2	+	c.147G>T	c.(145-147)ATG>ATT	p.M49I	CKAP2_uc001vgt.2_Missense_Mutation_p.M49I|CKAP2_uc001vgu.2_Missense_Mutation_p.M49I|CKAP2_uc010tha.1_Missense_Mutation_p.M1I	NM_001098525	NP_001091995	Q8WWK9	CKAP2_HUMAN	cytoskeleton associated protein 2 isoform 2	49					apoptosis|cell cycle	cytoplasm|microtubule|spindle pole				ovary(1)	1		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.6e-08)										0.223404	53.922729	60.53604	21	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53030734	53030734	3578	13	G	T	T	T	624	48	CKAP2	2	2
PCDH20	64881	broad.mit.edu	37	13	61985498	61985498	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:61985498A>T	uc001vid.3	-	c.2734T>A	c.(2734-2736)TGT>AGT	p.C912S	PCDH20_uc010thj.1_Missense_Mutation_p.C912S	NM_022843	NP_073754	Q8N6Y1	PCD20_HUMAN	protocadherin 20	885	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|breast(1)|central_nervous_system(1)	6		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)										0.21875	32.615168	37.280543	14	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61985498	61985498	11935	13	A	T	T	T	91	7	PCDH20	3	3
PCDH20	64881	broad.mit.edu	37	13	61985943	61985943	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:61985943C>A	uc001vid.3	-	c.2289G>T	c.(2287-2289)CCG>CCT	p.P763P	PCDH20_uc010thj.1_Silent_p.P763P	NM_022843	NP_073754	Q8N6Y1	PCD20_HUMAN	protocadherin 20	736	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|breast(1)|central_nervous_system(1)	6		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)										0.196721	50.926957	61.385088	24	98	KEEP	---	---	---	---	capture		Silent	SNP	61985943	61985943	11935	13	C	A	A	A	288	23	PCDH20	1	1
PCDH9	5101	broad.mit.edu	37	13	67801880	67801880	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:67801880C>A	uc001vik.2	-	c.693G>T	c.(691-693)CAG>CAT	p.Q231H	PCDH9_uc001vil.2_Missense_Mutation_p.Q231H|PCDH9_uc010thl.1_Missense_Mutation_p.Q231H|PCDH9_uc001vin.3_Missense_Mutation_p.Q231H	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	231	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)										0.147929	33.867845	53.98651	25	144	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67801880	67801880	11938	13	C	A	A	A	415	32	PCDH9	2	2
DACH1	1602	broad.mit.edu	37	13	72049909	72049909	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:72049909G>A	uc010thn.1	-	c.1943C>T	c.(1942-1944)ACG>ATG	p.T648M	DACH1_uc010tho.1_Missense_Mutation_p.T500M|DACH1_uc010thp.1_Missense_Mutation_p.T446M	NM_080759	NP_542937	Q9UI36	DACH1_HUMAN	dachshund homolog 1 isoform a	700	Potential.|Interaction with SIN3A (By similarity).				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)						202				0.266393	152.965008	164.99811	65	179	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72049909	72049909	4386	13	G	A	A	A	520	40	DACH1	1	1
MYCBP2	23077	broad.mit.edu	37	13	77632489	77632489	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:77632489C>A	uc001vkf.2	-	c.13079G>T	c.(13078-13080)GGG>GTG	p.G4360V	MYCBP2_uc010aev.2_Missense_Mutation_p.G3764V|MYCBP2_uc001vke.2_Missense_Mutation_p.G977V	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	4360					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)										0.095588	4.38141	26.696491	13	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77632489	77632489	10413	13	C	A	A	A	286	22	MYCBP2	2	2
MYCBP2	23077	broad.mit.edu	37	13	77669711	77669711	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:77669711C>A	uc001vkf.2	-	c.9867G>T	c.(9865-9867)ATG>ATT	p.M3289I	MYCBP2_uc010aev.2_Missense_Mutation_p.M2693I|MYCBP2_uc001vke.2_5'Flank	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	3289					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)										0.145455	26.522522	39.825696	16	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77669711	77669711	10413	13	C	A	A	A	325	25	MYCBP2	2	2
SLITRK1	114798	broad.mit.edu	37	13	84453896	84453896	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:84453896C>A	uc001vlk.2	-	c.1747G>T	c.(1747-1749)GCT>TCT	p.A583S		NM_052910	NP_443142	Q96PX8	SLIK1_HUMAN	slit and trk like 1 protein precursor	583	Extracellular (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)	3	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)										0.206897	28.677751	33.288014	12	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84453896	84453896	15240	13	C	A	A	A	351	27	SLITRK1	1	1
SOX21	11166	broad.mit.edu	37	13	95364147	95364147	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:95364147C>A	uc001vma.2	-	c.157G>T	c.(157-159)GAG>TAG	p.E53*		NM_007084	NP_009015	Q9Y651	SOX21_HUMAN	SRY-box 21	53	HMG box.				regulation of transcription from RNA polymerase II promoter|stem cell differentiation	nucleus	DNA binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity				0	all_neural(89;0.0646)|Medulloblastoma(90;0.163)													0.114583	9.460616	23.516232	11	85	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	95364147	95364147	15450	13	C	A	A	A	390	30	SOX21	5	2
DOCK9	23348	broad.mit.edu	37	13	99520503	99520503	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:99520503G>T	uc001vnt.2	-	c.3075C>A	c.(3073-3075)AGC>AGA	p.S1025R	DOCK9_uc001vnw.2_Missense_Mutation_p.S1024R|DOCK9_uc001vnv.1_Non-coding_Transcript|DOCK9_uc010tir.1_Missense_Mutation_p.S1025R|DOCK9_uc010tis.1_Missense_Mutation_p.S1024R|DOCK9_uc010tit.1_Missense_Mutation_p.S1025R|DOCK9_uc010tiq.1_5'Flank|DOCK9_uc010afu.1_Missense_Mutation_p.S871R	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a	1025					blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)													0.071429	-3.414407	12.482766	6	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99520503	99520503	4878	13	G	T	T	T	542	42	DOCK9	2	2
DYNC1H1	1778	broad.mit.edu	37	14	102446176	102446176	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:102446176C>T	uc001yks.2	+	c.639C>T	c.(637-639)ATC>ATT	p.I213I		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	213	Stem (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10														0.255034	91.470423	99.589088	38	111	KEEP	---	---	---	---	capture		Silent	SNP	102446176	102446176	5027	14	C	T	T	T	369	29	DYNC1H1	2	2
OR4Q3	441669	broad.mit.edu	37	14	20216346	20216346	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20216346C>T	uc010tkt.1	+	c.760C>T	c.(760-762)CCA>TCA	p.P254S		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	254	Helical; Name=6; (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)										0.086486	2.481907	34.504942	16	169	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20216346	20216346	11491	14	C	T	T	T	338	26	OR4Q3	2	2
OR4M1	441670	broad.mit.edu	37	14	20248994	20248994	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20248994C>A	uc010tku.1	+	c.513C>A	c.(511-513)CCC>CCA	p.P171P		NM_001005500	NP_001005500	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M,	171	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)										0.086826	5.400455	63.153943	29	305	KEEP	---	---	---	---	capture		Silent	SNP	20248994	20248994	11485	14	C	A	A	A	262	21	OR4M1	2	2
OR4K2	390431	broad.mit.edu	37	14	20344996	20344996	+	Silent	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20344996G>C	uc001vwh.1	+	c.570G>C	c.(568-570)GTG>GTC	p.V190V		NM_001005501	NP_001005501	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K,	190	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)										0.062016	-33.596172	69.613327	32	484	KEEP	---	---	---	---	capture		Silent	SNP	20344996	20344996	11482	14	G	C	C	C	600	47	OR4K2	3	3
OR4K1	79544	broad.mit.edu	37	14	20404275	20404275	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20404275G>A	uc001vwj.1	+	c.450G>A	c.(448-450)GCG>GCA	p.A150A		NM_001004063	NP_001004063	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K,	150	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)										0.091549	4.268679	28.138365	13	129	KEEP	---	---	---	---	capture		Silent	SNP	20404275	20404275	11477	14	G	A	A	A	496	39	OR4K1	1	1
OR11G2	390439	broad.mit.edu	37	14	20666364	20666364	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20666364C>A	uc010tlb.1	+	c.870C>A	c.(868-870)TAC>TAA	p.Y290*		NM_001005503	NP_001005503	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G,	290	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)										0.116935	37.799675	73.594663	29	219	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	20666364	20666364	11331	14	C	A	A	A	246	19	OR11G2	5	1
OR6S1	341799	broad.mit.edu	37	14	21109500	21109500	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:21109500C>T	uc001vxv.1	-	c.351G>A	c.(349-351)TTG>TTA	p.L117L		NM_001001968	NP_001001968	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S,	117	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)										0.096	8.898462	29.364779	12	113	KEEP	---	---	---	---	capture		Silent	SNP	21109500	21109500	11620	14	C	T	T	T	272	21	OR6S1	2	2
PSMB11	122706	broad.mit.edu	37	14	23512073	23512073	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23512073C>A	uc010ake.1	+	c.639C>A	c.(637-639)ACC>ACA	p.T213T		NM_001099780	NP_001093250	A5LHX3	PSB11_HUMAN	proteasome beta 11 subunit precursor	213					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00643)										0.114754	6.305515	15.209318	7	54	KEEP	---	---	---	---	capture		Silent	SNP	23512073	23512073	13129	14	C	A	A	A	275	22	PSMB11	2	2
NRL	4901	broad.mit.edu	37	14	24551747	24551747	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:24551747G>T	uc001wlo.2	-	c.311C>A	c.(310-312)CCA>CAA	p.P104Q	NRL_uc001wlp.2_Missense_Mutation_p.P104Q|NRL_uc001wlq.2_Missense_Mutation_p.P104Q	NM_006177	NP_006168	P54845	NRL_HUMAN	neural retina leucine zipper	104					response to stimulus|transcription from RNA polymerase II promoter|visual perception	nucleus	sequence-specific DNA binding|specific RNA polymerase II transcription factor activity				0				GBM - Glioblastoma multiforme(265;0.0181)										0.088608	1.617169	15.082648	7	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24551747	24551747	11061	14	G	T	T	T	611	47	NRL	2	2
GZMB	3002	broad.mit.edu	37	14	25101090	25101090	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:25101090G>C	uc001wps.2	-	c.574C>G	c.(574-576)CCA>GCA	p.P192A	GZMB_uc010ama.2_Missense_Mutation_p.P180A|GZMB_uc010amb.2_Non-coding_Transcript	NM_004131	NP_004122	P10144	GRAB_HUMAN	granzyme B precursor	192	Peptidase S1.				activation of pro-apoptotic gene products|cleavage of lamin|cytolysis|induction of apoptosis by intracellular signals	cytosol|immunological synapse|nucleus	protein binding|serine-type endopeptidase activity				0				GBM - Glioblastoma multiforme(265;0.028)										0.12605	46.042041	78.549986	30	208	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25101090	25101090	7196	14	G	C	C	C	559	43	GZMB	3	3
FAM177A1	283635	broad.mit.edu	37	14	35522515	35522515	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:35522515A>G	uc001wsq.2	+	c.197A>G	c.(196-198)GAA>GGA	p.E66G	FAM177A1_uc001wsp.2_Missense_Mutation_p.E43G	NM_173607	NP_775878	Q8N128	F177A_HUMAN	hypothetical protein LOC283635 isoform 1	43											0														0.127273	24.972984	39.873585	14	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35522515	35522515	5707	14	A	G	G	G	117	9	FAM177A1	4	4
FAM179B	23116	broad.mit.edu	37	14	45495057	45495057	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:45495057G>T	uc001wvw.2	+	c.3310G>T	c.(3310-3312)GTA>TTA	p.V1104L	FAM179B_uc001wvv.2_Missense_Mutation_p.V1104L|FAM179B_uc010anc.2_Non-coding_Transcript	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	1104	Ser-rich.						binding				0														0.131313	21.402766	34.48597	13	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45495057	45495057	5712	14	G	T	T	T	468	36	FAM179B	2	2
C14orf183	196913	broad.mit.edu	37	14	50550444	50550444	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:50550444G>A	uc010tqk.1	-	c.900C>T	c.(898-900)TCC>TCT	p.S300S		NM_001014830	NP_001014830	Q8WXQ3	CN183_HUMAN	hypothetical protein LOC196913	300											0														0.154321	45.574778	64.074615	25	137	KEEP	---	---	---	---	capture		Silent	SNP	50550444	50550444	1815	14	G	A	A	A	548	43	C14orf183	2	2
DDHD1	80821	broad.mit.edu	37	14	53529766	53529766	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:53529766C>A	uc001xai.2	-	c.1661G>T	c.(1660-1662)CGG>CTG	p.R554L	DDHD1_uc001xaj.2_Missense_Mutation_p.R561L|DDHD1_uc001xah.2_Missense_Mutation_p.R554L|DDHD1_uc001xag.2_Missense_Mutation_p.R136L|DDHD1_uc001xak.1_5'Flank	NM_001160148	NP_001153620	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1 isoform c	554					lipid catabolic process	cytoplasm	hydrolase activity|metal ion binding			ovary(1)	1	Breast(41;0.037)													0.159236	44.802091	62.149989	25	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53529766	53529766	4497	14	C	A	A	A	299	23	DDHD1	1	1
DDHD1	80821	broad.mit.edu	37	14	53619576	53619576	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:53619576C>A	uc001xai.2	-	c.241G>T	c.(241-243)GAC>TAC	p.D81Y	DDHD1_uc001xaj.2_Missense_Mutation_p.D81Y|DDHD1_uc001xah.2_Missense_Mutation_p.D81Y	NM_001160148	NP_001153620	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1 isoform c	81					lipid catabolic process	cytoplasm	hydrolase activity|metal ion binding			ovary(1)	1	Breast(41;0.037)													0.166667	9.661207	13.428187	6	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53619576	53619576	4497	14	C	A	A	A	390	30	DDHD1	2	2
BMP4	652	broad.mit.edu	37	14	54418875	54418875	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:54418875G>T	uc001xal.3	-	c.66C>A	c.(64-66)AGC>AGA	p.S22R	BMP4_uc010aoh.2_Missense_Mutation_p.S22R|BMP4_uc001xao.3_Missense_Mutation_p.S22R|BMP4_uc001xan.3_Missense_Mutation_p.S22R	NM_130851	NP_570912	P12644	BMP4_HUMAN	bone morphogenetic protein 4 preproprotein	22					activation of MAPKK activity|blood vessel endothelial cell proliferation involved in sprouting angiogenesis|BMP signaling pathway involved in nephric duct formation|branching involved in ureteric bud morphogenesis|bronchus development|bud dilation involved in lung branching|cardiac septum development|cartilage development|endocardial cushion development|epithelial cell proliferation involved in lung morphogenesis|intermediate mesodermal cell differentiation|lung alveolus development|lymphoid progenitor cell differentiation|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway|negative regulation of branching involved in ureteric bud morphogenesis|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of glomerular mesangial cell proliferation|negative regulation of glomerulus development|negative regulation of immature T cell proliferation in thymus|negative regulation of MAP kinase activity|negative regulation of metanephric comma-shaped body morphogenesis|negative regulation of metanephric S-shaped body morphogenesis|negative regulation of mitosis|negative regulation of myoblast differentiation|negative regulation of phosphorylation|negative regulation of striated muscle tissue development|negative regulation of thymocyte apoptosis|osteoblast differentiation|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cartilage development|positive regulation of collagen biosynthetic process|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of kidney development|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of smooth muscle cell proliferation|post-embryonic development|protein localization to nucleus|pulmonary artery endothelial tube morphogenesis|SMAD protein signal transduction|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway|steroid hormone mediated signaling pathway	extracellular space|proteinaceous extracellular matrix	BMP receptor binding|chemoattractant activity|cytokine activity|growth factor activity|transcription activator activity|transcription repressor activity				0									p.S22S(CW2-Tumor)	68				0.272727	83.17732	88.776667	33	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54418875	54418875	1487	14	G	T	T	T	542	42	BMP4	2	2
C14orf135	64430	broad.mit.edu	37	14	60591258	60591258	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:60591258A>T	uc001xer.3	+	c.1667A>T	c.(1666-1668)AAA>ATA	p.K556I	C14orf135_uc001xeq.2_Missense_Mutation_p.K556I|C14orf135_uc010apm.2_Non-coding_Transcript	NM_022495	NP_071940	Q63HM2	CN135_HUMAN	hepatitis C virus F protein-binding protein 2	790						integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)										0.278912	97.860446	104.295163	41	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60591258	60591258	1793	14	A	T	T	T	13	1	C14orf135	3	3
SNAPC1	6617	broad.mit.edu	37	14	62233743	62233743	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:62233743C>A	uc001xft.2	+	c.278C>A	c.(277-279)CCA>CAA	p.P93Q		NM_003082	NP_003073	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex,	93	SNAPC3-binding.				regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		NSCLC(27;223 907 37180 39193 46568)								0.16	15.165451	20.671273	8	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62233743	62233743	15334	14	C	A	A	A	273	21	SNAPC1	2	2
SYNE2	23224	broad.mit.edu	37	14	64408830	64408830	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:64408830G>T	uc001xgl.2	+	c.377G>T	c.(376-378)GGC>GTC	p.G126V	SYNE2_uc001xgk.2_Missense_Mutation_p.G126V|SYNE2_uc001xgm.2_Missense_Mutation_p.G126V	NM_182914	NP_878918	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	126	CH 1.|Cytoplasmic (Potential).|Actin-binding.				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)										0.220588	35.186482	40.075542	15	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64408830	64408830	15967	14	G	T	T	T	546	42	SYNE2	2	2
SYNE2	23224	broad.mit.edu	37	14	64635688	64635688	+	Silent	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:64635688A>C	uc001xgl.2	+	c.16999A>C	c.(16999-17001)AGA>CGA	p.R5667R	SYNE2_uc001xgm.2_Silent_p.R5667R|SYNE2_uc010apy.2_Silent_p.R2052R|SYNE2_uc001xgn.2_Silent_p.R629R|SYNE2_uc001xgo.2_Non-coding_Transcript|SYNE2_uc010aqa.2_5'UTR|SYNE2_uc001xgq.2_Silent_p.R32R	NM_182914	NP_878918	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5667	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)										0.43299	129.734369	130.114086	42	55	KEEP	---	---	---	---	capture		Silent	SNP	64635688	64635688	15967	14	A	C	C	C	88	7	SYNE2	4	4
ESR2	2100	broad.mit.edu	37	14	64746747	64746747	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:64746747C>T	uc001xha.1	-	c.487G>A	c.(487-489)GTC>ATC	p.V163I	ESR2_uc001xgu.2_Missense_Mutation_p.V163I|ESR2_uc001xgv.2_Missense_Mutation_p.V163I|ESR2_uc001xgw.2_Non-coding_Transcript|ESR2_uc001xgx.2_Missense_Mutation_p.V163I|ESR2_uc001xgy.1_Missense_Mutation_p.V163I|ESR2_uc001xgz.1_Missense_Mutation_p.V163I|ESR2_uc010aqb.1_Intron|ESR2_uc010aqc.1_Missense_Mutation_p.V163I	NM_001437	NP_001428	Q92731	ESR2_HUMAN	estrogen receptor beta isoform 1	163	NR C4-type.|Nuclear receptor.				cell-cell signaling|negative regulation of cell growth|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	mitochondrion|nucleoplasm	enzyme binding|estrogen receptor activity|receptor antagonist activity|sequence-specific DNA binding transcription factor activity|steroid binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Bicalutamide(DB01128)|Estradiol(DB00783)|Estramustine(DB01196)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)					196				0.35363	431.0657	439.145397	151	276	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64746747	64746747	5450	14	C	T	T	T	260	20	ESR2	2	2
PLEKHG3	26030	broad.mit.edu	37	14	65209851	65209851	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:65209851G>T	uc001xhp.2	+	c.3453G>T	c.(3451-3453)GGG>GGT	p.G1151G	PLEKHG3_uc001xhn.1_Silent_p.G974G|PLEKHG3_uc001xho.1_Silent_p.G1030G|PLEKHG3_uc010aqh.1_Silent_p.G572G|PLEKHG3_uc001xhq.1_Silent_p.G535G	NM_015549	NP_056364	A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G,	1030					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)										0.2607	159.617885	172.936086	67	190	KEEP	---	---	---	---	capture		Silent	SNP	65209851	65209851	12496	14	G	T	T	T	548	43	PLEKHG3	2	2
GALNTL1	57452	broad.mit.edu	37	14	69806305	69806305	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:69806305C>T	uc010aqu.1	+	c.1156C>T	c.(1156-1158)CGG>TGG	p.R386W	GALNTL1_uc001xla.1_Missense_Mutation_p.R386W|GALNTL1_uc001xlb.1_Missense_Mutation_p.R386W	NM_020692	NP_065743	Q8N428	GLTL1_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	386	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)	2				all cancers(60;0.00793)|BRCA - Breast invasive adenocarcinoma(234;0.0174)|OV - Ovarian serous cystadenocarcinoma(108;0.0656)										0.108696	13.504375	34.37439	15	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69806305	69806305	6485	14	C	T	T	T	295	23	GALNTL1	1	1
DPF3	8110	broad.mit.edu	37	14	73219972	73219972	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:73219972C>A	uc001xnc.2	-	c.301G>T	c.(301-303)GAA>TAA	p.E101*	DPF3_uc001xnf.2_Non-coding_Transcript|DPF3_uc010ari.1_Nonsense_Mutation_p.E101*|DPF3_uc010ttq.1_Nonsense_Mutation_p.E111*	NM_012074	NP_036206	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	101					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)										0.162162	10.525061	14.542154	6	31	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	73219972	73219972	4902	14	C	A	A	A	273	21	DPF3	5	2
ACOT6	641372	broad.mit.edu	37	14	74086095	74086096	+	Missense_Mutation	DNP	CT	GA	GA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:74086095_74086096CT>GA	uc001xop.2	+	c.176_177CT>GA	c.(175-177)CCT>CGA	p.P59R		NM_001037162	NP_001032239	Q3I5F7	ACOT6_HUMAN	acyl-CoA thioesterase 6	59						cytosol	carboxylesterase activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00331)										0.385542	198.250839	200.160424	64	102	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	74086095	74086096	155	14	CT	GA	GA	GA	312	24	ACOT6	3	3
PROX2	283571	broad.mit.edu	37	14	75330424	75330424	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:75330424G>T	uc001xqr.1	-	c.114C>A	c.(112-114)TCC>TCA	p.S38S	PROX2_uc001xqq.1_5'UTR	NM_001080408	NP_001073877	Q3B8N5	PROX2_HUMAN	prospero homeobox 2	38					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription regulator activity				0			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)										0.338235	58.893136	60.471943	23	45	KEEP	---	---	---	---	capture		Silent	SNP	75330424	75330424	13004	14	G	T	T	T	548	43	PROX2	2	2
NRXN3	9369	broad.mit.edu	37	14	79117635	79117635	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:79117635C>A	uc001xun.2	+	c.68C>A	c.(67-69)CCT>CAT	p.P23H	NRXN3_uc001xum.1_Non-coding_Transcript|NRXN3_uc010asv.1_Missense_Mutation_p.P157H	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	396	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)										0.068493	-7.7755	20.349218	10	136	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79117635	79117635	11072	14	C	A	A	A	312	24	NRXN3	2	2
NRXN3	9369	broad.mit.edu	37	14	79270162	79270162	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:79270162C>T	uc001xun.2	+	c.1125C>T	c.(1123-1125)AAC>AAT	p.N375N	NRXN3_uc001xum.1_Non-coding_Transcript|NRXN3_uc010asv.1_Silent_p.N509N	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	748	Laminin G-like 4.|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)										0.285714	61.817577	64.990655	22	55	KEEP	---	---	---	---	capture		Silent	SNP	79270162	79270162	11072	14	C	T	T	T	259	20	NRXN3	2	2
DIO2	1734	broad.mit.edu	37	14	80677676	80677676	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:80677676G>T	uc010tvp.1	-	c.140C>A	c.(139-141)ACT>AAT	p.T47N	DIO2_uc001xut.2_Non-coding_Transcript|DIO2_uc010asx.2_Missense_Mutation_p.T47N|DIO2_uc010tvq.1_Missense_Mutation_p.T47N|DIO2_uc010tvr.1_Missense_Mutation_p.T47N|DIO2_uc010asy.2_Missense_Mutation_p.T47N	NM_001007023	NP_001007024	Q92813	IOD2_HUMAN	deiodinase, iodothyronine, type II isoform b	47					hormone biosynthetic process|oxidation-reduction process|selenocysteine incorporation|thyroid hormone generation	integral to membrane|plasma membrane	selenium binding|thyroxine 5'-deiodinase activity|ubiquitin protein ligase binding				0				BRCA - Breast invasive adenocarcinoma(234;0.0281)										0.205128	17.575175	20.723775	8	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80677676	80677676	4704	14	G	T	T	T	468	36	DIO2	2	2
TRIP11	9321	broad.mit.edu	37	14	92480596	92480596	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:92480596T>A	uc001xzy.2	-	c.1149A>T	c.(1147-1149)TCA>TCT	p.S383S	TRIP11_uc010auf.1_Silent_p.S148S	NM_004239	NP_004230	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	383	Potential.				transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|kidney(2)|central_nervous_system(1)|breast(1)|skin(1)	11				COAD - Colon adenocarcinoma(157;0.223)		Ovarian(84;609 1888 9852 42686)				1481				0.404959	150.351202	151.306718	49	72	KEEP	---	---	---	---	capture		Silent	SNP	92480596	92480596	17105	14	T	A	A	A	704	55	TRIP11	3	3
SERPINA6	866	broad.mit.edu	37	14	94772489	94772489	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:94772489C>T	uc001ycv.2	-	c.951G>A	c.(949-951)GAG>GAA	p.E317E	SERPINA6_uc010auv.2_Non-coding_Transcript	NM_001756	NP_001747	P08185	CBG_HUMAN	corticosteroid binding globulin precursor	317					regulation of proteolysis|transport	extracellular space	serine-type endopeptidase inhibitor activity|steroid binding			skin(2)|ovary(1)|central_nervous_system(1)	4		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)									0.067961	-4.2538	15.638357	7	96	KEEP	---	---	---	---	capture		Silent	SNP	94772489	94772489	14581	14	C	T	T	T	311	24	SERPINA6	2	2
SERPINA11	256394	broad.mit.edu	37	14	94915071	94915071	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:94915071A>T	uc001ydd.1	-	c.41T>A	c.(40-42)CTG>CAG	p.L14Q		NM_001080451	NP_001073920	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1	14					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			kidney(1)	1				COAD - Colon adenocarcinoma(157;0.211)										0.110345	11.993439	33.80093	16	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94915071	94915071	14576	14	A	T	T	T	91	7	SERPINA11	3	3
ATG2B	55102	broad.mit.edu	37	14	96781496	96781496	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:96781496C>G	uc001yfi.2	-	c.3637G>C	c.(3637-3639)GAG>CAG	p.E1213Q		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	1213										ovary(1)|kidney(1)	2		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)										0.16129	13.45464	16.837892	5	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	96781496	96781496	1113	14	C	G	G	G	377	29	ATG2B	3	3
C14orf177	283598	broad.mit.edu	37	14	99183589	99183589	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:99183589T>C	uc001yfz.1	+	c.356T>C	c.(355-357)GTA>GCA	p.V119A		NM_182560	NP_872366	Q52M58	CN177_HUMAN	hypothetical protein LOC283598	119											0		Melanoma(154;0.128)												0.16	29.556899	37.808111	12	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99183589	99183589	1809	14	T	C	C	C	741	57	C14orf177	4	4
OR4F15	390649	broad.mit.edu	37	15	102358680	102358680	+	Nonsense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:102358680T>A	uc010uts.1	+	c.291T>A	c.(289-291)TGT>TGA	p.C97*		NM_001001674	NP_001001674	Q8NGB8	O4F15_HUMAN	olfactory receptor, family 4, subfamily F,	97	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)											0.176	43.584439	55.946298	22	103	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	102358680	102358680	11468	15	T	A	A	A	738	57	OR4F15	5	3
MAGEL2	54551	broad.mit.edu	37	15	23890547	23890547	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:23890547C>A	uc001ywj.3	-	c.534G>T	c.(532-534)GAG>GAT	p.E178D		NM_019066	NP_061939			MAGE-like protein 2												0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)										0.153846	18.143729	27.08822	12	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23890547	23890547	9572	15	C	A	A	A	415	32	MAGEL2	2	2
UBE3A	7337	broad.mit.edu	37	15	25585362	25585362	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:25585362T>A	uc001zaq.2	-	c.2377A>T	c.(2377-2379)ATC>TTC	p.I793F	UBE3A_uc001zar.2_Missense_Mutation_p.I770F|UBE3A_uc001zas.2_Missense_Mutation_p.I790F|UBE3A_uc001zat.2_Missense_Mutation_p.I770F	NM_000462	NP_000453	Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A isoform 2	793	HECT.				brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity				0		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)										0.169492	19.812897	25.912987	10	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25585362	25585362	17437	15	T	A	A	A	676	52	UBE3A	3	3
ATP10A	57194	broad.mit.edu	37	15	25940272	25940272	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:25940272C>A	uc010ayu.2	-	c.2782G>T	c.(2782-2784)GAC>TAC	p.D928Y		NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A	928	Cytoplasmic (Potential).				ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)						877				0.070423	-7.566434	19.477437	10	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25940272	25940272	1135	15	C	A	A	A	416	32	ATP10A	2	2
GABRB3	2562	broad.mit.edu	37	15	26806283	26806283	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:26806283G>T	uc001zbb.2	-	c.1044C>A	c.(1042-1044)CAC>CAA	p.H348Q	GABRB3_uc010uae.1_Missense_Mutation_p.H207Q|GABRB3_uc001zaz.2_Missense_Mutation_p.H292Q|GABRB3_uc001zba.2_Missense_Mutation_p.H292Q	NM_021912	NP_068712	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	292	Helical; (Probable).				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(1)|lung(1)|liver(1)|central_nervous_system(1)	4		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)									0.153846	40.649276	57.039328	22	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26806283	26806283	6419	15	G	T	T	T	568	44	GABRB3	2	2
TRPM1	4308	broad.mit.edu	37	15	31320594	31320594	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:31320594C>A	uc001zfm.2	-	c.3168G>T	c.(3166-3168)ATG>ATT	p.M1056I	TRPM1_uc010azy.2_Missense_Mutation_p.M963I|TRPM1_uc001zfl.2_Non-coding_Transcript	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	1056	Helical; (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)										0.112	9.654022	28.288636	14	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31320594	31320594	17136	15	C	A	A	A	273	21	TRPM1	2	2
TRPM1	4308	broad.mit.edu	37	15	31329943	31329943	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:31329943C>A	uc001zfm.2	-	c.2476G>T	c.(2476-2478)GCG>TCG	p.A826S	TRPM1_uc010azy.2_Missense_Mutation_p.A733S|TRPM1_uc001zfl.2_Non-coding_Transcript	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	826	Extracellular (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)										0.083333	2.923843	19.861701	8	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31329943	31329943	17136	15	C	A	A	A	351	27	TRPM1	1	1
TRPM1	4308	broad.mit.edu	37	15	31355409	31355409	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:31355409C>A	uc001zfm.2	-	c.811G>T	c.(811-813)GAG>TAG	p.E271*	TRPM1_uc010azy.2_Nonsense_Mutation_p.E184*|TRPM1_uc001zfl.2_Non-coding_Transcript	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	271	Extracellular (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)										0.201439	54.71382	66.23762	28	111	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	31355409	31355409	17136	15	C	A	A	A	416	32	TRPM1	5	2
RYR3	6263	broad.mit.edu	37	15	33941313	33941313	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:33941313C>A	uc001zhi.2	+	c.4019C>A	c.(4018-4020)CCA>CAA	p.P1340Q	RYR3_uc010bar.2_Missense_Mutation_p.P1340Q	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	1340	4 X approximate repeats.|B30.2/SPRY 3.|Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)										0.176471	53.425866	68.523935	27	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33941313	33941313	14250	15	C	A	A	A	273	21	RYR3	2	2
TMCO5A	145942	broad.mit.edu	37	15	38229100	38229100	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:38229100G>A	uc001zjw.2	+	c.193G>A	c.(193-195)GAG>AAG	p.E65K	TMCO5A_uc001zjv.1_Missense_Mutation_p.E65K|TMCO5A_uc010bbc.1_Missense_Mutation_p.E65K	NM_152453	NP_689666	Q8N6Q1	TMC5A_HUMAN	transmembrane and coiled-coil domains 5A	65	Potential.					integral to membrane				central_nervous_system(1)	1														0.186047	15.370937	19.346968	8	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38229100	38229100	16529	15	G	A	A	A	533	41	TMCO5A	2	2
DISP2	85455	broad.mit.edu	37	15	40659862	40659862	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:40659862C>A	uc001zlk.1	+	c.1549C>A	c.(1549-1551)CTG>ATG	p.L517M		NM_033510	NP_277045	A7MBM2	DISP2_HUMAN	dispatched B	517	Helical; (Potential).|SSD.				smoothened signaling pathway	integral to membrane				ovary(2)	2		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)										0.201754	48.255542	57.683268	23	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40659862	40659862	4719	15	C	A	A	A	363	28	DISP2	2	2
C15orf23	90417	broad.mit.edu	37	15	40678594	40678594	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:40678594C>A	uc001zll.2	+	c.336C>A	c.(334-336)CTC>CTA	p.L112L	C15orf23_uc010ucp.1_Silent_p.L112L|C15orf23_uc001zlo.2_Silent_p.L112L|C15orf23_uc001zlm.2_Non-coding_Transcript|C15orf23_uc001zln.2_Intron	NM_033286	NP_150628	Q9Y448	T4AF1_HUMAN	TRAF4 associated factor 1 isoform a	112						nucleus	protein binding			ovary(1)	1		all_cancers(109;2.34e-14)|all_epithelial(112;9.21e-12)|Lung NSC(122;2.95e-09)|all_lung(180;6.03e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;3.39e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0798)										0.115385	7.612317	18.986752	9	69	KEEP	---	---	---	---	capture		Silent	SNP	40678594	40678594	1835	15	C	A	A	A	405	32	C15orf23	2	2
BAHD1	22893	broad.mit.edu	37	15	40751731	40751731	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:40751731G>T	uc001zlu.2	+	c.1068G>T	c.(1066-1068)CCG>CCT	p.P356P	BAHD1_uc001zlt.2_Silent_p.P356P|BAHD1_uc010bbp.1_Silent_p.P356P|BAHD1_uc001zlv.2_Silent_p.P356P	NM_014952	NP_055767	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	356	Pro-rich.				heterochromatin formation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin silencing complex|chromosome	chromatin binding|DNA binding|protein binding				0		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)										0.276596	65.606689	69.831988	26	68	KEEP	---	---	---	---	capture		Silent	SNP	40751731	40751731	1318	15	G	T	T	T	470	37	BAHD1	1	1
TMEM87A	25963	broad.mit.edu	37	15	42529730	42529730	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:42529730C>G	uc010udd.1	-	c.768G>C	c.(766-768)CTG>CTC	p.L256L	TMEM87A_uc001zpf.3_Silent_p.L195L|TMEM87A_uc010bcu.1_Silent_p.L195L	NM_015497	NP_056312	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A isoform 1	256						integral to membrane				ovary(1)	1		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)										0.163265	20.566976	25.846675	8	41	KEEP	---	---	---	---	capture		Silent	SNP	42529730	42529730	16749	15	C	G	G	G	366	29	TMEM87A	3	3
TP53BP1	7158	broad.mit.edu	37	15	43749322	43749322	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:43749322G>A	uc001zrr.3	-	c.1484C>T	c.(1483-1485)TCT>TTT	p.S495F	TP53BP1_uc010udp.1_Missense_Mutation_p.S490F|TP53BP1_uc001zrq.3_Missense_Mutation_p.S495F|TP53BP1_uc001zrs.2_Missense_Mutation_p.S490F|TP53BP1_uc010udq.1_Missense_Mutation_p.S495F	NM_001141980	NP_001135452	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 1	490					double-strand break repair via homologous recombination|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome kinetochore|cytoplasm|nucleoplasm	protein binding|transcription activator activity			ovary(2)|large_intestine(1)|pancreas(1)|kidney(1)|skin(1)	6		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)						421				0.193548	26.760657	32.1973	12	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43749322	43749322	16925	15	G	A	A	A	429	33	TP53BP1	2	2
DUOX2	50506	broad.mit.edu	37	15	45386463	45386463	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:45386463T>A	uc010bea.2	-	c.4532A>T	c.(4531-4533)AAG>ATG	p.K1511M	DUOX2_uc001zun.2_Missense_Mutation_p.K1511M	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	1511	Cytoplasmic (Potential).				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)										0.087719	1.334288	11.131985	5	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45386463	45386463	4986	15	T	A	A	A	728	56	DUOX2	3	3
DUOX2	50506	broad.mit.edu	37	15	45387703	45387703	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:45387703G>A	uc010bea.2	-	c.4171C>T	c.(4171-4173)CCC>TCC	p.P1391S	DUOX2_uc001zun.2_Missense_Mutation_p.P1391S	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	1391	Cytoplasmic (Potential).				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)										0.168	39.813348	52.856797	21	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45387703	45387703	4986	15	G	A	A	A	559	43	DUOX2	2	2
DUOX2	50506	broad.mit.edu	37	15	45400285	45400285	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:45400285G>T	uc010bea.2	-	c.1534C>A	c.(1534-1536)CGG>AGG	p.R512R	DUOX2_uc001zun.2_Silent_p.R512R	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	512	Extracellular (Potential).|Peroxidase-like; mediates peroxidase activity (By similarity).				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)										0.162393	35.991934	48.638357	19	98	KEEP	---	---	---	---	capture		Silent	SNP	45400285	45400285	4986	15	G	T	T	T	493	38	DUOX2	1	1
SEMA6D	80031	broad.mit.edu	37	15	48056062	48056062	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:48056062G>T	uc010bek.2	+	c.763G>T	c.(763-765)GTG>TTG	p.V255L	SEMA6D_uc001zvw.2_Missense_Mutation_p.V255L|SEMA6D_uc001zvx.1_Missense_Mutation_p.V255L|SEMA6D_uc001zvy.2_Missense_Mutation_p.V255L|SEMA6D_uc001zvz.2_Missense_Mutation_p.V255L|SEMA6D_uc001zwa.2_Missense_Mutation_p.V255L|SEMA6D_uc001zwb.2_Missense_Mutation_p.V255L|SEMA6D_uc001zwc.2_Missense_Mutation_p.V255L	NM_153618	NP_705871	Q8NFY4	SEM6D_HUMAN	semaphorin 6D isoform 4 precursor	255	Sema.|Extracellular (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)										0.115183	26.643445	54.486293	22	169	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48056062	48056062	14528	15	G	T	T	T	520	40	SEMA6D	1	1
HDC	3067	broad.mit.edu	37	15	50546735	50546735	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:50546735A>T	uc001zxz.2	-	c.568T>A	c.(568-570)TCT>ACT	p.S190T	HDC_uc001zxy.2_5'Flank|HDC_uc010uff.1_Missense_Mutation_p.S190T|HDC_uc010bet.1_Missense_Mutation_p.S111T|HDC_uc010beu.1_Missense_Mutation_p.S190T	NM_002112	NP_002103	P19113	DCHS_HUMAN	histidine decarboxylase	190					catecholamine biosynthetic process|histidine metabolic process		histidine decarboxylase activity			large_intestine(2)|central_nervous_system(1)	3		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)	L-Histidine(DB00117)|Pyridoxal Phosphate(DB00114)	GBM(95;1627 1936 6910 9570)								0.102564	5.355526	17.623372	8	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50546735	50546735	7298	15	A	T	T	T	143	11	HDC	3	3
UNC13C	440279	broad.mit.edu	37	15	54306042	54306042	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:54306042T>A	uc002ack.2	+	c.942T>A	c.(940-942)CAT>CAA	p.H314Q		NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	314					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)						2691				0.185185	51.806868	64.3442	25	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54306042	54306042	17544	15	T	A	A	A	634	49	UNC13C	3	3
UNC13C	440279	broad.mit.edu	37	15	54914548	54914548	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:54914548G>T	uc002ack.2	+	c.6130G>T	c.(6130-6132)GGT>TGT	p.G2044C	UNC13C_uc002acm.2_5'UTR	NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	2044					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)						2691				0.086538	1.625374	19.605576	9	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54914548	54914548	17544	15	G	T	T	T	559	43	UNC13C	2	2
PRTG	283659	broad.mit.edu	37	15	56032678	56032678	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:56032678C>A	uc002adg.2	-	c.299G>T	c.(298-300)GGC>GTC	p.G100V		NM_173814	NP_776175	Q2VWP7	PRTG_HUMAN	protogenin precursor	100	Ig-like 1.				multicellular organismal development	integral to membrane				large_intestine(1)|ovary(1)	2				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)										0.195652	122.612526	150.455157	63	259	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56032678	56032678	13089	15	C	A	A	A	338	26	PRTG	2	2
ALDH1A2	8854	broad.mit.edu	37	15	58257929	58257929	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:58257929C>A	uc002aex.2	-	c.895G>T	c.(895-897)GCT>TCT	p.A299S	ALDH1A2_uc002aey.2_Missense_Mutation_p.A261S|ALDH1A2_uc010ugv.1_Missense_Mutation_p.A278S|ALDH1A2_uc010ugw.1_Missense_Mutation_p.A270S|ALDH1A2_uc002aew.2_Missense_Mutation_p.A203S	NM_003888	NP_003879	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 1	299					negative regulation of cell proliferation|neural tube development|oxidation-reduction process|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)									0.090909	2.225435	22.656923	11	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58257929	58257929	494	15	C	A	A	A	325	25	ALDH1A2	2	2
MYO1E	4643	broad.mit.edu	37	15	59494607	59494607	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:59494607C>A	uc002aga.2	-	c.1617_splice	c.e16-1	p.L539_splice		NM_004998	NP_004989			myosin IE						actin filament-based movement	myosin complex	actin binding|ATP binding|ATPase activity, coupled|calmodulin binding|microfilament motor activity			central_nervous_system(3)	3				all cancers(107;0.207)										0.099099	5.334096	23.183261	11	100	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	59494607	59494607	10467	15	C	A	A	A	312	24	MYO1E	5	2
VPS13C	54832	broad.mit.edu	37	15	62168014	62168014	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:62168014C>A	uc002agz.2	-	c.10255G>T	c.(10255-10257)GGG>TGG	p.G3419W	VPS13C_uc002aha.2_Missense_Mutation_p.G3376W|VPS13C_uc002ahb.1_Missense_Mutation_p.G3419W|VPS13C_uc002ahc.1_Missense_Mutation_p.G3376W	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	3419					protein localization					ovary(2)	2														0.12766	7.115886	13.470609	6	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62168014	62168014	17758	15	C	A	A	A	286	22	VPS13C	2	2
VPS13C	54832	broad.mit.edu	37	15	62320619	62320620	+	Splice_Site_DNP	DNP	CC	AA	AA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:62320619_62320620CC>AA	uc002agz.2	-	c.386_splice	c.e6-1	p.G129_splice	VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Splice_Site_DNP_p.G129_splice|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2														0.132353	12.823711	21.754931	9	59	KEEP	---	---	---	---	capture		Splice_Site_DNP	DNP	62320619	62320620	17758	15	CC	AA	AA	AA	338	26	VPS13C	5	2
RBPMS2	348093	broad.mit.edu	37	15	65041694	65041694	+	Splice_Site_SNP	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:65041694T>A	uc002anq.2	-	c.205_splice	c.e4-1	p.P69_splice		NM_194272	NP_919248			RNA binding protein with multiple splicing 2								nucleic acid binding|nucleotide binding				0														0.129496	23.462	42.032171	18	121	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	65041694	65041694	13633	15	T	A	A	A	689	53	RBPMS2	5	3
RASL12	51285	broad.mit.edu	37	15	65351719	65351719	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:65351719C>T	uc002aoi.1	-	c.198G>A	c.(196-198)CAG>CAA	p.Q66Q	RASL12_uc002aoj.1_Silent_p.Q47Q|RASL12_uc010uir.1_Silent_p.Q55Q	NM_016563	NP_057647	Q9NYN1	RASLC_HUMAN	RAS-like, family 12 protein	66					small GTPase mediated signal transduction	membrane	GTP binding|GTPase activity			skin(1)	1														0.09589	5.37176	17.326714	7	66	KEEP	---	---	---	---	capture		Silent	SNP	65351719	65351719	13544	15	C	T	T	T	363	28	RASL12	2	2
ITGA11	22801	broad.mit.edu	37	15	68643001	68643001	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:68643001C>G	uc010bib.2	-	c.1014G>C	c.(1012-1014)TTG>TTC	p.L338F	ITGA11_uc002ari.2_Missense_Mutation_p.L338F	NM_001004439	NP_001004439	Q9UKX5	ITA11_HUMAN	integrin, alpha 11 precursor	338	VWFA.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)									0.1	12.574163	28.55561	10	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68643001	68643001	8178	15	C	G	G	G	376	29	ITGA11	3	3
MYO9A	4649	broad.mit.edu	37	15	72186037	72186037	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:72186037C>A	uc002atl.3	-	c.5125G>T	c.(5125-5127)GGG>TGG	p.G1709W	MYO9A_uc002atn.1_Missense_Mutation_p.G1690W|MYO9A_uc002atk.2_Missense_Mutation_p.G433W|MYO9A_uc002atm.1_Missense_Mutation_p.G433W	NM_006901	NP_008832	B2RTY4	MYO9A_HUMAN	myosin IXA	1709	Tail.				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														0.086207	1.126614	11.191692	5	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72186037	72186037	10479	15	C	A	A	A	273	21	MYO9A	2	2
LMAN1L	79748	broad.mit.edu	37	15	75116016	75116016	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:75116016G>A	uc002ayt.1	+	c.1316G>A	c.(1315-1317)GGC>GAC	p.G439D	LMAN1L_uc010bke.1_Missense_Mutation_p.G427D|CPLX3_uc002ayu.1_5'Flank	NM_021819	NP_068591	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like precursor	439	Lumenal (Potential).					ER-Golgi intermediate compartment membrane|integral to membrane	sugar binding				0														0.11811	12.222857	30.4717	15	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75116016	75116016	9166	15	G	A	A	A	546	42	LMAN1L	2	2
NRG4	145957	broad.mit.edu	37	15	76254245	76254245	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:76254245T>C	uc002bbo.2	-	c.175A>G	c.(175-177)AGT>GGT	p.S59G	NRG4_uc010bkm.1_Non-coding_Transcript|NRG4_uc002bbn.2_Non-coding_Transcript|NRG4_uc010bkn.2_Non-coding_Transcript|NRG4_uc010bko.2_Non-coding_Transcript|NRG4_uc002bbp.2_Non-coding_Transcript	NM_138573	NP_612640	Q8WWG1	NRG4_HUMAN	neuregulin 4	59	Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	growth factor activity				0														0.134615	31.878282	45.337499	14	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76254245	76254245	11055	15	T	C	C	C	728	56	NRG4	4	4
LINGO1	84894	broad.mit.edu	37	15	77907381	77907381	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:77907381G>T	uc002bct.1	-	c.868C>A	c.(868-870)CGC>AGC	p.R290S	LINGO1_uc002bcu.1_Missense_Mutation_p.R284S	NM_032808	NP_116197	Q96FE5	LIGO1_HUMAN	leucine-rich repeat neuronal 6A	290	Extracellular (Potential).|LRR 9.				negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane				ovary(1)|lung(1)	2														0.112676	8.948077	19.464448	8	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77907381	77907381	9141	15	G	T	T	T	507	39	LINGO1	1	1
WDR61	80349	broad.mit.edu	37	15	78584957	78584957	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:78584957C>A	uc002bdn.2	-	c.319_splice	c.e5+1	p.V107_splice	WDR61_uc002bdo.2_Splice_Site_SNP_p.V107_splice|WDR61_uc010umz.1_Non-coding_Transcript|WDR61_uc010una.1_Missense_Mutation_p.G107V	NM_025234	NP_079510			WD repeat domain 61								protein binding			ovary(1)	1														0.122807	10.281515	18.221059	7	50	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	78584957	78584957	17885	15	C	A	A	A	234	18	WDR61	5	2
BNC1	646	broad.mit.edu	37	15	83931751	83931751	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:83931751G>T	uc002bjt.1	-	c.2252C>A	c.(2251-2253)ACA>AAA	p.T751K	BNC1_uc010uos.1_Missense_Mutation_p.T739K	NM_001717	NP_001708	Q01954	BNC1_HUMAN	basonuclin 1	751	C2H2-type 4.				epidermis development|positive regulation of cell proliferation|regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3														0.075949	-1.412792	13.147297	6	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83931751	83931751	1499	15	G	T	T	T	624	48	BNC1	2	2
AGBL1	123624	broad.mit.edu	37	15	87531247	87531247	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:87531247A>T	uc002blz.1	+	c.3113A>T	c.(3112-3114)CAT>CTT	p.H1038L		NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	1038					C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0														0.087805	9.095121	44.319364	18	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87531247	87531247	377	15	A	T	T	T	104	8	AGBL1	3	3
ANPEP	290	broad.mit.edu	37	15	90347593	90347593	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:90347593C>T	uc002bop.3	-	c.1070G>A	c.(1069-1071)TGG>TAG	p.W357*		NM_001150	NP_001141	P15144	AMPN_HUMAN	membrane alanine aminopeptidase precursor	357	Extracellular.|Metalloprotease.				angiogenesis|cell differentiation|interspecies interaction between organisms	cytosol|ER-Golgi intermediate compartment|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|receptor activity|zinc ion binding			ovary(3)	3	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)	NSCLC(30;827 977 2459 19669 26125)								0.120482	10.485403	22.217004	10	73	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	90347593	90347593	718	15	C	T	T	T	273	21	ANPEP	5	2
ANPEP	290	broad.mit.edu	37	15	90349243	90349243	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:90349243G>A	uc002bop.3	-	c.572C>T	c.(571-573)GCG>GTG	p.A191V		NM_001150	NP_001141	P15144	AMPN_HUMAN	membrane alanine aminopeptidase precursor	191	Extracellular.|Metalloprotease.				angiogenesis|cell differentiation|interspecies interaction between organisms	cytosol|ER-Golgi intermediate compartment|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|receptor activity|zinc ion binding			ovary(3)	3	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)	NSCLC(30;827 977 2459 19669 26125)								0.162791	33.520438	47.447367	21	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90349243	90349243	718	15	G	A	A	A	494	38	ANPEP	1	1
FURIN	5045	broad.mit.edu	37	15	91423004	91423004	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:91423004G>T	uc002bpu.1	+	c.1258G>T	c.(1258-1260)GTG>TTG	p.V420L		NM_002569	NP_002560	P09958	FURIN_HUMAN	furin preproprotein	420					cell proliferation|negative regulation of low-density lipoprotein particle receptor catabolic process|negative regulation of transforming growth factor-beta1 production|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|Notch signaling pathway|peptide biosynthetic process|peptidyl-glutamic acid carboxylation|positive regulation of membrane protein ectodomain proteolysis|post-translational protein modification|secretion by cell|signal peptide processing|transforming growth factor beta receptor signaling pathway|viral assembly, maturation, egress, and release	cell surface|Golgi lumen|Golgi membrane|integral to membrane|membrane raft|plasma membrane|trans-Golgi network|trans-Golgi network transport vesicle	metal ion binding|nerve growth factor binding|peptide binding|protease binding|serine-type endopeptidase activity|serine-type endopeptidase inhibitor activity			central_nervous_system(4)	4	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)							290				0.136	23.793282	39.83626	17	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91423004	91423004	6350	15	G	T	T	T	455	35	FURIN	2	2
ST8SIA2	8128	broad.mit.edu	37	15	92981651	92981651	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:92981651G>C	uc002bra.2	+	c.359G>C	c.(358-360)GGA>GCA	p.G120A	ST8SIA2_uc002brb.2_Missense_Mutation_p.G99A	NM_006011	NP_006002	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide	120	Lumenal (Potential).				axon guidance|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity				0	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)											0.132597	103.74584	151.191041	48	314	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92981651	92981651	15750	15	G	C	C	C	533	41	ST8SIA2	3	3
ATF7IP2	80063	broad.mit.edu	37	16	10574812	10574812	+	Silent	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:10574812T>C	uc002czu.2	+	c.1626T>C	c.(1624-1626)AAT>AAC	p.N542N	ATF7IP2_uc002czv.2_Missense_Mutation_p.M520T|ATF7IP2_uc010uyo.1_Non-coding_Transcript|ATF7IP2_uc010uyp.1_Silent_p.N86N|ATF7IP2_uc002czw.2_Silent_p.N542N|ATF7IP2_uc010uyq.1_Non-coding_Transcript	NM_024997	NP_079273	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting	542					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0														0.087379	9.100587	26.836463	9	94	KEEP	---	---	---	---	capture		Silent	SNP	10574812	10574812	1107	16	T	C	C	C	660	51	ATF7IP2	4	4
HN1L	90861	broad.mit.edu	37	16	1748976	1748976	+	Nonsense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1748976A>T	uc010uvi.1	+	c.634A>T	c.(634-636)AAA>TAA	p.K212*	HN1L_uc002cmg.2_Nonsense_Mutation_p.K184*|HN1L_uc010brt.2_Non-coding_Transcript|HN1L_uc010bru.2_3'UTR|HN1L_uc010uvj.1_3'UTR|HN1L_uc010uvk.1_Nonsense_Mutation_p.K171*	NM_144570	NP_653171	Q9H910	HN1L_HUMAN	hematological and neurological expressed 1-like	184						cytoplasm|nucleus					0														0.235669	79.830646	89.842461	37	120	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	1748976	1748976	7542	16	A	T	T	T	65	5	HN1L	5	3
GPR139	124274	broad.mit.edu	37	16	20043324	20043324	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20043324G>T	uc002dgu.1	-	c.795C>A	c.(793-795)ATC>ATA	p.I265I	GPR139_uc010vaw.1_Silent_p.I172I	NM_001002911	NP_001002911	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	265	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(2)	2														0.299213	88.679342	93.270016	38	89	KEEP	---	---	---	---	capture		Silent	SNP	20043324	20043324	6922	16	G	T	T	T	577	45	GPR139	2	2
UMOD	7369	broad.mit.edu	37	16	20352561	20352561	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20352561C>T	uc002dhb.2	-	c.1528G>A	c.(1528-1530)GTG>ATG	p.V510M	UMOD_uc002dgz.2_Missense_Mutation_p.V477M|UMOD_uc002dha.2_Missense_Mutation_p.V477M	NM_003361	NP_003352	P07911	UROM_HUMAN	uromodulin precursor	477	ZP.				cellular defense response|negative regulation of cell proliferation	anchored to membrane|apical plasma membrane|basolateral plasma membrane|cilium membrane|extrinsic to membrane|primary cilium|spindle pole	calcium ion binding			ovary(1)	1														0.2625	48.447903	52.525091	21	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20352561	20352561	17537	16	C	T	T	T	247	19	UMOD	1	1
UMOD	7369	broad.mit.edu	37	16	20362003	20362003	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20362003G>A	uc002dhb.2	-	c.57C>T	c.(55-57)ATC>ATT	p.I19I	UMOD_uc002dgz.2_Silent_p.I19I|UMOD_uc002dha.2_Silent_p.I19I	NM_003361	NP_003352	P07911	UROM_HUMAN	uromodulin precursor	19					cellular defense response|negative regulation of cell proliferation	anchored to membrane|apical plasma membrane|basolateral plasma membrane|cilium membrane|extrinsic to membrane|primary cilium|spindle pole	calcium ion binding			ovary(1)	1														0.388889	18.819728	19.014758	7	11	KEEP	---	---	---	---	capture		Silent	SNP	20362003	20362003	17537	16	G	A	A	A	577	45	UMOD	2	2
PDILT	204474	broad.mit.edu	37	16	20386220	20386220	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20386220G>T	uc002dhc.1	-	c.605C>A	c.(604-606)ACG>AAG	p.T202K		NM_174924	NP_777584	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis	202					cell differentiation|cell redox homeostasis|multicellular organismal development|spermatogenesis	endoplasmic reticulum	isomerase activity			large_intestine(1)	1														0.075949	-1.706418	27.39641	12	146	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20386220	20386220	12095	16	G	T	T	T	520	40	PDILT	1	1
ACSM2A	123876	broad.mit.edu	37	16	20471598	20471598	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20471598G>T	uc010bwe.2	+	c.162G>T	c.(160-162)TGG>TGT	p.W54C	ACSM2A_uc010bwd.1_Non-coding_Transcript|ACSM2A_uc010vax.1_Intron|ACSM2A_uc002dhf.3_Missense_Mutation_p.W54C|ACSM2A_uc002dhg.3_Missense_Mutation_p.W54C|ACSM2A_uc010vay.1_Intron	NM_001010845	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member	54					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			breast(1)	1														0.18	18.644496	23.4598	9	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20471598	20471598	184	16	G	T	T	T	559	43	ACSM2A	2	2
ACSM2B	348158	broad.mit.edu	37	16	20559428	20559428	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20559428G>T	uc002dhj.3	-	c.1054C>A	c.(1054-1056)CAG>AAG	p.Q352K	ACSM2B_uc002dhk.3_Missense_Mutation_p.Q352K|ACSM2B_uc010bwf.1_Missense_Mutation_p.Q352K	NM_182617	NP_872423	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member	352					fatty acid metabolic process|xenobiotic metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|CoA-ligase activity|metal ion binding			ovary(1)|central_nervous_system(1)	2														0.318182	264.432704	273.487666	98	210	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20559428	20559428	185	16	G	T	T	T	611	47	ACSM2B	2	2
LOC81691	81691	broad.mit.edu	37	16	20833145	20833145	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20833145G>T	uc002dhv.2	+	c.537G>T	c.(535-537)AAG>AAT	p.K179N	ERI2_uc002dht.3_Intron|LOC81691_uc002dhx.2_Missense_Mutation_p.K179N|LOC81691_uc002dhw.2_5'UTR|LOC81691_uc002dhy.3_Missense_Mutation_p.K179N	NM_030941	NP_112203	Q96IC2	REXON_HUMAN	exonuclease NEF-sp isoform 1	179						nucleolus	exonuclease activity|nucleotide binding|RNA binding			ovary(1)|kidney(1)	2														0.283465	99.142667	104.492832	36	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20833145	20833145	9262	16	G	T	T	T	464	36	LOC81691	2	2
DNAH3	55567	broad.mit.edu	37	16	21038383	21038383	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:21038383C>T	uc010vbe.1	-	c.5506G>A	c.(5506-5508)GAC>AAC	p.D1836N		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1836	AAA 2 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(10)|large_intestine(2)|central_nervous_system(2)	14				GBM - Glioblastoma multiforme(48;0.207)										0.195122	16.479002	20.031504	8	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21038383	21038383	4786	16	C	T	T	T	403	31	DNAH3	1	1
ZP2	7783	broad.mit.edu	37	16	21217083	21217083	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:21217083C>T	uc010bwn.1	-	c.614G>A	c.(613-615)CGG>CAG	p.R205Q	ZP2_uc002dii.2_Missense_Mutation_p.R166Q|ZP2_uc010bwo.2_Missense_Mutation_p.R205Q	NM_003460	NP_003451	Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 preproprotein	166	Extracellular (Potential).				binding of sperm to zona pellucida|intracellular protein transport	endoplasmic reticulum|Golgi apparatus|integral to membrane|multivesicular body|plasma membrane|proteinaceous extracellular matrix|stored secretory granule	acrosin binding|coreceptor activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(48;0.0573)										0.2	32.81114	38.669446	14	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21217083	21217083	18820	16	C	T	T	T	299	23	ZP2	1	1
PKD1	5310	broad.mit.edu	37	16	2168792	2168792	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:2168792T>A	uc002cos.1	-	c.414A>T	c.(412-414)CGA>CGT	p.R138R	PKD1_uc002cot.1_Silent_p.R138R	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	138	Extracellular (Potential).|LRRCT.			R -> Q (in Ref. 1; AAC50128).	calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(1)	1														0.3125	13.281666	13.775673	5	11	KEEP	---	---	---	---	capture		Silent	SNP	2168792	2168792	12387	16	T	A	A	A	639	50	PKD1	3	3
SCNN1G	6340	broad.mit.edu	37	16	23197833	23197833	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:23197833G>T	uc002dlm.1	+	c.241G>T	c.(241-243)GTC>TTC	p.V81F		NM_001039	NP_001030	P51170	SCNNG_HUMAN	sodium channel, nonvoltage-gated 1, gamma	81	Extracellular (By similarity).				excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(2)|large_intestine(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)									0.07377	-2.622641	20.151494	9	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23197833	23197833	14412	16	G	T	T	T	624	48	SCNN1G	2	2
CACNG3	10368	broad.mit.edu	37	16	24373044	24373044	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:24373044G>A	uc002dmf.2	+	c.808G>A	c.(808-810)GAC>AAC	p.D270N		NM_006539	NP_006530	O60359	CCG3_HUMAN	voltage-dependent calcium channel gamma-3	270					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0				GBM - Glioblastoma multiforme(48;0.0809)										0.15873	50.502696	71.434267	30	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24373044	24373044	2674	16	G	A	A	A	533	41	CACNG3	2	2
TNRC6A	27327	broad.mit.edu	37	16	24801619	24801619	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:24801619G>T	uc002dmm.2	+	c.1656G>T	c.(1654-1656)CAG>CAT	p.Q552H	TNRC6A_uc010bxs.2_Missense_Mutation_p.Q299H|TNRC6A_uc010vcc.1_Missense_Mutation_p.Q299H|TNRC6A_uc002dmn.2_Missense_Mutation_p.Q299H|TNRC6A_uc002dmo.2_Missense_Mutation_p.Q299H	NM_014494	NP_055309	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	552	Sufficient for interaction with EIF2C2.				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)										0.074468	-5.909241	29.057445	14	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24801619	24801619	16881	16	G	T	T	T	438	34	TNRC6A	2	2
IL4R	3566	broad.mit.edu	37	16	27373906	27373906	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:27373906C>T	uc002don.2	+	c.1233C>T	c.(1231-1233)TTC>TTT	p.F411F	IL4R_uc002dop.3_Silent_p.F396F|IL4R_uc010bxy.2_Silent_p.F411F|IL4R_uc002doo.2_Silent_p.F251F	NM_000418	NP_000409	P24394	IL4RA_HUMAN	interleukin 4 receptor alpha chain isoform a	411	Cytoplasmic (Potential).				immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity			ovary(1)|skin(1)	2														0.186441	41.563905	52.462307	22	96	KEEP	---	---	---	---	capture		Silent	SNP	27373906	27373906	7999	16	C	T	T	T	389	30	IL4R	2	2
IL21R	50615	broad.mit.edu	37	16	27460382	27460382	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:27460382G>T	uc002doq.1	+	c.1395G>T	c.(1393-1395)TGG>TGT	p.W465C	IL21R_uc002dor.1_Missense_Mutation_p.W465C|IL21R_uc002dos.1_Missense_Mutation_p.W465C	NM_181078	NP_851564	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor precursor	465	Cytoplasmic (Potential).				natural killer cell activation	integral to membrane	interleukin-21 receptor activity			ovary(2)	2										423				0.285714	56.186827	59.32	22	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27460382	27460382	7972	16	G	T	T	T	559	43	IL21R	2	2
GTF3C1	2975	broad.mit.edu	37	16	27476638	27476638	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:27476638G>A	uc002dov.1	-	c.5298C>T	c.(5296-5298)TTC>TTT	p.F1766F	GTF3C1_uc002dou.2_Silent_p.F1766F	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	1766					5S class rRNA transcription from RNA polymerase III type 1 promoter|tRNA transcription from RNA polymerase III promoter	transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|breast(1)|pancreas(1)	4														0.107692	12.046483	31.899206	14	116	KEEP	---	---	---	---	capture		Silent	SNP	27476638	27476638	7152	16	G	A	A	A	425	33	GTF3C1	2	2
SULT1A2	6799	broad.mit.edu	37	16	28603402	28603402	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:28603402C>T	uc002dqg.1	-	c.835G>A	c.(835-837)GAC>AAC	p.D279N	SULT1A2_uc002dqh.1_Missense_Mutation_p.D279N	NM_177528	NP_803564	P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A,	279					3'-phosphoadenosine 5'-phosphosulfate metabolic process|amine biosynthetic process|catecholamine metabolic process|steroid metabolic process|sulfation|xenobiotic metabolic process	cytosol	aryl sulfotransferase activity|flavonol 3-sulfotransferase activity				0														0.121212	3.573357	8.2229	4	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28603402	28603402	15893	16	C	T	T	T	390	30	SULT1A2	2	2
SPN	6693	broad.mit.edu	37	16	29675184	29675184	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:29675184C>A	uc002dtm.2	+	c.135C>A	c.(133-135)TAC>TAA	p.Y45*	BOLA2_uc010bzb.1_Intron|SPN_uc002dtn.2_Nonsense_Mutation_p.Y45*|SPN_uc010bzd.2_Non-coding_Transcript	NM_001030288	NP_001025459	P16150	LEUK_HUMAN	sialophorin precursor	45	Extracellular (Potential).				blood coagulation|cellular defense response|chemotaxis|defense response to bacterium|establishment or maintenance of cell polarity|immune response|leukocyte migration|negative regulation of cell adhesion|positive regulation of tumor necrosis factor biosynthetic process	extracellular space|integral to plasma membrane	bacterial cell surface binding|transmembrane receptor activity			central_nervous_system(2)	2														0.27907	163.601007	173.04347	60	155	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	29675184	29675184	15586	16	C	A	A	A	220	17	SPN	5	2
SEZ6L2	26470	broad.mit.edu	37	16	29884746	29884746	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:29884746T>A	uc010vec.1	-	c.2303A>T	c.(2302-2304)TAC>TTC	p.Y768F	BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Missense_Mutation_p.Y698F|SEZ6L2_uc002dur.3_Missense_Mutation_p.Y698F|SEZ6L2_uc002duq.3_Missense_Mutation_p.Y768F|SEZ6L2_uc002dus.3_Missense_Mutation_p.Y654F|SEZ6L2_uc010ved.1_Missense_Mutation_p.Y724F	NM_201575	NP_963869	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2 isoform	768	Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)	1														0.248227	76.991502	85.19459	35	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29884746	29884746	14633	16	T	A	A	A	741	57	SEZ6L2	3	3
TAOK2	9344	broad.mit.edu	37	16	29998855	29998855	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:29998855G>T	uc010bzm.1	+	c.3283G>T	c.(3283-3285)GTT>TTT	p.V1095F	BOLA2_uc010bzb.1_Intron|TAOK2_uc002dva.1_Missense_Mutation_p.V1088F|TAOK2_uc002dvb.1_Intron|TAOK2_uc002dvc.1_Intron|TAOK2_uc002dvd.1_Missense_Mutation_p.V915F	NM_016151	NP_057235	Q9UL54	TAOK2_HUMAN	TAO kinase 2 isoform 2	1088					actin cytoskeleton organization|activation of MAPKK activity|apoptosis|cell migration|focal adhesion assembly|positive regulation of JNK cascade|protein targeting to membrane|regulation of cell growth|regulation of cell shape|response to stress	cytoplasmic vesicle membrane|cytoskeleton|dendrite|integral to membrane|nucleolus	ATP binding|protein serine/threonine kinase activity			ovary(1)	1										143				0.261194	75.477997	82.39524	35	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29998855	29998855	16069	16	G	T	T	T	572	44	TAOK2	2	2
DOC2A	8448	broad.mit.edu	37	16	30021412	30021412	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30021412C>T	uc002dvm.2	-	c.132G>A	c.(130-132)GGG>GGA	p.G44G	BOLA2_uc010bzb.1_Intron|DOC2A_uc002dvl.2_Silent_p.G44G|DOC2A_uc002dvn.2_Silent_p.G44G|DOC2A_uc010vef.1_Intron|DOC2A_uc002dvo.2_Silent_p.G44G|DOC2A_uc002dvp.2_Silent_p.G44G|DOC2A_uc002dvq.2_Silent_p.G44G	NM_003586	NP_003577	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	44	Interaction with UNC13D and DYNLT1.				nervous system development|regulation of calcium ion-dependent exocytosis	cell junction|lysosome|synaptic vesicle membrane|synaptosome	calcium-dependent phospholipid binding|protein binding|transporter activity			ovary(2)	2														0.241379	33.078677	36.579518	14	44	KEEP	---	---	---	---	capture		Silent	SNP	30021412	30021412	4866	16	C	T	T	T	275	22	DOC2A	2	2
ITGAL	3683	broad.mit.edu	37	16	30507518	30507518	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30507518G>T	uc002dyi.3	+	c.1604G>T	c.(1603-1605)GGG>GTG	p.G535V	ITGAL_uc002dyj.3_Missense_Mutation_p.G452V|ITGAL_uc010vev.1_Intron	NM_002209	NP_002200	P20701	ITAL_HUMAN	integrin alpha L isoform a precursor	535	Potential.|FG-GAP 6.|Extracellular (Potential).				blood coagulation|heterophilic cell-cell adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	integrin complex	cell adhesion molecule binding|receptor activity			ovary(3)|central_nervous_system(3)|breast(1)	7					Efalizumab(DB00095)	NSCLC(110;1462 1641 3311 33990 49495)								0.207171	113.550231	133.431513	52	199	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30507518	30507518	8190	16	G	T	T	T	559	43	ITGAL	2	2
ITGAL	3683	broad.mit.edu	37	16	30510525	30510525	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30510525C>A	uc002dyi.3	+	c.1963C>A	c.(1963-1965)CAG>AAG	p.Q655K	ITGAL_uc002dyj.3_Missense_Mutation_p.Q572K|ITGAL_uc010vev.1_Intron	NM_002209	NP_002200	P20701	ITAL_HUMAN	integrin alpha L isoform a precursor	655	Extracellular (Potential).				blood coagulation|heterophilic cell-cell adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	integrin complex	cell adhesion molecule binding|receptor activity			ovary(3)|central_nervous_system(3)|breast(1)	7					Efalizumab(DB00095)	NSCLC(110;1462 1641 3311 33990 49495)								0.213115	88.616352	102.538945	39	144	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30510525	30510525	8190	16	C	A	A	A	273	21	ITGAL	2	2
SRCAP	10847	broad.mit.edu	37	16	30724540	30724540	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30724540G>A	uc002dze.1	+	c.2142G>A	c.(2140-2142)AAG>AAA	p.K714K	SRCAP_uc002dzf.2_Non-coding_Transcript|SRCAP_uc002dzg.1_Silent_p.K571K|SRCAP_uc010bzz.1_Silent_p.K284K	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	714	Helicase ATP-binding.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)	3			Colorectal(24;0.198)											0.273632	143.730946	153.016265	55	146	KEEP	---	---	---	---	capture		Silent	SNP	30724540	30724540	15649	16	G	A	A	A	438	34	SRCAP	2	2
PRSS36	146547	broad.mit.edu	37	16	31157193	31157193	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31157193G>A	uc002ebd.2	-	c.637C>T	c.(637-639)CCC>TCC	p.P213S	PRSS36_uc010vff.1_5'UTR|PRSS36_uc010vfg.1_Missense_Mutation_p.P213S|PRSS36_uc010vfh.1_Missense_Mutation_p.P213S	NM_173502	NP_775773	Q5K4E3	POLS2_HUMAN	protease, serine, 36 precursor	213	Peptidase S1 1.				proteolysis	cytoplasm|proteinaceous extracellular matrix	serine-type endopeptidase activity			ovary(1)	1														0.339806	88.218619	90.543048	35	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31157193	31157193	13075	16	G	A	A	A	546	42	PRSS36	2	2
ITGAX	3687	broad.mit.edu	37	16	31374570	31374570	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31374570G>T	uc002ebt.2	+	c.1585G>T	c.(1585-1587)GGG>TGG	p.G529W	ITGAX_uc002ebu.1_Missense_Mutation_p.G529W|ITGAX_uc010vfk.1_Missense_Mutation_p.G179W	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	529	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														0.203175	122.965231	148.72086	64	251	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31374570	31374570	8193	16	G	T	T	T	559	43	ITGAX	2	2
ABCC12	94160	broad.mit.edu	37	16	48130772	48130772	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:48130772A>T	uc002efc.1	-	c.3080T>A	c.(3079-3081)CTG>CAG	p.L1027Q	ABCC12_uc002eey.1_Non-coding_Transcript|ABCC12_uc002eez.1_Non-coding_Transcript|ABCC12_uc002efa.1_Non-coding_Transcript|ABCC12_uc002efb.1_Non-coding_Transcript|ABCC12_uc002efd.1_Non-coding_Transcript	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	1027	ABC transmembrane type-1 2.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)	2		all_cancers(37;0.0474)|all_lung(18;0.047)												0.116564	23.203356	46.790067	19	144	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48130772	48130772	53	16	A	T	T	T	91	7	ABCC12	3	3
ABCC12	94160	broad.mit.edu	37	16	48162380	48162380	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:48162380A>T	uc002efc.1	-	c.1505T>A	c.(1504-1506)GTG>GAG	p.V502E	ABCC12_uc002eey.1_Non-coding_Transcript|ABCC12_uc002eez.1_Non-coding_Transcript|ABCC12_uc002efa.1_Non-coding_Transcript|ABCC12_uc002efb.1_Non-coding_Transcript|ABCC12_uc002efd.1_Non-coding_Transcript|ABCC12_uc002efe.1_Missense_Mutation_p.V502E	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	502	ABC transporter 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)	2		all_cancers(37;0.0474)|all_lung(18;0.047)												0.154762	49.458592	68.57737	26	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48162380	48162380	53	16	A	T	T	T	78	6	ABCC12	3	3
ABCC12	94160	broad.mit.edu	37	16	48162469	48162469	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:48162469G>T	uc002efc.1	-	c.1416C>A	c.(1414-1416)TAC>TAA	p.Y472*	ABCC12_uc002eey.1_Non-coding_Transcript|ABCC12_uc002eez.1_Non-coding_Transcript|ABCC12_uc002efa.1_Non-coding_Transcript|ABCC12_uc002efb.1_Non-coding_Transcript|ABCC12_uc002efd.1_Non-coding_Transcript|ABCC12_uc002efe.1_Nonsense_Mutation_p.Y472*	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	472	ABC transporter 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)	2		all_cancers(37;0.0474)|all_lung(18;0.047)												0.149123	31.394506	44.862066	17	97	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	48162469	48162469	53	16	G	T	T	T	620	48	ABCC12	5	2
PPL	5493	broad.mit.edu	37	16	4933740	4933740	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:4933740C>T	uc002cyd.1	-	c.4916G>A	c.(4915-4917)CGC>CAC	p.R1639H		NM_002705	NP_002696	O60437	PEPL_HUMAN	periplakin	1639	Potential.				keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)	4														0.126761	9.729173	19.378835	9	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4933740	4933740	12769	16	C	T	T	T	351	27	PPL	1	1
RAB11FIP3	9727	broad.mit.edu	37	16	511444	511444	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:511444G>T	uc002chf.2	+	c.755G>T	c.(754-756)GGC>GTC	p.G252V		NM_014700	NP_055515	O75154	RFIP3_HUMAN	rab11-family interacting protein 3 isoform 1	252	EF-hand 2.|2 (Potential).				cell cycle|cytokinesis|endocytic recycling|protein transport	centrosome|cleavage furrow|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding				0		Hepatocellular(16;0.0218)				Melanoma(160;2366 2595 4474 8099)								0.066351	-14.676383	26.727188	14	197	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	511444	511444	13354	16	G	T	T	T	546	42	RAB11FIP3	2	2
CHD9	80205	broad.mit.edu	37	16	53331002	53331002	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:53331002G>T	uc002ehb.2	+	c.5645G>T	c.(5644-5646)AGT>ATT	p.S1882I	CHD9_uc002egy.2_Missense_Mutation_p.S1882I|CHD9_uc002ehc.2_Missense_Mutation_p.S1882I|CHD9_uc002ehf.2_Missense_Mutation_p.S996I|CHD9_uc010cbw.2_Missense_Mutation_p.S250I	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1882					cellular lipid metabolic process|chromatin assembly or disassembly|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|cytoplasm|nucleoplasm	ATP binding|chromatin binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)								1157				0.075	-4.039166	25.674821	12	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53331002	53331002	3466	16	G	T	T	T	468	36	CHD9	2	2
MMP2	4313	broad.mit.edu	37	16	55525859	55525859	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:55525859G>T	uc002ehz.3	+	c.1327G>T	c.(1327-1329)GAG>TAG	p.E443*	MMP2_uc010vhd.1_Nonsense_Mutation_p.E367*|MMP2_uc010ccc.2_Nonsense_Mutation_p.E393*|MMP2_uc002eia.3_5'Flank	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	443	Required for inhibitor TIMP2 binding.|Collagenase-like 2.				angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			ovary(3)|large_intestine(3)|lung(1)|central_nervous_system(1)|kidney(1)	9		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)					275				0.103896	4.1835	16.177415	8	69	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	55525859	55525859	10048	16	G	T	T	T	533	41	MMP2	5	2
MMP2	4313	broad.mit.edu	37	16	55530859	55530859	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:55530859G>A	uc002ehz.3	+	c.1494G>A	c.(1492-1494)ACG>ACA	p.T498T	MMP2_uc010vhd.1_Silent_p.T422T|MMP2_uc010ccc.2_Silent_p.T448T|MMP2_uc002eia.3_5'UTR	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	498	Required for inhibitor TIMP2 binding.|Hemopexin-like 1.		T -> M (in a colorectal cancer sample; somatic mutation).		angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			ovary(3)|large_intestine(3)|lung(1)|central_nervous_system(1)|kidney(1)	9		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)					275				0.175926	34.796611	45.462933	19	89	KEEP	---	---	---	---	capture		Silent	SNP	55530859	55530859	10048	16	G	A	A	A	483	38	MMP2	1	1
LPCAT2	54947	broad.mit.edu	37	16	55562356	55562356	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:55562356G>T	uc002eie.3	+	c.379G>T	c.(379-381)GCT>TCT	p.A127S		NM_017839	NP_060309	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2	127	Lumenal (Potential).				cellular membrane organization|platelet activating factor biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|Golgi stack|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding				0														0.090909	2.729259	17.582825	8	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55562356	55562356	9284	16	G	T	T	T	598	46	LPCAT2	2	2
GNAO1	2775	broad.mit.edu	37	16	56388845	56388845	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:56388845C>A	uc002eiu.3	+	c.945C>A	c.(943-945)CCC>CCA	p.P315P		NM_020988	NP_066268	P09471	GNAO_HUMAN	guanine nucleotide binding protein, alpha	315					dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|muscle contraction	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity				0		all_neural(199;0.159)												0.159574	25.258816	35.642274	15	79	KEEP	---	---	---	---	capture		Silent	SNP	56388845	56388845	6777	16	C	A	A	A	262	21	GNAO1	2	2
GPR56	9289	broad.mit.edu	37	16	57695812	57695812	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:57695812C>G	uc002emb.2	+	c.1886C>G	c.(1885-1887)TCC>TGC	p.S629C	GPR56_uc002ema.1_Missense_Mutation_p.S454C|GPR56_uc002emc.2_Missense_Mutation_p.S623C|GPR56_uc002emf.2_Missense_Mutation_p.S623C|GPR56_uc010vhs.1_Missense_Mutation_p.S629C|GPR56_uc002emd.2_Missense_Mutation_p.S623C|GPR56_uc002eme.2_Missense_Mutation_p.S623C|GPR56_uc010vht.1_Missense_Mutation_p.S628C|GPR56_uc002emg.3_Missense_Mutation_p.S623C|GPR56_uc010vhu.1_Missense_Mutation_p.S448C	NM_005682	NP_005673	Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56 isoform a	629	Helical; Name=6; (Potential).				brain development|cell adhesion|cell-cell signaling|neuropeptide signaling pathway	integral to plasma membrane	G-protein coupled receptor activity				0														0.107595	27.855194	51.983513	17	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57695812	57695812	6975	16	C	G	G	G	390	30	GPR56	3	3
GPR56	9289	broad.mit.edu	37	16	57697456	57697456	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:57697456C>T	uc002emb.2	+	c.2044C>T	c.(2044-2046)CCC>TCC	p.P682S	GPR56_uc002ema.1_Missense_Mutation_p.P507S|GPR56_uc002emc.2_Missense_Mutation_p.P676S|GPR56_uc002emf.2_Missense_Mutation_p.P676S|GPR56_uc010vhs.1_Missense_Mutation_p.P682S|GPR56_uc002emd.2_Missense_Mutation_p.P676S|GPR56_uc002eme.2_Missense_Mutation_p.P676S|GPR56_uc010vht.1_Missense_Mutation_p.P681S|GPR56_uc002emg.3_Missense_Mutation_p.P676S|GPR56_uc010vhu.1_Missense_Mutation_p.P501S	NM_005682	NP_005673	Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56 isoform a	682	Cytoplasmic (Potential).				brain development|cell adhesion|cell-cell signaling|neuropeptide signaling pathway	integral to plasma membrane	G-protein coupled receptor activity				0														0.11236	10.0828	23.294971	10	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57697456	57697456	6975	16	C	T	T	T	286	22	GPR56	2	2
C16orf80	29105	broad.mit.edu	37	16	58148824	58148824	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:58148824T>C	uc002enb.1	-	c.466A>G	c.(466-468)ATC>GTC	p.I156V		NM_013242	NP_037374	Q9Y6A4	CP080_HUMAN	transcription factor IIB	156					multicellular organismal development						0						Pancreas(103;1212 1612 18629 30162 52390)								0.123288	16.622767	26.760289	9	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58148824	58148824	1890	16	T	C	C	C	650	50	C16orf80	4	4
NDRG4	65009	broad.mit.edu	37	16	58541757	58541757	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:58541757C>A	uc002enm.2	+	c.822C>A	c.(820-822)GCC>GCA	p.A274A	NDRG4_uc002enk.2_Silent_p.A254A|NDRG4_uc010vif.1_Silent_p.A254A|NDRG4_uc010cdk.2_Silent_p.A240A|NDRG4_uc002eno.2_Silent_p.A222A|NDRG4_uc010vig.1_Silent_p.A252A|NDRG4_uc010vih.1_Silent_p.A167A|NDRG4_uc010vii.1_Silent_p.A240A|NDRG4_uc002enp.2_Silent_p.A222A|NDRG4_uc002enq.1_Intron	NM_001130487	NP_001123959	Q9ULP0	NDRG4_HUMAN	NDRG family member 4 isoform 2	222					cell differentiation|cell growth|multicellular organismal development|response to stress	cytoplasm					0														0.076923	-3.020266	18.425411	9	108	KEEP	---	---	---	---	capture		Silent	SNP	58541757	58541757	10653	16	C	A	A	A	262	21	NDRG4	2	2
CNOT1	23019	broad.mit.edu	37	16	58572800	58572800	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:58572800C>A	uc002env.2	-	c.5011G>T	c.(5011-5013)GAT>TAT	p.D1671Y	CNOT1_uc002enw.2_Non-coding_Transcript|CNOT1_uc002enu.3_Missense_Mutation_p.D1666Y|CNOT1_uc010vik.1_Missense_Mutation_p.D628Y	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1671					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)										0.192982	19.283552	24.309927	11	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58572800	58572800	3755	16	C	A	A	A	416	32	CNOT1	2	2
CDH8	1006	broad.mit.edu	37	16	61851501	61851501	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:61851501C>G	uc002eog.1	-	c.1159G>C	c.(1159-1161)GAG>CAG	p.E387Q	CDH8_uc002eoh.2_Missense_Mutation_p.E156Q	NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	387	Extracellular (Potential).|Cadherin 3.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|breast(1)	7		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)										0.087719	4.129916	13.930216	5	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61851501	61851501	3245	16	C	G	G	G	377	29	CDH8	3	3
CDH11	1009	broad.mit.edu	37	16	65005524	65005524	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:65005524C>T	uc002eoi.2	-	c.1600G>A	c.(1600-1602)GAA>AAA	p.E534K	CDH11_uc010cdn.2_Non-coding_Transcript|CDH11_uc002eoj.2_Missense_Mutation_p.E534K|CDH11_uc010vin.1_Missense_Mutation_p.E408K	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	534	Cadherin 5.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(7)|ovary(2)	9		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)						239	TSP Lung(24;0.17)			0.122222	12.555585	25.139997	11	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65005524	65005524	3226	16	C	T	T	T	377	29	CDH11	2	2
TSNAXIP1	55815	broad.mit.edu	37	16	67861260	67861260	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:67861260C>A	uc010vka.1	+	c.1773C>A	c.(1771-1773)TAC>TAA	p.Y591*	TSNAXIP1_uc010vjz.1_Nonsense_Mutation_p.Y414*|TSNAXIP1_uc002euf.3_Nonsense_Mutation_p.Y270*|TSNAXIP1_uc010vkb.1_Nonsense_Mutation_p.Y522*|TSNAXIP1_uc002eug.3_Nonsense_Mutation_p.Y245*|TSNAXIP1_uc002euh.3_Nonsense_Mutation_p.Y245*|TSNAXIP1_uc002eui.3_Nonsense_Mutation_p.Y245*|TSNAXIP1_uc002euj.2_Nonsense_Mutation_p.Y537*|TSNAXIP1_uc002euk.2_Nonsense_Mutation_p.Y270*	NM_018430	NP_060900	Q2TAA8	TXIP1_HUMAN	translin-associated factor X interacting protein	537					cell differentiation|multicellular organismal development|spermatogenesis	perinuclear region of cytoplasm					0		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00432)|Epithelial(162;0.0192)|all cancers(182;0.125)										0.113475	17.497282	38.283832	16	125	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	67861260	67861260	17183	16	C	A	A	A	233	18	TSNAXIP1	5	2
PDPR	55066	broad.mit.edu	37	16	70154618	70154618	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:70154618G>T	uc002eyf.1	+	c.223G>T	c.(223-225)GGC>TGC	p.G75C	CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Intron	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory	75					glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)										0.09589	3.806237	15.73213	7	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70154618	70154618	12110	16	G	T	T	T	559	43	PDPR	2	2
HYDIN	54768	broad.mit.edu	37	16	70900088	70900088	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:70900088G>T	uc002ezr.2	-	c.11452C>A	c.(11452-11454)CAG>AAG	p.Q3818K	HYDIN_uc010cfy.2_Non-coding_Transcript	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	3819										ovary(1)	1		Ovarian(137;0.0654)												0.176471	18.441551	23.474172	9	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70900088	70900088	7767	16	G	T	T	T	611	47	HYDIN	2	2
HYDIN	54768	broad.mit.edu	37	16	71015470	71015470	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:71015470C>A	uc002ezr.2	-	c.4331G>T	c.(4330-4332)GGC>GTC	p.G1444V		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	1445										ovary(1)	1		Ovarian(137;0.0654)												0.16	51.68961	73.697951	32	168	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71015470	71015470	7767	16	C	A	A	A	338	26	HYDIN	2	2
PHLPP2	23035	broad.mit.edu	37	16	71697944	71697944	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:71697944C>A	uc002fax.2	-	c.1843G>T	c.(1843-1845)GGA>TGA	p.G615*	PHLPP2_uc002fav.2_Non-coding_Transcript|PHLPP2_uc010cgf.2_Intron	NM_015020	NP_055835	Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein	615	LRR 16.					cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			central_nervous_system(1)	1														0.159574	27.559206	37.939966	15	79	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	71697944	71697944	12279	16	C	A	A	A	273	21	PHLPP2	5	2
RFWD3	55159	broad.mit.edu	37	16	74662537	74662537	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:74662537C>T	uc002fda.2	-	c.1782G>A	c.(1780-1782)ATG>ATA	p.M594I	RFWD3_uc010vmx.1_Missense_Mutation_p.M114I|RFWD3_uc010cgq.2_Missense_Mutation_p.M594I	NM_018124	NP_060594	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	594	WD 3.				DNA repair|mitotic cell cycle G1/S transition DNA damage checkpoint|response to ionizing radiation	nucleus	MDM2 binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding				0														0.068182	-17.720993	33.189287	18	246	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74662537	74662537	13733	16	C	T	T	T	325	25	RFWD3	2	2
WDR59	79726	broad.mit.edu	37	16	74976635	74976635	+	Splice_Site_SNP	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:74976635C>T	uc002fdh.1	-	c.534_splice	c.e7+1	p.R178_splice	WDR59_uc002fdi.2_Splice_Site_SNP_p.R178_splice|WDR59_uc002fdj.2_Splice_Site_SNP_p.R178_splice	NM_030581	NP_085058			WD repeat domain 59											ovary(1)|breast(1)	2														0.102564	4.938927	17.221818	8	70	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	74976635	74976635	17881	16	C	T	T	T	234	18	WDR59	5	2
TMEM231	79583	broad.mit.edu	37	16	75576504	75576504	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:75576504C>A	uc002fek.2	-	c.747G>T	c.(745-747)AGG>AGT	p.R249S	CHST5_uc002fej.1_5'UTR|TMEM231_uc002fel.2_Missense_Mutation_p.R104S|TMEM231_uc002fem.2_Missense_Mutation_p.R220S|TMEM231_uc010vne.1_Missense_Mutation_p.R73S|TMEM231_uc010cgx.1_Missense_Mutation_p.R184S	NM_001077416	NP_001070884	Q9H6L2	TM231_HUMAN	transmembrane protein 231 isoform 1	220						integral to membrane					0														0.23	48.371711	55.058023	23	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75576504	75576504	16686	16	C	A	A	A	389	30	TMEM231	2	2
ADAMTS18	170692	broad.mit.edu	37	16	77359870	77359870	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:77359870G>T	uc002ffc.3	-	c.1925C>A	c.(1924-1926)CCT>CAT	p.P642H	ADAMTS18_uc010chc.1_Missense_Mutation_p.P230H|ADAMTS18_uc002ffe.1_Missense_Mutation_p.P338H	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	642	TSP type-1 1.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|kidney(4)|skin(2)|pancreas(1)|ovary(1)	12									p.P642H(ISHIKAWAHERAKLIO02ER-Tumor)	1451				0.202899	31.209285	36.866801	14	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77359870	77359870	264	16	G	T	T	T	455	35	ADAMTS18	2	2
VAT1L	57687	broad.mit.edu	37	16	77896678	77896678	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:77896678C>G	uc002ffg.1	+	c.613C>G	c.(613-615)CCC>GCC	p.P205A		NM_020927	NP_065978	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport protein 1 homolog (T.	205					oxidation-reduction process		oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1														0.138889	31.562724	49.803546	20	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77896678	77896678	17695	16	C	G	G	G	286	22	VAT1L	3	3
CDYL2	124359	broad.mit.edu	37	16	80638384	80638384	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:80638384C>T	uc002ffs.2	-	c.1422G>A	c.(1420-1422)GTG>GTA	p.V474V		NM_152342	NP_689555	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	474					chromatin assembly or disassembly	chromatin|nucleus	catalytic activity|chromatin binding|protein binding			central_nervous_system(1)	1														0.079365	-3.502007	42.023908	20	232	KEEP	---	---	---	---	capture		Silent	SNP	80638384	80638384	3319	16	C	T	T	T	366	29	CDYL2	2	2
OSGIN1	29948	broad.mit.edu	37	16	83992864	83992864	+	Splice_Site_SNP	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:83992864G>T	uc002fha.2	+	c.317_splice	c.e4-1	p.G106_splice	OSGIN1_uc002fhb.2_Splice_Site_SNP_p.G23_splice|OSGIN1_uc002fhc.2_Splice_Site_SNP_p.G23_splice	NM_013370	NP_037502			oxidative stress induced growth inhibitor 1						cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0														0.125	18.927533	38.757499	18	126	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	83992864	83992864	11700	16	G	T	T	T	455	35	OSGIN1	5	2
LRRC50	123872	broad.mit.edu	37	16	84189346	84189346	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:84189346C>A	uc002fhl.3	+	c.733C>A	c.(733-735)CCC>ACC	p.P245T	LRRC50_uc010chi.1_Non-coding_Transcript	NM_178452	NP_848547	Q8NEP3	LRC50_HUMAN	leucine rich repeat containing 50	245					axonemal dynein complex assembly|cilium morphogenesis	cilium axoneme|cytoplasm|spindle pole	dynein binding			ovary(4)|pancreas(1)	5														0.177083	30.727459	40.151667	17	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84189346	84189346	9384	16	C	A	A	A	338	26	LRRC50	2	2
KIAA0513	9764	broad.mit.edu	37	16	85112585	85112585	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:85112585C>T	uc002fiu.2	+	c.878C>T	c.(877-879)ACG>ATG	p.T293M	KIAA0513_uc002fis.3_Missense_Mutation_p.T293M|KIAA0513_uc010voj.1_Missense_Mutation_p.T293M|KIAA0513_uc002fit.2_Missense_Mutation_p.T293M	NM_014732	NP_055547	O60268	K0513_HUMAN	hypothetical protein LOC9764	293						cytoplasm				breast(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.234)										0.12931	17.777359	33.284364	15	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85112585	85112585	8488	16	C	T	T	T	247	19	KIAA0513	1	1
JPH3	57338	broad.mit.edu	37	16	87677997	87677997	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:87677997C>T	uc002fkd.2	+	c.516C>T	c.(514-516)ACC>ACT	p.T172T	JPH3_uc010vou.1_Non-coding_Transcript	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3	172	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)										0.11811	14.631885	32.840381	15	112	KEEP	---	---	---	---	capture		Silent	SNP	87677997	87677997	8266	16	C	T	T	T	262	21	JPH3	2	2
JPH3	57338	broad.mit.edu	37	16	87678562	87678562	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:87678562G>T	uc002fkd.2	+	c.1081G>T	c.(1081-1083)GAG>TAG	p.E361*	JPH3_uc010vou.1_Non-coding_Transcript	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3	361	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)										0.173913	15.872142	20.489083	8	38	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	87678562	87678562	8266	16	G	T	T	T	481	37	JPH3	5	1
CA5A	763	broad.mit.edu	37	16	87921828	87921828	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:87921828C>T	uc002fkn.1	-	c.825G>A	c.(823-825)AAG>AAA	p.K275K		NM_001739	NP_001730	P35218	CAH5A_HUMAN	carbonic anhydrase VA, mitochondrial precursor	275					one-carbon metabolic process	mitochondrial matrix	carbonate dehydratase activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0513)										0.121212	11.450349	20.732935	8	58	KEEP	---	---	---	---	capture		Silent	SNP	87921828	87921828	2635	16	C	T	T	T	415	32	CA5A	2	2
USP7	7874	broad.mit.edu	37	16	9004656	9004656	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:9004656T>A	uc002czl.2	-	c.1107A>T	c.(1105-1107)GCA>GCT	p.A369A	USP7_uc010uyk.1_Silent_p.A270A|USP7_uc010uyj.1_Silent_p.A270A|USP7_uc002czk.2_Silent_p.A353A|USP7_uc010uyl.1_Non-coding_Transcript	NM_003470	NP_003461	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7	369					interspecies interaction between organisms|multicellular organismal development|protein deubiquitination|regulation of sequence-specific DNA binding transcription factor activity|ubiquitin-dependent protein catabolic process	cytoplasm|PML body	cysteine-type endopeptidase activity|p53 binding|protein C-terminus binding|transcription factor binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)	3														0.213675	60.710979	69.570503	25	92	KEEP	---	---	---	---	capture		Silent	SNP	9004656	9004656	17652	16	T	A	A	A	704	55	USP7	3	3
GRIN2A	2903	broad.mit.edu	37	16	9857801	9857801	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:9857801G>T	uc002czo.3	-	c.3600C>A	c.(3598-3600)CAC>CAA	p.H1200Q	GRIN2A_uc010uym.1_Missense_Mutation_p.H1200Q|GRIN2A_uc010uyn.1_Missense_Mutation_p.H1043Q|GRIN2A_uc002czr.3_Missense_Mutation_p.H1200Q	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1200	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)					324				0.19496	324.447142	389.912009	147	607	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9857801	9857801	7058	16	G	T	T	T	620	48	GRIN2A	2	2
MYH13	8735	broad.mit.edu	37	17	10209868	10209868	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10209868G>T	uc002gmk.1	-	c.5374C>A	c.(5374-5376)CAG>AAG	p.Q1792K		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1792	Potential.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)	4														0.205882	101.778669	120.854708	49	189	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10209868	10209868	10427	17	G	T	T	T	598	46	MYH13	2	2
MYH1	4619	broad.mit.edu	37	17	10409387	10409387	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10409387C>A	uc002gmo.2	-	c.1998G>T	c.(1996-1998)TTG>TTT	p.L666F		NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	666	Myosin head-like.|Actin-binding (By similarity).					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|breast(3)|kidney(1)|skin(1)	15										585				0.178862	39.254325	51.223066	22	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10409387	10409387	10424	17	C	A	A	A	376	29	MYH1	2	2
MYH1	4619	broad.mit.edu	37	17	10411224	10411224	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10411224C>G	uc002gmo.2	-	c.1947G>C	c.(1945-1947)CAG>CAC	p.Q649H		NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	649	Myosin head-like.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|breast(3)|kidney(1)|skin(1)	15										585				0.117647	20.123515	34.782552	12	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10411224	10411224	10424	17	C	G	G	G	415	32	MYH1	3	3
MYH3	4621	broad.mit.edu	37	17	10547773	10547773	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10547773C>T	uc002gmq.1	-	c.1305G>A	c.(1303-1305)AAG>AAA	p.K435K		NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,	435	Myosin head-like.				muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(1)|pancreas(1)	6														0.253333	95.445299	103.687837	38	112	KEEP	---	---	---	---	capture		Silent	SNP	10547773	10547773	10431	17	C	T	T	T	259	20	MYH3	2	2
DNAH9	1770	broad.mit.edu	37	17	11593083	11593083	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:11593083G>T	uc002gne.2	+	c.3944G>T	c.(3943-3945)AGC>ATC	p.S1315I	DNAH9_uc010coo.2_Missense_Mutation_p.S609I	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	1315	Stem (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	10		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)										0.262295	37.186797	40.29779	16	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11593083	11593083	4791	17	G	T	T	T	442	34	DNAH9	2	2
RICH2	9912	broad.mit.edu	37	17	12846933	12846933	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:12846933G>T	uc002gnr.3	+	c.680G>T	c.(679-681)AGG>ATG	p.R227M	RICH2_uc010vvk.1_Missense_Mutation_p.R227M|RICH2_uc010vvl.1_Missense_Mutation_p.R227M|RICH2_uc002gns.3_Missense_Mutation_p.R27M|RICH2_uc010vvm.1_Missense_Mutation_p.R227M|RICH2_uc010vvn.1_Non-coding_Transcript|RICH2_uc002gnt.1_5'Flank	NM_014859	NP_055674	Q17R89	RHG44_HUMAN	Rho GTPase-activating protein RICH2	227	BAR.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0														0.217054	58.915649	68.458216	28	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12846933	12846933	13832	17	G	T	T	T	455	35	RICH2	2	2
ELAC2	60528	broad.mit.edu	37	17	12915089	12915089	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:12915089C>A	uc002gnz.3	-	c.570G>T	c.(568-570)AGG>AGT	p.R190S	ELAC2_uc010vvo.1_Missense_Mutation_p.R13S|ELAC2_uc010vvp.1_Missense_Mutation_p.R171S|ELAC2_uc010vvq.1_Missense_Mutation_p.R190S|ELAC2_uc010vvr.1_Intron	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2 isoform 1	190					tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0														0.076923	-2.713976	11.584933	6	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12915089	12915089	5238	17	C	A	A	A	389	30	ELAC2	2	2
NCOR1	9611	broad.mit.edu	37	17	15989745	15989745	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:15989745C>A	uc002gpo.2	-	c.3028G>T	c.(3028-3030)GCT>TCT	p.A1010S	NCOR1_uc002gpn.2_Missense_Mutation_p.A1026S|NCOR1_uc002gpp.1_Missense_Mutation_p.A917S|NCOR1_uc002gpq.1_Missense_Mutation_p.A102S	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1	1010	Interaction with ETO.				cellular lipid metabolic process|chromatin modification|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of JNK cascade|regulation of fatty acid transport|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	spindle microtubule|transcriptional repressor complex	histone deacetylase binding|promoter binding|transcription corepressor activity			ovary(1)|kidney(1)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)										0.445946	97.562297	97.751198	33	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15989745	15989745	10634	17	C	A	A	A	325	25	NCOR1	2	2
TRPV2	51393	broad.mit.edu	37	17	16330853	16330853	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:16330853G>T	uc002gpy.2	+	c.1342G>T	c.(1342-1344)GTG>TTG	p.V448L	TRPV2_uc002gpz.2_Missense_Mutation_p.V18L	NM_016113	NP_057197	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel,	448	Helical; (Potential).				sensory perception	integral to plasma membrane|melanosome	calcium channel activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)										0.490909	174.644267	174.65225	54	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16330853	16330853	17147	17	G	T	T	T	520	40	TRPV2	1	1
FBXW10	10517	broad.mit.edu	37	17	18675739	18675739	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:18675739C>T	uc002gul.2	+	c.2108C>T	c.(2107-2109)ACA>ATA	p.T703I	FBXW10_uc002guj.2_Missense_Mutation_p.T674I|FBXW10_uc002guk.2_Missense_Mutation_p.T674I|FBXW10_uc010cqh.1_Missense_Mutation_p.T621I	NM_031456	NP_113644	Q5XX13	FBW10_HUMAN	F-box and WD-40 domain protein 10	674										ovary(1)	1														0.287402	179.360488	189.664526	73	181	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18675739	18675739	6000	17	C	T	T	T	221	17	FBXW10	2	2
KCNJ12	3768	broad.mit.edu	37	17	21319454	21319454	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:21319454C>A	uc002gyv.1	+	c.800C>A	c.(799-801)CCC>CAC	p.P267H		NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily	267	Cytoplasmic (By similarity).				blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)	3				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)						Prostate(3;0.18)			0.115789	9.953491	23.768554	11	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21319454	21319454	8351	17	C	A	A	A	286	22	KCNJ12	2	2
KIAA0664	23277	broad.mit.edu	37	17	2604050	2604050	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:2604050C>A	uc002fuy.1	-	c.981G>T	c.(979-981)GCG>GCT	p.A327A	KIAA0664_uc002fux.1_Silent_p.A259A	NM_015229	NP_056044	O75153	K0664_HUMAN	hypothetical protein LOC23277	327							binding			breast(2)	2														0.39759	94.997619	95.745569	33	50	KEEP	---	---	---	---	capture		Silent	SNP	2604050	2604050	8496	17	C	A	A	A	288	23	KIAA0664	1	1
EFCAB5	374786	broad.mit.edu	37	17	28435016	28435016	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:28435016C>G	uc002het.2	+	c.4486C>G	c.(4486-4488)CCA>GCA	p.P1496A	EFCAB5_uc010cse.2_Missense_Mutation_p.P1251A|EFCAB5_uc010csf.2_Missense_Mutation_p.P847A	NM_198529	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5 isoform a	1496							calcium ion binding			ovary(1)|skin(1)	2														0.288889	126.169072	131.562815	39	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28435016	28435016	5125	17	C	G	G	G	338	26	EFCAB5	3	3
PSMD11	5717	broad.mit.edu	37	17	30806346	30806346	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:30806346A>T	uc010cta.1	+	c.990A>T	c.(988-990)TTA>TTT	p.L330F	PSMD11_uc002hhm.2_Missense_Mutation_p.L330F	NM_002815	NP_002806	O00231	PSD11_HUMAN	proteasome 26S non-ATPase subunit 11	330	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	protein binding			ovary(1)	1		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.109)			Ovarian(130;1038 1716 9294 11987 19279)								0.090909	6.752564	43.85541	20	200	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30806346	30806346	13147	17	A	T	T	T	180	14	PSMD11	3	3
ACCN1	40	broad.mit.edu	37	17	31415952	31415952	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:31415952G>T	uc002hht.2	-	c.916C>A	c.(916-918)CCT>ACT	p.P306T	ACCN1_uc002hhu.2_Missense_Mutation_p.P255T	NM_183377	NP_899233	Q16515	ACCN1_HUMAN	amiloride-sensitive cation channel 1, neuronal	255	Extracellular (By similarity).				central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)									0.320755	93.40991	96.436744	34	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31415952	31415952	129	17	G	T	T	T	572	44	ACCN1	2	2
TMEM132E	124842	broad.mit.edu	37	17	32964379	32964379	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:32964379G>C	uc002hif.2	+	c.2083G>C	c.(2083-2085)GCA>CCA	p.A695P		NM_207313	NP_997196	Q6IEE7	T132E_HUMAN	transmembrane protein 132E precursor	695	Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(366;0.231)										0.165854	77.001715	98.788099	34	171	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32964379	32964379	16580	17	G	C	C	C	494	38	TMEM132E	3	3
RAD51L3	5892	broad.mit.edu	37	17	33428230	33428230	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:33428230G>T	uc010wcd.1	-	c.953C>A	c.(952-954)TCT>TAT	p.S318Y	RFFL_uc002hiq.2_Missense_Mutation_p.S139Y|RAD51L3_uc010ctj.2_Silent_p.I116I|RAD51L3_uc002hir.2_Missense_Mutation_p.S298Y|RAD51L3_uc002his.2_Missense_Mutation_p.S186Y|RAD51L3_uc010ctk.2_Missense_Mutation_p.S179Y|RAD51L3_uc010wce.1_Missense_Mutation_p.S179Y|RAD51L3_uc002hit.2_Missense_Mutation_p.S179Y|RAD51L3_uc002hiu.2_Missense_Mutation_p.S121Y	NM_001142571	NP_001136043	O75771	RA51D_HUMAN	RAD51-like 3 isoform 6	298					DNA repair|reciprocal meiotic recombination	nucleus	ATP binding|DNA binding|DNA-dependent ATPase activity|protein binding			lung(1)|breast(1)|central_nervous_system(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)										0.235897	94.843646	107.293682	46	149	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33428230	33428230	13450	17	G	T	T	T	429	33	RAD51L3	2	2
LYZL6	57151	broad.mit.edu	37	17	34263782	34263782	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:34263782G>A	uc002hkj.1	-	c.354C>T	c.(352-354)TCC>TCT	p.S118S	LYZL6_uc002hkk.1_Silent_p.S118S	NM_020426	NP_065159	O75951	LYZL6_HUMAN	lysozyme-like 6 precursor	118					cell wall macromolecule catabolic process	extracellular region	lysozyme activity				0				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)										0.35124	253.502171	258.226164	85	157	KEEP	---	---	---	---	capture		Silent	SNP	34263782	34263782	9511	17	G	A	A	A	496	39	LYZL6	1	1
LYZL6	57151	broad.mit.edu	37	17	34266291	34266291	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:34266291G>T	uc002hkj.1	-	c.70C>A	c.(70-72)CGC>AGC	p.R24S	LYZL6_uc002hkk.1_Missense_Mutation_p.R24S	NM_020426	NP_065159	O75951	LYZL6_HUMAN	lysozyme-like 6 precursor	24					cell wall macromolecule catabolic process	extracellular region	lysozyme activity				0				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)										0.28481	119.806535	126.376038	45	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34266291	34266291	9511	17	G	T	T	T	481	37	LYZL6	1	1
KRT28	162605	broad.mit.edu	37	17	38953456	38953456	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38953456C>A	uc002hvh.1	-	c.768G>T	c.(766-768)GCG>GCT	p.A256A		NM_181535	NP_853513	Q7Z3Y7	K1C28_HUMAN	keratin 25D	256	Rod.|Linker 12.					cytoplasm|intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)				Melanoma(19;789 869 15380 26882 39836)								0.289855	105.672387	111.117584	40	98	KEEP	---	---	---	---	capture		Silent	SNP	38953456	38953456	8780	17	C	A	A	A	288	23	KRT28	1	1
KRTAP4-4	84616	broad.mit.edu	37	17	39316800	39316800	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39316800G>A	uc002hwc.2	-	c.144C>T	c.(142-144)CCC>CCT	p.P48P		NM_032524	NP_115913	Q9BYR3	KRA44_HUMAN	keratin associated protein 4.4	48	6.|26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].		Missing (in allele KAP4.13).|Missing (in allele KAP4.4-v1).			keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)											0.316176	112.571548	116.661674	43	93	KEEP	---	---	---	---	capture		Silent	SNP	39316800	39316800	8875	17	G	A	A	A	548	43	KRTAP4-4	2	2
TUBG1	7283	broad.mit.edu	37	17	40766531	40766531	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40766531G>C	uc002ian.2	+	c.1014G>C	c.(1012-1014)CAG>CAC	p.Q338H		NM_001070	NP_001061	P23258	TBG1_HUMAN	tubulin, gamma 1	338					G2/M transition of mitotic cell cycle|meiotic spindle organization|protein polymerization	condensed nuclear chromosome|cytosol|gamma-tubulin complex|polar microtubule	GTP binding|GTPase activity|protein binding|structural constituent of cytoskeleton			ovary(1)	1		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.129)		Colon(20;114 698 11420 22864)								0.203125	35.83753	41.075151	13	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40766531	40766531	17319	17	G	C	C	C	425	33	TUBG1	3	3
AOC2	314	broad.mit.edu	37	17	40997103	40997103	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40997103G>T	uc002ibu.2	+	c.460G>T	c.(460-462)GAG>TAG	p.E154*	AOC2_uc002ibt.2_Nonsense_Mutation_p.E154*	NM_009590	NP_033720	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 isoform b	154					catecholamine metabolic process|oxidation-reduction process|visual perception	cytoplasm|plasma membrane	aliphatic-amine oxidase activity|aminoacetone:oxygen oxidoreductase(deaminating) activity|copper ion binding|electron carrier activity|phenethylamine:oxygen oxidoreductase (deaminating) activity|primary amine oxidase activity|quinone binding|tryptamine:oxygen oxidoreductase (deaminating) activity			ovary(2)	2		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)										0.224138	26.444636	30.503348	13	45	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	40997103	40997103	737	17	G	T	T	T	533	41	AOC2	5	2
NBR1	4077	broad.mit.edu	37	17	41345412	41345412	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:41345412G>T	uc010czd.2	+	c.1281G>T	c.(1279-1281)AAG>AAT	p.K427N	NBR1_uc010diz.2_Missense_Mutation_p.K427N|NBR1_uc010whu.1_Missense_Mutation_p.K427N|NBR1_uc010whv.1_Missense_Mutation_p.K427N|NBR1_uc010whw.1_Missense_Mutation_p.K406N|NBR1_uc010whx.1_Missense_Mutation_p.K236N	NM_031862	NP_114068	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	427					macroautophagy|protein oligomerization	autophagic vacuole|cytoplasmic vesicle|cytosol|late endosome|lysosome|sarcomere	ubiquitin binding|zinc ion binding			skin(1)	1		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)										0.239437	37.538498	41.947987	17	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41345412	41345412	10599	17	G	T	T	T	451	35	NBR1	2	2
ADAM11	4185	broad.mit.edu	37	17	42837203	42837203	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:42837203G>T	uc002ihh.2	+	c.175G>T	c.(175-177)GGG>TGG	p.G59W	ADAM11_uc010wjd.1_5'UTR	NM_002390	NP_002381	O75078	ADA11_HUMAN	ADAM metallopeptidase domain 11 preproprotein	59					integrin-mediated signaling pathway|proteolysis	integral to membrane|plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			pancreas(1)	1		Prostate(33;0.0959)												0.3125	48.137357	50.164132	20	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42837203	42837203	236	17	G	T	T	T	507	39	ADAM11	1	1
CRHR1	1394	broad.mit.edu	37	17	43910880	43910880	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:43910880C>A	uc010dap.2	+	c.993C>A	c.(991-993)ACC>ACA	p.T331T	CRHR1_uc010wjx.1_Silent_p.T127T|CRHR1_uc002ijp.2_Silent_p.T201T|CRHR1_uc002ijm.2_Silent_p.T302T|CRHR1_uc002ijn.2_Silent_p.T262T|CRHR1_uc010dar.2_Silent_p.T302T|CRHR1_uc010dao.2_Silent_p.T201T|CRHR1_uc010daq.2_Silent_p.T127T	NM_001145146	NP_001138618	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	331	Cytoplasmic (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)								0.315789	165.003374	170.754451	60	130	KEEP	---	---	---	---	capture		Silent	SNP	43910880	43910880	4010	17	C	A	A	A	262	21	CRHR1	2	2
MYBBP1A	10514	broad.mit.edu	37	17	4443107	4443107	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:4443107G>A	uc002fxz.3	-	c.3590C>T	c.(3589-3591)CCT>CTT	p.P1197L	MYBBP1A_uc002fyb.3_Missense_Mutation_p.P1197L|SPNS2_uc002fxx.2_3'UTR|SPNS2_uc002fxy.2_3'UTR|MYBBP1A_uc002fya.3_Missense_Mutation_p.P142L|MYBBP1A_uc010vsa.1_Missense_Mutation_p.P239L	NM_001105538	NP_001099008	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 1	1197	Required for nuclear and nucleolar localization (By similarity).				nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NLS-dependent protein nuclear import complex|nucleolus	DNA binding|DNA-directed DNA polymerase activity|transcription factor binding			ovary(1)|skin(1)	2														0.296296	98.841676	103.857064	40	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4443107	4443107	10403	17	G	A	A	A	455	35	MYBBP1A	2	2
WNT9B	7484	broad.mit.edu	37	17	44950057	44950057	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:44950057C>G	uc002ikw.1	+	c.252C>G	c.(250-252)CTC>CTG	p.L84L	WNT9B_uc002ikx.1_Silent_p.L84L	NM_003396	NP_003387	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family,	84					anterior/posterior pattern formation|axis specification|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|collecting duct development|cornea development in camera-type eye|endoderm development|establishment of planar polarity involved in nephron morphogenesis|kidney rudiment formation|male genitalia development|mesonephric duct formation|metanephric tubule development|negative regulation of gene-specific transcription from RNA polymerase II promoter|neuron differentiation|palate development|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|uterus morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway|Wnt receptor signaling pathway, planar cell polarity pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|G-protein-coupled receptor binding				0			BRCA - Breast invasive adenocarcinoma(9;0.0257)											0.323077	67.755286	69.560225	21	44	KEEP	---	---	---	---	capture		Silent	SNP	44950057	44950057	17973	17	C	G	G	G	392	31	WNT9B	3	3
CDC27	996	broad.mit.edu	37	17	45206824	45206824	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:45206824C>A	uc002ile.3	-	c.2113G>T	c.(2113-2115)GAT>TAT	p.D705Y	CDC27_uc002ild.3_Missense_Mutation_p.D699Y|CDC27_uc002ilf.3_Missense_Mutation_p.D698Y|CDC27_uc010wkp.1_Missense_Mutation_p.D638Y|CDC27_uc010wkq.1_Non-coding_Transcript	NM_001114091	NP_001107563	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 1	699	TPR 7.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein binding			lung(2)|breast(2)|ovary(1)	5														0.327103	91.880808	94.721644	35	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45206824	45206824	3194	17	C	A	A	A	377	29	CDC27	2	2
HOXB3	3213	broad.mit.edu	37	17	46628019	46628019	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:46628019G>T	uc002inn.2	-	c.973C>A	c.(973-975)CCG>ACG	p.P325T	HOXB3_uc010wlm.1_Missense_Mutation_p.P252T|HOXB3_uc010dbf.2_Missense_Mutation_p.P325T|HOXB3_uc010dbg.2_Missense_Mutation_p.P325T|HOXB3_uc002ino.2_Missense_Mutation_p.P325T|HOXB3_uc010wlk.1_Missense_Mutation_p.P193T|HOXB3_uc010wll.1_Missense_Mutation_p.P252T	NM_002146	NP_002137	P14651	HXB3_HUMAN	homeobox B3	325					angiogenesis|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0												OREG0024516	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.081633	-8.249681	18.10301	12	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46628019	46628019	7594	17	G	T	T	T	559	43	HOXB3	2	2
MPO	4353	broad.mit.edu	37	17	56357346	56357346	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:56357346G>C	uc002ivu.1	-	c.278C>G	c.(277-279)GCC>GGC	p.A93G		NM_000250	NP_000241	P05164	PERM_HUMAN	myeloperoxidase	93					anti-apoptosis|hydrogen peroxide catabolic process|low-density lipoprotein particle remodeling|oxidation-reduction process	extracellular space|lysosome|nucleus|stored secretory granule	chromatin binding|heme binding|heparin binding|peroxidase activity			ovary(2)|large_intestine(1)|pancreas(1)	4					Cefdinir(DB00535)									0.347826	48.407976	49.337963	16	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56357346	56357346	10124	17	G	C	C	C	546	42	MPO	3	3
TEX14	56155	broad.mit.edu	37	17	56729334	56729334	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:56729334G>T	uc010dcz.1	-	c.29C>A	c.(28-30)CCC>CAC	p.P10H	TEX14_uc002iwr.1_Missense_Mutation_p.P10H|TEX14_uc002iws.1_Missense_Mutation_p.P10H|TEX14_uc010dda.1_5'UTR	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a	10					protein phosphorylation	cytoplasm	ATP binding|protein kinase activity			stomach(4)|ovary(3)|large_intestine(1)|lung(1)|skin(1)|pancreas(1)	11	Medulloblastoma(34;0.127)|all_neural(34;0.237)									598				0.451613	125.05346	125.240313	42	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56729334	56729334	16305	17	G	T	T	T	559	43	TEX14	2	2
BRIP1	83990	broad.mit.edu	37	17	59820497	59820497	+	Splice_Site_SNP	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:59820497T>A	uc002izk.1	-	c.2258_splice	c.e16-1	p.D753_splice	BRIP1_uc002izl.1_Splice_Site_SNP_p.D134_splice	NM_032043	NP_114432			BRCA1 interacting protein C-terminal helicase 1						DNA damage checkpoint|double-strand break repair|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(1)	1										346				0.272727	45.017797	48.092854	18	48	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	59820497	59820497	1545	17	T	A	A	A	728	56	BRIP1	5	3
ACE	1636	broad.mit.edu	37	17	61558508	61558508	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:61558508G>A	uc002jau.1	+	c.904G>A	c.(904-906)GAC>AAC	p.D302N	ACE_uc010wpi.1_Missense_Mutation_p.D302N|ACE_uc010ddu.1_Missense_Mutation_p.D119N	NM_000789	NP_000780	P12821	ACE_HUMAN	angiotensin I converting enzyme 1 isoform 1	302	Extracellular (Potential).|Peptidase M2 1.				angiotensin catabolic process in blood|arachidonic acid secretion|blood vessel remodeling|hemopoietic stem cell differentiation|hormone catabolic process|kidney development|mononuclear cell proliferation|peptide catabolic process|regulation of renal output by angiotensin|regulation of smooth muscle cell migration|regulation of vasoconstriction|regulation of vasodilation	endosome|external side of plasma membrane|extracellular space|integral to membrane|membrane fraction|plasma membrane	actin binding|bradykinin receptor binding|carboxypeptidase activity|chloride ion binding|drug binding|metallopeptidase activity|peptidyl-dipeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3					Benazepril(DB00542)|Captopril(DB01197)|Deserpidine(DB01089)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)									0.065476	-9.823931	23.12859	11	157	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61558508	61558508	137	17	G	A	A	A	429	33	ACE	2	2
ACE	1636	broad.mit.edu	37	17	61568643	61568643	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:61568643C>G	uc002jau.1	+	c.2813C>G	c.(2812-2814)CCT>CGT	p.P938R	ACE_uc002jav.1_Missense_Mutation_p.P364R|ACE_uc010ddv.1_Missense_Mutation_p.P165R|ACE_uc010wpj.1_Missense_Mutation_p.P364R|ACE_uc002jaw.1_Non-coding_Transcript|ACE_uc010wpk.1_Missense_Mutation_p.P184R	NM_000789	NP_000780	P12821	ACE_HUMAN	angiotensin I converting enzyme 1 isoform 1	938	Extracellular (Potential).|Peptidase M2 2.				angiotensin catabolic process in blood|arachidonic acid secretion|blood vessel remodeling|hemopoietic stem cell differentiation|hormone catabolic process|kidney development|mononuclear cell proliferation|peptide catabolic process|regulation of renal output by angiotensin|regulation of smooth muscle cell migration|regulation of vasoconstriction|regulation of vasodilation	endosome|external side of plasma membrane|extracellular space|integral to membrane|membrane fraction|plasma membrane	actin binding|bradykinin receptor binding|carboxypeptidase activity|chloride ion binding|drug binding|metallopeptidase activity|peptidyl-dipeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3					Benazepril(DB00542)|Captopril(DB01197)|Deserpidine(DB01089)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)									0.092593	0.265521	18.329189	10	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61568643	61568643	137	17	C	G	G	G	312	24	ACE	3	3
SCN4A	6329	broad.mit.edu	37	17	62025295	62025295	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:62025295C>A	uc002jds.1	-	c.3273G>T	c.(3271-3273)GTG>GTT	p.V1091V		NM_000334	NP_000325	P35499	SCN4A_HUMAN	voltage-gated sodium channel type 4 alpha	1091	III.				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)									0.273973	54.972099	58.329485	20	53	KEEP	---	---	---	---	capture		Silent	SNP	62025295	62025295	14402	17	C	A	A	A	210	17	SCN4A	2	2
BPTF	2186	broad.mit.edu	37	17	65940369	65940369	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:65940369A>T	uc002jgf.2	+	c.6581A>T	c.(6580-6582)CAG>CTG	p.Q2194L	BPTF_uc002jge.2_Missense_Mutation_p.Q2320L|BPTF_uc002jgg.2_5'UTR	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2320					brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|transcription regulator activity|zinc ion binding			ovary(2)	2	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)											0.3625	248.356364	252.35027	87	153	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65940369	65940369	1523	17	A	T	T	T	91	7	BPTF	3	3
ABCA9	10350	broad.mit.edu	37	17	66980199	66980199	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:66980199C>A	uc002jhu.2	-	c.4497G>T	c.(4495-4497)CTG>CTT	p.L1499L	ABCA9_uc010dez.2_Silent_p.L1461L	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	1499	ABC transporter 2.				transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|central_nervous_system(1)	5	Breast(10;1.47e-12)													0.277778	68.347115	73.191896	30	78	KEEP	---	---	---	---	capture		Silent	SNP	66980199	66980199	40	17	C	A	A	A	366	29	ABCA9	2	2
BCL6B	255877	broad.mit.edu	37	17	6929781	6929781	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:6929781G>T	uc010clt.1	+	c.898G>T	c.(898-900)GAA>TAA	p.E300*	BCL6B_uc002geg.2_Nonsense_Mutation_p.E299*	NM_181844	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B (zinc finger	299						nucleus	zinc ion binding			skin(1)	1														0.21256	92.187542	107.998037	44	163	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	6929781	6929781	1398	17	G	T	T	T	585	45	BCL6B	5	2
TTYH2	94015	broad.mit.edu	37	17	72218757	72218757	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:72218757G>T	uc002jkc.2	+	c.263G>T	c.(262-264)TGC>TTC	p.C88F	TTYH2_uc010wqw.1_Missense_Mutation_p.C67F	NM_032646	NP_116035	Q9BSA4	TTYH2_HUMAN	tweety 2 isoform 1	88	Helical; Name=2; (Potential).					chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4														0.073394	-3.086062	17.306155	8	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72218757	72218757	17295	17	G	T	T	T	598	46	TTYH2	2	2
TP53	7157	broad.mit.edu	37	17	7577123	7577123	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7577123A>C	uc002gim.2	-	c.815T>G	c.(814-816)GTG>GGG	p.V272G	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.V272G|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.V140G|TP53_uc010cng.1_Missense_Mutation_p.V140G|TP53_uc002gii.1_Missense_Mutation_p.V140G|TP53_uc010cnh.1_Missense_Mutation_p.V272G|TP53_uc010cni.1_Missense_Mutation_p.V272G|TP53_uc002gij.2_Missense_Mutation_p.V272G	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	272	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		V -> M (in sporadic cancers; somatic mutation).|V -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|V -> A (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|V -> G (in sporadic cancers; somatic mutation).|V -> E (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.V272E(8)|p.V272A(7)|p.0?(6)|p.V272G(4)|p.?(2)|p.F270fs*72(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.E271fs*73(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111		690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.185185	24.022476	29.037686	10	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7577123	7577123	16923	17	A	C	C	C	78	6	TP53	4	4
AFMID	125061	broad.mit.edu	37	17	76202119	76202119	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:76202119C>T	uc002juz.3	+	c.888C>T	c.(886-888)AAC>AAT	p.N296N	AFMID_uc002jvb.3_3'UTR|AFMID_uc002jva.3_Silent_p.N291N	NM_001145526	NP_001138998	Q63HM1	AFMID_HUMAN	arylformamidase isoform 2	291						cytosol|nucleus	arylformamidase activity			large_intestine(1)|pancreas(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.134)											0.38961	85.725213	86.549256	30	47	KEEP	---	---	---	---	capture		Silent	SNP	76202119	76202119	363	17	C	T	T	T	246	19	AFMID	1	1
DNAH2	146754	broad.mit.edu	37	17	7722377	7722377	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7722377G>C	uc002giu.1	+	c.10811G>C	c.(10810-10812)CGG>CCG	p.R3604P	DNAH2_uc010cnm.1_Missense_Mutation_p.R542P	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	3604					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|central_nervous_system(1)	7		all_cancers(10;4.66e-07)|Prostate(122;0.081)												0.3	15.441741	16.15685	6	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7722377	7722377	4785	17	G	C	C	C	507	39	DNAH2	3	3
AZI1	22994	broad.mit.edu	37	17	79177294	79177294	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:79177294T>C	uc002jzp.1	-	c.629A>G	c.(628-630)AAC>AGC	p.N210S	AZI1_uc002jzn.1_Missense_Mutation_p.N210S|AZI1_uc002jzo.1_Missense_Mutation_p.N210S|AZI1_uc010wum.1_Missense_Mutation_p.N210S	NM_014984	NP_055799	Q9UPN4	AZI1_HUMAN	5-azacytidine induced 1 isoform a	210					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)											0.3	19.943169	20.657299	6	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79177294	79177294	1261	17	T	C	C	C	728	56	AZI1	4	4
GAS7	8522	broad.mit.edu	37	17	9830018	9830018	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:9830018G>T	uc002gmg.1	-	c.954C>A	c.(952-954)TGC>TGA	p.C318*	GAS7_uc010vvc.1_Nonsense_Mutation_p.C132*|GAS7_uc002gmh.1_Nonsense_Mutation_p.C178*|GAS7_uc010vvd.1_Nonsense_Mutation_p.C270*|GAS7_uc002gmi.2_Nonsense_Mutation_p.C254*|GAS7_uc002gmj.1_Nonsense_Mutation_p.C258*|GAS7_uc010coh.1_Nonsense_Mutation_p.C258*	NM_201433	NP_958839	O60861	GAS7_HUMAN	growth arrest-specific 7 isoform c	318	Potential.				cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			pancreas(1)	1										523				0.25	62.061425	67.510258	24	72	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	9830018	9830018	6514	17	G	T	T	T	490	38	GAS7	5	1
NAPG	8774	broad.mit.edu	37	18	10548349	10548349	+	Silent	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:10548349A>G	uc002kon.2	+	c.639A>G	c.(637-639)GCA>GCG	p.A213A	NAPG_uc010wzr.1_Silent_p.A131A|NAPG_uc002koo.2_Silent_p.A126A|NAPG_uc002kop.2_Silent_p.A126A	NM_003826	NP_003817	Q99747	SNAG_HUMAN	N-ethylmaleimide-sensitive factor attachment	213					cellular membrane fusion|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein complex assembly|protein stabilization	membrane|membrane fraction|mitochondrion	protein binding				0														0.133333	33.756388	51.369601	18	117	KEEP	---	---	---	---	capture		Silent	SNP	10548349	10548349	10560	18	A	G	G	G	80	7	NAPG	4	4
ZNF521	25925	broad.mit.edu	37	18	22806833	22806833	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:22806833C>A	uc002kvk.2	-	c.1049G>T	c.(1048-1050)GGC>GTC	p.G350V	ZNF521_uc010xbe.1_Non-coding_Transcript|ZNF521_uc010dly.2_Missense_Mutation_p.G350V|ZNF521_uc002kvl.2_Missense_Mutation_p.G130V	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521	350					cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)									266				0.178571	24.070085	32.170633	15	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22806833	22806833	18559	18	C	A	A	A	338	26	ZNF521	2	2
ZNF521	25925	broad.mit.edu	37	18	22807008	22807008	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:22807008C>A	uc002kvk.2	-	c.874G>T	c.(874-876)GAG>TAG	p.E292*	ZNF521_uc010xbe.1_Non-coding_Transcript|ZNF521_uc010dly.2_Nonsense_Mutation_p.E292*|ZNF521_uc002kvl.2_Nonsense_Mutation_p.E72*	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521	292	C2H2-type 7.				cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)									266				0.151899	17.552661	26.717582	12	67	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	22807008	22807008	18559	18	C	A	A	A	416	32	ZNF521	5	2
ZNF521	25925	broad.mit.edu	37	18	22807248	22807248	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:22807248G>T	uc002kvk.2	-	c.634C>A	c.(634-636)CTG>ATG	p.L212M	ZNF521_uc010xbe.1_Non-coding_Transcript|ZNF521_uc010dly.2_Missense_Mutation_p.L212M|ZNF521_uc002kvl.2_De_novo_Start_InFrame	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521	212	C2H2-type 5.				cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)									266				0.112903	6.17541	15.352084	7	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22807248	22807248	18559	18	G	T	T	T	425	33	ZNF521	2	2
CDH2	1000	broad.mit.edu	37	18	25532249	25532249	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:25532249A>T	uc002kwg.2	-	c.2589T>A	c.(2587-2589)AGT>AGA	p.S863R	CDH2_uc010xbn.1_Missense_Mutation_p.S832R	NM_001792	NP_001783	P19022	CADH2_HUMAN	cadherin 2, type 1 preproprotein	863	Ser-rich.|Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)	3										264		OREG0003876	type=REGULATORY REGION|Gene=CDH2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	0.178218	37.803819	47.637358	18	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25532249	25532249	3234	18	A	T	T	T	76	6	CDH2	3	3
DSC2	1824	broad.mit.edu	37	18	28662236	28662236	+	Nonsense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:28662236T>A	uc002kwl.3	-	c.1231A>T	c.(1231-1233)AAA>TAA	p.K411*	DSC2_uc002kwk.3_Nonsense_Mutation_p.K411*	NM_024422	NP_077740	Q02487	DSC2_HUMAN	desmocollin 2 isoform Dsc2a preproprotein	411	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(10;0.0241)											0.188679	19.217568	24.027037	10	43	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	28662236	28662236	4950	18	T	A	A	A	819	63	DSC2	5	3
DSG1	1828	broad.mit.edu	37	18	28916564	28916564	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:28916564C>T	uc002kwp.2	+	c.1253C>T	c.(1252-1254)TCA>TTA	p.S418L		NM_001942	NP_001933	Q02413	DSG1_HUMAN	desmoglein 1 preproprotein	418	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			ovary(2)|central_nervous_system(2)	4			OV - Ovarian serous cystadenocarcinoma(10;0.00559)											0.168831	23.522042	31.522893	13	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28916564	28916564	4960	18	C	T	T	T	377	29	DSG1	2	2
DSG1	1828	broad.mit.edu	37	18	28918286	28918286	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:28918286T>C	uc002kwp.2	+	c.1274T>C	c.(1273-1275)ATG>ACG	p.M425T		NM_001942	NP_001933	Q02413	DSG1_HUMAN	desmoglein 1 preproprotein	425	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			ovary(2)|central_nervous_system(2)	4			OV - Ovarian serous cystadenocarcinoma(10;0.00559)											0.15	20.437549	27.480875	9	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28918286	28918286	4960	18	T	C	C	C	663	51	DSG1	4	4
DSG3	1830	broad.mit.edu	37	18	29055792	29055792	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:29055792G>T	uc002kws.2	+	c.2569G>T	c.(2569-2571)GCA>TCA	p.A857S	DSG3_uc002kwt.2_Missense_Mutation_p.A139S	NM_001944	NP_001935	P32926	DSG3_HUMAN	desmoglein 3 preproprotein	857	Cytoplasmic (Potential).				cellular component disassembly involved in apoptosis|homophilic cell adhesion	cytosol|desmosome|integral to membrane	calcium ion binding			ovary(3)|lung(1)|central_nervous_system(1)	5			OV - Ovarian serous cystadenocarcinoma(10;0.00504)											0.109244	12.782636	30.782114	13	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29055792	29055792	4962	18	G	T	T	T	598	46	DSG3	2	2
DSG2	1829	broad.mit.edu	37	18	29125888	29125888	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:29125888A>T	uc002kwu.3	+	c.2539A>T	c.(2539-2541)ATA>TTA	p.I847L		NM_001943	NP_001934	Q14126	DSG2_HUMAN	desmoglein 2 preproprotein	847	Cytoplasmic (Potential).				cellular component disassembly involved in apoptosis|homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(2)|breast(1)	8			OV - Ovarian serous cystadenocarcinoma(10;0.0068)											0.166667	41.402024	54.670757	21	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29125888	29125888	4961	18	A	T	T	T	208	16	DSG2	3	3
DSG2	1829	broad.mit.edu	37	18	29125986	29125986	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:29125986G>C	uc002kwu.3	+	c.2637G>C	c.(2635-2637)GAG>GAC	p.E879D		NM_001943	NP_001934	Q14126	DSG2_HUMAN	desmoglein 2 preproprotein	879	Cytoplasmic (Potential).				cellular component disassembly involved in apoptosis|homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(2)|breast(1)	8			OV - Ovarian serous cystadenocarcinoma(10;0.0068)											0.125	31.107078	48.692431	16	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29125986	29125986	4961	18	G	C	C	C	425	33	DSG2	3	3
C18orf34	374864	broad.mit.edu	37	18	30926193	30926193	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:30926193G>A	uc010xbr.1	-	c.640C>T	c.(640-642)CCA>TCA	p.P214S	C18orf34_uc002kxn.2_Missense_Mutation_p.P214S|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Missense_Mutation_p.P214S|C18orf34_uc002kxp.2_Missense_Mutation_p.P214S	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1	214										ovary(1)	1														0.09434	6.263306	23.791938	10	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30926193	30926193	1963	18	G	A	A	A	559	43	C18orf34	2	2
C18orf34	374864	broad.mit.edu	37	18	30928890	30928890	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:30928890T>A	uc010xbr.1	-	c.421A>T	c.(421-423)ACA>TCA	p.T141S	C18orf34_uc002kxn.2_Missense_Mutation_p.T141S|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Missense_Mutation_p.T141S|C18orf34_uc002kxp.2_Missense_Mutation_p.T141S	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1	141										ovary(1)	1														0.109091	5.913045	14.234775	6	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30928890	30928890	1963	18	T	A	A	A	741	57	C18orf34	3	3
ASXL3	80816	broad.mit.edu	37	18	31325263	31325263	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:31325263A>T	uc010dmg.1	+	c.5451A>T	c.(5449-5451)CCA>CCT	p.P1817P	ASXL3_uc002kxq.2_Silent_p.P1524P	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1817					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3														0.143969	65.320095	96.671968	37	220	KEEP	---	---	---	---	capture		Silent	SNP	31325263	31325263	1087	18	A	T	T	T	67	6	ASXL3	3	3
DTNA	1837	broad.mit.edu	37	18	32459515	32459515	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:32459515A>T	uc010dmn.1	+	c.1913A>T	c.(1912-1914)GAG>GTG	p.E638V	DTNA_uc002kxw.2_Missense_Mutation_p.E581V|DTNA_uc010dmj.2_Missense_Mutation_p.E578V|DTNA_uc002kxz.2_Missense_Mutation_p.E585V|DTNA_uc002kxy.2_Missense_Mutation_p.E578V|DTNA_uc010xby.1_Missense_Mutation_p.E328V|DTNA_uc010xbz.1_Missense_Mutation_p.E347V|DTNA_uc010xca.1_Missense_Mutation_p.E290V|DTNA_uc002kye.2_Missense_Mutation_p.E286V	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1	638					neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0														0.1	4.004731	13.595898	6	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32459515	32459515	4973	18	A	T	T	T	143	11	DTNA	3	3
ELP2	55250	broad.mit.edu	37	18	33724961	33724961	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:33724961G>T	uc010xcg.1	+	c.1051G>T	c.(1051-1053)GTA>TTA	p.V351L	ELP2_uc002kzk.1_Missense_Mutation_p.V286L|ELP2_uc002kzl.1_Non-coding_Transcript|ELP2_uc002kzm.1_Missense_Mutation_p.V260L|ELP2_uc010xch.1_Missense_Mutation_p.V325L|ELP2_uc002kzn.1_Missense_Mutation_p.V260L|ELP2_uc002kzo.1_Missense_Mutation_p.V216L	NM_018255	NP_060725	Q6IA86	ELP2_HUMAN	elongator protein 2	286	WD 6.				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	DNA-directed RNA polymerase II, holoenzyme|Golgi apparatus|nucleolus|transcription elongation factor complex	RNA polymerase II transcription elongation factor activity			breast(2)|skin(1)	3														0.176471	45.613906	57.342963	21	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33724961	33724961	5272	18	G	T	T	T	572	44	ELP2	2	2
SYT4	6860	broad.mit.edu	37	18	40853820	40853820	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:40853820G>T	uc002law.2	-	c.574C>A	c.(574-576)CCA>ACA	p.P192T	SYT4_uc010dng.2_Intron|SYT4_uc010xcm.1_Missense_Mutation_p.P174T|SYT4_uc010dnh.2_Intron	NM_020783	NP_065834	Q9H2B2	SYT4_HUMAN	synaptotagmin IV	192	Phospholipid binding (Probable).|C2 1.|Cytoplasmic (Potential).					cell junction|integral to membrane|synaptic vesicle membrane	transporter activity				0						NSCLC(85;81 1419 2855 22820 35912)								0.081395	-0.945943	14.408773	7	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40853820	40853820	15997	18	G	T	T	T	559	43	SYT4	2	2
SETBP1	26040	broad.mit.edu	37	18	42643085	42643085	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:42643085G>C	uc010dni.2	+	c.4213G>C	c.(4213-4215)GAA>CAA	p.E1405Q		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	1405						nucleus	DNA binding			large_intestine(1)	1				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										0.203125	32.641876	37.877358	13	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42643085	42643085	14617	18	G	C	C	C	481	37	SETBP1	3	3
SLC14A2	8170	broad.mit.edu	37	18	43249357	43249357	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:43249357T>C	uc010dnj.2	+	c.2123T>C	c.(2122-2124)TTG>TCG	p.L708S	SLC14A2_uc002lbe.2_Missense_Mutation_p.L708S	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),	708	Helical; (Potential).					apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2														0.09396	15.478846	64.905782	28	270	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43249357	43249357	14892	18	T	C	C	C	819	63	SLC14A2	4	4
ST8SIA5	29906	broad.mit.edu	37	18	44260275	44260275	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:44260275G>T	uc010xcy.1	-	c.969C>A	c.(967-969)CGC>CGA	p.R323R	ST8SIA5_uc002lci.1_Silent_p.R134R|ST8SIA5_uc002lcj.1_Silent_p.R287R|ST8SIA5_uc010xcz.1_Silent_p.R256R	NM_013305	NP_037437	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide	287	Lumenal (Potential).				glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				ovary(1)|pancreas(1)	2														0.165138	31.677606	43.286173	18	91	KEEP	---	---	---	---	capture		Silent	SNP	44260275	44260275	15753	18	G	T	T	T	431	34	ST8SIA5	2	2
SMAD2	4087	broad.mit.edu	37	18	45368312	45368312	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:45368312C>A	uc002lcy.2	-	c.1290G>T	c.(1288-1290)ACG>ACT	p.T430T	SMAD2_uc002lcz.2_Silent_p.T430T|SMAD2_uc010xdc.1_Silent_p.T400T	NM_005901	NP_005892	Q15796	SMAD2_HUMAN	Sma- and Mad-related protein 2 isoform 1	430	MH2.				anterior/posterior pattern formation|cell fate commitment|common-partner SMAD protein phosphorylation|intracellular signal transduction|mesoderm formation|negative regulation of transcription, DNA-dependent|palate development|paraxial mesoderm morphogenesis|positive regulation of epithelial to mesenchymal transition|positive regulation of gene-specific transcription|positive regulation of transcription from RNA polymerase II promoter|primary microRNA processing|regulation of binding|regulation of transforming growth factor beta receptor signaling pathway|response to cholesterol|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|zygotic specification of dorsal/ventral axis	activin responsive factor complex|cytosol	co-SMAD binding|double-stranded DNA binding|I-SMAD binding|promoter binding|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription factor binding|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding			large_intestine(3)|lung(1)|central_nervous_system(1)	5									p.T430T(HEC108-Tumor)	268				0.084507	2.194169	14.634791	6	65	KEEP	---	---	---	---	capture		Silent	SNP	45368312	45368312	15256	18	C	A	A	A	288	23	SMAD2	1	1
MEX3C	51320	broad.mit.edu	37	18	48702765	48702765	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:48702765C>A	uc002lfc.3	-	c.1936G>T	c.(1936-1938)GTT>TTT	p.V646F		NM_016626	NP_057710	Q5U5Q3	MEX3C_HUMAN	ring finger and KH domain containing 2	646	RING-type.					cytoplasm|nucleus	RNA binding|zinc ion binding			ovary(1)|skin(1)	2		Colorectal(6;0.003)|all_epithelial(6;0.0473)		Colorectal(16;0.0175)|READ - Rectum adenocarcinoma(32;0.15)										0.137255	24.475502	37.465825	14	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48702765	48702765	9901	18	C	A	A	A	260	20	MEX3C	2	2
WDR7	23335	broad.mit.edu	37	18	54385314	54385314	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:54385314C>G	uc002lgk.1	+	c.1698C>G	c.(1696-1698)ATC>ATG	p.I566M	WDR7_uc010dpk.1_Non-coding_Transcript|WDR7_uc002lgl.1_Missense_Mutation_p.I566M	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	566	WD 7.									ovary(2)	2				Lung(128;0.0238)|Colorectal(16;0.0296)										0.123223	52.192421	81.500653	26	185	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54385314	54385314	17893	18	C	G	G	G	369	29	WDR7	3	3
CDH20	28316	broad.mit.edu	37	18	59203752	59203752	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:59203752C>A	uc010dps.1	+	c.1298C>A	c.(1297-1299)CCT>CAT	p.P433H	CDH20_uc002lif.2_Missense_Mutation_p.P427H	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	433	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)												0.066667	-15.924956	30.934121	16	224	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59203752	59203752	3235	18	C	A	A	A	312	24	CDH20	2	2
CDH20	28316	broad.mit.edu	37	18	59206354	59206354	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:59206354C>A	uc010dps.1	+	c.1506C>A	c.(1504-1506)GTC>GTA	p.V502V	CDH20_uc002lif.2_Silent_p.V496V	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	502	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)												0.125	34.105737	72.630132	35	245	KEEP	---	---	---	---	capture		Silent	SNP	59206354	59206354	3235	18	C	A	A	A	405	32	CDH20	2	2
ZCCHC2	54877	broad.mit.edu	37	18	60241759	60241759	+	Silent	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:60241759A>G	uc002lip.3	+	c.2445A>G	c.(2443-2445)CTA>CTG	p.L815L	ZCCHC2_uc002lio.2_Non-coding_Transcript|ZCCHC2_uc002liq.2_Silent_p.L285L	NM_017742	NP_060212	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	815					cell communication	cytoplasm	nucleic acid binding|phosphatidylinositol binding|zinc ion binding				0														0.176471	56.524681	68.243147	21	98	KEEP	---	---	---	---	capture		Silent	SNP	60241759	60241759	18175	18	A	G	G	G	158	13	ZCCHC2	4	4
PHLPP1	23239	broad.mit.edu	37	18	60506077	60506077	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:60506077C>T	uc002lis.2	+	c.298C>T	c.(298-300)CAG>TAG	p.Q100*		NM_194449	NP_919431	O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein	612	PH.				apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|membrane|nucleus	metal ion binding|protein serine/threonine phosphatase activity				0														0.298851	71.512818	74.660729	26	61	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	60506077	60506077	12278	18	C	T	T	T	273	21	PHLPP1	5	2
SERPINB12	89777	broad.mit.edu	37	18	61234147	61234147	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61234147C>T	uc010xeo.1	+	c.1181C>T	c.(1180-1182)TCT>TTT	p.S394F	SERPINB12_uc010xen.1_Missense_Mutation_p.S374F	NM_080474	NP_536722	Q96P63	SPB12_HUMAN	serine (or cysteine) proteinase inhibitor, clade	374					negative regulation of protein catabolic process|regulation of proteolysis	cytoplasm	enzyme binding|serine-type endopeptidase inhibitor activity				0														0.090909	4.293821	21.003652	9	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61234147	61234147	14587	18	C	T	T	T	416	32	SERPINB12	2	2
SERPINB7	8710	broad.mit.edu	37	18	61471509	61471509	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61471509G>C	uc002ljl.2	+	c.783G>C	c.(781-783)TGG>TGC	p.W261C	SERPINB7_uc002ljm.2_Missense_Mutation_p.W261C|SERPINB7_uc010xet.1_Missense_Mutation_p.W244C|SERPINB7_uc010dqg.2_Missense_Mutation_p.W261C	NM_001040147	NP_001035237	O75635	SPB7_HUMAN	serine (or cysteine) proteinase inhibitor, clade	261					regulation of proteolysis	cytoplasm	serine-type endopeptidase inhibitor activity			lung(2)|central_nervous_system(1)	3		Esophageal squamous(42;0.129)												0.156863	20.465256	26.195256	8	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61471509	61471509	14594	18	G	C	C	C	533	41	SERPINB7	3	3
LAMA1	284217	broad.mit.edu	37	18	6961756	6961756	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:6961756G>T	uc002knm.2	-	c.7455C>A	c.(7453-7455)CCC>CCA	p.P2485P	LAMA1_uc002knl.2_Intron|LAMA1_uc010wzj.1_Silent_p.P1961P	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	2485					axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.166667	13.395964	17.822815	7	35	KEEP	---	---	---	---	capture		Silent	SNP	6961756	6961756	8928	18	G	T	T	T	600	47	LAMA1	2	2
LAMA1	284217	broad.mit.edu	37	18	6966160	6966160	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:6966160C>A	uc002knm.2	-	c.7036G>T	c.(7036-7038)GGT>TGT	p.G2346C	LAMA1_uc002knl.2_5'Flank|LAMA1_uc010wzj.1_Missense_Mutation_p.G1822C	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	2346	Laminin G-like 2.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.209302	19.44846	22.814427	9	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6966160	6966160	8928	18	C	A	A	A	286	22	LAMA1	2	2
CBLN2	147381	broad.mit.edu	37	18	70209226	70209226	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:70209226G>T	uc002lku.2	-	c.170C>A	c.(169-171)CCC>CAC	p.P57H	CBLN2_uc002lkv.2_Missense_Mutation_p.P57H	NM_182511	NP_872317	Q8IUK8	CBLN2_HUMAN	cerebellin 2 precursor	57						integral to membrane					0		Esophageal squamous(42;0.131)												0.227273	10.287857	11.773552	5	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70209226	70209226	2824	18	G	T	T	T	559	43	CBLN2	2	2
LAMA1	284217	broad.mit.edu	37	18	7079972	7079972	+	Splice_Site_SNP	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:7079972A>G	uc002knm.2	-	c.345_splice	c.e3+1	p.Q115_splice	LAMA1_uc010wzj.1_Splice_Site_SNP	NM_005559	NP_005550			laminin, alpha 1 precursor						axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.144444	30.223892	41.16498	13	77	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	7079972	7079972	8928	18	A	G	G	G	182	14	LAMA1	5	4
MBP	4155	broad.mit.edu	37	18	74778254	74778254	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:74778254C>A	uc010xfd.1	-	c.139G>T	c.(139-141)GGA>TGA	p.G47*	MBP_uc002lmr.2_Nonsense_Mutation_p.G47*	NM_001025101	NP_001020272	P02686	MBP_HUMAN	Golli-mbp isoform 1	47					central nervous system development|immune response|synaptic transmission	plasma membrane	structural constituent of myelin sheath				0		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)		NSCLC(17;72 1131 19392)								0.19469	49.176433	59.010832	22	91	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	74778254	74778254	9748	18	C	A	A	A	299	23	MBP	5	1
SALL3	27164	broad.mit.edu	37	18	76753279	76753279	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:76753279G>T	uc002lmt.2	+	c.1288G>T	c.(1288-1290)GGC>TGC	p.G430C	SALL3_uc010dra.2_Missense_Mutation_p.G37C	NM_171999	NP_741996	Q9BXA9	SALL3_HUMAN	sal-like 3	430	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)										0.131579	6.141522	11.173893	5	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76753279	76753279	14292	18	G	T	T	T	507	39	SALL3	1	1
SALL3	27164	broad.mit.edu	37	18	76757283	76757283	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:76757283G>T	uc002lmt.2	+	c.3864G>T	c.(3862-3864)ACG>ACT	p.T1288T	SALL3_uc010dra.2_Silent_p.T823T	NM_171999	NP_741996	Q9BXA9	SALL3_HUMAN	sal-like 3	1288					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)										0.086331	3.839127	51.990634	24	254	KEEP	---	---	---	---	capture		Silent	SNP	76757283	76757283	14292	18	G	T	T	T	483	38	SALL3	1	1
KIAA0802	23255	broad.mit.edu	37	18	8824925	8824925	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:8824925G>T	uc002knr.2	+	c.3417G>T	c.(3415-3417)GGG>GGT	p.G1139G	KIAA0802_uc002knq.2_Silent_p.G1098G|KIAA0802_uc002kns.2_Silent_p.G479G	NM_015210	NP_056025	Q9Y4B5	K0802_HUMAN	hypothetical protein LOC23255	1449										ovary(6)|central_nervous_system(1)	7										468				0.203008	52.268247	63.163034	27	106	KEEP	---	---	---	---	capture		Silent	SNP	8824925	8824925	8501	18	G	T	T	T	535	42	KIAA0802	2	2
ZNF491	126069	broad.mit.edu	37	19	11917808	11917808	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11917808G>C	uc002mso.1	+	c.1040G>C	c.(1039-1041)AGG>ACG	p.R347T		NM_152356	NP_689569	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	347	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.129032	12.856812	21.16509	8	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11917808	11917808	18536	19	G	C	C	C	455	35	ZNF491	3	3
ZNF700	90592	broad.mit.edu	37	19	12060814	12060814	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:12060814A>G	uc002msu.2	+	c.1975A>G	c.(1975-1977)AAA>GAA	p.K659E	ZNF700_uc010xme.1_Missense_Mutation_p.K677E|ZNF763_uc010xmf.1_Intron	NM_144566	NP_653167	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	659	C2H2-type 16.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.151515	23.510348	31.181793	10	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12060814	12060814	18699	19	A	G	G	G	169	13	ZNF700	4	4
ZNF763	284390	broad.mit.edu	37	19	12087964	12087964	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:12087964A>T	uc010xmf.1	+	c.175A>T	c.(175-177)AAC>TAC	p.N59Y	ZNF763_uc002msv.2_Missense_Mutation_p.N42Y|ZNF763_uc002msw.2_Missense_Mutation_p.N39Y|ZNF763_uc010xmg.1_Intron	NM_001012753	NP_001012771	Q0D2J5	ZN763_HUMAN	zinc finger protein 763	39	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1														0.133803	19.911723	38.431079	19	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12087964	12087964	18735	19	A	T	T	T	117	9	ZNF763	3	3
CLEC17A	388512	broad.mit.edu	37	19	14694178	14694178	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:14694178A>C	uc010dzo.1	+	c.53A>C	c.(52-54)GAG>GCG	p.E18A	CLEC17A_uc002mzh.1_Missense_Mutation_p.E18A|CLEC17A_uc010xnt.1_Non-coding_Transcript|CLEC17A_uc010dzn.1_Missense_Mutation_p.E18A|CLEC17A_uc010xnu.1_Missense_Mutation_p.E18A	NM_207390	NP_997273	Q6ZS10	CL17A_HUMAN	C-type lectin domain family 17, member A	18	Cytoplasmic (Potential).|Poly-Glu.					cell surface|integral to membrane	fucose binding|mannose binding|metal ion binding|receptor activity				0														0.137931	6.581518	10.258324	4	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14694178	14694178	3638	19	A	C	C	C	143	11	CLEC17A	4	4
AKAP8	10270	broad.mit.edu	37	19	15483986	15483986	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15483986C>T	uc002nav.2	-	c.537G>A	c.(535-537)GAG>GAA	p.E179E	AKAP8_uc010dzy.2_5'UTR|AKAP8_uc010dzz.1_Non-coding_Transcript|AKAP8_uc010xog.1_5'UTR	NM_005858	NP_005849	O43823	AKAP8_HUMAN	A-kinase anchor protein 8	179					signal transduction	nuclear matrix				ovary(1)|breast(1)	2						GBM(190;1671 2163 3274 27186 30476)								0.134615	8.549817	15.232335	7	45	KEEP	---	---	---	---	capture		Silent	SNP	15483986	15483986	460	19	C	T	T	T	363	28	AKAP8	2	2
CYP4F22	126410	broad.mit.edu	37	19	15651462	15651463	+	Missense_Mutation	DNP	CG	GA	GA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15651462_15651463CG>GA	uc002nbh.3	+	c.873_874CG>GA	c.(871-876)GCCGAG>GCGAAG	p.E292K		NM_173483	NP_775754	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F,	292					oxidation-reduction process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|monooxygenase activity			pancreas(1)	1														0.116279	15.204608	27.651517	10	76	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	15651462	15651463	4354	19	CG	GA	GA	GA	288	23	CYP4F22	3	3
UQCR11	10975	broad.mit.edu	37	19	1599497	1599497	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:1599497C>A	uc002ltm.2	-	c.113G>T	c.(112-114)TGG>TTG	p.W38L		NM_006830	NP_006821	O14957	QCR10_HUMAN	ubiquinol-cytochrome c reductase, 6.4kDa	38					respiratory electron transport chain	integral to membrane|mitochondrial inner membrane|respiratory chain	electron carrier activity			ovary(1)|breast(1)	2														0.215385	61.920712	71.64898	28	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1599497	1599497	17578	19	C	A	A	A	273	21	UQCR11	2	2
AP1M1	8907	broad.mit.edu	37	19	16338502	16338502	+	Splice_Site_SNP	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:16338502G>T	uc002ndv.2	+	c.852_splice	c.e8+1	p.H284_splice	AP1M1_uc002ndu.2_Splice_Site_SNP_p.H272_splice|AP1M1_uc010xpd.1_Splice_Site_SNP_p.H272_splice	NM_001130524	NP_001123996			adaptor-related protein complex 1, mu 1 subunit						cellular membrane organization|endosome transport|interspecies interaction between organisms|intracellular protein transport|melanosome organization|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding			ovary(3)|breast(1)	4														0.077966	-1.206705	52.526051	23	272	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	16338502	16338502	744	19	G	T	T	T	520	40	AP1M1	5	1
JAK3	3718	broad.mit.edu	37	19	17937597	17937597	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17937597G>A	uc002nhn.3	-	c.3330C>T	c.(3328-3330)TTC>TTT	p.F1110F	JAK3_uc010ebh.2_Intron	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3	1110	Protein kinase 2.				B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(36)|lung(3)|ovary(3)|stomach(2)|breast(2)	46								2		364				0.088028	1.32128	50.167614	25	259	KEEP	---	---	---	---	capture		Silent	SNP	17937597	17937597	8243	19	G	A	A	A	581	45	JAK3	2	2
PDE4C	5143	broad.mit.edu	37	19	18329183	18329184	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:18329183_18329184GG>TT	uc010xqc.1	-	c.1190_1191CC>AA	c.(1189-1191)GCC>GAA	p.A397E	PDE4C_uc002nik.3_Missense_Mutation_p.A397E|PDE4C_uc002nil.3_Missense_Mutation_p.A397E|PDE4C_uc002nif.3_Missense_Mutation_p.A166E|PDE4C_uc002nig.3_Intron|PDE4C_uc002nih.3_Missense_Mutation_p.A167E|PDE4C_uc010ebk.2_Missense_Mutation_p.A291E|PDE4C_uc002nii.3_Missense_Mutation_p.A365E|PDE4C_uc010ebl.2_Missense_Mutation_p.A111E|PDE4C_uc010xqd.1_Missense_Mutation_p.A166E	NM_001098819	NP_001092289	Q08493	PDE4C_HUMAN	phosphodiesterase 4C isoform PDE4C-2	397					signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Dyphylline(DB00651)									0.256545	123.626047	133.86711	49	142	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	18329183	18329184	12062	19	GG	TT	TT	TT	548	43	PDE4C	2	2
TMEM59L	25789	broad.mit.edu	37	19	18731227	18731227	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:18731227C>T	uc002njy.3	+	c.910C>T	c.(910-912)CTG>TTG	p.L304L		NM_012109	NP_036241	Q9UK28	TM59L_HUMAN	brain-specific membrane-anchored protein	304						Golgi membrane|integral to membrane|membrane fraction				ovary(2)	2														0.135135	24.443616	38.769859	15	96	KEEP	---	---	---	---	capture		Silent	SNP	18731227	18731227	16725	19	C	T	T	T	311	24	TMEM59L	2	2
CILP2	148113	broad.mit.edu	37	19	19655944	19655944	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:19655944G>T	uc002nmw.3	+	c.2608G>T	c.(2608-2610)GCC>TCC	p.A870S	CILP2_uc002nmv.3_Missense_Mutation_p.A864S	NM_153221	NP_694953	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	864						proteinaceous extracellular matrix	carbohydrate binding|carboxypeptidase activity			ovary(1)	1														0.219512	19.66733	22.629483	9	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19655944	19655944	3564	19	G	T	T	T	494	38	CILP2	1	1
ZNF486	90649	broad.mit.edu	37	19	20308560	20308560	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:20308560G>A	uc002nou.2	+	c.1041G>A	c.(1039-1041)GAG>GAA	p.E347E		NM_052852	NP_443084	Q96H40	ZN486_HUMAN	zinc finger protein 486	347					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.095238	3.898569	14.260927	6	57	KEEP	---	---	---	---	capture		Silent	SNP	20308560	20308560	18533	19	G	A	A	A	425	33	ZNF486	2	2
ZNF676	163223	broad.mit.edu	37	19	22363680	22363680	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22363680G>C	uc002nqs.1	-	c.839C>G	c.(838-840)CCC>CGC	p.P280R		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	280					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)												0.078431	-0.67048	17.846397	8	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22363680	22363680	18678	19	G	C	C	C	559	43	ZNF676	3	3
ZNF99	7652	broad.mit.edu	37	19	22939970	22939970	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22939970T>A	uc010xrh.1	-	c.2361A>T	c.(2359-2361)TCA>TCT	p.S787S		NM_001080409	NP_001073878	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	787	C2H2-type 22.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)												0.288462	39.776963	41.883497	15	37	KEEP	---	---	---	---	capture		Silent	SNP	22939970	22939970	18808	19	T	A	A	A	756	59	ZNF99	3	3
ZNF99	7652	broad.mit.edu	37	19	22940130	22940130	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22940130C>G	uc010xrh.1	-	c.2201G>C	c.(2200-2202)AGA>ACA	p.R734T		NM_001080409	NP_001073878	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	734					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)												0.111111	11.776327	21.196479	7	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22940130	22940130	18808	19	C	G	G	G	416	32	ZNF99	3	3
POP4	10775	broad.mit.edu	37	19	30099608	30099608	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:30099608G>T	uc002nsf.2	+	c.52G>T	c.(52-54)GAT>TAT	p.D18Y	POP4_uc002nsg.2_Silent_p.P11P	NM_006627	NP_006618	O95707	RPP29_HUMAN	processing of precursor 4	18					mRNA cleavage|rRNA processing|tRNA processing	nucleolar ribonuclease P complex|ribonuclease MRP complex	identical protein binding|ribonuclease P activity|RNA binding				0	Ovarian(5;0.000567)|Breast(6;0.0602)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0623)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.225)			Melanoma(89;1165 1449 14085 34436 43672)								0.102941	14.410076	46.495618	21	183	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30099608	30099608	12681	19	G	T	T	T	481	37	POP4	1	1
ZNF536	9745	broad.mit.edu	37	19	30935448	30935448	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:30935448G>T	uc002nsu.1	+	c.979G>T	c.(979-981)GAG>TAG	p.E327*	ZNF536_uc010edd.1_Nonsense_Mutation_p.E327*	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	327					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)	9	Esophageal squamous(110;0.0834)													0.164609	67.746903	93.706013	40	203	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	30935448	30935448	18568	19	G	T	T	T	481	37	ZNF536	5	1
ZNF536	9745	broad.mit.edu	37	19	31039574	31039574	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:31039574G>T	uc002nsu.1	+	c.3048G>T	c.(3046-3048)ATG>ATT	p.M1016I	ZNF536_uc010edd.1_Missense_Mutation_p.M1016I	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	1016					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)	9	Esophageal squamous(110;0.0834)													0.079646	-1.807093	18.566543	9	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31039574	31039574	18568	19	G	T	T	T	611	47	ZNF536	2	2
ZNF536	9745	broad.mit.edu	37	19	31039763	31039763	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:31039763G>T	uc002nsu.1	+	c.3237G>T	c.(3235-3237)ATG>ATT	p.M1079I	ZNF536_uc010edd.1_Missense_Mutation_p.M1079I	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	1079					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)	9	Esophageal squamous(110;0.0834)													0.10084	8.717036	27.637501	12	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31039763	31039763	18568	19	G	T	T	T	611	47	ZNF536	2	2
TSHZ3	57616	broad.mit.edu	37	19	31769068	31769068	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:31769068C>T	uc002nsy.3	-	c.1631G>A	c.(1630-1632)TGG>TAG	p.W544*		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	544					regulation of respiratory gaseous exchange by neurological system process|regulation of transcription, DNA-dependent	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|skin(1)	7	Esophageal squamous(110;0.226)													0.114068	26.842259	65.516237	30	233	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	31769068	31769068	17176	19	C	T	T	T	273	21	TSHZ3	5	2
ANKRD27	84079	broad.mit.edu	37	19	33098606	33098606	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:33098606C>T	uc002ntn.1	-	c.2308G>A	c.(2308-2310)GCA>ACA	p.A770T		NM_032139	NP_115515	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	770	ANK 8.				early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|pancreas(1)	3	Esophageal squamous(110;0.137)													0.166667	12.09671	16.527142	7	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33098606	33098606	660	19	C	T	T	T	351	27	ANKRD27	1	1
GPI	2821	broad.mit.edu	37	19	34884875	34884875	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:34884875G>T	uc002nvf.2	+	c.1083G>T	c.(1081-1083)CTG>CTT	p.L361L	GPI_uc010xrv.1_Silent_p.L333L|GPI_uc002nvg.1_Silent_p.L322L|GPI_uc010xrw.1_Silent_p.L294L|GPI_uc010edl.1_Silent_p.L322L|GPI_uc002nvi.1_5'UTR	NM_000175	NP_000166	P06744	G6PI_HUMAN	glucose phosphate isomerase	322					angiogenesis|gluconeogenesis|glycolysis|hemostasis|humoral immune response	cytosol|extracellular space|nucleus|plasma membrane	cytokine activity|glucose-6-phosphate isomerase activity|growth factor activity			ovary(1)|kidney(1)	2	Esophageal squamous(110;0.162)													0.243542	162.910912	179.159911	66	205	KEEP	---	---	---	---	capture		Silent	SNP	34884875	34884875	6885	19	G	T	T	T	587	46	GPI	2	2
UBA2	10054	broad.mit.edu	37	19	34951384	34951384	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:34951384G>T	uc002nvk.2	+	c.1411G>T	c.(1411-1413)GAA>TAA	p.E471*	UBA2_uc010xrx.1_Nonsense_Mutation_p.E344*|UBA2_uc002nvl.2_Nonsense_Mutation_p.E375*	NM_005499	NP_005490	Q9UBT2	SAE2_HUMAN	SUMO-1 activating enzyme subunit 2	471					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)											0.233333	14.411578	16.364821	7	23	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	34951384	34951384	17385	19	G	T	T	T	429	33	UBA2	5	2
UBA2	10054	broad.mit.edu	37	19	34957912	34957912	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:34957912C>G	uc002nvk.2	+	c.1734C>G	c.(1732-1734)ACC>ACG	p.T578T	UBA2_uc002nvl.2_Silent_p.T482T	NM_005499	NP_005490	Q9UBT2	SAE2_HUMAN	SUMO-1 activating enzyme subunit 2	578					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)											0.181818	21.313716	26.547588	10	45	KEEP	---	---	---	---	capture		Silent	SNP	34957912	34957912	17385	19	C	G	G	G	301	24	UBA2	3	3
ZNF792	126375	broad.mit.edu	37	19	35451811	35451812	+	Missense_Mutation	DNP	CG	AA	AA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:35451811_35451812CG>AA	uc002nxh.1	-	c.120_121CG>TT	c.(118-123)TGCGAT>TGTTAT	p.D41Y		NM_175872	NP_787068	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	41	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GBM(1;7 183 21053 22581 22847)								0.189655	61.96493	77.649645	33	141	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	35451811	35451812	18762	19	CG	AA	AA	AA	403	31	ZNF792	1	1
GAPDHS	26330	broad.mit.edu	37	19	36027810	36027811	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36027810_36027811CC>AA	uc002oaf.1	+	c.163_164CC>AA	c.(163-165)CCG>AAG	p.P55K		NM_014364	NP_055179	O14556	G3PT_HUMAN	glyceraldehyde-3-phosphate dehydrogenase,	55					gluconeogenesis|glycolysis|oxidation-reduction process|positive regulation of glycolysis|sperm motility	cytosol	glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity|NAD binding|protein binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		NADH(DB00157)									0.142857	39.937299	60.550049	24	144	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	36027810	36027811	6501	19	CC	AA	AA	AA	234	18	GAPDHS	2	2
ATP4A	495	broad.mit.edu	37	19	36050770	36050770	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36050770G>A	uc002oal.1	-	c.993C>T	c.(991-993)GCC>GCT	p.A331A	ATP4A_uc010eee.1_5'Flank	NM_000704	NP_000695	P20648	ATP4A_HUMAN	hydrogen/potassium-exchanging ATPase 4A	331	Lumenal (Potential).				ATP biosynthetic process|ATP hydrolysis coupled proton transport	integral to plasma membrane	ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831)									0.132353	10.426427	19.358406	9	59	KEEP	---	---	---	---	capture		Silent	SNP	36050770	36050770	1164	19	G	A	A	A	600	47	ATP4A	2	2
KIRREL2	84063	broad.mit.edu	37	19	36350479	36350479	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36350479C>A	uc002ocb.3	+	c.619C>A	c.(619-621)CGG>AGG	p.R207R	KIRREL2_uc002obz.3_Silent_p.R207R|KIRREL2_uc002oca.3_Silent_p.R157R|KIRREL2_uc002occ.3_Silent_p.R154R|KIRREL2_uc002ocd.3_Silent_p.R204R	NM_199180	NP_954649	Q6UWL6	KIRR2_HUMAN	kin of IRRE-like 2 isoform c	207	Ig-like C2-type 2.|Extracellular (Potential).				cell adhesion	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)											0.191489	55.291723	67.797675	27	114	KEEP	---	---	---	---	capture		Silent	SNP	36350479	36350479	8637	19	C	A	A	A	295	23	KIRREL2	1	1
KIRREL2	84063	broad.mit.edu	37	19	36352122	36352122	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36352122G>T	uc002ocb.3	+	c.1155G>T	c.(1153-1155)CGG>CGT	p.R385R	KIRREL2_uc002obz.3_Silent_p.R385R|KIRREL2_uc002oca.3_Silent_p.R335R|KIRREL2_uc002occ.3_Silent_p.R332R|KIRREL2_uc002ocd.3_Silent_p.R382R	NM_199180	NP_954649	Q6UWL6	KIRR2_HUMAN	kin of IRRE-like 2 isoform c	385	Extracellular (Potential).|Ig-like C2-type 4.				cell adhesion	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)											0.192308	5.556194	7.871381	5	21	KEEP	---	---	---	---	capture		Silent	SNP	36352122	36352122	8637	19	G	T	T	T	548	43	KIRREL2	2	2
HCST	10870	broad.mit.edu	37	19	36394806	36394806	+	Splice_Site_SNP	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36394806G>T	uc002ocl.1	+	c.241_splice	c.e3+1	p.E81_splice	HCST_uc002ock.1_Splice_Site_SNP_p.D81_splice	NM_014266	NP_055081			hematopoietic cell signal transducer isoform 1						regulation of immune response	integral to membrane|plasma membrane					0	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)											0.130435	9.331633	15.431481	6	40	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	36394806	36394806	7286	19	G	T	T	T	572	44	HCST	5	2
CLIP3	25999	broad.mit.edu	37	19	36517911	36517911	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36517911C>T	uc010eeq.1	-	c.343G>A	c.(343-345)GGG>AGG	p.G115R	CLIP3_uc002ocz.1_Missense_Mutation_p.G115R	NM_015526	NP_056341	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	115					chaperone-mediated protein transport|fat cell differentiation|membrane biogenesis|negative regulation of microtubule polymerization|peptidyl-L-cysteine S-palmitoylation|positive regulation of apoptosis|positive regulation of endocytosis|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose transport|positive regulation of protein phosphorylation	early endosome membrane|Golgi stack|membrane raft|microsome|plasma membrane|recycling endosome membrane|trans-Golgi network membrane	ganglioside binding|microtubule binding			ovary(2)|pancreas(1)	3	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)											0.097561	6.237661	19.53602	8	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36517911	36517911	3672	19	C	T	T	T	299	23	CLIP3	1	1
FAM98C	147965	broad.mit.edu	37	19	38899416	38899416	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:38899416G>T	uc002oin.1	+	c.944G>T	c.(943-945)CGG>CTG	p.R315L	FAM98C_uc002oio.1_Missense_Mutation_p.R233L|FAM98C_uc010xtz.1_Silent_p.P181P	NM_174905	NP_777565	Q17RN3	FA98C_HUMAN	hypothetical protein LOC147965	315											0	all_cancers(60;3.95e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)											0.216867	85.315268	97.585141	36	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38899416	38899416	5894	19	G	T	T	T	507	39	FAM98C	1	1
CEACAM5	1048	broad.mit.edu	37	19	42221645	42221645	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42221645T>G	uc002ork.2	+	c.1230T>G	c.(1228-1230)AAT>AAG	p.N410K	CEACAM5_uc002orj.1_Missense_Mutation_p.N409K|CEACAM5_uc002orl.2_Missense_Mutation_p.N410K	NM_004363	NP_004354	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion	410	Ig-like 4.					anchored to membrane|basolateral plasma membrane|integral to plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)										0.155172	105.004845	137.927666	45	245	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42221645	42221645	3328	19	T	G	G	G	660	51	CEACAM5	4	4
PSG8	440533	broad.mit.edu	37	19	43268410	43268410	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43268410G>T	uc002ouo.2	-	c.88C>A	c.(88-90)CCA>ACA	p.P30T	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG8_uc002oui.2_Intron|PSG8_uc002ouh.2_Missense_Mutation_p.P30T|PSG8_uc010ein.2_Intron|PSG8_uc002ouj.3_5'UTR|PSG8_uc002ouk.3_Intron|PSG8_uc002oul.3_Missense_Mutation_p.P30T|PSG8_uc002oum.3_Missense_Mutation_p.P30T|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Missense_Mutation_p.P30T	NM_182707	NP_874366	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8 isoform	30						extracellular region					0		Prostate(69;0.00899)												0.204724	161.439618	192.271557	78	303	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43268410	43268410	13114	19	G	T	T	T	559	43	PSG8	2	2
PSG5	5673	broad.mit.edu	37	19	43680093	43680093	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43680093C>A	uc002ovv.2	-	c.917G>T	c.(916-918)GGA>GTA	p.G306V	PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_Intron|PSG5_uc002ovu.2_Missense_Mutation_p.G213V|PSG5_uc002ovx.2_Missense_Mutation_p.G213V|PSG5_uc002ovw.2_Intron	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	213	Ig-like C2-type 1.				female pregnancy	extracellular region					0		Prostate(69;0.00899)												0.265781	187.040546	201.978715	80	221	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43680093	43680093	13111	19	C	A	A	A	390	30	PSG5	2	2
XRCC1	7515	broad.mit.edu	37	19	44058904	44058904	+	Nonsense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44058904G>C	uc002owt.2	-	c.308C>G	c.(307-309)TCA>TGA	p.S103*	XRCC1_uc010xwp.1_Nonsense_Mutation_p.S72*	NM_006297	NP_006288	P18887	XRCC1_HUMAN	X-ray repair cross complementing protein 1	103					base-excision repair|single strand break repair	nucleoplasm	damaged DNA binding|protein binding			ovary(2)|large_intestine(1)|lung(1)	4		Prostate(69;0.0153)												0.098039	36.953631	86.401617	30	276	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	44058904	44058904	18035	19	G	C	C	C	585	45	XRCC1	5	3
IRGC	56269	broad.mit.edu	37	19	44222873	44222873	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44222873C>G	uc002oxh.2	+	c.163C>G	c.(163-165)CTG>GTG	p.L55V		NM_019612	NP_062558	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	55						membrane	GTP binding|hydrolase activity, acting on acid anhydrides			ovary(1)	1		Prostate(69;0.0435)				Colon(189;350 2037 11447 13433 38914)								0.184783	39.318152	47.892403	17	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44222873	44222873	8141	19	C	G	G	G	311	24	IRGC	3	3
CHAF1A	10036	broad.mit.edu	37	19	4433496	4433496	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:4433496G>T	uc002mal.2	+	c.2633G>T	c.(2632-2634)TGC>TTC	p.C878F		NM_005483	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	878	Binds to p60.				cell cycle|DNA repair|DNA replication|DNA replication-dependent nucleosome assembly|protein complex assembly|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin assembly complex|WINAC complex	chromatin binding|chromo shadow domain binding|unfolded protein binding			ovary(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)										0.118812	14.426425	28.84026	12	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4433496	4433496	3445	19	G	T	T	T	598	46	CHAF1A	2	2
ZNF404	342908	broad.mit.edu	37	19	44377026	44377026	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44377026G>T	uc002oxs.3	-	c.1331C>A	c.(1330-1332)ACC>AAC	p.T444N		NM_001033719	NP_001028891	Q494X3	ZN404_HUMAN	zinc finger protein 404	447	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)												0.307692	8.646261	9.105975	4	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44377026	44377026	18479	19	G	T	T	T	572	44	ZNF404	2	2
ZNF155	7711	broad.mit.edu	37	19	44500732	44500732	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44500732C>G	uc010xwt.1	+	c.756C>G	c.(754-756)TTC>TTG	p.F252L	ZNF155_uc002oxy.1_Missense_Mutation_p.F241L|ZNF155_uc002oxz.1_Missense_Mutation_p.F241L	NM_198089	NP_932355	Q12901	ZN155_HUMAN	zinc finger protein 155	241	C2H2-type 3.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)	2		Prostate(69;0.0352)				NSCLC(61;554 1277 20909 42067 42312)								0.194444	114.518123	133.332622	42	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44500732	44500732	18327	19	C	G	G	G	376	29	ZNF155	3	3
ZNF234	10780	broad.mit.edu	37	19	44661726	44661726	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44661726G>T	uc002oym.2	+	c.1557G>T	c.(1555-1557)AAG>AAT	p.K519N	ZNF234_uc002oyl.3_Missense_Mutation_p.K519N	NM_006630	NP_006621	Q14588	ZN234_HUMAN	zinc finger protein 234	519	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)												0.291045	99.962697	105.209453	39	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44661726	44661726	18378	19	G	T	T	T	451	35	ZNF234	2	2
ZNF229	7772	broad.mit.edu	37	19	44936498	44936498	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44936498T>G	uc002oze.1	-	c.137A>C	c.(136-138)GAG>GCG	p.E46A	ZNF229_uc010ejk.1_5'UTR|ZNF229_uc010ejl.1_Missense_Mutation_p.E46A	NM_014518	NP_055333	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	46	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Prostate(69;0.0352)												0.13198	43.131575	69.041429	26	171	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44936498	44936498	18373	19	T	G	G	G	702	54	ZNF229	4	4
PPP1R15A	23645	broad.mit.edu	37	19	49376908	49376908	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:49376908G>T	uc002pky.3	+	c.418G>T	c.(418-420)GCT>TCT	p.A140S		NM_014330	NP_055145	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	140	Required for localization in the endoplasmic reticulum.				apoptosis|cell cycle arrest|regulation of translation|response to DNA damage stimulus	endoplasmic reticulum	protein binding			lung(1)	1		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)										0.073955	-10.029424	48.035727	23	288	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49376908	49376908	12798	19	G	T	T	T	598	46	PPP1R15A	2	2
HRC	3270	broad.mit.edu	37	19	49657621	49657621	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:49657621C>T	uc002pmv.2	-	c.874G>A	c.(874-876)GAC>AAC	p.D292N		NM_002152	NP_002143	P23327	SRCH_HUMAN	histidine rich calcium binding protein	292	2-5.|6 X approximate tandem repeats.|4 X tandem repeats, acidic.				muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding			ovary(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		Melanoma(37;75 1097 24567 25669 30645)								0.228916	45.424134	50.988921	19	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49657621	49657621	7644	19	C	T	T	T	403	31	HRC	1	1
ALDH16A1	126133	broad.mit.edu	37	19	49964950	49964950	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:49964950G>T	uc002pnt.2	+	c.652G>T	c.(652-654)GGC>TGC	p.G218C	ALDH16A1_uc010yar.1_Missense_Mutation_p.G218C|ALDH16A1_uc010yas.1_Missense_Mutation_p.G53C|ALDH16A1_uc010yat.1_Missense_Mutation_p.G55C	NM_153329	NP_699160	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	218					oxidation-reduction process		oxidoreductase activity|protein binding				0		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)										0.3125	12.81563	13.291721	5	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49964950	49964950	491	19	G	T	T	T	559	43	ALDH16A1	2	2
NUP62	23636	broad.mit.edu	37	19	50412420	50412420	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:50412420G>T	uc002pqx.2	-	c.645C>A	c.(643-645)ACC>ACA	p.T215T	IL4I1_uc002pqv.1_Intron|IL4I1_uc010eno.1_Intron|IL4I1_uc002pqw.1_Intron|IL4I1_uc002pqu.1_Intron|NUP62_uc002pqy.2_Silent_p.T215T|NUP62_uc002pqz.2_Silent_p.T215T|NUP62_uc002pra.2_Silent_p.T215T|NUP62_uc002prb.2_Silent_p.T215T|NUP62_uc002prc.2_Silent_p.T215T	NM_153719	NP_714941	P37198	NUP62_HUMAN	nucleoporin 62kDa	215	15 X 9 AA approximate repeats.|Ala-rich.|Thr-rich.				carbohydrate metabolic process|cell death|cell surface receptor linked signaling pathway|glucose transport|hormone-mediated signaling pathway|mRNA transport|negative regulation of apoptosis|negative regulation of cell proliferation|nucleocytoplasmic transport|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription, DNA-dependent|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleocytoplasmic shuttling complex|ribonucleoprotein complex|spindle pole	chromatin binding|protein serine/threonine kinase activity|receptor signaling complex scaffold activity|SH2 domain binding|structural constituent of nuclear pore|thyroid hormone receptor binding|transcription regulator activity|ubiquitin binding				0		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)										0.263158	108.09191	116.773713	45	126	KEEP	---	---	---	---	capture		Silent	SNP	50412420	50412420	11173	19	G	T	T	T	600	47	NUP62	2	2
GPR32	2854	broad.mit.edu	37	19	51274316	51274316	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51274316C>T	uc010ycf.1	+	c.459C>T	c.(457-459)CGC>CGT	p.R153R		NM_001506	NP_001497	O75388	GPR32_HUMAN	G protein-coupled receptor 32	153	Cytoplasmic (Potential).					integral to plasma membrane	N-formyl peptide receptor activity				0		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		Esophageal Squamous(113;152 1581 5732 15840 44398)								0.325967	142.737339	147.614359	59	122	KEEP	---	---	---	---	capture		Silent	SNP	51274316	51274316	6963	19	C	T	T	T	314	25	GPR32	2	2
GPR32	2854	broad.mit.edu	37	19	51274424	51274424	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51274424G>T	uc010ycf.1	+	c.567G>T	c.(565-567)ACG>ACT	p.T189T		NM_001506	NP_001497	O75388	GPR32_HUMAN	G protein-coupled receptor 32	189	Extracellular (Potential).					integral to plasma membrane	N-formyl peptide receptor activity				0		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		Esophageal Squamous(113;152 1581 5732 15840 44398)								0.102273	6.708732	20.588032	9	79	KEEP	---	---	---	---	capture		Silent	SNP	51274424	51274424	6963	19	G	T	T	T	483	38	GPR32	1	1
FPR2	2358	broad.mit.edu	37	19	52272029	52272029	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52272029G>T	uc002pxr.2	+	c.118G>T	c.(118-120)GGG>TGG	p.G40W	FPR2_uc002pxs.3_Missense_Mutation_p.G40W|FPR2_uc010epf.2_Missense_Mutation_p.G40W	NM_001005738	NP_001005738	P25090	FPR2_HUMAN	formyl peptide receptor-like 1	40	Helical; Name=1; (Potential).				cell adhesion|cellular component movement|chemotaxis|inflammatory response	integral to membrane|plasma membrane	N-formyl peptide receptor activity			ovary(1)	1														0.268293	87.53336	93.486598	33	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52272029	52272029	6285	19	G	T	T	T	507	39	FPR2	1	1
FPR2	2358	broad.mit.edu	37	19	52272799	52272799	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52272799C>A	uc002pxr.2	+	c.888C>A	c.(886-888)TGC>TGA	p.C296*	FPR2_uc002pxs.3_Nonsense_Mutation_p.C296*|FPR2_uc010epf.2_Nonsense_Mutation_p.C296*	NM_001005738	NP_001005738	P25090	FPR2_HUMAN	formyl peptide receptor-like 1	296	Helical; Name=7; (Potential).				cell adhesion|cellular component movement|chemotaxis|inflammatory response	integral to membrane|plasma membrane	N-formyl peptide receptor activity			ovary(1)	1														0.194631	59.78333	72.749329	29	120	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	52272799	52272799	6285	19	C	A	A	A	337	26	FPR2	5	2
ZNF649	65251	broad.mit.edu	37	19	52394293	52394293	+	Nonsense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52394293T>A	uc002pxy.2	-	c.1096A>T	c.(1096-1098)AGA>TGA	p.R366*	ZNF577_uc010ydf.1_5'Flank	NM_023074	NP_075562	Q9BS31	ZN649_HUMAN	zinc finger protein 649	366	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00152)|OV - Ovarian serous cystadenocarcinoma(262;0.0185)										0.252427	61.699732	67.434417	26	77	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	52394293	52394293	18659	19	T	A	A	A	700	54	ZNF649	5	3
ZNF432	9668	broad.mit.edu	37	19	52537917	52537917	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52537917G>C	uc002pyk.2	-	c.1015C>G	c.(1015-1017)CAT>GAT	p.H339D		NM_014650	NP_055465	O94892	ZN432_HUMAN	zinc finger protein 432	339	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|pancreas(1)	3		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.0054)|OV - Ovarian serous cystadenocarcinoma(262;0.0182)										0.131148	33.311504	49.448312	16	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52537917	52537917	18499	19	G	C	C	C	585	45	ZNF432	3	3
ZNF480	147657	broad.mit.edu	37	19	52825630	52825630	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52825630G>T	uc010ydl.1	+	c.1127G>T	c.(1126-1128)TGT>TTT	p.C376F	ZNF480_uc002pyv.2_Missense_Mutation_p.C299F|ZNF480_uc010ydm.1_Missense_Mutation_p.C333F|ZNF480_uc010epn.2_Missense_Mutation_p.C207F	NM_144684	NP_653285	Q8WV37	ZN480_HUMAN	zinc finger protein 480	376	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)										0.22093	45.875524	52.043276	19	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52825630	52825630	18529	19	G	T	T	T	624	48	ZNF480	2	2
VN1R4	317703	broad.mit.edu	37	19	53770647	53770647	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53770647C>T	uc010ydu.1	-	c.272G>A	c.(271-273)AGG>AAG	p.R91K		NM_173857	NP_776256	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	91	Helical; Name=3; (Potential).				response to pheromone	actin cytoskeleton|cytoplasm|integral to membrane|plasma membrane	pheromone receptor activity			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.00294)										0.307692	24.290062	25.14728	8	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53770647	53770647	17747	19	C	T	T	T	312	24	VN1R4	2	2
LILRB4	11006	broad.mit.edu	37	19	55175709	55175709	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:55175709T>A	uc002qgr.2	+	c.551T>A	c.(550-552)CTG>CAG	p.L184Q	LILRB4_uc002qgp.2_Missense_Mutation_p.L143Q|LILRB4_uc002qgq.2_Missense_Mutation_p.L143Q|LILRB4_uc010ers.1_Missense_Mutation_p.L56Q|LILRB4_uc010ert.2_Missense_Mutation_p.L184Q|LILRB4_uc010eru.2_Missense_Mutation_p.L172Q	NM_006847	NP_006838	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor,	143	Ig-like C2-type 2.|Extracellular (Potential).					integral to membrane|plasma membrane	antigen binding|receptor activity			ovary(3)	3				GBM - Glioblastoma multiforme(193;0.035)										0.130178	31.93581	54.423041	22	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55175709	55175709	9119	19	T	A	A	A	715	55	LILRB4	3	3
PTPRH	5794	broad.mit.edu	37	19	55697269	55697269	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:55697269C>G	uc002qjq.2	-	c.2862G>C	c.(2860-2862)GTG>GTC	p.V954V	PTPRH_uc010esv.2_Silent_p.V776V	NM_002842	NP_002833	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	954	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.				apoptosis	cytoplasm|integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|large_intestine(1)	3		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)										0.21028	128.153325	144.772002	45	169	KEEP	---	---	---	---	capture		Silent	SNP	55697269	55697269	13260	19	C	G	G	G	366	29	PTPRH	3	3
NLRP4	147945	broad.mit.edu	37	19	56369120	56369120	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56369120C>T	uc002qmd.3	+	c.361C>T	c.(361-363)CTA>TTA	p.L121L	NLRP4_uc002qmf.2_Silent_p.L46L|NLRP4_uc010etf.2_5'UTR	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	121							ATP binding			ovary(5)|lung(3)|kidney(1)|pancreas(1)	10		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)										0.290323	127.407781	133.516494	45	110	KEEP	---	---	---	---	capture		Silent	SNP	56369120	56369120	10882	19	C	T	T	T	311	24	NLRP4	2	2
NLRP4	147945	broad.mit.edu	37	19	56369305	56369305	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56369305C>A	uc002qmd.3	+	c.546C>A	c.(544-546)TTC>TTA	p.F182L	NLRP4_uc002qmf.2_Missense_Mutation_p.F107L|NLRP4_uc010etf.2_Missense_Mutation_p.F13L	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	182	NACHT.						ATP binding			ovary(5)|lung(3)|kidney(1)|pancreas(1)	10		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)										0.298165	154.153713	162.116369	65	153	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56369305	56369305	10882	19	C	A	A	A	389	30	NLRP4	2	2
NLRP13	126204	broad.mit.edu	37	19	56443578	56443578	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56443578G>T	uc010ygg.1	-	c.100C>A	c.(100-102)CTT>ATT	p.L34I		NM_176810	NP_789780	Q86W25	NAL13_HUMAN	NACHT, leucine rich repeat and PYD containing	34	DAPIN.						ATP binding			ovary(3)|skin(2)|pancreas(1)|lung(1)	7		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)										0.2125	70.779847	82.992822	34	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56443578	56443578	10878	19	G	T	T	T	442	34	NLRP13	2	2
NLRP8	126205	broad.mit.edu	37	19	56473435	56473435	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56473435C>T	uc002qmh.2	+	c.2045C>T	c.(2044-2046)GCG>GTG	p.A682V	NLRP8_uc010etg.2_Missense_Mutation_p.A682V	NM_176811	NP_789781	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	682						cytoplasm	ATP binding			ovary(4)|breast(3)|large_intestine(1)|kidney(1)|skin(1)	10		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)										0.245192	114.547469	126.834376	51	157	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56473435	56473435	10886	19	C	T	T	T	351	27	NLRP8	1	1
ZSCAN5B	342933	broad.mit.edu	37	19	56701251	56701251	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56701251T>A	uc010ygh.1	-	c.1433A>T	c.(1432-1434)CAG>CTG	p.Q478L		NM_001080456	NP_001073925	A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	478	C2H2-type 5.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.285714	59.920335	63.091982	22	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56701251	56701251	18843	19	T	A	A	A	715	55	ZSCAN5B	3	3
ZSCAN5B	342933	broad.mit.edu	37	19	56701293	56701293	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56701293T>A	uc010ygh.1	-	c.1391A>T	c.(1390-1392)GAG>GTG	p.E464V		NM_001080456	NP_001073925	A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	464					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.142857	15.071066	24.539953	11	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56701293	56701293	18843	19	T	A	A	A	702	54	ZSCAN5B	3	3
ZNF667	63934	broad.mit.edu	37	19	56953439	56953439	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56953439G>T	uc002qnd.2	-	c.925C>A	c.(925-927)CCT>ACT	p.P309T	ZNF667_uc010etl.2_Missense_Mutation_p.P91T|ZNF667_uc002qne.2_Missense_Mutation_p.P309T|ZNF667_uc010etm.2_Missense_Mutation_p.P252T	NM_022103	NP_071386	Q5HYK9	ZN667_HUMAN	zinc finger protein 667	309					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)										0.25	67.888252	74.224213	28	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56953439	56953439	18669	19	G	T	T	T	559	43	ZNF667	2	2
PEG3	5178	broad.mit.edu	37	19	57328676	57328676	+	Silent	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57328676A>G	uc002qnu.2	-	c.1134T>C	c.(1132-1134)AAT>AAC	p.N378N	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Silent_p.N349N|PEG3_uc002qnv.2_Silent_p.N378N|PEG3_uc002qnw.2_Silent_p.N254N|PEG3_uc002qnx.2_Silent_p.N252N|PEG3_uc010etr.2_Silent_p.N378N	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	378					apoptosis|regulation of transcription, DNA-dependent|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|large_intestine(1)|pancreas(1)	9		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)										0.227027	118.863753	131.509474	42	143	KEEP	---	---	---	---	capture		Silent	SNP	57328676	57328676	12141	19	A	G	G	G	50	4	PEG3	4	4
PEG3	5178	broad.mit.edu	37	19	57333091	57333091	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57333091C>A	uc002qnu.2	-	c.597G>T	c.(595-597)GTG>GTT	p.V199V	ZIM2_uc010ygq.1_5'UTR|ZIM2_uc010ygr.1_5'UTR|ZIM2_uc002qnr.2_Silent_p.V74V|ZIM2_uc002qnq.2_Silent_p.V74V|ZIM2_uc010etp.2_Silent_p.V74V|ZIM2_uc010ygs.1_Silent_p.V74V|PEG3_uc002qnt.2_Silent_p.V200V|PEG3_uc002qnv.2_Silent_p.V199V|PEG3_uc002qnw.2_Silent_p.V74V|PEG3_uc002qnx.2_Silent_p.V73V|PEG3_uc010etr.2_Silent_p.V199V	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	199					apoptosis|regulation of transcription, DNA-dependent|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|large_intestine(1)|pancreas(1)	9		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)										0.076655	-6.292247	46.400684	22	265	KEEP	---	---	---	---	capture		Silent	SNP	57333091	57333091	12141	19	C	A	A	A	262	21	PEG3	2	2
ZNF460	10794	broad.mit.edu	37	19	57802137	57802137	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57802137C>T	uc002qog.2	+	c.228C>T	c.(226-228)CTC>CTT	p.L76L	ZNF460_uc010ygv.1_Silent_p.L35L	NM_006635	NP_006626	Q14592	ZN460_HUMAN	zinc finger protein 460	76	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)										0.172414	27.86551	36.691453	15	72	KEEP	---	---	---	---	capture		Silent	SNP	57802137	57802137	18517	19	C	T	T	T	379	30	ZNF460	2	2
ZNF134	7693	broad.mit.edu	37	19	58132534	58132534	+	Missense_Mutation	SNP	C	G	G	rs34357677	by1000genomes	TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:58132534C>G	uc002qpn.2	+	c.1047C>G	c.(1045-1047)TGC>TGG	p.C349W	ZNF134_uc002qpo.2_Missense_Mutation_p.C176W|ZNF211_uc010yhb.1_5'UTR	NM_003435	NP_003426	P52741	ZN134_HUMAN	zinc finger protein 134	349	C2H2-type 9.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)										0.188235	121.747652	144.947445	48	207	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58132534	58132534	18315	19	C	G	G	G	350	27	ZNF134	3	3
ZNF135	7694	broad.mit.edu	37	19	58579104	58579104	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:58579104G>T	uc010yhq.1	+	c.1288G>T	c.(1288-1290)GCC>TCC	p.A430S	ZNF135_uc002qre.2_Missense_Mutation_p.A418S|ZNF135_uc002qrd.1_Intron|ZNF135_uc002qrf.2_Missense_Mutation_p.A376S|ZNF135_uc002qrg.2_Missense_Mutation_p.A388S|ZNF135_uc010yhr.1_Missense_Mutation_p.A239S	NM_003436	NP_003427	B4DHH9	B4DHH9_HUMAN	zinc finger protein 135 isoform 2	430					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)										0.160714	15.135573	21.275522	9	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58579104	58579104	18316	19	G	T	T	T	442	34	ZNF135	2	2
ZNF274	10782	broad.mit.edu	37	19	58718367	58718367	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:58718367G>T	uc002qrq.1	+	c.538G>T	c.(538-540)GAC>TAC	p.D180Y	ZNF274_uc010yhu.1_Non-coding_Transcript|ZNF274_uc010yhv.1_Non-coding_Transcript|ZNF274_uc002qrr.1_Missense_Mutation_p.D148Y|ZNF274_uc002qrs.1_Missense_Mutation_p.D75Y|ZNF274_uc010eum.1_5'UTR	NM_133502	NP_598009	Q96GC6	ZN274_HUMAN	zinc finger protein 274 isoform c	180	SCAN box.				regulation of transcription, DNA-dependent|viral reproduction	centrosome|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)										0.2	5.114335	6.372955	3	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58718367	58718367	18401	19	G	T	T	T	533	41	ZNF274	2	2
FBN3	84467	broad.mit.edu	37	19	8196580	8196580	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:8196580C>A	uc002mjf.2	-	c.1848G>T	c.(1846-1848)GTG>GTT	p.V616V		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	616						proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|central_nervous_system(1)|pancreas(1)	8														0.138462	11.226737	19.447634	9	56	KEEP	---	---	---	---	capture		Silent	SNP	8196580	8196580	5940	19	C	A	A	A	314	25	FBN3	2	2
MUC16	94025	broad.mit.edu	37	19	9018138	9018138	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9018138C>G	uc002mkp.2	-	c.37800G>C	c.(37798-37800)TTG>TTC	p.L12600F		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	12602	SEA 4.|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														0.141593	32.220589	46.222007	16	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9018138	9018138	10367	19	C	G	G	G	324	25	MUC16	3	3
MUC16	94025	broad.mit.edu	37	19	9056877	9056877	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9056877G>T	uc002mkp.2	-	c.30569C>A	c.(30568-30570)CCT>CAT	p.P10190H		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	10192	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.1375	15.869922	26.042025	11	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9056877	9056877	10367	19	G	T	T	T	455	35	MUC16	2	2
MUC16	94025	broad.mit.edu	37	19	9065903	9065903	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9065903T>A	uc002mkp.2	-	c.21543A>T	c.(21541-21543)ACA>ACT	p.T7181T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	7183	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.125	26.523528	47.402851	19	133	KEEP	---	---	---	---	capture		Silent	SNP	9065903	9065903	10367	19	T	A	A	A	704	55	MUC16	3	3
ZNF317	57693	broad.mit.edu	37	19	9269576	9269576	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9269576G>T	uc002mku.2	+	c.460G>T	c.(460-462)GTG>TTG	p.V154L	ZNF317_uc002mkv.2_Missense_Mutation_p.V13L|ZNF317_uc002mkw.2_Missense_Mutation_p.V122L|ZNF317_uc002mkx.2_Missense_Mutation_p.V69L|ZNF317_uc002mky.2_Missense_Mutation_p.V37L	NM_020933	NP_065984	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	154					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.117117	17.291327	33.297316	13	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9269576	9269576	18427	19	G	T	T	T	624	48	ZNF317	2	2
OR7E24	26648	broad.mit.edu	37	19	9362498	9362498	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9362498G>C	uc002mlb.1	+	c.779G>C	c.(778-780)GGC>GCC	p.G260A		NM_001079935	NP_001073404	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E,	260	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.130435	6.409789	9.464092	3	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9362498	9362498	11632	19	G	C	C	C	546	42	OR7E24	3	3
FRRS1	391059	broad.mit.edu	37	1	100183082	100183082	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:100183082C>A	uc001dsh.1	-	c.1121_splice	c.e11-1	p.G374_splice		NM_001013660	NP_001013682			stromal cell derived factor receptor 2 homolog						electron transport chain|transport	integral to membrane	ferric-chelate reductase activity|metal ion binding				0		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)										0.078652	-2.149839	14.001051	7	82	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	100183082	100183082	6310	1	C	A	A	A	312	24	FRRS1	5	2
KIF1B	23095	broad.mit.edu	37	1	10335490	10335490	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:10335490A>T	uc001aqz.2	+	c.887A>T	c.(886-888)AAA>ATA	p.K296I	KIF1B_uc001aqv.3_Missense_Mutation_p.K290I|KIF1B_uc001aqw.3_Missense_Mutation_p.K290I|KIF1B_uc001aqx.3_Missense_Mutation_p.K296I|KIF1B_uc001aqy.2_Missense_Mutation_p.K296I|KIF1B_uc001ara.2_Missense_Mutation_p.K296I|KIF1B_uc001arb.2_Missense_Mutation_p.K296I	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	296	Kinesin-motor.|Interaction with KBP.				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)										0.074468	-3.653751	13.831478	7	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10335490	10335490	8595	1	A	T	T	T	13	1	KIF1B	3	3
COL11A1	1301	broad.mit.edu	37	1	103453205	103453205	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:103453205C>A	uc001dum.2	-	c.2522G>T	c.(2521-2523)GGT>GTT	p.G841V	COL11A1_uc001duk.2_Missense_Mutation_p.V20F|COL11A1_uc001dul.2_Missense_Mutation_p.G829V|COL11A1_uc001dun.2_Missense_Mutation_p.G790V|COL11A1_uc009weh.2_Missense_Mutation_p.G713V	NM_080629	NP_542196	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform B	829	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|central_nervous_system(1)|pancreas(1)	11		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)										0.213333	40.15754	45.852054	16	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103453205	103453205	3805	1	C	A	A	A	234	18	COL11A1	2	2
AMY2B	280	broad.mit.edu	37	1	104115874	104115874	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:104115874G>T	uc001duq.2	+	c.505G>T	c.(505-507)GCT>TCT	p.A169S	AMY2B_uc010ouo.1_Non-coding_Transcript|LOC648740_uc001dur.2_Missense_Mutation_p.A169S|AMY2B_uc001dus.1_5'Flank	NM_020978	NP_066188	P19961	AMY2B_HUMAN	amylase, pancreatic, alpha-2B precursor	169					carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)										0.067376	-15.123279	39.569578	19	263	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104115874	104115874	598	1	G	T	T	T	598	46	AMY2B	2	2
VAV3	10451	broad.mit.edu	37	1	108299900	108299900	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:108299900C>A	uc010ouw.1	-	c.1069G>T	c.(1069-1071)GCT>TCT	p.A357S	VAV3_uc001dvk.1_Missense_Mutation_p.A357S|VAV3_uc001dvl.1_Missense_Mutation_p.A181S|VAV3_uc010oux.1_Missense_Mutation_p.A357S	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform	357	DH.				angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(4)|lung(2)|breast(2)	8		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)										0.145455	14.275494	20.91471	8	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108299900	108299900	17698	1	C	A	A	A	338	26	VAV3	2	2
PROK1	84432	broad.mit.edu	37	1	110996662	110996662	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:110996662C>A	uc001dzs.2	+	c.152C>A	c.(151-153)ACC>AAC	p.T51N		NM_032414	NP_115790	P58294	PROK1_HUMAN	prokineticin 1 precursor	51					angiogenesis|positive regulation of cell division	extracellular region	growth factor activity				0		all_cancers(81;6.23e-06)|all_epithelial(167;2.12e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0239)|all cancers(265;0.0699)|Epithelial(280;0.0753)|Colorectal(144;0.105)|LUSC - Lung squamous cell carcinoma(189;0.135)										0.15625	15.35624	22.539284	10	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110996662	110996662	12993	1	C	A	A	A	234	18	PROK1	2	2
SYT6	148281	broad.mit.edu	37	1	114680353	114680353	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:114680353A>C	uc001eev.2	-	c.580T>G	c.(580-582)TGC>GGC	p.C194G		NM_205848	NP_995320	Q5T7P8	SYT6_HUMAN	synaptotagmin VI	279	Cytoplasmic (Potential).|C2 1.					cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)										0.195489	64.297591	76.057327	26	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114680353	114680353	15999	1	A	C	C	C	104	8	SYT6	4	4
SYCP1	6847	broad.mit.edu	37	1	115523985	115523985	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:115523985C>A	uc001efr.2	+	c.2411C>A	c.(2410-2412)CCT>CAT	p.P804H	SYCP1_uc010owt.1_Non-coding_Transcript|SYCP1_uc001efq.2_Missense_Mutation_p.P804H|SYCP1_uc009wgw.2_Missense_Mutation_p.P779H	NM_003176	NP_003167	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	804					cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding				0	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)										0.293103	45.14882	47.373388	17	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115523985	115523985	15952	1	C	A	A	A	312	24	SYCP1	2	2
IGSF3	3321	broad.mit.edu	37	1	117131682	117131682	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:117131682C>A	uc001egq.1	-	c.2134G>T	c.(2134-2136)GTG>TTG	p.V712L	IGSF3_uc001egr.1_Missense_Mutation_p.V692L|IGSF3_uc001egs.1_Missense_Mutation_p.V365L	NM_001542	NP_001533	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 1	692	Ig-like C2-type 6.|Extracellular (Potential).					integral to membrane				ovary(2)	2	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)										0.096552	6.852015	30.507217	14	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117131682	117131682	7902	1	C	A	A	A	234	18	IGSF3	2	2
PTGFRN	5738	broad.mit.edu	37	1	117527322	117527322	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:117527322T>C	uc001egv.1	+	c.2188T>C	c.(2188-2190)TCC>CCC	p.S730P		NM_020440	NP_065173	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor negative regulator	730	Ig-like C2-type 6.|Extracellular (Potential).					endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	protein binding			liver(1)	1	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)										0.157895	44.690833	59.54077	21	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117527322	117527322	13205	1	T	C	C	C	754	58	PTGFRN	4	4
UBE2J2	118424	broad.mit.edu	37	1	1190769	1190769	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:1190769G>A	uc001ado.2	-	c.642C>T	c.(640-642)GTC>GTT	p.V214V	UBE2J2_uc001adm.2_Silent_p.V163V|UBE2J2_uc001adn.2_Silent_p.V198V|UBE2J2_uc001adp.2_Silent_p.V198V|UBE2J2_uc001adq.2_Silent_p.V146V|UBE2J2_uc001adr.2_Silent_p.V146V|UBE2J2_uc001ads.2_Silent_p.V146V	NM_194315	NP_919296	Q8N2K1	UB2J2_HUMAN	ubiquitin conjugating enzyme E2, J2 isoform 1	198	Cytoplasmic (Potential).				post-translational protein modification|response to unfolded protein	endoplasmic reticulum membrane|integral to membrane	ATP binding|ubiquitin-protein ligase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.66e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.53e-21)|Colorectal(212;0.00019)|COAD - Colon adenocarcinoma(227;0.000215)|Kidney(185;0.00255)|BRCA - Breast invasive adenocarcinoma(365;0.00266)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0371)|Lung(427;0.205)										0.184358	64.673417	81.401914	33	146	KEEP	---	---	---	---	capture		Silent	SNP	1190769	1190769	17418	1	G	A	A	A	522	41	UBE2J2	2	2
HSD3B2	3284	broad.mit.edu	37	1	119958100	119958100	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:119958100C>T	uc001ehs.2	+	c.58C>T	c.(58-60)CGC>TGC	p.R20C	HSD3B2_uc001eht.2_Missense_Mutation_p.R20C|HSD3B2_uc001ehu.2_Missense_Mutation_p.R20C	NM_000198	NP_000189	P26439	3BHS2_HUMAN	3 beta-hydroxysteroid dehydrogenase 2	20					androgen biosynthetic process|glucocorticoid biosynthetic process|mineralocorticoid biosynthetic process|oxidation-reduction process	integral to membrane|microsome|mitochondrial inner membrane|mitochondrial intermembrane space|smooth endoplasmic reticulum membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|steroid delta-isomerase activity			ovary(2)	2	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.015)|LUSC - Lung squamous cell carcinoma(189;0.0836)	NADH(DB00157)|Trilostane(DB01108)									0.075	-3.021015	19.221124	9	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119958100	119958100	7686	1	C	T	T	T	299	23	HSD3B2	1	1
NOTCH2	4853	broad.mit.edu	37	1	120478159	120478159	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:120478159C>T	uc001eik.2	-	c.3591G>A	c.(3589-3591)CAG>CAA	p.Q1197Q	NOTCH2_uc001eil.2_Silent_p.Q1197Q	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	1197	EGF-like 31; calcium-binding (Potential).|Extracellular (Potential).				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(7)|ovary(4)|lung(3)|central_nervous_system(2)|kidney(2)|breast(1)	19	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)						581				0.215789	98.75834	112.933761	41	149	KEEP	---	---	---	---	capture		Silent	SNP	120478159	120478159	10951	1	C	T	T	T	415	32	NOTCH2	2	2
AADACL3	126767	broad.mit.edu	37	1	12785391	12785391	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:12785391C>T	uc009vnn.1	+	c.481C>T	c.(481-483)CAG>TAG	p.Q161*	AADACL3_uc001aug.1_Nonsense_Mutation_p.Q91*	NM_001103170	NP_001096640	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3 isoform 1	161							hydrolase activity				0	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)										0.152239	78.996573	117.801362	51	284	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	12785391	12785391	13	1	C	T	T	T	377	29	AADACL3	5	2
PRAMEF12	390999	broad.mit.edu	37	1	12837328	12837328	+	Silent	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:12837328T>G	uc001aui.2	+	c.1038T>G	c.(1036-1038)GCT>GCG	p.A346A		NM_001080830	NP_001074299	O95522	PRA12_HUMAN	PRAME family member 12	346										ovary(3)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)										0.19697	63.102553	74.375143	26	106	KEEP	---	---	---	---	capture		Silent	SNP	12837328	12837328	12864	1	T	G	G	G	704	55	PRAMEF12	4	4
PRAMEF4	400735	broad.mit.edu	37	1	12941888	12941888	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:12941888G>T	uc001aun.2	-	c.662C>A	c.(661-663)CCC>CAC	p.P221H		NM_001009611	NP_001009611	O60810	PRAM4_HUMAN	PRAME family member 4	221										ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)										0.09375	10.932048	58.695586	27	261	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12941888	12941888	12877	1	G	T	T	T	559	43	PRAMEF4	2	2
TXNIP	10628	broad.mit.edu	37	1	145439780	145439780	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:145439780C>G	uc001enn.3	+	c.326C>G	c.(325-327)CCT>CGT	p.P109R	NBPF10_uc001emp.3_Intron|TXNIP_uc001enm.1_Intron|TXNIP_uc010oys.1_Missense_Mutation_p.P54R	NM_006472	NP_006463	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	109					cell cycle|keratinocyte differentiation|transcription, DNA-dependent		ubiquitin protein ligase binding			ovary(2)	2	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)													0.061947	-12.547647	32.692415	14	212	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145439780	145439780	17359	1	C	G	G	G	312	24	TXNIP	3	3
TXNIP	10628	broad.mit.edu	37	1	145439809	145439809	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:145439809G>T	uc001enn.3	+	c.355G>T	c.(355-357)GGG>TGG	p.G119W	NBPF10_uc001emp.3_Intron|TXNIP_uc001enm.1_Intron|TXNIP_uc010oys.1_Missense_Mutation_p.G64W	NM_006472	NP_006463	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	119					cell cycle|keratinocyte differentiation|transcription, DNA-dependent		ubiquitin protein ligase binding			ovary(2)	2	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)													0.060729	-18.391158	31.411694	15	232	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145439809	145439809	17359	1	G	T	T	T	611	47	TXNIP	2	2
ITGA10	8515	broad.mit.edu	37	1	145539090	145539090	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:145539090C>T	uc001eoa.2	+	c.3030C>T	c.(3028-3030)AAC>AAT	p.N1010N	NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Silent_p.N879N|ITGA10_uc009wiw.2_Silent_p.N867N|ITGA10_uc010oyw.1_Silent_p.N955N	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor	1010	Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)	7	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)									450				0.150602	37.153243	56.588759	25	141	KEEP	---	---	---	---	capture		Silent	SNP	145539090	145539090	8177	1	C	T	T	T	220	17	ITGA10	2	2
ANKRD35	148741	broad.mit.edu	37	1	145563069	145563069	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:145563069C>A	uc001eob.1	+	c.2757C>A	c.(2755-2757)CTC>CTA	p.L919L	NBPF10_uc001emp.3_Intron|ANKRD35_uc010oyx.1_Silent_p.L762L	NM_144698	NP_653299	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	919	Potential.									ovary(4)	4	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					Melanoma(9;127 754 22988 51047)								0.112245	8.796261	23.317961	11	87	KEEP	---	---	---	---	capture		Silent	SNP	145563069	145563069	672	1	C	A	A	A	366	29	ANKRD35	2	2
OTUD7B	56957	broad.mit.edu	37	1	149916312	149916312	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:149916312C>A	uc001etn.2	-	c.1976G>T	c.(1975-1977)GGT>GTT	p.G659V		NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne	659					negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding				0	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)											0.077922	-6.422451	49.592827	24	284	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149916312	149916312	11732	1	C	A	A	A	234	18	OTUD7B	2	2
VPS45	11311	broad.mit.edu	37	1	150040772	150040772	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:150040772G>A	uc001etp.2	+	c.179G>A	c.(178-180)CGA>CAA	p.R60Q	VPS45_uc010pbp.1_Non-coding_Transcript|VPS45_uc010pbq.1_Missense_Mutation_p.R24Q|VPS45_uc010pbs.1_Missense_Mutation_p.R24Q|VPS45_uc009wlm.1_Missense_Mutation_p.R60Q|VPS45_uc010pbr.1_Missense_Mutation_p.R24Q	NM_007259	NP_009190	Q9NRW7	VPS45_HUMAN	vacuolar protein sorting 45A	60					blood coagulation|intracellular protein transport|vesicle docking involved in exocytosis	endosome membrane|Golgi membrane|integral to membrane of membrane fraction				central_nervous_system(1)	1	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)											0.063927	-14.635989	28.695886	14	205	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150040772	150040772	17778	1	G	A	A	A	481	37	VPS45	1	1
PSMD4	5710	broad.mit.edu	37	1	151239025	151239025	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:151239025G>T	uc001exn.2	+	c.934G>T	c.(934-936)GAT>TAT	p.D312Y	PSMD4_uc001exl.2_Missense_Mutation_p.D309Y	NM_002810	NP_002801	P55036	PSMD4_HUMAN	proteasome 26S non-ATPase subunit 4	309					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	protein binding|zinc ion binding				0	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)											0.514563	149.729609	149.747127	53	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151239025	151239025	13153	1	G	T	T	T	585	45	PSMD4	2	2
THEM4	117145	broad.mit.edu	37	1	151867517	151867517	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:151867517C>T	uc001ezj.1	-	c.253G>A	c.(253-255)GAA>AAA	p.E85K	THEM4_uc001ezk.1_Non-coding_Transcript	NM_053055	NP_444283	Q5T1C6	THEM4_HUMAN	thioesterase superfamily member 4	85					insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|ruffle membrane					0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)											0.0625	-19.922612	31.168151	16	240	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151867517	151867517	16386	1	C	T	T	T	377	29	THEM4	2	2
HRNR	388697	broad.mit.edu	37	1	152192277	152192277	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152192277G>T	uc001ezt.1	-	c.1828C>A	c.(1828-1830)CAT>AAT	p.H610N		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	610	6.				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)											0.078261	-13.245238	112.325884	54	636	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152192277	152192277	7653	1	G	T	T	T	611	47	HRNR	2	2
FLG	2312	broad.mit.edu	37	1	152279055	152279055	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152279055C>T	uc001ezu.1	-	c.8307G>A	c.(8305-8307)CAG>CAA	p.Q2769Q		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2769	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.196375	303.452348	360.334114	130	532	KEEP	---	---	---	---	capture		Silent	SNP	152279055	152279055	6160	1	C	T	T	T	311	24	FLG	2	2
FLG	2312	broad.mit.edu	37	1	152282354	152282354	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152282354G>T	uc001ezu.1	-	c.5008C>A	c.(5008-5010)CAG>AAG	p.Q1670K		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1670	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.385057	933.63497	943.735118	335	535	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152282354	152282354	6160	1	G	T	T	T	611	47	FLG	2	2
FLG	2312	broad.mit.edu	37	1	152283677	152283677	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152283677C>A	uc001ezu.1	-	c.3685G>T	c.(3685-3687)GGC>TGC	p.G1229C		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1229	Ser-rich.|Filaggrin 7.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.073341	-30.450215	130.417374	63	796	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152283677	152283677	6160	1	C	A	A	A	299	23	FLG	1	1
FLG2	388698	broad.mit.edu	37	1	152326453	152326453	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152326453G>T	uc001ezw.3	-	c.3809C>A	c.(3808-3810)TCT>TAT	p.S1270Y		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1270	Ser-rich.						calcium ion binding|structural molecule activity			ovary(9)|breast(1)	10	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.063248	-45.841931	70.402717	37	548	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152326453	152326453	6161	1	G	T	T	T	429	33	FLG2	2	2
LCE2B	26239	broad.mit.edu	37	1	152659626	152659626	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152659626T>A	uc001fai.2	+	c.307T>A	c.(307-309)TGC>AGC	p.C103S		NM_014357	NP_055172	O14633	LCE2B_HUMAN	late cornified envelope 2B	103	Cys-rich.				keratinization					ovary(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.271028	74.127673	79.187746	29	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152659626	152659626	8989	1	T	A	A	A	715	55	LCE2B	3	3
LCE1E	353135	broad.mit.edu	37	1	152759971	152759971	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152759971G>T	uc001fan.2	+	c.196G>T	c.(196-198)GGC>TGC	p.G66C		NM_178353	NP_848130	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	66	Cys-rich.				keratinization						0	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;0.206)											0.119565	11.963692	25.029733	11	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152759971	152759971	8986	1	G	T	T	T	559	43	LCE1E	2	2
LCE1C	353133	broad.mit.edu	37	1	152777761	152777761	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152777761C>A	uc001fap.1	-	c.194G>T	c.(193-195)GGG>GTG	p.G65V		NM_178351	NP_848128	Q5T751	LCE1C_HUMAN	late cornified envelope 1C	65	Gly-rich.				keratinization						0	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)											0.275591	84.479353	90.23487	35	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152777761	152777761	8984	1	C	A	A	A	286	22	LCE1C	2	2
NUP210L	91181	broad.mit.edu	37	1	154099789	154099789	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154099789C>T	uc001fdw.2	-	c.1183G>A	c.(1183-1185)GAT>AAT	p.D395N	NUP210L_uc009woq.2_5'UTR|NUP210L_uc010peh.1_Missense_Mutation_p.D395N	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1	395						integral to membrane				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)											0.159091	25.089168	34.837637	14	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154099789	154099789	11166	1	C	T	T	T	416	32	NUP210L	2	2
PBXIP1	57326	broad.mit.edu	37	1	154919271	154919271	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154919271C>G	uc001ffr.2	-	c.879G>C	c.(877-879)AAG>AAC	p.K293N	PBXIP1_uc001ffs.2_Missense_Mutation_p.K264N|PBXIP1_uc010pep.1_Missense_Mutation_p.K138N	NM_020524	NP_065385	Q96AQ6	PBIP1_HUMAN	pre-B-cell leukemia homeobox interacting protein	293	Potential.				cell differentiation|multicellular organismal development|negative regulation of transcription, DNA-dependent	cytosol|microtubule|nucleus	protein binding|transcription corepressor activity			large_intestine(1)	1	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)											0.088889	10.553157	41.2913	16	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154919271	154919271	11916	1	C	G	G	G	311	24	PBXIP1	3	3
KRTCAP2	200185	broad.mit.edu	37	1	155145212	155145212	+	Splice_Site_SNP	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155145212A>G	uc001fho.2	-	c.237_splice	c.e2+1	p.T79_splice	RAG1AP1_uc010pey.1_Intron|KRTCAP2_uc001fhp.1_Splice_Site_SNP_p.T79_splice|TRIM46_uc009wpe.1_5'Flank|TRIM46_uc010pez.1_5'Flank|TRIM46_uc001fhq.2_5'Flank|TRIM46_uc001fhr.2_5'Flank|TRIM46_uc001fhs.1_5'Flank|TRIM46_uc001fht.1_5'Flank|TRIM46_uc010pfa.1_5'Flank|TRIM46_uc001fhu.1_5'Flank|TRIM46_uc009wpg.1_5'Flank|TRIM46_uc009wpf.2_5'Flank|TRIM46_uc001fhv.3_5'Flank|TRIM46_uc001fhw.1_5'Flank	NM_173852	NP_776251			keratinocyte associated protein 2							integral to membrane					0	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.18e-10)|all cancers(21;8.39e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)											0.24031	95.171792	103.102311	31	98	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	155145212	155145212	8901	1	A	G	G	G	182	14	KRTCAP2	5	4
SCAMP3	10067	broad.mit.edu	37	1	155228631	155228631	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155228631T>G	uc001fjs.2	-	c.503A>C	c.(502-504)TAC>TCC	p.Y168S	RAG1AP1_uc010pey.1_Intron|SCAMP3_uc001fjr.2_Missense_Mutation_p.Y15S|SCAMP3_uc001fju.2_Missense_Mutation_p.Y154S|SCAMP3_uc001fjv.2_Missense_Mutation_p.Y168S|SCAMP3_uc001fjt.2_Missense_Mutation_p.Y142S	NM_005698	NP_005689	O14828	SCAM3_HUMAN	secretory carrier membrane protein 3 isoform 1	168	Cytoplasmic (Potential).				post-Golgi vesicle-mediated transport|protein transport	integral to membrane				ovary(3)	3	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)											0.208247	275.50601	313.763879	101	384	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155228631	155228631	14353	1	T	G	G	G	741	57	SCAMP3	4	4
BCAN	63827	broad.mit.edu	37	1	156622600	156622600	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156622600C>A	uc001fpp.2	+	c.1858C>A	c.(1858-1860)CCA>ACA	p.P620T	BCAN_uc001fpo.2_Missense_Mutation_p.P620T	NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	brevican isoform 1	620					cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			ovary(1)|pancreas(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)													0.197674	37.42874	44.746369	17	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156622600	156622600	1366	1	C	A	A	A	286	22	BCAN	2	2
HDGF	3068	broad.mit.edu	37	1	156714928	156714928	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156714928C>A	uc010phr.1	-	c.223G>T	c.(223-225)GGC>TGC	p.G75C	HDGF_uc009wsd.2_Missense_Mutation_p.G27C|HDGF_uc001fpy.3_Missense_Mutation_p.G59C|HDGF_uc001fpz.3_Missense_Mutation_p.G52C|HDGF_uc009wse.2_Missense_Mutation_p.G75C|HDGF_uc009wsf.2_Missense_Mutation_p.G27C|HDGF_uc009wsg.2_Missense_Mutation_p.G59C	NM_001126050	NP_001119522	P51858	HDGF_HUMAN	hepatoma-derived growth factor isoform b	59	PWWP.				cell proliferation|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus	DNA binding|growth factor activity|heparin binding|nucleotide binding			lung(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)										0.176471	22.658191	29.367774	12	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156714928	156714928	7301	1	C	A	A	A	286	22	HDGF	2	2
INSRR	3645	broad.mit.edu	37	1	156818752	156818752	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156818752G>T	uc010pht.1	-	c.1532C>A	c.(1531-1533)GCC>GAC	p.A511D	NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron	NM_014215	NP_055030	P14616	INSRR_HUMAN	insulin receptor-related receptor precursor	511	Fibronectin type-III 1.				protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity			lung(7)|ovary(4)|kidney(1)|central_nervous_system(1)|skin(1)	14	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)									299				0.157895	4.827214	6.93638	3	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156818752	156818752	8075	1	G	T	T	T	546	42	INSRR	2	2
ETV3L	440695	broad.mit.edu	37	1	157062580	157062580	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:157062580G>T	uc001fqq.1	-	c.947C>A	c.(946-948)CCC>CAC	p.P316H		NM_001004341	NP_001004341	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	316					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Hepatocellular(266;0.158)	Prostate(1639;0.184)												0.258427	55.879482	60.588327	23	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157062580	157062580	5473	1	G	T	T	T	559	43	ETV3L	2	2
FCRL4	83417	broad.mit.edu	37	1	157555977	157555977	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:157555977C>G	uc001fqw.2	-	c.1116G>C	c.(1114-1116)GTG>GTC	p.V372V	FCRL4_uc010phy.1_Non-coding_Transcript	NM_031282	NP_112572	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4 precursor	372	Ig-like C2-type 4.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(2)|kidney(1)	3	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)								315		OREG0007229	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=FCRL4|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	0.301471	133.717262	138.507202	41	95	KEEP	---	---	---	---	capture		Silent	SNP	157555977	157555977	6034	1	C	G	G	G	314	25	FCRL4	3	3
CD5L	922	broad.mit.edu	37	1	157803248	157803248	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:157803248T>A	uc001frk.3	-	c.773A>T	c.(772-774)GAG>GTG	p.E258V		NM_005894	NP_005885	O43866	CD5L_HUMAN	CD5 molecule-like precursor	258	SRCR 3.				apoptosis|cellular defense response	extracellular space|membrane	scavenger receptor activity			ovary(1)	1	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)											0.121339	28.618413	62.20286	29	210	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157803248	157803248	3155	1	T	A	A	A	702	54	CD5L	3	3
CD1C	911	broad.mit.edu	37	1	158262614	158262614	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158262614G>T	uc001fru.2	+	c.839G>T	c.(838-840)TGT>TTT	p.C280F	CD1C_uc001frv.2_Missense_Mutation_p.C83F	NM_001765	NP_001756	P29017	CD1C_HUMAN	CD1C antigen precursor	280	Extracellular (Potential).|Ig-like.				antigen processing and presentation|T cell activation involved in immune response	endosome membrane|integral to plasma membrane	endogenous lipid antigen binding|exogenous lipid antigen binding|glycolipid binding|lipopeptide binding			ovary(2)|pancreas(1)	3	all_hematologic(112;0.0378)													0.141026	19.79919	29.474731	11	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158262614	158262614	3103	1	G	T	T	T	624	48	CD1C	2	2
CASP9	842	broad.mit.edu	37	1	15831140	15831140	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:15831140C>A	uc001awn.2	-	c.834G>T	c.(832-834)AAG>AAT	p.K278N	CASP9_uc001awm.1_Missense_Mutation_p.K278N|CASP9_uc001awo.2_Intron|CASP9_uc001awp.2_Missense_Mutation_p.K122N|CASP9_uc009voi.2_Missense_Mutation_p.K122N|CASP9_uc010obm.1_Missense_Mutation_p.K195N|CASP9_uc001awq.2_Missense_Mutation_p.K195N	NM_001229	NP_001220	P55211	CASP9_HUMAN	caspase 9 isoform alpha preproprotein	278					activation of caspase activity by cytochrome c|induction of apoptosis by intracellular signals|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol	cysteine-type endopeptidase activity|enzyme activator activity|protein binding			central_nervous_system(1)|kidney(1)	2		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)						893				0.188679	18.913874	23.728155	10	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15831140	15831140	2798	1	C	A	A	A	363	28	CASP9	2	2
OR6Y1	391112	broad.mit.edu	37	1	158517593	158517593	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158517593G>T	uc010pil.1	-	c.303C>A	c.(301-303)GGC>GGA	p.G101G		NM_001005189	NP_001005189	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y,	101	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)													0.107143	11.912216	33.363609	15	125	KEEP	---	---	---	---	capture		Silent	SNP	158517593	158517593	11624	1	G	T	T	T	431	34	OR6Y1	2	2
OR10Z1	128368	broad.mit.edu	37	1	158576967	158576967	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158576967G>C	uc010pio.1	+	c.739G>C	c.(739-741)GTG>CTG	p.V247L		NM_001004478	NP_001004478	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z,	247	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1	all_hematologic(112;0.0378)													0.216912	167.774893	187.876193	59	213	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158576967	158576967	11329	1	G	C	C	C	468	36	OR10Z1	3	3
SPTA1	6708	broad.mit.edu	37	1	158644206	158644207	+	Nonsense_Mutation	DNP	AG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158644206_158644207AG>TT	uc001fst.1	-	c.1262_1263CT>AA	c.(1261-1263)TCT>TAA	p.S421*		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	421	Spectrin 5.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.107955	20.894212	47.715501	19	157	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	158644206	158644207	15630	1	AG	TT	TT	TT	28	3	SPTA1	5	3
OR6K2	81448	broad.mit.edu	37	1	158669885	158669885	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158669885C>G	uc001fsu.1	-	c.558G>C	c.(556-558)CTG>CTC	p.L186L		NM_001005279	NP_001005279	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K,	186	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1	all_hematologic(112;0.0378)													0.166667	40.876975	52.258228	18	90	KEEP	---	---	---	---	capture		Silent	SNP	158669885	158669885	11612	1	C	G	G	G	262	21	OR6K2	3	3
VANGL2	57216	broad.mit.edu	37	1	160389247	160389247	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:160389247G>T	uc001fwb.1	+	c.648G>T	c.(646-648)GTG>GTT	p.V216V	VANGL2_uc001fwc.1_Silent_p.V216V	NM_020335	NP_065068	Q9ULK5	VANG2_HUMAN	vang-like 2	216	Extracellular (Potential).				apical protein localization|heart looping|sensory cilium assembly	apical plasma membrane|integral to membrane				ovary(1)	1	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)											0.07438	-6.237608	38.773963	18	224	KEEP	---	---	---	---	capture		Silent	SNP	160389247	160389247	17685	1	G	T	T	T	587	46	VANGL2	2	2
SLAMF7	57823	broad.mit.edu	37	1	160719714	160719714	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:160719714G>T	uc001fwq.2	+	c.480G>T	c.(478-480)GTG>GTT	p.V160V	SLAMF7_uc010pjn.1_Silent_p.V53V|SLAMF7_uc001fws.2_Silent_p.V53V|SLAMF7_uc001fwr.2_Silent_p.V160V|SLAMF7_uc010pjo.1_Intron|SLAMF7_uc010pjp.1_Silent_p.V53V|SLAMF7_uc010pjq.1_Intron|SLAMF7_uc010pjr.1_Silent_p.V53V	NM_021181	NP_067004	Q9NQ25	SLAF7_HUMAN	SLAM family member 7	160	Ig-like C2-type.|Extracellular (Potential).				cell adhesion|natural killer cell activation|natural killer cell mediated cytotoxicity	integral to membrane	receptor activity			ovary(1)	1	all_cancers(52;2.63e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)											0.096916	7.283527	44.251711	22	205	KEEP	---	---	---	---	capture		Silent	SNP	160719714	160719714	14864	1	G	T	T	T	574	45	SLAMF7	2	2
ITLN1	55600	broad.mit.edu	37	1	160849175	160849175	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:160849175T>A	uc001fxc.2	-	c.715A>T	c.(715-717)AGG>TGG	p.R239W		NM_017625	NP_060095	Q8WWA0	ITLN1_HUMAN	intelectin precursor	239	Fibrinogen C-terminal.				positive regulation of glucose import|positive regulation of protein phosphorylation|response to nematode|signal transduction	anchored to membrane|brush border membrane|extracellular region|membrane raft	receptor binding|sugar binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)											0.082734	8.129489	57.329918	23	255	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160849175	160849175	8214	1	T	A	A	A	713	55	ITLN1	3	3
OLFML2B	25903	broad.mit.edu	37	1	161987227	161987227	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:161987227G>T	uc010pkq.1	-	c.509C>A	c.(508-510)ACC>AAC	p.T170N	OLFML2B_uc001gbu.2_Missense_Mutation_p.T170N	NM_015441	NP_056256	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B precursor	170											0	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)											0.077419	-1.816068	26.500599	12	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161987227	161987227	11263	1	G	T	T	T	572	44	OLFML2B	2	2
DDR2	4921	broad.mit.edu	37	1	162724443	162724443	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:162724443G>T	uc001gcf.2	+	c.215G>T	c.(214-216)TGG>TTG	p.W72L	DDR2_uc001gcg.2_Missense_Mutation_p.W72L	NM_001014796	NP_001014796	Q16832	DDR2_HUMAN	discoidin domain receptor family, member 2	72	Extracellular (Potential).|F5/8 type C.				cell adhesion|protein phosphorylation	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)			NSCLC(161;314 2006 8283 19651 23192)				497				0.285714	110.02408	116.378929	44	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	162724443	162724443	4508	1	G	T	T	T	611	47	DDR2	2	2
RGS5	8490	broad.mit.edu	37	1	163122409	163122409	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:163122409G>T	uc001gcn.2	-	c.315C>A	c.(313-315)TCC>TCA	p.S105S	RGS5_uc009wvb.2_Non-coding_Transcript	NM_003617	NP_003608	O15539	RGS5_HUMAN	regulator of G-protein signalling 5	105	RGS.				negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity				0			LUSC - Lung squamous cell carcinoma(543;0.187)											0.247423	164.145354	181.055105	72	219	KEEP	---	---	---	---	capture		Silent	SNP	163122409	163122409	13782	1	G	T	T	T	548	43	RGS5	2	2
RXRG	6258	broad.mit.edu	37	1	165380317	165380317	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:165380317C>G	uc001gda.2	-	c.652G>C	c.(652-654)GAG>CAG	p.E218Q		NM_006917	NP_008848	P48443	RXRG_HUMAN	retinoid X receptor, gamma isoform a	218	Hinge.				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tretinoin(DB00755)									0.084337	5.672646	20.21666	7	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165380317	165380317	14245	1	C	G	G	G	416	32	RXRG	3	3
DCAF6	55827	broad.mit.edu	37	1	167974027	167974027	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167974027G>C	uc001gex.2	+	c.1374G>C	c.(1372-1374)CAG>CAC	p.Q458H	DCAF6_uc001gev.2_Missense_Mutation_p.Q458H|DCAF6_uc001gew.2_Missense_Mutation_p.Q458H|DCAF6_uc010plk.1_Missense_Mutation_p.Q427H|DCAF6_uc001gey.2_Missense_Mutation_p.Q311H	NM_018442	NP_060912	Q58WW2	DCAF6_HUMAN	IQ motif and WD repeats 1 isoform a	458					positive regulation of transcription from RNA polymerase II promoter|protein ubiquitination	CUL4 RING ubiquitin ligase complex|nucleus	ligand-dependent nuclear receptor transcription coactivator activity			ovary(1)|central_nervous_system(1)	2														0.130435	18.524565	27.691795	9	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167974027	167974027	4445	1	G	C	C	C	464	36	DCAF6	3	3
F5	2153	broad.mit.edu	37	1	169526046	169526046	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:169526046G>T	uc001ggg.1	-	c.790C>A	c.(790-792)CCA>ACA	p.P264T	F5_uc010plr.1_Non-coding_Transcript	NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	264	F5/8 type A 1.|Plastocyanin-like 2.				cell adhesion|oxidation-reduction process|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)	5	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)									0.253968	37.196505	40.641549	16	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169526046	169526046	5542	1	G	T	T	T	546	42	F5	2	2
MYOC	4653	broad.mit.edu	37	1	171621555	171621555	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:171621555T>A	uc001ghu.2	-	c.197A>T	c.(196-198)CAG>CTG	p.Q66L	MYOC_uc010pmk.1_Missense_Mutation_p.Q66L	NM_000261	NP_000252	Q99972	MYOC_HUMAN	myocilin precursor	66					anatomical structure morphogenesis	cilium|extracellular space|rough endoplasmic reticulum	structural molecule activity			lung(1)	1	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)													0.08	0.956959	23.444875	10	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	171621555	171621555	10481	1	T	A	A	A	715	55	MYOC	3	3
KLHL20	27252	broad.mit.edu	37	1	173702931	173702931	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:173702931G>A	uc001gjc.2	+	c.103G>A	c.(103-105)GAA>AAA	p.E35K	KLHL20_uc010pmr.1_Intron|KLHL20_uc009wwf.2_Missense_Mutation_p.E17K|KLHL20_uc001gjd.2_Missense_Mutation_p.E35K	NM_014458	NP_055273	Q9Y2M5	KLH20_HUMAN	kelch-like 20	35					cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity			ovary(1)	1						GBM(159;862 2695 6559 23041)								0.195489	59.06575	70.569928	26	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	173702931	173702931	8687	1	G	A	A	A	429	33	KLHL20	2	2
SERPINC1	462	broad.mit.edu	37	1	173883690	173883690	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:173883690C>A	uc001gjt.2	-	c.408_splice	c.e2+1	p.E136_splice		NM_000488	NP_000479			serpin peptidase inhibitor, clade C, member 1						blood coagulation|regulation of proteolysis	extracellular space|plasma membrane	heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(1)	1					Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)							OREG0013990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.1	6.181096	22.161656	10	90	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	173883690	173883690	14597	1	C	A	A	A	234	18	SERPINC1	5	2
PADI3	51702	broad.mit.edu	37	1	17593246	17593246	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:17593246C>A	uc001bai.2	+	c.441C>A	c.(439-441)GGC>GGA	p.G147G		NM_016233	NP_057317	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	147					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity			ovary(1)|breast(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)									0.084906	2.005119	20.52484	9	97	KEEP	---	---	---	---	capture		Silent	SNP	17593246	17593246	11795	1	C	A	A	A	340	27	PADI3	1	1
PAPPA2	60676	broad.mit.edu	37	1	176526098	176526099	+	Missense_Mutation	DNP	GG	TC	TC			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:176526098_176526099GG>TC	uc001gkz.2	+	c.640_641GG>TC	c.(640-642)GGT>TCT	p.G214S	PAPPA2_uc001gky.1_Missense_Mutation_p.G214S|PAPPA2_uc009www.2_Non-coding_Transcript	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	214					cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|lung(1)|breast(1)	14														0.253165	138.116665	151.217929	60	177	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	176526098	176526099	11850	1	GG	TC	TC	TC	507	39	PAPPA2	1	1
ASTN1	460	broad.mit.edu	37	1	176992707	176992707	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:176992707C>A	uc001glc.2	-	c.1271G>T	c.(1270-1272)GGG>GTG	p.G424V	ASTN1_uc001glb.1_Missense_Mutation_p.G424V|ASTN1_uc001gld.1_Missense_Mutation_p.G424V|ASTN1_uc009wwx.1_Missense_Mutation_p.G424V|ASTN1_uc001gle.3_Intron	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	424					cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	11										849				0.216216	16.98238	19.730123	8	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176992707	176992707	1083	1	C	A	A	A	286	22	ASTN1	2	2
ASTN1	460	broad.mit.edu	37	1	177001826	177001826	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:177001826C>T	uc001glc.2	-	c.631G>A	c.(631-633)GGG>AGG	p.G211R	ASTN1_uc001glb.1_Missense_Mutation_p.G211R|ASTN1_uc001gld.1_Missense_Mutation_p.G211R|ASTN1_uc009wwx.1_Missense_Mutation_p.G211R|ASTN1_uc001gle.3_Non-coding_Transcript	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	211					cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	11										849				0.36	73.733957	75.015187	27	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	177001826	177001826	1083	1	C	T	T	T	299	23	ASTN1	1	1
FAM5B	57795	broad.mit.edu	37	1	177247804	177247804	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:177247804A>T	uc001glf.2	+	c.1118A>T	c.(1117-1119)CAG>CTG	p.Q373L	FAM5B_uc010pna.1_Missense_Mutation_p.Q123L|FAM5B_uc001glg.2_Missense_Mutation_p.Q268L	NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B	373						extracellular region				ovary(2)	2														0.085174	3.983123	59.3229	27	290	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	177247804	177247804	5816	1	A	T	T	T	91	7	FAM5B	3	3
RALGPS2	55103	broad.mit.edu	37	1	178846684	178846684	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:178846684G>T	uc001glz.2	+	c.659G>T	c.(658-660)GGC>GTC	p.G220V	RALGPS2_uc001gly.1_Missense_Mutation_p.G220V|RALGPS2_uc010pnb.1_Missense_Mutation_p.G220V	NM_152663	NP_689876	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	220	Ras-GEF.				small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity|protein binding				0														0.278689	43.84504	46.535155	17	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	178846684	178846684	13478	1	G	T	T	T	546	42	RALGPS2	2	2
ABL2	27	broad.mit.edu	37	1	179078178	179078178	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179078178C>A	uc001gmj.3	-	c.2224G>T	c.(2224-2226)GGG>TGG	p.G742W	ABL2_uc010pnf.1_Intron|ABL2_uc010png.1_Intron|ABL2_uc010pnh.1_Missense_Mutation_p.G721W|ABL2_uc001gmg.3_Intron|ABL2_uc001gmi.3_Missense_Mutation_p.G727W|ABL2_uc001gmh.3_Missense_Mutation_p.G706W|ABL2_uc010pne.1_Intron	NM_007314	NP_009298	P42684	ABL2_HUMAN	arg tyrosine kinase isoform b	742					axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|ovary(2)|breast(2)|central_nervous_system(1)	9					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)				p.G742R(KMRC1-Tumor)	285				0.372549	53.309991	54.038384	19	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179078178	179078178	94	1	C	A	A	A	273	21	ABL2	2	2
C1orf125	126859	broad.mit.edu	37	1	179338107	179338107	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179338107G>T	uc001gmo.2	+	c.270G>T	c.(268-270)AAG>AAT	p.K90N	C1orf125_uc009wxg.2_Non-coding_Transcript|C1orf125_uc001gmn.1_Intron|C1orf125_uc010pnl.1_Non-coding_Transcript|C1orf125_uc001gmp.2_Missense_Mutation_p.K90N	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1	90											0														0.290698	65.036288	68.41424	25	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179338107	179338107	2060	1	G	T	T	T	451	35	C1orf125	2	2
TDRD5	163589	broad.mit.edu	37	1	179631268	179631268	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179631268G>T	uc010pnp.1	+	c.2352G>T	c.(2350-2352)CTG>CTT	p.L784L	TDRD5_uc001gnf.1_Silent_p.L730L|TDRD5_uc001gnh.1_Silent_p.L285L	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	781					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|central_nervous_system(1)|skin(1)	4														0.062201	-13.904373	27.867943	13	196	KEEP	---	---	---	---	capture		Silent	SNP	179631268	179631268	16260	1	G	T	T	T	600	47	TDRD5	2	2
TDRD5	163589	broad.mit.edu	37	1	179659901	179659901	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179659901C>A	uc010pnp.1	+	c.2931C>A	c.(2929-2931)GAC>GAA	p.D977E	TDRD5_uc001gnf.1_Missense_Mutation_p.D923E|TDRD5_uc001gnh.1_Missense_Mutation_p.D478E	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	923					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|central_nervous_system(1)|skin(1)	4														0.336066	116.131348	119.034938	41	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179659901	179659901	16260	1	C	A	A	A	220	17	TDRD5	2	2
TDRD5	163589	broad.mit.edu	37	1	179660007	179660007	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179660007G>T	uc010pnp.1	+	c.3037G>T	c.(3037-3039)GCT>TCT	p.A1013S	TDRD5_uc001gnf.1_Missense_Mutation_p.A959S|TDRD5_uc001gnh.1_Missense_Mutation_p.A514S	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	959					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|central_nervous_system(1)|skin(1)	4														0.230769	35.388574	39.708305	15	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179660007	179660007	16260	1	G	T	T	T	598	46	TDRD5	2	2
CACNA1E	777	broad.mit.edu	37	1	181705562	181705562	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:181705562C>T	uc001gow.2	+	c.3414C>T	c.(3412-3414)ACC>ACT	p.T1138T	CACNA1E_uc009wxs.2_Silent_p.T1026T|CACNA1E_uc001gox.1_Silent_p.T364T|CACNA1E_uc009wxt.2_Silent_p.T364T	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	1138	Cytoplasmic (Potential).				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6														0.25	20.05382	22.102645	9	27	KEEP	---	---	---	---	capture		Silent	SNP	181705562	181705562	2658	1	C	T	T	T	262	21	CACNA1E	2	2
RNF2	6045	broad.mit.edu	37	1	185069342	185069342	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:185069342G>T	uc001grc.1	+	c.920G>T	c.(919-921)GGC>GTC	p.G307V	RNF2_uc001grd.1_Missense_Mutation_p.G235V|RNF2_uc001gre.1_Non-coding_Transcript	NM_007212	NP_009143	Q99496	RING2_HUMAN	ring finger protein 2	307					transcription, DNA-dependent	MLL1 complex|ubiquitin ligase complex	RING-like zinc finger domain binding|zinc ion binding				0		Breast(1374;0.000496)		Colorectal(1306;6.9e-08)|KIRC - Kidney renal clear cell carcinoma(1967;8.12e-06)										0.254237	35.293562	38.530252	15	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185069342	185069342	13950	1	G	T	T	T	546	42	RNF2	2	2
HMCN1	83872	broad.mit.edu	37	1	185704050	185704050	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:185704050G>T	uc001grq.1	+	c.139G>T	c.(139-141)GAT>TAT	p.D47Y		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	47	VWFA.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.089109	1.481311	35.950796	18	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185704050	185704050	7511	1	G	T	T	T	585	45	HMCN1	2	2
PRG4	10216	broad.mit.edu	37	1	186266034	186266034	+	Nonsense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:186266034C>G	uc001gru.3	+	c.27C>G	c.(25-27)TAC>TAG	p.Y9*	PRG4_uc001grt.3_Nonsense_Mutation_p.Y9*|PRG4_uc009wyl.2_Nonsense_Mutation_p.Y9*|PRG4_uc009wym.2_Nonsense_Mutation_p.Y9*|PRG4_uc010poo.1_Non-coding_Transcript	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	9					cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity				0														0.087719	4.529307	14.328839	5	52	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	186266034	186266034	12924	1	C	G	G	G	233	18	PRG4	5	3
TAS1R2	80834	broad.mit.edu	37	1	19166909	19166909	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:19166909A>T	uc001bba.1	-	c.1704T>A	c.(1702-1704)GCT>GCA	p.A568A		NM_152232	NP_689418	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2 precursor	568	Helical; Name=1; (Potential).				detection of chemical stimulus involved in sensory perception of sweet taste	integral to membrane|plasma membrane	protein heterodimerization activity|taste receptor activity			ovary(1)|central_nervous_system(1)	2		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)									0.12037	15.902612	31.164823	13	95	KEEP	---	---	---	---	capture		Silent	SNP	19166909	19166909	16085	1	A	T	T	T	80	7	TAS1R2	3	3
KIAA1751	85452	broad.mit.edu	37	1	1920390	1920390	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:1920390C>G	uc009vkz.1	-	c.90G>C	c.(88-90)CCG>CCC	p.P30P	KIAA1751_uc001aim.1_Silent_p.P30P|KIAA1751_uc001ain.1_Silent_p.P30P	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452	30										pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-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)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)										0.116883	14.317824	25.434927	9	68	KEEP	---	---	---	---	capture		Silent	SNP	1920390	1920390	8567	1	C	G	G	G	288	23	KIAA1751	3	3
KCNT2	343450	broad.mit.edu	37	1	196398799	196398799	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:196398799C>A	uc001gtd.1	-	c.727G>T	c.(727-729)GTG>TTG	p.V243L	KCNT2_uc009wyt.1_Non-coding_Transcript|KCNT2_uc001gte.1_Missense_Mutation_p.V243L|KCNT2_uc001gtf.1_Missense_Mutation_p.V243L|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Missense_Mutation_p.V243L|KCNT2_uc009wyv.1_Missense_Mutation_p.V218L	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	243						voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|catalytic activity|voltage-gated potassium channel activity			ovary(4)|breast(1)	5														0.258427	60.08098	64.788335	23	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196398799	196398799	8397	1	C	A	A	A	221	17	KCNT2	2	2
CFH	3075	broad.mit.edu	37	1	196654312	196654312	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:196654312G>T	uc001gtj.3	+	c.909G>T	c.(907-909)CGG>CGT	p.R303R	CFH_uc001gti.3_Silent_p.R303R|CFH_uc009wyw.2_Silent_p.R303R|CFH_uc009wyx.2_Silent_p.R239R	NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	303	Sushi 5.				complement activation, alternative pathway	extracellular space				ovary(1)|breast(1)|skin(1)	3														0.271605	52.911434	56.724431	22	59	KEEP	---	---	---	---	capture		Silent	SNP	196654312	196654312	3416	1	G	T	T	T	548	43	CFH	2	2
CFHR5	81494	broad.mit.edu	37	1	196977662	196977662	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:196977662A>G	uc001gts.3	+	c.1559A>G	c.(1558-1560)CAG>CGG	p.Q520R		NM_030787	NP_110414	Q9BXR6	FHR5_HUMAN	complement factor H-related 5 precursor	520	Sushi 9.				complement activation, alternative pathway	extracellular region				breast(1)	1														0.15	18.035497	25.081303	9	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196977662	196977662	3421	1	A	G	G	G	91	7	CFHR5	4	4
ASPM	259266	broad.mit.edu	37	1	197072368	197072368	+	Silent	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197072368T>G	uc001gtu.2	-	c.6013A>C	c.(6013-6015)AGG>CGG	p.R2005R	ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	2005					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6														0.307692	93.464502	96.891121	32	72	KEEP	---	---	---	---	capture		Silent	SNP	197072368	197072368	1075	1	T	G	G	G	687	53	ASPM	4	4
ASPM	259266	broad.mit.edu	37	1	197094181	197094181	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197094181T>A	uc001gtu.2	-	c.3077A>T	c.(3076-3078)GAG>GTG	p.E1026V	ASPM_uc001gtv.2_Missense_Mutation_p.E1026V|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	1026	CH 1.				mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6														0.129032	10.256186	18.567463	8	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197094181	197094181	1075	1	T	A	A	A	702	54	ASPM	3	3
CRB1	23418	broad.mit.edu	37	1	197396583	197396583	+	Splice_Site_SNP	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197396583G>A	uc001gtz.2	+	c.2129_splice	c.e7-1	p.E710_splice	CRB1_uc010poz.1_Splice_Site_SNP_p.E641_splice|CRB1_uc010ppa.1_Splice_Site_SNP|CRB1_uc009wza.2_Splice_Site_SNP_p.E598_splice|CRB1_uc010ppb.1_Intron|CRB1_uc010ppc.1_Splice_Site_SNP|CRB1_uc010ppd.1_Splice_Site_SNP_p.E191_splice|CRB1_uc001gub.1_Splice_Site_SNP_p.E359_splice	NM_201253	NP_957705			crumbs homolog 1 precursor						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														0.176471	19.741632	24.773773	9	42	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	197396583	197396583	3987	1	G	A	A	A	429	33	CRB1	5	2
DENND1B	163486	broad.mit.edu	37	1	197479885	197479885	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197479885C>G	uc010ppe.1	-	c.1973G>C	c.(1972-1974)AGT>ACT	p.S658T	DENND1B_uc010ppf.1_Non-coding_Transcript	NM_001142795	NP_001136267	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B isoform 1	Error:Variant_position_missing_in_Q6P3S1_after_alignment						clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0														0.173913	31.95553	38.880681	12	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197479885	197479885	4606	1	C	G	G	G	260	20	DENND1B	3	3
PLA2G2E	30814	broad.mit.edu	37	1	20246811	20246811	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:20246811G>T	uc001bct.1	-	c.418C>A	c.(418-420)CCG>ACG	p.P140T		NM_014589	NP_055404	Q9NZK7	PA2GE_HUMAN	phospholipase A2, group IIE precursor	140					inflammatory response|lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|phospholipase A2 activity				0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|COAD - Colon adenocarcinoma(152;1.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|GBM - Glioblastoma multiforme(114;0.000146)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)										0.115942	8.15018	18.171155	8	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20246811	20246811	12424	1	G	T	T	T	559	43	PLA2G2E	2	2
KDM5B	10765	broad.mit.edu	37	1	202715449	202715449	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:202715449T>A	uc009xag.2	-	c.2127A>T	c.(2125-2127)GGA>GGT	p.G709G	KDM5B_uc001gyf.2_Silent_p.G673G|KDM5B_uc001gyg.1_Silent_p.G515G	NM_006618	NP_006609	Q9UGL1	KDM5B_HUMAN	jumonji, AT rich interactive domain 1B	673					negative regulation of transcription, DNA-dependent|oxidation-reduction process	nucleolus	DNA binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-trimethyl-K4 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(2)|urinary_tract(1)	5														0.291667	49.93946	52.743233	21	51	KEEP	---	---	---	---	capture		Silent	SNP	202715449	202715449	8440	1	T	A	A	A	691	54	KDM5B	3	3
KLHL12	59349	broad.mit.edu	37	1	202878154	202878154	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:202878154C>T	uc010pqc.1	-	c.930G>A	c.(928-930)AGG>AGA	p.R310R	KLHL12_uc001gym.1_Silent_p.R5R|KLHL12_uc001gyn.1_Silent_p.R122R|KLHL12_uc001gyo.1_Silent_p.R272R|KLHL12_uc009xah.1_Silent_p.R272R	NM_021633	NP_067646	Q53G59	KLH12_HUMAN	kelch-like 12	272					Wnt receptor signaling pathway		protein binding				0			BRCA - Breast invasive adenocarcinoma(75;0.166)											0.20438	61.416608	72.532098	28	109	KEEP	---	---	---	---	capture		Silent	SNP	202878154	202878154	8680	1	C	T	T	T	389	30	KLHL12	2	2
NFASC	23114	broad.mit.edu	37	1	204951081	204951081	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:204951081C>T	uc001hbj.2	+	c.2403C>T	c.(2401-2403)GTC>GTT	p.V801V	NFASC_uc010pra.1_Silent_p.V797V|NFASC_uc001hbi.2_Silent_p.V797V|NFASC_uc010prb.1_Silent_p.V812V|NFASC_uc010prc.1_Silent_p.V368V|NFASC_uc001hbk.1_Silent_p.V607V|NFASC_uc001hbl.1_Silent_p.V51V	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor	801	Extracellular (Potential).|Fibronectin type-III 2.				axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)	4	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)											0.209302	19.849644	23.214639	9	34	KEEP	---	---	---	---	capture		Silent	SNP	204951081	204951081	10759	1	C	T	T	T	379	30	NFASC	2	2
DYRK3	8444	broad.mit.edu	37	1	206821658	206821658	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:206821658C>G	uc001hej.2	+	c.1115C>G	c.(1114-1116)TCT>TGT	p.S372C	DYRK3_uc001hek.2_Intron|DYRK3_uc001hei.2_Missense_Mutation_p.S352C	NM_003582	NP_003573	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	372	Protein kinase.				erythrocyte differentiation|protein phosphorylation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(1)|central_nervous_system(1)	2	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			Melanoma(164;427 2622 26826 51707)				219				0.146497	46.713463	65.574559	23	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	206821658	206821658	5043	1	C	G	G	G	416	32	DYRK3	3	3
PIGR	5284	broad.mit.edu	37	1	207111097	207111097	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:207111097C>A	uc001hez.2	-	c.389_splice	c.e4-1	p.G130_splice	PIGR_uc009xbz.2_Splice_Site_SNP_p.G130_splice	NM_002644	NP_002635			polymeric immunoglobulin receptor precursor							extracellular region|integral to plasma membrane	protein binding			ovary(1)|central_nervous_system(1)	2														0.170732	11.693589	15.90649	7	34	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	207111097	207111097	12321	1	C	A	A	A	312	24	PIGR	5	2
CR1	1378	broad.mit.edu	37	1	207782848	207782848	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:207782848C>T	uc001hfx.2	+	c.6110C>T	c.(6109-6111)TCT>TTT	p.S2037F	CR1_uc009xcl.1_Missense_Mutation_p.S1137F|CR1_uc001hfy.2_Missense_Mutation_p.S1587F	NM_000651	NP_000642	P17927	CR1_HUMAN	complement receptor 1 isoform S precursor	1587	Extracellular (Potential).|Sushi 24.				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3														0.090909	2.530494	11.812098	5	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	207782848	207782848	3979	1	C	T	T	T	416	32	CR1	2	2
PLXNA2	5362	broad.mit.edu	37	1	208212308	208212308	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:208212308C>A	uc001hgz.2	-	c.4522G>T	c.(4522-4524)GAC>TAC	p.D1508Y		NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor	1508	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.199)										0.192771	32.94607	40.266247	16	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	208212308	208212308	12546	1	C	A	A	A	377	29	PLXNA2	2	2
PLXNA2	5362	broad.mit.edu	37	1	208390214	208390214	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:208390214C>A	uc001hgz.2	-	c.1054G>T	c.(1054-1056)GAC>TAC	p.D352Y	PLXNA2_uc001hha.3_Missense_Mutation_p.D406Y	NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor	352	Extracellular (Potential).|Sema.				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.199)										0.21519	34.725	40.647073	17	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	208390214	208390214	12546	1	C	A	A	A	377	29	PLXNA2	2	2
SYT14	255928	broad.mit.edu	37	1	210273453	210273453	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:210273453G>T	uc001hhs.3	+	c.946G>T	c.(946-948)GAC>TAC	p.D316Y	SYT14_uc001hht.3_Missense_Mutation_p.D271Y|SYT14_uc001hhu.3_Non-coding_Transcript|SYT14_uc010psn.1_Missense_Mutation_p.D316Y|SYT14_uc010pso.1_Missense_Mutation_p.D233Y|SYT14_uc009xcv.2_Missense_Mutation_p.D271Y	NM_001146261	NP_001139733	Q8NB59	SYT14_HUMAN	synaptotagmin XIV isoform 1	271	Cytoplasmic (Potential).					integral to membrane				ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.085)										0.144578	17.53922	27.636631	12	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	210273453	210273453	15991	1	G	T	T	T	585	45	SYT14	2	2
KCNK2	3776	broad.mit.edu	37	1	215259913	215259913	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:215259913G>A	uc001hkq.2	+	c.249G>A	c.(247-249)TTG>TTA	p.L83L	KCNK2_uc001hko.2_Silent_p.L79L|KCNK2_uc009xdm.2_Non-coding_Transcript|KCNK2_uc001hkp.2_Non-coding_Transcript|KCNK2_uc010pua.1_Non-coding_Transcript|KCNK2_uc001hkr.3_Silent_p.L68L	NM_001017425	NP_001017425	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2 isoform	83							outward rectifier potassium channel activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)									0.109756	12.821643	37.560096	18	146	KEEP	---	---	---	---	capture		Silent	SNP	215259913	215259913	8371	1	G	A	A	A	607	47	KCNK2	2	2
USH2A	7399	broad.mit.edu	37	1	216370014	216370014	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216370014G>C	uc001hku.1	-	c.4132C>G	c.(4132-4134)CTC>GTC	p.L1378V	USH2A_uc001hkv.2_Missense_Mutation_p.L1378V	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1378	Extracellular (Potential).|Fibronectin type-III 4.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.093333	9.264363	21.737345	7	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	216370014	216370014	17598	1	G	C	C	C	429	33	USH2A	3	3
GPATCH2	55105	broad.mit.edu	37	1	217784288	217784288	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:217784288C>A	uc001hlf.1	-	c.961G>T	c.(961-963)GTC>TTC	p.V321F	GPATCH2_uc001hlg.3_Missense_Mutation_p.V321F	NM_018040	NP_060510	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	321						intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)										0.142857	18.099309	26.70533	10	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	217784288	217784288	6865	1	C	A	A	A	221	17	GPATCH2	2	2
TGFB2	7042	broad.mit.edu	37	1	218607769	218607769	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:218607769G>T	uc001hln.2	+	c.817G>T	c.(817-819)GAA>TAA	p.E273*	TGFB2_uc001hlm.2_Nonsense_Mutation_p.E245*|TGFB2_uc010pue.1_Non-coding_Transcript|TGFB2_uc001hlo.2_Non-coding_Transcript	NM_001135599	NP_001129071	P61812	TGFB2_HUMAN	transforming growth factor, beta 2 isoform 1	245					activation of protein kinase activity|angiogenesis|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cardioblast differentiation|catagen|cell cycle arrest|cell death|cell growth|cell-cell junction organization|cell-cell signaling|collagen fibril organization|dopamine biosynthetic process|embryonic digestive tract development|eye development|glial cell migration|hair follicle morphogenesis|hemopoiesis|menstrual cycle phase|negative regulation of alkaline phosphatase activity|negative regulation of cell growth|negative regulation of epithelial cell proliferation|negative regulation of immune response|negative regulation of macrophage cytokine production|neuron development|neutrophil chemotaxis|odontogenesis|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of cardioblast differentiation|positive regulation of catagen|positive regulation of cell adhesion mediated by integrin|positive regulation of cell cycle|positive regulation of cell division|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of epithelial cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of heart contraction|positive regulation of immune response|positive regulation of integrin biosynthetic process|positive regulation of neuron apoptosis|positive regulation of ossification|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein secretion|positive regulation of stress-activated MAPK cascade|regulation of transforming growth factor-beta2 production|response to hypoxia|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein import into nucleus|somatic stem cell division|transforming growth factor beta receptor signaling pathway	axon|extracellular matrix|extracellular space|neuronal cell body|platelet alpha granule lumen	beta-amyloid binding|cytokine activity|growth factor activity|protein heterodimerization activity|protein homodimerization activity|receptor signaling protein serine/threonine kinase activity|type II transforming growth factor beta receptor binding				0				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)						137				0.188679	19.415729	24.225811	10	43	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	218607769	218607769	16346	1	G	T	T	T	429	33	TGFB2	5	2
MARK1	4139	broad.mit.edu	37	1	220791840	220791840	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:220791840C>T	uc009xdw.2	+	c.741C>T	c.(739-741)CTC>CTT	p.L247L	MARK1_uc001hmn.3_Silent_p.L247L|MARK1_uc010pun.1_Silent_p.L247L|MARK1_uc001hmm.3_Silent_p.L225L	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1	247	Protein kinase.				intracellular protein kinase cascade|protein phosphorylation	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|central_nervous_system(2)|stomach(1)|lung(1)	7				GBM - Glioblastoma multiforme(131;0.0407)						258				0.093023	3.328916	17.666294	8	78	KEEP	---	---	---	---	capture		Silent	SNP	220791840	220791840	9695	1	C	T	T	T	405	32	MARK1	2	2
TAF1A	9015	broad.mit.edu	37	1	222757545	222757545	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:222757545T>A	uc009xdz.1	-	c.216A>T	c.(214-216)CAA>CAT	p.Q72H	TAF1A_uc001hni.1_Intron|TAF1A_uc001hnj.2_Missense_Mutation_p.Q72H|TAF1A_uc001hnk.2_Intron|TAF1A_uc010pur.1_Missense_Mutation_p.Q72H	NM_139352	NP_647603	Q15573	TAF1A_HUMAN	TBP-associated factor 1A isoform 2	72					regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter	RNA polymerase I transcription factor complex	DNA binding|general RNA polymerase II transcription factor activity|RNA polymerase I transcription factor activity				0				GBM - Glioblastoma multiforme(131;0.0186)										0.10231	17.194337	64.980476	31	272	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	222757545	222757545	16040	1	T	A	A	A	725	56	TAF1A	3	3
PARP1	142	broad.mit.edu	37	1	226566929	226566929	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:226566929G>T	uc001hqd.3	-	c.1659C>A	c.(1657-1659)TTC>TTA	p.F553L		NM_001618	NP_001609	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase family, member 1	553					cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nuclear envelope|nucleolus|transcription factor complex	DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding			ovary(2)|breast(2)|lung(1)	5	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)						1012				0.096429	10.602954	56.346016	27	253	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	226566929	226566929	11871	1	G	T	T	T	581	45	PARP1	2	2
OBSCN	84033	broad.mit.edu	37	1	228468497	228468497	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228468497G>T	uc009xez.1	+	c.8197G>T	c.(8197-8199)GAT>TAT	p.D2733Y	OBSCN_uc001hsn.2_Missense_Mutation_p.D2733Y|OBSCN_uc001hsp.1_Missense_Mutation_p.D432Y|OBSCN_uc001hsq.1_5'UTR	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	2733					apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)								4006				0.2	15.110277	18.036282	7	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228468497	228468497	11217	1	G	T	T	T	507	39	OBSCN	1	1
NUP133	55746	broad.mit.edu	37	1	229588382	229588382	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:229588382C>A	uc001htn.2	-	c.2989G>T	c.(2989-2991)GAG>TAG	p.E997*		NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	997					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)								578				0.178571	19.312818	24.761557	10	46	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	229588382	229588382	11159	1	C	A	A	A	377	29	NUP133	5	2
TAF5L	27097	broad.mit.edu	37	1	229730411	229730411	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:229730411C>G	uc001htq.2	-	c.1403G>C	c.(1402-1404)CGT>CCT	p.R468P		NM_014409	NP_055224	O75529	TAF5L_HUMAN	PCAF associated factor 65 beta isoform a	468	WD 5.				histone H3 acetylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	STAGA complex|transcription factor TFTC complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulator activity			ovary(1)	1	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)												0.085106	6.880882	40.04386	16	172	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	229730411	229730411	16050	1	C	G	G	G	247	19	TAF5L	3	3
SIPA1L2	57568	broad.mit.edu	37	1	232596806	232596806	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:232596806C>A	uc001hvg.2	-	c.2922G>T	c.(2920-2922)GTG>GTT	p.V974V	SIPA1L2_uc001hvf.2_Silent_p.V48V	NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	974	PDZ.				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)												0.064103	-22.560587	39.136348	20	292	KEEP	---	---	---	---	capture		Silent	SNP	232596806	232596806	14825	1	C	A	A	A	262	21	SIPA1L2	2	2
GPR137B	7107	broad.mit.edu	37	1	236341796	236341796	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:236341796G>T	uc001hxq.2	+	c.547G>T	c.(547-549)GGA>TGA	p.G183*	GPR137B_uc001hxr.1_5'UTR|GPR137B_uc009xge.2_Non-coding_Transcript	NM_003272	NP_003263	O60478	G137B_HUMAN	G protein-coupled receptor 137B	183	Extracellular (Potential).					integral to plasma membrane|membrane fraction					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.197)|Prostate(94;0.219)|Acute lymphoblastic leukemia(190;0.226)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)											0.178571	45.094417	58.709978	25	115	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	236341796	236341796	6920	1	G	T	T	T	559	43	GPR137B	5	2
RYR2	6262	broad.mit.edu	37	1	237774140	237774140	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237774140G>T	uc001hyl.1	+	c.4762G>T	c.(4762-4764)GTG>TTG	p.V1588L		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1588	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.407407	31.517325	31.72012	11	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237774140	237774140	14249	1	G	T	T	T	520	40	RYR2	1	1
RYR2	6262	broad.mit.edu	37	1	237798224	237798224	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237798224G>T	uc001hyl.1	+	c.6724G>T	c.(6724-6726)GTG>TTG	p.V2242L		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2242	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.411765	21.021108	21.136911	7	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237798224	237798224	14249	1	G	T	T	T	624	48	RYR2	2	2
RYR2	6262	broad.mit.edu	37	1	237802371	237802371	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237802371G>A	uc001hyl.1	+	c.6985G>A	c.(6985-6987)GAG>AAG	p.E2329K		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2329	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.227273	10.661151	12.165307	5	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237802371	237802371	14249	1	G	A	A	A	585	45	RYR2	2	2
ZP4	57829	broad.mit.edu	37	1	238050727	238050727	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:238050727G>T	uc001hym.2	-	c.688C>A	c.(688-690)CAA>AAA	p.Q230K	LOC100130331_uc010pyc.1_Intron	NM_021186	NP_067009	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4 preproprotein	230	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)								0.21875	67.823092	77.160332	28	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	238050727	238050727	18822	1	G	T	T	T	624	48	ZP4	2	2
RGS7	6000	broad.mit.edu	37	1	240969465	240969465	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:240969465C>A	uc001hyv.2	-	c.1244G>T	c.(1243-1245)GGA>GTA	p.G415V	RGS7_uc010pyh.1_Missense_Mutation_p.G389V|RGS7_uc010pyj.1_Missense_Mutation_p.G331V|RGS7_uc001hyu.2_Missense_Mutation_p.G415V|RGS7_uc009xgn.1_Missense_Mutation_p.G362V|RGS7_uc001hyw.2_Missense_Mutation_p.G415V|RGS7_uc001hyt.2_Missense_Mutation_p.G247V	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7	415	RGS.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|kidney(1)	5		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)											0.171875	37.762491	50.799577	22	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	240969465	240969465	13784	1	C	A	A	A	390	30	RGS7	2	2
KMO	8564	broad.mit.edu	37	1	241752098	241752098	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:241752098C>G	uc009xgp.2	+	c.1064C>G	c.(1063-1065)GCG>GGG	p.A355G	KMO_uc001hyy.2_Missense_Mutation_p.A355G|KMO_uc009xgo.1_Missense_Mutation_p.A355G	NM_003679	NP_003670	O15229	KMO_HUMAN	kynurenine 3-monooxygenase	355					oxidation-reduction process|pyridine nucleotide biosynthetic process|response to salt stress	cytosol|integral to membrane|mitochondrial outer membrane	electron carrier activity|flavin adenine dinucleotide binding|kynurenine 3-monooxygenase activity|NAD(P)H oxidase activity			ovary(2)	2	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)											0.174757	43.986992	54.264607	18	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	241752098	241752098	8738	1	C	G	G	G	351	27	KMO	3	3
EXO1	9156	broad.mit.edu	37	1	242016740	242016740	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:242016740G>C	uc001hzh.2	+	c.362G>C	c.(361-363)CGG>CCG	p.R121P	EXO1_uc001hzi.2_Missense_Mutation_p.R121P|EXO1_uc001hzj.2_Missense_Mutation_p.R121P|EXO1_uc009xgq.2_Missense_Mutation_p.R121P	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b	121					meiosis|mismatch repair	nucleus	double-stranded DNA specific 5'-3' exodeoxyribonuclease activity|flap endonuclease activity|metal ion binding|protein binding|protein binding|ribonuclease H activity|single-stranded DNA specific 5'-3' exodeoxyribonuclease activity			ovary(2)|skin(1)	3	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)											0.215385	103.000528	117.539069	42	153	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	242016740	242016740	5493	1	G	C	C	C	507	39	EXO1	3	3
KIF26B	55083	broad.mit.edu	37	1	245530532	245530532	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:245530532G>T	uc001ibf.1	+	c.862G>T	c.(862-864)GCC>TCC	p.A288S	KIF26B_uc010pyq.1_Missense_Mutation_p.A288S|KIF26B_uc010pyr.1_Missense_Mutation_p.A88S	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	288					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)											0.15625	8.053114	11.66444	5	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	245530532	245530532	8606	1	G	T	T	T	546	42	KIF26B	2	2
CNST	163882	broad.mit.edu	37	1	246811284	246811284	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:246811284C>T	uc001ibp.2	+	c.1781C>T	c.(1780-1782)TCT>TTT	p.S594F	CNST_uc001ibo.3_Missense_Mutation_p.S594F	NM_152609	NP_689822	Q6PJW8	CNST_HUMAN	hypothetical protein LOC163882 isoform 1	594					positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding				0														0.076628	-3.925891	44.010376	20	241	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	246811284	246811284	3772	1	C	T	T	T	416	32	CNST	2	2
C1orf201	90529	broad.mit.edu	37	1	24700270	24700270	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:24700270T>A	uc001bja.2	-	c.352A>T	c.(352-354)AAC>TAC	p.N118Y	C1orf201_uc010oej.1_5'UTR|C1orf201_uc001bjb.2_Missense_Mutation_p.N73Y|C1orf201_uc001bjc.2_Missense_Mutation_p.N165Y|C1orf201_uc001bjd.2_Missense_Mutation_p.N165Y|C1orf201_uc001bje.1_Missense_Mutation_p.N118Y|C1orf201_uc001bjf.2_Missense_Mutation_p.N33Y	NM_178122	NP_835223	Q5TH74	CA201_HUMAN	hypothetical protein LOC90529	165										ovary(1)|breast(1)	2		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.0191)|all_lung(284;0.0251)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.056)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.48e-25)|Colorectal(126;7.29e-08)|COAD - Colon adenocarcinoma(152;3.85e-06)|GBM - Glioblastoma multiforme(114;0.000399)|BRCA - Breast invasive adenocarcinoma(304;0.00107)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00393)|READ - Rectum adenocarcinoma(331;0.0672)|Lung(427;0.145)										0.137856	102.947821	160.91327	63	394	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24700270	24700270	2095	1	T	A	A	A	819	63	C1orf201	3	3
AHCTF1	25909	broad.mit.edu	37	1	247057967	247057967	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247057967T>C	uc001ibv.1	-	c.1825A>G	c.(1825-1827)AGA>GGA	p.R609G	AHCTF1_uc001ibu.1_Missense_Mutation_p.R600G|AHCTF1_uc009xgs.1_5'UTR	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	600	Necessary for cytoplasmic localization (By similarity).				cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)	5	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			Colon(145;197 1800 4745 15099 26333)								0.069767	0.677509	17.113342	6	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247057967	247057967	411	1	T	C	C	C	713	55	AHCTF1	4	4
ZNF496	84838	broad.mit.edu	37	1	247464362	247464362	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247464362C>A	uc009xgv.2	-	c.1331G>T	c.(1330-1332)TGT>TTT	p.C444F	ZNF496_uc001ico.2_Missense_Mutation_p.C408F|ZNF496_uc001icp.2_Missense_Mutation_p.C408F	NM_032752	NP_116141	Q96IT1	ZN496_HUMAN	zinc finger protein 496	408	C2H2-type 1; degenerate.				positive regulation of transcription, DNA-dependent|viral reproduction		DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)											0.175573	41.332057	54.35006	23	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247464362	247464362	18539	1	C	A	A	A	221	17	ZNF496	2	2
NLRP3	114548	broad.mit.edu	37	1	247588039	247588039	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247588039C>A	uc001icr.2	+	c.1294C>A	c.(1294-1296)CTT>ATT	p.L432I	NLRP3_uc001ics.2_Missense_Mutation_p.L432I|NLRP3_uc001icu.2_Missense_Mutation_p.L432I|NLRP3_uc001icw.2_Missense_Mutation_p.L432I|NLRP3_uc001icv.2_Missense_Mutation_p.L432I|NLRP3_uc010pyw.1_Missense_Mutation_p.L430I|NLRP3_uc001ict.1_Missense_Mutation_p.L430I	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	432	NACHT.				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding			ovary(5)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	11	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)							412				0.165138	28.443284	40.110952	18	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247588039	247588039	10881	1	C	A	A	A	312	24	NLRP3	2	2
NLRP3	114548	broad.mit.edu	37	1	247597508	247597508	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247597508G>C	uc001icr.2	+	c.2431G>C	c.(2431-2433)GGT>CGT	p.G811R	NLRP3_uc001ics.2_Missense_Mutation_p.G811R|NLRP3_uc001icu.2_Missense_Mutation_p.G811R|NLRP3_uc001icw.2_Missense_Mutation_p.G754R|NLRP3_uc001icv.2_Missense_Mutation_p.G754R|NLRP3_uc010pyw.1_Missense_Mutation_p.G789R	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	811	LRR 3.				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding			ovary(5)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	11	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)						p.G811S(JHUEM1-Tumor)|p.G811S(YH13-Tumor)|p.G811S(HGC27-Tumor)|p.G811S(YKG1-Tumor)|p.G811S(MKN7-Tumor)|p.G811S(NALM19-Tumor)|p.G811S(SET2-Tumor)|p.G811S(LC1SQSF-Tumor)|p.G811S(JHOC5-Tumor)|p.G811S(KHM1B-Tumor)|p.G811S(LC1F-Tumor)	412				0.100478	16.05158	49.354719	21	188	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247597508	247597508	10881	1	G	C	C	C	507	39	NLRP3	3	3
OR2G2	81470	broad.mit.edu	37	1	247751880	247751880	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247751880C>A	uc010pyy.1	+	c.219C>A	c.(217-219)TAC>TAA	p.Y73*		NM_001001915	NP_001001915	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G,	73	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)											0.121528	35.613822	76.058939	35	253	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	247751880	247751880	11404	1	C	A	A	A	233	18	OR2G2	5	2
OR13G1	441933	broad.mit.edu	37	1	247835749	247835749	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247835749C>A	uc001idi.1	-	c.595G>T	c.(595-597)GCT>TCT	p.A199S		NM_001005487	NP_001005487	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G,	199	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)											0.09434	4.275523	21.797094	10	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247835749	247835749	11348	1	C	A	A	A	325	25	OR13G1	2	2
OR13G1	441933	broad.mit.edu	37	1	247836100	247836101	+	Missense_Mutation	DNP	TG	AT	AT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247836100_247836101TG>AT	uc001idi.1	-	c.243_244CA>AT	c.(241-246)ACCATG>ACATTG	p.M82L		NM_001005487	NP_001005487	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G,	82	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)											0.235294	28.679571	31.944819	12	39	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	247836100	247836101	11348	1	TG	AT	AT	AT	663	51	OR13G1	3	3
OR6F1	343169	broad.mit.edu	37	1	247875377	247875377	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247875377C>A	uc001idj.1	-	c.681G>T	c.(679-681)AGG>AGT	p.R227S		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	227	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)											0.08046	-7.4366	39.430022	21	240	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247875377	247875377	11611	1	C	A	A	A	389	30	OR6F1	2	2
OR2L8	391190	broad.mit.edu	37	1	248112310	248112310	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248112310G>T	uc001idt.1	+	c.151G>T	c.(151-153)GAC>TAC	p.D51Y	OR2L13_uc001ids.2_Intron	NM_001001963	NP_001001963	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L,	51	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	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)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)											0.089127	6.983606	102.700867	50	511	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248112310	248112310	11415	1	G	T	T	T	533	41	OR2L8	2	2
OR2AK2	391191	broad.mit.edu	37	1	248128725	248128725	+	Missense_Mutation	SNP	G	T	T	rs74153215	byFrequency;by1000genomes	TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248128725G>T	uc010pzd.1	+	c.92G>T	c.(91-93)GGT>GTT	p.G31V	OR2L13_uc001ids.2_Intron	NM_001004491	NP_001004491	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK,	31	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2	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)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			Melanoma(45;390 1181 23848 28461 41504)								0.101351	12.108251	35.579323	15	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248128725	248128725	11392	1	G	T	T	T	572	44	OR2AK2	2	2
OR2L3	391192	broad.mit.edu	37	1	248224093	248224093	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248224093C>A	uc001idx.1	+	c.110C>A	c.(109-111)GCT>GAT	p.A37D	OR2L13_uc001ids.2_Intron	NM_001004687	NP_001004687	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L,	37	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	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;0.0278)											0.219316	245.679366	281.779381	109	388	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248224093	248224093	11414	1	C	A	A	A	364	28	OR2L3	2	2
OR2L3	391192	broad.mit.edu	37	1	248224537	248224537	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248224537C>A	uc001idx.1	+	c.554C>A	c.(553-555)ACT>AAT	p.T185N	OR2L13_uc001ids.2_Intron	NM_001004687	NP_001004687	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L,	185	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	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;0.0278)											0.082474	1.037418	35.455265	16	178	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248224537	248224537	11414	1	C	A	A	A	260	20	OR2L3	2	2
OR2M2	391194	broad.mit.edu	37	1	248343733	248343733	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248343733G>T	uc010pzf.1	+	c.446G>T	c.(445-447)TGG>TTG	p.W149L		NM_001004688	NP_001004688	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M,	149	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	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;0.0245)											0.229607	168.282481	190.527114	76	255	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248343733	248343733	11416	1	G	T	T	T	611	47	OR2M2	2	2
OR2M3	127062	broad.mit.edu	37	1	248366486	248366486	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248366486C>A	uc010pzg.1	+	c.117C>A	c.(115-117)TTC>TTA	p.F39L		NM_001004689	NP_001004689	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M,	39	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)											0.095823	12.983781	79.738482	39	368	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248366486	248366486	11417	1	C	A	A	A	376	29	OR2M3	2	2
OR2T12	127064	broad.mit.edu	37	1	248458331	248458331	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248458331G>A	uc010pzj.1	-	c.550C>T	c.(550-552)CGT>TGT	p.R184C		NM_001004692	NP_001004692	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T,	184	Extracellular (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)											0.225962	103.843634	118.172353	47	161	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248458331	248458331	11425	1	G	A	A	A	494	38	OR2T12	1	1
OR2T12	127064	broad.mit.edu	37	1	248458840	248458840	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248458840C>A	uc010pzj.1	-	c.41G>T	c.(40-42)GGA>GTA	p.G14V		NM_001004692	NP_001004692	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T,	14	Extracellular (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)											0.10231	17.286643	65.08331	31	272	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248458840	248458840	11425	1	C	A	A	A	390	30	OR2T12	2	2
OR2T4	127074	broad.mit.edu	37	1	248525336	248525336	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248525336T>A	uc001ieh.1	+	c.454T>A	c.(454-456)TAT>AAT	p.Y152N		NM_001004696	NP_001004696	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T,	152	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(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;0.0265)											0.280899	193.349937	204.848161	75	192	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248525336	248525336	11433	1	T	A	A	A	689	53	OR2T4	3	3
OR2T1	26696	broad.mit.edu	37	1	248569885	248569885	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248569885G>T	uc010pzm.1	+	c.590G>T	c.(589-591)GGT>GTT	p.G197V		NM_030904	NP_112166	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T,	197	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(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;0.0265)											0.184397	56.262773	69.439754	26	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248569885	248569885	11422	1	G	T	T	T	572	44	OR2T1	2	2
OR2T10	127069	broad.mit.edu	37	1	248756307	248756307	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248756307C>T	uc010pzn.1	-	c.763G>A	c.(763-765)GCT>ACT	p.A255T		NM_001004693	NP_001004693	Q8NGZ9	O2T10_HUMAN	olfactory receptor, family 2, subfamily T,	255	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.10989	7.281259	20.994475	10	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248756307	248756307	11423	1	C	T	T	T	325	25	OR2T10	2	2
OR14I1	401994	broad.mit.edu	37	1	248845057	248845057	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248845057C>A	uc001ieu.1	-	c.549G>T	c.(547-549)TTG>TTT	p.L183F		NM_001004734	NP_001004734	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I,	183	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.208333	33.281865	38.956888	15	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248845057	248845057	11353	1	C	A	A	A	272	21	OR14I1	2	2
SLC30A2	7780	broad.mit.edu	37	1	26370836	26370836	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26370836G>C	uc001blg.1	-	c.371C>G	c.(370-372)TCC>TGC	p.S124C	SLC30A2_uc001blh.1_Intron	NM_001004434	NP_001004434	Q9BRI3	ZNT2_HUMAN	solute carrier family 30, member 2 isoform 1	90	Cytoplasmic (Potential).				positive regulation of sequestering of zinc ion|zinc ion transport	integral to membrane|late endosome|lysosomal membrane	cation transmembrane transporter activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.09e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00614)|READ - Rectum adenocarcinoma(331;0.0649)										0.111111	7.146574	13.874277	5	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26370836	26370836	15052	1	G	C	C	C	533	41	SLC30A2	3	3
CATSPER4	378807	broad.mit.edu	37	1	26526438	26526438	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26526438C>A	uc010oez.1	+	c.876C>A	c.(874-876)ACC>ACA	p.T292T	CATSPER4_uc010oey.1_Silent_p.T114T|CATSPER4_uc009vsf.2_Non-coding_Transcript	NM_198137	NP_937770	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	292	Helical; Name=Segment S6; (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|voltage-gated ion channel activity			ovary(1)	1		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)										0.34	50.76449	51.893661	17	33	KEEP	---	---	---	---	capture		Silent	SNP	26526438	26526438	2809	1	C	A	A	A	262	21	CATSPER4	2	2
ARID1A	8289	broad.mit.edu	37	1	27105667	27105667	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:27105667G>T	uc001bmv.1	+	c.5278G>T	c.(5278-5280)GAG>TAG	p.E1760*	ARID1A_uc001bmu.1_Nonsense_Mutation_p.E1543*|ARID1A_uc001bmx.1_Nonsense_Mutation_p.E606*|ARID1A_uc009vsm.1_Nonsense_Mutation_p.E88*|ARID1A_uc009vsn.1_Nonsense_Mutation_p.E2*	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1760					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding|transcription activator activity			ovary(124)|endometrium(3)|kidney(3)|central_nervous_system(2)|pancreas(2)|lung(1)|skin(1)	136		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)						478				0.202381	64.235637	78.081946	34	134	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	27105667	27105667	928	1	G	T	T	T	533	41	ARID1A	5	2
FAM46B	115572	broad.mit.edu	37	1	27333053	27333053	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:27333053C>A	uc010ofj.1	-	c.660G>T	c.(658-660)CAG>CAT	p.Q220H		NM_052943	NP_443175	Q96A09	FA46B_HUMAN	hypothetical protein LOC115572	220										central_nervous_system(1)	1		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)										0.076923	-1.891255	12.384847	6	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27333053	27333053	5787	1	C	A	A	A	415	32	FAM46B	2	2
KPNA6	23633	broad.mit.edu	37	1	32626214	32626214	+	Splice_Site_SNP	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:32626214A>T	uc010ogy.1	+	c.574_splice	c.e7-2	p.A192_splice	KPNA6_uc001bug.2_Splice_Site_SNP_p.A187_splice|KPNA6_uc001buh.2_Intron|KPNA6_uc010ogx.1_Splice_Site_SNP_p.A184_splice|KPNA6_uc009vtz.2_Splice_Site_SNP_p.A82_splice	NM_012316	NP_036448			karyopherin alpha 6						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)												0.211382	63.495754	72.959915	26	97	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	32626214	32626214	8748	1	A	T	T	T	91	7	KPNA6	5	3
AK2	204	broad.mit.edu	37	1	33480187	33480187	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:33480187T>A	uc001bwp.1	-	c.434A>T	c.(433-435)CAC>CTC	p.H145L	AK2_uc001bwo.1_Missense_Mutation_p.H145L|AK2_uc010ohq.1_Missense_Mutation_p.H137L|AK2_uc009vud.1_Missense_Mutation_p.H103L|AK2_uc010ohr.1_Missense_Mutation_p.H97L|AK2_uc001bwq.1_Missense_Mutation_p.H97L	NM_001625	NP_001616	P54819	KAD2_HUMAN	adenylate kinase 2 isoform a	145					nucleobase, nucleoside and nucleotide interconversion	mitochondrial intermembrane space	adenylate kinase activity|ATP binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)												0.224189	198.843131	222.527286	76	263	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33480187	33480187	443	1	T	A	A	A	767	59	AK2	3	3
DLGAP3	58512	broad.mit.edu	37	1	35370074	35370074	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:35370074C>A	uc001byc.2	-	c.911G>T	c.(910-912)CGC>CTC	p.R304L		NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated	304					cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)												0.06338	-8.388669	19.742474	9	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35370074	35370074	4741	1	C	A	A	A	351	27	DLGAP3	1	1
CCDC27	148870	broad.mit.edu	37	1	3669282	3669282	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:3669282G>T	uc001akv.2	+	c.237G>T	c.(235-237)CGG>CGT	p.R79R		NM_152492	NP_689705	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	79											0	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)										0.138462	15.669881	23.850555	9	56	KEEP	---	---	---	---	capture		Silent	SNP	3669282	3669282	2923	1	G	T	T	T	561	44	CCDC27	2	2
GRIK3	2899	broad.mit.edu	37	1	37267485	37267485	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:37267485G>T	uc001caz.2	-	c.2727C>A	c.(2725-2727)GCC>GCA	p.A909A		NM_000831	NP_000822	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	909	Cytoplasmic (Potential).				negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|large_intestine(1)|breast(1)	5		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)									0.132653	18.013999	30.85136	13	85	KEEP	---	---	---	---	capture		Silent	SNP	37267485	37267485	7054	1	G	T	T	T	444	35	GRIK3	2	2
GRIK3	2899	broad.mit.edu	37	1	37291209	37291209	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:37291209G>A	uc001caz.2	-	c.1749C>T	c.(1747-1749)ATC>ATT	p.I583I	GRIK3_uc001cba.1_Silent_p.I583I	NM_000831	NP_000822	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	583	Helical; (Potential).				negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|large_intestine(1)|breast(1)	5		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)									0.384615	43.216153	43.671209	15	24	KEEP	---	---	---	---	capture		Silent	SNP	37291209	37291209	7054	1	G	A	A	A	473	37	GRIK3	1	1
GNL2	29889	broad.mit.edu	37	1	38034454	38034454	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:38034454G>A	uc001cbk.2	-	c.1866C>T	c.(1864-1866)GTC>GTT	p.V622V		NM_013285	NP_037417	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2	622					ribosome biogenesis	nucleolus	GTP binding|GTPase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(586;0.0393)												0.092732	8.839001	75.480945	37	362	KEEP	---	---	---	---	capture		Silent	SNP	38034454	38034454	6805	1	G	A	A	A	574	45	GNL2	2	2
C1orf174	339448	broad.mit.edu	37	1	3807396	3807396	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:3807396G>A	uc001alf.2	-	c.355C>T	c.(355-357)CTT>TTT	p.L119F	C1orf174_uc009vls.2_Non-coding_Transcript	NM_207356	NP_997239	Q8IYL3	CA174_HUMAN	hypothetical protein LOC339448	119											0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)										0.103448	6.204776	15.287064	6	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3807396	3807396	2082	1	G	A	A	A	429	33	C1orf174	2	2
CCDC30	728621	broad.mit.edu	37	1	43111812	43111812	+	Nonsense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:43111812A>T	uc009vwk.1	+	c.1897A>T	c.(1897-1899)AAG>TAG	p.K633*	CCDC30_uc001chm.2_Nonsense_Mutation_p.K331*|CCDC30_uc001chn.2_Nonsense_Mutation_p.K422*	NM_001080850	NP_001074319	Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	633											0														0.263158	11.666216	12.630371	5	14	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	43111812	43111812	2927	1	A	T	T	T	169	13	CCDC30	5	3
EBNA1BP2	10969	broad.mit.edu	37	1	43637203	43637203	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:43637203G>A	uc010ojx.1	-	c.435C>T	c.(433-435)AAC>AAT	p.N145N	EBNA1BP2_uc001cio.2_Silent_p.N145N|WDR65_uc010ojz.1_5'Flank|WDR65_uc001cip.1_5'Flank|WDR65_uc001ciq.1_5'Flank|EBNA1BP2_uc001cim.2_5'UTR|EBNA1BP2_uc001cin.2_Silent_p.N90N	NM_001159936	NP_001153408	Q99848	EBP2_HUMAN	EBNA1 binding protein 2 isoform 1	90					ribosome biogenesis	membrane fraction|nucleolus	protein binding				0	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)												0.150418	77.586628	119.674596	54	305	KEEP	---	---	---	---	capture		Silent	SNP	43637203	43637203	5072	1	G	A	A	A	620	48	EBNA1BP2	2	2
MPL	4352	broad.mit.edu	37	1	43803815	43803815	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:43803815C>A	uc001ciw.2	+	c.125C>A	c.(124-126)TCC>TAC	p.S42Y	MPL_uc001civ.2_Missense_Mutation_p.S42Y|MPL_uc009vwr.2_Missense_Mutation_p.S35Y	NM_005373	NP_005364	P40238	TPOR_HUMAN	myeloproliferative leukemia virus oncogene	42	Extracellular (Potential).				cell proliferation|platelet activation	integral to plasma membrane	cytokine receptor activity			haematopoietic_and_lymphoid_tissue(359)|pancreas(1)	360	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				NSCLC(52;534 1204 10016 41452 44427)				169				0.100917	6.13754	23.473403	11	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43803815	43803815	10122	1	C	A	A	A	390	30	MPL	2	2
IPO13	9670	broad.mit.edu	37	1	44429990	44429990	+	Silent	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:44429990A>C	uc001ckx.2	+	c.2394A>C	c.(2392-2394)GCA>GCC	p.A798A	IPO13_uc001cky.2_5'Flank	NM_014652	NP_055467	O94829	IPO13_HUMAN	importin 13	798	HEAT 14.				protein import into nucleus	cytoplasm|nucleus	protein binding|protein transporter activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)												0.150685	72.238016	97.836413	33	186	KEEP	---	---	---	---	capture		Silent	SNP	44429990	44429990	8095	1	A	C	C	C	67	6	IPO13	4	4
DMRTB1	63948	broad.mit.edu	37	1	53925146	53925146	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:53925146G>T	uc001cvq.1	+	c.20G>T	c.(19-21)CGC>CTC	p.R7L		NM_033067	NP_149056	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal,	7					regulation of transcription, DNA-dependent|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0														0.145833	11.114174	16.886746	7	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53925146	53925146	4770	1	G	T	T	T	494	38	DMRTB1	1	1
DMRTB1	63948	broad.mit.edu	37	1	53932273	53932273	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:53932273C>A	uc001cvq.1	+	c.967C>A	c.(967-969)CAG>AAG	p.Q323K		NM_033067	NP_149056	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal,	323					regulation of transcription, DNA-dependent|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0														0.194672	200.725168	243.175614	95	393	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53932273	53932273	4770	1	C	A	A	A	273	21	DMRTB1	2	2
CDCP2	200008	broad.mit.edu	37	1	54610303	54610303	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:54610303A>T	uc001cwv.1	-	c.263T>A	c.(262-264)CTG>CAG	p.L88Q		NM_201546	NP_963840	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2 precursor	88	CUB 1.					extracellular region				ovary(1)	1														0.093333	3.267025	15.745947	7	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54610303	54610303	3223	1	A	T	T	T	91	7	CDCP2	3	3
C8B	732	broad.mit.edu	37	1	57411562	57411562	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:57411562G>T	uc001cyp.2	-	c.1037C>A	c.(1036-1038)ACA>AAA	p.T346K	C8B_uc010oon.1_Missense_Mutation_p.T284K|C8B_uc010ooo.1_Missense_Mutation_p.T294K	NM_000066	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	346	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	membrane attack complex				central_nervous_system(2)|large_intestine(1)|ovary(1)	4														0.1625	26.320172	34.985801	13	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57411562	57411562	2526	1	G	T	T	T	624	48	C8B	2	2
NPHP4	261734	broad.mit.edu	37	1	5967250	5967250	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:5967250C>A	uc001alq.1	-	c.1536G>T	c.(1534-1536)CGG>CGT	p.R512R	NPHP4_uc001als.1_Non-coding_Transcript|NPHP4_uc009vlt.1_Intron|NPHP4_uc001alt.1_Intron|NPHP4_uc009vlu.1_5'Flank	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	512					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cilium|membrane|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)										0.181818	7.587571	9.679852	4	18	KEEP	---	---	---	---	capture		Silent	SNP	5967250	5967250	10985	1	C	A	A	A	223	18	NPHP4	2	2
HOOK1	51361	broad.mit.edu	37	1	60328550	60328550	+	Splice_Site_SNP	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:60328550G>T	uc009wad.2	+	c.1626_splice	c.e17+1	p.S542_splice	HOOK1_uc001czo.2_Splice_Site_SNP_p.S542_splice|HOOK1_uc001czp.2_Splice_Site_SNP|HOOK1_uc010oor.1_Splice_Site_SNP_p.S500_splice	NM_015888	NP_056972			hook homolog 1						early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|multicellular organismal development|protein transport	FHF complex|microtubule	identical protein binding			ovary(1)|breast(1)	2	all_cancers(7;0.000129)													0.128571	14.222958	23.632682	9	61	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	60328550	60328550	7574	1	G	T	T	T	624	48	HOOK1	5	2
KCNAB2	8514	broad.mit.edu	37	1	6147562	6147562	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:6147562G>T	uc001aly.1	+	c.461G>T	c.(460-462)TGG>TTG	p.W154L	KCNAB2_uc009vlv.1_Missense_Mutation_p.W121L|KCNAB2_uc001alv.1_Missense_Mutation_p.W121L|KCNAB2_uc001alw.1_Missense_Mutation_p.W107L|KCNAB2_uc001alx.1_Missense_Mutation_p.W121L|KCNAB2_uc009vlw.1_Missense_Mutation_p.W54L|KCNAB2_uc001alu.2_Missense_Mutation_p.W121L	NM_172130	NP_742128	Q13303	KCAB2_HUMAN	potassium voltage-gated channel, shaker-related	121					oxidation-reduction process	cytoplasm|integral to membrane|juxtaparanode region of axon	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity				0	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)										0.192308	38.834142	48.037088	20	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6147562	6147562	8315	1	G	T	T	T	611	47	KCNAB2	2	2
CHD5	26038	broad.mit.edu	37	1	6196657	6196657	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:6196657C>G	uc001amb.1	-	c.2616G>C	c.(2614-2616)CTG>CTC	p.L872L	CHD5_uc001ama.1_Non-coding_Transcript|CHD5_uc001amc.1_Non-coding_Transcript|CHD5_uc009vlx.1_Non-coding_Transcript	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	872	Helicase ATP-binding.				chromatin assembly or disassembly|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|zinc ion binding			breast(3)|central_nervous_system(3)|ovary(1)|lung(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)						2304				0.111801	28.046524	52.005942	18	143	KEEP	---	---	---	---	capture		Silent	SNP	6196657	6196657	3462	1	C	G	G	G	314	25	CHD5	3	3
INADL	10207	broad.mit.edu	37	1	62582842	62582842	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:62582842C>G	uc001dab.2	+	c.4842C>G	c.(4840-4842)CTC>CTG	p.L1614L	INADL_uc001dac.2_Non-coding_Transcript|INADL_uc010oot.1_Silent_p.L428L|INADL_uc009wag.2_Silent_p.L398L	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	1614	PDZ 9.				intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)	3														0.147541	22.140439	29.411349	9	52	KEEP	---	---	---	---	capture		Silent	SNP	62582842	62582842	8032	1	C	G	G	G	379	30	INADL	3	3
CACHD1	57685	broad.mit.edu	37	1	65157120	65157120	+	Missense_Mutation	SNP	C	A	A	rs72673394	by1000genomes	TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:65157120C>A	uc001dbo.1	+	c.3548C>A	c.(3547-3549)CCC>CAC	p.P1183H	CACHD1_uc001dbp.1_Missense_Mutation_p.P938H|CACHD1_uc001dbq.1_Missense_Mutation_p.P938H|CACHD1_uc010opa.1_Missense_Mutation_p.P427H	NM_020925	NP_065976	Q5VU97	CAHD1_HUMAN	cache domain containing 1	1234	Cytoplasmic (Potential).				calcium ion transport	integral to membrane				ovary(2)	2														0.15625	20.754605	31.600794	15	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65157120	65157120	2653	1	C	A	A	A	286	22	CACHD1	2	2
IL12RB2	3595	broad.mit.edu	37	1	67816660	67816660	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:67816660C>T	uc001ddu.2	+	c.1146C>T	c.(1144-1146)TCC>TCT	p.S382S	IL12RB2_uc010oqi.1_Silent_p.S382S|IL12RB2_uc010oqj.1_Silent_p.S382S|IL12RB2_uc010oqk.1_Non-coding_Transcript|IL12RB2_uc010oql.1_Silent_p.S382S|IL12RB2_uc010oqm.1_Silent_p.S382S|IL12RB2_uc010oqn.1_Non-coding_Transcript	NM_001559	NP_001550	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2 precursor	382	Fibronectin type-III 3.|Extracellular (Potential).				positive regulation of cell proliferation|positive regulation of interferon-gamma production	integral to plasma membrane	cytokine receptor activity			ovary(2)|central_nervous_system(1)	3														0.109589	9.642722	20.660755	8	65	KEEP	---	---	---	---	capture		Silent	SNP	67816660	67816660	7928	1	C	T	T	T	301	24	IL12RB2	2	2
TNNI3K	51086	broad.mit.edu	37	1	74957895	74957895	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:74957895C>T	uc001dge.1	+	c.2599C>T	c.(2599-2601)CGT>TGT	p.R867C	TNNI3K_uc001dgf.1_Missense_Mutation_p.R766C	NM_001112808	NP_001106279	Q59H18	TNI3K_HUMAN	TNNI3 interacting kinase isoform a	766					protein phosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10										765				0.078947	-1.510344	32.881343	15	175	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74957895	74957895	16870	1	C	T	T	T	403	31	TNNI3K	1	1
ACADM	34	broad.mit.edu	37	1	76205759	76205759	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:76205759A>T	uc009wbr.2	+	c.662A>T	c.(661-663)CAG>CTG	p.Q221L	ACADM_uc010orc.1_3'UTR|ACADM_uc010ord.1_Missense_Mutation_p.Q102L|ACADM_uc001dgw.3_Missense_Mutation_p.Q188L|ACADM_uc009wbp.2_Missense_Mutation_p.Q192L|ACADM_uc010ore.1_Missense_Mutation_p.Q152L|ACADM_uc010orf.1_5'UTR|ACADM_uc001dgx.3_Missense_Mutation_p.Q102L|ACADM_uc010org.1_Missense_Mutation_p.Q58L	NM_000016	NP_000007	P11310	ACADM_HUMAN	medium-chain acyl-CoA dehydrogenase isoform a	188					carnitine biosynthetic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|medium-chain fatty acid catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|identical protein binding|medium-chain-acyl-CoA dehydrogenase activity			breast(2)|ovary(1)	3														0.178218	40.186689	50.032662	18	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76205759	76205759	114	1	A	T	T	T	91	7	ACADM	3	3
RABGGTB	5876	broad.mit.edu	37	1	76254898	76254898	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:76254898G>A	uc001dgy.1	+	c.166G>A	c.(166-168)GTA>ATA	p.V56I	RABGGTB_uc009wbt.1_Non-coding_Transcript|RABGGTB_uc001dha.1_Missense_Mutation_p.V10I|SNORD45B_uc009wbv.1_5'Flank	NM_004582	NP_004573	P53611	PGTB2_HUMAN	RAB geranylgeranyltransferase, beta subunit	56	PFTB 1.				protein modification process|visual perception		metal ion binding|protein binding|Rab geranylgeranyltransferase activity			ovary(1)	1														0.228571	79.321542	88.786499	32	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76254898	76254898	13427	1	G	A	A	A	468	36	RABGGTB	2	2
LPHN2	23266	broad.mit.edu	37	1	82436173	82436173	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:82436173G>T	uc001dit.3	+	c.2858G>T	c.(2857-2859)GGA>GTA	p.G953V	LPHN2_uc001dis.2_Intron|LPHN2_uc001diu.2_Missense_Mutation_p.G953V|LPHN2_uc001div.2_Missense_Mutation_p.G953V|LPHN2_uc009wcd.2_Missense_Mutation_p.G953V|LPHN2_uc001diw.2_Missense_Mutation_p.G537V|LPHN2_uc009wce.1_Missense_Mutation_p.G39V	NM_012302	NP_036434	O95490	LPHN2_HUMAN	latrophilin 2 precursor	966	Helical; Name=4; (Potential).				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)										0.191781	26.60272	33.086589	14	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82436173	82436173	9289	1	G	T	T	T	533	41	LPHN2	2	2
RERE	473	broad.mit.edu	37	1	8425871	8425871	+	Splice_Site_SNP	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:8425871C>T	uc001ape.2	-	c.1447_splice	c.e14+1	p.L483_splice	RERE_uc001apf.2_Splice_Site_SNP_p.L483_splice|RERE_uc010nzx.1_Splice_Site_SNP_p.L215_splice|RERE_uc001apd.2_Splice_Site_SNP	NM_012102	NP_036234			atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus|regulation of transcription, DNA-dependent	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)										0.16	18.546024	26.8099	12	63	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	8425871	8425871	13700	1	C	T	T	T	221	17	RERE	5	2
SYDE2	84144	broad.mit.edu	37	1	85656358	85656358	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:85656358C>A	uc009wcm.2	-	c.823G>T	c.(823-825)GGT>TGT	p.G275C	SYDE2_uc001dku.3_Missense_Mutation_p.G275C	NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	275					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)										0.165899	66.458134	89.451657	36	181	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85656358	85656358	15957	1	C	A	A	A	312	24	SYDE2	2	2
GBP4	115361	broad.mit.edu	37	1	89654458	89654458	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:89654458T>G	uc001dnb.2	-	c.1217A>C	c.(1216-1218)AAG>ACG	p.K406T		NM_052941	NP_443173	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	406				IEKKKGDFV -> KKKKKKKKK (in Ref. 5; AAH17889).		cytoplasm	GTP binding|GTPase activity				0				all cancers(265;0.00723)|Epithelial(280;0.0291)										0.070111	-3.982336	47.691059	19	252	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89654458	89654458	6542	1	T	G	G	G	728	56	GBP4	4	4
GBP6	163351	broad.mit.edu	37	1	89849270	89849270	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:89849270G>C	uc001dnf.2	+	c.1425G>C	c.(1423-1425)TTG>TTC	p.L475F	GBP6_uc010ost.1_Missense_Mutation_p.L345F	NM_198460	NP_940862	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	475							GTP binding|GTPase activity			ovary(2)	2		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)										0.213592	66.091508	73.895759	22	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89849270	89849270	6544	1	G	C	C	C	594	46	GBP6	3	3
HFM1	164045	broad.mit.edu	37	1	91818090	91818090	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:91818090C>T	uc001doa.3	-	c.1950G>A	c.(1948-1950)CAG>CAA	p.Q650Q	HFM1_uc009wdb.2_Non-coding_Transcript|HFM1_uc010osu.1_Silent_p.Q329Q|HFM1_uc010osv.1_Silent_p.Q334Q	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein	650	Helicase C-terminal.						ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)										0.227273	38.989232	43.495334	15	51	KEEP	---	---	---	---	capture		Silent	SNP	91818090	91818090	7366	1	C	T	T	T	415	32	HFM1	2	2
FAM69A	388650	broad.mit.edu	37	1	93341943	93341943	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:93341943C>A	uc001dpg.2	-	c.99G>T	c.(97-99)TGG>TGT	p.W33C	FAM69A_uc001dpc.2_Missense_Mutation_p.W33C|FAM69A_uc010otg.1_Missense_Mutation_p.W26C	NM_001006605	NP_001006606	Q5T7M9	FA69A_HUMAN	family with sequence similarity 69, member A	33	Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane					0		all_lung(203;0.00265)|Lung NSC(277;0.00562)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000563)|all cancers(265;0.000751)|Epithelial(280;0.127)										0.148936	10.453639	16.097435	7	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93341943	93341943	5825	1	C	A	A	A	234	18	FAM69A	2	2
CCDC18	343099	broad.mit.edu	37	1	93691946	93691946	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:93691946G>C	uc001dpq.2	+	c.2586G>C	c.(2584-2586)TTG>TTC	p.L862F	CCDC18_uc009wdl.1_Missense_Mutation_p.L379F	NM_206886	NP_996769			sarcoma antigen NY-SAR-41											ovary(2)|breast(2)|pancreas(1)	5		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)										0.15873	24.507025	31.500207	10	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93691946	93691946	2916	1	G	C	C	C	581	45	CCDC18	3	3
ABCA4	24	broad.mit.edu	37	1	94574175	94574175	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:94574175G>T	uc001dqh.2	-	c.400C>A	c.(400-402)CAA>AAA	p.Q134K	ABCA4_uc010otn.1_Missense_Mutation_p.Q134K	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	134	Extracellular.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|central_nervous_system(2)|breast(1)	7		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)										0.075	-3.121121	19.120277	9	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94574175	94574175	35	1	G	T	T	T	611	47	ABCA4	2	2
LPPR4	9890	broad.mit.edu	37	1	99772270	99772270	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:99772270C>G	uc001dse.2	+	c.1996C>G	c.(1996-1998)CTC>GTC	p.L666V	LPPR4_uc010oue.1_Missense_Mutation_p.L608V	NM_014839	NP_055654	Q7Z2D5	LPPR4_HUMAN	plasticity related gene 1	666							phosphatidate phosphatase activity			ovary(3)	3		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)										0.14	13.68881	19.948047	7	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99772270	99772270	9300	1	C	G	G	G	416	32	LPPR4	3	3
ISM1	140862	broad.mit.edu	37	20	13260326	13260326	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:13260326G>A	uc010gce.1	+	c.424G>A	c.(424-426)GAT>AAT	p.D142N	TASP1_uc010zri.1_Intron	NM_080826	NP_543016	B1AKI9	ISM1_HUMAN	isthmin 1 homolog precursor	142						extracellular region					0														0.095238	4.200425	14.561051	6	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13260326	13260326	8164	20	G	A	A	A	429	33	ISM1	2	2
ISM1	140862	broad.mit.edu	37	20	13260371	13260371	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:13260371G>A	uc010gce.1	+	c.469G>A	c.(469-471)GAC>AAC	p.D157N	TASP1_uc010zri.1_Intron	NM_080826	NP_543016	B1AKI9	ISM1_HUMAN	isthmin 1 homolog precursor	157						extracellular region					0														0.163934	19.111411	25.654836	10	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13260371	13260371	8164	20	G	A	A	A	481	37	ISM1	1	1
CD93	22918	broad.mit.edu	37	20	23066263	23066263	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:23066263C>T	uc002wsv.2	-	c.567G>A	c.(565-567)CGG>CGA	p.R189R		NM_012072	NP_036204	Q9NPY3	C1QR1_HUMAN	CD93 antigen precursor	189	Extracellular (Potential).				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	integral to membrane|plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding			large_intestine(2)	2	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)													0.227273	78.138977	88.661048	35	119	KEEP	---	---	---	---	capture		Silent	SNP	23066263	23066263	3175	20	C	T	T	T	327	26	CD93	2	2
CD93	22918	broad.mit.edu	37	20	23066266	23066266	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:23066266G>T	uc002wsv.2	-	c.564C>A	c.(562-564)TGC>TGA	p.C188*		NM_012072	NP_036204	Q9NPY3	C1QR1_HUMAN	CD93 antigen precursor	188	Extracellular (Potential).				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	integral to membrane|plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding			large_intestine(2)	2	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)													0.233766	83.524889	93.513247	36	118	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	23066266	23066266	3175	20	G	T	T	T	542	42	CD93	5	2
DEFB115	245929	broad.mit.edu	37	20	29847348	29847348	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:29847348G>T	uc002wvp.1	+	c.180G>T	c.(178-180)GGG>GGT	p.G60G		NM_001037730	NP_001032819	Q30KQ5	DB115_HUMAN	beta-defensin 115 precursor	60					defense response to bacterium	extracellular region				ovary(1)	1			Colorectal(19;0.00445)|COAD - Colon adenocarcinoma(19;0.0347)											0.25641	48.461541	52.659733	20	58	KEEP	---	---	---	---	capture		Silent	SNP	29847348	29847348	4581	20	G	T	T	T	548	43	DEFB115	2	2
REM1	28954	broad.mit.edu	37	20	30065698	30065698	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:30065698G>T	uc002wwa.2	+	c.408G>T	c.(406-408)TGG>TGT	p.W136C		NM_014012	NP_054731	O75628	REM1_HUMAN	RAS-like GTP-binding protein REM	136					small GTPase mediated signal transduction	membrane	calmodulin binding|GTP binding|GTPase activity			pancreas(2)	2	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)							265				0.222222	16.577855	19.136466	8	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30065698	30065698	13691	20	G	T	T	T	559	43	REM1	2	2
REM1	28954	broad.mit.edu	37	20	30070104	30070104	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:30070104C>G	uc002wwa.2	+	c.438C>G	c.(436-438)AGC>AGG	p.S146R		NM_014012	NP_054731	O75628	REM1_HUMAN	RAS-like GTP-binding protein REM	146					small GTPase mediated signal transduction	membrane	calmodulin binding|GTP binding|GTPase activity			pancreas(2)	2	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)							265				0.07767	1.714428	20.50985	8	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30070104	30070104	13691	20	C	G	G	G	337	26	REM1	3	3
XKR7	343702	broad.mit.edu	37	20	30584558	30584558	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:30584558G>A	uc002wxe.2	+	c.1038G>A	c.(1036-1038)GGG>GGA	p.G346G		NM_001011718	NP_001011718	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related	346						integral to membrane				ovary(1)|breast(1)	2			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)											0.220779	39.234408	44.76187	17	60	KEEP	---	---	---	---	capture		Silent	SNP	30584558	30584558	18017	20	G	A	A	A	548	43	XKR7	2	2
HCK	3055	broad.mit.edu	37	20	30659585	30659585	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:30659585G>A	uc002wxh.2	+	c.183G>A	c.(181-183)CCG>CCA	p.P61P	HCK_uc010gdy.2_Silent_p.P40P|HCK_uc002wxi.2_Silent_p.P40P	NM_002110	NP_002101	P08631	HCK_HUMAN	hemopoietic cell kinase isoform p61HCK	61					interspecies interaction between organisms|mesoderm development|protein phosphorylation|regulation of defense response to virus by virus|viral reproduction	caveola|cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|ovary(2)|central_nervous_system(2)|pancreas(1)	9			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)							262				0.192982	25.295572	30.308294	11	46	KEEP	---	---	---	---	capture		Silent	SNP	30659585	30659585	7276	20	G	A	A	A	496	39	HCK	1	1
ASXL1	171023	broad.mit.edu	37	20	31021302	31021302	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:31021302G>T	uc002wxs.2	+	c.1301G>T	c.(1300-1302)GGG>GTG	p.G434V	ASXL1_uc010geb.2_Missense_Mutation_p.G325V	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1	434					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(131)|large_intestine(6)|central_nervous_system(2)|ovary(1)	140														0.197861	75.825897	91.681558	37	150	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31021302	31021302	1085	20	G	T	T	T	559	43	ASXL1	2	2
NCOA6	23054	broad.mit.edu	37	20	33337364	33337364	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:33337364C>A	uc002xav.2	-	c.2634G>T	c.(2632-2634)AAG>AAT	p.K878N	NCOA6_uc002xaw.2_Missense_Mutation_p.K878N	NM_014071	NP_054790	Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	878	TBP/GTF2A-binding region.|NCOA1-binding region.|NCOA6IP-binding region.|CREBBP-binding region.|Gln-rich.				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding|transcription activator activity			ovary(3)|breast(3)|central_nervous_system(1)	7														0.074074	-4.437304	25.75927	12	150	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33337364	33337364	10632	20	C	A	A	A	311	24	NCOA6	2	2
EIF6	3692	broad.mit.edu	37	20	33867799	33867799	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:33867799C>A	uc002xbv.1	-	c.492G>T	c.(490-492)AAG>AAT	p.K164N	EDEM2_uc010zuv.1_5'Flank|EIF6_uc002xbx.1_Missense_Mutation_p.K164N|EIF6_uc002xbz.1_Missense_Mutation_p.K145N|EIF6_uc002xby.1_Non-coding_Transcript	NM_181468	NP_852133	P56537	IF6_HUMAN	eukaryotic translation initiation factor 6	164					mature ribosome assembly	cytoplasm|nucleolus	protein binding|ribosome binding|translation initiation factor activity			pancreas(1)	1			BRCA - Breast invasive adenocarcinoma(18;0.00252)											0.214085	162.981952	189.80401	76	279	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33867799	33867799	5236	20	C	A	A	A	415	32	EIF6	2	2
CEP250	11190	broad.mit.edu	37	20	34092529	34092529	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:34092529T>A	uc002xcm.2	+	c.6332T>A	c.(6331-6333)CTG>CAG	p.L2111Q	CEP250_uc010zve.1_Missense_Mutation_p.L1479Q	NM_007186	NP_009117	Q9BV73	CP250_HUMAN	centrosomal protein 2	2111	Gln/Glu-rich.|Potential.				centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)											0.25	116.086545	126.314087	45	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34092529	34092529	3385	20	T	A	A	A	715	55	CEP250	3	3
VSTM2L	128434	broad.mit.edu	37	20	36560130	36560130	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:36560130A>G	uc002xhk.3	+	c.215A>G	c.(214-216)TAC>TGC	p.Y72C		NM_080607	NP_542174	Q96N03	VTM2L_HUMAN	V-set and transmembrane domain containing 2 like	72	Ig-like.									ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)												0.27933	151.598938	159.421851	50	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36560130	36560130	17799	20	A	G	G	G	182	14	VSTM2L	4	4
KIAA1755	85449	broad.mit.edu	37	20	36841717	36841717	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:36841717A>T	uc002xhy.1	-	c.3330T>A	c.(3328-3330)CCT>CCA	p.P1110P	KIAA1755_uc002xhv.1_Silent_p.P174P|KIAA1755_uc002xhw.1_Silent_p.P165P|KIAA1755_uc002xhx.1_Silent_p.P388P	NM_001029864	NP_001025035	Q5JYT7	K1755_HUMAN	hypothetical protein LOC85449	1110										ovary(4)|pancreas(1)	5		Myeloproliferative disorder(115;0.00874)												0.243902	24.329492	26.780277	10	31	KEEP	---	---	---	---	capture		Silent	SNP	36841717	36841717	8568	20	A	T	T	T	80	7	KIAA1755	3	3
PTPRT	11122	broad.mit.edu	37	20	40757458	40757458	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:40757458C>A	uc010ggj.2	-	c.2840G>T	c.(2839-2841)CGG>CTG	p.R947L	PTPRT_uc002xkg.2_Missense_Mutation_p.R928L|PTPRT_uc010ggi.2_Missense_Mutation_p.R131L	NM_133170	NP_573400	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	928	Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential).				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			ovary(7)|lung(5)|skin(2)	14		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)								646				0.204819	41.049037	47.742707	17	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40757458	40757458	13270	20	C	A	A	A	299	23	PTPRT	1	1
PTPRT	11122	broad.mit.edu	37	20	40790177	40790178	+	Missense_Mutation	DNP	CA	AT	AT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:40790177_40790178CA>AT	uc010ggj.2	-	c.2553_2554TG>AT	c.(2551-2556)GATGGC>GAATGC	p.851_852DG>EC	PTPRT_uc002xkg.2_Missense_Mutation_p.832_833DG>EC|PTPRT_uc010ggi.2_Missense_Mutation_p.35_36DG>EC	NM_133170	NP_573400	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	832_833	Cytoplasmic (Potential).				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			ovary(7)|lung(5)|skin(2)	14		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)								646				0.293233	96.962773	102.059159	39	94	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	40790177	40790178	13270	20	CA	AT	AT	AT	273	21	PTPRT	2	2
RIMS4	140730	broad.mit.edu	37	20	43386739	43386739	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:43386739C>A	uc010ggu.2	-	c.326G>T	c.(325-327)CGC>CTC	p.R109L	RIMS4_uc002xms.2_Missense_Mutation_p.R108L	NM_182970	NP_892015	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4	108					exocytosis|neurotransmitter transport	cell junction|synapse				ovary(4)|central_nervous_system(1)	5		Myeloproliferative disorder(115;0.0122)												0.092437	3.456064	23.350672	11	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43386739	43386739	13847	20	C	A	A	A	351	27	RIMS4	1	1
STK4	6789	broad.mit.edu	37	20	43629814	43629814	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:43629814G>A	uc002xnb.2	+	c.967G>A	c.(967-969)GAT>AAT	p.D323N	STK4_uc010ggx.2_Missense_Mutation_p.D323N|STK4_uc010ggy.2_Missense_Mutation_p.D268N	NM_006282	NP_006273	Q13043	STK4_HUMAN	serine/threonine kinase 4	323					apoptosis|cell morphogenesis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of apoptosis|protein autophosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein homodimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity|transcription factor binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				GBM(187;1039 2137 11798 21916 33213)				296				0.108108	4.071752	9.705921	4	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43629814	43629814	15826	20	G	A	A	A	533	41	STK4	2	2
RBPJL	11317	broad.mit.edu	37	20	43941003	43941003	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:43941003C>G	uc002xns.2	+	c.587C>G	c.(586-588)TCG>TGG	p.S196W	RBPJL_uc002xnt.2_Missense_Mutation_p.S196W	NM_014276	NP_055091	Q9UBG7	RBPJL_HUMAN	recombining binding protein L	196					regulation of transcription, DNA-dependent|signal transduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)												0.27451	40.662771	42.977157	14	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43941003	43941003	13631	20	C	G	G	G	403	31	RBPJL	3	3
ZNF335	63925	broad.mit.edu	37	20	44588902	44588902	+	Silent	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:44588902G>C	uc002xqw.2	-	c.1965C>G	c.(1963-1965)CCC>CCG	p.P655P	ZNF335_uc010zxk.1_Silent_p.P500P	NM_022095	NP_071378	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	655	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)												0.102041	8.269866	23.76555	10	88	KEEP	---	---	---	---	capture		Silent	SNP	44588902	44588902	18444	20	G	C	C	C	444	35	ZNF335	3	3
MMP9	4318	broad.mit.edu	37	20	44642321	44642321	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:44642321A>T	uc002xqz.2	+	c.1636A>T	c.(1636-1638)AGG>TGG	p.R546W		NM_004994	NP_004985	P14780	MMP9_HUMAN	matrix metalloproteinase 9 preproprotein	546	Hemopexin-like 1.				collagen catabolic process|macrophage differentiation|positive regulation of keratinocyte migration|proteolysis	extracellular space|proteinaceous extracellular matrix	collagen binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)			Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)|Simvastatin(DB00641)					462		OREG0025990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.179487	15.417974	19.17368	7	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44642321	44642321	10060	20	A	T	T	T	88	7	MMP9	3	3
PARD6B	84612	broad.mit.edu	37	20	49366767	49366767	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:49366767G>T	uc002xvo.2	+	c.861G>T	c.(859-861)GAG>GAT	p.E287D		NM_032521	NP_115910	Q9BYG5	PAR6B_HUMAN	PAR-6 beta	287					axonogenesis|cell cycle|cell division|establishment or maintenance of cell polarity|protein complex assembly|regulation of cell migration|tight junction assembly	cytosol|tight junction	protein binding			kidney(1)	1														0.081081	-4.056298	29.150383	15	170	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49366767	49366767	11863	20	G	T	T	T	451	35	PARD6B	2	2
TSHZ2	128553	broad.mit.edu	37	20	51870276	51870276	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:51870276G>T	uc002xwo.2	+	c.279G>T	c.(277-279)TCG>TCT	p.S93S		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	93					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(23;0.1)											0.259615	70.17755	75.619566	27	77	KEEP	---	---	---	---	capture		Silent	SNP	51870276	51870276	17175	20	G	T	T	T	496	39	TSHZ2	1	1
PROKR2	128674	broad.mit.edu	37	20	5294854	5294854	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:5294854G>A	uc010zqw.1	-	c.162C>T	c.(160-162)ATC>ATT	p.I54I	PROKR2_uc010zqx.1_Silent_p.I54I|PROKR2_uc010zqy.1_Silent_p.I54I	NM_144773	NP_658986	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	54	Extracellular (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5														0.109195	17.095383	43.419854	19	155	KEEP	---	---	---	---	capture		Silent	SNP	5294854	5294854	12996	20	G	A	A	A	473	37	PROKR2	1	1
MC3R	4159	broad.mit.edu	37	20	54823861	54823861	+	De_novo_Start_InFrame	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:54823861C>A	uc002xxb.2	+	c.-38C>A	c.(-40--36)CCCTG>CCATG			NM_019888	NP_063941			melanocortin 3 receptor						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|protein binding			ovary(2)	2			Colorectal(105;0.202)											0.199017	167.236876	201.563849	81	326	KEEP	---	---	---	---	capture		De_novo_Start_InFrame	SNP	54823861	54823861	9754	20	C	A	A	A	300	24	MC3R	5	2
C20orf106	200232	broad.mit.edu	37	20	55100027	55100027	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:55100027T>C	uc002xxx.2	+	c.163T>C	c.(163-165)TGG>CGG	p.W55R	GCNT7_uc010zzg.1_Intron|C20orf107_uc010zzh.1_Missense_Mutation_p.W55R	NM_001012971	NP_001012989	Q5JX71	CT106_HUMAN	hypothetical protein LOC200232 precursor	55	Helical; (Potential).					integral to membrane					0			Colorectal(105;0.202)											0.073034	0.54045	33.903871	13	165	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55100027	55100027	2152	20	T	C	C	C	715	55	C20orf106	4	4
GNAS	2778	broad.mit.edu	37	20	57430252	57430252	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:57430252G>A	uc002xzw.2	+	c.1932G>A	c.(1930-1932)AAG>AAA	p.K644K	GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_Non-coding_Transcript	NM_080425	NP_536350	P63092	GNAS2_HUMAN	GNAS complex locus XLas	Error:Variant_position_missing_in_P63092_after_alignment					activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|large_intestine(5)|parathyroid(5)|kidney(5)|lung(2)|testis(1)|autonomic_ganglia(1)	279	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			Colon(117;935 1597 6045 8307 46442)				461	TSP Lung(22;0.16)			0.304348	17.414425	18.201126	7	16	KEEP	---	---	---	---	capture		Silent	SNP	57430252	57430252	6779	20	G	A	A	A	442	34	GNAS	2	2
ZNF831	128611	broad.mit.edu	37	20	57769381	57769381	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:57769381C>T	uc002yan.2	+	c.3307C>T	c.(3307-3309)CTG>TTG	p.L1103L		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1103						intracellular	nucleic acid binding|zinc ion binding			ovary(1)|skin(1)	2	all_lung(29;0.0085)													0.219048	49.773096	57.407739	23	82	KEEP	---	---	---	---	capture		Silent	SNP	57769381	57769381	18784	20	C	T	T	T	363	28	ZNF831	2	2
LAMA5	3911	broad.mit.edu	37	20	60892796	60892796	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:60892796C>A	uc002ycq.2	-	c.7278G>T	c.(7276-7278)CTG>CTT	p.L2426L		NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor	2426	Domain II and I.|Potential.				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)									0.266667	18.167181	19.659326	8	22	KEEP	---	---	---	---	capture		Silent	SNP	60892796	60892796	8932	20	C	A	A	A	314	25	LAMA5	2	2
COL20A1	57642	broad.mit.edu	37	20	61951687	61951687	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:61951687C>A	uc011aau.1	+	c.3120C>A	c.(3118-3120)GCC>GCA	p.A1040A	COL20A1_uc011aav.1_Silent_p.A861A	NM_020882	NP_065933	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	1040					cell adhesion	collagen|extracellular space	structural molecule activity				0	all_cancers(38;1.39e-10)													0.178218	36.665594	46.452092	18	83	KEEP	---	---	---	---	capture		Silent	SNP	61951687	61951687	3817	20	C	A	A	A	288	23	COL20A1	1	1
ZNF512B	57473	broad.mit.edu	37	20	62596021	62596021	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62596021C>A	uc002yhl.1	-	c.1083G>T	c.(1081-1083)AGG>AGT	p.R361S		NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B	361					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)													0.240964	45.114361	50.159787	20	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62596021	62596021	18551	20	C	A	A	A	337	26	ZNF512B	2	2
USP25	29761	broad.mit.edu	37	21	17197314	17197314	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:17197314G>A	uc011aby.1	+	c.1238G>A	c.(1237-1239)AGA>AAA	p.R413K	USP25_uc002yjy.1_Missense_Mutation_p.R413K|USP25_uc002yjz.1_Missense_Mutation_p.R413K|USP25_uc010gla.1_Intron	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	413					protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)										0.277778	41.500302	43.900506	15	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17197314	17197314	17619	21	G	A	A	A	429	33	USP25	2	2
NCAM2	4685	broad.mit.edu	37	21	22370902	22370902	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:22370902C>T	uc002yld.1	+	c.21C>T	c.(19-21)TTC>TTT	p.F7F	NCAM2_uc011acb.1_Silent_p.F7F	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor	7					neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)										0.116883	11.915078	23.036011	9	68	KEEP	---	---	---	---	capture		Silent	SNP	22370902	22370902	10602	21	C	T	T	T	415	32	NCAM2	2	2
ADAMTS1	9510	broad.mit.edu	37	21	28216549	28216549	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:28216549G>T	uc002ymf.2	-	c.725C>A	c.(724-726)CCC>CAC	p.P242H		NM_006988	NP_008919	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1	242					integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)		Lung(58;0.215)								OREG0026151	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.121212	4.575962	9.217376	4	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28216549	28216549	256	21	G	T	T	T	559	43	ADAMTS1	2	2
RNF160	26046	broad.mit.edu	37	21	30303583	30303583	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:30303583C>A	uc002ymr.2	-	c.5270G>T	c.(5269-5271)GGT>GTT	p.G1757V		NM_015565	NP_056380	O94822	LTN1_HUMAN	zinc finger protein 294	1711							ligase activity|zinc ion binding				0														0.138889	13.208987	22.280536	10	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30303583	30303583	13932	21	C	A	A	A	234	18	RNF160	2	2
CLDN17	26285	broad.mit.edu	37	21	31538373	31538373	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:31538373C>A	uc011acv.1	-	c.563G>T	c.(562-564)TGC>TTC	p.C188F		NM_012131	NP_036263	P56750	CLD17_HUMAN	claudin 17	188	Cytoplasmic (Potential).				calcium-independent cell-cell adhesion|tight junction assembly	Golgi apparatus|integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(2)	2														0.12	10.918658	21.546388	9	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31538373	31538373	3614	21	C	A	A	A	325	25	CLDN17	2	2
KRTAP6-2	337967	broad.mit.edu	37	21	31971073	31971073	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:31971073C>A	uc011adc.1	-	c.121G>T	c.(121-123)GGT>TGT	p.G41C	KRTAP22-1_uc011add.1_5'Flank	NM_181604	NP_853635	Q3LI66	KRA62_HUMAN	keratin associated protein 6-2	41						intermediate filament					0														0.146341	9.120909	14.052285	6	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31971073	31971073	8892	21	C	A	A	A	273	21	KRTAP6-2	2	2
KRTAP20-1	337975	broad.mit.edu	37	21	31988931	31988931	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:31988931A>T	uc011ade.1	+	c.158A>T	c.(157-159)TAT>TTT	p.Y53F	KRTAP6-1_uc002yop.2_5'Flank	NM_181615	NP_853646	Q3LI63	KR201_HUMAN	keratin associated protein 20-1	53						intermediate filament				breast(1)	1														0.080357	3.025112	23.099129	9	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31988931	31988931	8854	21	A	T	T	T	208	16	KRTAP20-1	3	3
TIAM1	7074	broad.mit.edu	37	21	32589888	32589888	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:32589888C>A	uc002yow.1	-	c.2123G>T	c.(2122-2124)GGA>GTA	p.G708V	TIAM1_uc011adk.1_Missense_Mutation_p.G708V|TIAM1_uc011adl.1_Missense_Mutation_p.G708V|TIAM1_uc002yox.1_Missense_Mutation_p.G316V	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	708					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|lung(1)	5										780				0.121212	24.043438	56.546584	28	203	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32589888	32589888	16418	21	C	A	A	A	390	30	TIAM1	2	2
SON	6651	broad.mit.edu	37	21	34922655	34922655	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:34922655A>G	uc002yse.1	+	c.1118A>G	c.(1117-1119)CAG>CGG	p.Q373R	SON_uc002ysb.1_Missense_Mutation_p.Q373R|SON_uc002ysc.2_Missense_Mutation_p.Q373R|SON_uc002ysd.2_5'UTR|SON_uc002ysf.1_Intron|SON_uc002ysg.2_5'Flank	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F	373					anti-apoptosis	nuclear speck	DNA binding|double-stranded RNA binding			ovary(3)	3														0.088	7.931151	29.381325	11	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34922655	34922655	15426	21	A	G	G	G	91	7	SON	4	4
ITSN1	6453	broad.mit.edu	37	21	35183306	35183306	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:35183306G>T	uc002yta.1	+	c.2347G>T	c.(2347-2349)GGC>TGC	p.G783C	DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_Non-coding_Transcript|ITSN1_uc002ysz.2_Missense_Mutation_p.G778C|ITSN1_uc010gmg.2_Missense_Mutation_p.G741C|ITSN1_uc010gmh.2_Non-coding_Transcript|ITSN1_uc002ysw.2_Missense_Mutation_p.G783C|ITSN1_uc010gmi.2_Missense_Mutation_p.G746C|ITSN1_uc010gmj.2_Missense_Mutation_p.G662C|ITSN1_uc002ysy.2_Missense_Mutation_p.G778C|ITSN1_uc002ysx.2_Missense_Mutation_p.G741C|ITSN1_uc002ytb.1_Missense_Mutation_p.G778C|ITSN1_uc002ytc.1_Missense_Mutation_p.G778C|ITSN1_uc002ytd.2_Non-coding_Transcript|ITSN1_uc010gmk.2_Missense_Mutation_p.G746C|ITSN1_uc010gml.2_Non-coding_Transcript|ITSN1_uc002ytj.2_Missense_Mutation_p.G778C|ITSN1_uc010gmm.1_Non-coding_Transcript|ITSN1_uc002yte.2_Missense_Mutation_p.G717C|ITSN1_uc002ytf.1_Non-coding_Transcript	NM_003024	NP_003015	Q15811	ITSN1_HUMAN	intersectin 1 isoform ITSN-l	783	SH3 1.				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 vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)	3														0.106719	26.077104	64.886289	27	226	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35183306	35183306	8230	21	G	T	T	T	507	39	ITSN1	1	1
AGPAT3	56894	broad.mit.edu	37	21	45402211	45402211	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:45402211G>T	uc002zdx.2	+	c.1330G>T	c.(1330-1332)GGA>TGA	p.G444*	AGPAT3_uc002zdv.2_Nonsense_Mutation_p.G357*|AGPAT3_uc002zdw.2_Nonsense_Mutation_p.G357*|AGPAT3_uc002zdy.2_Nonsense_Mutation_p.G295*	NM_020132	NP_064517	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3	357	Cytoplasmic (Potential).				phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		Pancreas(60;623 1650 5574 52796)								0.142857	76.844901	119.007204	49	294	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	45402211	45402211	391	21	G	T	T	T	455	35	AGPAT3	5	2
PFKL	5211	broad.mit.edu	37	21	45745937	45745937	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:45745937C>T	uc002zel.2	+	c.2083C>T	c.(2083-2085)CGC>TGC	p.R695C	PFKL_uc002zek.2_Missense_Mutation_p.R742C|PFKL_uc002zem.2_Missense_Mutation_p.R282C|PFKL_uc002zen.2_Missense_Mutation_p.R282C	NM_002626	NP_002617	P17858	K6PL_HUMAN	liver phosphofructokinase	695					fructose 6-phosphate metabolic process|glycolysis|protein oligomerization	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|fructose-6-phosphate binding|identical protein binding|kinase binding|metal ion binding				0				Colorectal(79;0.0811)										0.170213	15.972325	20.806815	8	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45745937	45745937	12186	21	C	T	T	T	299	23	PFKL	1	1
KRTAP10-10	353333	broad.mit.edu	37	21	46057504	46057504	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:46057504G>T	uc002zfq.2	+	c.170G>T	c.(169-171)TGT>TTT	p.C57F	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_181688	NP_859016	P60014	KR10A_HUMAN	keratin associated protein 10-10	57	15 X 5 AA repeats of C-C-X(3).					keratin filament					0														0.090909	0.388138	17.123446	9	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46057504	46057504	8821	21	G	T	T	T	624	48	KRTAP10-10	2	2
KRTAP12-4	386684	broad.mit.edu	37	21	46074485	46074485	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:46074485C>A	uc002zfs.1	-	c.47G>T	c.(46-48)GGC>GTC	p.G16V	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198698	NP_941971	P60329	KR124_HUMAN	keratin associated protein 12-4	16	15 X 5 AA approximate repeats.					keratin filament				ovary(1)	1														0.238095	8.860779	10.289099	5	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46074485	46074485	8836	21	C	A	A	A	338	26	KRTAP12-4	2	2
COL18A1	80781	broad.mit.edu	37	21	46888412	46888412	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:46888412G>T	uc011afs.1	+	c.1608G>T	c.(1606-1608)CTG>CTT	p.L536L	COL18A1_uc002zhg.2_Silent_p.L121L|COL18A1_uc002zhi.2_Silent_p.L301L	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	536	TSP N-terminal.				cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)						1836				0.09816	7.31541	33.642733	16	147	KEEP	---	---	---	---	capture		Silent	SNP	46888412	46888412	3813	21	G	T	T	T	600	47	COL18A1	2	2
PCNT	5116	broad.mit.edu	37	21	47754562	47754562	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:47754562A>T	uc002zji.3	+	c.519A>T	c.(517-519)ACA>ACT	p.T173T	PCNT_uc002zjj.2_Silent_p.T55T|PCNT_uc010gqk.1_Non-coding_Transcript	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	173					cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)													0.131579	28.199585	48.24899	20	132	KEEP	---	---	---	---	capture		Silent	SNP	47754562	47754562	12010	21	A	T	T	T	54	5	PCNT	3	3
PCNT	5116	broad.mit.edu	37	21	47851463	47851463	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:47851463G>A	uc002zji.3	+	c.8085G>A	c.(8083-8085)GAG>GAA	p.E2695E	PCNT_uc002zjj.2_Silent_p.E2577E	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	2695	Potential.				cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)													0.092593	6.362632	24.406183	10	98	KEEP	---	---	---	---	capture		Silent	SNP	47851463	47851463	12010	21	G	A	A	A	425	33	PCNT	2	2
DIP2A	23181	broad.mit.edu	37	21	47987386	47987386	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:47987386G>T	uc002zjo.2	+	c.4567G>T	c.(4567-4569)GAG>TAG	p.E1523*	DIP2A_uc011afz.1_Nonsense_Mutation_p.E1519*|DIP2A_uc002zjs.2_Nonsense_Mutation_p.E203*|DIP2A_uc002zjt.2_Non-coding_Transcript	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a	1523					multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)										0.163934	15.608261	22.157243	10	51	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	47987386	47987386	4706	21	G	T	T	T	533	41	DIP2A	5	2
TRMT2A	27037	broad.mit.edu	37	22	20100126	20100126	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:20100126T>C	uc002zrn.1	-	c.1892A>G	c.(1891-1893)GAT>GGT	p.D631G	TRMT2A_uc002zrk.1_Missense_Mutation_p.D613G|TRMT2A_uc002zrl.1_Missense_Mutation_p.D613G|TRMT2A_uc002zrm.1_Missense_Mutation_p.D435G	NM_182984	NP_892029	Q8IZ69	TRM2A_HUMAN	HpaII tiny fragments locus 9C	613					RNA processing		nucleotide binding|RNA binding|RNA methyltransferase activity			breast(1)	1														0.204819	44.250351	50.942646	17	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20100126	20100126	17115	22	T	C	C	C	650	50	TRMT2A	4	4
PI4KA	5297	broad.mit.edu	37	22	21157610	21157610	+	Splice_Site_SNP	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:21157610T>A	uc002zsz.3	-	c.1288_splice	c.e13-1	p.G430_splice	PI4KA_uc010gsq.1_Splice_Site_SNP_p.G488_splice	NM_058004	NP_477352			phosphatidylinositol 4-kinase type 3 alpha						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|salivary_gland(1)	3	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			GBM(136;1332 1831 3115 23601 50806)				873				0.094891	7.573173	30.146653	13	124	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	21157610	21157610	12297	22	T	A	A	A	715	55	PI4KA	5	3
PRAME	23532	broad.mit.edu	37	22	22890546	22890546	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:22890546C>A	uc002zwf.2	-	c.1473G>T	c.(1471-1473)GGG>GGT	p.G491G	LOC96610_uc011aim.1_Intron|PRAME_uc011air.1_Silent_p.G475G|PRAME_uc010gtr.2_Silent_p.G491G|PRAME_uc002zwg.2_Silent_p.G491G|PRAME_uc002zwh.2_Silent_p.G491G|PRAME_uc002zwi.2_Silent_p.G491G|PRAME_uc002zwj.2_Silent_p.G491G|PRAME_uc002zwk.2_Silent_p.G491G	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	491	Mediates interaction with RARA.				apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|positive regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding|transcription repressor activity			central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		Melanoma(73;1707 1838 15168 27201)				1184				0.108434	23.804747	74.199671	36	296	KEEP	---	---	---	---	capture		Silent	SNP	22890546	22890546	12860	22	C	A	A	A	275	22	PRAME	2	2
PRAME	23532	broad.mit.edu	37	22	22892504	22892504	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:22892504C>T	uc002zwf.2	-	c.597G>A	c.(595-597)GTG>GTA	p.V199V	LOC96610_uc011aim.1_Intron|PRAME_uc011air.1_Silent_p.V183V|PRAME_uc010gtr.2_Silent_p.V199V|PRAME_uc002zwg.2_Silent_p.V199V|PRAME_uc002zwh.2_Silent_p.V199V|PRAME_uc002zwi.2_Silent_p.V199V|PRAME_uc002zwj.2_Silent_p.V199V|PRAME_uc002zwk.2_Silent_p.V199V	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	199					apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|positive regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding|transcription repressor activity			central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		Melanoma(73;1707 1838 15168 27201)				1184				0.158371	59.673654	84.27272	35	186	KEEP	---	---	---	---	capture		Silent	SNP	22892504	22892504	12860	22	C	T	T	T	366	29	PRAME	2	2
PRAME	23532	broad.mit.edu	37	22	22899246	22899246	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:22899246G>A	uc002zwf.2	-	c.7C>T	c.(7-9)CGA>TGA	p.R3*	LOC96610_uc011aim.1_Intron|PRAME_uc011air.1_5'Flank|PRAME_uc010gtr.2_Nonsense_Mutation_p.R3*|PRAME_uc002zwg.2_Nonsense_Mutation_p.R3*|PRAME_uc002zwh.2_Nonsense_Mutation_p.R3*|PRAME_uc002zwi.2_Nonsense_Mutation_p.R3*|PRAME_uc002zwj.2_Nonsense_Mutation_p.R3*|PRAME_uc002zwk.2_Nonsense_Mutation_p.R3*|LOC648691_uc011ais.1_5'Flank	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	3					apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|positive regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding|transcription repressor activity			central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		Melanoma(73;1707 1838 15168 27201)				1184				0.1875	82.309792	102.803727	42	182	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	22899246	22899246	12860	22	G	A	A	A	519	40	PRAME	5	1
SEZ6L	23544	broad.mit.edu	37	22	26688679	26688679	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26688679C>G	uc003acb.2	+	c.402C>G	c.(400-402)CCC>CCG	p.P134P	SEZ6L_uc003acc.2_Silent_p.P134P|SEZ6L_uc011akc.1_Silent_p.P134P|SEZ6L_uc003acd.2_Silent_p.P134P|SEZ6L_uc011akd.1_Silent_p.P134P|SEZ6L_uc003ace.2_Silent_p.P134P|SEZ6L_uc003acf.1_5'UTR|SEZ6L_uc010gvc.1_5'UTR	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	134	Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6														0.183673	18.29516	22.858821	9	40	KEEP	---	---	---	---	capture		Silent	SNP	26688679	26688679	14632	22	C	G	G	G	262	21	SEZ6L	3	3
CRYBB1	1414	broad.mit.edu	37	22	26995455	26995455	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26995455C>T	uc003acy.1	-	c.758G>A	c.(757-759)TGA>TAA	p.*253*		NM_001887	NP_001878	P53674	CRBB1_HUMAN	crystallin, beta B1	253					visual perception		structural constituent of eye lens			ovary(1)	1														0.069182	-10.20435	20.305584	11	148	KEEP	---	---	---	---	capture		Silent	SNP	26995455	26995455	4049	22	C	T	T	T	376	29	CRYBB1	2	2
CRYBB1	1414	broad.mit.edu	37	22	27008146	27008146	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:27008146G>A	uc003acy.1	-	c.189C>T	c.(187-189)GTC>GTT	p.V63V		NM_001887	NP_001878	P53674	CRBB1_HUMAN	crystallin, beta B1	63	Beta/gamma crystallin 'Greek key' 1.				visual perception		structural constituent of eye lens			ovary(1)	1														0.079545	-1.948097	13.937558	7	81	KEEP	---	---	---	---	capture		Silent	SNP	27008146	27008146	4049	22	G	A	A	A	418	33	CRYBB1	2	2
SEC14L3	266629	broad.mit.edu	37	22	30857304	30857304	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:30857304G>A	uc003ahy.2	-	c.1074C>T	c.(1072-1074)GCC>GCT	p.A358A	SEC14L3_uc003ahz.2_Silent_p.A281A|SEC14L3_uc003aia.2_Silent_p.A299A|SEC14L3_uc003aib.2_Silent_p.A299A	NM_174975	NP_777635	Q9UDX4	S14L3_HUMAN	SEC14-like 3	358	GOLD.					integral to membrane|intracellular	lipid binding|transporter activity			ovary(3)|pancreas(1)	4					Vitamin E(DB00163)	Esophageal Squamous(108;290 1516 3584 23771 37333)								0.091837	6.132015	38.99796	18	178	KEEP	---	---	---	---	capture		Silent	SNP	30857304	30857304	14469	22	G	A	A	A	496	39	SEC14L3	1	1
PLA2G3	50487	broad.mit.edu	37	22	31533822	31533822	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:31533822G>C	uc003aka.2	-	c.940C>G	c.(940-942)CAT>GAT	p.H314D		NM_015715	NP_056530	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III precursor	314					cilium morphogenesis|lipid catabolic process|phospholipid metabolic process	centriole|extracellular space|plasma membrane	calcium ion binding|calcium-dependent phospholipase A2 activity				0														0.111888	51.050628	93.555552	32	254	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31533822	31533822	12426	22	G	C	C	C	624	48	PLA2G3	3	3
C22orf42	150297	broad.mit.edu	37	22	32546305	32546305	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:32546305C>A	uc003amd.2	-	c.654_splice	c.e7+1	p.M218_splice		NM_001010859	NP_001010859			chromosome 22 open reading frame 42											ovary(1)	1														0.152632	53.94156	75.888723	29	161	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	32546305	32546305	2231	22	C	A	A	A	234	18	C22orf42	5	2
ISX	91464	broad.mit.edu	37	22	35481642	35481642	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:35481642C>T	uc003anj.2	+	c.694C>T	c.(694-696)CCT>TCT	p.P232S	ISX_uc011amg.1_Missense_Mutation_p.P220S	NM_001008494	NP_001008494	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	232					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(3)	3														0.147239	35.197391	54.684645	24	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35481642	35481642	8169	22	C	T	T	T	234	18	ISX	2	2
HMGXB4	10042	broad.mit.edu	37	22	35679974	35679974	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:35679974C>T	uc003anl.2	+	c.1235C>T	c.(1234-1236)TCG>TTG	p.S412L	HMGXB4_uc003ank.2_Missense_Mutation_p.S303L	NM_001003681	NP_001003681	Q9UGU5	HMGX4_HUMAN	high-mobility group protein 2-like 1	412	HMG box.				endosome to lysosome transport|negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	NURF complex	DNA binding			breast(1)	1														0.216867	41.703209	47.840975	18	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35679974	35679974	7531	22	C	T	T	T	403	31	HMGXB4	1	1
C1QTNF6	114904	broad.mit.edu	37	22	37578327	37578327	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:37578327C>A	uc003aqx.1	-	c.738G>T	c.(736-738)GTG>GTT	p.V246V	C1QTNF6_uc003aqw.1_Silent_p.V227V|C1QTNF6_uc003aqy.1_Silent_p.V246V|C1QTNF6_uc003aqz.1_Non-coding_Transcript	NM_182486	NP_872292	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	227	C1q.					collagen					0														0.236111	39.735929	44.322035	17	55	KEEP	---	---	---	---	capture		Silent	SNP	37578327	37578327	2034	22	C	A	A	A	314	25	C1QTNF6	2	2
GTPBP1	9567	broad.mit.edu	37	22	39112749	39112749	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:39112749G>A	uc003awg.2	+	c.578G>A	c.(577-579)CGC>CAC	p.R193H		NM_004286	NP_004277	O00178	GTPB1_HUMAN	GTP binding protein 1	193					immune response|signal transduction		GTP binding|GTPase activity			ovary(1)	1	Melanoma(58;0.04)													0.222222	50.008414	57.028531	22	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39112749	39112749	7158	22	G	A	A	A	494	38	GTPBP1	1	1
TAB1	10454	broad.mit.edu	37	22	39813767	39813767	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:39813767C>A	uc003axr.2	+	c.691C>A	c.(691-693)CTC>ATC	p.L231I	TAB1_uc003axt.2_Missense_Mutation_p.L155I|TAB1_uc011aok.1_5'UTR|TAB1_uc003axu.1_Missense_Mutation_p.L155I	NM_006116	NP_006107	Q15750	TAB1_HUMAN	mitogen-activated protein kinase kinase kinase 7	155	PP2C-like.				activation of MAPK activity|activation of MAPKKK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane	catalytic activity|protein binding				0										336				0.130435	19.438422	34.725498	15	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39813767	39813767	16016	22	C	A	A	A	260	20	TAB1	2	2
CACNA1I	8911	broad.mit.edu	37	22	40037036	40037036	+	Missense_Mutation	SNP	A	T	T	rs59635914		TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:40037036A>T	uc003ayc.2	+	c.905A>T	c.(904-906)GAC>GTC	p.D302V	CACNA1I_uc003ayd.2_Missense_Mutation_p.D302V|CACNA1I_uc003aye.2_Missense_Mutation_p.D217V|CACNA1I_uc003ayf.2_Missense_Mutation_p.D217V	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,	302	I.|Extracellular (Potential).				axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)									0.086022	-1.059573	15.093149	8	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40037036	40037036	2662	22	A	T	T	T	130	10	CACNA1I	3	3
PMM1	5372	broad.mit.edu	37	22	41982110	41982110	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:41982110T>A	uc003bal.2	-	c.175A>T	c.(175-177)ATC>TTC	p.I59F		NM_002676	NP_002667	Q92871	PMM1_HUMAN	phosphomannomutase 1	59					dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	cytosol	metal ion binding|phosphomannomutase activity				0														0.102128	14.628516	51.762864	24	211	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41982110	41982110	12562	22	T	A	A	A	650	50	PMM1	3	3
SEPT3	55964	broad.mit.edu	37	22	42383628	42383628	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:42383628G>T	uc003bbr.3	+	c.416G>T	c.(415-417)TGG>TTG	p.W139L	WBP2NL_uc011ape.1_Intron|SEPT3_uc003bbs.3_Missense_Mutation_p.W139L|SEPT3_uc010gyr.2_Missense_Mutation_p.W75L|SEPT3_uc011apj.1_Missense_Mutation_p.W75L|SEPT3_uc010gys.2_5'UTR	NM_145733	NP_663786	Q9UH03	SEPT3_HUMAN	septin 3 isoform A	139					cell cycle|cytokinesis	cell junction|septin complex	GTP binding				0										112				0.070175	-5.02747	16.654207	8	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42383628	42383628	14551	22	G	T	T	T	611	47	SEPT3	2	2
TCF20	6942	broad.mit.edu	37	22	42609766	42609766	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:42609766C>G	uc003bcj.1	-	c.1546G>C	c.(1546-1548)GCA>CCA	p.A516P	TCF20_uc003bck.1_Missense_Mutation_p.A516P|TCF20_uc003bnt.2_Missense_Mutation_p.A516P	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1	516					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)	4														0.120087	94.695858	159.539672	55	403	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42609766	42609766	16216	22	C	G	G	G	338	26	TCF20	3	3
PNPLA5	150379	broad.mit.edu	37	22	44285403	44285403	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:44285403C>A	uc003beg.2	-	c.508G>T	c.(508-510)GCT>TCT	p.A170S	PNPLA5_uc011aqc.1_Intron|PNPLA5_uc003beh.2_Intron	NM_138814	NP_620169	Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	170	Patatin.				lipid catabolic process		hydrolase activity				0		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)												0.188	85.610871	108.377436	47	203	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44285403	44285403	12595	22	C	A	A	A	338	26	PNPLA5	2	2
FBLN1	2192	broad.mit.edu	37	22	45943050	45943050	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:45943050C>A	uc010gzz.2	+	c.1521C>A	c.(1519-1521)TAC>TAA	p.Y507*	FBLN1_uc003bgg.1_Nonsense_Mutation_p.Y469*|FBLN1_uc003bgh.2_Nonsense_Mutation_p.Y469*|FBLN1_uc003bgi.1_Nonsense_Mutation_p.Y469*|FBLN1_uc003bgj.1_Nonsense_Mutation_p.Y469*	NM_001996	NP_001987	P23142	FBLN1_HUMAN	fibulin 1 isoform C precursor	469	EGF-like 7; calcium-binding.				interspecies interaction between organisms	extracellular space|soluble fraction	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)										0.112903	5.381728	14.55413	7	55	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	45943050	45943050	5934	22	C	A	A	A	233	18	FBLN1	5	2
ZBED4	9889	broad.mit.edu	37	22	50278436	50278436	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:50278436C>T	uc003bix.2	+	c.1126C>T	c.(1126-1128)CCA>TCA	p.P376S		NM_014838	NP_055653	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	376						cytoplasm|nucleus	DNA binding|metal ion binding|protein dimerization activity			ovary(2)	2		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)										0.119658	15.271309	31.879675	14	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50278436	50278436	18104	22	C	T	T	T	390	30	ZBED4	2	2
TBC1D8	11138	broad.mit.edu	37	2	101655070	101655070	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:101655070G>T	uc010fiv.2	-	c.1083C>A	c.(1081-1083)CCC>CCA	p.P361P	TBC1D8_uc010yvw.1_Silent_p.P376P|TBC1D8_uc002tau.3_Silent_p.P118P	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8	361					blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3														0.152284	50.274601	73.033408	30	167	KEEP	---	---	---	---	capture		Silent	SNP	101655070	101655070	16151	2	G	T	T	T	600	47	TBC1D8	2	2
IL18R1	8809	broad.mit.edu	37	2	103013214	103013214	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:103013214G>A	uc002tbw.3	+	c.1494G>A	c.(1492-1494)CTG>CTA	p.L498L	IL18R1_uc010ywc.1_Silent_p.L497L|IL18R1_uc010ywd.1_Silent_p.L342L|IL18R1_uc010fiy.2_Silent_p.L498L	NM_003855	NP_003846	Q13478	IL18R_HUMAN	interleukin 18 receptor 1 precursor	498	TIR.|Cytoplasmic (Potential).				innate immune response	integral to membrane|plasma membrane	interleukin-1 receptor activity			ovary(2)|pancreas(1)	3														0.128205	23.179352	44.210419	20	136	KEEP	---	---	---	---	capture		Silent	SNP	103013214	103013214	7948	2	G	A	A	A	574	45	IL18R1	2	2
SLC5A7	60482	broad.mit.edu	37	2	108608567	108608567	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:108608567T>A	uc002tdv.2	+	c.184T>A	c.(184-186)TGG>AGG	p.W62R	SLC5A7_uc010ywm.1_5'UTR|SLC5A7_uc010fjj.2_Missense_Mutation_p.W62R|SLC5A7_uc010ywn.1_5'UTR	NM_021815	NP_068587	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (choline transporter),	62	Helical; (Potential).				acetylcholine biosynthetic process|neurotransmitter secretion	integral to membrane|plasma membrane	choline:sodium symporter activity			ovary(2)|central_nervous_system(1)	3					Choline(DB00122)									0.121622	10.320221	20.705218	9	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108608567	108608567	15167	2	T	A	A	A	715	55	SLC5A7	3	3
SLC5A7	60482	broad.mit.edu	37	2	108618378	108618378	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:108618378C>A	uc002tdv.2	+	c.623C>A	c.(622-624)TCA>TAA	p.S208*	SLC5A7_uc010ywm.1_Intron|SLC5A7_uc010fjj.2_Nonsense_Mutation_p.S208*|SLC5A7_uc010ywn.1_Nonsense_Mutation_p.S95*	NM_021815	NP_068587	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (choline transporter),	208	Helical; (Potential).				acetylcholine biosynthetic process|neurotransmitter secretion	integral to membrane|plasma membrane	choline:sodium symporter activity			ovary(2)|central_nervous_system(1)	3					Choline(DB00122)									0.156566	49.789791	72.091806	31	167	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	108618378	108618378	15167	2	C	A	A	A	377	29	SLC5A7	5	2
ATP6V1C2	245973	broad.mit.edu	37	2	10912016	10912016	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:10912016C>A	uc002ras.2	+	c.522C>A	c.(520-522)TTC>TTA	p.F174L	ATP6V1C2_uc002rat.2_Missense_Mutation_p.F174L	NM_001039362	NP_001034451	Q8NEY4	VATC2_HUMAN	vacuolar H+ ATPase C2 isoform a	174					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting V-type ATPase, V1 domain				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		NSCLC(188;1042 2136 10807 16813 47705)								0.09396	15.375036	64.751391	28	270	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10912016	10912016	1200	2	C	A	A	A	402	31	ATP6V1C2	1	1
PDIA6	10130	broad.mit.edu	37	2	10929942	10929942	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:10929942C>T	uc002rav.2	-	c.929G>A	c.(928-930)AGA>AAA	p.R310K	PDIA6_uc002rau.2_Missense_Mutation_p.R258K|PDIA6_uc010yjg.1_Missense_Mutation_p.R255K|PDIA6_uc010yjh.1_Missense_Mutation_p.R263K|PDIA6_uc002raw.2_Missense_Mutation_p.R306K	NM_005742	NP_005733	Q15084	PDIA6_HUMAN	protein disulfide isomerase A6 precursor	258	Thioredoxin 2.				cell redox homeostasis|glycerol ether metabolic process|protein folding	endoplasmic reticulum lumen|ER-Golgi intermediate compartment|melanosome|plasma membrane	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		GBM(73;509 1219 34219 41343 41551)								0.116071	14.131128	30.353829	13	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10929942	10929942	12093	2	C	T	T	T	416	32	PDIA6	2	2
RANBP2	5903	broad.mit.edu	37	2	109352661	109352661	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:109352661G>T	uc002tem.3	+	c.738G>T	c.(736-738)ACG>ACT	p.T246T		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	246					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														0.152709	51.919583	75.49912	31	172	KEEP	---	---	---	---	capture		Silent	SNP	109352661	109352661	13488	2	G	T	T	T	483	38	RANBP2	1	1
SH3RF3	344558	broad.mit.edu	37	2	109964320	109964320	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:109964320C>G	uc010ywt.1	+	c.764C>G	c.(763-765)CCA>CGA	p.P255R		NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	255							zinc ion binding			ovary(1)	1														0.162162	9.521608	13.545624	6	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109964320	109964320	14752	2	C	G	G	G	273	21	SH3RF3	3	3
ANKRD57	65124	broad.mit.edu	37	2	110373544	110373544	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:110373544A>T	uc002tfb.2	+	c.1478A>T	c.(1477-1479)CAG>CTG	p.Q493L	SEPT10_uc010ywu.1_5'Flank|SEPT10_uc002tew.2_5'Flank|SEPT10_uc002tex.2_5'Flank|SEPT10_uc002tey.2_5'Flank|SEPT10_uc010ywv.1_5'Flank	NM_023016	NP_075392	Q53LP3	ANR57_HUMAN	ankyrin repeat domain 57	493											0														0.2	21.023378	25.207858	10	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110373544	110373544	691	2	A	T	T	T	91	7	ANKRD57	3	3
KCNF1	3754	broad.mit.edu	37	2	11053201	11053201	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:11053201G>T	uc002rax.2	+	c.649G>T	c.(649-651)GTG>TTG	p.V217L		NM_002236	NP_002227	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F,	217						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)										0.112676	9.270765	19.767228	8	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11053201	11053201	8331	2	G	T	T	T	520	40	KCNF1	1	1
NPHP1	4867	broad.mit.edu	37	2	110881445	110881445	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:110881445C>T	uc002tfl.3	-	c.2125G>A	c.(2125-2127)GAC>AAC	p.D709N	NPHP1_uc002tfm.3_Missense_Mutation_p.D653N|NPHP1_uc002tfn.3_Missense_Mutation_p.D708N|NPHP1_uc002tfo.3_Missense_Mutation_p.D590N|NPHP1_uc010ywx.1_Missense_Mutation_p.D652N	NM_000272	NP_000263	O15259	NPHP1_HUMAN	nephrocystin 1 isoform 1	708					actin cytoskeleton organization|cell projection organization|cell-cell adhesion|excretion|retina development in camera-type eye|signal transduction|spermatid differentiation|visual behavior	adherens junction|cilium axoneme|cytoplasm|cytoskeleton|motile cilium|photoreceptor connecting cilium	protein binding|structural molecule activity			ovary(2)	2														0.171053	49.647214	65.206982	26	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110881445	110881445	10983	2	C	T	T	T	416	32	NPHP1	2	2
ACTR3	10096	broad.mit.edu	37	2	114699825	114699825	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:114699825G>T	uc002tkx.1	+	c.747G>T	c.(745-747)GGG>GGT	p.G249G	ACTR3_uc010yyc.1_Silent_p.G187G|ACTR3_uc010yyd.1_Silent_p.G198G	NM_005721	NP_005712	P61158	ARP3_HUMAN	ARP3 actin-related protein 3 homolog	249					cellular component movement|cilium morphogenesis	Arp2/3 protein complex	actin binding|ATP binding				0														0.163934	18.809986	25.354909	10	51	KEEP	---	---	---	---	capture		Silent	SNP	114699825	114699825	213	2	G	T	T	T	561	44	ACTR3	2	2
MARCO	8685	broad.mit.edu	37	2	119750717	119750717	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:119750717G>A	uc002tln.1	+	c.1270G>A	c.(1270-1272)GTC>ATC	p.V424I	MARCO_uc010yyf.1_Missense_Mutation_p.V346I	NM_006770	NP_006761	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	424	SRCR.|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)								0.19697	82.014315	98.951176	39	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119750717	119750717	9694	2	G	A	A	A	520	40	MARCO	1	1
GLI2	2736	broad.mit.edu	37	2	121744024	121744024	+	Silent	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:121744024G>C	uc010flp.2	+	c.2127G>C	c.(2125-2127)CTG>CTC	p.L709L	GLI2_uc002tmq.1_Silent_p.L381L|GLI2_uc002tmr.1_Silent_p.L364L|GLI2_uc002tmt.3_Silent_p.L381L|GLI2_uc002tmu.3_Silent_p.L364L|GLI2_uc002tmw.1_Silent_p.L692L	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	709					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|zinc ion binding			ovary(7)|central_nervous_system(1)	8	Renal(3;0.0496)	Prostate(154;0.0623)								376				0.123288	13.220494	23.358109	9	64	KEEP	---	---	---	---	capture		Silent	SNP	121744024	121744024	6706	2	G	C	C	C	600	47	GLI2	3	3
CNTNAP5	129684	broad.mit.edu	37	2	125504945	125504945	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:125504945C>A	uc010flu.2	+	c.2217C>A	c.(2215-2217)GAC>GAA	p.D739E	CNTNAP5_uc002tno.2_Missense_Mutation_p.D738E	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	738	Extracellular (Potential).|Fibrinogen C-terminal.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)										0.091346	13.961649	48.962623	19	189	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125504945	125504945	3788	2	C	A	A	A	246	19	CNTNAP5	1	1
MYO7B	4648	broad.mit.edu	37	2	128387322	128387322	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:128387322G>T	uc002top.2	+	c.4649G>T	c.(4648-4650)AGG>ATG	p.R1550M	MYO7B_uc002tor.1_Missense_Mutation_p.R403M	NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	1550	SH3 1.					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)										0.24	12.970128	14.491326	6	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128387322	128387322	10478	2	G	T	T	T	455	35	MYO7B	2	2
UGGT1	56886	broad.mit.edu	37	2	128873837	128873837	+	Splice_Site_SNP	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:128873837A>G	uc002tps.2	+	c.794_splice	c.e8-2	p.G265_splice	UGGT1_uc010fme.1_Splice_Site_SNP_p.G140_splice|UGGT1_uc002tpr.2_Splice_Site_SNP_p.G241_splice	NM_020120	NP_064505			UDP-glucose ceramide glucosyltransferase-like 1						'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1														0.131313	28.521565	41.586856	13	86	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	128873837	128873837	17499	2	A	G	G	G	195	15	UGGT1	5	4
UGGT1	56886	broad.mit.edu	37	2	128880772	128880772	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:128880772A>C	uc002tps.2	+	c.1086A>C	c.(1084-1086)AAA>AAC	p.K362N	UGGT1_uc010fme.1_Missense_Mutation_p.K237N|UGGT1_uc002tpr.2_Missense_Mutation_p.K338N	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1	362					'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1														0.092593	5.332579	14.351922	5	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128880772	128880772	17499	2	A	C	C	C	11	1	UGGT1	4	4
FAM123C	205147	broad.mit.edu	37	2	131520421	131520421	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:131520421C>A	uc002trw.2	+	c.776C>A	c.(775-777)TCG>TAG	p.S259*	FAM123C_uc010fmv.2_Nonsense_Mutation_p.S259*|FAM123C_uc010fms.1_Nonsense_Mutation_p.S259*|FAM123C_uc010fmt.1_Nonsense_Mutation_p.S259*|FAM123C_uc010fmu.1_Nonsense_Mutation_p.S259*	NM_152698	NP_689911	Q8N944	F123C_HUMAN	hypothetical protein LOC205147	259										pancreas(2)|ovary(1)	3	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.13)										0.166667	55.567311	73.899095	29	145	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	131520421	131520421	5621	2	C	A	A	A	403	31	FAM123C	5	1
POTEE	445582	broad.mit.edu	37	2	132021400	132021400	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:132021400A>G	uc002tsn.2	+	c.2372A>G	c.(2371-2373)TAC>TGC	p.Y791C	PLEKHB2_uc002tsh.2_Intron|POTEE_uc002tsk.2_Missense_Mutation_p.Y391C|POTEE_uc002tsl.2_Missense_Mutation_p.Y373C|POTEE_uc010fmy.1_Missense_Mutation_p.Y255C	NM_001083538	NP_001077007	Q6S8J3	POTEE_HUMAN	protein expressed in prostate, ovary, testis,	791	Actin-like.						ATP binding				0														0.165644	67.938851	85.210529	27	136	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132021400	132021400	12694	2	A	G	G	G	182	14	POTEE	4	4
MGAT5	4249	broad.mit.edu	37	2	135119873	135119873	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:135119873G>T	uc002ttv.1	+	c.1274G>T	c.(1273-1275)GGG>GTG	p.G425V		NM_002410	NP_002401	Q09328	MGT5A_HUMAN	N-acetylglucosaminyltransferase V	425	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0964)										0.219457	214.813994	246.879735	97	345	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135119873	135119873	9938	2	G	T	T	T	559	43	MGAT5	2	2
ACMSD	130013	broad.mit.edu	37	2	135628551	135628551	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:135628551C>G	uc002ttz.2	+	c.597C>G	c.(595-597)ACC>ACG	p.T199T	ACMSD_uc002tua.2_Silent_p.T141T	NM_138326	NP_612199	Q8TDX5	ACMSD_HUMAN	aminocarboxymuconate semialdehyde decarboxylase	199					quinolinate metabolic process|tryptophan catabolic process	cytosol	aminocarboxymuconate-semialdehyde decarboxylase activity|metal ion binding				0				BRCA - Breast invasive adenocarcinoma(221;0.115)										0.12987	16.927184	27.166254	10	67	KEEP	---	---	---	---	capture		Silent	SNP	135628551	135628551	145	2	C	G	G	G	262	21	ACMSD	3	3
LRP1B	53353	broad.mit.edu	37	2	141032110	141032110	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141032110C>T	uc002tvj.1	-	c.13025G>A	c.(13024-13026)AGT>AAT	p.S4342N		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4342	Extracellular (Potential).|EGF-like 13.				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)			0.11828	13.25283	26.571993	11	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141032110	141032110	9328	2	C	T	T	T	260	20	LRP1B	2	2
LRP1B	53353	broad.mit.edu	37	2	141283457	141283457	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141283457C>A	uc002tvj.1	-	c.7982G>T	c.(7981-7983)GGG>GTG	p.G2661V		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2661	Extracellular (Potential).|LDL-receptor class A 14.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)			p.G2661E(IPC298-Tumor)	2546	TSP Lung(27;0.18)			0.075	-1.806082	13.013536	6	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141283457	141283457	9328	2	C	A	A	A	286	22	LRP1B	2	2
LRP1B	53353	broad.mit.edu	37	2	141299535	141299535	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141299535T>A	uc002tvj.1	-	c.7200A>T	c.(7198-7200)ATA>ATT	p.I2400I		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2400	Extracellular (Potential).|LDL-receptor class B 26.				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)			0.208333	20.959485	24.715472	10	38	KEEP	---	---	---	---	capture		Silent	SNP	141299535	141299535	9328	2	T	A	A	A	680	53	LRP1B	3	3
LRP1B	53353	broad.mit.edu	37	2	141473549	141473549	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141473549C>A	uc002tvj.1	-	c.6016G>T	c.(6016-6018)GAG>TAG	p.E2006*		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2006	Extracellular (Potential).|LDL-receptor class B 20.				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)			0.098592	2.966452	14.41833	7	64	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	141473549	141473549	9328	2	C	A	A	A	416	32	LRP1B	5	2
LRP1B	53353	broad.mit.edu	37	2	141597618	141597618	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141597618C>A	uc002tvj.1	-	c.5151G>T	c.(5149-5151)ATG>ATT	p.M1717I		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1717	Extracellular (Potential).|LDL-receptor class B 16.				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)			0.2	10.959331	13.053102	5	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141597618	141597618	9328	2	C	A	A	A	273	21	LRP1B	2	2
LRP1B	53353	broad.mit.edu	37	2	141660594	141660594	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141660594G>T	uc002tvj.1	-	c.3661C>A	c.(3661-3663)CAT>AAT	p.H1221N	LRP1B_uc010fnl.1_Missense_Mutation_p.H403N	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1221	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)			0.088235	1.889538	19.381219	9	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141660594	141660594	9328	2	G	T	T	T	585	45	LRP1B	2	2
LRP1B	53353	broad.mit.edu	37	2	141812791	141812791	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141812791C>G	uc002tvj.1	-	c.1446G>C	c.(1444-1446)ATG>ATC	p.M482I	LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	482	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)			0.133333	20.094431	29.882375	10	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141812791	141812791	9328	2	C	G	G	G	325	25	LRP1B	3	3
ARHGAP15	55843	broad.mit.edu	37	2	143959748	143959748	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:143959748G>T	uc002tvm.3	+	c.211G>T	c.(211-213)GTC>TTC	p.V71F	ARHGAP15_uc010zbl.1_Missense_Mutation_p.V71F	NM_018460	NP_060930	Q53QZ3	RHG15_HUMAN	ARHGAP15	71					regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.151)										0.241379	53.928645	59.238681	21	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143959748	143959748	877	2	G	T	T	T	624	48	ARHGAP15	2	2
RIF1	55183	broad.mit.edu	37	2	152311424	152311424	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:152311424C>T	uc002txm.2	+	c.2360C>T	c.(2359-2361)TCA>TTA	p.S787L	RIF1_uc002txl.2_Missense_Mutation_p.S787L|RIF1_uc010fnv.1_Missense_Mutation_p.S751L|RIF1_uc002txn.2_Missense_Mutation_p.S787L|RIF1_uc002txo.2_Missense_Mutation_p.S787L	NM_018151	NP_060621	Q5UIP0	RIF1_HUMAN	RAP1 interacting factor 1	787					cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|lung(2)|kidney(1)	12				BRCA - Breast invasive adenocarcinoma(221;0.0429)						950				0.125	10.351805	19.147779	8	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152311424	152311424	13834	2	C	T	T	T	377	29	RIF1	2	2
SLC4A10	57282	broad.mit.edu	37	2	162757507	162757507	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:162757507C>A	uc002ubx.3	+	c.1428C>A	c.(1426-1428)CTC>CTA	p.L476L	SLC4A10_uc010fpa.1_Silent_p.L488L|SLC4A10_uc010zcr.1_Non-coding_Transcript|SLC4A10_uc002uby.3_Silent_p.L446L|SLC4A10_uc010zcs.1_Silent_p.L457L	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate	476	Cytoplasmic (Potential).				bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5														0.428571	8.623598	8.654806	3	4	KEEP	---	---	---	---	capture		Silent	SNP	162757507	162757507	15148	2	C	A	A	A	379	30	SLC4A10	2	2
SCN2A	6326	broad.mit.edu	37	2	166226697	166226697	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:166226697A>T	uc002udc.2	+	c.3737A>T	c.(3736-3738)GAC>GTC	p.D1246V	SCN2A_uc002udd.2_Missense_Mutation_p.D1246V|SCN2A_uc002ude.2_Missense_Mutation_p.D1246V	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	1246	Helical; Name=S2 of repeat III; (Potential).|III.				myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)									0.148387	37.029499	55.418056	23	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166226697	166226697	14398	2	A	T	T	T	130	10	SCN2A	3	3
CSRNP3	80034	broad.mit.edu	37	2	166536110	166536110	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:166536110G>C	uc002udf.2	+	c.1605G>C	c.(1603-1605)TTG>TTC	p.L535F	CSRNP3_uc002udg.2_Missense_Mutation_p.L535F	NM_024969	NP_079245	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	535					apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)	4														0.118644	25.159176	42.016589	14	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166536110	166536110	4106	2	G	C	C	C	581	45	CSRNP3	3	3
TTC21B	79809	broad.mit.edu	37	2	166737205	166737205	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:166737205C>A	uc002udk.2	-	c.3789G>T	c.(3787-3789)CGG>CGT	p.R1263R	TTC21B_uc002udj.1_Non-coding_Transcript	NM_024753	NP_079029	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	1263	TPR 18.					cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5														0.254545	31.523644	34.531555	14	41	KEEP	---	---	---	---	capture		Silent	SNP	166737205	166737205	17242	2	C	A	A	A	379	30	TTC21B	2	2
TTC21B	79809	broad.mit.edu	37	2	166788366	166788366	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:166788366C>A	uc002udk.2	-	c.796G>T	c.(796-798)GCT>TCT	p.A266S	TTC21B_uc002udl.2_Missense_Mutation_p.A266S	NM_024753	NP_079029	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	266						cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5														0.189189	13.700989	17.047139	7	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166788366	166788366	17242	2	C	A	A	A	338	26	TTC21B	2	2
SCN9A	6335	broad.mit.edu	37	2	167168062	167168062	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:167168062C>G	uc010fpl.2	-	c.205G>C	c.(205-207)GGC>CGC	p.G69R		NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	69						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)	11					Lamotrigine(DB00555)|Lidocaine(DB00281)									0.159292	33.274784	45.773607	18	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167168062	167168062	14407	2	C	G	G	G	299	23	SCN9A	3	3
XIRP2	129446	broad.mit.edu	37	2	168100460	168100460	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168100460T>A	uc002udx.2	+	c.2558T>A	c.(2557-2559)CTA>CAA	p.L853Q	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.L678Q|XIRP2_uc010fpq.2_Missense_Mutation_p.L631Q|XIRP2_uc010fpr.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	678					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.11976	22.783622	46.477463	20	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168100460	168100460	18011	2	T	A	A	A	689	53	XIRP2	3	3
XIRP2	129446	broad.mit.edu	37	2	168101337	168101337	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168101337A>T	uc002udx.2	+	c.3435A>T	c.(3433-3435)ACA>ACT	p.T1145T	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.T970T|XIRP2_uc010fpq.2_Silent_p.T923T|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	970					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.213483	46.586244	53.32774	19	70	KEEP	---	---	---	---	capture		Silent	SNP	168101337	168101337	18011	2	A	T	T	T	80	7	XIRP2	3	3
XIRP2	129446	broad.mit.edu	37	2	168107012	168107012	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168107012C>A	uc002udx.2	+	c.9110C>A	c.(9109-9111)TCC>TAC	p.S3037Y	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.S2862Y|XIRP2_uc010fpq.2_Missense_Mutation_p.S2815Y|XIRP2_uc010fpr.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	2862					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.115385	14.422122	33.375089	15	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168107012	168107012	18011	2	C	A	A	A	390	30	XIRP2	2	2
LRP2	4036	broad.mit.edu	37	2	170042197	170042197	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:170042197G>A	uc002ues.2	-	c.9661C>T	c.(9661-9663)CTC>TTC	p.L3221F		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	3221	Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	23				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)					2055				0.099631	24.405328	67.828796	27	244	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170042197	170042197	9329	2	G	A	A	A	455	35	LRP2	2	2
KBTBD10	10324	broad.mit.edu	37	2	170356090	170356090	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:170356090C>G	uc010zdh.1	+	c.776C>G	c.(775-777)GCC>GGC	p.A259G	BBS5_uc002uet.2_Missense_Mutation_p.A259G|BBS5_uc010fpw.2_Missense_Mutation_p.A238G	NM_152384	NP_689597	O60662	KBTBA_HUMAN	Bardet-Biedl syndrome 5	Error:Variant_position_missing_in_O60662_after_alignment					striated muscle contraction	centrosome|nucleolus|plasma membrane|pseudopodium|ruffle					0														0.208	76.377228	86.250127	26	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170356090	170356090	8294	2	C	G	G	G	338	26	KBTBD10	3	3
RAPGEF4	11069	broad.mit.edu	37	2	173916400	173916400	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:173916400C>G	uc002uhv.3	+	c.2941C>G	c.(2941-2943)CAG>GAG	p.Q981E	RAPGEF4_uc002uhw.3_Missense_Mutation_p.Q837E	NM_007023	NP_008954	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	981	Ras-GEF.				blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|kidney(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.194)											0.070423	1.315013	14.831895	5	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	173916400	173916400	13506	2	C	G	G	G	377	29	RAPGEF4	3	3
ATF2	1386	broad.mit.edu	37	2	175986270	175986270	+	Splice_Site_SNP	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:175986270T>A	uc002ujl.2	-	c.103_splice	c.e5-1	p.R35_splice	ATF2_uc010fqv.2_Splice_Site_SNP_p.A9_splice|ATF2_uc002ujv.2_Splice_Site_SNP|ATF2_uc002ujm.2_Intron|ATF2_uc002ujn.2_Intron|ATF2_uc002ujo.2_Intron|ATF2_uc002ujp.2_Splice_Site_SNP|ATF2_uc002ujq.2_Splice_Site_SNP_p.R35_splice|ATF2_uc002ujr.2_Splice_Site_SNP|ATF2_uc010fqu.2_Splice_Site_SNP_p.R17_splice|ATF2_uc002ujs.2_Intron|ATF2_uc002ujt.2_Splice_Site_SNP|ATF2_uc002uju.2_Intron|ATF2_uc002ujw.1_Intron|ATF2_uc002ujx.1_Splice_Site_SNP|ATF2_uc002ujy.1_Splice_Site_SNP_p.R35_splice	NM_001880	NP_001871			activating transcription factor 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|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	nucleoplasm	protein dimerization activity|RNA polymerase II transcription factor activity|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			breast(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.125)			Pancreas(17;87 705 4534 15538 30988)				377				0.177778	18.073069	22.471964	8	37	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	175986270	175986270	1099	2	T	A	A	A	715	55	ATF2	5	3
HOXD3	3232	broad.mit.edu	37	2	177036982	177036982	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:177036982C>T	uc002ukt.1	+	c.1279C>T	c.(1279-1281)CCC>TCC	p.P427S		NM_006898	NP_008829	P31249	HXD3_HUMAN	homeobox D3	427					anterior/posterior pattern formation|cartilage development|cell-matrix adhesion|embryonic skeletal system morphogenesis|Notch signaling pathway|positive regulation of gene expression|positive regulation of neuron differentiation|regulation of transcription, DNA-dependent|thyroid gland development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)										0.111111	5.309912	13.386006	6	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	177036982	177036982	7615	2	C	T	T	T	390	30	HOXD3	2	2
AGPS	8540	broad.mit.edu	37	2	178305762	178305762	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:178305762G>T	uc002ull.2	+	c.707G>T	c.(706-708)GGT>GTT	p.G236V	AGPS_uc010zfb.1_Missense_Mutation_p.G146V	NM_003659	NP_003650	O00116	ADAS_HUMAN	alkyldihydroxyacetone phosphate synthase	236	FAD-binding PCMH-type.				ether lipid biosynthetic process	peroxisomal matrix|peroxisomal membrane|plasma membrane	alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity			ovary(2)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)											0.135135	17.699332	27.246092	10	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	178305762	178305762	397	2	G	T	T	T	572	44	AGPS	2	2
TTN	7273	broad.mit.edu	37	2	179403316	179403316	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179403316C>T	uc010zfg.1	-	c.91536G>A	c.(91534-91536)GGG>GGA	p.G30512G	TTN_uc010zfh.1_Silent_p.G24207G|TTN_uc010zfi.1_Silent_p.G24140G|TTN_uc010zfj.1_Silent_p.G24015G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	925										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				0.169935	44.943658	60.728124	26	127	KEEP	---	---	---	---	capture		Silent	SNP	179403316	179403316	17290	2	C	T	T	T	327	26	TTN	2	2
TTN	7273	broad.mit.edu	37	2	179435496	179435496	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179435496G>T	uc010zfg.1	-	c.67659C>A	c.(67657-67659)ATC>ATA	p.I22553I	TTN_uc010zfh.1_Silent_p.I16248I|TTN_uc010zfi.1_Silent_p.I16181I|TTN_uc010zfj.1_Silent_p.I16056I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3068										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)						p.I22553I(SNU1040-Tumor)	8722				0.122727	33.160102	63.822785	27	193	KEEP	---	---	---	---	capture		Silent	SNP	179435496	179435496	17290	2	G	T	T	T	473	37	TTN	1	1
TTN	7273	broad.mit.edu	37	2	179468758	179468758	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179468758G>T	uc010zfg.1	-	c.46952C>A	c.(46951-46953)GCA>GAA	p.A15651E	TTN_uc010zfh.1_Missense_Mutation_p.A9346E|TTN_uc010zfi.1_Missense_Mutation_p.A9279E|TTN_uc010zfj.1_Missense_Mutation_p.A9154E	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	Error:Variant_position_missing_in_Q4ZG20_after_alignment										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				0.064599	-24.149653	52.11453	25	362	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179468758	179468758	17290	2	G	T	T	T	598	46	TTN	2	2
TTN	7273	broad.mit.edu	37	2	179479056	179479056	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179479056A>T	uc010zfg.1	-	c.41364T>A	c.(41362-41364)GCT>GCA	p.A13788A	TTN_uc010zfh.1_Silent_p.A7483A|TTN_uc010zfi.1_Silent_p.A7416A|TTN_uc010zfj.1_Silent_p.A7291A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	201										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				0.217391	48.849144	55.624555	20	72	KEEP	---	---	---	---	capture		Silent	SNP	179479056	179479056	17290	2	A	T	T	T	80	7	TTN	3	3
TTN	7273	broad.mit.edu	37	2	179590276	179590276	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179590276G>T	uc010zfg.1	-	c.16923C>A	c.(16921-16923)GTC>GTA	p.V5641V	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.V2302V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2650										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				0.094118	1.627286	15.716632	8	77	KEEP	---	---	---	---	capture		Silent	SNP	179590276	179590276	17290	2	G	T	T	T	522	41	TTN	2	2
TTN	7273	broad.mit.edu	37	2	179596304	179596304	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179596304G>A	uc010zfg.1	-	c.13457C>T	c.(13456-13458)CCA>CTA	p.P4486L	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.P1147L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1457										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				0.133333	8.725079	14.593818	6	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179596304	179596304	17290	2	G	A	A	A	611	47	TTN	2	2
TTN	7273	broad.mit.edu	37	2	179598427	179598427	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179598427A>G	uc010zfg.1	-	c.11957T>C	c.(11956-11958)GTT>GCT	p.V3986A	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.V647A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2236										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				0.143564	67.039265	91.750835	29	173	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179598427	179598427	17290	2	A	G	G	G	26	2	TTN	4	4
TTN	7273	broad.mit.edu	37	2	179633572	179633572	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179633572G>T	uc010zfg.1	-	c.8991C>A	c.(8989-8991)ATC>ATA	p.I2997I	TTN_uc010zfh.1_Silent_p.I2951I|TTN_uc010zfi.1_Silent_p.I2951I|TTN_uc010zfj.1_Silent_p.I2951I|TTN_uc002unb.2_Silent_p.I2997I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2997										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				0.146667	15.869136	24.874673	11	64	KEEP	---	---	---	---	capture		Silent	SNP	179633572	179633572	17290	2	G	T	T	T	421	33	TTN	2	2
TTN	7273	broad.mit.edu	37	2	179648929	179648929	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179648929G>T	uc010zfg.1	-	c.2643C>A	c.(2641-2643)TTC>TTA	p.F881L	TTN_uc010zfh.1_Missense_Mutation_p.F835L|TTN_uc010zfi.1_Missense_Mutation_p.F835L|TTN_uc010zfj.1_Missense_Mutation_p.F835L|TTN_uc002unb.2_Missense_Mutation_p.F881L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	881										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				0.160584	32.353293	47.392298	22	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179648929	179648929	17290	2	G	T	T	T	529	41	TTN	2	2
MSGN1	343930	broad.mit.edu	37	2	17998056	17998056	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:17998056G>T	uc010yjt.1	+	c.271G>T	c.(271-273)GTA>TTA	p.V91L		NM_001105569	NP_001099039	A6NI15	MSGN1_HUMAN	mesogenin 1	91					cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription regulator activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					Melanoma(127;325 1712 14802 40657 49130)								0.160377	33.51374	45.151332	17	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17998056	17998056	10262	2	G	T	T	T	572	44	MSGN1	2	2
ITGA4	3676	broad.mit.edu	37	2	182389954	182389954	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:182389954C>A	uc002unu.2	+	c.2275C>A	c.(2275-2277)CTA>ATA	p.L759I	ITGA4_uc010frj.1_Missense_Mutation_p.L241I|ITGA4_uc002unv.2_Missense_Mutation_p.L4I	NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor	759	Extracellular (Potential).				B cell differentiation|blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)									0.196721	23.572355	28.795536	12	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	182389954	182389954	8182	2	C	A	A	A	415	32	ITGA4	2	2
NCKAP1	10787	broad.mit.edu	37	2	183902768	183902768	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:183902768G>A	uc002upb.2	-	c.60C>T	c.(58-60)CTC>CTT	p.L20L	NCKAP1_uc002upc.2_Silent_p.L20L	NM_205842	NP_995314	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1 isoform 2	20					apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)											0.181818	7.288	9.38006	4	18	KEEP	---	---	---	---	capture		Silent	SNP	183902768	183902768	10620	2	G	A	A	A	574	45	NCKAP1	2	2
ZNF804A	91752	broad.mit.edu	37	2	185800875	185800875	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:185800875G>T	uc002uph.2	+	c.752G>T	c.(751-753)AGA>ATA	p.R251I		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	251						intracellular	zinc ion binding			ovary(6)|large_intestine(1)|pancreas(1)	8														0.158824	43.604093	62.475833	27	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185800875	185800875	18768	2	G	T	T	T	429	33	ZNF804A	2	2
ZNF804A	91752	broad.mit.edu	37	2	185803359	185803359	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:185803359C>A	uc002uph.2	+	c.3236C>A	c.(3235-3237)ACA>AAA	p.T1079K		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	1079						intracellular	zinc ion binding			ovary(6)|large_intestine(1)|pancreas(1)	8														0.073593	-6.792932	36.367755	17	214	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185803359	185803359	18768	2	C	A	A	A	221	17	ZNF804A	2	2
ZSWIM2	151112	broad.mit.edu	37	2	187702135	187702135	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:187702135G>T	uc002upu.1	-	c.641C>A	c.(640-642)TCT>TAT	p.S214Y		NM_182521	NP_872327	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM domain containing 2	214					apoptosis		zinc ion binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)											0.078431	-2.988397	15.549599	8	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	187702135	187702135	18845	2	G	T	T	T	429	33	ZSWIM2	2	2
WDR75	84128	broad.mit.edu	37	2	190323581	190323582	+	Missense_Mutation	DNP	TG	AT	AT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:190323581_190323582TG>AT	uc002uql.1	+	c.672_673TG>AT	c.(670-675)GATGGC>GAATGC	p.224_225DG>EC	WDR75_uc002uqm.1_Missense_Mutation_p.160_161DG>EC|WDR75_uc002uqn.1_Missense_Mutation_p.2_3DG>EC|WDR75_uc002uqo.1_Missense_Mutation_p.2_3DG>EC	NM_032168	NP_115544	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	224_225	WD 3.					nucleolus				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)											0.145161	48.707845	71.230777	27	159	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	190323581	190323582	17898	2	TG	AT	AT	AT	660	51	WDR75	3	3
ANKAR	150709	broad.mit.edu	37	2	190554279	190554279	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:190554279G>T	uc002uqw.1	+	c.415G>T	c.(415-417)GAC>TAC	p.D139Y	ANKAR_uc002uqu.2_Non-coding_Transcript|ANKAR_uc002uqv.1_Missense_Mutation_p.D210Y	NM_144708	NP_653309	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	210						integral to membrane	binding			ovary(2)|pancreas(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)											0.122449	13.623358	27.308376	12	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	190554279	190554279	626	2	G	T	T	T	429	33	ANKAR	2	2
PMS1	5378	broad.mit.edu	37	2	190660675	190660675	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:190660675G>T	uc002urh.3	+	c.313G>T	c.(313-315)GAG>TAG	p.E105*	PMS1_uc010zga.1_Nonsense_Mutation_p.E105*|PMS1_uc010zgb.1_Intron|PMS1_uc002urk.3_Nonsense_Mutation_p.E105*|PMS1_uc002uri.3_Nonsense_Mutation_p.E105*|PMS1_uc010zgc.1_5'UTR|PMS1_uc010zgd.1_Intron|PMS1_uc002urj.2_Non-coding_Transcript|PMS1_uc010fry.1_Nonsense_Mutation_p.E105*|PMS1_uc010frz.2_Nonsense_Mutation_p.E105*|PMS1_uc010zfz.1_Nonsense_Mutation_p.E105*	NM_000534	NP_000525	P54277	PMS1_HUMAN	postmeiotic segregation 1 isoform a	105					mismatch repair|reciprocal meiotic recombination	MutLalpha complex	ATP binding|ATPase activity|mismatched DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)							236				0.133858	21.778048	38.307425	17	110	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	190660675	190660675	12568	2	G	T	T	T	585	45	PMS1	5	2
STAT4	6775	broad.mit.edu	37	2	191941029	191941029	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:191941029A>G	uc002usm.1	-	c.296T>C	c.(295-297)ATG>ACG	p.M99T	STAT4_uc002usn.1_Missense_Mutation_p.M99T|STAT4_uc002uso.2_Missense_Mutation_p.M99T|STAT4_uc002usp.3_Missense_Mutation_p.M99T	NM_003151	NP_003142	Q14765	STAT4_HUMAN	signal transducer and activator of transcription	99					JAK-STAT cascade|regulation of transcription, DNA-dependent	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(2)|ovary(1)|pancreas(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)											0.089286	6.270539	25.341271	10	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	191941029	191941029	15787	2	A	G	G	G	104	8	STAT4	4	4
MYO1B	4430	broad.mit.edu	37	2	192194697	192194697	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:192194697A>T	uc010fsg.2	+	c.288A>T	c.(286-288)CGA>CGT	p.R96R	MYO1B_uc002usq.2_Silent_p.R96R|MYO1B_uc002usr.2_Silent_p.R96R|MYO1B_uc002uss.1_Silent_p.R96R	NM_001130158	NP_001123630	O43795	MYO1B_HUMAN	myosin IB isoform 1	96	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(5)|large_intestine(2)|ovary(1)	8			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)											0.085546	3.527333	62.559905	29	310	KEEP	---	---	---	---	capture		Silent	SNP	192194697	192194697	10464	2	A	T	T	T	132	11	MYO1B	3	3
MYT1L	23040	broad.mit.edu	37	2	1926489	1926489	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:1926489G>T	uc002qxe.2	-	c.1052C>A	c.(1051-1053)CCG>CAG	p.P351Q	MYT1L_uc002qxd.2_Missense_Mutation_p.P351Q|MYT1L_uc010ewl.1_Non-coding_Transcript	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	351					cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)										0.1	2.007928	11.604574	6	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1926489	1926489	10502	2	G	T	T	T	507	39	MYT1L	1	1
MYT1L	23040	broad.mit.edu	37	2	1926757	1926757	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:1926757C>G	uc002qxe.2	-	c.784G>C	c.(784-786)GTG>CTG	p.V262L	MYT1L_uc002qxd.2_Missense_Mutation_p.V262L|MYT1L_uc010ewl.1_Non-coding_Transcript	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	262					cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)										0.098859	28.635455	70.976218	26	237	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1926757	1926757	10502	2	C	G	G	G	260	20	MYT1L	3	3
CCDC150	284992	broad.mit.edu	37	2	197541345	197541345	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:197541345G>C	uc002utp.1	+	c.1330G>C	c.(1330-1332)GTG>CTG	p.V444L	CCDC150_uc010zgq.1_Non-coding_Transcript|CCDC150_uc010zgr.1_Non-coding_Transcript|CCDC150_uc010zgs.1_Missense_Mutation_p.V112L	NM_001080539	NP_001074008	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	444	Potential.										0														0.290909	51.478978	53.632245	16	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197541345	197541345	2905	2	G	C	C	C	624	48	CCDC150	3	3
PLCL1	5334	broad.mit.edu	37	2	198950911	198950912	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:198950911_198950912GG>TT	uc010fsp.2	+	c.2670_2671GG>TT	c.(2668-2673)GCGGTT>GCTTTT	p.V891F	PLCL1_uc002uuv.3_Missense_Mutation_p.V812F	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;	891					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)	1					Quinacrine(DB01103)									0.117647	4.577876	9.462536	4	30	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	198950911	198950912	12465	2	GG	TT	TT	TT	496	39	PLCL1	1	1
SGOL2	151246	broad.mit.edu	37	2	201448175	201448175	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:201448175G>A	uc002uvw.2	+	c.3786G>A	c.(3784-3786)AAG>AAA	p.K1262K	AOX1_uc002uvx.2_5'Flank|SGOL2_uc010zhe.1_Missense_Mutation_p.R1260K	NM_152524	NP_689737	Q562F6	SGOL2_HUMAN	shugoshin-like 2 isoform 1	1262					cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding			ovary(2)	2														0.116883	11.314718	22.435975	9	68	KEEP	---	---	---	---	capture		Silent	SNP	201448175	201448175	14708	2	G	A	A	A	429	33	SGOL2	2	2
NRP2	8828	broad.mit.edu	37	2	206617571	206617571	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:206617571A>T	uc002vaw.2	+	c.1916A>T	c.(1915-1917)CAG>CTG	p.Q639L	NRP2_uc002vau.2_Missense_Mutation_p.Q639L|NRP2_uc002vav.2_Missense_Mutation_p.Q639L|NRP2_uc002vax.2_Missense_Mutation_p.Q639L|NRP2_uc002vay.2_Missense_Mutation_p.Q639L	NM_201266	NP_957718	O60462	NRP2_HUMAN	neuropilin 2 isoform 1 precursor	639	Extracellular (Potential).				axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			ovary(1)|central_nervous_system(1)	2														0.082192	0.692676	13.660331	6	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	206617571	206617571	11066	2	A	T	T	T	91	7	NRP2	3	3
NDUFS1	4719	broad.mit.edu	37	2	207008741	207008742	+	Splice_Site_DNP	DNP	CC	AA	AA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:207008741_207008742CC>AA	uc010ziq.1	-	c.1029_splice	c.e10+1	p.M343_splice	NDUFS1_uc002vbe.2_Splice_Site_DNP_p.M329_splice|NDUFS1_uc010zir.1_Splice_Site_DNP_p.M293_splice|NDUFS1_uc010zis.1_Splice_Site_DNP_p.M272_splice|NDUFS1_uc010zit.1_Splice_Site_DNP_p.M218_splice|NDUFS1_uc010ziu.1_Splice_Site_DNP_p.M213_splice	NM_005006	NP_004997			NADH dehydrogenase (ubiquinone) Fe-S protein 1,						apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)									0.182927	34.873618	42.614191	15	67	KEEP	---	---	---	---	capture		Splice_Site_DNP	DNP	207008741	207008742	10690	2	CC	AA	AA	AA	234	18	NDUFS1	5	2
ZDBF2	57683	broad.mit.edu	37	2	207176120	207176120	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:207176120C>G	uc002vbp.2	+	c.6868C>G	c.(6868-6870)CCT>GCT	p.P2290A		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	2290							nucleic acid binding|zinc ion binding			ovary(3)	3														0.26087	18.439291	19.62975	6	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	207176120	207176120	18187	2	C	G	G	G	390	30	ZDBF2	3	3
ZDBF2	57683	broad.mit.edu	37	2	207176151	207176151	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:207176151G>C	uc002vbp.2	+	c.6899G>C	c.(6898-6900)CGC>CCC	p.R2300P		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	2300							nucleic acid binding|zinc ion binding			ovary(3)	3														0.193548	16.132297	18.848555	6	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	207176151	207176151	18187	2	G	C	C	C	494	38	ZDBF2	3	3
CRYGB	1419	broad.mit.edu	37	2	209010557	209010557	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:209010557C>A	uc002vcp.3	-	c.193G>T	c.(193-195)GAC>TAC	p.D65Y		NM_005210	NP_005201	P07316	CRGB_HUMAN	crystallin, gamma B	65	Beta/gamma crystallin 'Greek key' 2.				visual perception		structural constituent of eye lens				0				Epithelial(149;0.0641)|LUSC - Lung squamous cell carcinoma(261;0.0703)|Lung(261;0.132)										0.112903	13.771079	32.104146	14	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	209010557	209010557	4054	2	C	A	A	A	377	29	CRYGB	2	2
CPS1	1373	broad.mit.edu	37	2	211464252	211464252	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:211464252C>A	uc010fur.2	+	c.1534C>A	c.(1534-1536)CTG>ATG	p.L512M	CPS1_uc002vee.3_Missense_Mutation_p.L506M|CPS1_uc010fus.2_Missense_Mutation_p.L55M	NM_001122633	NP_001116105	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform a	506					carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)	12				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)										0.173077	32.278011	42.783473	18	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	211464252	211464252	3961	2	C	A	A	A	415	32	CPS1	2	2
CPS1	1373	broad.mit.edu	37	2	211539650	211539650	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:211539650G>T	uc010fur.2	+	c.4144G>T	c.(4144-4146)GGT>TGT	p.G1382C	CPS1_uc002vee.3_Missense_Mutation_p.G1376C|CPS1_uc010fus.2_Missense_Mutation_p.G925C	NM_001122633	NP_001116105	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform a	1376			G -> S (polymorphism with no functional consequences).		carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)	12				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)										0.186441	47.077736	57.949681	22	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	211539650	211539650	3961	2	G	T	T	T	611	47	CPS1	2	2
ERBB4	2066	broad.mit.edu	37	2	212288980	212288980	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:212288980A>T	uc002veg.1	-	c.2766T>A	c.(2764-2766)GAT>GAA	p.D922E	ERBB4_uc002veh.1_Missense_Mutation_p.D922E|ERBB4_uc010zji.1_Missense_Mutation_p.D912E|ERBB4_uc010zjj.1_Missense_Mutation_p.D912E	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	922	Protein kinase.|Cytoplasmic (Potential).				cell proliferation|protein phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(12)|large_intestine(1)|breast(1)	14		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)						777	TSP Lung(8;0.080)			0.140625	16.934486	24.909107	9	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	212288980	212288980	5402	2	A	T	T	T	102	8	ERBB4	3	3
APOB	338	broad.mit.edu	37	2	21231857	21231857	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:21231857G>A	uc002red.2	-	c.7883C>T	c.(7882-7884)TCA>TTA	p.S2628L		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	2628					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)									0.092486	3.954558	32.892768	16	157	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21231857	21231857	796	2	G	A	A	A	585	45	APOB	2	2
APOB	338	broad.mit.edu	37	2	21234088	21234088	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:21234088G>T	uc002red.2	-	c.5652C>A	c.(5650-5652)AAC>AAA	p.N1884K		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	1884					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)									0.210227	84.578509	98.253096	37	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21234088	21234088	796	2	G	T	T	T	464	36	APOB	2	2
APOB	338	broad.mit.edu	37	2	21235298	21235298	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:21235298A>T	uc002red.2	-	c.4442T>A	c.(4441-4443)GTC>GAC	p.V1481D		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	1481					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)									0.192308	50.697685	62.196524	25	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21235298	21235298	796	2	A	T	T	T	130	10	APOB	3	3
APOB	338	broad.mit.edu	37	2	21238276	21238276	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:21238276G>T	uc002red.2	-	c.3474C>A	c.(3472-3474)GGC>GGA	p.G1158G		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	1158					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)									0.257576	41.941958	45.45907	17	49	KEEP	---	---	---	---	capture		Silent	SNP	21238276	21238276	796	2	G	T	T	T	431	34	APOB	2	2
PECR	55825	broad.mit.edu	37	2	216914082	216914082	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:216914082G>A	uc002vft.2	-	c.618C>T	c.(616-618)TCC>TCT	p.S206S	PECR_uc010zjq.1_Non-coding_Transcript|PECR_uc002vfr.2_Silent_p.S68S|PECR_uc002vfs.2_Silent_p.S60S	NM_018441	NP_060911	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	206					fatty acid biosynthetic process|oxidation-reduction process|regulation of apoptosis	peroxisome	binding|trans-2-enoyl-CoA reductase (NADPH) activity				0		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)									0.081522	4.372819	37.191101	15	169	KEEP	---	---	---	---	capture		Silent	SNP	216914082	216914082	12138	2	G	A	A	A	548	43	PECR	2	2
MARCH4	57574	broad.mit.edu	37	2	217124200	217124200	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:217124200G>T	uc002vgb.2	-	c.1068C>A	c.(1066-1068)GCC>GCA	p.A356A		NM_020814	NP_065865	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4	356						Golgi membrane|Golgi stack|integral to membrane|trans-Golgi network	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)										0.148515	21.700788	33.64612	15	86	KEEP	---	---	---	---	capture		Silent	SNP	217124200	217124200	9686	2	G	T	T	T	548	43	MARCH4	2	2
CCDC108	255101	broad.mit.edu	37	2	219893021	219893021	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:219893021G>T	uc002vjl.1	-	c.1753C>A	c.(1753-1755)CGG>AGG	p.R585R	CCDC108_uc010fwa.1_Silent_p.R28R|CCDC108_uc010zkp.1_Silent_p.R574R|CCDC108_uc010zkq.1_Silent_p.R520R	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	585						integral to membrane	structural molecule activity			ovary(2)|pancreas(1)	3		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.171975	51.541811	67.419118	27	130	KEEP	---	---	---	---	capture		Silent	SNP	219893021	219893021	2863	2	G	T	T	T	506	39	CCDC108	1	1
CCDC108	255101	broad.mit.edu	37	2	219894146	219894146	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:219894146C>T	uc002vjl.1	-	c.1629G>A	c.(1627-1629)GTG>GTA	p.V543V	CCDC108_uc010fwa.1_5'UTR|CCDC108_uc010zkp.1_Silent_p.V532V|CCDC108_uc010zkq.1_Silent_p.V478V	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	543						integral to membrane	structural molecule activity			ovary(2)|pancreas(1)	3		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)								OREG0015211	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.177778	17.070293	21.471828	8	37	KEEP	---	---	---	---	capture		Silent	SNP	219894146	219894146	2863	2	C	T	T	T	262	21	CCDC108	2	2
FAM134A	79137	broad.mit.edu	37	2	220046857	220046857	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220046857A>T	uc002vjw.3	+	c.1138A>T	c.(1138-1140)AGG>TGG	p.R380W	FAM134A_uc010fwc.2_Missense_Mutation_p.R173W|FAM134A_uc002vjx.2_Missense_Mutation_p.R173W	NM_024293	NP_077269	Q8NC44	F134A_HUMAN	hypothetical protein LOC79137	380						endoplasmic reticulum|integral to membrane				ovary(1)|central_nervous_system(1)	2		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.136986	54.305996	91.55273	40	252	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220046857	220046857	5642	2	A	T	T	T	36	3	FAM134A	3	3
FAM134A	79137	broad.mit.edu	37	2	220046971	220046971	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220046971C>T	uc002vjw.3	+	c.1252C>T	c.(1252-1254)CCC>TCC	p.P418S	FAM134A_uc010fwc.2_Missense_Mutation_p.P211S|FAM134A_uc002vjx.2_Missense_Mutation_p.P211S	NM_024293	NP_077269	Q8NC44	F134A_HUMAN	hypothetical protein LOC79137	418						endoplasmic reticulum|integral to membrane				ovary(1)|central_nervous_system(1)	2		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.101695	26.902107	82.862358	36	318	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220046971	220046971	5642	2	C	T	T	T	286	22	FAM134A	2	2
SPEG	10290	broad.mit.edu	37	2	220352934	220352934	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220352934A>T	uc010fwg.2	+	c.7760A>T	c.(7759-7761)CAC>CTC	p.H2587L		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	2587	Ig-like 9.				muscle organ development|negative regulation of cell proliferation|protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity			ovary(4)|stomach(2)|central_nervous_system(1)	7		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)						482				0.1875	62.661946	77.290644	30	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220352934	220352934	15548	2	A	T	T	T	78	6	SPEG	3	3
TMEM198	130612	broad.mit.edu	37	2	220413975	220413975	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220413975C>A	uc002vme.2	+	c.844C>A	c.(844-846)CTC>ATC	p.L282I	TMEM198_uc002vmf.2_Missense_Mutation_p.L282I	NM_001005209	NP_001005209	Q66K66	TM198_HUMAN	transmembrane protein 198	282	Arg-rich.					integral to membrane				ovary(1)	1		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)										0.142857	35.372802	58.657677	27	162	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220413975	220413975	16654	2	C	A	A	A	312	24	TMEM198	2	2
OBSL1	23363	broad.mit.edu	37	2	220418377	220418377	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220418377G>T	uc010fwk.2	-	c.4908C>A	c.(4906-4908)CAC>CAA	p.H1636Q		NM_015311	NP_056126	O75147	OBSL1_HUMAN	obscurin-like 1	1636	Ig-like 13.				cardiac myofibril assembly	intercalated disc|M band|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity				0		Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)								OREG0003989	type=REGULATORY REGION|Gene=AK092118|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	0.102564	4.380278	10.509973	4	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220418377	220418377	11218	2	G	T	T	T	516	40	OBSL1	1	1
PAX3	5077	broad.mit.edu	37	2	223096856	223096856	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:223096856C>A	uc002vmt.1	-	c.733G>T	c.(733-735)GAC>TAC	p.D245Y	PAX3_uc002vmy.1_Missense_Mutation_p.D244Y|PAX3_uc002vmv.1_Missense_Mutation_p.D245Y|PAX3_uc002vmw.1_Missense_Mutation_p.D245Y|PAX3_uc002vmx.1_Missense_Mutation_p.D245Y|PAX3_uc010fwo.2_Missense_Mutation_p.D245Y	NM_181459	NP_852124	P23760	PAX3_HUMAN	paired box 3 isoform PAX3e	245	Homeobox.				apoptosis|organ morphogenesis|positive regulation of gene-specific transcription from RNA polymerase II promoter|sensory perception of sound|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity		PAX3/FOXO1(749)|PAX3/NCOA1(8)|PAX3/NCOA2(4)	soft_tissue(761)|ovary(4)	765		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)						141				0.134752	25.41862	43.66598	19	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	223096856	223096856	11900	2	C	A	A	A	377	29	PAX3	2	2
IRS1	3667	broad.mit.edu	37	2	227663167	227663167	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:227663167C>A	uc002voh.3	-	c.288G>T	c.(286-288)GCG>GCT	p.A96A		NM_005544	NP_005535	P35568	IRS1_HUMAN	insulin receptor substrate 1	96	PH.|Mediates interaction with PHIP (By similarity).				fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity	caveola|cytosol|insulin receptor complex|microsome|nucleus	insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity			central_nervous_system(4)|lung(3)|ovary(1)|pancreas(1)	9		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)						143		OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.221198	102.118095	117.637549	48	169	KEEP	---	---	---	---	capture		Silent	SNP	227663167	227663167	8144	2	C	A	A	A	288	23	IRS1	1	1
SPHKAP	80309	broad.mit.edu	37	2	228883020	228883020	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228883020C>A	uc002vpq.2	-	c.2550G>T	c.(2548-2550)GAG>GAT	p.E850D	SPHKAP_uc002vpp.2_Missense_Mutation_p.E850D|SPHKAP_uc010zlx.1_Missense_Mutation_p.E850D	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	850						cytoplasm	protein binding			ovary(4)|lung(1)	5		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)										0.063169	-75.57459	110.104232	59	875	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228883020	228883020	15560	2	C	A	A	A	415	32	SPHKAP	2	2
SPHKAP	80309	broad.mit.edu	37	2	228973593	228973593	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228973593G>T	uc002vpq.2	-	c.201C>A	c.(199-201)CCC>CCA	p.P67P	SPHKAP_uc002vpp.2_Silent_p.P67P|SPHKAP_uc010zlx.1_Silent_p.P67P	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	67						cytoplasm	protein binding			ovary(4)|lung(1)	5		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)										0.147727	20.311371	30.803474	13	75	KEEP	---	---	---	---	capture		Silent	SNP	228973593	228973593	15560	2	G	T	T	T	444	35	SPHKAP	2	2
DNER	92737	broad.mit.edu	37	2	230456378	230456378	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:230456378C>A	uc002vpv.2	-	c.503G>T	c.(502-504)CGC>CTC	p.R168L		NM_139072	NP_620711	Q8NFT8	DNER_HUMAN	delta-notch-like EGF repeat-containing	168	Extracellular (Potential).				central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			ovary(1)	1		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)										0.182609	44.736766	55.593642	21	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	230456378	230456378	4850	2	C	A	A	A	351	27	DNER	1	1
SP140L	93349	broad.mit.edu	37	2	231193546	231193546	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:231193546G>T	uc010fxm.1	+	c.107G>T	c.(106-108)AGG>ATG	p.R36M	SP140_uc010zma.1_Intron	NM_138402	NP_612411	Q9H930	LY10L_HUMAN	SP140 nuclear body protein-like	36	HSR.					nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1														0.103448	4.203432	13.289137	6	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	231193546	231193546	15463	2	G	T	T	T	455	35	SP140L	2	2
NMUR1	10316	broad.mit.edu	37	2	232390050	232390050	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:232390050C>A	uc002vry.3	-	c.985G>T	c.(985-987)GGC>TGC	p.G329C		NM_006056	NP_006047	Q9HB89	NMUR1_HUMAN	neuromedin U receptor 1	329	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|calcium ion transport|calcium-mediated signaling|chloride transport|smooth muscle contraction	integral to plasma membrane|membrane fraction	neuromedin U receptor activity			central_nervous_system(1)|pancreas(1)	2		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;8.37e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)										0.271845	63.218862	68.082433	28	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	232390050	232390050	10909	2	C	A	A	A	273	21	NMUR1	2	2
NEU2	4759	broad.mit.edu	37	2	233898903	233898903	+	Silent	SNP	G	T	T	rs2233387		TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:233898903G>T	uc010zmn.1	+	c.279G>T	c.(277-279)GCG>GCT	p.A93A		NM_005383	NP_005374	Q9Y3R4	NEUR2_HUMAN	neuraminidase 2	93							exo-alpha-sialidase activity				0		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)										0.144105	55.027284	82.947836	33	196	KEEP	---	---	---	---	capture		Silent	SNP	233898903	233898903	10741	2	G	T	T	T	483	38	NEU2	1	1
TRPM8	79054	broad.mit.edu	37	2	234835272	234835272	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:234835272G>T	uc002vvh.2	+	c.90G>T	c.(88-90)CGG>CGT	p.R30R	TRPM8_uc010fyj.2_5'UTR	NM_024080	NP_076985	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel,	30	Cytoplasmic (Potential).					integral to membrane					0		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)					505				0.246154	34.267682	38.082856	16	49	KEEP	---	---	---	---	capture		Silent	SNP	234835272	234835272	17143	2	G	T	T	T	522	41	TRPM8	2	2
SH3BP4	23677	broad.mit.edu	37	2	235950023	235950023	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:235950023G>T	uc002vvp.2	+	c.610G>T	c.(610-612)GAA>TAA	p.E204*	SH3BP4_uc010fym.2_Nonsense_Mutation_p.E204*|SH3BP4_uc002vvq.2_Nonsense_Mutation_p.E204*	NM_014521	NP_055336	Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	204					endocytosis	clathrin-coated vesicle|coated pit|nucleus	protein binding			ovary(1)|skin(1)	2		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)										0.18797	107.100117	131.352357	50	216	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	235950023	235950023	14737	2	G	T	T	T	481	37	SH3BP4	5	1
IQCA1	79781	broad.mit.edu	37	2	237406078	237406078	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:237406078C>A	uc002vwb.2	-	c.85G>T	c.(85-87)GAT>TAT	p.D29Y	IQCA1_uc002vvz.1_Missense_Mutation_p.D22Y|IQCA1_uc002vwa.1_Non-coding_Transcript|IQCA1_uc010zni.1_Missense_Mutation_p.D22Y	NM_024726	NP_079002	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	22							ATP binding			ovary(1)	1														0.096154	3.434659	11.939829	5	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237406078	237406078	8103	2	C	A	A	A	403	31	IQCA1	1	1
COL6A3	1293	broad.mit.edu	37	2	238249368	238249368	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:238249368G>T	uc002vwl.2	-	c.8191C>A	c.(8191-8193)CCA>ACA	p.P2731T	COL6A3_uc002vwo.2_Missense_Mutation_p.P2525T|COL6A3_uc010znj.1_Missense_Mutation_p.P2124T|COL6A3_uc002vwj.2_Missense_Mutation_p.P112T	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2731	VWFA 12.|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)										0.182292	65.611102	83.818473	35	157	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	238249368	238249368	3839	2	G	T	T	T	559	43	COL6A3	2	2
COL6A3	1293	broad.mit.edu	37	2	238303368	238303368	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:238303368C>A	uc002vwl.2	-	c.571G>T	c.(571-573)GAA>TAA	p.E191*	COL6A3_uc002vwo.2_Intron|COL6A3_uc010znj.1_Intron|COL6A3_uc002vwq.2_Intron|COL6A3_uc002vwr.2_Intron|COL6A3_uc010znk.1_Nonsense_Mutation_p.E191*	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	191	VWFA 1.|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)										0.071429	-7.772474	18.746109	10	130	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	238303368	238303368	3839	2	C	A	A	A	377	29	COL6A3	5	2
HDAC4	9759	broad.mit.edu	37	2	240056263	240056263	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:240056263G>A	uc002vyk.3	-	c.1055C>T	c.(1054-1056)CCC>CTC	p.P352L	HDAC4_uc010fyz.1_Missense_Mutation_p.P347L|HDAC4_uc010zoa.1_Missense_Mutation_p.P347L|HDAC4_uc010fza.2_Missense_Mutation_p.P352L|HDAC4_uc010fyy.2_Missense_Mutation_p.P304L|HDAC4_uc010znz.1_Missense_Mutation_p.P235L|HDAC4_uc010fzb.1_Non-coding_Transcript	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4	352					B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|specific transcriptional repressor activity|transcription activator activity|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)						606				0.089888	3.082946	18.144343	8	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	240056263	240056263	7292	2	G	A	A	A	559	43	HDAC4	2	2
HDLBP	3069	broad.mit.edu	37	2	242195624	242195624	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:242195624C>A	uc002waz.2	-	c.848G>T	c.(847-849)CGC>CTC	p.R283L	HDLBP_uc002wba.2_Missense_Mutation_p.R283L|HDLBP_uc002wbb.2_Missense_Mutation_p.R304L|HDLBP_uc010fzn.1_Missense_Mutation_p.R35L	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	283	KH 2.				cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)	3		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)						532				0.184466	37.614059	47.20034	19	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	242195624	242195624	7308	2	C	A	A	A	351	27	HDLBP	1	1
D2HGDH	728294	broad.mit.edu	37	2	242707190	242707190	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:242707190G>T	uc002wce.1	+	c.1372G>T	c.(1372-1374)GAG>TAG	p.E458*	D2HGDH_uc010fzq.1_Nonsense_Mutation_p.E324*|D2HGDH_uc002wcg.1_Non-coding_Transcript|D2HGDH_uc002wch.2_Non-coding_Transcript|D2HGDH_uc002wci.2_Nonsense_Mutation_p.E157*	NM_152783	NP_689996	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase precursor	458					2-oxoglutarate metabolic process|cellular protein metabolic process|oxidation-reduction process|response to cobalt ion|response to manganese ion|response to zinc ion	mitochondrial matrix	(R)-2-hydroxyglutarate dehydrogenase activity|flavin adenine dinucleotide binding|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)										0.191176	21.026098	27.101415	13	55	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	242707190	242707190	4379	2	G	T	T	T	533	41	D2HGDH	5	2
C2orf84	653140	broad.mit.edu	37	2	24406434	24406434	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:24406434C>T	uc002rfc.2	+	c.321C>T	c.(319-321)TTC>TTT	p.F107F	C2orf84_uc010eyc.2_Non-coding_Transcript	NM_001040710	NP_001035800	Q86W67	CB084_HUMAN	hypothetical protein LOC653140	107											0														0.137255	10.187025	16.683876	7	44	KEEP	---	---	---	---	capture		Silent	SNP	24406434	24406434	2291	2	C	T	T	T	376	29	C2orf84	2	2
HADHB	3032	broad.mit.edu	37	2	26502894	26502894	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:26502894C>T	uc002rgz.2	+	c.844C>T	c.(844-846)CGT>TGT	p.R282C	HADHB_uc010ykv.1_Missense_Mutation_p.R260C|HADHB_uc010ykw.1_Missense_Mutation_p.R267C|HADHB_uc002rha.2_Missense_Mutation_p.R159C|HADHB_uc010ykx.1_Missense_Mutation_p.R208C	NM_000183	NP_000174	P55084	ECHB_HUMAN	mitochondrial trifunctional protein, beta	282					fatty acid beta-oxidation	mitochondrial nucleoid	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acyltransferase activity|enoyl-CoA hydratase activity|protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.129252	31.418448	51.093193	19	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26502894	26502894	7226	2	C	T	T	T	299	23	HADHB	1	1
C2orf39	92749	broad.mit.edu	37	2	26644177	26644177	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:26644177T>A	uc002rhg.2	+	c.265T>A	c.(265-267)TGT>AGT	p.C89S	C2orf39_uc010eym.1_Non-coding_Transcript	NM_145038	NP_659475	Q96MC2	CC164_HUMAN	hypothetical protein LOC92749	89											0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.071429	-4.428445	19.42237	9	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26644177	26644177	2252	2	T	A	A	A	715	55	C2orf39	3	3
C2orf18	54978	broad.mit.edu	37	2	27001138	27001138	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27001138G>A	uc002rhp.1	+	c.875G>A	c.(874-876)CGC>CAC	p.R292H	C2orf18_uc002rhq.1_Missense_Mutation_p.R209H|C2orf18_uc010eyo.1_Missense_Mutation_p.R239H|C2orf18_uc010ylc.1_Missense_Mutation_p.R145H	NM_017877	NP_060347	Q8N357	CB018_HUMAN	ANT2-binding protein precursor	292						integral to membrane|lysosomal membrane					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.195652	70.663792	86.602135	36	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27001138	27001138	2244	2	G	A	A	A	494	38	C2orf18	1	1
CENPA	1058	broad.mit.edu	37	2	27016114	27016114	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27016114G>T	uc002rhr.2	+	c.390G>T	c.(388-390)CGG>CGT	p.R130R	CENPA_uc002rht.2_Non-coding_Transcript|CENPA_uc002rhs.2_Silent_p.R104R	NM_001809	NP_001800	P49450	CENPA_HUMAN	centromere protein A isoform a	130	H3-like.				CenH3-containing nucleosome assembly at centromere|establishment of mitotic spindle orientation|interspecies interaction between organisms|kinetochore assembly|mitotic prometaphase|protein localization to chromosome, centromeric region	condensed nuclear chromosome kinetochore|cytosol|nucleoplasm|nucleosome	chromatin binding|DNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					Pancreas(28;769 878 30250 30578 41330)								0.057441	-39.76826	38.985868	22	361	KEEP	---	---	---	---	capture		Silent	SNP	27016114	27016114	3359	2	G	T	T	T	522	41	CENPA	2	2
KHK	3795	broad.mit.edu	37	2	27322123	27322123	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27322123G>C	uc002rin.2	+	c.627G>C	c.(625-627)TTG>TTC	p.L209F	KHK_uc002ril.2_Missense_Mutation_p.L208F|KHK_uc002rim.2_Missense_Mutation_p.L208F|KHK_uc002rio.2_Missense_Mutation_p.L124F|CGREF1_uc010ylf.1_3'UTR|CGREF1_uc002rip.1_3'UTR	NM_000221	NP_000212	P50053	KHK_HUMAN	ketohexokinase isoform a	208					fructose catabolic process	cytosol	ATP binding|ketohexokinase activity|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.167702	68.021989	84.866385	27	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27322123	27322123	8455	2	G	C	C	C	581	45	KHK	3	3
C2orf53	339779	broad.mit.edu	37	2	27360383	27360383	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27360383G>T	uc002rjb.2	-	c.815C>A	c.(814-816)CCC>CAC	p.P272H	PREB_uc002rix.1_5'Flank|PREB_uc002riy.1_5'Flank|PREB_uc002riz.1_5'Flank|PREB_uc002rja.1_5'Flank	NM_178553	NP_848648	Q53SZ7	CB053_HUMAN	hypothetical protein LOC339779	272											0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.123457	11.595273	22.829547	10	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27360383	27360383	2262	2	G	T	T	T	559	43	C2orf53	2	2
PLB1	151056	broad.mit.edu	37	2	28761238	28761238	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:28761238T>A	uc002rmb.1	+	c.608T>A	c.(607-609)CTG>CAG	p.L203Q	PLB1_uc010ezj.1_Missense_Mutation_p.L214Q	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor	203	4 X 308-326 AA approximate repeats.|Extracellular (Potential).|1.				lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|breast(1)	7	Acute lymphoblastic leukemia(172;0.155)													0.104167	4.050417	11.524713	5	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28761238	28761238	12450	2	T	A	A	A	715	55	PLB1	3	3
C2orf71	388939	broad.mit.edu	37	2	29293581	29293581	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:29293581C>T	uc002rmt.1	-	c.3547G>A	c.(3547-3549)GCC>ACC	p.A1183T		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	1183					response to stimulus|visual perception	photoreceptor outer segment					0														0.189873	26.896617	33.992708	15	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29293581	29293581	2279	2	C	T	T	T	325	25	C2orf71	2	2
C2orf71	388939	broad.mit.edu	37	2	29296449	29296449	+	Nonsense_Mutation	SNP	C	A	A	rs114057537	by1000genomes	TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:29296449C>A	uc002rmt.1	-	c.679G>T	c.(679-681)GAG>TAG	p.E227*		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	227					response to stimulus|visual perception	photoreceptor outer segment					0														0.105263	12.750286	42.193661	20	170	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	29296449	29296449	2279	2	C	A	A	A	377	29	C2orf71	5	2
ALK	238	broad.mit.edu	37	2	29416585	29416585	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:29416585G>T	uc002rmy.2	-	c.4368C>A	c.(4366-4368)CCC>CCA	p.P1456P	ALK_uc010ymo.1_Silent_p.P388P	NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	1456	Cytoplasmic (Potential).				protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(191)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(14)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(200)|autonomic_ganglia(95)|soft_tissue(59)|kidney(4)|large_intestine(3)|ovary(3)|central_nervous_system(1)|breast(1)|pancreas(1)	1093	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)					777				0.126214	30.908071	59.00576	26	180	KEEP	---	---	---	---	capture		Silent	SNP	29416585	29416585	528	2	G	T	T	T	600	47	ALK	2	2
CAPN13	92291	broad.mit.edu	37	2	30975918	30975918	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:30975918C>A	uc002rnn.2	-	c.1087_splice	c.e10+1	p.G363_splice	CAPN13_uc002rnp.1_Splice_Site_SNP_p.G363_splice	NM_144575	NP_653176			calpain 13						proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)													0.100503	29.231166	92.658666	40	358	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	30975918	30975918	2743	2	C	A	A	A	234	18	CAPN13	5	2
GALNT14	79623	broad.mit.edu	37	2	31168704	31168704	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:31168704A>T	uc002rns.2	-	c.702T>A	c.(700-702)GAT>GAA	p.D234E	GALNT14_uc002rnq.2_Missense_Mutation_p.D209E|GALNT14_uc002rnr.2_Missense_Mutation_p.D229E|GALNT14_uc010ymr.1_Missense_Mutation_p.D194E|GALNT14_uc010ezo.1_Missense_Mutation_p.D196E|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14	229	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	Acute lymphoblastic leukemia(172;0.155)													0.089888	3.839093	18.939253	8	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31168704	31168704	6476	2	A	T	T	T	206	16	GALNT14	3	3
GALNT14	79623	broad.mit.edu	37	2	31168710	31168710	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:31168710C>A	uc002rns.2	-	c.696G>T	c.(694-696)GTG>GTT	p.V232V	GALNT14_uc002rnq.2_Silent_p.V207V|GALNT14_uc002rnr.2_Silent_p.V227V|GALNT14_uc010ymr.1_Silent_p.V192V|GALNT14_uc010ezo.1_Silent_p.V194V|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14	227	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	Acute lymphoblastic leukemia(172;0.155)													0.223529	40.673227	46.652893	19	66	KEEP	---	---	---	---	capture		Silent	SNP	31168710	31168710	6476	2	C	A	A	A	366	29	GALNT14	2	2
BIRC6	57448	broad.mit.edu	37	2	32640813	32640813	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:32640813G>T	uc010ezu.2	+	c.2454G>T	c.(2452-2454)AGG>AGT	p.R818S		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	818					anti-apoptosis|apoptosis|post-translational protein modification	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					Pancreas(94;175 1509 16028 18060 45422)				1555				0.148148	11.460221	17.882841	8	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32640813	32640813	1463	2	G	T	T	T	529	41	BIRC6	2	2
BIRC6	57448	broad.mit.edu	37	2	32740258	32740258	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:32740258A>T	uc010ezu.2	+	c.10770A>T	c.(10768-10770)TCA>TCT	p.S3590S		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	3590					anti-apoptosis|apoptosis|post-translational protein modification	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					Pancreas(94;175 1509 16028 18060 45422)				1555				0.089552	4.199493	15.592001	6	61	KEEP	---	---	---	---	capture		Silent	SNP	32740258	32740258	1463	2	A	T	T	T	93	8	BIRC6	3	3
COLEC11	78989	broad.mit.edu	37	2	3691447	3691447	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:3691447C>T	uc002qya.2	+	c.555C>T	c.(553-555)GCC>GCT	p.A185A	COLEC11_uc002qxz.2_Silent_p.A182A|COLEC11_uc002qyb.2_Silent_p.A161A|COLEC11_uc002qyc.2_Silent_p.A161A|COLEC11_uc010ewo.2_Silent_p.A137A|COLEC11_uc010ewp.2_Silent_p.A159A|COLEC11_uc010ewq.2_Silent_p.A135A|COLEC11_uc010ewr.2_Silent_p.A135A|COLEC11_uc010ews.2_Silent_p.A111A	NM_024027	NP_076932	Q9BWP8	COL11_HUMAN	collectin sub-family member 11 isoform a	185	C-type lectin.					collagen	mannose binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)										0.138889	6.64793	11.189135	5	31	KEEP	---	---	---	---	capture		Silent	SNP	3691447	3691447	3849	2	C	T	T	T	262	21	COLEC11	2	2
QPCT	25797	broad.mit.edu	37	2	37599510	37599510	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:37599510C>T	uc002rqg.2	+	c.835C>T	c.(835-837)CAT>TAT	p.H279Y	QPCT_uc002rqh.2_Missense_Mutation_p.H230Y	NM_012413	NP_036545	Q16769	QPCT_HUMAN	glutaminyl-peptide cyclotransferase precursor	279					peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase|proteolysis	extracellular region	acyltransferase activity|glutaminyl-peptide cyclotransferase activity|peptidase activity|zinc ion binding			central_nervous_system(1)	1		Ovarian(717;0.051)|all_hematologic(82;0.21)												0.175355	71.334417	92.318248	37	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37599510	37599510	13332	2	C	T	T	T	377	29	QPCT	2	2
CDKL4	344387	broad.mit.edu	37	2	39405784	39405784	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:39405784C>A	uc010fal.1	-	c.1044G>T	c.(1042-1044)CAG>CAT	p.Q348H	CDKL4_uc002rrm.2_3'UTR	NM_001009565	NP_001009565	Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4	Error:Variant_position_missing_in_Q5MAI5_after_alignment					protein phosphorylation	cytoplasm	ATP binding|cyclin-dependent protein kinase activity			ovary(1)	1		all_hematologic(82;0.248)								219				0.321429	22.161602	22.956564	9	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39405784	39405784	3285	2	C	A	A	A	404	32	CDKL4	2	2
KCNG3	170850	broad.mit.edu	37	2	42671100	42671100	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:42671100T>A	uc002rsn.2	-	c.1285A>T	c.(1285-1287)AGC>TGC	p.S429C	KCNG3_uc002rsm.2_Missense_Mutation_p.S418C	NM_133329	NP_579875	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G,	429	Cytoplasmic (Potential).					endoplasmic reticulum|voltage-gated potassium channel complex	protein binding			central_nervous_system(1)	1														0.125	16.298843	30.591551	13	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42671100	42671100	8334	2	T	A	A	A	702	54	KCNG3	3	3
PLEKHH2	130271	broad.mit.edu	37	2	43953436	43953436	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:43953436G>C	uc010yny.1	+	c.2567G>C	c.(2566-2568)TGG>TCG	p.W856S	PLEKHH2_uc002rtf.3_Missense_Mutation_p.W855S	NM_172069	NP_742066	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H	856	PH 2.					cytoplasm|cytoskeleton|integral to membrane	binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)												0.1	8.170235	19.359152	7	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43953436	43953436	12503	2	G	C	C	C	611	47	PLEKHH2	3	3
SLC3A1	6519	broad.mit.edu	37	2	44527217	44527217	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:44527217G>T	uc002ruc.3	+	c.999G>T	c.(997-999)AAG>AAT	p.K333N	SLC3A1_uc002rty.2_Missense_Mutation_p.K333N|SLC3A1_uc002rtz.2_Missense_Mutation_p.K333N|SLC3A1_uc002rua.2_Missense_Mutation_p.K333N|SLC3A1_uc002rub.2_Missense_Mutation_p.K333N|SLC3A1_uc002rud.3_Missense_Mutation_p.K55N	NM_000341	NP_000332	Q07837	SLC31_HUMAN	solute carrier family 3, member 1	333	Extracellular (Potential).				carbohydrate metabolic process|cellular amino acid metabolic process|ion transport	integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity|catalytic activity|cation binding|L-cystine transmembrane transporter activity				0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)									0.163265	25.83046	36.398312	16	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44527217	44527217	15123	2	G	T	T	T	425	33	SLC3A1	2	2
FBXO11	80204	broad.mit.edu	37	2	48059590	48059590	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:48059590C>A	uc010fbl.2	-	c.1044G>T	c.(1042-1044)GCG>GCT	p.A348A	FBXO11_uc002rwe.2_Silent_p.A348A|FBXO11_uc002rwf.2_Silent_p.A348A|FBXO11_uc002rwg.1_Silent_p.A348A|FBXO11_uc010fbk.2_5'UTR	NM_025133	NP_079409	Q86XK2	FBX11_HUMAN	F-box only protein 11 isoform 1	432	PbH1 2.				ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|ubiquitin ligase complex	protein binding|protein-arginine N-methyltransferase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)							2				0.163934	21.710932	28.253759	10	51	KEEP	---	---	---	---	capture		Silent	SNP	48059590	48059590	5964	2	C	A	A	A	236	19	FBXO11	1	1
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48896865	48896865	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:48896865C>T	uc002rwp.1	+	c.3095C>T	c.(3094-3096)TCT>TTT	p.S1032F	STON1-GTF2A1L_uc010yol.1_Missense_Mutation_p.S985F|GTF2A1L_uc002rws.1_Missense_Mutation_p.S328F|GTF2A1L_uc010yom.1_Missense_Mutation_p.S294F|GTF2A1L_uc002rwt.2_Missense_Mutation_p.S328F	NM_172311	NP_758515	B7ZL16	B7ZL16_HUMAN	STON1-GTF2A1L protein	985					endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex	RNA polymerase II transcription factor activity			ovary(3)|pancreas(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)											0.092025	7.589808	34.918616	15	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48896865	48896865	15837	2	C	T	T	T	416	32	STON1-GTF2A1L	2	2
FSHR	2492	broad.mit.edu	37	2	49190600	49190600	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:49190600C>A	uc002rww.2	-	c.1360G>T	c.(1360-1362)GAG>TAG	p.E454*	FSHR_uc002rwx.2_Nonsense_Mutation_p.E392*|FSHR_uc010fbn.2_Nonsense_Mutation_p.E428*	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	454	Helical; Name=3; (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)	4		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									0.134328	10.418301	19.130288	9	58	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	49190600	49190600	6324	2	C	A	A	A	377	29	FSHR	5	2
NRXN1	9378	broad.mit.edu	37	2	50149359	50149359	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:50149359G>T	uc010fbq.2	-	c.4367C>A	c.(4366-4368)CCG>CAG	p.P1456Q	NRXN1_uc010fbp.2_Missense_Mutation_p.P351Q|NRXN1_uc002rxb.3_Missense_Mutation_p.P1085Q|NRXN1_uc002rxe.3_Missense_Mutation_p.P1386Q|NRXN1_uc010yon.1_Missense_Mutation_p.P51Q|NRXN1_uc002rxa.3_Missense_Mutation_p.P48Q	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	351	Extracellular (Potential).				neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)											0.150943	14.565562	20.752047	8	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50149359	50149359	11070	2	G	T	T	T	507	39	NRXN1	1	1
NRXN1	9378	broad.mit.edu	37	2	50847255	50847255	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:50847255C>A	uc010fbq.2	-	c.1345G>T	c.(1345-1347)GGG>TGG	p.G449W	NRXN1_uc002rxb.3_Missense_Mutation_p.G81W|NRXN1_uc002rxe.3_Missense_Mutation_p.G409W|NRXN1_uc002rxc.1_Non-coding_Transcript	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	Error:Variant_position_missing_in_P58400_after_alignment					neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)											0.117647	3.071925	7.965994	4	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50847255	50847255	11070	2	C	A	A	A	286	22	NRXN1	2	2
PSME4	23198	broad.mit.edu	37	2	54125016	54125016	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:54125016T>A	uc002rxp.2	-	c.3597A>T	c.(3595-3597)GTA>GTT	p.V1199V	PSME4_uc010yop.1_Silent_p.V1085V|PSME4_uc010yoq.1_Non-coding_Transcript|PSME4_uc010fbu.1_Silent_p.V574V|PSME4_uc010fbv.1_Silent_p.V343V	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator	1199	HEAT 3.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)											0.24359	93.273933	102.621159	38	118	KEEP	---	---	---	---	capture		Silent	SNP	54125016	54125016	13162	2	T	A	A	A	678	53	PSME4	3	3
C2orf86	51057	broad.mit.edu	37	2	63401863	63401863	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:63401863A>T	uc002sch.2	-	c.2020T>A	c.(2020-2022)TCT>ACT	p.S674T	C2orf86_uc002sce.2_Non-coding_Transcript|C2orf86_uc002scf.2_Missense_Mutation_p.S515T|C2orf86_uc010ypu.1_Non-coding_Transcript|C2orf86_uc002scg.2_Missense_Mutation_p.S482T	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2	674					cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0														0.104478	9.647118	30.506932	14	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63401863	63401863	2293	2	A	T	T	T	143	11	C2orf86	3	3
MEIS1	4211	broad.mit.edu	37	2	66670112	66670112	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:66670112G>T	uc002sdv.2	+	c.556G>T	c.(556-558)GAC>TAC	p.D186Y	MEIS1_uc002sdt.2_Missense_Mutation_p.D188Y|MEIS1_uc002sdu.2_Missense_Mutation_p.D188Y|MEIS1_uc010yqh.1_Non-coding_Transcript|MEIS1_uc010yqi.1_Missense_Mutation_p.D123Y|MEIS1_uc002sdw.1_Missense_Mutation_p.D44Y	NM_002398	NP_002389	O00470	MEIS1_HUMAN	Meis homeobox 1	188					regulation of transcription, DNA-dependent		RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity				0														0.23913	119.690425	134.000086	55	175	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66670112	66670112	9856	2	G	T	T	T	429	33	MEIS1	2	2
PPP3R1	5534	broad.mit.edu	37	2	68415748	68415748	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:68415748C>A	uc002sei.1	-	c.118G>T	c.(118-120)GTG>TTG	p.V40L		NM_000945	NP_000936	P63098	CANB1_HUMAN	protein phosphatase 3, regulatory subunit B,	40	EF-hand 1.|1.				activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	calcineurin complex|cytosol	calcium ion binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding				0					Pimecrolimus(DB00337)					75				0.129032	15.956254	28.402813	12	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68415748	68415748	12836	2	C	A	A	A	221	17	PPP3R1	2	2
AAK1	22848	broad.mit.edu	37	2	69706164	69706164	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:69706164C>A	uc002sfp.2	-	c.2599G>T	c.(2599-2601)GAT>TAT	p.D867Y		NM_014911	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	867					protein phosphorylation	coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0										752				0.075862	-4.199785	22.549497	11	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69706164	69706164	17	2	C	A	A	A	377	29	AAK1	2	2
PCBP1	5093	broad.mit.edu	37	2	70315923	70315923	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:70315923G>C	uc002sgf.2	+	c.1048G>C	c.(1048-1050)GAG>CAG	p.E350Q	ASPRV1_uc002sga.2_5'Flank	NM_006196	NP_006187	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	350					nuclear mRNA splicing, via spliceosome	cytoplasm|nucleoplasm|ribonucleoprotein complex	protein binding|RNA binding|single-stranded DNA binding				0						Colon(85;1146 1307 3484 18706 25380)								0.1	8.202618	17.792819	6	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70315923	70315923	11920	2	G	C	C	C	585	45	PCBP1	3	3
ATP6V1B1	525	broad.mit.edu	37	2	71190322	71190322	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:71190322C>A	uc002shj.2	+	c.940C>A	c.(940-942)CGC>AGC	p.R314S	ATP6V1B1_uc010fdv.2_Missense_Mutation_p.R314S|ATP6V1B1_uc010fdw.2_Non-coding_Transcript|ATP6V1B1_uc010fdx.2_Missense_Mutation_p.R272S	NM_001692	NP_001683	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1	314					ATP hydrolysis coupled proton transport|calcium ion homeostasis|cellular iron ion homeostasis|excretion|inner ear morphogenesis|insulin receptor signaling pathway|ossification|pH reduction|sensory perception of sound|transferrin transport	apical plasma membrane|basolateral plasma membrane|cytosol|endomembrane system|lateral plasma membrane|microvillus|proton-transporting V-type ATPase, V1 domain|vacuolar proton-transporting V-type ATPase complex	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism				0														0.180851	70.182781	88.073786	34	154	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71190322	71190322	1197	2	C	A	A	A	351	27	ATP6V1B1	1	1
CYP26B1	56603	broad.mit.edu	37	2	72359460	72359460	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:72359460C>T	uc002sih.1	-	c.1435G>A	c.(1435-1437)GTC>ATC	p.V479I	CYP26B1_uc010yra.1_Missense_Mutation_p.V462I|CYP26B1_uc010yrb.1_Missense_Mutation_p.V404I	NM_019885	NP_063938	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily b,	479			V -> I.		cell fate determination|embryonic limb morphogenesis|male meiosis|negative regulation of retinoic acid receptor signaling pathway|oxidation-reduction process|proximal/distal pattern formation|retinoic acid catabolic process|spermatogenesis|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity|retinoic acid binding				0														0.290323	20.251212	21.480509	9	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72359460	72359460	4321	2	C	T	T	T	247	19	CYP26B1	1	1
ALMS1	7840	broad.mit.edu	37	2	73799562	73799562	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:73799562G>T	uc002sje.1	+	c.10561G>T	c.(10561-10563)GAC>TAC	p.D3521Y	ALMS1_uc002sjf.1_Missense_Mutation_p.D3477Y|ALMS1_uc002sjg.2_Missense_Mutation_p.D2907Y|ALMS1_uc002sjh.1_Missense_Mutation_p.D2907Y	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3519					G2/M transition of mitotic cell cycle|visual perception	centrosome|cilium|cytosol|microtubule basal body|spindle pole				ovary(2)|breast(2)|lung(1)|pancreas(1)	6														0.352941	62.775395	64.073976	24	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73799562	73799562	538	2	G	T	T	T	429	33	ALMS1	2	2
ALMS1	7840	broad.mit.edu	37	2	73800051	73800051	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:73800051G>C	uc002sje.1	+	c.11050G>C	c.(11050-11052)GAG>CAG	p.E3684Q	ALMS1_uc002sjf.1_Missense_Mutation_p.E3640Q|ALMS1_uc002sjg.2_Missense_Mutation_p.E3070Q|ALMS1_uc002sjh.1_Missense_Mutation_p.E3070Q	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3682					G2/M transition of mitotic cell cycle|visual perception	centrosome|cilium|cytosol|microtubule basal body|spindle pole				ovary(2)|breast(2)|lung(1)|pancreas(1)	6														0.152381	34.728485	46.873911	16	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73800051	73800051	538	2	G	C	C	C	429	33	ALMS1	3	3
ACTG2	72	broad.mit.edu	37	2	74140716	74140716	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74140716C>A	uc002sjw.2	+	c.556C>A	c.(556-558)CTC>ATC	p.L186I	ACTG2_uc010fey.2_Missense_Mutation_p.L186I|ACTG2_uc010yrn.1_Missense_Mutation_p.L143I	NM_001615	NP_001606	P63267	ACTH_HUMAN	actin, gamma 2 propeptide	186					muscle contraction	cytoskeleton|cytosol	ATP binding				0														0.102941	5.434672	26.847754	14	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74140716	74140716	198	2	C	A	A	A	312	24	ACTG2	2	2
TET3	200424	broad.mit.edu	37	2	74328907	74328907	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74328907C>A	uc002skb.3	+	c.4587C>A	c.(4585-4587)CTC>CTA	p.L1529L		NM_144993	NP_659430	O43151	TET3_HUMAN	tet oncogene family member 3	1529					oxidation-reduction process		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0														0.130952	14.163021	25.292142	11	73	KEEP	---	---	---	---	capture		Silent	SNP	74328907	74328907	16298	2	C	A	A	A	366	29	TET3	2	2
C2orf3	6936	broad.mit.edu	37	2	75928379	75928379	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:75928379C>A	uc002sno.2	-	c.654G>T	c.(652-654)CAG>CAT	p.Q218H	C2orf3_uc010ffs.2_De_novo_Start_OutOfFrame|C2orf3_uc002snn.2_Missense_Mutation_p.Q49H|C2orf3_uc010fft.2_De_novo_Start_InFrame	NM_003203	NP_003194	P16383	GCF_HUMAN	hypothetical protein LOC6936	218					regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			ovary(1)|central_nervous_system(1)	2						Esophageal Squamous(141;1502 1784 15043 37622 47064)								0.142857	10.889153	16.914773	7	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75928379	75928379	2250	2	C	A	A	A	311	24	C2orf3	2	2
LRRTM4	80059	broad.mit.edu	37	2	77746569	77746569	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:77746569G>T	uc002snr.2	-	c.426C>A	c.(424-426)TAC>TAA	p.Y142*	LRRTM4_uc002snq.2_Nonsense_Mutation_p.Y142*|LRRTM4_uc002sns.2_Nonsense_Mutation_p.Y142*|LRRTM4_uc002snt.2_Nonsense_Mutation_p.Y143*	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	142	LRR 4.|Extracellular (Potential).					integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)										0.30303	56.372422	58.659364	20	46	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	77746569	77746569	9418	2	G	T	T	T	620	48	LRRTM4	5	2
DNAH6	1768	broad.mit.edu	37	2	84784942	84784942	+	Silent	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:84784942T>G	uc010fgb.2	+	c.1686T>G	c.(1684-1686)GCT>GCG	p.A562A	DNAH6_uc002soo.2_Silent_p.A141A|DNAH6_uc002sop.2_Silent_p.A141A	NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy polypeptide 6	562	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1														0.097015	22.669387	66.254425	26	242	KEEP	---	---	---	---	capture		Silent	SNP	84784942	84784942	4788	2	T	G	G	G	717	56	DNAH6	4	4
DNAH6	1768	broad.mit.edu	37	2	84784945	84784945	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:84784945C>T	uc010fgb.2	+	c.1689C>T	c.(1687-1689)TTC>TTT	p.F563F	DNAH6_uc002soo.2_Silent_p.F142F|DNAH6_uc002sop.2_Silent_p.F142F	NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy polypeptide 6	563	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1														0.092593	4.747983	49.887126	25	245	KEEP	---	---	---	---	capture		Silent	SNP	84784945	84784945	4788	2	C	T	T	T	376	29	DNAH6	2	2
ELMOD3	84173	broad.mit.edu	37	2	85590289	85590290	+	Splice_Site_DNP	DNP	GG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:85590289_85590290GG>TT	uc010ysn.1	+	c.199_splice	c.e4+1	p.V67_splice	ELMOD3_uc010fgg.2_Intron|ELMOD3_uc002spf.3_Splice_Site_DNP_p.V67_splice|ELMOD3_uc002spg.3_Splice_Site_DNP_p.V67_splice|ELMOD3_uc002sph.3_Splice_Site_DNP_p.V67_splice|ELMOD3_uc010yso.1_Splice_Site_DNP|ELMOD3_uc010ysp.1_Splice_Site_DNP	NM_032213	NP_115589			ELMO/CED-12 domain containing 3 isoform a						phagocytosis	cytoskeleton				ovary(2)	2														0.170213	16.467737	21.309248	8	39	KEEP	---	---	---	---	capture		Splice_Site_DNP	DNP	85590289	85590290	5262	2	GG	TT	TT	TT	611	47	ELMOD3	5	2
CD8B	926	broad.mit.edu	37	2	87085311	87085311	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:87085311G>T	uc002ssa.2	-	c.272C>A	c.(271-273)GCT>GAT	p.A91D	RMND5A_uc002srs.3_Intron|CD8B_uc002srw.2_Missense_Mutation_p.A91D|CD8B_uc002srx.2_Missense_Mutation_p.A91D|CD8B_uc002sry.2_Missense_Mutation_p.A91D|CD8B_uc010fgt.2_Missense_Mutation_p.A91D|CD8B_uc002srz.2_Missense_Mutation_p.A91D|CD8B_uc010yto.1_Missense_Mutation_p.A91D	NM_172099	NP_742097	P10966	CD8B_HUMAN	CD8b antigen isoform 1 precursor	91	Ig-like V-type.|Extracellular (Potential).				immune response|regulation of defense response to virus by virus|regulation of immune response|T cell activation|transmembrane receptor protein tyrosine kinase signaling pathway|viral reproduction	early endosome|extracellular region|integral to plasma membrane|T cell receptor complex	coreceptor activity|MHC class I protein binding				0														0.076142	-3.518756	32.736761	15	182	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87085311	87085311	3173	2	G	T	T	T	442	34	CD8B	2	2
SMYD1	150572	broad.mit.edu	37	2	88409926	88409926	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:88409926C>A	uc002ssr.2	+	c.1368C>A	c.(1366-1368)TTC>TTA	p.F456L	SMYD1_uc002ssq.1_Intron|SMYD1_uc002sss.2_Missense_Mutation_p.F152L	NM_198274	NP_938015	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	456					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3														0.130435	6.213385	12.333762	6	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88409926	88409926	15321	2	C	A	A	A	376	29	SMYD1	2	2
MRPS5	64969	broad.mit.edu	37	2	95774150	95774150	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:95774150C>A	uc002sub.2	-	c.407G>T	c.(406-408)CGT>CTT	p.R136L	MRPS5_uc002suc.2_Non-coding_Transcript|MRPS5_uc010yud.1_Missense_Mutation_p.R136L	NM_031902	NP_114108	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	136					translation	mitochondrion|ribosome	protein binding|RNA binding|structural constituent of ribosome			ovary(2)|central_nervous_system(1)	3														0.232323	60.476351	66.97039	23	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95774150	95774150	10239	2	C	A	A	A	247	19	MRPS5	1	1
ADRA2B	151	broad.mit.edu	37	2	96781416	96781416	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:96781416G>T	uc002svi.2	-	c.473C>A	c.(472-474)CCG>CAG	p.P158Q		NM_000682	NP_000673	P18089	ADA2B_HUMAN	alpha-2B-adrenergic receptor	158	Extracellular (By similarity).				activation of MAPK activity by adrenergic receptor signaling pathway|activation of protein kinase B activity|blood coagulation|cell-cell signaling|epidermal growth factor receptor transactivation by G-protein coupled receptor signaling pathway|negative regulation of epinephrine secretion|negative regulation of norepinephrine secretion|positive regulation of neuron differentiation	integral to plasma membrane	alpha2-adrenergic receptor activity|epinephrine binding|protein binding			ovary(2)|lung(1)	3					Bethanidine(DB00217)|Brimonidine(DB00484)|Debrisoquin(DB04840)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Lofexidine(DB04948)|Norepinephrine(DB00368)|Yohimbine(DB01392)									0.176471	24.362748	31.067229	12	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	96781416	96781416	339	2	G	T	T	T	507	39	ADRA2B	1	1
CNGA3	1261	broad.mit.edu	37	2	98996642	98996642	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:98996642T>C	uc002syt.2	+	c.220T>C	c.(220-222)TCG>CCG	p.S74P	CNGA3_uc002syu.2_Missense_Mutation_p.S74P|CNGA3_uc010fij.2_Missense_Mutation_p.S78P	NM_001298	NP_001289	Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3 isoform	74					signal transduction|visual perception	integral to membrane	cGMP binding			ovary(5)	5														0.201754	59.373166	68.785215	23	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98996642	98996642	3736	2	T	C	C	C	754	58	CNGA3	4	4
INPP4A	3631	broad.mit.edu	37	2	99169339	99169339	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:99169339C>T	uc002syy.2	+	c.1269C>T	c.(1267-1269)ACC>ACT	p.T423T	INPP4A_uc010yvj.1_Silent_p.T423T|INPP4A_uc010yvk.1_Silent_p.T423T|INPP4A_uc002syx.2_Silent_p.T418T|INPP4A_uc010fik.2_Intron	NM_001134224	NP_001127696	Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type 1	423					signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1														0.255814	26.596898	28.929487	11	32	KEEP	---	---	---	---	capture		Silent	SNP	99169339	99169339	8053	2	C	T	T	T	275	22	INPP4A	2	2
C2orf55	343990	broad.mit.edu	37	2	99413910	99413910	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:99413910C>A	uc002szf.1	-	c.2507G>T	c.(2506-2508)GGG>GTG	p.G836V		NM_207362	NP_997245	Q6NV74	CB055_HUMAN	hypothetical protein LOC343990	836											0														0.147059	31.991251	56.484935	30	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99413910	99413910	2264	2	C	A	A	A	286	22	C2orf55	2	2
ATP2B2	491	broad.mit.edu	37	3	10391822	10391822	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:10391822G>A	uc003bvt.2	-	c.2378C>T	c.(2377-2379)CCA>CTA	p.P793L	ATP2B2_uc003bvv.2_Missense_Mutation_p.P748L|ATP2B2_uc003bvw.2_Missense_Mutation_p.P748L|ATP2B2_uc010hdo.2_Missense_Mutation_p.P498L	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1	793	Cytoplasmic (Potential).				ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|central_nervous_system(1)	4						Ovarian(125;1619 1709 15675 19819 38835)								0.2	14.972064	18.326413	8	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10391822	10391822	1159	3	G	A	A	A	611	47	ATP2B2	2	2
CD200R1	131450	broad.mit.edu	37	3	112643989	112643989	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:112643989G>T	uc003dzj.1	-	c.821C>A	c.(820-822)ACT>AAT	p.T274N	CD200R1_uc003dzk.1_Missense_Mutation_p.T251N|CD200R1_uc011bhx.1_Intron	NM_138806	NP_620161	Q8TD46	MO2R1_HUMAN	CD200 receptor 1 isoform a	251	Helical; (Potential).				interspecies interaction between organisms|regulation of immune response	extracellular region|integral to membrane|plasma membrane	receptor activity			ovary(2)|pancreas(1)	3														0.166667	6.812873	8.709478	3	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112643989	112643989	3108	3	G	T	T	T	468	36	CD200R1	2	2
BOC	91653	broad.mit.edu	37	3	112989746	112989746	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:112989746C>A	uc003dzz.2	+	c.622C>A	c.(622-624)CAG>AAG	p.Q208K	BOC_uc003dzx.2_Missense_Mutation_p.Q208K|BOC_uc010hqi.2_Missense_Mutation_p.Q208K|BOC_uc003dzy.2_Missense_Mutation_p.Q208K|BOC_uc003eab.2_5'UTR	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	208	Extracellular (Potential).|Ig-like C2-type 2.				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)											0.125	42.105864	77.29282	32	224	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112989746	112989746	1506	3	C	A	A	A	273	21	BOC	2	2
BOC	91653	broad.mit.edu	37	3	112991432	112991432	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:112991432G>A	uc003dzz.2	+	c.843G>A	c.(841-843)CTG>CTA	p.L281L	BOC_uc003dzx.2_Silent_p.L281L|BOC_uc003dzy.2_Silent_p.L281L|BOC_uc003eab.2_5'UTR	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	281	Ig-like C2-type 3.|Extracellular (Potential).				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)											0.091787	6.286728	41.016168	19	188	KEEP	---	---	---	---	capture		Silent	SNP	112991432	112991432	1506	3	G	A	A	A	574	45	BOC	2	2
C3orf30	152405	broad.mit.edu	37	3	118865608	118865608	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:118865608C>A	uc003ecb.1	+	c.572C>A	c.(571-573)TCC>TAC	p.S191Y	IGSF11_uc003eby.2_5'Flank|IGSF11_uc003ebz.2_5'Flank|IGSF11_uc010hqs.2_5'Flank|C3orf30_uc011biw.1_Missense_Mutation_p.S191Y	NM_152539	NP_689752	Q96M34	CC030_HUMAN	hypothetical protein LOC152405	191										ovary(2)	2				GBM - Glioblastoma multiforme(114;0.222)										0.126761	17.764153	37.066249	18	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118865608	118865608	2313	3	C	A	A	A	390	30	C3orf30	2	2
PARP15	165631	broad.mit.edu	37	3	122340333	122340333	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:122340333G>T	uc003efm.2	+	c.1106G>T	c.(1105-1107)TGC>TTC	p.C369F	PARP15_uc003efn.2_Missense_Mutation_p.C243F|PARP15_uc003efo.1_Missense_Mutation_p.C116F|PARP15_uc003efp.1_Missense_Mutation_p.C135F|PARP15_uc011bjt.1_Missense_Mutation_p.C135F	NM_001113523	NP_001106995	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	347	Macro 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	NAD+ ADP-ribosyltransferase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0531)										0.129944	31.494655	55.089573	23	154	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122340333	122340333	11876	3	G	T	T	T	598	46	PARP15	2	2
MYLK	4638	broad.mit.edu	37	3	123452994	123452994	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:123452994C>A	uc003ego.2	-	c.849G>T	c.(847-849)TCG>TCT	p.S283S	MYLK_uc011bjw.1_Silent_p.S283S|MYLK_uc003egp.2_Silent_p.S283S|MYLK_uc003egq.2_Silent_p.S283S|MYLK_uc003egr.2_Silent_p.S283S|MYLK_uc003egs.2_Silent_p.S107S	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	283					aorta smooth muscle tissue morphogenesis|muscle contraction|protein phosphorylation	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)	6		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)						766				0.135417	15.703998	28.08312	13	83	KEEP	---	---	---	---	capture		Silent	SNP	123452994	123452994	10451	3	C	A	A	A	392	31	MYLK	1	1
MYLK	4638	broad.mit.edu	37	3	123456333	123456333	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:123456333G>T	uc003ego.2	-	c.646C>A	c.(646-648)CAG>AAG	p.Q216K	MYLK_uc011bjw.1_Missense_Mutation_p.Q216K|MYLK_uc003egp.2_Missense_Mutation_p.Q216K|MYLK_uc003egq.2_Missense_Mutation_p.Q216K|MYLK_uc003egr.2_Missense_Mutation_p.Q216K|MYLK_uc003egs.2_Missense_Mutation_p.Q40K|MYLK_uc010hrs.1_Missense_Mutation_p.Q216K	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	216	Ig-like C2-type 2.				aorta smooth muscle tissue morphogenesis|muscle contraction|protein phosphorylation	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)	6		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)						766				0.098113	15.645359	58.489993	26	239	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123456333	123456333	10451	3	G	T	T	T	598	46	MYLK	2	2
ITGB5	3693	broad.mit.edu	37	3	124492670	124492670	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:124492670G>A	uc003eho.2	-	c.1783C>T	c.(1783-1785)CGG>TGG	p.R595W	ITGB5_uc010hrx.2_Non-coding_Transcript|ITGB5_uc003ehp.1_Non-coding_Transcript	NM_002213	NP_002204	P18084	ITB5_HUMAN	integrin, beta 5 precursor	595	IV.|Extracellular (Potential).|Cysteine-rich tandem repeats.				cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|muscle contraction	integrin complex	receptor activity			skin(1)	1				GBM - Glioblastoma multiforme(114;0.163)										0.197917	41.875084	50.02873	19	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124492670	124492670	8202	3	G	A	A	A	506	39	ITGB5	1	1
SLC12A8	84561	broad.mit.edu	37	3	124829095	124829095	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:124829095G>A	uc003ehw.3	-	c.1084C>T	c.(1084-1086)CGC>TGC	p.R362C	SLC12A8_uc003ehv.3_Missense_Mutation_p.R333C|SLC12A8_uc003eht.3_Missense_Mutation_p.R134C|SLC12A8_uc003ehu.3_Missense_Mutation_p.R86C|SLC12A8_uc010hry.2_Missense_Mutation_p.R86C	NM_024628	NP_078904	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	333					potassium ion transport	integral to membrane	symporter activity				0														0.116788	21.022511	40.795158	16	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124829095	124829095	14884	3	G	A	A	A	507	39	SLC12A8	1	1
TSEN2	80746	broad.mit.edu	37	3	12545147	12545147	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:12545147G>T	uc003bxc.2	+	c.695G>T	c.(694-696)CGT>CTT	p.R232L	TSEN2_uc003bwy.2_Missense_Mutation_p.R232L|TSEN2_uc003bwz.2_Missense_Mutation_p.R173L|TSEN2_uc003bxa.2_Missense_Mutation_p.R232L|TSEN2_uc011auq.1_Missense_Mutation_p.R232L|TSEN2_uc003bxb.2_Missense_Mutation_p.R232L|TSEN2_uc011aur.1_Missense_Mutation_p.R141L	NM_025265	NP_079541	Q8NCE0	SEN2_HUMAN	tRNA-intron nuclease 2 isoform 1	232					mRNA processing|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|nucleolus|tRNA-intron endonuclease complex	nucleic acid binding|tRNA-intron endonuclease activity			central_nervous_system(1)	1														0.263158	23.82384	25.760039	10	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12545147	12545147	17163	3	G	T	T	T	520	40	TSEN2	1	1
ALDH1L1	10840	broad.mit.edu	37	3	125877313	125877313	+	Silent	SNP	C	A	A	rs113434283		TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:125877313C>A	uc003eim.1	-	c.297G>T	c.(295-297)CGG>CGT	p.R99R	ALDH1L1_uc010hse.1_Non-coding_Transcript|ALDH1L1_uc011bki.1_Silent_p.R99R|ALDH1L1_uc003eio.2_5'Flank|ALDH1L1_uc010hsf.1_Silent_p.R125R|ALDH1L1_uc003eip.1_Silent_p.R8R|ALDH1L1_uc011bkj.1_Intron	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	99	GART.				10-formyltetrahydrofolate catabolic process|biosynthetic process|oxidation-reduction process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)									0.102041	3.335544	11.076093	5	44	KEEP	---	---	---	---	capture		Silent	SNP	125877313	125877313	497	3	C	A	A	A	327	26	ALDH1L1	2	2
MCM2	4171	broad.mit.edu	37	3	127336223	127336223	+	Silent	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:127336223G>C	uc003ejp.2	+	c.1875G>C	c.(1873-1875)ACG>ACC	p.T625T	MCM2_uc011bkm.1_Silent_p.T495T|MCM2_uc010hsl.2_Non-coding_Transcript|MCM2_uc011bkn.1_Silent_p.T578T	NM_004526	NP_004517	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	625	MCM.				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|helicase activity|metal ion binding			ovary(3)|skin(1)	4														0.166667	9.891757	14.330549	7	35	KEEP	---	---	---	---	capture		Silent	SNP	127336223	127336223	9775	3	G	C	C	C	496	39	MCM2	3	3
COL6A6	131873	broad.mit.edu	37	3	130282042	130282042	+	Silent	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:130282042T>C	uc010htl.2	+	c.195T>C	c.(193-195)CGT>CGC	p.R65R		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	65	Nonhelical region.|VWFA 1.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8														0.147651	36.451877	54.216763	22	127	KEEP	---	---	---	---	capture		Silent	SNP	130282042	130282042	3841	3	T	C	C	C	756	59	COL6A6	4	4
ACAD11	84129	broad.mit.edu	37	3	132360962	132360962	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:132360962C>T	uc003eov.3	-	c.391G>A	c.(391-393)GAT>AAT	p.D131N	ACAD11_uc003eoy.2_Missense_Mutation_p.D131N	NM_032169	NP_115545	Q709F0	ACD11_HUMAN	putative acyl-CoA dehydrogenase	131					oxidation-reduction process	peroxisome	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding			ovary(1)	1														0.11236	7.678888	20.896232	10	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132360962	132360962	110	3	C	T	T	T	377	29	ACAD11	2	2
EPHB1	2047	broad.mit.edu	37	3	134898709	134898709	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:134898709A>T	uc003eqt.2	+	c.1767A>T	c.(1765-1767)CCA>CCT	p.P589P	EPHB1_uc003equ.2_Silent_p.P150P	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	589	Cytoplasmic (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(7)|ovary(4)|stomach(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	18										376				0.12	37.350447	72.834342	30	220	KEEP	---	---	---	---	capture		Silent	SNP	134898709	134898709	5367	3	A	T	T	T	80	7	EPHB1	3	3
EPHB1	2047	broad.mit.edu	37	3	134920489	134920489	+	Nonsense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:134920489C>G	uc003eqt.2	+	c.2304C>G	c.(2302-2304)TAC>TAG	p.Y768*	EPHB1_uc003equ.2_Nonsense_Mutation_p.Y329*	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	768	Cytoplasmic (Potential).|Protein kinase.				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(7)|ovary(4)|stomach(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	18										376				0.106796	14.827271	30.563656	11	92	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	134920489	134920489	5367	3	C	G	G	G	233	18	EPHB1	5	3
WNT7A	7476	broad.mit.edu	37	3	13896298	13896298	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:13896298T>A	uc003bye.1	-	c.301A>T	c.(301-303)AGC>TGC	p.S101C		NM_004625	NP_004616	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family,	101					activation of JUN kinase activity|anterior/posterior pattern formation|canonical Wnt receptor signaling pathway|cell proliferation in forebrain|cellular response to transforming growth factor beta stimulus|central nervous system vasculogenesis|cerebellar granule cell differentiation|dorsal/ventral pattern formation|embryonic axis specification|embryonic digit morphogenesis|embryonic forelimb morphogenesis|embryonic leg morphogenesis|lens fiber cell development|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of neurogenesis|palate development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of JNK cascade|positive regulation of synaptogenesis|regulation of axon diameter|satellite cell activation|satellite cell maintenance involved in skeletal muscle regeneration|sex differentiation|uterus development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	cytokine activity|frizzled binding|receptor agonist activity|signal transducer activity			ovary(2)	2														0.171429	27.898809	38.61013	18	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13896298	13896298	17968	3	T	A	A	A	702	54	WNT7A	3	3
CLSTN2	64084	broad.mit.edu	37	3	140284952	140284952	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:140284952G>A	uc003etn.2	+	c.2725G>A	c.(2725-2727)GCC>ACC	p.A909T		NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	909	Glu-rich (highly acidic).|Cytoplasmic (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						GBM(45;858 913 3709 36904 37282)								0.098592	4.865991	16.318769	7	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140284952	140284952	3700	3	G	A	A	A	442	34	CLSTN2	2	2
TRIM42	287015	broad.mit.edu	37	3	140397271	140397271	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:140397271G>T	uc003eto.1	+	c.200G>T	c.(199-201)TGC>TTC	p.C67F		NM_152616	NP_689829	Q8IWZ5	TRI42_HUMAN	tripartite motif-containing 42	67	Cys-rich.					intracellular	zinc ion binding			lung(2)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)|skin(1)	6										261				0.129252	24.414071	44.097586	19	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140397271	140397271	17061	3	G	T	T	T	598	46	TRIM42	2	2
GRIP2	80852	broad.mit.edu	37	3	14547155	14547155	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:14547155C>T	uc011avi.1	-	c.2835G>A	c.(2833-2835)GAG>GAA	p.E945E	GRIP2_uc010heh.2_Non-coding_Transcript|GRIP2_uc011avh.1_Silent_p.E476E	NM_001080423	NP_001073892	Q9C0E4	GRIP2_HUMAN	glutamate receptor interacting protein 2	847					synaptic transmission	cytosol|plasma membrane	protein binding			pancreas(1)	1														0.25	9.99157	10.901139	4	12	KEEP	---	---	---	---	capture		Silent	SNP	14547155	14547155	7067	3	C	T	T	T	311	24	GRIP2	2	2
HLTF	6596	broad.mit.edu	37	3	148759310	148759310	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:148759310T>A	uc003ewq.1	-	c.2343A>T	c.(2341-2343)AAA>AAT	p.K781N	HLTF_uc003ewr.1_Missense_Mutation_p.K781N|HLTF_uc003ews.1_Missense_Mutation_p.K780N|HLTF_uc010hve.1_Missense_Mutation_p.K780N	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor	781	RING-type.				chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding				0			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)											0.178571	31.378744	39.543515	15	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148759310	148759310	7506	3	T	A	A	A	777	60	HLTF	3	3
HLTF	6596	broad.mit.edu	37	3	148791089	148791089	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:148791089T>A	uc003ewq.1	-	c.550A>T	c.(550-552)AGT>TGT	p.S184C	HLTF_uc003ewr.1_Missense_Mutation_p.S184C|HLTF_uc003ews.1_Missense_Mutation_p.S184C|HLTF_uc010hve.1_Missense_Mutation_p.S184C	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor	184					chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding				0			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)											0.123077	9.352337	18.39173	8	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148791089	148791089	7506	3	T	A	A	A	728	56	HLTF	3	3
IGSF10	285313	broad.mit.edu	37	3	151163172	151163172	+	Nonsense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:151163172T>A	uc011bod.1	-	c.4597A>T	c.(4597-4599)AAG>TAG	p.K1533*		NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	1533					cell differentiation|multicellular organismal development|ossification	extracellular region				ovary(4)|central_nervous_system(1)	5			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)											0.110266	29.193092	68.715407	29	234	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	151163172	151163172	7898	3	T	A	A	A	819	63	IGSF10	5	3
SI	6476	broad.mit.edu	37	3	164730802	164730802	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:164730802A>G	uc003fei.2	-	c.4028T>C	c.(4027-4029)ATA>ACA	p.I1343T		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	1343	Sucrase.|Lumenal.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|pancreas(1)	8		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)									0.356522	145.05281	147.134067	41	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	164730802	164730802	14792	3	A	G	G	G	208	16	SI	4	4
SI	6476	broad.mit.edu	37	3	164739041	164739041	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:164739041C>A	uc003fei.2	-	c.3230G>T	c.(3229-3231)CGA>CTA	p.R1077L		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	1077	Sucrase.|Lumenal.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|pancreas(1)	8		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)									0.179487	39.998881	51.312262	21	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	164739041	164739041	14792	3	C	A	A	A	403	31	SI	1	1
ZBBX	79740	broad.mit.edu	37	3	167045790	167045790	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:167045790G>T	uc011bpc.1	-	c.802C>A	c.(802-804)CAA>AAA	p.Q268K	ZBBX_uc003fep.2_Missense_Mutation_p.Q268K|ZBBX_uc003feq.2_Missense_Mutation_p.Q239K	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	268						intracellular	zinc ion binding			ovary(2)	2														0.100503	12.642303	44.366461	20	179	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167045790	167045790	18100	3	G	T	T	T	585	45	ZBBX	2	2
CLDN11	5010	broad.mit.edu	37	3	170140990	170140990	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:170140990C>A	uc003fgx.2	+	c.266C>A	c.(265-267)TCG>TAG	p.S89*	CLDN11_uc011bpt.1_Nonsense_Mutation_p.S89*|CLDN11_uc003fgy.2_Nonsense_Mutation_p.S5*	NM_005602	NP_005593	O75508	CLD11_HUMAN	claudin 11	89	Helical; (Potential).				calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)											0.136029	45.244395	80.294676	37	235	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	170140990	170140990	3609	3	C	A	A	A	403	31	CLDN11	5	1
SLC7A14	57709	broad.mit.edu	37	3	170198101	170198101	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:170198101C>A	uc003fgz.2	-	c.1970G>T	c.(1969-1971)CGG>CTG	p.R657L	CLDN11_uc011bpt.1_Intron	NM_020949	NP_066000	Q8TBB6	S7A14_HUMAN	solute carrier family 7 (cationic amino acid	657	Helical; (Potential).					integral to membrane	amino acid transmembrane transporter activity			ovary(2)|liver(1)|central_nervous_system(1)	4	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)											0.208333	124.868938	145.676423	55	209	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170198101	170198101	15193	3	C	A	A	A	299	23	SLC7A14	1	1
SLC2A2	6514	broad.mit.edu	37	3	170716031	170716031	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:170716031C>A	uc003fhe.1	-	c.1325G>T	c.(1324-1326)AGC>ATC	p.S442I	SLC2A2_uc003fhf.1_Missense_Mutation_p.S269I|SLC2A2_uc011bpu.1_Missense_Mutation_p.S315I	NM_000340	NP_000331	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose	442	Helical; Name=11; (Potential).				carbohydrate metabolic process|cellular lipid metabolic process|endocrine pancreas development|energy reserve metabolic process|regulation of insulin secretion	integral to plasma membrane|membrane fraction	D-glucose transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)											0.122449	15.325127	29.006892	12	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170716031	170716031	15041	3	C	A	A	A	364	28	SLC2A2	2	2
NLGN1	22871	broad.mit.edu	37	3	173997440	173997440	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:173997440G>C	uc003fio.1	+	c.1649G>C	c.(1648-1650)GGT>GCT	p.G550A	NLGN1_uc010hww.1_3'UTR|NLGN1_uc003fip.1_Missense_Mutation_p.G550A	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	567	Extracellular (Potential).				calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of excitatory postsynaptic membrane potential|regulation of N-methyl-D-aspartate selective glutamate receptor activity|regulation of synaptic transmission|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	carboxylesterase activity|cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	6	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)											0.168317	33.811637	44.335701	17	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	173997440	173997440	10864	3	G	C	C	C	559	43	NLGN1	3	3
TBC1D5	9779	broad.mit.edu	37	3	17447954	17447954	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:17447954T>A	uc010hev.2	-	c.232A>T	c.(232-234)AAT>TAT	p.N78Y	TBC1D5_uc003cbf.2_Missense_Mutation_p.N78Y|TBC1D5_uc003cbe.2_Missense_Mutation_p.N78Y|TBC1D5_uc010hew.1_Missense_Mutation_p.N30Y	NM_001134381	NP_001127853	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5 isoform a	78						intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1														0.081633	-2.005345	24.191441	12	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17447954	17447954	16149	3	T	A	A	A	793	61	TBC1D5	3	3
CCDC39	339829	broad.mit.edu	37	3	180366130	180366130	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:180366130C>A	uc010hxe.2	-	c.1185G>T	c.(1183-1185)CTG>CTT	p.L395L	CCDC39_uc003fkn.2_Non-coding_Transcript	NM_181426	NP_852091	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	395	Potential.				axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium axoneme|cytoplasm|cytoskeleton				ovary(4)	4	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)											0.203704	48.18235	56.989402	22	86	KEEP	---	---	---	---	capture		Silent	SNP	180366130	180366130	2933	3	C	A	A	A	366	29	CCDC39	2	2
ATP11B	23200	broad.mit.edu	37	3	182605388	182605388	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:182605388C>T	uc003flb.2	+	c.2730C>T	c.(2728-2730)AGC>AGT	p.S910S	ATP11B_uc003flc.2_Silent_p.S494S|ATP11B_uc011bqm.1_Intron|ATP11B_uc010hxf.1_Silent_p.S72S	NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	910	Extracellular (Potential).				aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)											0.107143	5.612408	18.481749	9	75	KEEP	---	---	---	---	capture		Silent	SNP	182605388	182605388	1139	3	C	T	T	T	350	27	ATP11B	1	1
ALG3	10195	broad.mit.edu	37	3	183960709	183960709	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:183960709C>A	uc003fne.2	-	c.1046G>T	c.(1045-1047)GGC>GTC	p.G349V	ALG3_uc011brc.1_Missense_Mutation_p.G314V|ALG3_uc011brd.1_Missense_Mutation_p.G293V|ALG3_uc011bre.1_Missense_Mutation_p.G301V	NM_005787	NP_005778	Q92685	ALG3_HUMAN	alpha-1,3-mannosyltransferase ALG3 isoform a	349	Helical; (Potential).				dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity|dolichyl-phosphate-mannose-glycolipid alpha-mannosyltransferase activity				0	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)											0.265306	30.052499	32.492657	13	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	183960709	183960709	523	3	C	A	A	A	338	26	ALG3	2	2
ETV5	2119	broad.mit.edu	37	3	185798879	185798879	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:185798879C>A	uc003fpy.2	-	c.444G>T	c.(442-444)CAG>CAT	p.Q148H	ETV5_uc003fpz.2_Missense_Mutation_p.Q106H	NM_004454	NP_004445	P41161	ETV5_HUMAN	ets variant gene 5 (ets-related molecule)	106					cellular response to oxidative stress|regulation of transcription, DNA-dependent	nucleus	promoter binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)							170				0.1571	83.513356	120.645329	52	279	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185798879	185798879	5475	3	C	A	A	A	311	24	ETV5	2	2
AHSG	197	broad.mit.edu	37	3	186338719	186338719	+	Nonstop_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:186338719G>T	uc003fql.3	+	c.1107G>T	c.(1105-1107)TAG>TAT	p.*369Y	AHSG_uc003fqk.3_Nonstop_Mutation_p.*368Y|AHSG_uc003fqm.3_Nonstop_Mutation_p.*367Y|AHSG_uc010hyp.2_Nonstop_Mutation_p.*331Y	NM_001622	NP_001613	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	369					acute-phase response|negative regulation of bone mineralization|negative regulation of insulin receptor signaling pathway|pinocytosis|positive regulation of phagocytosis|regulation of inflammatory response|skeletal system development	extracellular space	cysteine-type endopeptidase inhibitor activity|protein binding				0	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)										0.152174	11.194059	16.523772	7	39	KEEP	---	---	---	---	capture		Nonstop_Mutation	SNP	186338719	186338719	423	3	G	T	T	T	451	35	AHSG	5	2
ARPP21	10777	broad.mit.edu	37	3	35723372	35723372	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:35723372G>A	uc011axy.1	+	c.129G>A	c.(127-129)CAG>CAA	p.Q43Q	ARPP21_uc003cga.2_Silent_p.Q43Q|ARPP21_uc003cgb.2_Silent_p.Q43Q|ARPP21_uc003cfz.2_Non-coding_Transcript|ARPP21_uc003cgc.2_Silent_p.Q43Q|ARPP21_uc003cgd.2_Silent_p.Q43Q|ARPP21_uc011axx.1_Non-coding_Transcript|ARPP21_uc003cge.2_Silent_p.Q43Q	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	cyclic AMP-regulated phosphoprotein, 21 kD	43	Potential.					cytoplasm	nucleic acid binding			ovary(2)	2														0.116279	7.442179	13.674096	5	38	KEEP	---	---	---	---	capture		Silent	SNP	35723372	35723372	996	3	G	A	A	A	451	35	ARPP21	2	2
ARPP21	10777	broad.mit.edu	37	3	35731613	35731613	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:35731613G>T	uc011axy.1	+	c.526G>T	c.(526-528)GAT>TAT	p.D176Y	ARPP21_uc003cga.2_Missense_Mutation_p.D176Y|ARPP21_uc003cgb.2_Missense_Mutation_p.D176Y|ARPP21_uc003cgf.2_Missense_Mutation_p.D12Y	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	cyclic AMP-regulated phosphoprotein, 21 kD	176	R3H.					cytoplasm	nucleic acid binding			ovary(2)	2														0.196078	20.016842	24.410971	10	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35731613	35731613	996	3	G	T	T	T	585	45	ARPP21	2	2
DCLK3	85443	broad.mit.edu	37	3	36779327	36779327	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:36779327C>A	uc003cgi.2	-	c.824G>T	c.(823-825)TGG>TTG	p.W275L		NM_033403	NP_208382	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	275					protein phosphorylation	cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			lung(3)|large_intestine(2)|ovary(1)|breast(1)|kidney(1)	8										128				0.242268	109.852986	121.589407	47	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36779327	36779327	4464	3	C	A	A	A	273	21	DCLK3	2	2
ACVR2B	93	broad.mit.edu	37	3	38519453	38519453	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:38519453G>T	uc003cif.2	+	c.362G>T	c.(361-363)GGC>GTC	p.G121V	ACVR2B_uc003cig.2_5'UTR	NM_001106	NP_001097	Q13705	AVR2B_HUMAN	activin A receptor, type IIB precursor	121	Extracellular (Potential).				activin receptor signaling pathway|anterior/posterior pattern formation|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|protein phosphorylation|regulation of transcription, DNA-dependent	cell surface|cytoplasm|integral to plasma membrane	activin receptor activity|ATP binding|growth factor binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)						107				0.145299	51.855674	80.132862	34	200	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38519453	38519453	225	3	G	T	T	T	546	42	ACVR2B	2	2
SCN5A	6331	broad.mit.edu	37	3	38627390	38627390	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:38627390A>G	uc003cio.2	-	c.2579T>C	c.(2578-2580)CTC>CCC	p.L860P	SCN5A_uc003cin.2_Missense_Mutation_p.L860P|SCN5A_uc003cil.3_Missense_Mutation_p.L860P|SCN5A_uc010hhi.2_Missense_Mutation_p.L860P|SCN5A_uc010hhk.2_Missense_Mutation_p.L860P|SCN5A_uc011ayr.1_Missense_Mutation_p.L860P|SCN5A_uc010hhj.1_Missense_Mutation_p.L471P	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha	860	Helical; Name=S5 of repeat II; (Potential).				blood circulation|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|central_nervous_system(1)	7	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)									0.159763	65.322527	83.946175	27	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38627390	38627390	14404	3	A	G	G	G	143	11	SCN5A	4	4
XIRP1	165904	broad.mit.edu	37	3	39228545	39228545	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:39228545C>T	uc003cjk.1	-	c.2392G>A	c.(2392-2394)GGG>AGG	p.G798R	XIRP1_uc003cji.2_Missense_Mutation_p.G798R|XIRP1_uc003cjj.2_Intron	NM_194293	NP_919269	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	798							actin binding			ovary(4)|breast(2)|central_nervous_system(1)|pancreas(1)	8				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)										0.09434	4.484631	22.013273	10	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39228545	39228545	18010	3	C	T	T	T	312	24	XIRP1	2	2
LIMD1	8994	broad.mit.edu	37	3	45637310	45637310	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:45637310A>T	uc003coq.2	+	c.939A>T	c.(937-939)AGA>AGT	p.R313S		NM_014240	NP_055055	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	313					cytoplasmic mRNA processing body assembly|gene silencing by miRNA|multicellular organismal development|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasmic mRNA processing body|nucleus|RNA-induced silencing complex	protein binding|transcription repressor activity|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)										0.078947	-3.206797	17.43746	9	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45637310	45637310	9124	3	A	T	T	T	154	12	LIMD1	3	3
LIMD1	8994	broad.mit.edu	37	3	45707201	45707201	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:45707201G>A	uc003coq.2	+	c.1570G>A	c.(1570-1572)GAC>AAC	p.D524N		NM_014240	NP_055055	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	524	Necessary for nuclear localization.|LIM zinc-binding 1.				cytoplasmic mRNA processing body assembly|gene silencing by miRNA|multicellular organismal development|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasmic mRNA processing body|nucleus|RNA-induced silencing complex	protein binding|transcription repressor activity|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)										0.087379	5.684145	41.181142	18	188	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45707201	45707201	9124	3	G	A	A	A	429	33	LIMD1	2	2
C3orf75	54859	broad.mit.edu	37	3	47543343	47543343	+	Splice_Site_SNP	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:47543343T>A	uc003crk.2	-	c.324_splice	c.e5-1	p.R108_splice	C3orf75_uc003crj.2_Splice_Site_SNP_p.R35_splice|C3orf75_uc011bba.1_Splice_Site_SNP_p.R59_splice|C3orf75_uc003crl.1_Splice_Site_SNP_p.R108_splice	NM_001031703	NP_001026873			transmembrane protein 103												0														0.214286	13.143543	15.250362	6	22	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	47543343	47543343	2338	3	T	A	A	A	715	55	C3orf75	5	3
CELSR3	1951	broad.mit.edu	37	3	48677941	48677941	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:48677941G>A	uc003cuf.1	-	c.9371C>T	c.(9370-9372)GCC>GTC	p.A3124V	CELSR3_uc010hkf.2_Missense_Mutation_p.A316V|CELSR3_uc010hkg.2_Missense_Mutation_p.A1009V|CELSR3_uc003cul.2_Missense_Mutation_p.A3026V	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	3026	Cytoplasmic (Potential).				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|central_nervous_system(2)|skin(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)										0.177778	12.172437	16.577018	8	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48677941	48677941	3356	3	G	A	A	A	546	42	CELSR3	2	2
WDR6	11180	broad.mit.edu	37	3	49049550	49049550	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49049550G>C	uc003cvj.2	+	c.673G>C	c.(673-675)GAC>CAC	p.D225H	WDR6_uc011bbx.1_Missense_Mutation_p.D96H|WDR6_uc011bby.1_Intron|WDR6_uc010hkn.2_Missense_Mutation_p.D169H|WDR6_uc011bbz.1_Missense_Mutation_p.D144H	NM_018031	NP_060501	Q9NNW5	WDR6_HUMAN	WD repeat domain 6 protein	195	WD 2.				cell cycle arrest|negative regulation of cell proliferation	cytoplasm				central_nervous_system(1)	1				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)										0.154762	28.416341	37.986322	13	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49049550	49049550	17883	3	G	C	C	C	429	33	WDR6	3	3
MST1	4485	broad.mit.edu	37	3	49725033	49725033	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49725033G>T	uc003cxg.2	-	c.311C>A	c.(310-312)ACG>AAG	p.T104K	MST1_uc011bcs.1_Missense_Mutation_p.T104K|MST1_uc010hkx.2_Silent_p.R15R|MST1_uc011bct.1_Missense_Mutation_p.T104K|MST1_uc011bcu.1_Non-coding_Transcript|RNF123_uc003cxh.2_5'Flank	NM_020998	NP_066278	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth	90	PAN.				proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GBM(110;181 1524 8005 22865 46297)								0.151515	20.008697	27.68234	10	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49725033	49725033	10283	3	G	T	T	T	520	40	MST1	1	1
CDHR4	389118	broad.mit.edu	37	3	49836286	49836286	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49836286G>T	uc010hkz.2	-	c.468C>A	c.(466-468)CTC>CTA	p.L156L	CDHR4_uc003cxp.2_Missense_Mutation_p.P182T|CDHR4_uc011bcw.1_Silent_p.L156L	NM_001007540	NP_001007541	A6H8M9	CDHR4_HUMAN	cadherin-like 29 precursor	156	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.155556	11.004301	16.097548	7	38	KEEP	---	---	---	---	capture		Silent	SNP	49836286	49836286	3250	3	G	T	T	T	522	41	CDHR4	2	2
PCBP4	57060	broad.mit.edu	37	3	51994299	51994299	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:51994299G>C	uc003dcc.1	-	c.191C>G	c.(190-192)TCC>TGC	p.S64C	PCBP4_uc003dcb.1_Missense_Mutation_p.S64C|PCBP4_uc003dcd.1_Missense_Mutation_p.S98C|PCBP4_uc003dce.1_Missense_Mutation_p.S98C|PCBP4_uc003dcf.1_Missense_Mutation_p.S98C|PCBP4_uc003dcg.1_Missense_Mutation_p.S64C|PCBP4_uc003dch.1_Missense_Mutation_p.S98C|PCBP4_uc003dci.1_Missense_Mutation_p.S21C|PCBP4_uc003dcj.1_Missense_Mutation_p.S98C|PCBP4_uc003dck.1_Missense_Mutation_p.S98C|PCBP4_uc003dcl.1_Missense_Mutation_p.S98C	NM_020418	NP_065151	P57723	PCBP4_HUMAN	poly(rC) binding protein 4 isoform a	98						cytoplasm|ribonucleoprotein complex	DNA binding|RNA binding				0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)										0.093023	5.165475	12.329599	4	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51994299	51994299	11923	3	G	C	C	C	533	41	PCBP4	3	3
PBRM1	55193	broad.mit.edu	37	3	52643680	52643680	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:52643680T>C	uc003des.2	-	c.2216A>G	c.(2215-2217)AAT>AGT	p.N739S	PBRM1_uc003dex.2_Non-coding_Transcript|PBRM1_uc003deq.2_Missense_Mutation_p.N739S|PBRM1_uc003der.2_Missense_Mutation_p.N707S|PBRM1_uc003det.2_Missense_Mutation_p.N754S|PBRM1_uc003deu.2_Missense_Mutation_p.N754S|PBRM1_uc003dev.2_Non-coding_Transcript|PBRM1_uc003dew.2_Missense_Mutation_p.N739S|PBRM1_uc010hmk.1_Missense_Mutation_p.N739S|PBRM1_uc003dey.2_Missense_Mutation_p.N739S|PBRM1_uc003dez.1_Missense_Mutation_p.N739S|PBRM1_uc003dfb.1_Missense_Mutation_p.N652S|PBRM1_uc003dfa.1_Missense_Mutation_p.N85S|PBRM1_uc003dfc.2_Missense_Mutation_p.N106S	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	739	Bromo 5.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding	p.S652*(1)|p.Y85fs*10(1)|p.Y738_N739delYN(1)		kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)										0.225434	116.853473	128.817315	39	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52643680	52643680	11911	3	T	C	C	C	676	52	PBRM1	4	4
ITIH1	3697	broad.mit.edu	37	3	52816058	52816058	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:52816058C>A	uc003dfs.2	+	c.790C>A	c.(790-792)CGA>AGA	p.R264R	ITIH1_uc010hmn.1_Non-coding_Transcript|ITIH1_uc003dft.2_5'Flank|ITIH1_uc010hmo.1_5'Flank	NM_002215	NP_002206	P19827	ITIH1_HUMAN	inter-alpha (globulin) inhibitor H1	264					hyaluronan metabolic process|leukocyte activation	extracellular region	calcium ion binding|serine-type endopeptidase inhibitor activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)										0.145299	26.595854	40.759272	17	100	KEEP	---	---	---	---	capture		Silent	SNP	52816058	52816058	8207	3	C	A	A	A	399	31	ITIH1	1	1
RFT1	91869	broad.mit.edu	37	3	53137994	53137994	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:53137994T>A	uc003dgj.2	-	c.1077A>T	c.(1075-1077)GGA>GGT	p.G359G	RFT1_uc003dgk.2_Silent_p.G320G	NM_052859	NP_443091	Q96AA3	RFT1_HUMAN	RFT1 homolog	359					carbohydrate transport|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane	lipid transporter activity				0				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)										0.216667	27.04255	31.486557	13	47	KEEP	---	---	---	---	capture		Silent	SNP	53137994	53137994	13729	3	T	A	A	A	691	54	RFT1	3	3
ARHGEF3	50650	broad.mit.edu	37	3	56779328	56779328	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:56779328G>A	uc003dih.2	-	c.871C>T	c.(871-873)CCA>TCA	p.P291S	ARHGEF3_uc011bew.1_Missense_Mutation_p.P259S|ARHGEF3_uc011bev.1_Missense_Mutation_p.P230S|ARHGEF3_uc003dif.2_Missense_Mutation_p.P265S|ARHGEF3_uc003dig.2_Missense_Mutation_p.P259S|ARHGEF3_uc010hmy.1_Missense_Mutation_p.P57S|ARHGEF3_uc003dii.2_Missense_Mutation_p.P259S	NM_001128615	NP_001122087	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor 3 isoform	259	DH.				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)										0.218659	172.725251	197.755101	75	268	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56779328	56779328	918	3	G	A	A	A	533	41	ARHGEF3	2	2
CADPS	8618	broad.mit.edu	37	3	62751548	62751548	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:62751548C>A	uc003dll.2	-	c.553G>T	c.(553-555)GAG>TAG	p.E185*	CADPS_uc003dlm.2_Nonsense_Mutation_p.E185*|CADPS_uc003dln.2_Nonsense_Mutation_p.E185*	NM_003716	NP_003707	Q9ULU8	CAPS1_HUMAN	Ca2+-dependent secretion activator isoform 1	185					exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)										0.204819	34.624085	41.338025	17	66	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	62751548	62751548	2686	3	C	A	A	A	377	29	CADPS	5	2
PSMD6	9861	broad.mit.edu	37	3	64004980	64004980	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:64004980C>A	uc003dmb.1	-	c.648G>T	c.(646-648)AAG>AAT	p.K216N	PSMD6_uc003dlz.1_Missense_Mutation_p.K114N|PSMD6_uc003dma.1_Missense_Mutation_p.K163N|PSMD6_uc003dmc.1_Missense_Mutation_p.K124N|PSMD6_uc003dmd.1_Missense_Mutation_p.K125N	NM_014814	NP_055629	Q15008	PSMD6_HUMAN	proteasome (prosome, macropain) 26S subunit,	163					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	ATPase activity|protein binding			central_nervous_system(1)	1		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000805)|Kidney(15;0.00188)|KIRC - Kidney renal clear cell carcinoma(15;0.00212)										0.127273	18.474372	33.37715	14	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64004980	64004980	13155	3	C	A	A	A	311	24	PSMD6	2	2
ADAMTS9	56999	broad.mit.edu	37	3	64526878	64526878	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:64526878T>C	uc003dmg.2	-	c.5414A>G	c.(5413-5415)TAT>TGT	p.Y1805C	ADAMTS9_uc011bfo.1_Missense_Mutation_p.Y1777C|ADAMTS9_uc011bfp.1_Missense_Mutation_p.Y716C	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1805	GON.				glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)	3		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)										0.111111	21.038788	41.213091	15	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64526878	64526878	274	3	T	C	C	C	637	49	ADAMTS9	4	4
ADAMTS9	56999	broad.mit.edu	37	3	64601143	64601143	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:64601143C>A	uc003dmg.2	-	c.3043G>T	c.(3043-3045)GGT>TGT	p.G1015C	ADAMTS9_uc011bfo.1_Missense_Mutation_p.G987C|ADAMTS9_uc003dmh.1_Missense_Mutation_p.G844C|ADAMTS9_uc003dmk.1_Missense_Mutation_p.G1015C|ADAMTS9_uc011bfp.1_5'UTR	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1015	TSP type-1 4.				glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)	3		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)										0.191176	29.556723	35.600982	13	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64601143	64601143	274	3	C	A	A	A	299	23	ADAMTS9	1	1
GRM7	2917	broad.mit.edu	37	3	7456833	7456833	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:7456833C>A	uc003bql.2	+	c.1157C>A	c.(1156-1158)ACA>AAA	p.T386K	GRM7_uc011ata.1_Non-coding_Transcript|GRM7_uc011atb.1_Non-coding_Transcript|GRM7_uc010hcf.2_Non-coding_Transcript|GRM7_uc011atc.1_Non-coding_Transcript|GRM7_uc010hcg.2_Missense_Mutation_p.T386K|GRM7_uc003bqm.2_Missense_Mutation_p.T386K|GRM7_uc003bqn.1_5'UTR	NM_181874	NP_870989	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform b	386	Extracellular (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)	4					L-Glutamic Acid(DB00142)									0.22549	56.569051	63.630708	23	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7456833	7456833	7081	3	C	A	A	A	221	17	GRM7	2	2
EPHA6	285220	broad.mit.edu	37	3	97167557	97167557	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:97167557T>A	uc010how.1	+	c.1877T>A	c.(1876-1878)TTT>TAT	p.F626Y	EPHA6_uc011bgo.1_Non-coding_Transcript|EPHA6_uc011bgp.1_De_novo_Start_OutOfFrame|EPHA6_uc003drs.3_De_novo_Start_InFrame|EPHA6_uc003drr.3_De_novo_Start_InFrame|EPHA6_uc003drt.2_De_novo_Start_InFrame|EPHA6_uc010hox.1_Non-coding_Transcript	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	531	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				0.25	40.43988	44.305207	17	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97167557	97167557	5364	3	T	A	A	A	832	64	EPHA6	3	3
OR5H15	403274	broad.mit.edu	37	3	97887789	97887789	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:97887789G>A	uc011bgu.1	+	c.246G>A	c.(244-246)CTG>CTA	p.L82L		NM_001005515	NP_001005515	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H,	82	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.107595	11.648493	35.796344	17	141	KEEP	---	---	---	---	capture		Silent	SNP	97887789	97887789	11571	3	G	A	A	A	574	45	OR5H15	2	2
OR5H6	79295	broad.mit.edu	37	3	97984066	97984066	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:97984066T>C	uc003dsi.1	+	c.938T>C	c.(937-939)GTA>GCA	p.V313A		NM_001005479	NP_001005479	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H,	313	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|skin(1)	2														0.213333	47.264497	52.953225	16	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97984066	97984066	11573	3	T	C	C	C	741	57	OR5H6	4	4
C4orf17	84103	broad.mit.edu	37	4	100458876	100458876	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:100458876T>A	uc003huw.2	+	c.597T>A	c.(595-597)GTT>GTA	p.V199V	C4orf17_uc003hux.2_Non-coding_Transcript	NM_032149	NP_115525	Q53FE4	CD017_HUMAN	hypothetical protein LOC84103	199											0				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)										0.085106	0.623316	17.0417	8	86	KEEP	---	---	---	---	capture		Silent	SNP	100458876	100458876	2347	4	T	A	A	A	821	64	C4orf17	3	3
CENPE	1062	broad.mit.edu	37	4	104061453	104061453	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:104061453T>G	uc003hxb.1	-	c.5873A>C	c.(5872-5874)CAA>CCA	p.Q1958P	CENPE_uc003hxc.1_Missense_Mutation_p.Q1933P|CENPE_uc003hxd.1_Non-coding_Transcript	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	1958	Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)										0.14	16.592892	22.847252	7	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104061453	104061453	3363	4	T	G	G	G	819	63	CENPE	4	4
LEF1	51176	broad.mit.edu	37	4	108985506	108985506	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:108985506T>A	uc003hyt.1	-	c.1151A>T	c.(1150-1152)CAG>CTG	p.Q384L	LEF1_uc011cfj.1_Missense_Mutation_p.Q241L|LEF1_uc011cfk.1_Missense_Mutation_p.Q288L|LEF1_uc003hyu.1_Missense_Mutation_p.Q356L|LEF1_uc003hyv.1_Missense_Mutation_p.Q356L|LEF1_uc010imb.1_Non-coding_Transcript|LEF1_uc003hys.1_Non-coding_Transcript|LEF1_uc010ima.1_Missense_Mutation_p.Q72L	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1	384					canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of caspase activity|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of gene-specific transcription|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|promoter binding|transcription activator activity|transcription repressor activity			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)										0.097826	6.203181	21.10284	9	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108985506	108985506	9038	4	T	A	A	A	715	55	LEF1	3	3
OSTC	58505	broad.mit.edu	37	4	109571951	109571951	+	Splice_Site_SNP	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:109571951G>T	uc003hzb.1	+	c.139_splice	c.e1+1	p.G47_splice		NM_021227	NP_067050			DC2 protein						protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				breast(1)	1														0.102564	7.699109	19.925578	8	70	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	109571951	109571951	11708	4	G	T	T	T	572	44	OSTC	5	2
AGXT2L1	64850	broad.mit.edu	37	4	109672096	109672096	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:109672096C>A	uc003hzc.2	-	c.697G>T	c.(697-699)GCA>TCA	p.A233S	AGXT2L1_uc010imc.2_Missense_Mutation_p.A227S|AGXT2L1_uc011cfm.1_Missense_Mutation_p.A193S|AGXT2L1_uc011cfn.1_Missense_Mutation_p.A160S|AGXT2L1_uc011cfo.1_Missense_Mutation_p.A175S	NM_031279	NP_112569	Q8TBG4	AT2L1_HUMAN	alanine-glyoxylate aminotransferase 2-like 1	233					cellular amino acid metabolic process	mitochondrion	alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000281)										0.084	2.867645	46.820039	21	229	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109672096	109672096	409	4	C	A	A	A	338	26	AGXT2L1	2	2
ALPK1	80216	broad.mit.edu	37	4	113356453	113356453	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:113356453G>T	uc003iap.3	+	c.3184G>T	c.(3184-3186)GGG>TGG	p.G1062W	ALPK1_uc003ian.3_Missense_Mutation_p.G1062W|ALPK1_uc011cfx.1_Missense_Mutation_p.G984W|ALPK1_uc003iao.3_Non-coding_Transcript|ALPK1_uc010imo.2_Missense_Mutation_p.G890W	NM_025144	NP_079420	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	1062	Alpha-type protein kinase.				protein phosphorylation		ATP binding|protein serine/threonine kinase activity			ovary(5)	5		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)						252				0.064171	-12.449834	24.488391	12	175	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113356453	113356453	547	4	G	T	T	T	559	43	ALPK1	2	2
ANK2	287	broad.mit.edu	37	4	114278434	114278434	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:114278434C>T	uc003ibe.3	+	c.8660C>T	c.(8659-8661)CCA>CTA	p.P2887L	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_Missense_Mutation_p.P189L|ANK2_uc011cgb.1_Missense_Mutation_p.P2902L	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	2854					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)	13		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)										0.108949	28.665735	67.551888	28	229	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114278434	114278434	624	4	C	T	T	T	273	21	ANK2	2	2
ANK2	287	broad.mit.edu	37	4	114279550	114279551	+	Nonsense_Mutation	DNP	CC	AA	AA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:114279550_114279551CC>AA	uc003ibe.3	+	c.9776_9777CC>AA	c.(9775-9777)TCC>TAA	p.S3259*	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_Nonsense_Mutation_p.S561*|ANK2_uc011cgb.1_Nonsense_Mutation_p.S3274*	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	3226					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)	13		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)										0.137931	24.117624	42.722648	20	125	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	114279550	114279551	624	4	CC	AA	AA	AA	390	30	ANK2	5	2
FAT4	79633	broad.mit.edu	37	4	126240586	126240586	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:126240586A>T	uc003ifj.3	+	c.3020A>T	c.(3019-3021)GAG>GTG	p.E1007V		NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	1007	Cadherin 10.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(8)|pancreas(2)	10														0.158879	28.002716	39.873172	17	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126240586	126240586	5928	4	A	T	T	T	143	11	FAT4	3	3
PCDH10	57575	broad.mit.edu	37	4	134072236	134072236	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:134072236G>T	uc003iha.2	+	c.941G>T	c.(940-942)GGC>GTC	p.G314V	PCDH10_uc003igz.2_Missense_Mutation_p.G314V	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	314	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1				LUSC - Lung squamous cell carcinoma(193;0.227)										0.155844	33.445994	50.838264	24	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134072236	134072236	11927	4	G	T	T	T	546	42	PCDH10	2	2
PCDH10	57575	broad.mit.edu	37	4	134072870	134072870	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:134072870G>T	uc003iha.2	+	c.1575G>T	c.(1573-1575)TTG>TTT	p.L525F	PCDH10_uc003igz.2_Missense_Mutation_p.L525F	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	525	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1				LUSC - Lung squamous cell carcinoma(193;0.227)										0.114094	19.787603	41.650945	17	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134072870	134072870	11927	4	G	T	T	T	620	48	PCDH10	2	2
BOD1L	259282	broad.mit.edu	37	4	13603372	13603372	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:13603372C>A	uc003gmz.1	-	c.5152G>T	c.(5152-5154)GGT>TGT	p.G1718C	BOD1L_uc010idr.1_Missense_Mutation_p.G1055C	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	1718							DNA binding			ovary(5)|breast(1)	6														0.152263	61.301957	89.444273	37	206	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13603372	13603372	1508	4	C	A	A	A	286	22	BOD1L	2	2
BOD1L	259282	broad.mit.edu	37	4	13606630	13606630	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:13606630G>A	uc003gmz.1	-	c.1894C>T	c.(1894-1896)CGG>TGG	p.R632W	BOD1L_uc010idr.1_5'UTR	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	632	Lys-rich.						DNA binding			ovary(5)|breast(1)	6														0.179104	26.357592	32.850377	12	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13606630	13606630	1508	4	G	A	A	A	506	39	BOD1L	1	1
INPP4B	8821	broad.mit.edu	37	4	143235915	143235915	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:143235915C>T	uc003iix.3	-	c.373G>A	c.(373-375)GTT>ATT	p.V125I	INPP4B_uc003iiw.3_Missense_Mutation_p.V125I|INPP4B_uc011chm.1_Non-coding_Transcript|INPP4B_uc011cho.1_Non-coding_Transcript	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,	125	C2.				signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)									564				0.098684	9.310162	33.799295	15	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143235915	143235915	8054	4	C	T	T	T	234	18	INPP4B	2	2
TTC29	83894	broad.mit.edu	37	4	147830185	147830185	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:147830185C>G	uc003ikx.3	-	c.471G>C	c.(469-471)GAG>GAC	p.E157D	TTC29_uc003ikw.3_Missense_Mutation_p.E131D|TTC29_uc010ipc.2_Non-coding_Transcript|TTC29_uc010ipd.1_Missense_Mutation_p.E131D	NM_031956	NP_114162	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	131							binding				0	all_hematologic(180;0.151)													0.087379	9.39014	27.135298	9	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	147830185	147830185	17251	4	C	G	G	G	415	32	TTC29	3	3
DCHS2	54798	broad.mit.edu	37	4	155256115	155256115	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:155256115G>T	uc003inw.2	-	c.1121C>A	c.(1120-1122)CCT>CAT	p.P374H	DCHS2_uc003inx.2_Missense_Mutation_p.P873H	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	374	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)										0.086957	2.324741	18.217824	8	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155256115	155256115	4459	4	G	T	T	T	455	35	DCHS2	2	2
FGB	2244	broad.mit.edu	37	4	155487754	155487754	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:155487754C>T	uc003ioa.3	+	c.420C>T	c.(418-420)ACC>ACT	p.T140T	FGB_uc010ipu.1_Non-coding_Transcript|FGB_uc003iob.3_Silent_p.T137T|FGB_uc010ipv.2_Silent_p.T78T|FGB_uc010ipw.2_Silent_p.T137T|FGB_uc003ioc.3_Intron	NM_005141	NP_005132	P02675	FIBB_HUMAN	fibrinogen, beta chain preproprotein	140					platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen|soluble fraction	chaperone binding|eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)	2	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	NSCLC(106;1133 1613 21870 46110 52656)								0.124031	22.208598	40.042687	16	113	KEEP	---	---	---	---	capture		Silent	SNP	155487754	155487754	6068	4	C	T	T	T	301	24	FGB	2	2
GUCY1A3	2982	broad.mit.edu	37	4	156634571	156634571	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:156634571C>A	uc003iov.2	+	c.1408C>A	c.(1408-1410)CAA>AAA	p.Q470K	GUCY1A3_uc010iqc.2_Missense_Mutation_p.Q470K|GUCY1A3_uc003iow.2_Missense_Mutation_p.Q470K|GUCY1A3_uc010iqd.2_Missense_Mutation_p.Q469K|GUCY1A3_uc003iox.2_Missense_Mutation_p.Q470K|GUCY1A3_uc003ioz.2_Missense_Mutation_p.Q235K|GUCY1A3_uc003ioy.2_Missense_Mutation_p.Q470K|GUCY1A3_uc010iqe.2_Missense_Mutation_p.Q235K|GUCY1A3_uc003ipa.2_Intron|GUCY1A3_uc003ipb.2_Missense_Mutation_p.Q470K	NM_000856	NP_000847	Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3 isoform A	470					blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble	GTP binding|guanylate cyclase activity|heme binding|receptor activity			central_nervous_system(2)|ovary(1)	3	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)										0.135135	11.880426	21.477912	10	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156634571	156634571	7174	4	C	A	A	A	325	25	GUCY1A3	2	2
GUCY1B3	2983	broad.mit.edu	37	4	156711063	156711063	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:156711063G>T	uc011cio.1	+	c.561G>T	c.(559-561)AAG>AAT	p.K187N	GUCY1B3_uc003ipc.2_Missense_Mutation_p.K165N|GUCY1B3_uc011cip.1_Missense_Mutation_p.K145N|GUCY1B3_uc003ipd.2_Missense_Mutation_p.K93N|GUCY1B3_uc010iqf.2_Missense_Mutation_p.K165N|GUCY1B3_uc010iqg.2_Missense_Mutation_p.K93N|GUCY1B3_uc011ciq.1_Missense_Mutation_p.K93N	NM_000857	NP_000848	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	165					blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble|intracellular membrane-bounded organelle	GTP binding|guanylate cyclase activity|receptor activity				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)										0.149425	21.312355	31.573347	13	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156711063	156711063	7175	4	G	T	T	T	451	35	GUCY1B3	2	2
RXFP1	59350	broad.mit.edu	37	4	159566095	159566095	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:159566095C>A	uc011cje.1	+	c.1231C>A	c.(1231-1233)CCA>ACA	p.P411T	RXFP1_uc010iqj.1_Missense_Mutation_p.P213T|RXFP1_uc003ipz.2_Missense_Mutation_p.P384T|RXFP1_uc011cja.1_Missense_Mutation_p.P279T|RXFP1_uc010iqo.2_Missense_Mutation_p.P336T|RXFP1_uc011cjb.1_Missense_Mutation_p.P282T|RXFP1_uc010iqk.2_Missense_Mutation_p.P252T|RXFP1_uc011cjc.1_Missense_Mutation_p.P303T|RXFP1_uc011cjd.1_Missense_Mutation_p.P303T|RXFP1_uc010iql.2_Missense_Mutation_p.P228T|RXFP1_uc010iqm.2_Missense_Mutation_p.P351T|RXFP1_uc011cjf.1_Missense_Mutation_p.P253T|RXFP1_uc010iqn.2_Missense_Mutation_p.P329T	NM_021634	NP_067647	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	384	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)										0.125	7.907161	14.523825	6	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	159566095	159566095	14239	4	C	A	A	A	234	18	RXFP1	2	2
RAPGEF2	9693	broad.mit.edu	37	4	160251586	160251586	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:160251586C>G	uc003iqg.3	+	c.920C>G	c.(919-921)TCT>TGT	p.S307C		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	307	N-terminal Ras-GEF.				cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			upper_aerodigestive_tract(1)|skin(1)	2	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)						322				0.091667	10.625782	30.788136	11	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160251586	160251586	13504	4	C	G	G	G	416	32	RAPGEF2	3	3
ANP32C	23520	broad.mit.edu	37	4	165118375	165118375	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:165118375C>A	uc011cjk.1	-	c.489G>T	c.(487-489)CTG>CTT	p.L163L	MARCH1_uc003iqs.1_Intron	NM_012403	NP_036535	O43423	AN32C_HUMAN	acidic nuclear phosphoprotein 32C	163	Asp/Glu-rich (highly acidic).										0	all_hematologic(180;0.203)	Prostate(90;0.0138)|Melanoma(52;0.18)|all_neural(102;0.223)		KIRC - Kidney renal clear cell carcinoma(143;0.242)										0.08	-0.612258	12.887916	6	69	KEEP	---	---	---	---	capture		Silent	SNP	165118375	165118375	715	4	C	A	A	A	262	21	ANP32C	2	2
LDB2	9079	broad.mit.edu	37	4	16590406	16590406	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:16590406A>T	uc003goz.2	-	c.458T>A	c.(457-459)ATG>AAG	p.M153K	LDB2_uc003gpa.2_Missense_Mutation_p.M153K|LDB2_uc003gpb.2_Missense_Mutation_p.M153K|LDB2_uc011bxh.1_Missense_Mutation_p.M153K|LDB2_uc010iee.2_Missense_Mutation_p.M153K|LDB2_uc003goy.2_Missense_Mutation_p.M29K|LDB2_uc011bxi.1_Missense_Mutation_p.M29K	NM_001290	NP_001281	O43679	LDB2_HUMAN	LIM domain binding 2 isoform a	153							LIM domain binding|transcription cofactor activity				0														0.163265	33.341583	43.896669	16	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16590406	16590406	9020	4	A	T	T	T	104	8	LDB2	3	3
TLL1	7092	broad.mit.edu	37	4	166976235	166976235	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:166976235G>C	uc011cjn.1	+	c.1601G>C	c.(1600-1602)AGA>ACA	p.R534T	TLL1_uc003irh.1_Missense_Mutation_p.R511T|TLL1_uc011cjo.1_Missense_Mutation_p.R335T	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor	511	CUB 2.				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)|central_nervous_system(1)	4	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)										0.071429	-0.659785	17.895419	7	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166976235	166976235	16475	4	G	C	C	C	429	33	TLL1	3	3
TLL1	7092	broad.mit.edu	37	4	166999115	166999115	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:166999115A>T	uc011cjn.1	+	c.2444A>T	c.(2443-2445)GAC>GTC	p.D815V	TLL1_uc003irh.1_Missense_Mutation_p.D792V|TLL1_uc011cjo.1_Missense_Mutation_p.D616V	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor	792	CUB 4.				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)|central_nervous_system(1)	4	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)										0.142857	11.56279	18.44833	8	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	166999115	166999115	16475	4	A	T	T	T	130	10	TLL1	3	3
PALLD	23022	broad.mit.edu	37	4	169432821	169432821	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:169432821G>A	uc011cjx.1	+	c.166G>A	c.(166-168)GAA>AAA	p.E56K	PALLD_uc003iru.2_Missense_Mutation_p.E56K	NM_016081	NP_057165	Q8WX93	PALLD_HUMAN	palladin isoform 2	56					cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		Esophageal Squamous(109;1482 1532 18347 40239 51172)								0.136364	9.917805	15.552986	6	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169432821	169432821	11823	4	G	A	A	A	429	33	PALLD	2	2
GALNTL6	442117	broad.mit.edu	37	4	172735780	172735780	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:172735780G>T	uc003isv.2	+	c.49G>T	c.(49-51)GTG>TTG	p.V17L		NM_001034845	NP_001030017	Q49A17	GLTL6_HUMAN	N-acetylgalactosaminyltransferase-like 6	17	Helical; Signal-anchor for type II membrane protein; (Potential).					Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)	3														0.160714	32.394865	44.822966	18	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	172735780	172735780	6489	4	G	T	T	T	572	44	GALNTL6	2	2
WDR17	116966	broad.mit.edu	37	4	177067216	177067216	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:177067216C>A	uc003iuj.2	+	c.1672C>A	c.(1672-1674)CCA>ACA	p.P558T	WDR17_uc003iuk.2_Missense_Mutation_p.P534T|WDR17_uc003ium.3_Missense_Mutation_p.P534T|WDR17_uc003iul.1_Intron	NM_170710	NP_733828	Q8IZU2	WDR17_HUMAN	WD repeat domain 17 isoform 1	558	WD 9.									ovary(2)|pancreas(1)	3		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)										0.144144	26.43782	39.995622	16	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	177067216	177067216	17850	4	C	A	A	A	234	18	WDR17	2	2
VEGFC	7424	broad.mit.edu	37	4	177608675	177608675	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:177608675C>A	uc003ius.1	-	c.812_splice	c.e6-1	p.D271_splice		NM_005429	NP_005420			vascular endothelial growth factor C						angiogenesis|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of mast cell chemotaxis|substrate-dependent cell migration|vascular endothelial growth factor receptor signaling pathway	membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity			lung(2)	2		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)						148				0.263158	12.565338	13.529928	5	14	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	177608675	177608675	17719	4	C	A	A	A	416	32	VEGFC	5	2
DCAF16	54876	broad.mit.edu	37	4	17805188	17805188	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:17805188C>G	uc003gpn.2	-	c.577G>C	c.(577-579)GAA>CAA	p.E193Q	DCAF16_uc003gpo.2_Non-coding_Transcript	NM_017741	NP_060211	Q9NXF7	DCA16_HUMAN	DDB1 and CUL4 associated factor 16	193					protein ubiquitination	CUL4 RING ubiquitin ligase complex				ovary(1)	1														0.186916	51.933115	61.760011	20	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17805188	17805188	4439	4	C	G	G	G	377	29	DCAF16	3	3
ODZ3	55714	broad.mit.edu	37	4	183714264	183714264	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:183714264A>T	uc003ivd.1	+	c.6439A>T	c.(6439-6441)ATA>TTA	p.I2147L		NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	2147	Extracellular (Potential).|YD 18.				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)										0.181818	43.47344	54.989935	22	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	183714264	183714264	11241	4	A	T	T	T	156	12	ODZ3	3	3
SLIT2	9353	broad.mit.edu	37	4	20552452	20552452	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:20552452C>A	uc003gpr.1	+	c.2492C>A	c.(2491-2493)TCT>TAT	p.S831Y	SLIT2_uc003gps.1_Missense_Mutation_p.S823Y	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor	831	LRR 20.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|initiation of Roundabout signal transduction|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|ovary(3)	7														0.09375	1.697128	12.321574	6	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20552452	20552452	15238	4	C	A	A	A	416	32	SLIT2	2	2
GPR125	166647	broad.mit.edu	37	4	22436933	22436933	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:22436933C>A	uc003gqm.1	-	c.1443_splice	c.e10+1	p.E481_splice	GPR125_uc010ieo.1_Splice_Site_SNP_p.E355_splice|GPR125_uc003gqn.1_Splice_Site_SNP_p.E255_splice|GPR125_uc003gqo.2_Splice_Site_SNP_p.E481_splice	NM_145290	NP_660333			G protein-coupled receptor 125 precursor						neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity				0		Breast(46;0.198)												0.180556	26.869191	33.880362	13	59	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	22436933	22436933	6913	4	C	A	A	A	234	18	GPR125	5	2
ADD1	118	broad.mit.edu	37	4	2883688	2883689	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:2883688_2883689GG>TT	uc003gfq.2	+	c.259_260GG>TT	c.(259-261)GGC>TTC	p.G87F	ADD1_uc003gfn.2_Intron|ADD1_uc010ico.1_Missense_Mutation_p.G87F|ADD1_uc003gfo.2_Missense_Mutation_p.G87F|ADD1_uc003gfp.2_Missense_Mutation_p.G87F|ADD1_uc003gfr.2_Missense_Mutation_p.G87F|ADD1_uc003gfs.2_Missense_Mutation_p.G87F|ADD1_uc003gft.3_Missense_Mutation_p.G87F	NM_014189	NP_054908	P35611	ADDA_HUMAN	adducin 1 (alpha) isoform b	87					actin filament bundle assembly|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|positive regulation of protein binding	cytosol|F-actin capping protein complex|nucleus|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding|transcription factor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		Esophageal Squamous(71;505 1201 20414 34538 37449)								0.141935	32.945322	52.111245	22	133	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	2883688	2883689	305	4	GG	TT	TT	TT	455	35	ADD1	2	2
C4orf44	345222	broad.mit.edu	37	4	3265616	3265616	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:3265616C>T	uc003ggt.2	+	c.734C>T	c.(733-735)TCC>TTC	p.S245F		NM_001012982	NP_001013000	Q6ZTZ1	CD044_HUMAN	hypothetical protein LOC345222 isoform b	245											0														0.116945	50.255044	110.777539	49	370	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3265616	3265616	2367	4	C	T	T	T	378	30	C4orf44	2	2
ZBTB49	166793	broad.mit.edu	37	4	4304252	4304252	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:4304252G>T	uc003ghu.2	+	c.689G>T	c.(688-690)GGT>GTT	p.G230V	ZBTB49_uc003ghv.2_5'UTR|ZBTB49_uc010icy.2_Non-coding_Transcript|ZBTB49_uc010icz.2_5'UTR	NM_145291	NP_660334	Q6ZSB9	ZBT49_HUMAN	zinc finger protein 509	230					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.146154	28.637004	44.291702	19	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4304252	4304252	18137	4	G	T	T	T	572	44	ZBTB49	2	2
GABRA2	2555	broad.mit.edu	37	4	46314638	46314638	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:46314638C>A	uc003gxc.3	-	c.351G>T	c.(349-351)ATG>ATT	p.M117I	GABRA2_uc010igc.2_Missense_Mutation_p.M117I|GABRA2_uc011bzc.1_Missense_Mutation_p.M62I|GABRA2_uc003gxe.2_Missense_Mutation_p.M117I	NM_001114175	NP_001107647	P47869	GBRA2_HUMAN	gamma-aminobutyric acid A receptor, alpha 2	117	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels	cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)									0.309091	45.051268	46.839357	17	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46314638	46314638	6412	4	C	A	A	A	273	21	GABRA2	2	2
ATP10D	57205	broad.mit.edu	37	4	47570974	47570974	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:47570974G>T	uc003gxk.1	+	c.2974G>T	c.(2974-2976)GGG>TGG	p.G992W	ATP10D_uc003gxl.1_Missense_Mutation_p.G240W	NM_020453	NP_065186	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	992	Cytoplasmic (Potential).				ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3														0.099174	7.101341	26.546151	12	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47570974	47570974	1137	4	G	T	T	T	455	35	ATP10D	2	2
CORIN	10699	broad.mit.edu	37	4	47667122	47667122	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:47667122G>T	uc003gxm.2	-	c.1516C>A	c.(1516-1518)CTC>ATC	p.L506I	CORIN_uc011bzf.1_Missense_Mutation_p.L367I|CORIN_uc011bzg.1_Missense_Mutation_p.L439I|CORIN_uc011bzh.1_Missense_Mutation_p.L469I|CORIN_uc011bzi.1_Missense_Mutation_p.L469I	NM_006587	NP_006578	Q9Y5Q5	CORIN_HUMAN	corin	506	Extracellular (Potential).|FZ 2.				peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)	1														0.089888	1.424492	16.548605	8	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47667122	47667122	3890	4	G	T	T	T	455	35	CORIN	2	2
FRYL	285527	broad.mit.edu	37	4	48621362	48621362	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:48621362A>G	uc003gyh.1	-	c.340T>C	c.(340-342)TAT>CAT	p.Y114H	FRYL_uc003gyk.2_Missense_Mutation_p.Y114H|FRYL_uc003gyl.1_Missense_Mutation_p.Y165H	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	114					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1														0.233333	21.312567	23.26287	7	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48621362	48621362	6314	4	A	G	G	G	169	13	FRYL	4	4
CWH43	80157	broad.mit.edu	37	4	49032885	49032885	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:49032885C>A	uc003gyv.2	+	c.1416C>A	c.(1414-1416)CCC>CCA	p.P472P	CWH43_uc011bzl.1_Silent_p.P445P	NM_025087	NP_079363	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog	472					GPI anchor biosynthetic process	integral to membrane				ovary(1)	1														0.144828	34.671144	52.278041	21	124	KEEP	---	---	---	---	capture		Silent	SNP	49032885	49032885	4233	4	C	A	A	A	301	24	CWH43	2	2
LRRC66	339977	broad.mit.edu	37	4	52860889	52860889	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:52860889T>G	uc003gzi.2	-	c.2299A>C	c.(2299-2301)AAG>CAG	p.K767Q		NM_001024611	NP_001019782	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	767						integral to membrane				ovary(1)|central_nervous_system(1)	2														0.086957	9.496709	33.332786	12	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52860889	52860889	9393	4	T	G	G	G	819	63	LRRC66	4	4
LRRC66	339977	broad.mit.edu	37	4	52861975	52861975	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:52861975A>G	uc003gzi.2	-	c.1213T>C	c.(1213-1215)TGG>CGG	p.W405R		NM_001024611	NP_001019782	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	405						integral to membrane				ovary(1)|central_nervous_system(1)	2														0.102857	19.216003	46.766372	18	157	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52861975	52861975	9393	4	A	G	G	G	78	6	LRRC66	4	4
STK32B	55351	broad.mit.edu	37	4	5332984	5332984	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:5332984G>C	uc003gih.1	+	c.298G>C	c.(298-300)GTG>CTG	p.V100L	STK32B_uc010ida.1_Missense_Mutation_p.V53L	NM_018401	NP_060871	Q9NY57	ST32B_HUMAN	serine/threonine kinase 32B	100	Protein kinase.				protein phosphorylation		ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5										175				0.217742	79.359269	88.463794	27	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5332984	5332984	15818	4	G	C	C	C	572	44	STK32B	3	3
PDGFRA	5156	broad.mit.edu	37	4	55139722	55139722	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:55139722C>G	uc003han.3	+	c.1383C>G	c.(1381-1383)TCC>TCG	p.S461S	PDGFRA_uc003haa.2_Intron|PDGFRA_uc010igq.1_Silent_p.S355S|PDGFRA_uc003ham.2_Non-coding_Transcript	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	461	Ig-like C2-type 5.|Extracellular (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(532)|small_intestine(40)|stomach(16)|central_nervous_system(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|ovary(3)|skin(2)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|bone(1)	625	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	Pancreas(151;208 1913 7310 23853 37092)				1045	TSP Lung(21;0.16)			0.103448	7.005586	20.633512	9	78	KEEP	---	---	---	---	capture		Silent	SNP	55139722	55139722	12082	4	C	G	G	G	301	24	PDGFRA	3	3
PDGFRA	5156	broad.mit.edu	37	4	55140699	55140699	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:55140699C>T	uc003han.3	+	c.1560C>T	c.(1558-1560)ACC>ACT	p.T520T	PDGFRA_uc003haa.2_Intron|PDGFRA_uc010igq.1_Silent_p.T414T|PDGFRA_uc003ham.2_Non-coding_Transcript|PDGFRA_uc003hao.1_5'Flank	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	520	Extracellular (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(532)|small_intestine(40)|stomach(16)|central_nervous_system(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|ovary(3)|skin(2)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|bone(1)	625	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	Pancreas(151;208 1913 7310 23853 37092)				1045	TSP Lung(21;0.16)			0.129496	27.957127	46.528288	18	121	KEEP	---	---	---	---	capture		Silent	SNP	55140699	55140699	12082	4	C	T	T	T	275	22	PDGFRA	2	2
KDR	3791	broad.mit.edu	37	4	55968157	55968157	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:55968157G>A	uc003has.2	-	c.2173C>T	c.(2173-2175)CGC>TGC	p.R725C	KDR_uc003hat.1_Missense_Mutation_p.R725C	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	725	Ig-like C2-type 7.|Extracellular (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|protein phosphorylation|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(9)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|ovary(2)|kidney(1)	22	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)					1022	TSP Lung(20;0.16)			0.122449	21.842492	42.363689	18	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55968157	55968157	8445	4	G	A	A	A	507	39	KDR	1	1
CEP135	9662	broad.mit.edu	37	4	56865740	56865740	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:56865740G>A	uc003hbi.2	+	c.2209G>A	c.(2209-2211)GAC>AAC	p.D737N	CEP135_uc003hbj.2_Missense_Mutation_p.D443N	NM_025009	NP_079285	Q66GS9	CP135_HUMAN	centrosome protein 4	737	Potential.				centriole replication|centriole-centriole cohesion|G2/M transition of mitotic cell cycle	centriole|cytosol	protein C-terminus binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4	Glioma(25;0.08)|all_neural(26;0.101)													0.090909	4.11004	20.803642	9	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56865740	56865740	3380	4	G	A	A	A	429	33	CEP135	2	2
LPHN3	23284	broad.mit.edu	37	4	62812745	62812745	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:62812745G>T	uc010ihh.2	+	c.2329G>T	c.(2329-2331)GTC>TTC	p.V777F	LPHN3_uc003hcq.3_Missense_Mutation_p.V777F|LPHN3_uc003hct.2_Missense_Mutation_p.V170F	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	764	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.15847	56.225857	76.628381	29	154	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62812745	62812745	9290	4	G	T	T	T	624	48	LPHN3	2	2
EPHA5	2044	broad.mit.edu	37	4	66280039	66280039	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:66280039G>T	uc011cah.1	-	c.1650C>A	c.(1648-1650)GTC>GTA	p.V550V	EPHA5_uc003hcx.2_Silent_p.V481V|EPHA5_uc003hcy.2_Silent_p.V550V|EPHA5_uc003hcz.2_Silent_p.V550V|EPHA5_uc011cai.1_Silent_p.V550V|EPHA5_uc003hda.2_Silent_p.V550V	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	550	Extracellular (Potential).|Fibronectin type-III 2.				cAMP-mediated signaling|ephrin receptor signaling pathway|neuron development|protein phosphorylation	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(12)|ovary(2)|central_nervous_system(1)	15										537	TSP Lung(17;0.13)			0.109375	10.752758	30.10139	14	114	KEEP	---	---	---	---	capture		Silent	SNP	66280039	66280039	5363	4	G	T	T	T	418	33	EPHA5	2	2
UBA6	55236	broad.mit.edu	37	4	68504786	68504786	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:68504786C>A	uc003hdg.3	-	c.1611G>T	c.(1609-1611)AAG>AAT	p.K537N	UBA6_uc003hdh.1_Missense_Mutation_p.K63N	NM_018227	NP_060697	A0AVT1	UBA6_HUMAN	ubiquitin-activating enzyme E1-like 2	537					protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0														0.155172	14.632849	21.226067	9	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68504786	68504786	17389	4	C	A	A	A	415	32	UBA6	2	2
TMPRSS11F	389208	broad.mit.edu	37	4	68934426	68934426	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:68934426G>C	uc003hdt.1	-	c.665C>G	c.(664-666)GCC>GGC	p.A222G	LOC550112_uc003hdl.3_Intron	NM_207407	NP_997290	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	222	Peptidase S1.|Extracellular (Potential).				proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1														0.181818	19.002585	23.164697	8	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68934426	68934426	16784	4	G	C	C	C	546	42	TMPRSS11F	3	3
UGT2B10	7365	broad.mit.edu	37	4	69693259	69693259	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:69693259G>T	uc003hee.2	+	c.1300G>T	c.(1300-1302)GAT>TAT	p.D434Y	UGT2B10_uc011cam.1_Missense_Mutation_p.D350Y	NM_001075	NP_001066	P36537	UDB10_HUMAN	UDP glucuronosyltransferase 2B10 isoform 1	434					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(2)	2						Melanoma(133;755 1763 25578 26334 46021)								0.117117	10.284403	26.310664	13	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69693259	69693259	17514	4	G	T	T	T	585	45	UGT2B10	2	2
UGT2B7	7364	broad.mit.edu	37	4	69962824	69962824	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:69962824G>A	uc003heg.3	+	c.586G>A	c.(586-588)GTT>ATT	p.V196I	UGT2B7_uc010ihq.2_Missense_Mutation_p.V196I	NM_001074	NP_001065	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2B7 precursor	196					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)	1														0.179104	21.455242	27.95201	12	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69962824	69962824	17520	4	G	A	A	A	624	48	UGT2B7	2	2
MUC7	4589	broad.mit.edu	37	4	71346841	71346841	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:71346841C>G	uc011cat.1	+	c.380C>G	c.(379-381)CCA>CGA	p.P127R	MUC7_uc011cau.1_Missense_Mutation_p.P127R|MUC7_uc003hfj.2_Missense_Mutation_p.P127R	NM_001145006	NP_001138478	Q8TAX7	MUC7_HUMAN	mucin 7, secreted precursor	127	Thr-rich.					extracellular region	protein binding			ovary(2)|central_nervous_system(1)	3			Lung(101;0.211)											0.116022	26.735341	53.014857	21	160	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71346841	71346841	10375	4	C	G	G	G	273	21	MUC7	3	3
MUC7	4589	broad.mit.edu	37	4	71347516	71347516	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:71347516G>T	uc011cat.1	+	c.1055G>T	c.(1054-1056)GGC>GTC	p.G352V	MUC7_uc011cau.1_Missense_Mutation_p.G352V|MUC7_uc003hfj.2_Missense_Mutation_p.G352V	NM_001145006	NP_001138478	Q8TAX7	MUC7_HUMAN	mucin 7, secreted precursor	352						extracellular region	protein binding			ovary(2)|central_nervous_system(1)	3			Lung(101;0.211)											0.112676	16.793323	37.829387	16	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71347516	71347516	10375	4	G	T	T	T	546	42	MUC7	2	2
ENAM	10117	broad.mit.edu	37	4	71497577	71497577	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:71497577C>A	uc011caw.1	+	c.135C>A	c.(133-135)CCC>CCA	p.P45P		NM_031889	NP_114095	Q9NRM1	ENAM_HUMAN	enamelin precursor	45					bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)											0.125749	26.014531	48.808102	21	146	KEEP	---	---	---	---	capture		Silent	SNP	71497577	71497577	5305	4	C	A	A	A	275	22	ENAM	2	2
ANKRD17	26057	broad.mit.edu	37	4	74007528	74007528	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:74007528C>A	uc003hgp.2	-	c.2262G>T	c.(2260-2262)ATG>ATT	p.M754I	ANKRD17_uc003hgo.2_Missense_Mutation_p.M641I|ANKRD17_uc003hgq.2_Missense_Mutation_p.M754I|ANKRD17_uc003hgr.2_Missense_Mutation_p.M754I|ANKRD17_uc011cbd.1_Missense_Mutation_p.M319I	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	754					interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(2)|lung(1)	8	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)											0.137255	10.888246	17.383572	7	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74007528	74007528	649	4	C	A	A	A	273	21	ANKRD17	2	2
RASSF6	166824	broad.mit.edu	37	4	74447533	74447533	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:74447533C>A	uc003hhd.1	-	c.817_splice	c.e8+1	p.E273_splice	RASSF6_uc003hhc.1_Splice_Site_SNP_p.E241_splice|RASSF6_uc010iik.1_Splice_Site_SNP_p.E207_splice|RASSF6_uc010iil.1_Splice_Site_SNP_p.E229_splice	NM_201431	NP_958834			Ras association (RalGDS/AF-6) domain family 6						apoptosis|signal transduction		protein binding			pancreas(2)	2	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)											0.092308	0.795374	11.682944	6	59	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	74447533	74447533	13551	4	C	A	A	A	234	18	RASSF6	5	2
CDKL2	8999	broad.mit.edu	37	4	76532502	76532502	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:76532502T>A	uc011cbp.1	-	c.407A>T	c.(406-408)CAG>CTG	p.Q136L	CDKL2_uc003hiq.2_Missense_Mutation_p.Q136L|CDKL2_uc010iix.1_Intron	NM_003948	NP_003939	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2	136	Protein kinase.				protein phosphorylation|sex differentiation|signal transduction	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(2)|breast(2)	4			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)							284				0.134831	20.237935	31.742896	12	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76532502	76532502	3283	4	T	A	A	A	715	55	CDKL2	3	3
PPEF2	5470	broad.mit.edu	37	4	76787428	76787428	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:76787428G>A	uc003hix.2	-	c.1834C>T	c.(1834-1836)CCA>TCA	p.P612S	PPEF2_uc003hiy.2_Non-coding_Transcript|PPEF2_uc003hiz.1_3'UTR	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	612					detection of stimulus involved in sensory perception|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			NSCLC(105;1359 1603 15961 44567 47947)								0.113402	8.094275	22.370602	11	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76787428	76787428	12738	4	G	A	A	A	546	42	PPEF2	2	2
ANKRD56	345079	broad.mit.edu	37	4	77817798	77817798	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:77817798C>G	uc003hki.2	-	c.1205G>C	c.(1204-1206)AGT>ACT	p.S402T		NM_001029870	NP_001025041	A6NEL2	ANR56_HUMAN	ankyrin repeat domain 56	402											0														0.108808	32.227692	61.488306	21	172	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77817798	77817798	690	4	C	G	G	G	260	20	ANKRD56	3	3
ANXA3	306	broad.mit.edu	37	4	79522677	79522677	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:79522677G>T	uc003hld.2	+	c.744G>T	c.(742-744)AGG>AGT	p.R248S	ANXA3_uc003hle.2_Missense_Mutation_p.R209S|ANXA3_uc010ijk.2_Missense_Mutation_p.R209S	NM_005139	NP_005130	P12429	ANXA3_HUMAN	annexin A3	248					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)								0.090909	1.970172	20.529241	10	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79522677	79522677	727	4	G	T	T	T	529	41	ANXA3	2	2
NAA11	84779	broad.mit.edu	37	4	80246689	80246689	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:80246689T>A	uc003hlt.3	-	c.343A>T	c.(343-345)AAC>TAC	p.N115Y		NM_032693	NP_116082	Q9BSU3	NAA11_HUMAN	alpha-N-acetyltransferase 1B	115	N-acetyltransferase.					cytoplasm|nucleus	peptide alpha-N-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2														0.117647	7.555346	17.3267	8	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80246689	80246689	10512	4	T	A	A	A	793	61	NAA11	3	3
PRKG2	5593	broad.mit.edu	37	4	82090872	82090872	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:82090872T>A	uc003hmh.2	-	c.793A>T	c.(793-795)ATA>TTA	p.I265L	PRKG2_uc011cch.1_Missense_Mutation_p.I265L	NM_006259	NP_006250	Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	265	cGMP 1.				platelet activation|protein phosphorylation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7										728				0.10084	10.613633	29.536438	12	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82090872	82090872	12966	4	T	A	A	A	637	49	PRKG2	3	3
HTRA3	94031	broad.mit.edu	37	4	8307701	8307701	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:8307701C>A	uc003gla.2	+	c.1200C>A	c.(1198-1200)GGC>GGA	p.G400G		NM_053044	NP_444272	P83110	HTRA3_HUMAN	HtrA serine peptidase 3 precursor	400	PDZ.				proteolysis|regulation of cell growth	extracellular region	insulin-like growth factor binding|serine-type endopeptidase activity			ovary(1)	1														0.065217	-9.736358	26.187085	12	172	KEEP	---	---	---	---	capture		Silent	SNP	8307701	8307701	7755	4	C	A	A	A	340	27	HTRA3	1	1
ACOX3	8310	broad.mit.edu	37	4	8418141	8418141	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:8418141C>T	uc010idk.2	-	c.108G>A	c.(106-108)GCG>GCA	p.A36A	ACOX3_uc003glc.3_Silent_p.A36A|ACOX3_uc003gld.3_Silent_p.A36A|ACOX3_uc003gle.1_5'Flank	NM_003501	NP_003492	O15254	ACOX3_HUMAN	acyl-Coenzyme A oxidase 3 isoform a	36					bile acid metabolic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|pristanoyl-CoA oxidase activity			central_nervous_system(1)	1														0.15748	33.55255	47.739143	20	107	KEEP	---	---	---	---	capture		Silent	SNP	8418141	8418141	161	4	C	T	T	T	340	27	ACOX3	1	1
GPR78	27201	broad.mit.edu	37	4	8584301	8584301	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:8584301C>A	uc003glk.2	+	c.712C>A	c.(712-714)CGC>AGC	p.R238S	CPZ_uc003gll.2_Non-coding_Transcript	NM_080819	NP_543009	Q96P69	GPR78_HUMAN	G protein-coupled receptor 78	238	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(4)|ovary(2)	6														0.104478	9.854784	30.70926	14	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8584301	8584301	6985	4	C	A	A	A	299	23	GPR78	1	1
SLC10A6	345274	broad.mit.edu	37	4	87770121	87770121	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:87770121C>A	uc003hqd.2	-	c.148G>T	c.(148-150)GGA>TGA	p.G50*		NM_197965	NP_932069	Q3KNW5	SOAT_HUMAN	sodium-dependent organic anion transporter	50	Helical; (Potential).					integral to membrane|plasma membrane	bile acid:sodium symporter activity				0		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.00099)										0.125	6.380079	14.085395	7	49	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	87770121	87770121	14873	4	C	A	A	A	286	22	SLC10A6	5	2
MEPE	56955	broad.mit.edu	37	4	88767462	88767462	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:88767462G>T	uc003hqy.2	+	c.1442G>T	c.(1441-1443)CGG>CTG	p.R481L	MEPE_uc010ikn.2_Missense_Mutation_p.R368L	NM_020203	NP_064588	Q9NQ76	MEPE_HUMAN	matrix, extracellular phosphoglycoprotein with	481					skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding			ovary(1)|lung(1)	2		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)										0.155039	38.415768	53.083711	20	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88767462	88767462	9867	4	G	T	T	T	507	39	MEPE	1	1
FAM13A	10144	broad.mit.edu	37	4	89679943	89679943	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:89679943G>C	uc003hse.1	-	c.1688C>G	c.(1687-1689)TCG>TGG	p.S563W	FAM13A_uc003hsa.1_Missense_Mutation_p.S34W|FAM13A_uc003hsb.1_Missense_Mutation_p.S237W|FAM13A_uc003hsd.1_Missense_Mutation_p.S237W|FAM13A_uc003hsc.1_Missense_Mutation_p.S223W|FAM13A_uc011cdq.1_Missense_Mutation_p.S209W|FAM13A_uc003hsf.1_Missense_Mutation_p.S149W|FAM13A_uc003hsg.1_Missense_Mutation_p.S34W|FAM13A_uc010ikr.1_Missense_Mutation_p.S59W	NM_014883	NP_055698	O94988	FA13A_HUMAN	family with sequence similarity 13, member A1	563					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2														0.1375	19.571265	29.74127	11	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89679943	89679943	5649	4	G	C	C	C	481	37	FAM13A	3	3
SNCA	6622	broad.mit.edu	37	4	90743477	90743477	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:90743477C>A	uc003hsq.2	-	c.226G>T	c.(226-228)GCA>TCA	p.A76S	SNCA_uc010ikt.2_Missense_Mutation_p.A62S|SNCA_uc003hso.2_Missense_Mutation_p.A76S|SNCA_uc003hsp.2_Missense_Mutation_p.A76S|SNCA_uc003hsr.2_Missense_Mutation_p.A76S	NM_001146054	NP_001139526	P37840	SYUA_HUMAN	alpha-synuclein isoform NACP140	76				Missing: Impairs polymerization into amyloid fibrils.|Missing: Impairs polymerization into amyloid fibrils.|Missing: Does not affect polymerization into amyloid fibrils.	activation of caspase activity|anti-apoptosis|negative regulation of caspase activity|negative regulation of dopamine uptake|negative regulation of exocytosis|negative regulation of histone acetylation|negative regulation of microtubule polymerization|negative regulation of monooxygenase activity|negative regulation of norepinephrine uptake|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of serotonin uptake|negative regulation of thrombin receptor signaling pathway|negative regulation of transporter activity|positive regulation of endocytosis|positive regulation of inositol phosphate biosynthetic process|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein serine/threonine kinase activity|positive regulation of receptor recycling|positive regulation of release of sequestered calcium ion into cytosol|receptor internalization|regulation of phospholipase activity|response to interferon-gamma|response to interleukin-1|response to iron(II) ion|response to lipopolysaccharide|response to magnesium ion|synaptic vesicle endocytosis	actin cytoskeleton|axon|cell cortex|cell junction|cytosol|fibril|growth cone|nucleus|synapse	alpha-tubulin binding|calcium ion binding|caspase inhibitor activity|dynein binding|ferrous iron binding|histone binding|Hsp70 protein binding|kinesin binding|magnesium ion binding|phosphoprotein binding|tau protein binding|zinc ion binding				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.42e-05)	Melatonin(DB01065)									0.117647	7.545913	17.326212	8	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90743477	90743477	15340	4	C	A	A	A	364	28	SNCA	2	2
MMRN1	22915	broad.mit.edu	37	4	90844382	90844382	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:90844382G>T	uc003hst.2	+	c.914G>T	c.(913-915)GGA>GTA	p.G305V	MMRN1_uc010iku.2_Missense_Mutation_p.G271V|MMRN1_uc011cds.1_Missense_Mutation_p.G47V	NM_007351	NP_031377	Q13201	MMRN1_HUMAN	multimerin 1	305					cell adhesion|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen				ovary(4)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)										0.12381	21.179787	50.322182	26	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90844382	90844382	10061	4	G	T	T	T	533	41	MMRN1	2	2
MMRN1	22915	broad.mit.edu	37	4	90857618	90857618	+	Silent	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:90857618A>G	uc003hst.2	+	c.2787A>G	c.(2785-2787)ACA>ACG	p.T929T	MMRN1_uc010iku.2_Intron|MMRN1_uc011cds.1_Silent_p.T671T	NM_007351	NP_031377	Q13201	MMRN1_HUMAN	multimerin 1	929					cell adhesion|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen				ovary(4)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)										0.119403	9.851705	19.378605	8	59	KEEP	---	---	---	---	capture		Silent	SNP	90857618	90857618	10061	4	A	G	G	G	54	5	MMRN1	4	4
MMRN1	22915	broad.mit.edu	37	4	90874276	90874276	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:90874276C>A	uc003hst.2	+	c.3394C>A	c.(3394-3396)CCA>ACA	p.P1132T	MMRN1_uc010iku.2_Missense_Mutation_p.P435T|MMRN1_uc011cds.1_Missense_Mutation_p.P874T	NM_007351	NP_031377	Q13201	MMRN1_HUMAN	multimerin 1	1132	C1q.				cell adhesion|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen				ovary(4)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)										0.098765	3.934854	16.984006	8	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90874276	90874276	10061	4	C	A	A	A	286	22	MMRN1	2	2
SMARCAD1	56916	broad.mit.edu	37	4	95162122	95162122	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:95162122G>C	uc003htb.3	+	c.670G>C	c.(670-672)GAT>CAT	p.D224H	SMARCAD1_uc003htc.3_Missense_Mutation_p.D224H|SMARCAD1_uc003htd.3_Missense_Mutation_p.D224H|SMARCAD1_uc010ila.2_Missense_Mutation_p.D87H	NM_001128430	NP_001121902	Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated	224					chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)										0.103448	5.002317	9.542803	3	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95162122	95162122	15270	4	G	C	C	C	585	45	SMARCAD1	3	3
BMPR1B	658	broad.mit.edu	37	4	96051084	96051084	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:96051084G>T	uc003htm.3	+	c.657G>T	c.(655-657)TGG>TGT	p.W219C	BMPR1B_uc010ilb.2_Missense_Mutation_p.W219C|BMPR1B_uc003htn.3_Missense_Mutation_p.W219C	NM_001203	NP_001194	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB	219	Cytoplasmic (Potential).|Protein kinase.				BMP signaling pathway|cartilage condensation|eye development|limb morphogenesis|ovarian cumulus expansion|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|protein phosphorylation	integral to plasma membrane|receptor complex	ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta receptor activity			lung(2)|stomach(1)|skin(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)						166				0.101449	3.389524	14.312531	7	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	96051084	96051084	1495	4	G	T	T	T	533	41	BMPR1B	2	2
PAM	5066	broad.mit.edu	37	5	102361025	102361025	+	Silent	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:102361025A>C	uc003knt.2	+	c.2676A>C	c.(2674-2676)TCA>TCC	p.S892S	PAM_uc003kns.2_Silent_p.S785S|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc003knw.2_Silent_p.S892S|PAM_uc011cuz.1_Silent_p.S794S|PAM_uc003knz.2_Silent_p.S132S	NM_000919	NP_000910	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	892	Cytoplasmic (Potential).				oxidation-reduction process|peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)									0.098214	15.24337	33.330002	11	101	KEEP	---	---	---	---	capture		Silent	SNP	102361025	102361025	11829	5	A	C	C	C	54	5	PAM	4	4
MARCH6	10299	broad.mit.edu	37	5	10423937	10423937	+	Splice_Site_SNP	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:10423937G>T	uc003jet.1	+	c.2373_splice	c.e23+1	p.Q791_splice	MARCH6_uc011cmu.1_Splice_Site_SNP_p.Q743_splice|MARCH6_uc003jeu.1_Splice_Site_SNP_p.Q489_splice|MARCH6_uc011cmv.1_Splice_Site_SNP_p.Q686_splice	NM_005885	NP_005876			membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding				0														0.15	17.032933	24.081267	9	51	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	10423937	10423937	9688	5	G	T	T	T	572	44	MARCH6	5	2
APC	324	broad.mit.edu	37	5	112175975	112175975	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:112175975G>A	uc010jby.2	+	c.4684G>A	c.(4684-4686)GAC>AAC	p.D1562N	APC_uc011cvt.1_Missense_Mutation_p.D1544N|APC_uc003kpz.3_Missense_Mutation_p.D1562N|APC_uc003kpy.3_Missense_Mutation_p.D1562N|APC_uc010jbz.2_Missense_Mutation_p.D1279N|APC_uc010jca.2_Missense_Mutation_p.D862N	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli	1562	Ser-rich.|Asp/Glu-rich (acidic).				canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of protein catabolic process|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity	p.K1192fs*3(1)|p.?(1)		large_intestine(2012)|stomach(123)|soft_tissue(55)|small_intestine(34)|pancreas(25)|breast(23)|urinary_tract(20)|lung(18)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|upper_aerodigestive_tract(6)|adrenal_gland(6)|NS(5)|bone(5)|skin(4)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2396		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		12		629	TSP Lung(16;0.13)			0.148515	26.157065	38.132854	15	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112175975	112175975	773	5	G	A	A	A	533	41	APC	2	2
CEP120	153241	broad.mit.edu	37	5	122734967	122734967	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:122734967G>C	uc003ktk.2	-	c.475C>G	c.(475-477)CTG>GTG	p.L159V	CEP120_uc011cwq.1_5'UTR|CEP120_uc010jcz.1_Missense_Mutation_p.L133V	NM_153223	NP_694955	Q8N960	CE120_HUMAN	coiled-coil domain containing 100	159										ovary(1)	1														0.254237	40.294946	43.530126	15	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122734967	122734967	3379	5	G	C	C	C	451	35	CEP120	3	3
SLC6A18	348932	broad.mit.edu	37	5	1242871	1242871	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:1242871T>C	uc003jby.1	+	c.1024T>C	c.(1024-1026)TCC>CCC	p.S342P		NM_182632	NP_872438	Q96N87	S6A18_HUMAN	solute carrier family 6, member 18	342	Extracellular (Potential).				cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			ovary(1)	1	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)											0.080292	5.030684	29.625878	11	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1242871	1242871	15178	5	T	C	C	C	702	54	SLC6A18	4	4
MEGF10	84466	broad.mit.edu	37	5	126674906	126674906	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:126674906C>A	uc003kuh.3	+	c.211C>A	c.(211-213)CGG>AGG	p.R71R	MEGF10_uc010jdc.1_Silent_p.R71R|MEGF10_uc010jdd.1_Silent_p.R71R|MEGF10_uc003kui.3_Silent_p.R71R	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor	71	Extracellular (Potential).|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.|EMI.				cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)										0.182927	33.677226	41.41532	15	67	KEEP	---	---	---	---	capture		Silent	SNP	126674906	126674906	9849	5	C	A	A	A	347	27	MEGF10	1	1
SLC27A6	28965	broad.mit.edu	37	5	128302064	128302064	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:128302064C>T	uc003kuy.2	+	c.234C>T	c.(232-234)GAC>GAT	p.D78D	SLC27A6_uc003kuz.2_Silent_p.D78D	NM_014031	NP_054750	Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid	78					long-chain fatty acid transport|transmembrane transport|very long-chain fatty acid metabolic process	integral to membrane|sarcolemma	fatty acid transporter activity|long-chain fatty acid-CoA ligase activity|nucleotide binding				0		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)										0.19	34.457794	43.45396	19	81	KEEP	---	---	---	---	capture		Silent	SNP	128302064	128302064	15027	5	C	T	T	T	220	17	SLC27A6	2	2
IL3	3562	broad.mit.edu	37	5	131398035	131398035	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:131398035G>T	uc003kwe.1	+	c.235G>T	c.(235-237)GCA>TCA	p.A79S		NM_000588	NP_000579	P08700	IL3_HUMAN	interleukin 3 precursor	79					cell-cell signaling|immune response|nervous system development|positive regulation of cell proliferation|positive regulation of DNA replication|positive regulation of survival gene product expression|positive regulation of tyrosine phosphorylation of Stat5 protein	extracellular space	cytokine activity|growth factor activity|interleukin-3 receptor binding			ovary(2)|central_nervous_system(1)	3		all_cancers(142;7.42e-12)|Lung NSC(810;4.25e-07)|all_lung(232;1.93e-06)|Prostate(281;0.00741)|Breast(839;0.0544)|Lung SC(612;0.122)|Ovarian(839;0.223)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	GBM - Glioblastoma multiforme(465;0.0161)|Lung(113;0.105)	Amlexanox(DB01025)					56				0.080906	-1.578144	53.75191	25	284	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131398035	131398035	7990	5	G	T	T	T	546	42	IL3	2	2
PITX1	5307	broad.mit.edu	37	5	134366998	134366998	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:134366998C>T	uc010jea.2	-	c.370G>A	c.(370-372)GTG>ATG	p.V124M	PITX1_uc011cxy.1_Missense_Mutation_p.V124M	NM_002653	NP_002644	P78337	PITX1_HUMAN	paired-like homeodomain transcription factor 1	124	Homeobox.					nucleolus	sequence-specific DNA binding|transcription regulator activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	READ - Rectum adenocarcinoma(2;0.0607)										0.122449	6.251285	13.061661	6	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134366998	134366998	12378	5	C	T	T	T	247	19	PITX1	1	1
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139889656	139889656	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:139889656G>T	uc003lfs.1	+	c.3994G>T	c.(3994-3996)GCA>TCA	p.A1332S	ANKHD1_uc003lfq.1_Missense_Mutation_p.A1351S|ANKHD1_uc003lfr.2_Missense_Mutation_p.A1332S|ANKHD1_uc003lft.1_Missense_Mutation_p.A543S|ANKHD1_uc003lfu.1_Missense_Mutation_p.A812S|ANKHD1_uc003lfv.1_Missense_Mutation_p.A409S|ANKHD1-EIF4EBP3_uc011czh.1_Missense_Mutation_p.A71S|ANKHD1_uc003lfw.2_5'UTR	NM_020690	NP_065741	Q8IWZ2	Q8IWZ2_HUMAN	ANKHD1-EIF4EBP3 protein	1332						cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.142857	21.986118	34.868989	15	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139889656	139889656	632	5	G	T	T	T	546	42	ANKHD1-EIF4EBP3	2	2
IK	3550	broad.mit.edu	37	5	140041211	140041211	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140041211A>G	uc003lgq.2	+	c.1420A>G	c.(1420-1422)AAG>GAG	p.K474E		NM_006083	NP_006074	Q13123	RED_HUMAN	RED protein	474					cell-cell signaling|immune response	extracellular space|nucleus|soluble fraction				large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.3	8.121087	8.478551	3	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140041211	140041211	7909	5	A	G	G	G	65	5	IK	4	4
PCDHA2	56146	broad.mit.edu	37	5	140175321	140175321	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140175321G>T	uc003lhd.2	+	c.772G>T	c.(772-774)GGG>TGG	p.G258W	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Missense_Mutation_p.G258W|PCDHA2_uc011czy.1_Missense_Mutation_p.G258W	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	258	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.070866	-9.765683	38.480938	18	236	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140175321	140175321	11944	5	G	T	T	T	611	47	PCDHA2	2	2
PCDHA3	56145	broad.mit.edu	37	5	140182121	140182121	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140182121G>T	uc003lhf.2	+	c.1339G>T	c.(1339-1341)GAC>TAC	p.D447Y	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Missense_Mutation_p.D447Y	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	447	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(5)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.251908	76.314284	83.639026	33	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140182121	140182121	11945	5	G	T	T	T	481	37	PCDHA3	1	1
PCDHA8	56140	broad.mit.edu	37	5	140222067	140222067	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140222067C>A	uc003lhs.2	+	c.1161C>A	c.(1159-1161)TGC>TGA	p.C387*	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_uc003lhr.1_Nonsense_Mutation_p.C387*	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	387	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.198083	125.654595	152.243845	62	251	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	140222067	140222067	11950	5	C	A	A	A	363	28	PCDHA8	5	2
PCDHA10	56139	broad.mit.edu	37	5	140235754	140235754	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140235754G>T	uc003lhx.2	+	c.121G>T	c.(121-123)GGC>TGC	p.G41C	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_Missense_Mutation_p.G41C|PCDHA10_uc011dad.1_Missense_Mutation_p.G41C	NM_018901	NP_061724	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10 isoform 1 precursor	41	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|breast(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.148148	25.131053	37.973827	16	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140235754	140235754	11940	5	G	T	T	T	507	39	PCDHA10	1	1
PCDHAC2	56134	broad.mit.edu	37	5	140347671	140347671	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140347671A>T	uc003lii.2	+	c.1320A>T	c.(1318-1320)ACA>ACT	p.T440T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_Intron|PCDHAC2_uc011dag.1_Silent_p.T440T	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1	440	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			Melanoma(190;638 2083 3390 11909 52360)								0.273292	113.347795	120.794697	44	117	KEEP	---	---	---	---	capture		Silent	SNP	140347671	140347671	11953	5	A	T	T	T	80	7	PCDHAC2	3	3
PCDHB12	56124	broad.mit.edu	37	5	140590170	140590170	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140590170C>A	uc003liz.2	+	c.1691C>A	c.(1690-1692)CCG>CAG	p.P564Q	PCDHB12_uc011dak.1_Missense_Mutation_p.P227Q	NM_018932	NP_061755	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12 precursor	564	Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.183333	21.094353	26.740324	11	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140590170	140590170	11957	5	C	A	A	A	299	23	PCDHB12	1	1
PCDHB15	56121	broad.mit.edu	37	5	140627195	140627195	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140627195C>A	uc003lje.2	+	c.2049C>A	c.(2047-2049)GCC>GCA	p.A683A		NM_018935	NP_061758	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15 precursor	683	Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|breast(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.116438	17.810641	38.833093	17	129	KEEP	---	---	---	---	capture		Silent	SNP	140627195	140627195	11960	5	C	A	A	A	288	23	PCDHB15	1	1
PCDHGA2	56113	broad.mit.edu	37	5	140720200	140720200	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140720200C>G	uc003ljk.1	+	c.1662C>G	c.(1660-1662)GAC>GAG	p.D554E	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Missense_Mutation_p.D554E	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	554	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.067568	-10.684535	46.702466	20	276	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140720200	140720200	11974	5	C	G	G	G	233	18	PCDHGA2	3	3
PCDHGA4	56111	broad.mit.edu	37	5	140737049	140737049	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140737049C>A	uc003ljq.1	+	c.2282C>A	c.(2281-2283)GCG>GAG	p.A761E	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGB2_uc003ljs.1_5'Flank|PCDHGA4_uc003ljp.1_Missense_Mutation_p.A761E|PCDHGB2_uc011dar.1_5'Flank	NM_018917	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4 isoform 1	761	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)											0.1875	52.72637	64.430027	24	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140737049	140737049	11976	5	C	A	A	A	351	27	PCDHGA4	1	1
PCDHGB2	56103	broad.mit.edu	37	5	140740131	140740131	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140740131C>G	uc003ljs.1	+	c.429C>G	c.(427-429)GGC>GGG	p.G143G	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_uc011dar.1_Silent_p.G143G	NM_018923	NP_061746	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2 isoform 1	143	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.175258	41.933866	51.566239	17	80	KEEP	---	---	---	---	capture		Silent	SNP	140740131	140740131	11983	5	C	G	G	G	340	27	PCDHGB2	3	3
PCDHGA6	56109	broad.mit.edu	37	5	140753939	140753939	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140753939G>T	uc003ljy.1	+	c.289G>T	c.(289-291)GCT>TCT	p.A97S	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_uc011dau.1_Missense_Mutation_p.A97S	NM_018919	NP_061742	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6 isoform 1	97	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)											0.188119	41.886321	50.990456	19	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140753939	140753939	11978	5	G	T	T	T	598	46	PCDHGA6	2	2
ARAP3	64411	broad.mit.edu	37	5	141059632	141059632	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:141059632G>A	uc003llm.2	-	c.422C>T	c.(421-423)TCC>TTC	p.S141F	ARAP3_uc003lln.2_Missense_Mutation_p.S63F|ARAP3_uc003llo.1_Missense_Mutation_p.S141F	NM_022481	NP_071926	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	141					cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding			breast(5)|ovary(1)|large_intestine(1)	7														0.072978	-16.651198	78.469085	37	470	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141059632	141059632	851	5	G	A	A	A	533	41	ARAP3	2	2
ARHGAP26	23092	broad.mit.edu	37	5	142273824	142273824	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:142273824G>C	uc011dbj.1	+	c.508G>C	c.(508-510)GTC>CTC	p.V170L	ARHGAP26_uc003lmt.2_Missense_Mutation_p.V170L|ARHGAP26_uc003lmw.2_Missense_Mutation_p.V170L	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal	170					actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)							831				0.258621	47.39809	50.459061	15	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142273824	142273824	887	5	G	C	C	C	572	44	ARHGAP26	3	3
LARS	51520	broad.mit.edu	37	5	145499985	145499985	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:145499985T>A	uc003lnx.1	-	c.3274A>T	c.(3274-3276)AAC>TAC	p.N1092Y	LARS_uc003lnw.1_Missense_Mutation_p.N250Y|LARS_uc011dbq.1_Missense_Mutation_p.N1046Y|LARS_uc011dbr.1_Missense_Mutation_p.N1038Y|LARS_uc011dbs.1_Missense_Mutation_p.N1065Y	NM_020117	NP_064502	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	1092					leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)									0.248175	81.788168	89.688936	34	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145499985	145499985	8957	5	T	A	A	A	793	61	LARS	3	3
PPP2R2B	5521	broad.mit.edu	37	5	146257616	146257616	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:146257616T>C	uc011dbv.1	-	c.193A>G	c.(193-195)ACC>GCC	p.T65A	PPP2R2B_uc003loe.2_Missense_Mutation_p.T7A|PPP2R2B_uc010jgm.2_De_novo_Start_InFrame|PPP2R2B_uc003log.3_Missense_Mutation_p.T7A|PPP2R2B_uc003lof.3_Missense_Mutation_p.T7A|PPP2R2B_uc003loi.3_Intron|PPP2R2B_uc003loh.3_Missense_Mutation_p.T7A|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron	NM_181675	NP_858061	Q00005	2ABB_HUMAN	beta isoform of regulatory subunit B55, protein	7					apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.077778	0.967471	17.362578	7	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	146257616	146257616	12821	5	T	C	C	C	741	57	PPP2R2B	4	4
AFAP1L1	134265	broad.mit.edu	37	5	148685935	148685935	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:148685935C>A	uc003lqh.2	+	c.503C>A	c.(502-504)GCA>GAA	p.A168E	AFAP1L1_uc003lqg.3_Missense_Mutation_p.A168E|AFAP1L1_uc010jgy.2_Missense_Mutation_p.A168E	NM_152406	NP_689619	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	168							protein binding			breast(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.269231	18.112156	19.362488	7	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148685935	148685935	355	5	C	A	A	A	325	25	AFAP1L1	2	2
PDE6A	5145	broad.mit.edu	37	5	149264109	149264109	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:149264109G>A	uc003lrg.3	-	c.1960C>T	c.(1960-1962)CAG>TAG	p.Q654*		NM_000440	NP_000431	P16499	PDE6A_HUMAN	phosphodiesterase 6A	654					cytosolic calcium ion homeostasis|GMP metabolic process|platelet activation|signal transduction|visual perception	cytosol|plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)											0.205882	40.69875	48.906369	21	81	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	149264109	149264109	12066	5	G	A	A	A	624	48	PDE6A	5	2
GRIA1	2890	broad.mit.edu	37	5	153182038	153182038	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:153182038C>T	uc011dcy.1	+	c.2538C>T	c.(2536-2538)TCC>TCT	p.S846S	GRIA1_uc003lva.3_Silent_p.S836S|GRIA1_uc003luy.3_Silent_p.S836S|GRIA1_uc003luz.3_Silent_p.S741S|GRIA1_uc011dcv.1_Non-coding_Transcript|GRIA1_uc011dcw.1_Silent_p.S756S|GRIA1_uc011dcx.1_Silent_p.S767S|GRIA1_uc011dcz.1_Silent_p.S846S	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	836	Cytoplasmic (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(1)	5		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)									0.098976	16.241329	63.507448	29	264	KEEP	---	---	---	---	capture		Silent	SNP	153182038	153182038	7045	5	C	T	T	T	262	21	GRIA1	2	2
ADAM19	8728	broad.mit.edu	37	5	156991421	156991421	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:156991421C>G	uc003lwz.2	-	c.211G>C	c.(211-213)GCT>CCT	p.A71P	ADAM19_uc003lww.1_5'UTR|ADAM19_uc011ddr.1_Missense_Mutation_p.A2P	NM_033274	NP_150377	Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19 preproprotein	71					proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	7	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)											0.166667	38.839126	48.951592	16	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156991421	156991421	241	5	C	G	G	G	338	26	ADAM19	3	3
CLINT1	9685	broad.mit.edu	37	5	157214823	157214823	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:157214823G>A	uc011ddv.1	-	c.1763C>T	c.(1762-1764)CCG>CTG	p.P588L	CLINT1_uc003lxg.1_Missense_Mutation_p.P107L|CLINT1_uc003lxh.1_Missense_Mutation_p.P144L|CLINT1_uc003lxi.1_Missense_Mutation_p.P570L|CLINT1_uc003lxj.1_Missense_Mutation_p.P570L	NM_014666	NP_055481	Q14677	EPN4_HUMAN	epsin 4	570	Met-rich.				endocytosis|post-Golgi vesicle-mediated transport	clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm	clathrin binding|lipid binding			ovary(2)|pancreas(1)	3	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)			Colon(22;427 587 2170 6147 14291)								0.221053	52.62473	59.428151	21	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157214823	157214823	3669	5	G	A	A	A	507	39	CLINT1	1	1
CLINT1	9685	broad.mit.edu	37	5	157233056	157233056	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:157233056C>A	uc011ddv.1	-	c.760G>T	c.(760-762)GAG>TAG	p.E254*	CLINT1_uc003lxi.1_Nonsense_Mutation_p.E236*|CLINT1_uc003lxj.1_Nonsense_Mutation_p.E254*	NM_014666	NP_055481	Q14677	EPN4_HUMAN	epsin 4	254					endocytosis|post-Golgi vesicle-mediated transport	clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm	clathrin binding|lipid binding			ovary(2)|pancreas(1)	3	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)			Colon(22;427 587 2170 6147 14291)								0.16129	15.804768	22.57912	10	52	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	157233056	157233056	3669	5	C	A	A	A	416	32	CLINT1	5	2
FBXL7	23194	broad.mit.edu	37	5	15936789	15936789	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:15936789G>T	uc003jfn.1	+	c.970G>T	c.(970-972)GCC>TCC	p.A324S		NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	324	LRR 6.				ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3														0.272727	21.361776	22.89771	9	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15936789	15936789	5961	5	G	T	T	T	494	38	FBXL7	1	1
FBXL7	23194	broad.mit.edu	37	5	15936818	15936818	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:15936818C>A	uc003jfn.1	+	c.999C>A	c.(997-999)GAC>GAA	p.D333E		NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	333	LRR 6.				ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3														0.357143	13.57019	13.822232	5	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15936818	15936818	5961	5	C	A	A	A	259	20	FBXL7	2	2
GABRB2	2561	broad.mit.edu	37	5	160763691	160763691	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:160763691C>A	uc003lys.1	-	c.627G>T	c.(625-627)CAG>CAT	p.Q209H	GABRB2_uc011deh.1_Missense_Mutation_p.Q48H|GABRB2_uc003lyr.1_Missense_Mutation_p.Q209H|GABRB2_uc003lyt.1_Missense_Mutation_p.Q209H|GABRB2_uc010jiu.1_Missense_Mutation_p.Q146H	NM_021911	NP_068711	P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	209	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)									0.177778	33.841291	42.643682	16	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160763691	160763691	6418	5	C	A	A	A	259	20	GABRB2	2	2
CCDC99	54908	broad.mit.edu	37	5	169015427	169015427	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:169015427G>C	uc003mae.3	+	c.7G>C	c.(7-9)GCA>CCA	p.A3P	CCDC99_uc010jjj.2_5'UTR|CCDC99_uc011deq.1_5'UTR|CCDC99_uc010jjk.2_5'UTR	NM_017785	NP_060255	Q96EA4	SPDLY_HUMAN	coiled-coil domain containing 99	3	Potential.				cell division|establishment of mitotic spindle orientation|mitotic metaphase plate congression|mitotic prometaphase|protein localization to kinetochore	condensed chromosome outer kinetochore|cytosol|microtubule organizing center|nucleus|spindle pole	kinetochore binding|protein binding			ovary(1)|liver(1)	2	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)											0.113636	6.639205	13.125006	5	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169015427	169015427	3001	5	G	C	C	C	546	42	CCDC99	3	3
FOXI1	2299	broad.mit.edu	37	5	169535124	169535124	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:169535124A>G	uc003mai.3	+	c.646A>G	c.(646-648)AGG>GGG	p.R216G	FOXI1_uc003maj.3_Intron	NM_012188	NP_036320	Q12951	FOXI1_HUMAN	forkhead box I1 isoform a	216	Fork-head.				epidermal cell fate specification|negative regulation of gene-specific transcription from RNA polymerase II promoter|otic placode formation|pattern specification process|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter 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			breast(3)|central_nervous_system(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)											0.111111	18.616131	34.774611	12	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169535124	169535124	6254	5	A	G	G	G	36	3	FOXI1	4	4
STK10	6793	broad.mit.edu	37	5	171509466	171509466	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:171509466C>T	uc003mbo.1	-	c.1853G>A	c.(1852-1854)CGT>CAT	p.R618H		NM_005990	NP_005981	O94804	STK10_HUMAN	serine/threonine kinase 10	618	Potential.				protein phosphorylation		ATP binding|protein serine/threonine kinase activity			ovary(3)|testis(1)|lung(1)|pancreas(1)	6	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)							570				0.18125	58.478829	73.756636	29	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	171509466	171509466	15806	5	C	T	T	T	247	19	STK10	1	1
C5orf25	375484	broad.mit.edu	37	5	175716848	175716848	+	Silent	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:175716848G>C	uc011dfk.1	+	c.321G>C	c.(319-321)GCG>GCC	p.A107A	C5orf25_uc003mdt.3_Intron|C5orf25_uc003mds.3_Silent_p.A88A|C5orf25_uc003mdr.3_Intron	NM_198567	NP_940969	Q8NDZ2	CE025_HUMAN	hypothetical protein LOC375484	88											0	all_cancers(89;0.00381)|Renal(175;0.000269)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.119)										0.164384	26.75543	34.561325	12	61	KEEP	---	---	---	---	capture		Silent	SNP	175716848	175716848	2386	5	G	C	C	C	495	39	C5orf25	3	3
GPRIN1	114787	broad.mit.edu	37	5	176024932	176024932	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176024932C>A	uc003meo.1	-	c.1904G>T	c.(1903-1905)GGT>GTT	p.G635V		NM_052899	NP_443131	Q7Z2K8	GRIN1_HUMAN	G protein-regulated inducer of neurite outgrowth	635						growth cone|plasma membrane				ovary(2)	2	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.123077	8.851054	17.893315	8	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176024932	176024932	7005	5	C	A	A	A	234	18	GPRIN1	2	2
HK3	3101	broad.mit.edu	37	5	176315748	176315748	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176315748T>A	uc003mfa.2	-	c.1032A>T	c.(1030-1032)CAA>CAT	p.Q344H	HK3_uc003mez.2_De_novo_Start_OutOfFrame	NM_002115	NP_002106	P52790	HXK3_HUMAN	hexokinase 3	344	Regulatory.				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)											0.119266	13.99693	29.510602	13	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176315748	176315748	7483	5	T	A	A	A	725	56	HK3	3	3
PROP1	5626	broad.mit.edu	37	5	177421183	177421183	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:177421183C>T	uc003mif.1	-	c.266G>A	c.(265-267)GGG>GAG	p.G89E		NM_006261	NP_006252	O75360	PROP1_HUMAN	PROP paired-like homeobox 1	89	Homeobox.				central nervous system development|regulation of transcription, DNA-dependent	nucleus	RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.119048	28.166975	58.059308	25	185	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	177421183	177421183	13000	5	C	T	T	T	286	22	PROP1	2	2
ADAMTS2	9509	broad.mit.edu	37	5	178634575	178634575	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:178634575G>A	uc003mjw.2	-	c.830C>T	c.(829-831)TCT>TTT	p.S277F	ADAMTS2_uc011dgm.1_Missense_Mutation_p.S277F	NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	277	Peptidase M12B.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)						1974				0.147186	60.801351	88.41928	34	197	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	178634575	178634575	266	5	G	A	A	A	429	33	ADAMTS2	2	2
MAPK9	5601	broad.mit.edu	37	5	179696296	179696296	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:179696296C>A	uc003mls.3	-	c.236G>T	c.(235-237)TGT>TTT	p.C79F	MAPK9_uc003mlt.3_Missense_Mutation_p.C79F|MAPK9_uc010jlc.2_Missense_Mutation_p.C79F|MAPK9_uc003mlv.3_Missense_Mutation_p.C79F|MAPK9_uc011dgx.1_Missense_Mutation_p.C79F	NM_002752	NP_002743	P45984	MK09_HUMAN	mitogen-activated protein kinase 9 isoform JNK2	79	Protein kinase.				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				0.208333	47.84511	55.409164	20	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179696296	179696296	9670	5	C	A	A	A	221	17	MAPK9	2	2
MGAT1	4245	broad.mit.edu	37	5	180219359	180219359	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:180219359C>A	uc003mmg.3	-	c.613G>T	c.(613-615)GCC>TCC	p.A205S	MGAT1_uc010jlf.2_Missense_Mutation_p.A205S|MGAT1_uc010jlg.2_Missense_Mutation_p.A205S|MGAT1_uc003mmh.3_Missense_Mutation_p.A205S|MGAT1_uc010jlh.2_Missense_Mutation_p.A205S|MGAT1_uc003mmi.3_Missense_Mutation_p.A205S	NM_002406	NP_002397	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein	205	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity			ovary(1)	1	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.22619	39.976637	45.764951	19	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	180219359	180219359	9932	5	C	A	A	A	338	26	MGAT1	2	2
CDH12	1010	broad.mit.edu	37	5	21765193	21765193	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:21765193G>T	uc010iuc.2	-	c.1409C>A	c.(1408-1410)ACC>AAC	p.T470N	CDH12_uc011cno.1_Missense_Mutation_p.T430N|CDH12_uc003jgk.2_Missense_Mutation_p.T470N	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	470	Extracellular (Potential).|Cadherin 4.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2														0.230769	56.026774	62.071514	21	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21765193	21765193	3227	5	G	T	T	T	572	44	CDH12	2	2
CDH12	1010	broad.mit.edu	37	5	21854814	21854814	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:21854814C>A	uc010iuc.2	-	c.612G>T	c.(610-612)CAG>CAT	p.Q204H	CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Missense_Mutation_p.Q204H	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	204	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2														0.166667	20.981496	27.936193	11	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21854814	21854814	3227	5	C	A	A	A	311	24	CDH12	2	2
CDH10	1008	broad.mit.edu	37	5	24491830	24491830	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:24491830G>C	uc003jgr.1	-	c.1731C>G	c.(1729-1731)AGC>AGG	p.S577R	CDH10_uc011cnu.1_Non-coding_Transcript	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	577	Cadherin 5.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)										0.220588	39.386062	44.275502	15	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24491830	24491830	3225	5	G	C	C	C	594	46	CDH10	3	3
CDH9	1007	broad.mit.edu	37	5	26906170	26906170	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:26906170G>T	uc003jgs.1	-	c.709C>A	c.(709-711)CAG>AAG	p.Q237K	CDH9_uc010iug.2_Missense_Mutation_p.Q237K	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	237	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)	5						Melanoma(8;187 585 15745 40864 52829)								0.121795	26.812164	48.671453	19	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26906170	26906170	3246	5	G	T	T	T	624	48	CDH9	2	2
PDZD2	23037	broad.mit.edu	37	5	32089569	32089569	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:32089569C>A	uc003jhl.2	+	c.6015C>A	c.(6013-6015)GTC>GTA	p.V2005V	PDZD2_uc003jhm.2_Silent_p.V2005V	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	2005					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|large_intestine(1)	7														0.072539	-22.170024	50.425155	28	358	KEEP	---	---	---	---	capture		Silent	SNP	32089569	32089569	12122	5	C	A	A	A	379	30	PDZD2	2	2
ZFR	51663	broad.mit.edu	37	5	32355983	32355983	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:32355983C>G	uc003jhr.1	-	c.3108G>C	c.(3106-3108)CCG>CCC	p.P1036P	ZFR_uc010ium.1_Silent_p.P167P|ZFR_uc011cny.1_Non-coding_Transcript	NM_016107	NP_057191	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	1036	DZF.				multicellular organismal development	chromosome|cytoplasm|nucleus	DNA binding|RNA binding|zinc ion binding				0				STAD - Stomach adenocarcinoma(35;0.19)										0.131707	50.60425	77.608086	27	178	KEEP	---	---	---	---	capture		Silent	SNP	32355983	32355983	18249	5	C	G	G	G	340	27	ZFR	3	3
TARS	6897	broad.mit.edu	37	5	33453500	33453500	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:33453500G>T	uc011coc.1	+	c.499G>T	c.(499-501)GAT>TAT	p.D167Y	TARS_uc011cob.1_Missense_Mutation_p.D134Y|TARS_uc010iup.1_Missense_Mutation_p.D87Y|TARS_uc003jhy.2_Missense_Mutation_p.D146Y|TARS_uc003jhz.2_Missense_Mutation_p.D42Y|TARS_uc011cod.1_Intron	NM_152295	NP_689508	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	146					threonyl-tRNA aminoacylation	cytosol	ATP binding|protein homodimerization activity|threonine-tRNA ligase activity			ovary(2)	2					L-Threonine(DB00156)									0.150289	35.410481	55.737794	26	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33453500	33453500	16081	5	G	T	T	T	533	41	TARS	2	2
ADAMTS12	81792	broad.mit.edu	37	5	33576991	33576991	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:33576991G>T	uc003jia.1	-	c.3140C>A	c.(3139-3141)GCA>GAA	p.A1047E	ADAMTS12_uc010iuq.1_Missense_Mutation_p.A962E	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1047	Spacer 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.141304	20.509027	31.932138	13	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33576991	33576991	258	5	G	T	T	T	598	46	ADAMTS12	2	2
RXFP3	51289	broad.mit.edu	37	5	33937208	33937208	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:33937208C>A	uc003jic.1	+	c.363C>A	c.(361-363)GTC>GTA	p.V121V		NM_016568	NP_057652	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	121	Helical; Name=2; (Potential).					integral to plasma membrane	N-formyl peptide receptor activity				0														0.087912	0.946011	32.235876	16	166	KEEP	---	---	---	---	capture		Silent	SNP	33937208	33937208	14241	5	C	A	A	A	366	29	RXFP3	2	2
PRKAA1	5562	broad.mit.edu	37	5	40775031	40775031	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:40775031T>C	uc003jmb.2	-	c.407A>G	c.(406-408)GAG>GGG	p.E136G	PRKAA1_uc003jmc.2_Intron	NM_206907	NP_996790	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic	121	Protein kinase.				activation of MAPK activity|cell cycle arrest|cholesterol biosynthetic process|fatty acid biosynthetic process|insulin receptor signaling pathway|negative regulation of glucosylceramide biosynthetic process|positive regulation of anti-apoptosis|positive regulation of cholesterol biosynthetic process|regulation of fatty acid oxidation|response to hypoxia	cytosol	ATP binding|cAMP-dependent protein kinase activity|metal ion binding|protein binding			breast(1)	1					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)					149				0.091954	5.730781	20.654206	8	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40775031	40775031	12936	5	T	C	C	C	702	54	PRKAA1	4	4
HEATR7B2	133558	broad.mit.edu	37	5	41038867	41038867	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:41038867C>T	uc003jmj.3	-	c.2185G>A	c.(2185-2187)GTC>ATC	p.V729I	HEATR7B2_uc003jmi.3_Missense_Mutation_p.V284I	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	729							binding			ovary(6)|central_nervous_system(2)	8														0.195122	16.26405	19.836062	8	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41038867	41038867	7318	5	C	T	T	T	260	20	HEATR7B2	2	2
C6	729	broad.mit.edu	37	5	41181563	41181563	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:41181563C>A	uc003jmk.2	-	c.825G>T	c.(823-825)GGG>GGT	p.G275G	C6_uc003jml.1_Silent_p.G275G	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	275	MACPF.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)	5		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)												0.176471	31.297164	41.355363	18	84	KEEP	---	---	---	---	capture		Silent	SNP	41181563	41181563	2416	5	C	A	A	A	275	22	C6	2	2
ZNF131	7690	broad.mit.edu	37	5	43174846	43174846	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:43174846G>T	uc011cpw.1	+	c.1483G>T	c.(1483-1485)GTG>TTG	p.V495L	ZNF131_uc003jnj.3_Missense_Mutation_p.V216L|ZNF131_uc003jnk.2_Missense_Mutation_p.V461L|ZNF131_uc003jnn.3_Missense_Mutation_p.V216L|ZNF131_uc003jnl.1_Intron|ZNF131_uc010ivm.1_Intron	NM_003432	NP_003423	P52739	ZN131_HUMAN	zinc finger protein 131	495					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.269841	46.545385	49.557414	17	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43174846	43174846	18312	5	G	T	T	T	624	48	ZNF131	2	2
PELO	53918	broad.mit.edu	37	5	52097598	52097598	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:52097598G>T	uc003jos.2	+	c.1082G>T	c.(1081-1083)GGG>GTG	p.G361V	ITGA1_uc003jov.2_Intron|ITGA1_uc003jou.2_Intron|PELO_uc003jot.1_Intron	NM_015946	NP_057030	Q9BRX2	PELO_HUMAN	pelota homolog	361					cell cycle|cell division|translation	cytoplasm|nucleus	endonuclease activity|metal ion binding|protein binding				0		Lung NSC(810;4.94e-05)|Breast(144;0.0848)												0.243902	21.727818	24.180287	10	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52097598	52097598	12145	5	G	T	T	T	559	43	PELO	2	2
GPX8	493869	broad.mit.edu	37	5	54456891	54456891	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:54456891C>T	uc003jpq.2	+	c.274C>T	c.(274-276)CTG>TTG	p.L92L	CDC20B_uc003jpn.1_Intron|CDC20B_uc010ivu.1_Intron|CDC20B_uc003jpo.1_Intron|CDC20B_uc010ivv.1_Intron|CDC20B_uc003jpp.2_Intron|GPX8_uc003jpr.2_Intron|GPX8_uc003jps.2_Non-coding_Transcript|GPX8_uc003jpt.2_Silent_p.L41L	NM_001008397	NP_001008398	Q8TED1	GPX8_HUMAN	glutathione peroxidase 8	92					oxidation-reduction process|response to oxidative stress	integral to membrane	glutathione peroxidase activity				0					Glutathione(DB00143)									0.141026	16.872534	26.572051	11	67	KEEP	---	---	---	---	capture		Silent	SNP	54456891	54456891	7022	5	C	T	T	T	259	20	GPX8	2	2
SGTB	54557	broad.mit.edu	37	5	64976515	64976515	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:64976515C>A	uc003jud.2	-	c.586G>T	c.(586-588)GCA>TCA	p.A196S		NM_019072	NP_061945	Q96EQ0	SGTB_HUMAN	small glutamine-rich tetratricopeptide repeat	196							binding				0		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)										0.066225	-9.782967	19.70023	10	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64976515	64976515	14717	5	C	A	A	A	364	28	SGTB	2	2
IQGAP2	10788	broad.mit.edu	37	5	75954354	75954354	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:75954354T>A	uc003kek.2	+	c.2391T>A	c.(2389-2391)GAT>GAA	p.D797E	IQGAP2_uc010izv.2_Missense_Mutation_p.D350E|IQGAP2_uc011csv.1_Missense_Mutation_p.D293E|IQGAP2_uc003kel.2_Missense_Mutation_p.D293E	NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	797					small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)										0.209524	52.190729	60.391366	22	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75954354	75954354	8118	5	T	A	A	A	673	52	IQGAP2	3	3
CRHBP	1393	broad.mit.edu	37	5	76259265	76259265	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:76259265G>T	uc003ker.2	+	c.791G>T	c.(790-792)TGC>TTC	p.C264F		NM_001882	NP_001873	P24387	CRHBP_HUMAN	corticotropin releasing hormone binding protein	264					female pregnancy|learning or memory|signal transduction	soluble fraction					0		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-51)|Epithelial(54;8.79e-46)|all cancers(79;2.49e-41)										0.168724	78.026273	103.277251	41	202	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76259265	76259265	4009	5	G	T	T	T	598	46	CRHBP	2	2
DMGDH	29958	broad.mit.edu	37	5	78347268	78347268	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:78347268T>C	uc003kfs.2	-	c.587A>G	c.(586-588)TAT>TGT	p.Y196C	DMGDH_uc011cte.1_Missense_Mutation_p.Y46C|DMGDH_uc011ctf.1_Intron|DMGDH_uc011ctg.1_Intron	NM_013391	NP_037523	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase precursor	196					choline metabolic process|glycine catabolic process|oxidation-reduction process	mitochondrial matrix	aminomethyltransferase activity|dimethylglycine dehydrogenase activity|electron carrier activity			ovary(2)|liver(1)	3		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)										0.081818	6.797138	26.368318	9	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78347268	78347268	4761	5	T	C	C	C	637	49	DMGDH	4	4
DMGDH	29958	broad.mit.edu	37	5	78350088	78350088	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:78350088C>A	uc003kfs.2	-	c.459G>T	c.(457-459)CGG>CGT	p.R153R	DMGDH_uc011cte.1_Silent_p.R3R|DMGDH_uc011ctf.1_Intron|DMGDH_uc011ctg.1_Intron	NM_013391	NP_037523	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase precursor	153					choline metabolic process|glycine catabolic process|oxidation-reduction process	mitochondrial matrix	aminomethyltransferase activity|dimethylglycine dehydrogenase activity|electron carrier activity			ovary(2)|liver(1)	3		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)										0.116667	6.579541	15.257894	7	53	KEEP	---	---	---	---	capture		Silent	SNP	78350088	78350088	4761	5	C	A	A	A	379	30	DMGDH	2	2
JMY	133746	broad.mit.edu	37	5	78573766	78573766	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:78573766G>T	uc003kfx.3	+	c.1066G>T	c.(1066-1068)GTG>TTG	p.V356L	JMY_uc003kfw.1_Missense_Mutation_p.V2L	NM_152405	NP_689618	Q8N9B5	JMY_HUMAN	junction-mediating and regulatory protein	356	Potential.				'de novo' actin filament nucleation|actin polymerization-dependent cell motility|Arp2/3 complex-mediated actin nucleation|cell cycle arrest|DNA repair|induction of apoptosis|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter	cell leading edge|cytoplasm|cytoskeleton|nucleus	actin binding|transcription coactivator activity				0		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)										0.120301	18.284154	37.141896	16	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78573766	78573766	8261	5	G	T	T	T	572	44	JMY	2	2
ACOT12	134526	broad.mit.edu	37	5	80655832	80655832	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:80655832A>G	uc003khl.3	-	c.386T>C	c.(385-387)CTA>CCA	p.L129P	RNU5E_uc011cto.1_Intron|ACOT12_uc003khm.2_Missense_Mutation_p.L129P	NM_130767	NP_570123	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	129					acyl-CoA metabolic process|fatty acid metabolic process	cytosol	acetyl-CoA hydrolase activity|carboxylesterase activity			ovary(1)|kidney(1)	2		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)										0.152941	30.821847	40.613385	13	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80655832	80655832	151	5	A	G	G	G	195	15	ACOT12	4	4
VCAN	1462	broad.mit.edu	37	5	82816053	82816053	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82816053C>T	uc003kii.3	+	c.1928C>T	c.(1927-1929)ACA>ATA	p.T643I	VCAN_uc003kij.3_Intron|VCAN_uc010jau.2_Missense_Mutation_p.T643I|VCAN_uc003kik.3_Intron	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	643	GAG-alpha (glucosaminoglycan attachment domain).				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(3)|lung(2)|central_nervous_system(1)	13		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)										0.084416	-4.656711	22.400116	13	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82816053	82816053	17703	5	C	T	T	T	221	17	VCAN	2	2
VCAN	1462	broad.mit.edu	37	5	82816423	82816423	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82816423G>A	uc003kii.3	+	c.2298G>A	c.(2296-2298)ATG>ATA	p.M766I	VCAN_uc003kij.3_Intron|VCAN_uc010jau.2_Missense_Mutation_p.M766I|VCAN_uc003kik.3_Intron	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	766	GAG-alpha (glucosaminoglycan attachment domain).				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(3)|lung(2)|central_nervous_system(1)	13		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)										0.083333	1.058322	15.881629	7	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82816423	82816423	17703	5	G	A	A	A	611	47	VCAN	2	2
VCAN	1462	broad.mit.edu	37	5	82832966	82832966	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82832966G>C	uc003kii.3	+	c.4144G>C	c.(4144-4146)GAC>CAC	p.D1382H	VCAN_uc003kij.3_Missense_Mutation_p.D395H|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Missense_Mutation_p.D46H	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	1382	GAG-beta.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(3)|lung(2)|central_nervous_system(1)	13		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)										0.224138	37.442507	41.500736	13	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82832966	82832966	17703	5	G	C	C	C	429	33	VCAN	3	3
VCAN	1462	broad.mit.edu	37	5	82837427	82837427	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82837427C>G	uc003kii.3	+	c.8605C>G	c.(8605-8607)CAT>GAT	p.H2869D	VCAN_uc003kij.3_Missense_Mutation_p.H1882D|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Missense_Mutation_p.H1533D	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	2869	GAG-beta.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(3)|lung(2)|central_nervous_system(1)	13		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)										0.065041	-1.306464	22.865281	8	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82837427	82837427	17703	5	C	G	G	G	377	29	VCAN	3	3
HAPLN1	1404	broad.mit.edu	37	5	82937398	82937398	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82937398T>C	uc003kim.2	-	c.982A>G	c.(982-984)ACT>GCT	p.T328A	HAPLN1_uc003kin.2_Missense_Mutation_p.T328A	NM_001884	NP_001875	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	328	Link 2.				cell adhesion	proteinaceous extracellular matrix	hyaluronic acid binding			large_intestine(3)|ovary(1)	4		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)						115				0.201754	121.237243	140.085189	46	182	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82937398	82937398	7236	5	T	C	C	C	741	57	HAPLN1	4	4
HAPLN1	1404	broad.mit.edu	37	5	82948412	82948412	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82948412C>T	uc003kim.2	-	c.332G>A	c.(331-333)AGA>AAA	p.R111K	HAPLN1_uc003kin.2_Missense_Mutation_p.R111K	NM_001884	NP_001875	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	111	Ig-like V-type.				cell adhesion	proteinaceous extracellular matrix	hyaluronic acid binding			large_intestine(3)|ovary(1)	4		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)						115				0.150442	29.898384	43.133635	17	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82948412	82948412	7236	5	C	T	T	T	416	32	HAPLN1	2	2
GPR98	84059	broad.mit.edu	37	5	90012412	90012412	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:90012412C>A	uc003kju.2	+	c.9313C>A	c.(9313-9315)CGG>AGG	p.R3105R	GPR98_uc003kjt.2_Silent_p.R811R|GPR98_uc003kjv.2_Silent_p.R705R	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	3105	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)										0.25	29.978397	32.704632	12	36	KEEP	---	---	---	---	capture		Silent	SNP	90012412	90012412	6997	5	C	A	A	A	399	31	GPR98	1	1
SEMA5A	9037	broad.mit.edu	37	5	9337872	9337872	+	Silent	SNP	C	A	A	rs111523371		TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:9337872C>A	uc003jek.2	-	c.177G>T	c.(175-177)TCG>TCT	p.S59S		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	59	Sema.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2														0.119048	14.703474	26.65959	10	74	KEEP	---	---	---	---	capture		Silent	SNP	9337872	9337872	14523	5	C	A	A	A	340	27	SEMA5A	1	1
MCTP1	79772	broad.mit.edu	37	5	94248658	94248658	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:94248658T>A	uc003kkx.2	-	c.1374A>T	c.(1372-1374)CTA>CTT	p.L458L	MCTP1_uc003kkv.2_Silent_p.L237L|MCTP1_uc003kkw.2_Silent_p.L191L|MCTP1_uc003kkz.2_Silent_p.L119L|MCTP1_uc003kku.2_5'UTR	NM_024717	NP_078993	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1 isoform L	458	C2 2.				calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)										0.076364	-2.220246	48.315456	21	254	KEEP	---	---	---	---	capture		Silent	SNP	94248658	94248658	9789	5	T	A	A	A	626	49	MCTP1	3	3
GRIK2	2898	broad.mit.edu	37	6	102483357	102483357	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:102483357G>C	uc003pqp.3	+	c.2227G>C	c.(2227-2229)GAG>CAG	p.E743Q	GRIK2_uc003pqo.3_Missense_Mutation_p.E743Q|GRIK2_uc010kcw.2_Missense_Mutation_p.E743Q	NM_021956	NP_068775	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	743	Extracellular (Potential).				glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|breast(1)|pancreas(1)	4		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)									0.074468	3.29039	38.268966	14	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102483357	102483357	7053	6	G	C	C	C	481	37	GRIK2	3	3
LAMA4	3910	broad.mit.edu	37	6	112476088	112476088	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:112476088T>C	uc003pvu.2	-	c.2021A>G	c.(2020-2022)AAT>AGT	p.N674S	LAMA4_uc003pvv.2_Missense_Mutation_p.N667S|LAMA4_uc003pvt.2_Missense_Mutation_p.N667S	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	674	Domain II and I.|Potential.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)										0.133858	34.589154	51.10226	17	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112476088	112476088	8931	6	T	C	C	C	676	52	LAMA4	4	4
NCOA7	135112	broad.mit.edu	37	6	126203632	126203632	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:126203632G>A	uc010kes.2	+	c.634G>A	c.(634-636)GAA>AAA	p.E212K	NCOA7_uc003qae.3_Missense_Mutation_p.E212K|NCOA7_uc003qah.2_Missense_Mutation_p.E212K|NCOA7_uc003qai.2_Missense_Mutation_p.E212K|NCOA7_uc010ket.2_Missense_Mutation_p.E108K|NCOA7_uc003qaf.2_Missense_Mutation_p.E212K|NCOA7_uc003qag.2_Missense_Mutation_p.E212K	NM_181782	NP_861447	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7 isoform 1	212					cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)										0.130435	7.815519	13.929816	6	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126203632	126203632	10633	6	G	A	A	A	585	45	NCOA7	2	2
ECHDC1	55862	broad.mit.edu	37	6	127611311	127611311	+	Silent	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:127611311G>C	uc003qax.2	-	c.627C>G	c.(625-627)CTC>CTG	p.L209L	ECHDC1_uc003qaz.3_Silent_p.L203L|ECHDC1_uc010key.2_Silent_p.L128L|ECHDC1_uc003qay.3_3'UTR|ECHDC1_uc010kez.2_3'UTR|ECHDC1_uc010kex.2_Non-coding_Transcript	NM_001139510	NP_001132982	Q9NTX5	ECHD1_HUMAN	enoyl Coenzyme A hydratase domain containing 1	209							catalytic activity				0				GBM - Glioblastoma multiforme(226;0.0423)|all cancers(137;0.156)										0.071429	2.767894	26.614913	9	117	KEEP	---	---	---	---	capture		Silent	SNP	127611311	127611311	5080	6	G	C	C	C	574	45	ECHDC1	3	3
C6orf58	352999	broad.mit.edu	37	6	127898540	127898540	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:127898540G>C	uc003qbh.2	+	c.210G>C	c.(208-210)CAG>CAC	p.Q70H		NM_001010905	NP_001010905	Q6P5S2	CF058_HUMAN	hypothetical protein LOC352999 precursor	70						extracellular region					0				GBM - Glioblastoma multiforme(226;0.0405)|all cancers(137;0.156)										0.124031	30.004118	47.833788	16	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	127898540	127898540	2473	6	G	C	C	C	425	33	C6orf58	3	3
TMEM200A	114801	broad.mit.edu	37	6	130761606	130761606	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:130761606C>A	uc003qca.2	+	c.39C>A	c.(37-39)GCC>GCA	p.A13A	TMEM200A_uc010kfh.2_Silent_p.A13A|TMEM200A_uc010kfi.2_Silent_p.A13A|TMEM200A_uc003qcb.2_Silent_p.A13A	NM_052913	NP_443145	Q86VY9	T200A_HUMAN	transmembrane protein 200A	13	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)						66				0.19598	76.830048	93.963585	39	160	KEEP	---	---	---	---	capture		Silent	SNP	130761606	130761606	16658	6	C	A	A	A	301	24	TMEM200A	2	2
TMEM200A	114801	broad.mit.edu	37	6	130762699	130762699	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:130762699G>T	uc003qca.2	+	c.1132G>T	c.(1132-1134)GCC>TCC	p.A378S	TMEM200A_uc010kfh.2_Missense_Mutation_p.A378S|TMEM200A_uc010kfi.2_Missense_Mutation_p.A378S|TMEM200A_uc003qcb.2_Missense_Mutation_p.A378S	NM_052913	NP_443145	Q86VY9	T200A_HUMAN	transmembrane protein 200A	378	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)						66				0.257576	42.241172	45.758863	17	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130762699	130762699	16658	6	G	T	T	T	598	46	TMEM200A	2	2
EPB41L2	2037	broad.mit.edu	37	6	131201331	131201331	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:131201331C>A	uc003qch.2	-	c.1849G>T	c.(1849-1851)GTA>TTA	p.V617L	EPB41L2_uc003qce.1_Intron|EPB41L2_uc003qcf.1_Non-coding_Transcript|EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc010kfl.1_Intron|EPB41L2_uc003qcj.1_5'Flank	NM_001431	NP_001422	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	617	Spectrin--actin-binding.				cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)										0.222222	27.494741	31.321009	12	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131201331	131201331	5346	6	C	A	A	A	260	20	EPB41L2	2	2
MED23	9439	broad.mit.edu	37	6	131917827	131917827	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:131917827G>C	uc003qcs.1	-	c.2609C>G	c.(2608-2610)GCC>GGC	p.A870G	MED23_uc003qcq.2_Missense_Mutation_p.A876G|MED23_uc011eca.1_Missense_Mutation_p.A511G	NM_004830	NP_004821	Q9ULK4	MED23_HUMAN	mediator complex subunit 23 isoform a	870					regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity|transcription regulator activity			ovary(1)|kidney(1)	2	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)										0.160714	20.637626	26.77338	9	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131917827	131917827	9830	6	G	C	C	C	546	42	MED23	3	3
TAAR8	83551	broad.mit.edu	37	6	132874334	132874334	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:132874334A>T	uc011ecj.1	+	c.503A>T	c.(502-504)TAC>TTC	p.Y168F		NM_053278	NP_444508	Q969N4	TAAR8_HUMAN	trace amine associated receptor 8	168	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00412)|GBM - Glioblastoma multiforme(226;0.00792)										0.06367	-17.827949	35.05836	17	250	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132874334	132874334	16014	6	A	T	T	T	182	14	TAAR8	3	3
C6orf192	116843	broad.mit.edu	37	6	133094199	133094199	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:133094199C>A	uc003qdw.1	-	c.1018G>T	c.(1018-1020)GTT>TTT	p.V340F	C6orf192_uc010kgd.1_Non-coding_Transcript|C6orf192_uc011eco.1_Missense_Mutation_p.V214F	NM_052831	NP_439896	Q6NT16	CF192_HUMAN	hypothetical protein LOC116843	340	Helical; (Potential).				transmembrane transport	integral to membrane				ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(155;0.00303)|GBM - Glioblastoma multiforme(226;0.0265)										0.119048	6.342675	12.329394	5	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133094199	133094199	2454	6	C	A	A	A	260	20	C6orf192	2	2
ADAT2	134637	broad.mit.edu	37	6	143759805	143759805	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:143759805T>A	uc003qjj.2	-	c.123A>T	c.(121-123)GAA>GAT	p.E41D	ADAT2_uc003qjk.1_Non-coding_Transcript	NM_182503	NP_872309	Q7Z6V5	ADAT2_HUMAN	deaminase domain containing 1	41					tRNA processing		hydrolase activity|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(155;5.61e-06)|GBM - Glioblastoma multiforme(68;0.0115)										0.094118	3.731287	17.807002	8	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143759805	143759805	286	6	T	A	A	A	725	56	ADAT2	3	3
ULBP1	80329	broad.mit.edu	37	6	150289779	150289779	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:150289779C>T	uc003qnp.2	+	c.122C>T	c.(121-123)CCT>CTT	p.P41L		NM_025218	NP_079494	Q9BZM6	N2DL1_HUMAN	UL16 binding protein 1 precursor	41	MHC class I alpha-1 like.				antigen processing and presentation|immune response|natural killer cell activation|regulation of immune response	anchored to membrane|endoplasmic reticulum|MHC class I protein complex	MHC class I receptor activity			pancreas(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.14e-11)										0.178862	98.44452	122.322315	44	202	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150289779	150289779	17530	6	C	T	T	T	312	24	ULBP1	2	2
MTHFD1L	25902	broad.mit.edu	37	6	151265679	151265679	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:151265679G>T	uc011eeo.1	+	c.1501G>T	c.(1501-1503)GCT>TCT	p.A501S	MTHFD1L_uc011een.1_Non-coding_Transcript|MTHFD1L_uc003qob.2_Missense_Mutation_p.A500S|MTHFD1L_uc003qoc.2_Missense_Mutation_p.A448S	NM_015440	NP_056255	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+	500	Formyltetrahydrofolate synthetase.				folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)										0.162162	10.327981	14.343085	6	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151265679	151265679	10321	6	G	T	T	T	546	42	MTHFD1L	2	2
NOX3	50508	broad.mit.edu	37	6	155761165	155761165	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:155761165G>T	uc003qqm.2	-	c.593C>A	c.(592-594)GCC>GAC	p.A198D		NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	198	Ferric oxidoreductase.|Cytoplasmic (Potential).				oxidation-reduction process		electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)										0.130435	15.583066	27.768059	12	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155761165	155761165	10961	6	G	T	T	T	546	42	NOX3	2	2
LPA	4018	broad.mit.edu	37	6	160968856	160968856	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:160968856G>T	uc003qtl.2	-	c.5269C>A	c.(5269-5271)CCA>ACA	p.P1757T		NM_005577	NP_005568	P08519	APOA_HUMAN	lipoprotein Lp(a) precursor	4265	Kringle 38.				blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|pancreas(1)	4		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)									0.079755	-6.272936	23.163547	13	150	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160968856	160968856	9276	6	G	T	T	T	533	41	LPA	2	2
C6orf118	168090	broad.mit.edu	37	6	165711483	165711483	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:165711483G>T	uc003qum.3	-	c.1044C>A	c.(1042-1044)GCC>GCA	p.A348A	C6orf118_uc011egi.1_Non-coding_Transcript	NM_144980	NP_659417	Q5T5N4	CF118_HUMAN	hypothetical protein LOC168090	348	Potential.										0		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)										0.163265	56.668913	77.80751	32	164	KEEP	---	---	---	---	capture		Silent	SNP	165711483	165711483	2425	6	G	T	T	T	548	43	C6orf118	2	2
PDE10A	10846	broad.mit.edu	37	6	165801829	165801829	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:165801829G>T	uc003quo.2	-	c.1770C>A	c.(1768-1770)ACC>ACA	p.T590T	PDE10A_uc011egj.1_Non-coding_Transcript|PDE10A_uc011egk.1_Silent_p.T510T|PDE10A_uc003qun.2_Silent_p.T580T	NM_001130690	NP_001124162	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 1	580					platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)	3		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	Esophageal Squamous(22;308 615 5753 12038 40624)								0.136	24.591681	40.633177	17	108	KEEP	---	---	---	---	capture		Silent	SNP	165801829	165801829	12051	6	G	T	T	T	600	47	PDE10A	2	2
UNC93A	54346	broad.mit.edu	37	6	167711556	167711556	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:167711556C>A	uc003qvq.2	+	c.623C>A	c.(622-624)ACT>AAT	p.T208N	UNC93A_uc003qvr.2_Intron	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1	208	Helical; (Potential).					integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)										0.19697	54.165718	65.466278	26	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167711556	167711556	17555	6	C	A	A	A	260	20	UNC93A	2	2
SLC17A4	10050	broad.mit.edu	37	6	25777118	25777118	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:25777118T>A	uc003nfe.2	+	c.1199T>A	c.(1198-1200)GTG>GAG	p.V400E	SLC17A4_uc011djx.1_Missense_Mutation_p.V170E|SLC17A4_uc003nff.1_Missense_Mutation_p.V189E|SLC17A4_uc003nfg.2_Missense_Mutation_p.V337E|SLC17A4_uc010jqa.2_Intron	NM_005495	NP_005486	Q9Y2C5	S17A4_HUMAN	solute carrier family 17 (sodium phosphate),	400	Helical; (Potential).				phosphate metabolic process	integral to plasma membrane|membrane fraction	sodium:phosphate symporter activity				0														0.188889	75.957442	92.248121	34	146	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25777118	25777118	14915	6	T	A	A	A	767	59	SLC17A4	3	3
SLC17A1	6568	broad.mit.edu	37	6	25819932	25819932	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:25819932C>A	uc003nfh.3	-	c.419G>T	c.(418-420)CGA>CTA	p.R140L	SLC17A1_uc011djy.1_Non-coding_Transcript|SLC17A1_uc010jqb.1_Missense_Mutation_p.R138L|SLC17A1_uc010jqc.1_Missense_Mutation_p.R138L	NM_005074	NP_005065	Q14916	NPT1_HUMAN	solute carrier family 17 (sodium phosphate),	140					sodium ion transport|urate metabolic process	integral to plasma membrane|membrane fraction	sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(3)|pancreas(1)	4														0.202381	35.625533	42.540035	17	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25819932	25819932	14912	6	C	A	A	A	403	31	SLC17A1	1	1
HIST1H3A	8350	broad.mit.edu	37	6	26021048	26021048	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26021048T>A	uc003nfp.1	+	c.331T>A	c.(331-333)TGC>AGC	p.C111S	HIST1H4A_uc003nfq.2_5'Flank	NM_003529	NP_003520	P68431	H31_HUMAN	histone cluster 1, H3a	111					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)|pancreas(1)	2														0.126582	13.013606	23.749369	10	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26021048	26021048	7440	6	T	A	A	A	767	59	HIST1H3A	3	3
HIST1H3B	8358	broad.mit.edu	37	6	26032069	26032069	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26032069C>T	uc003nfs.1	-	c.220G>A	c.(220-222)GAA>AAA	p.E74K		NM_003537	NP_003528	P68431	H31_HUMAN	histone cluster 1, H3b	74					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(2)	2														0.168	40.00841	53.052559	21	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26032069	26032069	7441	6	C	T	T	T	416	32	HIST1H3B	2	2
HIST1H2AC	8334	broad.mit.edu	37	6	26124779	26124779	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26124779G>T	uc003ngm.2	+	c.319G>T	c.(319-321)GGC>TGC	p.G107C	HIST1H2BC_uc003ngk.3_5'Flank|HIST1H2BC_uc003ngl.2_5'Flank|HIST1H2AC_uc003ngn.2_Non-coding_Transcript|HIST1H2AC_uc003ngo.2_Non-coding_Transcript|HIST1H2AC_uc003ngp.2_Missense_Mutation_p.G107C	NM_003512	NP_003503	Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	107					nucleosome assembly	nucleosome|nucleus	DNA binding				0														0.205714	80.701886	94.757053	36	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26124779	26124779	7415	6	G	T	T	T	507	39	HIST1H2AC	1	1
HIST1H2BF	8343	broad.mit.edu	37	6	26199826	26199826	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26199826G>T	uc003ngx.2	+	c.40G>T	c.(40-42)GGC>TGC	p.G14C	HIST1H3D_uc003ngv.2_5'Flank|HIST1H2AD_uc003ngw.2_5'Flank	NM_003522	NP_003513	P62807	H2B1C_HUMAN	histone cluster 1, H2bf	14					defense response to bacterium|nucleosome assembly	nucleosome|nucleus	DNA binding|protein binding				0		all_hematologic(11;0.196)												0.107143	14.00417	43.96576	21	175	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26199826	26199826	7430	6	G	T	T	T	559	43	HIST1H2BF	2	2
BTN2A2	10385	broad.mit.edu	37	6	26388252	26388253	+	Missense_Mutation	DNP	AA	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26388252_26388253AA>TT	uc003nhq.2	+	c.454_455AA>TT	c.(454-456)AAG>TTG	p.K152L	BTN2A2_uc011dkf.1_Missense_Mutation_p.K36L|BTN2A2_uc011dkg.1_Intron|BTN2A2_uc003nhr.2_Missense_Mutation_p.K36L|BTN2A2_uc011dkh.1_Intron|BTN2A2_uc003nhs.2_Missense_Mutation_p.K152L|BTN2A2_uc003nht.2_Missense_Mutation_p.K152L|BTN2A2_uc011dki.1_5'Flank	NM_006995	NP_008926	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2 isoform a	152	Extracellular (Potential).				negative regulation of activated T cell proliferation|negative regulation of cellular metabolic process|negative regulation of cytokine secretion	integral to membrane					0														0.320755	47.759197	49.270343	17	36	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	26388252	26388253	1595	6	AA	TT	TT	TT	169	13	BTN2A2	3	3
BTN1A1	696	broad.mit.edu	37	6	26501952	26501952	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26501952C>A	uc003nif.3	+	c.214C>A	c.(214-216)CCG>ACG	p.P72T		NM_001732	NP_001723	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1 precursor	72	Extracellular (Potential).|Ig-like V-type 1.					extracellular region|integral to plasma membrane	receptor activity			ovary(1)	1														0.14	9.993092	16.250048	7	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26501952	26501952	1593	6	C	A	A	A	338	26	BTN1A1	2	2
MYLK4	340156	broad.mit.edu	37	6	2749382	2749382	+	Silent	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:2749382A>G	uc003mty.3	-	c.147T>C	c.(145-147)TCT>TCC	p.S49S		NM_001012418	NP_001012418	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4	49					protein phosphorylation		ATP binding|protein serine/threonine kinase activity			breast(3)|ovary(1)	4	Ovarian(93;0.0412)	all_hematologic(90;0.0897)								535				0.122363	41.102657	74.198993	29	208	KEEP	---	---	---	---	capture		Silent	SNP	2749382	2749382	10454	6	A	G	G	G	80	7	MYLK4	4	4
OR2J3	442186	broad.mit.edu	37	6	29079941	29079941	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:29079941G>T	uc011dll.1	+	c.274G>T	c.(274-276)GAA>TAA	p.E92*		NM_001005216	NP_001005216	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J,	92	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.08547	-4.596849	36.228711	20	214	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	29079941	29079941	11410	6	G	T	T	T	533	41	OR2J3	5	2
OR12D2	26529	broad.mit.edu	37	6	29364690	29364690	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:29364690T>C	uc003nmf.3	+	c.214T>C	c.(214-216)TCT>CCT	p.S72P		NM_013936	NP_039224	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D,	72	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.12766	35.056359	54.106215	18	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29364690	29364690	11337	6	T	C	C	C	702	54	OR12D2	4	4
MOG	4340	broad.mit.edu	37	6	29633942	29633943	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:29633942_29633943GG>TT	uc003nmy.1	+	c.450_451GG>TT	c.(448-453)TGGGTG>TGTTTG	p.150_151WV>CL	MOG_uc003nmz.2_3'UTR|MOG_uc011dlt.1_Missense_Mutation_p.80_81WV>CL|MOG_uc003nna.2_Missense_Mutation_p.34_35WV>CL|MOG_uc011dlu.1_Missense_Mutation_p.34_35WV>CL|MOG_uc011dlv.1_Missense_Mutation_p.34_35WV>CL|MOG_uc003nnd.2_3'UTR|MOG_uc003nne.2_Missense_Mutation_p.150_151WV>CL|MOG_uc003nnf.2_Missense_Mutation_p.150_151WV>CL|MOG_uc003nng.2_Missense_Mutation_p.150_151WV>CL|MOG_uc003nnh.2_Missense_Mutation_p.150_151WV>CL|MOG_uc003nni.2_Missense_Mutation_p.150_151WV>CL|MOG_uc003nnj.2_Missense_Mutation_p.150_151WV>CL|MOG_uc003nnk.2_Missense_Mutation_p.150_151WV>CL	NM_206809	NP_996532	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein isoform	150_151	Extracellular (Potential).				cell adhesion|central nervous system development|positive regulation of MyD88-dependent toll-like receptor signaling pathway	integral to membrane|plasma membrane				ovary(1)	1														0.186246	130.163078	162.364698	65	284	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	29633942	29633943	10084	6	GG	TT	TT	TT	559	43	MOG	2	2
TRIM15	89870	broad.mit.edu	37	6	30131749	30131749	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:30131749C>G	uc010jrx.2	+	c.288C>G	c.(286-288)AAC>AAG	p.N96K		NM_033229	NP_150232	Q9C019	TRI15_HUMAN	tripartite motif protein 15	96	B box-type.				mesodermal cell fate determination	intracellular	zinc ion binding				0														0.142857	38.396988	53.018574	17	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30131749	30131749	17034	6	C	G	G	G	246	19	TRIM15	3	3
TRIM15	89870	broad.mit.edu	37	6	30138348	30138348	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:30138348C>T	uc010jrx.2	+	c.802C>T	c.(802-804)CAC>TAC	p.H268Y		NM_033229	NP_150232	Q9C019	TRI15_HUMAN	tripartite motif protein 15	268					mesodermal cell fate determination	intracellular	zinc ion binding				0														0.22314	62.145387	70.69013	27	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30138348	30138348	17034	6	C	T	T	T	273	21	TRIM15	2	2
HSPA1L	3305	broad.mit.edu	37	6	31777852	31777852	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:31777852G>A	uc003nxh.2	-	c.1898C>T	c.(1897-1899)ACA>ATA	p.T633I	HSPA1L_uc010jte.2_Missense_Mutation_p.T633I	NM_005527	NP_005518	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	633					response to unfolded protein		ATP binding			ovary(3)|kidney(1)|pleura(1)	5										2				0.246914	46.761581	51.483662	20	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31777852	31777852	7709	6	G	A	A	A	624	48	HSPA1L	2	2
CYP21A2	1589	broad.mit.edu	37	6	32006974	32006974	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32006974C>T	uc003nze.1	+	c.396C>T	c.(394-396)ATC>ATT	p.I132I	CYP21A2_uc003nzf.1_Silent_p.I102I	NM_000500	NP_000491	P08686	CP21A_HUMAN	cytochrome P450, family 21, subfamily A,	131					glucocorticoid biosynthetic process|mineralocorticoid biosynthetic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|steroid 21-monooxygenase activity|steroid binding				0						Melanoma(174;1669 1998 3915 34700 46447)								0.190476	7.686265	9.56863	4	17	KEEP	---	---	---	---	capture		Silent	SNP	32006974	32006974	4318	6	C	T	T	T	382	30	CYP21A2	2	2
BRD2	6046	broad.mit.edu	37	6	32942346	32942346	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32942346C>T	uc010juh.2	+	c.137C>T	c.(136-138)CCC>CTC	p.P46L	BRD2_uc003ocn.3_Missense_Mutation_p.P46L|BRD2_uc003oco.2_Non-coding_Transcript|BRD2_uc003ocq.3_Missense_Mutation_p.P46L|BRD2_uc003ocp.3_5'UTR	NM_005104	NP_005095	P25440	BRD2_HUMAN	bromodomain containing 2	46					spermatogenesis	nucleus	protein serine/threonine kinase activity			central_nervous_system(3)|stomach(2)	5										227				0.080745	0.259808	29.096387	13	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32942346	32942346	1533	6	C	T	T	T	286	22	BRD2	2	2
ITPR3	3710	broad.mit.edu	37	6	33646533	33646533	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:33646533G>T	uc011drk.1	+	c.3889G>T	c.(3889-3891)GTG>TTG	p.V1297L		NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	1297	Cytoplasmic (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			central_nervous_system(5)|ovary(3)|lung(1)|kidney(1)	10														0.24	13.32791	14.880614	6	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33646533	33646533	8226	6	G	T	T	T	624	48	ITPR3	2	2
ITPR3	3710	broad.mit.edu	37	6	33648392	33648392	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:33648392G>T	uc011drk.1	+	c.4411G>T	c.(4411-4413)GTT>TTT	p.V1471F		NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	1471	Cytoplasmic (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			central_nervous_system(5)|ovary(3)|lung(1)|kidney(1)	10														0.251337	127.454895	137.947214	47	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33648392	33648392	8226	6	G	T	T	T	520	40	ITPR3	1	1
GRM4	2914	broad.mit.edu	37	6	33996102	33996102	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:33996102C>G	uc003oir.3	-	c.2484G>C	c.(2482-2484)CTG>CTC	p.L828L	GRM4_uc011dsn.1_Silent_p.L781L|GRM4_uc010jvh.2_Silent_p.L828L|GRM4_uc010jvi.2_Silent_p.L520L|GRM4_uc003oio.2_Silent_p.L520L|GRM4_uc003oip.2_Non-coding_Transcript|GRM4_uc011dsl.1_Silent_p.L688L|GRM4_uc003oiq.2_Silent_p.L695L|GRM4_uc011dsm.1_Silent_p.L659L	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor	828	Helical; Name=7; (Potential).				activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			ovary(1)	1					L-Glutamic Acid(DB00142)									0.071146	-0.666534	47.403115	18	235	KEEP	---	---	---	---	capture		Silent	SNP	33996102	33996102	7078	6	C	G	G	G	366	29	GRM4	3	3
TCP11	6954	broad.mit.edu	37	6	35090037	35090037	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:35090037G>T	uc003okd.2	-	c.474C>A	c.(472-474)CTC>CTA	p.L158L	TCP11_uc003ojz.1_Silent_p.L83L|TCP11_uc003oka.2_Silent_p.L83L|TCP11_uc003okb.2_Silent_p.L82L|TCP11_uc003okc.2_Silent_p.L82L|TCP11_uc011dsu.1_Silent_p.L140L|TCP11_uc011dsv.1_Silent_p.L107L|TCP11_uc011dsw.1_Silent_p.L112L	NM_001093728	NP_001087197	Q8WWU5	TCP11_HUMAN	t-complex 11 isoform 1	145					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)	3														0.115607	16.864516	42.058573	20	153	KEEP	---	---	---	---	capture		Silent	SNP	35090037	35090037	16239	6	G	T	T	T	574	45	TCP11	2	2
KCTD20	222658	broad.mit.edu	37	6	36442578	36442578	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:36442578A>C	uc003ome.2	+	c.173A>C	c.(172-174)GAC>GCC	p.D58A	KCTD20_uc011dtm.1_Intron|KCTD20_uc011dtn.1_Intron|KCTD20_uc010jwk.2_Intron|KCTD20_uc011dto.1_Intron	NM_173562	NP_775833	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerisation domain	58						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2														0.198276	60.760686	70.588835	23	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36442578	36442578	8414	6	A	C	C	C	130	10	KCTD20	4	4
MDGA1	266727	broad.mit.edu	37	6	37620025	37620025	+	Silent	SNP	G	A	A	rs2273108		TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:37620025G>A	uc003onu.1	-	c.1074C>T	c.(1072-1074)CAC>CAT	p.H358H	MDGA1_uc003onw.3_Non-coding_Transcript	NM_153487	NP_705691	Q8NFP4	MDGA1_HUMAN	MAM domain containing	358	Ig-like 4.				brain development|neuron migration|spinal cord association neuron differentiation	anchored to plasma membrane				central_nervous_system(2)	2														0.1875	35.188914	43.972595	18	78	KEEP	---	---	---	---	capture		Silent	SNP	37620025	37620025	9795	6	G	A	A	A	516	40	MDGA1	1	1
DNAH8	1769	broad.mit.edu	37	6	38885138	38885138	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:38885138C>G	uc003ooe.1	+	c.9613C>G	c.(9613-9615)CCA>GCA	p.P3205A		NM_001371	NP_001362	Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy polypeptide 8	3205	Stalk (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(5)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	17										2979				0.067164	-0.940225	25.066641	9	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38885138	38885138	4790	6	C	G	G	G	390	30	DNAH8	3	3
DNAH8	1769	broad.mit.edu	37	6	38980322	38980322	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:38980322T>A	uc003ooe.1	+	c.12972T>A	c.(12970-12972)ACT>ACA	p.T4324T		NM_001371	NP_001362	Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy polypeptide 8	4324					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(5)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	17										2979				0.107527	28.238355	70.8745	30	249	KEEP	---	---	---	---	capture		Silent	SNP	38980322	38980322	4790	6	T	A	A	A	704	55	DNAH8	3	3
UBR2	23304	broad.mit.edu	37	6	42582899	42582899	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:42582899A>T	uc011dur.1	+	c.1076A>T	c.(1075-1077)GAT>GTT	p.D359V	UBR2_uc011dus.1_Missense_Mutation_p.D4V|UBR2_uc010jxv.1_5'Flank|UBR2_uc003osh.2_5'Flank|UBR2_uc003osf.2_Missense_Mutation_p.D359V	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	359						nucleus|plasma membrane	zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)											0.144444	24.219135	35.166337	13	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42582899	42582899	17460	6	A	T	T	T	156	12	UBR2	3	3
UBR2	23304	broad.mit.edu	37	6	42650816	42650816	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:42650816A>T	uc011dur.1	+	c.4742A>T	c.(4741-4743)AAA>ATA	p.K1581I	UBR2_uc011dus.1_Missense_Mutation_p.K1226I|UBR2_uc003osh.2_Non-coding_Transcript|UBR2_uc011dut.1_Missense_Mutation_p.K169I	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	1581						nucleus|plasma membrane	zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)											0.078125	-1.678644	9.971712	5	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42650816	42650816	17460	6	A	T	T	T	13	1	UBR2	3	3
MRPL14	64928	broad.mit.edu	37	6	44081782	44081782	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:44081782C>G	uc003owp.2	-	c.236G>C	c.(235-237)GGA>GCA	p.G79A		NM_032111	NP_115487	Q6P1L8	RM14_HUMAN	mitochondrial ribosomal protein L14 precursor	79					translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0181)											0.109409	73.961814	142.960684	50	407	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44081782	44081782	10172	6	C	G	G	G	390	30	MRPL14	3	3
PKHD1	5314	broad.mit.edu	37	6	51497480	51497480	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:51497480G>A	uc003pah.1	-	c.11548C>T	c.(11548-11550)CCT>TCT	p.P3850S		NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	3850	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			ovary(12)|large_intestine(5)|central_nervous_system(3)	20	Lung NSC(77;0.0605)									1537				0.084746	-1.247807	19.41345	10	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51497480	51497480	12396	6	G	A	A	A	546	42	PKHD1	2	2
PKHD1	5314	broad.mit.edu	37	6	51915060	51915060	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:51915060C>A	uc003pah.1	-	c.2174G>T	c.(2173-2175)GGG>GTG	p.G725V	PKHD1_uc003pai.2_Missense_Mutation_p.G725V	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	725	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			ovary(12)|large_intestine(5)|central_nervous_system(3)	20	Lung NSC(77;0.0605)									1537		OREG0017493	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.169231	20.384822	27.118022	11	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51915060	51915060	12396	6	C	A	A	A	286	22	PKHD1	2	2
FAM83B	222584	broad.mit.edu	37	6	54791332	54791332	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:54791332G>T	uc003pck.2	+	c.608G>T	c.(607-609)AGG>ATG	p.R203M		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	203										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)													0.136364	17.737092	29.007457	12	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54791332	54791332	5860	6	G	T	T	T	455	35	FAM83B	2	2
HCRTR2	3062	broad.mit.edu	37	6	55113565	55113565	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:55113565G>C	uc003pcl.2	+	c.352G>C	c.(352-354)GAG>CAG	p.E118Q	HCRTR2_uc010jzv.2_Non-coding_Transcript|HCRTR2_uc010jzw.1_Missense_Mutation_p.E53Q	NM_001526	NP_001517	O43614	OX2R_HUMAN	orexin receptor 2	118	Extracellular (Potential).				feeding behavior	integral to plasma membrane	neuropeptide receptor activity			ovary(2)	2	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)											0.083612	19.330715	71.999391	25	274	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55113565	55113565	7285	6	G	C	C	C	585	45	HCRTR2	3	3
HCRTR2	3062	broad.mit.edu	37	6	55145212	55145212	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:55145212G>T	uc003pcl.2	+	c.1075G>T	c.(1075-1077)GCG>TCG	p.A359S	HCRTR2_uc010jzv.2_Non-coding_Transcript	NM_001526	NP_001517	O43614	OX2R_HUMAN	orexin receptor 2	359	Helical; Name=7; (Potential).				feeding behavior	integral to plasma membrane	neuropeptide receptor activity			ovary(2)	2	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)											0.086614	2.824019	24.805604	11	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55145212	55145212	7285	6	G	T	T	T	598	46	HCRTR2	2	2
COL21A1	81578	broad.mit.edu	37	6	55924961	55924961	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:55924961C>A	uc003pcs.2	-	c.2463G>T	c.(2461-2463)CTG>CTT	p.L821L	COL21A1_uc010jzz.2_Silent_p.L206L|COL21A1_uc011dxg.1_Silent_p.L194L|COL21A1_uc011dxh.1_Intron|COL21A1_uc003pcr.2_Silent_p.L178L	NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor	821					cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)											0.25	15.837922	17.201723	6	18	KEEP	---	---	---	---	capture		Silent	SNP	55924961	55924961	3818	6	C	A	A	A	210	17	COL21A1	2	2
DST	667	broad.mit.edu	37	6	56504070	56504070	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:56504070C>A	uc003pdf.2	-	c.2852G>T	c.(2851-2853)CGG>CTG	p.R951L	DST_uc003pcz.3_Missense_Mutation_p.R773L|DST_uc011dxj.1_Missense_Mutation_p.R802L|DST_uc011dxk.1_Missense_Mutation_p.R813L|DST_uc011dxl.1_Missense_Mutation_p.R802L|DST_uc003pcy.3_Missense_Mutation_p.R447L|DST_uc003pdb.2_Missense_Mutation_p.R447L|DST_uc003pdc.3_Missense_Mutation_p.R447L|DST_uc003pdd.3_Missense_Mutation_p.R447L|DST_uc003pde.2_Missense_Mutation_p.R889L	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	773	Spectrin 1.				cell adhesion|cell cycle arrest|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasmic membrane-bounded vesicle|hemidesmosome|microtubule plus end|nucleus	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein C-terminus binding			ovary(7)|central_nervous_system(6)	13	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)							2498				0.108696	5.239624	12.219784	5	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56504070	56504070	4967	6	C	A	A	A	299	23	DST	1	1
COL9A1	1297	broad.mit.edu	37	6	70948970	70948970	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:70948970C>T	uc003pfg.3	-	c.2099G>A	c.(2098-2100)GGC>GAC	p.G700D	COL9A1_uc003pfe.3_Missense_Mutation_p.G249D|COL9A1_uc003pff.3_Missense_Mutation_p.G457D	NM_001851	NP_001842	P20849	CO9A1_HUMAN	alpha 1 type IX collagen isoform 1 precursor	700	Triple-helical region (COL2).				axon guidance|cell adhesion|organ morphogenesis	collagen type IX	extracellular matrix structural constituent conferring tensile strength|metal ion binding			ovary(4)	4														0.092593	2.630477	11.653445	5	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70948970	70948970	3845	6	C	T	T	T	338	26	COL9A1	2	2
TXNDC5	81567	broad.mit.edu	37	6	7899820	7899820	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:7899820C>T	uc003mxv.2	-	c.508G>A	c.(508-510)GAG>AAG	p.E170K	TXNDC5_uc003mxw.2_Missense_Mutation_p.E127K|TXNDC5_uc010jnz.2_Missense_Mutation_p.E62K|TXNDC5_uc010joa.1_Missense_Mutation_p.E62K	NM_030810	NP_110437	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 isoform 1	170	Thioredoxin 2.				anti-apoptosis|cell redox homeostasis|cellular membrane organization|glycerol ether metabolic process|post-Golgi vesicle-mediated transport	endoplasmic reticulum lumen|lysosomal lumen	electron carrier activity|isomerase activity|protein disulfide oxidoreductase activity				0	Ovarian(93;0.0398)					Ovarian(119;1430 1625 3928 26125 34589)								0.126437	13.563892	25.413624	11	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7899820	7899820	17355	6	C	T	T	T	403	31	TXNDC5	1	1
LCA5	167691	broad.mit.edu	37	6	80197277	80197277	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:80197277T>A	uc003pix.2	-	c.1538A>T	c.(1537-1539)GAA>GTA	p.E513V	LCA5_uc003piy.2_Missense_Mutation_p.E513V	NM_001122769	NP_001116241	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	513					protein transport	cilium axoneme|microtubule basal body	protein binding				0		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)										0.067568	-9.77202	18.892972	10	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80197277	80197277	8979	6	T	A	A	A	806	62	LCA5	3	3
TTK	7272	broad.mit.edu	37	6	80746240	80746240	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:80746240G>T	uc003pjc.2	+	c.1973G>T	c.(1972-1974)GGA>GTA	p.G658V	TTK_uc003pjb.3_Missense_Mutation_p.G657V	NM_003318	NP_003309	P33981	TTK_HUMAN	TTK protein kinase	658	Protein kinase.				mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation|protein phosphorylation	spindle	ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(4)|stomach(2)|large_intestine(2)|pancreas(1)	9		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)						471				0.08	-1.613856	11.890746	6	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80746240	80746240	17275	6	G	T	T	T	533	41	TTK	2	2
TBX18	9096	broad.mit.edu	37	6	85470001	85470001	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:85470001T>A	uc003pkl.1	-	c.571A>T	c.(571-573)ATT>TTT	p.I191F	TBX18_uc010kbq.1_Missense_Mutation_p.I33F	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18	191	T-box.				multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)						300				0.121212	5.877813	10.516714	4	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85470001	85470001	16179	6	T	A	A	A	637	49	TBX18	3	3
HTR1E	3354	broad.mit.edu	37	6	87725346	87725346	+	Nonsense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:87725346G>A	uc003pli.2	+	c.294G>A	c.(292-294)TGG>TGA	p.W98*		NM_000865	NP_000856	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E	98	Helical; Name=3; (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane	protein binding|serotonin binding|serotonin receptor activity			ovary(2)	2		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Eletriptan(DB00216)									0.085937	-0.375955	21.877693	11	117	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	87725346	87725346	7739	6	G	A	A	A	546	42	HTR1E	5	2
CGA	1081	broad.mit.edu	37	6	87796106	87796106	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:87796106C>A	uc003plj.1	-	c.135G>T	c.(133-135)CCG>CCT	p.P45P		NM_000735	NP_000726	P01215	GLHA_HUMAN	glycoprotein hormones, alpha polypeptide	45					hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity			ovary(1)	1		all_cancers(76;5.98e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000102)		BRCA - Breast invasive adenocarcinoma(108;0.0484)										0.179191	68.042609	84.777598	31	142	KEEP	---	---	---	---	capture		Silent	SNP	87796106	87796106	3428	6	C	A	A	A	288	23	CGA	1	1
ZNF292	23036	broad.mit.edu	37	6	87969756	87969756	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:87969756G>T	uc003plm.3	+	c.6409G>T	c.(6409-6411)GCT>TCT	p.A2137S		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	2137	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)										0.090909	2.162749	15.158779	7	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87969756	87969756	18418	6	G	T	T	T	546	42	ZNF292	2	2
BACH2	60468	broad.mit.edu	37	6	90661411	90661411	+	Silent	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:90661411A>G	uc011eab.1	-	c.414T>C	c.(412-414)GAT>GAC	p.D138D	BACH2_uc003pnw.2_Silent_p.D138D|BACH2_uc010kch.2_Silent_p.D138D	NM_021813	NP_068585	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper	138					regulation of transcription, DNA-dependent	nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|lung(1)|pancreas(1)	5		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)										0.082192	1.407357	14.364664	6	67	KEEP	---	---	---	---	capture		Silent	SNP	90661411	90661411	1305	6	A	G	G	G	102	8	BACH2	4	4
TSC22D4	81628	broad.mit.edu	37	7	100075602	100075602	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100075602C>A	uc003uva.2	-	c.60G>T	c.(58-60)GAG>GAT	p.E20D	TSC22D4_uc003uvb.2_Intron|TSC22D4_uc011kjv.1_Intron|TSC22D4_uc010lgx.2_Missense_Mutation_p.E20D|TSC22D4_uc003uvc.3_Missense_Mutation_p.E20D	NM_030935	NP_112197	Q9Y3Q8	T22D4_HUMAN	TSC22 domain family, member 4	20					regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			breast(2)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)													0.285714	10.09332	10.67079	4	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100075602	100075602	17161	7	C	A	A	A	311	24	TSC22D4	2	2
FBXO24	26261	broad.mit.edu	37	7	100190547	100190547	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100190547C>T	uc011kjz.1	+	c.814C>T	c.(814-816)CGG>TGG	p.R272W	FBXO24_uc010lha.1_Non-coding_Transcript|FBXO24_uc003uvl.1_Missense_Mutation_p.R220W|FBXO24_uc003uvm.1_Missense_Mutation_p.R234W|FBXO24_uc003uvn.1_Intron|FBXO24_uc011kka.1_Missense_Mutation_p.R222W	NM_012172	NP_036304	O75426	FBX24_HUMAN	F-box only protein 24 isoform 3	234						ubiquitin ligase complex	ubiquitin-protein ligase activity			ovary(3)|skin(1)	4	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)													0.10989	8.291806	21.994375	10	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100190547	100190547	5972	7	C	T	T	T	347	27	FBXO24	1	1
ZAN	7455	broad.mit.edu	37	7	100349995	100349995	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100349995C>A	uc003uwj.2	+	c.2267C>A	c.(2266-2268)CCA>CAA	p.P756Q	ZAN_uc003uwk.2_Missense_Mutation_p.P756Q|ZAN_uc003uwl.2_Non-coding_Transcript|ZAN_uc010lhh.2_Non-coding_Transcript|ZAN_uc010lhi.2_Non-coding_Transcript	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	756	66 X heptapeptide repeats (approximate) (mucin-like domain).|Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)											0.152174	19.178177	29.853457	14	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100349995	100349995	18096	7	C	A	A	A	273	21	ZAN	2	2
MUC17	140453	broad.mit.edu	37	7	100675863	100675863	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100675863G>C	uc003uxp.1	+	c.1166G>C	c.(1165-1167)AGT>ACT	p.S389T	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	389	Extracellular (Potential).|59 X approximate tandem repeats.|4.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|breast(3)|lung(2)	19	Lung NSC(181;0.136)|all_lung(186;0.182)													0.102236	44.652737	94.019821	32	281	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100675863	100675863	10368	7	G	C	C	C	468	36	MUC17	3	3
MYL10	93408	broad.mit.edu	37	7	101256815	101256815	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:101256815G>A	uc003uyr.2	-	c.621C>T	c.(619-621)TGC>TGT	p.C207C		NM_138403	NP_612412	Q9BUA6	MYL10_HUMAN	myosin, light chain 10, regulatory	207	EF-hand 3.					mitochondrion	calcium ion binding			ovary(1)|breast(1)	2						Esophageal Squamous(24;575 709 17516 40384 51639)								0.1	8.63174	35.902658	17	153	KEEP	---	---	---	---	capture		Silent	SNP	101256815	101256815	10439	7	G	A	A	A	490	38	MYL10	1	1
RELN	5649	broad.mit.edu	37	7	103138649	103138649	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:103138649C>T	uc003vca.2	-	c.8718G>A	c.(8716-8718)TGG>TGA	p.W2906*	RELN_uc010liz.2_Nonsense_Mutation_p.W2906*	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2906					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		NSCLC(146;835 1944 15585 22231 52158)								0.183486	41.728908	51.982366	20	89	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	103138649	103138649	13689	7	C	T	T	T	390	30	RELN	5	2
RELN	5649	broad.mit.edu	37	7	103162509	103162509	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:103162509C>A	uc003vca.2	-	c.7628G>T	c.(7627-7629)TGT>TTT	p.C2543F	RELN_uc010liz.2_Missense_Mutation_p.C2543F	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2543					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		NSCLC(146;835 1944 15585 22231 52158)								0.107143	7.669143	25.00463	12	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103162509	103162509	13689	7	C	A	A	A	221	17	RELN	2	2
RELN	5649	broad.mit.edu	37	7	103252227	103252227	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:103252227G>T	uc003vca.2	-	c.2726C>A	c.(2725-2727)GCC>GAC	p.A909D	RELN_uc010liz.2_Missense_Mutation_p.A909D	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	909					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		NSCLC(146;835 1944 15585 22231 52158)								0.214286	33.182424	38.463116	15	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103252227	103252227	13689	7	G	T	T	T	546	42	RELN	2	2
PIK3CG	5294	broad.mit.edu	37	7	106522623	106522623	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:106522623A>G	uc003vdv.3	+	c.2600A>G	c.(2599-2601)TAT>TGT	p.Y867C	PIK3CG_uc003vdu.2_Missense_Mutation_p.Y867C|PIK3CG_uc003vdw.2_Missense_Mutation_p.Y867C	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	867	PI3K/PI4K.				G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21										292				0.09375	6.906532	17.516785	6	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106522623	106522623	12340	7	A	G	G	G	208	16	PIK3CG	4	4
GPR22	2845	broad.mit.edu	37	7	107114721	107114721	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:107114721A>T	uc003vef.2	+	c.216A>T	c.(214-216)TTA>TTT	p.L72F	COG5_uc003vec.2_Intron|COG5_uc003ved.2_Intron|COG5_uc003vee.2_Intron	NM_005295	NP_005286	Q99680	GPR22_HUMAN	G protein-coupled receptor 22	72	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(1)	1														0.104575	10.489839	34.287753	16	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107114721	107114721	6957	7	A	T	T	T	167	13	GPR22	3	3
BCAP29	55973	broad.mit.edu	37	7	107224400	107224400	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:107224400A>T	uc011kma.1	+	c.166A>T	c.(166-168)ATC>TTC	p.I56F	BCAP29_uc003vej.2_Missense_Mutation_p.I56F|BCAP29_uc011kly.1_5'UTR|BCAP29_uc011klz.1_Missense_Mutation_p.I56F	NM_001008405	NP_001008405	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein BAP29 isoform	56	Helical; (Potential).				apoptosis|intracellular protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|integral to membrane				large_intestine(1)|ovary(1)	2														0.087719	5.164551	24.760643	10	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107224400	107224400	1367	7	A	T	T	T	208	16	BCAP29	3	3
LAMB4	22798	broad.mit.edu	37	7	107671272	107671272	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:107671272G>T	uc010ljo.1	-	c.4971C>A	c.(4969-4971)CAC>CAA	p.H1657Q	LAMB4_uc003vey.2_Missense_Mutation_p.H1657Q|LAMB4_uc010ljp.1_Missense_Mutation_p.H626Q	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	1657	Potential.|Domain I.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)	7														0.118182	32.187284	63.707682	26	194	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107671272	107671272	8936	7	G	T	T	T	568	44	LAMB4	2	2
NRCAM	4897	broad.mit.edu	37	7	107880434	107880434	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:107880434C>G	uc003vfb.2	-	c.75G>C	c.(73-75)CAG>CAC	p.Q25H	NRCAM_uc003vfc.2_Missense_Mutation_p.Q25H|NRCAM_uc011kmk.1_Missense_Mutation_p.Q20H|NRCAM_uc003vfd.2_Missense_Mutation_p.Q20H|NRCAM_uc003vfe.2_Missense_Mutation_p.Q20H	NM_001037132	NP_001032209	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule isoform A	25	Extracellular (Potential).				angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5														0.073171	3.370338	26.412737	9	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107880434	107880434	11049	7	C	G	G	G	415	32	NRCAM	3	3
IMMP2L	83943	broad.mit.edu	37	7	110526731	110526731	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:110526731C>A	uc003vfq.1	-	c.326G>T	c.(325-327)CGG>CTG	p.R109L	IMMP2L_uc010ljr.1_Missense_Mutation_p.R109L	NM_032549	NP_115938	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane protease-like	109					protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)										0.157895	17.438615	23.799278	9	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110526731	110526731	8018	7	C	A	A	A	299	23	IMMP2L	1	1
LRRN3	54674	broad.mit.edu	37	7	110764016	110764016	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:110764016C>G	uc003vft.3	+	c.1188C>G	c.(1186-1188)TGC>TGG	p.C396W	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Missense_Mutation_p.C396W|LRRN3_uc003vfs.3_Missense_Mutation_p.C396W	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	396	Extracellular (Potential).|LRRCT.					integral to membrane				ovary(2)|pancreas(2)|central_nervous_system(1)	5				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)										0.072289	1.681504	17.309253	6	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110764016	110764016	9412	7	C	G	G	G	350	27	LRRN3	3	3
GPR85	54329	broad.mit.edu	37	7	112723879	112723879	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:112723879G>T	uc010ljv.2	-	c.898C>A	c.(898-900)CCC>ACC	p.P300T	GPR85_uc003vgp.1_Missense_Mutation_p.P300T|GPR85_uc003vgq.2_Missense_Mutation_p.P300T|GPR85_uc010ljw.1_Missense_Mutation_p.P300T	NM_001146266	NP_001139738	P60893	GPR85_HUMAN	G protein-coupled receptor 85	300	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|central_nervous_system(1)	2														0.164062	35.292801	49.016551	21	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112723879	112723879	6990	7	G	T	T	T	559	43	GPR85	2	2
THSD7A	221981	broad.mit.edu	37	7	11468710	11468710	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:11468710C>A	uc003ssf.3	-	c.3107G>T	c.(3106-3108)TGC>TTC	p.C1036F		NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1036	TSP type-1 11.|Extracellular (Potential).					integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)										0.260274	141.561416	152.965179	57	162	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11468710	11468710	16407	7	C	A	A	A	325	25	THSD7A	2	2
TFEC	22797	broad.mit.edu	37	7	115614261	115614261	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:115614261T>A	uc003vhj.1	-	c.230A>T	c.(229-231)GAG>GTG	p.E77V	TFEC_uc003vhk.1_Intron|TFEC_uc003vhl.3_Intron|TFEC_uc011kmw.1_Missense_Mutation_p.E167V	NM_012252	NP_036384	O14948	TFEC_HUMAN	transcription factor EC isoform a	77	Necessary for transcriptional transactivation.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulator activity			large_intestine(1)	1			STAD - Stomach adenocarcinoma(10;0.00878)											0.107692	6.17755	16.099394	7	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115614261	115614261	16330	7	T	A	A	A	702	54	TFEC	3	3
PTPRZ1	5803	broad.mit.edu	37	7	121650958	121650958	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:121650958G>C	uc003vjy.2	+	c.1858G>C	c.(1858-1860)GAT>CAT	p.D620H	PTPRZ1_uc003vjz.2_Missense_Mutation_p.D620H|PTPRZ1_uc011knt.1_Missense_Mutation_p.D70H	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	620	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														0.120482	18.296402	30.012749	10	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121650958	121650958	13272	7	G	C	C	C	585	45	PTPRZ1	3	3
PTPRZ1	5803	broad.mit.edu	37	7	121651806	121651806	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:121651806G>T	uc003vjy.2	+	c.2706G>T	c.(2704-2706)ACG>ACT	p.T902T	PTPRZ1_uc003vjz.2_Intron|PTPRZ1_uc011knt.1_Intron	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	902	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														0.131868	18.234894	30.220493	12	79	KEEP	---	---	---	---	capture		Silent	SNP	121651806	121651806	13272	7	G	T	T	T	483	38	PTPRZ1	1	1
FEZF1	389549	broad.mit.edu	37	7	121942191	121942191	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:121942191C>T	uc003vkd.2	-	c.1288G>A	c.(1288-1290)GCC>ACC	p.A430T	FEZF1_uc003vkc.2_Missense_Mutation_p.A380T	NM_001024613	NP_001019784	A0PJY2	FEZF1_HUMAN	FEZ family zinc finger 1 isoform 1	430					cell differentiation|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|breast(1)	3														0.085106	-0.481027	15.853842	8	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121942191	121942191	6062	7	C	T	T	T	338	26	FEZF1	2	2
RNF133	168433	broad.mit.edu	37	7	122338605	122338605	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:122338605C>G	uc003vkj.1	-	c.368G>C	c.(367-369)GGA>GCA	p.G123A	CADPS2_uc010lkp.2_Intron|CADPS2_uc010lkq.2_Intron	NM_139175	NP_631914	Q8WVZ7	RN133_HUMAN	ring finger protein 133	123	PA.					endoplasmic reticulum membrane|integral to membrane	ligase activity|zinc ion binding				0						Colon(198;1778 2057 7449 19869 45985)								0.158192	66.893592	86.598613	28	149	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122338605	122338605	13916	7	C	G	G	G	390	30	RNF133	3	3
POT1	25913	broad.mit.edu	37	7	124467351	124467351	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:124467351T>A	uc003vlm.2	-	c.1603A>T	c.(1603-1605)ATT>TTT	p.I535F	POT1_uc011koe.1_Non-coding_Transcript|POT1_uc003vlk.2_Non-coding_Transcript|POT1_uc003vll.2_Non-coding_Transcript|POT1_uc003vlo.2_Missense_Mutation_p.I404F|POT1_uc003vln.2_Non-coding_Transcript	NM_015450	NP_056265	Q9NUX5	POTE1_HUMAN	protection of telomeres 1 isoform 1	535					DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1						Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)								0.102564	1.873389	8.013698	4	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124467351	124467351	12689	7	T	A	A	A	637	49	POT1	3	3
POT1	25913	broad.mit.edu	37	7	124532324	124532324	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:124532324T>A	uc003vlm.2	-	c.120A>T	c.(118-120)GGA>GGT	p.G40G	POT1_uc011koe.1_Non-coding_Transcript|POT1_uc003vlk.2_Non-coding_Transcript|POT1_uc003vll.2_Non-coding_Transcript|POT1_uc003vlo.2_5'UTR|POT1_uc003vln.2_Non-coding_Transcript	NM_015450	NP_056265	Q9NUX5	POTE1_HUMAN	protection of telomeres 1 isoform 1	40	DNA binding.				DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1						Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)								0.087805	0.800464	36.033166	18	187	KEEP	---	---	---	---	capture		Silent	SNP	124532324	124532324	12689	7	T	A	A	A	795	62	POT1	3	3
C7orf45	136263	broad.mit.edu	37	7	129855823	129855823	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:129855823A>T	uc003vpp.2	+	c.248A>T	c.(247-249)GAG>GTG	p.E83V		NM_145268	NP_660311	Q8WWF3	CG045_HUMAN	hypothetical protein LOC136263	83						integral to membrane					0	Melanoma(18;0.0435)													0.113924	7.026926	18.636812	9	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129855823	129855823	2502	7	A	T	T	T	143	11	C7orf45	3	3
KLF14	136259	broad.mit.edu	37	7	130418206	130418206	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:130418206G>T	uc003vqk.1	-	c.655C>A	c.(655-657)CAC>AAC	p.H219N		NM_138693	NP_619638	Q8TD94	KLF14_HUMAN	Kruppel-like factor 14	219	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Melanoma(18;0.0435)													0.139535	9.218651	14.617884	6	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130418206	130418206	8654	7	G	T	T	T	611	47	KLF14	2	2
PLXNA4	91584	broad.mit.edu	37	7	131849037	131849037	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:131849037C>A	uc003vra.3	-	c.4364G>T	c.(4363-4365)GGG>GTG	p.G1455V		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1455	Cytoplasmic (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1														0.087719	0.53206	10.333177	5	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131849037	131849037	12548	7	C	A	A	A	286	22	PLXNA4	2	2
PLXNA4	91584	broad.mit.edu	37	7	131866287	131866288	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:131866287_131866288GG>TT	uc003vra.3	-	c.3344_3345CC>AA	c.(3343-3345)CCC>CAA	p.P1115Q		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1115	Extracellular (Potential).|IPT/TIG 3.					integral to membrane|intracellular|plasma membrane				ovary(1)	1														0.202797	69.894384	81.624217	29	114	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	131866287	131866288	12548	7	GG	TT	TT	TT	496	39	PLXNA4	1	1
PLXNA4	91584	broad.mit.edu	37	7	131913153	131913153	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:131913153C>A	uc003vra.3	-	c.1680G>T	c.(1678-1680)CGG>CGT	p.R560R		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	560	Extracellular (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1														0.089744	0.665796	13.921852	7	71	KEEP	---	---	---	---	capture		Silent	SNP	131913153	131913153	12548	7	C	A	A	A	327	26	PLXNA4	2	2
STRA8	346673	broad.mit.edu	37	7	134928142	134928142	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:134928142C>A	uc011kpx.1	+	c.399C>A	c.(397-399)AGC>AGA	p.S133R		NM_182489	NP_872295	Q7Z7C7	STRA8_HUMAN	STRA8	133					DNA replication	cytoplasm|nucleus	transcription regulator activity				0														0.142857	17.669883	27.137021	11	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134928142	134928142	15843	7	C	A	A	A	324	25	STRA8	2	2
DGKI	9162	broad.mit.edu	37	7	137293720	137293720	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:137293720C>A	uc003vtt.2	-	c.1159G>T	c.(1159-1161)GGC>TGC	p.G387C	DGKI_uc003vtu.2_Missense_Mutation_p.G87C	NM_004717	NP_004708	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	387	DAGKc.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)	2														0.155172	15.234665	21.825741	9	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	137293720	137293720	4650	7	C	A	A	A	312	24	DGKI	2	2
KIAA1549	57670	broad.mit.edu	37	7	138536986	138536986	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:138536986C>A	uc011kql.1	-	c.5277G>T	c.(5275-5277)CCG>CCT	p.P1759P	KIAA1549_uc011kqi.1_Silent_p.P543P|KIAA1549_uc003vuk.3_Silent_p.P1709P|KIAA1549_uc011kqj.1_Silent_p.P1759P|KIAA1549_uc011kqk.1_Silent_p.P543P	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	1759						integral to membrane			KIAA1549/BRAF(211)	central_nervous_system(211)|pancreas(1)	212						NSCLC(119;1534 1718 44213 46230 50068)			p.P1709P(SNU1040-Tumor)|p.P1709P(JK1-Tumor)	967				0.269231	17.013401	18.26307	7	19	KEEP	---	---	---	---	capture		Silent	SNP	138536986	138536986	8553	7	C	A	A	A	392	31	KIAA1549	1	1
HIPK2	28996	broad.mit.edu	37	7	139416276	139416276	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:139416276C>G	uc003vvf.3	-	c.558G>C	c.(556-558)CTG>CTC	p.L186L	HIPK2_uc003vvd.3_Silent_p.L186L	NM_022740	NP_073577	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2 isoform	186	Transcriptional corepression (By similarity).				apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)									363				0.161538	40.831156	54.966725	21	109	KEEP	---	---	---	---	capture		Silent	SNP	139416276	139416276	7402	7	C	G	G	G	262	21	HIPK2	3	3
TRYX3	136541	broad.mit.edu	37	7	141955042	141955042	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:141955042T>A	uc003vxb.2	-	c.269A>T	c.(268-270)CAT>CTT	p.H90L	TRYX3_uc003vxc.3_Missense_Mutation_p.H90L	NM_001001317	NP_001001317	Q8IYP2	PRS58_HUMAN	trypsin X3 precursor	90	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity				0	Melanoma(164;0.0272)													0.08805	7.931375	35.208062	14	145	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141955042	141955042	17155	7	T	A	A	A	663	51	TRYX3	3	3
PRSS1	5644	broad.mit.edu	37	7	142459775	142459775	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142459775A>T	uc003wak.2	+	c.351A>T	c.(349-351)GCA>GCT	p.A117A	TRY6_uc011ksn.1_Intron|PRSS1_uc011ksm.1_3'UTR|PRSS1_uc003wam.2_Silent_p.A57A	NM_002769	NP_002760	P07477	TRY1_HUMAN	protease, serine, 1 preproprotein	117	Peptidase S1.				digestion|proteolysis	extracellular space	metal ion binding|protein binding|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)											0.136564	48.972664	77.998828	31	196	KEEP	---	---	---	---	capture		Silent	SNP	142459775	142459775	13064	7	A	T	T	T	80	7	PRSS1	3	3
OR6V1	346517	broad.mit.edu	37	7	142749798	142749798	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142749798T>A	uc011ksv.1	+	c.361T>A	c.(361-363)TTT>ATT	p.F121I		NM_001001667	NP_001001667	Q8N148	OR6V1_HUMAN	olfactory receptor, family 6, subfamily V,	121	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Melanoma(164;0.059)													0.172185	42.0174	57.420503	26	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142749798	142749798	11622	7	T	A	A	A	728	56	OR6V1	3	3
PIP	5304	broad.mit.edu	37	7	142836648	142836648	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142836648G>T	uc003wcf.1	+	c.354G>T	c.(352-354)CGG>CGT	p.R118R		NM_002652	NP_002643	P12273	PIP_HUMAN	prolactin-induced protein precursor	118						extracellular region	actin binding			ovary(1)	1	Melanoma(164;0.059)	Ovarian(593;2.82e-05)|Breast(660;0.012)		BRCA - Breast invasive adenocarcinoma(188;0.0026)|LUSC - Lung squamous cell carcinoma(290;0.0733)|Lung(243;0.08)										0.170909	84.24982	112.42212	47	228	KEEP	---	---	---	---	capture		Silent	SNP	142836648	142836648	12359	7	G	T	T	T	548	43	PIP	2	2
TMEM139	135932	broad.mit.edu	37	7	142983814	142983814	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142983814G>A	uc010lov.2	+	c.543G>A	c.(541-543)GCG>GCA	p.A181A	CASP2_uc003wco.2_5'Flank|CASP2_uc003wcp.2_5'Flank|CASP2_uc011kta.1_5'Flank|CASP2_uc003wcq.2_5'Flank|TMEM139_uc003wck.3_Silent_p.A181A|TMEM139_uc003wcl.2_Silent_p.A181A|TMEM139_uc003wcm.2_Silent_p.A181A|TMEM139_uc003wcn.2_Non-coding_Transcript	NM_153345	NP_699176	Q8IV31	TM139_HUMAN	transmembrane protein 139 precursor	181	Cytoplasmic (Potential).					integral to membrane					0	Melanoma(164;0.059)													0.125786	24.190153	45.936501	20	139	KEEP	---	---	---	---	capture		Silent	SNP	142983814	142983814	16586	7	G	A	A	A	496	39	TMEM139	1	1
EPHA1	2041	broad.mit.edu	37	7	143092462	143092462	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143092462C>A	uc003wcz.2	-	c.2033G>T	c.(2032-2034)GGC>GTC	p.G678V		NM_005232	NP_005223	P21709	EPHA1_HUMAN	ephrin receptor EphA1 precursor	678	Protein kinase.|Cytoplasmic (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(3)|lung(1)|breast(1)	5	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)								379		OREG0018405	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.07131	-31.206919	82.894658	43	560	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143092462	143092462	5358	7	C	A	A	A	338	26	EPHA1	2	2
OR2A5	393046	broad.mit.edu	37	7	143748015	143748015	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143748015T>A	uc011ktw.1	+	c.521T>A	c.(520-522)ATC>AAC	p.I174N		NM_012365	NP_036497	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A,	174	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Melanoma(164;0.0783)													0.071739	-20.062969	66.849292	33	427	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143748015	143748015	11387	7	T	A	A	A	650	50	OR2A5	3	3
OR2A25	392138	broad.mit.edu	37	7	143771324	143771324	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143771324T>A	uc011ktx.1	+	c.12T>A	c.(10-12)AAT>AAA	p.N4K		NM_001004488	NP_001004488	A4D2G3	O2A25_HUMAN	olfactory receptor, family 2, subfamily A,	4	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Melanoma(164;0.0783)													0.171642	46.753604	60.401274	23	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143771324	143771324	11384	7	T	A	A	A	647	50	OR2A25	3	3
ZNF862	643641	broad.mit.edu	37	7	149557754	149557754	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:149557754G>T	uc010lpn.2	+	c.1505G>T	c.(1504-1506)CGG>CTG	p.R502L	ZNF862_uc003wgm.2_Non-coding_Transcript	NM_001099220	NP_001092690	O60290	ZN862_HUMAN	zinc finger protein 862	502	TTF-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|nucleic acid binding|protein dimerization activity			skin(1)	1														0.11236	24.169731	50.583786	20	158	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149557754	149557754	18798	7	G	T	T	T	507	39	ZNF862	1	1
GIMAP1	170575	broad.mit.edu	37	7	150416163	150416163	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150416163G>T	uc003whp.2	+	c.52G>T	c.(52-54)GAA>TAA	p.E18*	GIMAP1_uc003whq.2_Nonsense_Mutation_p.E10*	NM_130759	NP_570115	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	10	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										0.114035	12.790979	29.540962	13	101	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	150416163	150416163	6647	7	G	T	T	T	585	45	GIMAP1	5	2
GIMAP1	170575	broad.mit.edu	37	7	150417496	150417496	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150417496T>A	uc003whp.2	+	c.428T>A	c.(427-429)GTG>GAG	p.V143E	GIMAP1_uc003whq.2_Missense_Mutation_p.V135E	NM_130759	NP_570115	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	135	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										0.179104	24.072696	30.555253	12	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150417496	150417496	6647	7	T	A	A	A	767	59	GIMAP1	3	3
KCNH2	3757	broad.mit.edu	37	7	150647499	150647499	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150647499C>A	uc003wic.2	-	c.2155G>T	c.(2155-2157)GGC>TGC	p.G719C	KCNH2_uc003wib.2_Missense_Mutation_p.G379C|KCNH2_uc011kux.1_Missense_Mutation_p.G623C|KCNH2_uc003wid.2_Missense_Mutation_p.G379C|KCNH2_uc003wie.2_Missense_Mutation_p.G719C	NM_000238	NP_000229	Q12809	KCNH2_HUMAN	voltage-gated potassium channel, subfamily H,	719	Cytoplasmic (Potential).				blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|two-component sensor activity			ovary(1)|skin(1)	2	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661)	GBM(137;110 1844 13671 20123 45161)				314				0.138889	21.151952	34.765064	15	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150647499	150647499	8337	7	C	A	A	A	286	22	KCNH2	2	2
TMUB1	83590	broad.mit.edu	37	7	150779566	150779566	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150779566C>A	uc003wjb.2	-	c.85G>T	c.(85-87)GTC>TTC	p.V29F	FASTK_uc003wiw.1_5'Flank|FASTK_uc003wix.1_5'Flank|FASTK_uc003wiy.1_5'Flank|FASTK_uc003wiz.1_5'Flank|FASTK_uc003wja.1_5'Flank|TMUB1_uc003wjc.2_Missense_Mutation_p.V29F|TMUB1_uc003wjd.2_Missense_Mutation_p.V29F	NM_031434	NP_113622	Q9BVT8	TMUB1_HUMAN	transmembrane and ubiquitin-like domain	29						cytoplasm|integral to membrane|nucleus					0			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										0.06993	-7.840176	19.447446	10	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150779566	150779566	16805	7	C	A	A	A	234	18	TMUB1	2	2
TMEM195	392636	broad.mit.edu	37	7	15425104	15425104	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:15425104C>A	uc003stb.1	-	c.1041G>T	c.(1039-1041)TTG>TTT	p.L347F		NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195	347	Helical; (Potential).				ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process|oxidation-reduction process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0														0.125984	22.004003	39.352929	16	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15425104	15425104	16652	7	C	A	A	A	272	21	TMEM195	2	2
DPP6	1804	broad.mit.edu	37	7	154679411	154679411	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:154679411G>C	uc003wlk.2	+	c.2271G>C	c.(2269-2271)TTG>TTC	p.L757F	DPP6_uc003wli.2_Missense_Mutation_p.L693F|DPP6_uc003wlm.2_Missense_Mutation_p.L695F|DPP6_uc011kvq.1_Missense_Mutation_p.L650F	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1	757	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)								0.173536	176.027213	222.409697	80	381	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154679411	154679411	4914	7	G	C	C	C	607	47	DPP6	3	3
SHH	6469	broad.mit.edu	37	7	155596253	155596253	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:155596253G>A	uc003wmk.1	-	c.730C>T	c.(730-732)CGC>TGC	p.R244C	SHH_uc003wmh.1_Intron|SHH_uc003wmi.1_Intron|SHH_uc003wmj.1_Missense_Mutation_p.R157C	NM_000193	NP_000184	Q15465	SHH_HUMAN	sonic hedgehog preproprotein	244					androgen metabolic process|axon guidance|branching involved in ureteric bud morphogenesis|CD4-positive or CD8-positive, alpha-beta T cell lineage commitment|embryonic digit morphogenesis|hindbrain development|intein-mediated protein splicing|lymphoid progenitor cell differentiation|metanephric mesenchymal cell proliferation involved in metanephros development|midbrain development|negative regulation of cell migration|negative regulation of kidney smooth muscle cell differentiation|negative regulation of ureter smooth muscle cell differentiation|negative thymic T cell selection|neural crest cell migration|neuroblast proliferation|patterning of blood vessels|positive regulation of alpha-beta T cell differentiation|positive regulation of immature T cell proliferation in thymus|positive regulation of kidney smooth muscle cell differentiation|positive regulation of T cell differentiation in thymus|positive regulation of ureter smooth muscle cell differentiation|positive thymic T cell selection|proteolysis|regulation of mesenchymal cell proliferation involved in ureter development|sclerotome development|stem cell development|thymus development|vasculogenesis|ventral midline development	cell surface|extracellular space|membrane raft|plasma membrane	calcium ion binding|laminin-1 binding|peptidase activity|signal transducer activity|transcription activator activity|zinc ion binding			central_nervous_system(3)	3	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00882)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)						109				0.4	11.199061	11.286135	4	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155596253	155596253	14771	7	G	A	A	A	507	39	SHH	1	1
LMBR1	64327	broad.mit.edu	37	7	156518501	156518501	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:156518501T>C	uc010lqn.2	-	c.1147A>G	c.(1147-1149)ACG>GCG	p.T383A	LMBR1_uc003wmv.3_Missense_Mutation_p.T190A|LMBR1_uc003wmw.3_Missense_Mutation_p.T342A|LMBR1_uc003wmx.3_Missense_Mutation_p.T190A|LMBR1_uc011kvx.1_Missense_Mutation_p.T321A	NM_022458	NP_071903	Q8WVP7	LMBR1_HUMAN	limb region 1 protein	342	Helical; (Potential).					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)										0.071429	1.358054	11.951473	4	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156518501	156518501	9169	7	T	C	C	C	741	57	LMBR1	4	4
NCAPG2	54892	broad.mit.edu	37	7	158482646	158482646	+	Splice_Site_SNP	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:158482646C>T	uc011kwe.1	-	c.538_splice	c.e6-1	p.G180_splice	NCAPG2_uc010lqu.1_Splice_Site_SNP|NCAPG2_uc003wnv.1_Splice_Site_SNP_p.G180_splice|NCAPG2_uc003wnw.1_Splice_Site_SNP|NCAPG2_uc003wnx.1_Splice_Site_SNP_p.G180_splice	NM_017760	NP_060230			leucine zipper protein 5						cell division|chromosome condensation|mitosis	nucleus	methylated histone residue binding			ovary(1)|breast(1)|kidney(1)	3	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)										0.153846	11.622834	16.092188	6	33	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	158482646	158482646	10607	7	C	T	T	T	312	24	NCAPG2	5	2
WDR60	55112	broad.mit.edu	37	7	158669353	158669353	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:158669353G>A	uc003woe.3	+	c.544G>A	c.(544-546)GAT>AAT	p.D182N		NM_018051	NP_060521	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	182										ovary(2)|breast(1)	3	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)										0.222222	9.389617	10.667907	4	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158669353	158669353	17884	7	G	A	A	A	429	33	WDR60	2	2
PSMG3	84262	broad.mit.edu	37	7	1608771	1608771	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:1608771C>A	uc003skx.2	-	c.205G>T	c.(205-207)GGG>TGG	p.G69W	PSMG3_uc011jvx.1_Missense_Mutation_p.G69W|KIAA1908_uc003sla.2_5'Flank|KIAA1908_uc003sky.1_5'Flank|KIAA1908_uc003skz.1_5'Flank	NM_032302	NP_115678	Q9BT73	PSMG3_HUMAN	proteasome assembling chaperone 3	69											0		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.63e-15)										0.169591	56.080754	73.739007	29	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1608771	1608771	13166	7	C	A	A	A	286	22	PSMG3	2	2
SOSTDC1	25928	broad.mit.edu	37	7	16502317	16502317	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:16502317T>A	uc003sth.2	-	c.549A>T	c.(547-549)GTA>GTT	p.V183V	SOSTDC1_uc003stg.2_Silent_p.V159V	NM_015464	NP_056279	Q6X4U4	SOSD1_HUMAN	sclerostin domain containing 1 precursor	159	CTCK.				Wnt receptor signaling pathway					ovary(2)|central_nervous_system(1)	3	Lung NSC(10;0.185)			UCEC - Uterine corpus endometrioid carcinoma (126;0.177)										0.28479	217.430191	230.309305	88	221	KEEP	---	---	---	---	capture		Silent	SNP	16502317	16502317	15439	7	T	A	A	A	678	53	SOSTDC1	3	3
ANKMY2	57037	broad.mit.edu	37	7	16666731	16666731	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:16666731C>A	uc003sti.2	-	c.205G>T	c.(205-207)GGA>TGA	p.G69*	ANKMY2_uc010ktz.2_Non-coding_Transcript	NM_020319	NP_064715	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	69	ANK 1.					cilium	zinc ion binding			central_nervous_system(1)	1	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)										0.186047	16.871907	20.845988	8	35	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	16666731	16666731	638	7	C	A	A	A	273	21	ANKMY2	5	2
TMEM196	256130	broad.mit.edu	37	7	19761705	19761705	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:19761705C>A	uc011jyg.1	-	c.512G>T	c.(511-513)AGA>ATA	p.R171I	TMEM196_uc003sur.2_Non-coding_Transcript	NM_152774	NP_689987	Q5HYL7	TM196_HUMAN	transmembrane protein 196	177						integral to membrane					0														0.22449	23.595513	27.016821	11	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19761705	19761705	16653	7	C	A	A	A	416	32	TMEM196	2	2
ABCB5	340273	broad.mit.edu	37	7	20784905	20784906	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:20784905_20784906CC>AA	uc010kuh.2	+	c.3273_3274CC>AA	c.(3271-3276)TCCCAA>TCAAAA	p.Q1092K	ABCB5_uc003suw.3_Missense_Mutation_p.Q647K	NM_001163941	NP_001157413	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5	647	Cytoplasmic (Potential).|ABC transporter 2.				regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			large_intestine(1)|ovary(1)|pancreas(1)	3														0.259615	65.798806	71.227868	27	77	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	20784905	20784906	45	7	CC	AA	AA	AA	275	22	ABCB5	2	2
KLHL7	55975	broad.mit.edu	37	7	23180421	23180421	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:23180421C>A	uc003svs.3	+	c.476C>A	c.(475-477)CCT>CAT	p.P159H	KLHL7_uc003svr.3_Missense_Mutation_p.P137H|KLHL7_uc011jys.1_Missense_Mutation_p.P83H|KLHL7_uc011jyt.1_De_novo_Start_OutOfFrame|KLHL7_uc003svt.2_Missense_Mutation_p.P111H|KLHL7_uc011jyv.1_De_novo_Start_OutOfFrame	NM_001031710	NP_001026880	Q8IXQ5	KLHL7_HUMAN	kelch-like 7 isoform 1	159					response to stimulus|visual perception	Golgi apparatus|nucleolus|plasma membrane					0														0.193798	53.60031	64.887002	25	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23180421	23180421	8708	7	C	A	A	A	312	24	KLHL7	2	2
KLHL7	55975	broad.mit.edu	37	7	23180432	23180432	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:23180432G>A	uc003svs.3	+	c.487G>A	c.(487-489)GCA>ACA	p.A163T	KLHL7_uc003svr.3_Missense_Mutation_p.A141T|KLHL7_uc011jys.1_Missense_Mutation_p.A87T|KLHL7_uc011jyt.1_5'UTR|KLHL7_uc003svt.2_Missense_Mutation_p.A115T|KLHL7_uc011jyv.1_5'UTR	NM_001031710	NP_001026880	Q8IXQ5	KLHL7_HUMAN	kelch-like 7 isoform 1	163					response to stimulus|visual perception	Golgi apparatus|nucleolus|plasma membrane					0														0.194245	60.544606	72.667573	27	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23180432	23180432	8708	7	G	A	A	A	442	34	KLHL7	2	2
KLHL7	55975	broad.mit.edu	37	7	23205441	23205441	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:23205441G>C	uc003svs.3	+	c.1061G>C	c.(1060-1062)TGC>TCC	p.C354S	KLHL7_uc003svr.3_Missense_Mutation_p.C332S|KLHL7_uc011jys.1_Missense_Mutation_p.C278S|KLHL7_uc011jyt.1_Missense_Mutation_p.C129S|KLHL7_uc003svt.2_Missense_Mutation_p.C306S|KLHL7_uc011jyv.1_Missense_Mutation_p.C129S	NM_001031710	NP_001026880	Q8IXQ5	KLHL7_HUMAN	kelch-like 7 isoform 1	354	Kelch 2.				response to stimulus|visual perception	Golgi apparatus|nucleolus|plasma membrane					0														0.241379	43.522196	47.059519	14	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23205441	23205441	8708	7	G	C	C	C	598	46	KLHL7	3	3
NPY	4852	broad.mit.edu	37	7	24324910	24324910	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:24324910C>T	uc003sww.1	+	c.51C>T	c.(49-51)TCC>TCT	p.S17S		NM_000905	NP_000896	P01303	NPY_HUMAN	neuropeptide Y precursor	17					adult feeding behavior|calcium ion transport|cell proliferation|cellular component movement|digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|neuropeptide signaling pathway|positive regulation of appetite|synaptic transmission	cell|extracellular space	calcium channel regulator activity|G-protein coupled receptor activity|neuropeptide hormone activity				0														0.195122	48.475926	59.10475	24	99	KEEP	---	---	---	---	capture		Silent	SNP	24324910	24324910	11012	7	C	T	T	T	275	22	NPY	2	2
CHST12	55501	broad.mit.edu	37	7	2472659	2472659	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:2472659C>T	uc003smc.2	+	c.385C>T	c.(385-387)CGG>TGG	p.R129W	CHST12_uc003smd.2_Missense_Mutation_p.R129W	NM_018641	NP_061111	Q9NRB3	CHSTC_HUMAN	carbohydrate sulfotransferase 12	129	Lumenal (Potential).				dermatan sulfate biosynthetic process	integral to Golgi membrane	3'-phosphoadenosine 5'-phosphosulfate binding|chondroitin 4-sulfotransferase activity|protein binding			kidney(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)										0.117647	10.845642	25.494207	12	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2472659	2472659	3534	7	C	T	T	T	347	27	CHST12	1	1
OSBPL3	26031	broad.mit.edu	37	7	24870410	24870410	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:24870410C>T	uc003sxf.2	-	c.1861G>A	c.(1861-1863)GGC>AGC	p.G621S	OSBPL3_uc003sxd.2_Non-coding_Transcript|OSBPL3_uc003sxe.2_Non-coding_Transcript|OSBPL3_uc003sxg.2_Missense_Mutation_p.G585S|OSBPL3_uc003sxh.2_Missense_Mutation_p.G590S|OSBPL3_uc003sxi.2_Missense_Mutation_p.G554S	NM_015550	NP_056365	Q9H4L5	OSBL3_HUMAN	oxysterol-binding protein-like protein 3 isoform	621					lipid transport		lipid binding|protein binding			skin(1)	1														0.065041	-21.92152	50.529823	24	345	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24870410	24870410	11690	7	C	T	T	T	286	22	OSBPL3	2	2
C7orf27	221927	broad.mit.edu	37	7	2581099	2581099	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:2581099C>A	uc003smi.2	-	c.1154G>T	c.(1153-1155)TGG>TTG	p.W385L	C7orf27_uc003smh.3_5'UTR	NM_152743	NP_689956	Q6PJG6	BRAT1_HUMAN	hypothetical protein LOC221927 precursor	385					response to ionizing radiation	nucleus	protein binding				0		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;2.91e-14)										0.5	11.799403	11.799403	4	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2581099	2581099	2489	7	C	A	A	A	273	21	C7orf27	2	2
HOXA1	3198	broad.mit.edu	37	7	27134253	27134253	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:27134253G>C	uc003sye.2	-	c.814C>G	c.(814-816)CAA>GAA	p.Q272E	HOXA1_uc003syd.2_3'UTR	NM_005522	NP_005513	P49639	HXA1_HUMAN	homeobox A1 isoform a	272	Homeobox.					nucleus	protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)	3														0.114286	19.20855	39.741145	16	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27134253	27134253	7580	7	G	C	C	C	611	47	HOXA1	3	3
TAX1BP1	8887	broad.mit.edu	37	7	27827145	27827145	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:27827145G>T	uc003szl.2	+	c.961G>T	c.(961-963)GAG>TAG	p.E321*	TAX1BP1_uc011jzo.1_Nonsense_Mutation_p.E321*|TAX1BP1_uc003szk.2_Nonsense_Mutation_p.E321*|TAX1BP1_uc011jzp.1_Nonsense_Mutation_p.E164*	NM_006024	NP_006015	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I)	321	Oligomerization.|Potential.				anti-apoptosis|apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production	cytosol	identical protein binding|kinase binding|zinc ion binding			breast(1)	1			GBM - Glioblastoma multiforme(3;0.0823)											0.129412	12.358991	23.733522	11	74	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	27827145	27827145	16116	7	G	T	T	T	429	33	TAX1BP1	5	2
GHRHR	2692	broad.mit.edu	37	7	31014634	31014634	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:31014634G>T	uc003tbx.2	+	c.861G>T	c.(859-861)GGG>GGT	p.G287G	GHRHR_uc003tbw.1_Silent_p.G287G|GHRHR_uc003tby.2_Silent_p.G223G|GHRHR_uc003tbz.2_Missense_Mutation_p.A54S	NM_000823	NP_000814	Q02643	GHRHR_HUMAN	growth hormone releasing hormone receptor	287	Helical; Name=5; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of cell proliferation|positive regulation of growth hormone secretion|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of multicellular organism growth|response to estrogen stimulus|response to glucocorticoid stimulus	cell surface|integral to membrane|nuclear inner membrane|nuclear matrix|nuclear outer membrane|plasma membrane|stored secretory granule	growth factor binding|growth hormone-releasing hormone receptor activity|peptide hormone binding			large_intestine(1)|ovary(1)	2					Sermorelin(DB00010)							OREG0017943	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.101523	14.395631	45.563691	20	177	KEEP	---	---	---	---	capture		Silent	SNP	31014634	31014634	6641	7	G	T	T	T	535	42	GHRHR	2	2
ADCYAP1R1	117	broad.mit.edu	37	7	31146224	31146224	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:31146224C>A	uc003tcc.1	+	c.1417C>A	c.(1417-1419)CAG>AAG	p.Q473K	ADCYAP1R1_uc003tca.1_Missense_Mutation_p.Q445K|ADCYAP1R1_uc003tcb.1_Missense_Mutation_p.Q424K|ADCYAP1R1_uc003tcd.1_Missense_Mutation_p.Q473K|ADCYAP1R1_uc003tce.1_Missense_Mutation_p.Q472K	NM_001118	NP_001109	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1	445	Cytoplasmic (Potential).				activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|spermatogenesis	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			ovary(1)	1						Ovarian(44;225 1186 2158 11092)								0.184211	27.200165	34.315251	14	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31146224	31146224	304	7	C	A	A	A	273	21	ADCYAP1R1	2	2
CCDC129	223075	broad.mit.edu	37	7	31592660	31592660	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:31592660G>T	uc011kae.1	+	c.100G>T	c.(100-102)GGA>TGA	p.G34*	CCDC129_uc011kad.1_Nonsense_Mutation_p.G18*|CCDC129_uc003tcj.1_Nonsense_Mutation_p.G8*|CCDC129_uc003tci.1_Nonsense_Mutation_p.G7*|CCDC129_uc003tck.1_5'Flank	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	8											0														0.208333	10.96019	12.852235	5	19	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	31592660	31592660	2884	7	G	T	T	T	455	35	CCDC129	5	2
CCDC129	223075	broad.mit.edu	37	7	31617853	31617853	+	Silent	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:31617853A>G	uc011kae.1	+	c.1053A>G	c.(1051-1053)CTA>CTG	p.L351L	CCDC129_uc011kad.1_Silent_p.L335L|CCDC129_uc003tcj.1_Silent_p.L325L|CCDC129_uc003tci.1_Intron|CCDC129_uc003tck.1_Silent_p.L233L	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	325											0														0.197531	43.862892	50.755766	16	65	KEEP	---	---	---	---	capture		Silent	SNP	31617853	31617853	2884	7	A	G	G	G	171	14	CCDC129	4	4
BMPER	168667	broad.mit.edu	37	7	33945247	33945247	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:33945247G>A	uc011kap.1	+	c.22G>A	c.(22-24)GGG>AGG	p.G8R		NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor	8					blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3														0.19697	24.74488	30.388154	13	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33945247	33945247	1493	7	G	A	A	A	507	39	BMPER	1	1
BMPER	168667	broad.mit.edu	37	7	34125411	34125412	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:34125411_34125412GG>TT	uc011kap.1	+	c.1452_1453GG>TT	c.(1450-1455)ATGGCT>ATTTCT	p.484_485MA>IS		NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor	484_485	VWFD.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3														0.147059	15.299511	23.443876	10	58	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	34125411	34125412	1493	7	GG	TT	TT	TT	611	47	BMPER	2	2
BMPER	168667	broad.mit.edu	37	7	34182962	34182962	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:34182962G>A	uc011kap.1	+	c.1866G>A	c.(1864-1866)CAG>CAA	p.Q622Q		NM_133468	NP_597725	Q8N8U9	BMPER_HUMAN	BMP-binding endothelial regulator precursor	622					blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3														0.083333	0.453715	15.281252	7	77	KEEP	---	---	---	---	capture		Silent	SNP	34182962	34182962	1493	7	G	A	A	A	425	33	BMPER	2	2
ELMO1	9844	broad.mit.edu	37	7	37253043	37253043	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:37253043C>A	uc003tfk.1	-	c.851G>T	c.(850-852)CGG>CTG	p.R284L	ELMO1_uc011kbc.1_Missense_Mutation_p.R188L|ELMO1_uc010kxg.1_Missense_Mutation_p.R284L	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	284					actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)	3														0.254237	36.036043	39.249579	15	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37253043	37253043	5257	7	C	A	A	A	299	23	ELMO1	1	1
TXNDC3	51314	broad.mit.edu	37	7	37936532	37936532	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:37936532G>T	uc003tfn.2	+	c.1605G>T	c.(1603-1605)TTG>TTT	p.L535F		NM_016616	NP_057700	Q8N427	TXND3_HUMAN	thioredoxin domain containing 3	535	NDK 3.				cell differentiation|cell redox homeostasis|CTP biosynthetic process|GTP biosynthetic process|multicellular organismal development|spermatogenesis|UTP biosynthetic process	cytoplasm|microtubule cytoskeleton	ATP binding|nucleoside diphosphate kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3						Ovarian(108;903 1537 27096 29907 47400)								0.070175	-5.899725	15.84757	8	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37936532	37936532	17354	7	G	T	T	T	581	45	TXNDC3	2	2
AMPH	273	broad.mit.edu	37	7	38500951	38500951	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:38500951G>T	uc003tgu.2	-	c.949C>A	c.(949-951)CAG>AAG	p.Q317K	AMPH_uc003tgv.2_Missense_Mutation_p.Q317K|AMPH_uc003tgt.2_Missense_Mutation_p.Q70K	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1	317					endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)	4														0.101124	13.104857	41.377742	18	160	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38500951	38500951	591	7	G	T	T	T	598	46	AMPH	2	2
C7orf36	57002	broad.mit.edu	37	7	39610208	39610208	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:39610208G>T	uc003thc.3	+	c.233G>T	c.(232-234)CGA>CTA	p.R78L		NM_020192	NP_064577	Q9NRH1	CG036_HUMAN	hypothetical protein LOC57002	78											0														0.153374	42.261715	61.003322	25	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39610208	39610208	2497	7	G	T	T	T	481	37	C7orf36	1	1
SDK1	221935	broad.mit.edu	37	7	4026893	4026893	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:4026893G>T	uc003smx.2	+	c.2070G>T	c.(2068-2070)TGG>TGT	p.W690C		NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	690	Fibronectin type-III 1.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)	5		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)										0.27451	277.871412	296.531112	112	296	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4026893	4026893	14454	7	G	T	T	T	559	43	SDK1	2	2
SDK1	221935	broad.mit.edu	37	7	4116809	4116810	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:4116809_4116810GG>TT	uc003smx.2	+	c.3190_3191GG>TT	c.(3190-3192)GGA>TTA	p.G1064L	SDK1_uc010kso.2_Missense_Mutation_p.G340L	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	1064					cell adhesion	integral to membrane				large_intestine(3)|ovary(2)	5		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)										0.138462	14.828035	23.043997	9	56	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	4116809	4116810	14454	7	GG	TT	TT	TT	611	47	SDK1	2	2
HECW1	23072	broad.mit.edu	37	7	43436462	43436462	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:43436462G>C	uc003tid.1	+	c.605G>C	c.(604-606)CGG>CCG	p.R202P	HECW1_uc011kbi.1_Missense_Mutation_p.R202P|HECW1_uc003tie.1_Missense_Mutation_p.R234P	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	202	C2.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(7)|breast(2)|skin(2)|pancreas(1)|lung(1)	13										944				0.117021	15.062238	28.619675	11	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43436462	43436462	7325	7	G	C	C	C	507	39	HECW1	3	3
HECW1	23072	broad.mit.edu	37	7	43484004	43484004	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:43484004G>A	uc003tid.1	+	c.1233G>A	c.(1231-1233)GAG>GAA	p.E411E	HECW1_uc011kbi.1_Silent_p.E411E	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	411					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(7)|breast(2)|skin(2)|pancreas(1)|lung(1)	13										944				0.104167	5.071981	20.050626	10	86	KEEP	---	---	---	---	capture		Silent	SNP	43484004	43484004	7325	7	G	A	A	A	438	34	HECW1	2	2
HECW1	23072	broad.mit.edu	37	7	43547716	43547716	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:43547716T>A	uc003tid.1	+	c.3852T>A	c.(3850-3852)TTT>TTA	p.F1284L	HECW1_uc011kbi.1_Missense_Mutation_p.F1250L	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	1284	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(7)|breast(2)|skin(2)|pancreas(1)|lung(1)	13										944				0.086957	2.99704	14.912646	6	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43547716	43547716	7325	7	T	A	A	A	816	63	HECW1	3	3
IGFBP1	3484	broad.mit.edu	37	7	45930211	45930212	+	Missense_Mutation	DNP	CC	GA	GA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:45930211_45930212CC>GA	uc003tnp.2	+	c.414_415CC>GA	c.(412-417)TTCCAT>TTGAAT	p.138_139FH>LN	IGFBP1_uc003tno.3_Missense_Mutation_p.138_139FH>LN|IGFBP1_uc010kyn.2_Missense_Mutation_p.138_139FH>LN	NM_000596	NP_000587	P08833	IBP1_HUMAN	insulin-like growth factor binding protein 1	138_139						extracellular space	insulin-like growth factor binding				0												OREG0018048	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.081395	9.542716	40.208706	14	158	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	45930211	45930212	7879	7	CC	GA	GA	GA	389	30	IGFBP1	3	3
TNS3	64759	broad.mit.edu	37	7	47342932	47342932	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:47342932C>A	uc003tnv.2	-	c.3073G>T	c.(3073-3075)GCC>TCC	p.A1025S	TNS3_uc003tnw.2_Missense_Mutation_p.A1025S	NM_022748	NP_073585	Q68CZ2	TENS3_HUMAN	tensin 3	1025						focal adhesion	protein binding			ovary(4)	4														0.166667	11.426962	15.219946	6	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47342932	47342932	16885	7	C	A	A	A	351	27	TNS3	1	1
PKD1L1	168507	broad.mit.edu	37	7	47942094	47942094	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:47942094G>C	uc003tny.1	-	c.1946C>G	c.(1945-1947)ACA>AGA	p.T649R		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	649	Extracellular (Potential).|PKD 2.				cell-cell adhesion	integral to membrane				ovary(7)|breast(1)	8														0.212766	59.153573	66.31485	20	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47942094	47942094	12388	7	G	C	C	C	624	48	PKD1L1	3	3
RADIL	55698	broad.mit.edu	37	7	4839071	4839071	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:4839071G>T	uc003snj.1	-	c.3166C>A	c.(3166-3168)CTG>ATG	p.L1056M	RADIL_uc003sng.1_Non-coding_Transcript|RADIL_uc003sni.1_Missense_Mutation_p.L561M|RADIL_uc011jwc.1_Missense_Mutation_p.L816M|RADIL_uc011jwd.1_Non-coding_Transcript|RADIL_uc003snh.1_Missense_Mutation_p.L352M	NM_018059	NP_060529	Q96JH8	RADIL_HUMAN	Rap GTPase interactor	1056	PDZ.				cell adhesion|multicellular organismal development|signal transduction		protein binding			central_nervous_system(2)|pancreas(2)|breast(1)	5		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)										0.132743	14.646819	29.465795	15	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4839071	4839071	13457	7	G	T	T	T	451	35	RADIL	2	2
RADIL	55698	broad.mit.edu	37	7	4874578	4874578	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:4874578G>C	uc003snj.1	-	c.1076C>G	c.(1075-1077)GCG>GGG	p.A359G	RADIL_uc003sng.1_Non-coding_Transcript|RADIL_uc003sni.1_5'Flank|RADIL_uc011jwc.1_Missense_Mutation_p.A119G|RADIL_uc011jwd.1_Non-coding_Transcript	NM_018059	NP_060529	Q96JH8	RADIL_HUMAN	Rap GTPase interactor	359	FHA.				cell adhesion|multicellular organismal development|signal transduction		protein binding			central_nervous_system(2)|pancreas(2)|breast(1)	5		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)										0.206897	16.836995	19.143125	6	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4874578	4874578	13457	7	G	C	C	C	494	38	RADIL	3	3
IKZF1	10320	broad.mit.edu	37	7	50444306	50444306	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:50444306C>A	uc003tow.3	+	c.236C>A	c.(235-237)GCG>GAG	p.A79E	IKZF1_uc003tox.3_Missense_Mutation_p.A79E|IKZF1_uc003toy.3_Missense_Mutation_p.A79E|IKZF1_uc011kck.1_Intron|IKZF1_uc003toz.3_Missense_Mutation_p.A49E|IKZF1_uc010kyx.2_Intron	NM_006060	NP_006051	Q13422	IKZF1_HUMAN	zinc finger protein, subfamily 1A, 1 (Ikaros)	79					cell cycle|chromatin modification|mesoderm development	cytoplasm|nucleus	zinc ion binding	p.?(74)		haematopoietic_and_lymphoid_tissue(147)|lung(1)	148	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)								226				0.103226	16.111585	40.387191	16	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50444306	50444306	7915	7	C	A	A	A	351	27	IKZF1	1	1
WIPI2	26100	broad.mit.edu	37	7	5239262	5239262	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:5239262G>T	uc003snv.2	+	c.184G>T	c.(184-186)GAT>TAT	p.D62Y	WIPI2_uc003snw.2_Missense_Mutation_p.D62Y|WIPI2_uc003snx.2_Missense_Mutation_p.D44Y|WIPI2_uc003sny.2_Missense_Mutation_p.D44Y|WIPI2_uc010ksv.2_5'UTR	NM_015610	NP_056425	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2	62					autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)										0.149682	70.897496	107.876702	47	267	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5239262	5239262	17945	7	G	T	T	T	533	41	WIPI2	2	2
POM121L12	285877	broad.mit.edu	37	7	53103526	53103526	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:53103526C>G	uc003tpz.2	+	c.162C>G	c.(160-162)CCC>CCG	p.P54P		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	POM121 membrane glycoprotein-like 12	54											0														0.15625	25.8426	36.713025	15	81	KEEP	---	---	---	---	capture		Silent	SNP	53103526	53103526	12669	7	C	G	G	G	275	22	POM121L12	3	3
EGFR	1956	broad.mit.edu	37	7	55231427	55231427	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:55231427G>C	uc003tqk.2	+	c.1633G>C	c.(1633-1635)GAG>CAG	p.E545Q	EGFR_uc003tqi.2_Missense_Mutation_p.E545Q|EGFR_uc003tqj.2_Missense_Mutation_p.E545Q|EGFR_uc010kzg.1_Missense_Mutation_p.E500Q|EGFR_uc011kco.1_Missense_Mutation_p.E492Q|EGFR_uc011kcp.1_Intron|EGFR_uc011kcq.1_Intron|EGFR_uc003tqn.2_5'Flank	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	545	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.103226	20.879196	45.180918	16	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55231427	55231427	5156	7	G	C	C	C	585	45	EGFR	3	3
PRKAR1B	5575	broad.mit.edu	37	7	591043	591043	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:591043C>G	uc003siu.1	-	c.956G>C	c.(955-957)GGA>GCA	p.G319A	PRKAR1B_uc003siv.2_Missense_Mutation_p.G319A|PRKAR1B_uc003siw.1_Missense_Mutation_p.G319A	NM_002735	NP_002726	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type	319	cAMP 2.				activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)						35				0.153846	4.84123	6.330534	2	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	591043	591043	12947	7	C	G	G	G	390	30	PRKAR1B	3	3
RSPH10B2	728194	broad.mit.edu	37	7	6006566	6006566	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:6006566C>A	uc003sph.1	-	c.182G>T	c.(181-183)CGC>CTC	p.R61L	RSPH10B2_uc010ktd.1_Missense_Mutation_p.R61L	NM_173565	NP_775836	B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B	61										ovary(1)|pancreas(1)	2														0.167488	65.316151	86.595444	34	169	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6006566	6006566	14184	7	C	A	A	A	351	27	RSPH10B2	1	1
ASL	435	broad.mit.edu	37	7	65552346	65552346	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:65552346G>T	uc003tuo.2	+	c.628G>T	c.(628-630)GGT>TGT	p.G210C	ASL_uc003tup.2_Missense_Mutation_p.G210C|ASL_uc003tur.2_Missense_Mutation_p.G184C|ASL_uc003tuq.2_Missense_Mutation_p.G210C	NM_000048	NP_000039	P04424	ARLY_HUMAN	argininosuccinate lyase isoform 1	210					arginine biosynthetic process via ornithine|arginine catabolic process|urea cycle	cytosol	argininosuccinate lyase activity			breast(2)	2					L-Arginine(DB00125)									0.119565	12.659192	25.728208	11	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65552346	65552346	1063	7	G	T	T	T	559	43	ASL	2	2
WBSCR17	64409	broad.mit.edu	37	7	70853231	70853231	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:70853231C>A	uc003tvy.2	+	c.433C>A	c.(433-435)CTC>ATC	p.L145I	WBSCR17_uc003tvz.2_5'UTR	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	145	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)												0.076923	-3.162432	20.674557	10	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70853231	70853231	17836	7	C	A	A	A	364	28	WBSCR17	2	2
FKBP6	8468	broad.mit.edu	37	7	72744205	72744205	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:72744205G>C	uc003tya.2	+	c.318G>C	c.(316-318)GAG>GAC	p.E106D	FKBP6_uc003twz.2_Intron|FKBP6_uc011kew.1_Missense_Mutation_p.E101D|FKBP6_uc010lbe.1_Non-coding_Transcript|TRIM50_uc003txy.1_5'Flank|TRIM50_uc003txz.1_5'Flank	NM_003602	NP_003593	O75344	FKBP6_HUMAN	FK506 binding protein 6 isoform a	106	PPIase FKBP-type.				protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)												0.175	33.597441	41.570588	14	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72744205	72744205	6150	7	G	C	C	C	438	34	FKBP6	3	3
COL28A1	340267	broad.mit.edu	37	7	7413034	7413034	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:7413034C>A	uc003src.1	-	c.2503G>T	c.(2503-2505)GCC>TCC	p.A835S	COL28A1_uc011jxe.1_Missense_Mutation_p.A518S	NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN	collagen, type XXVIII precursor	835	VWFA 2.				cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity				0		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)										0.288889	119.663193	126.838621	52	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7413034	7413034	3824	7	C	A	A	A	338	26	COL28A1	2	2
HIP1	3092	broad.mit.edu	37	7	75203140	75203140	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:75203140G>A	uc003uds.1	-	c.671C>T	c.(670-672)CCG>CTG	p.P224L	HIP1_uc011kfz.1_Missense_Mutation_p.P101L	NM_005338	NP_005329	O00291	HIP1_HUMAN	huntingtin interacting protein 1	224					activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			pancreas(2)|ovary(1)|central_nervous_system(1)	4										1179				0.176471	35.48541	45.563707	18	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75203140	75203140	7399	7	G	A	A	A	507	39	HIP1	1	1
RHBDD2	57414	broad.mit.edu	37	7	75517556	75517556	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:75517556G>A	uc003udw.1	+	c.984G>A	c.(982-984)CTG>CTA	p.L328L	RHBDD2_uc003udv.1_Silent_p.L187L	NM_001040456	NP_001035546	Q6NTF9	RHBD2_HUMAN	rhomboid domain containing 2 isoform a	328						integral to membrane	serine-type endopeptidase activity				0														0.064615	-25.150429	38.941272	21	304	KEEP	---	---	---	---	capture		Silent	SNP	75517556	75517556	13792	7	G	A	A	A	600	47	RHBDD2	2	2
POMZP3	22932	broad.mit.edu	37	7	76254966	76254966	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:76254966G>T	uc003uft.2	-	c.100C>A	c.(100-102)CCA>ACA	p.P34T	POMZP3_uc003ufu.2_Missense_Mutation_p.P34T|POMZP3_uc003ufv.2_Non-coding_Transcript|POMZP3_uc011kgm.1_Non-coding_Transcript	NM_012230	NP_036362	Q6PJE2	POZP3_HUMAN	POMZP3 fusion protein isoform 1	34											0		Myeloproliferative disorder(862;0.204)												0.068884	-18.492021	62.472472	29	392	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76254966	76254966	12676	7	G	T	T	T	572	44	POMZP3	2	2
MAGI2	9863	broad.mit.edu	37	7	77756539	77756539	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:77756539G>T	uc003ugx.2	-	c.3398C>A	c.(3397-3399)CCT>CAT	p.P1133H	MAGI2_uc003ugy.2_Missense_Mutation_p.P1119H|MAGI2_uc010ldx.1_Missense_Mutation_p.P726H	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	1133						cell junction|synapse|synaptosome	phosphatase binding			ovary(5)	5		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)												0.171756	80.799326	107.499958	45	217	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77756539	77756539	9574	7	G	T	T	T	455	35	MAGI2	2	2
HGF	3082	broad.mit.edu	37	7	81335050	81335050	+	Missense_Mutation	SNP	A	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:81335050A>C	uc003uhl.2	-	c.1777T>G	c.(1777-1779)TTT>GTT	p.F593V	HGF_uc003uhm.2_Missense_Mutation_p.F588V	NM_000601	NP_000592	P14210	HGF_HUMAN	hepatocyte growth factor isoform 1	593	Peptidase S1.				epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4										800				0.086957	4.400905	16.312552	6	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81335050	81335050	7369	7	A	C	C	C	13	1	HGF	4	4
HGF	3082	broad.mit.edu	37	7	81355333	81355333	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:81355333C>A	uc003uhl.2	-	c.1041G>T	c.(1039-1041)AAG>AAT	p.K347N	HGF_uc003uhm.2_Missense_Mutation_p.K342N	NM_000601	NP_000592	P14210	HGF_HUMAN	hepatocyte growth factor isoform 1	347	Kringle 3.				epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4										800				0.186047	29.444007	37.394441	16	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81355333	81355333	7369	7	C	A	A	A	285	22	HGF	2	2
PCLO	27445	broad.mit.edu	37	7	82474642	82474642	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:82474642C>A	uc003uhx.2	-	c.13991G>T	c.(13990-13992)AGC>ATC	p.S4664I	PCLO_uc003uhv.2_Missense_Mutation_p.S4664I|PCLO_uc003uht.1_Missense_Mutation_p.S115I|PCLO_uc003uhu.1_Missense_Mutation_p.S94I	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	4552					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.12766	7.81597	14.169794	6	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82474642	82474642	12003	7	C	A	A	A	364	28	PCLO	2	2
PCLO	27445	broad.mit.edu	37	7	82476482	82476482	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:82476482C>A	uc003uhx.2	-	c.13736G>T	c.(13735-13737)AGT>ATT	p.S4579I	PCLO_uc003uhv.2_Missense_Mutation_p.S4579I|PCLO_uc003uht.1_Missense_Mutation_p.S30I|PCLO_uc003uhu.1_Missense_Mutation_p.V12L	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	4467	PDZ.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.25	16.147704	17.504974	6	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82476482	82476482	12003	7	C	A	A	A	260	20	PCLO	2	2
PCLO	27445	broad.mit.edu	37	7	82579983	82579983	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:82579983C>A	uc003uhx.2	-	c.9921G>T	c.(9919-9921)CTG>CTT	p.L3307L	PCLO_uc003uhv.2_Silent_p.L3307L|PCLO_uc010lec.2_Silent_p.L272L	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3238	Gln-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.233129	87.95518	98.594237	38	125	KEEP	---	---	---	---	capture		Silent	SNP	82579983	82579983	12003	7	C	A	A	A	262	21	PCLO	2	2
SEMA3A	10371	broad.mit.edu	37	7	83689790	83689790	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:83689790G>T	uc003uhz.2	-	c.538C>A	c.(538-540)CTT>ATT	p.L180I		NM_006080	NP_006071	Q14563	SEM3A_HUMAN	semaphorin 3A precursor	180	Sema.				axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4														0.133333	27.798163	47.371266	20	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83689790	83689790	14510	7	G	T	T	T	455	35	SEMA3A	2	2
GATAD1	57798	broad.mit.edu	37	7	92083958	92083958	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:92083958C>G	uc003ulx.1	+	c.578C>G	c.(577-579)TCT>TGT	p.S193C	GATAD1_uc011khq.1_Non-coding_Transcript	NM_021167	NP_066990	Q8WUU5	GATD1_HUMAN	GATA zinc finger domain containing 1	193					regulation of transcription, DNA-dependent		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(62;1.63e-10)|all_epithelial(64;8.33e-10)|Breast(17;0.00311)|all_lung(186;0.0498)|Lung NSC(181;0.0676)		STAD - Stomach adenocarcinoma(171;4.51e-05)|GBM - Glioblastoma multiforme(5;8.83e-05)|all cancers(6;0.000136)|Lung(22;0.123)|Epithelial(20;0.179)|LUSC - Lung squamous cell carcinoma(200;0.225)											0.127389	36.380404	57.648966	20	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92083958	92083958	6523	7	C	G	G	G	416	32	GATAD1	3	3
CALCR	799	broad.mit.edu	37	7	93067561	93067561	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:93067561G>T	uc003umv.1	-	c.926C>A	c.(925-927)ACT>AAT	p.T309N	CALCR_uc011kia.1_Missense_Mutation_p.T89N|CALCR_uc003ums.1_Non-coding_Transcript|CALCR_uc003umt.1_Non-coding_Transcript|CALCR_uc003umu.1_Missense_Mutation_p.T275N|CALCR_uc003umw.2_Missense_Mutation_p.T275N	NM_001742	NP_001733	P30988	CALCR_HUMAN	calcitonin receptor isoform 2 precursor	291	Helical; Name=4; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|elevation of cytosolic calcium ion concentration|positive regulation of adenylate cyclase activity|response to glucocorticoid stimulus	integral to plasma membrane	calcitonin binding|calcitonin binding|calcitonin receptor activity|calcitonin receptor activity|protein binding			ovary(3)|lung(1)|pancreas(1)	5	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Salmon Calcitonin(DB00017)									0.111111	7.778383	17.198723	7	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93067561	93067561	2695	7	G	T	T	T	468	36	CALCR	2	2
DLX6	1750	broad.mit.edu	37	7	96637038	96637038	+	Silent	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:96637038C>G	uc003uom.2	+	c.441C>G	c.(439-441)TCC>TCG	p.S147S	DLX6AS_uc003uol.2_Intron|DLX6AS_uc010lfo.1_Intron	NM_005222	NP_005213	P56179	DLX6_HUMAN	distal-less homeobox 6	57	Homeobox.				nervous system development|regulation of transcription, DNA-dependent|skeletal system development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(2)	2	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)													0.181818	8.785495	10.879331	4	18	KEEP	---	---	---	---	capture		Silent	SNP	96637038	96637038	4755	7	C	G	G	G	262	21	DLX6	3	3
TRRAP	8295	broad.mit.edu	37	7	98589832	98589833	+	Missense_Mutation	DNP	CG	AT	AT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:98589832_98589833CG>AT	uc003upp.2	+	c.9841_9842CG>AT	c.(9841-9843)CGG>ATG	p.R3281M	TRRAP_uc011kis.1_Missense_Mutation_p.R3252M|TRRAP_uc003upr.2_Missense_Mutation_p.R2969M	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	3281					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|stomach(2)|lung(1)|liver(1)	27	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)							1847				0.127072	54.913567	104.015003	46	316	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	98589832	98589833	17152	7	CG	AT	AT	AT	347	27	TRRAP	1	1
GAL3ST4	79690	broad.mit.edu	37	7	99764641	99764641	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:99764641C>T	uc003utt.2	-	c.78G>A	c.(76-78)ATG>ATA	p.M26I	GAL3ST4_uc003utu.2_Missense_Mutation_p.M26I|GAL3ST4_uc010lgq.2_Missense_Mutation_p.D66N	NM_024637	NP_078913	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4	26	Helical; Signal-anchor for type II membrane protein; (Potential).				cell-cell signaling|oligosaccharide metabolic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi cisterna membrane|integral to membrane|membrane fraction	3'-phosphoadenosine 5'-phosphosulfate binding|galactosylceramide sulfotransferase activity|proteoglycan sulfotransferase activity			ovary(3)	3	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)													0.333333	12.56843	12.938225	5	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99764641	99764641	6464	7	C	T	T	T	377	29	GAL3ST4	2	2
RGS22	26166	broad.mit.edu	37	8	101075759	101075759	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:101075759T>C	uc003yjb.1	-	c.1237A>G	c.(1237-1239)AAG>GAG	p.K413E	RGS22_uc003yja.1_Missense_Mutation_p.K232E|RGS22_uc003yjc.1_Missense_Mutation_p.K401E|RGS22_uc011lgz.1_Non-coding_Transcript|RGS22_uc010mbo.1_Non-coding_Transcript	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	413					negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|breast(1)|central_nervous_system(1)	5			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)							790				0.058824	-10.269025	31.314879	12	192	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101075759	101075759	13779	8	T	C	C	C	832	64	RGS22	4	4
UBR5	51366	broad.mit.edu	37	8	103301722	103301722	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:103301722C>A	uc003ykr.1	-	c.4672G>T	c.(4672-4674)GAT>TAT	p.D1558Y	UBR5_uc003yks.1_Missense_Mutation_p.D1558Y	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	1558					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(5)|ovary(3)|large_intestine(3)|kidney(1)|central_nervous_system(1)	13	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			Ovarian(131;96 1741 5634 7352 27489)				1024				0.604839	454.669332	457.047951	150	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103301722	103301722	17463	8	C	A	A	A	416	32	UBR5	2	2
UBR5	51366	broad.mit.edu	37	8	103317410	103317410	+	Silent	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:103317410T>C	uc003ykr.1	-	c.2730A>G	c.(2728-2730)ACA>ACG	p.T910T	UBR5_uc003yks.1_Silent_p.T910T	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	910					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(5)|ovary(3)|large_intestine(3)|kidney(1)|central_nervous_system(1)	13	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			Ovarian(131;96 1741 5634 7352 27489)				1024				0.51632	534.03642	534.114307	174	163	KEEP	---	---	---	---	capture		Silent	SNP	103317410	103317410	17463	8	T	C	C	C	652	51	UBR5	4	4
UBR5	51366	broad.mit.edu	37	8	103327008	103327008	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:103327008C>A	uc003ykr.1	-	c.1858G>T	c.(1858-1860)GCA>TCA	p.A620S	UBR5_uc003yks.1_Missense_Mutation_p.A620S	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	620					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(5)|ovary(3)|large_intestine(3)|kidney(1)|central_nervous_system(1)	13	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			Ovarian(131;96 1741 5634 7352 27489)				1024				0.641791	138.038017	139.222593	43	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103327008	103327008	17463	8	C	A	A	A	325	25	UBR5	2	2
CTHRC1	115908	broad.mit.edu	37	8	104390389	104390389	+	Silent	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:104390389T>A	uc003ylk.2	+	c.507T>A	c.(505-507)CCT>CCA	p.P169P		NM_138455	NP_612464	Q96CG8	CTHR1_HUMAN	collagen triple helix repeat containing 1	169						collagen				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)											0.073529	-12.214166	38.647263	20	252	KEEP	---	---	---	---	capture		Silent	SNP	104390389	104390389	4169	8	T	A	A	A	691	54	CTHRC1	3	3
RP1L1	94137	broad.mit.edu	37	8	10465408	10465408	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:10465408G>T	uc003wtc.2	-	c.6200C>A	c.(6199-6201)GCT>GAT	p.A2067D		NM_178857	NP_849188	A6NKC6	A6NKC6_HUMAN	retinitis pigmentosa 1-like 1	2067					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)										0.311321	253.492382	263.534022	99	219	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10465408	10465408	14012	8	G	T	T	T	442	34	RP1L1	2	2
RP1L1	94137	broad.mit.edu	37	8	10465814	10465814	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:10465814C>A	uc003wtc.2	-	c.5794G>T	c.(5794-5796)GAG>TAG	p.E1932*		NM_178857	NP_849188	A6NKC6	A6NKC6_HUMAN	retinitis pigmentosa 1-like 1	1932					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)										0.307443	249.502953	259.721541	95	214	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	10465814	10465814	14012	8	C	A	A	A	403	31	RP1L1	5	1
DPYS	1807	broad.mit.edu	37	8	105441800	105441800	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:105441800G>T	uc003yly.3	-	c.923C>A	c.(922-924)CCC>CAC	p.P308H		NM_001385	NP_001376	Q14117	DPYS_HUMAN	dihydropyrimidinase	308					protein homotetramerization|pyrimidine nucleoside catabolic process|thymine catabolic process|uracil catabolic process	cytosol	dihydropyrimidinase activity|zinc ion binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)											0.109091	9.514134	26.172038	12	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105441800	105441800	4930	8	G	T	T	T	559	43	DPYS	2	2
LRP12	29967	broad.mit.edu	37	8	105510277	105510277	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:105510277C>A	uc003yma.2	-	c.503G>T	c.(502-504)TGT>TTT	p.C168F	LRP12_uc003ymb.2_Missense_Mutation_p.C149F|LRP12_uc003ylz.2_5'Flank	NM_013437	NP_038465	Q9Y561	LRP12_HUMAN	low density lipoprotein-related protein 12	168	Extracellular (Potential).|LDL-receptor class A 1.				endocytosis|regulation of growth	coated pit|integral to plasma membrane	low-density lipoprotein receptor activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)											0.07619	-0.58964	18.738476	8	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105510277	105510277	9327	8	C	A	A	A	221	17	LRP12	2	2
XKR6	286046	broad.mit.edu	37	8	11058274	11058274	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:11058274C>A	uc003wtk.1	-	c.575G>T	c.(574-576)GGG>GTG	p.G192V		NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related	192						integral to membrane				ovary(1)	1				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)										0.195652	18.346645	22.321221	9	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11058274	11058274	18016	8	C	A	A	A	286	22	XKR6	2	2
CSMD3	114788	broad.mit.edu	37	8	113304930	113304930	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113304930C>A	uc003ynu.2	-	c.8624G>T	c.(8623-8625)TGT>TTT	p.C2875F	CSMD3_uc003yns.2_Missense_Mutation_p.C2077F|CSMD3_uc003ynt.2_Missense_Mutation_p.C2835F|CSMD3_uc011lhx.1_Missense_Mutation_p.C2706F	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2875	Extracellular (Potential).|Sushi 19.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.078125	-0.979291	10.669739	5	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113304930	113304930	4087	8	C	A	A	A	221	17	CSMD3	2	2
CSMD3	114788	broad.mit.edu	37	8	113317037	113317037	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113317037G>T	uc003ynu.2	-	c.8179C>A	c.(8179-8181)CCT>ACT	p.P2727T	CSMD3_uc003yns.2_Missense_Mutation_p.P1929T|CSMD3_uc003ynt.2_Missense_Mutation_p.P2687T|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2727	Extracellular (Potential).|Sushi 16.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52									p.P2727T(NCIH520-Tumor)	2888	TCGA Ovarian(7;0.080)			0.109375	5.274153	14.951126	7	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113317037	113317037	4087	8	G	T	T	T	559	43	CSMD3	2	2
CSMD3	114788	broad.mit.edu	37	8	113326690	113326690	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113326690T>C	uc003ynu.2	-	c.7517A>G	c.(7516-7518)GAA>GGA	p.E2506G	CSMD3_uc003yns.2_Missense_Mutation_p.E1708G|CSMD3_uc003ynt.2_Missense_Mutation_p.E2466G|CSMD3_uc011lhx.1_Missense_Mutation_p.E2402G|CSMD3_uc003ynw.1_Missense_Mutation_p.E217G	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2506	CUB 14.|Extracellular (Potential).					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.135135	20.500943	30.045489	10	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113326690	113326690	4087	8	T	C	C	C	806	62	CSMD3	4	4
CSMD3	114788	broad.mit.edu	37	8	113933969	113933969	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113933969G>T	uc003ynu.2	-	c.1520C>A	c.(1519-1521)ACT>AAT	p.T507N	CSMD3_uc003ynt.2_Missense_Mutation_p.T467N|CSMD3_uc011lhx.1_Missense_Mutation_p.T403N	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	507	Extracellular (Potential).|Sushi 2.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.078947	-0.121849	20.52921	9	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113933969	113933969	4087	8	G	T	T	T	468	36	CSMD3	2	2
COL14A1	7373	broad.mit.edu	37	8	121262964	121262964	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:121262964C>G	uc003yox.2	+	c.2711C>G	c.(2710-2712)GCC>GGC	p.A904G	COL14A1_uc003yoy.2_Missense_Mutation_p.A582G	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	904	Fibronectin type-III 7.				cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)							1131				0.082353	1.007533	16.297733	7	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121262964	121262964	3809	8	C	G	G	G	338	26	COL14A1	3	3
WDYHV1	55093	broad.mit.edu	37	8	124449469	124449469	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:124449469G>T	uc003yqn.1	+	c.403G>T	c.(403-405)GCA>TCA	p.A135S	WDYHV1_uc011lij.1_Missense_Mutation_p.A75S|WDYHV1_uc003yqo.1_Non-coding_Transcript	NM_018024	NP_060494	Q96HA8	NTAQ1_HUMAN	WDYHV motif containing 1	135					protein modification process	cytosol|nucleus	protein binding|protein N-terminal glutamine amidohydrolase activity			ovary(1)	1														0.090909	2.129585	11.411952	5	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124449469	124449469	17917	8	G	T	T	T	598	46	WDYHV1	2	2
FER1L6	654463	broad.mit.edu	37	8	125113558	125113558	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:125113558C>A	uc003yqw.2	+	c.5104C>A	c.(5104-5106)CTG>ATG	p.L1702M		NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	1702	C2 6.|Cytoplasmic (Potential).					integral to membrane				ovary(5)|central_nervous_system(1)|skin(1)	7	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)											0.128571	11.225854	20.63537	9	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125113558	125113558	6052	8	C	A	A	A	363	28	FER1L6	2	2
LRRC6	23639	broad.mit.edu	37	8	133644985	133644985	+	Splice_Site_SNP	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:133644985C>A	uc003ytk.2	-	c.653_splice	c.e5+1	p.L218_splice	LRRC6_uc003ytl.2_Splice_Site_SNP	NM_012472	NP_036604			leucine rich repeat containing 6							cytoplasm				ovary(1)|kidney(1)	2	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)											0.090047	10.452853	46.241211	19	192	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	133644985	133644985	9391	8	C	A	A	A	221	17	LRRC6	5	2
FAM135B	51059	broad.mit.edu	37	8	139163907	139163907	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139163907C>A	uc003yuy.2	-	c.2811G>T	c.(2809-2811)TTG>TTT	p.L937F	FAM135B_uc003yux.2_Missense_Mutation_p.L838F|FAM135B_uc003yuz.2_Non-coding_Transcript|FAM135B_uc003yva.2_Missense_Mutation_p.L499F|FAM135B_uc003yvb.2_Missense_Mutation_p.L499F	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	937										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)											0.134615	26.666017	46.868947	21	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139163907	139163907	5646	8	C	A	A	A	376	29	FAM135B	2	2
COL22A1	169044	broad.mit.edu	37	8	139768047	139768047	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139768047G>A	uc003yvd.2	-	c.1928C>T	c.(1927-1929)CCT>CTT	p.P643L	COL22A1_uc011ljo.1_5'UTR	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	643	Pro-rich.|Gly-rich.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(10)|pancreas(1)	11	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)											0.079365	1.248568	24.007994	10	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139768047	139768047	3819	8	G	A	A	A	455	35	COL22A1	2	2
PLEC	5339	broad.mit.edu	37	8	145012823	145012823	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145012823C>A	uc003zaf.1	-	c.561G>T	c.(559-561)AAG>AAT	p.K187N	PLEC_uc003zab.1_Missense_Mutation_p.K50N|PLEC_uc003zac.1_Missense_Mutation_p.K54N|PLEC_uc003zad.2_Missense_Mutation_p.K50N|PLEC_uc003zae.1_Missense_Mutation_p.K18N|PLEC_uc003zag.1_Missense_Mutation_p.K28N|PLEC_uc003zah.2_Missense_Mutation_p.K36N|PLEC_uc003zaj.2_Missense_Mutation_p.K77N	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	187	CH 1.|Globular 1.|Actin-binding.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|central_nervous_system(1)	7														0.135135	23.546524	37.870658	15	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145012823	145012823	12478	8	C	A	A	A	259	20	PLEC	2	2
SPATC1	375686	broad.mit.edu	37	8	145095278	145095278	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145095278C>A	uc011lkw.1	+	c.680C>A	c.(679-681)CCA>CAA	p.P227Q	SPATC1_uc011lkx.1_Missense_Mutation_p.P227Q	NM_198572	NP_940974	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	227										ovary(1)|central_nervous_system(1)	2	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)											0.169492	17.915364	24.014726	10	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145095278	145095278	15527	8	C	A	A	A	273	21	SPATC1	2	2
NAT2	10	broad.mit.edu	37	8	18257576	18257576	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:18257576G>C	uc003wyw.1	+	c.63G>C	c.(61-63)TTG>TTC	p.L21F		NM_000015	NP_000006	P11245	ARY2_HUMAN	N-acetyltransferase 2	21					xenobiotic metabolic process	cytosol	arylamine N-acetyltransferase activity			ovary(1)|skin(1)	2				Colorectal(111;0.0531)|COAD - Colon adenocarcinoma(73;0.21)										0.306818	153.573262	159.436281	54	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18257576	18257576	10573	8	G	C	C	C	607	47	NAT2	3	3
HR	55806	broad.mit.edu	37	8	21986489	21986489	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:21986489G>T	uc003xas.2	-	c.195C>A	c.(193-195)TTC>TTA	p.F65L	HR_uc003xat.2_Missense_Mutation_p.F65L|HR_uc010lts.2_Missense_Mutation_p.F65L	NM_005144	NP_005135	O43593	HAIR_HUMAN	hairless protein isoform a	65							DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|ovary(1)	2		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)										0.096386	1.761612	15.307464	8	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21986489	21986489	7639	8	G	T	T	T	529	41	HR	2	2
ADRA1A	148	broad.mit.edu	37	8	26721659	26721659	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:26721659G>T	uc003xfc.1	-	c.828C>A	c.(826-828)ATC>ATA	p.I276I	ADRA1A_uc010lul.1_Silent_p.I276I|ADRA1A_uc003xfd.1_Non-coding_Transcript|ADRA1A_uc003xfe.1_Silent_p.I276I|ADRA1A_uc010lum.1_Silent_p.I276I|ADRA1A_uc003xff.1_Non-coding_Transcript|ADRA1A_uc003xfg.1_Silent_p.I276I|ADRA1A_uc003xfh.1_Silent_p.I276I	NM_033303	NP_150646	P35348	ADA1A_HUMAN	alpha-1A-adrenergic receptor isoform 2	276	Helical; Name=6; (By similarity).				activation of phospholipase C activity|aging|apoptosis|calcium ion transport into cytosol|cell-cell signaling|intracellular protein kinase cascade|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of synaptic transmission, GABAergic|positive regulation of action potential|positive regulation of cardiac muscle contraction|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase C signaling cascade|positive regulation of vasoconstriction|response to drug|response to hormone stimulus|response to stress|smooth muscle contraction	integral to plasma membrane	alpha1-adrenergic receptor activity			ovary(1)|breast(1)|skin(1)	3		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amphetamine(DB00182)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Carvedilol(DB01136)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Maprotiline(DB00934)|Mephentermine(DB01365)|Metaraminol(DB00610)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Midodrine(DB00211)|Nefazodone(DB01149)|Nicergoline(DB00699)|Nilutamide(DB00665)|Norepinephrine(DB00368)|Norgestrel(DB00506)|Oxymetazoline(DB00935)|Perphenazine(DB00850)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Prazosin(DB00457)|Promazine(DB00420)|Promethazine(DB01069)|Propericiazine(DB01608)|Propiomazine(DB00777)|Pseudoephedrine(DB00852)|Risperidone(DB00734)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioridazine(DB00679)|Tolazoline(DB00797)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Ziprasidone(DB00246)									0.24	40.619118	45.243693	18	57	KEEP	---	---	---	---	capture		Silent	SNP	26721659	26721659	335	8	G	T	T	T	473	37	ADRA1A	1	1
KCNU1	157855	broad.mit.edu	37	8	36793116	36793116	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:36793116G>T	uc010lvw.2	+	c.3128G>T	c.(3127-3129)TGT>TTT	p.C1043F		NM_001031836	NP_001027006	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	1043	Cytoplasmic (Potential).					voltage-gated potassium channel complex	binding|catalytic activity|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)										0.097403	13.501591	38.504045	15	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36793116	36793116	8398	8	G	T	T	T	624	48	KCNU1	2	2
ANK1	286	broad.mit.edu	37	8	41543692	41543692	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:41543692G>T	uc003xom.2	-	c.4491C>A	c.(4489-4491)ATC>ATA	p.I1497I	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Silent_p.I772I|ANK1_uc003xoi.2_Silent_p.I1456I|ANK1_uc003xoj.2_Silent_p.I1456I|ANK1_uc003xok.2_Silent_p.I1456I|ANK1_uc003xol.2_Silent_p.I1456I	NM_001142446	NP_001135918	P16157	ANK1_HUMAN	ankyrin 1 isoform 9	1456	55 kDa regulatory domain.|Death.				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)											0.119718	13.360636	33.538625	17	125	KEEP	---	---	---	---	capture		Silent	SNP	41543692	41543692	623	8	G	T	T	T	525	41	ANK1	2	2
PLAT	5327	broad.mit.edu	37	8	42038086	42038087	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:42038086_42038087GG>TT	uc003xos.2	-	c.1006_1007CC>AA	c.(1006-1008)CCC>AAC	p.P336N	PLAT_uc010lxf.1_Missense_Mutation_p.P253N|PLAT_uc010lxg.1_Missense_Mutation_p.P161N|PLAT_uc003xot.2_Missense_Mutation_p.P290N|PLAT_uc011lcm.1_Missense_Mutation_p.P247N|PLAT_uc011lcn.1_Missense_Mutation_p.P210N	NM_000930	NP_000921	P00750	TPA_HUMAN	plasminogen activator, tissue isoform 1	336	Peptidase S1.				blood coagulation|fibrinolysis|negative regulation of proteolysis|protein modification process|proteolysis	cell surface|cytoplasm|extracellular space	protein binding|serine-type endopeptidase activity			breast(1)|skin(1)	2	all_cancers(6;3.84e-26)|all_epithelial(6;9.61e-28)|all_lung(13;7.2e-13)|Lung NSC(13;1.18e-11)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000378)|Lung NSC(58;0.00145)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00135)|Colorectal(10;0.00165)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)		Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Iloprost(DB01088)|Reteplase(DB00015)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)					176				0.080214	0.930238	34.412533	15	172	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	42038086	42038087	12447	8	GG	TT	TT	TT	559	43	PLAT	2	2
HGSNAT	138050	broad.mit.edu	37	8	43037331	43037331	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:43037331G>T	uc003xpx.3	+	c.1056G>T	c.(1054-1056)TTG>TTT	p.L352F		NM_152419	NP_689632	Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	380	Helical; (Potential).				lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)											0.252632	422.291599	459.237952	168	497	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43037331	43037331	7372	8	G	T	T	T	607	47	HGSNAT	2	2
PRKDC	5591	broad.mit.edu	37	8	48711843	48711843	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:48711843C>A	uc003xqi.2	-	c.10225G>T	c.(10225-10227)GTG>TTG	p.V3409L	PRKDC_uc003xqj.2_Missense_Mutation_p.V3409L|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	3409	FAT.				cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of gene-specific transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				Esophageal Squamous(79;1091 1253 12329 31680 40677)				1566				0.078788	-0.760269	29.155277	13	152	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48711843	48711843	12964	8	C	A	A	A	234	18	PRKDC	2	2
PXDNL	137902	broad.mit.edu	37	8	52321213	52321213	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:52321213G>T	uc003xqu.3	-	c.2971C>A	c.(2971-2973)CAC>AAC	p.H991N	PXDNL_uc003xqt.3_Non-coding_Transcript	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	991					hydrogen peroxide catabolic process|oxidation-reduction process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)												0.344828	27.440069	28.057258	10	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52321213	52321213	13306	8	G	T	T	T	611	47	PXDNL	2	2
ST18	9705	broad.mit.edu	37	8	53030987	53030987	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:53030987C>T	uc003xqz.2	-	c.2770G>A	c.(2770-2772)GAA>AAA	p.E924K	ST18_uc011ldq.1_Missense_Mutation_p.E571K|ST18_uc011ldr.1_Missense_Mutation_p.E889K|ST18_uc011lds.1_Missense_Mutation_p.E829K|ST18_uc003xra.2_Missense_Mutation_p.E924K	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	924	Potential.					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)												0.147059	14.198762	22.344997	10	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53030987	53030987	15730	8	C	T	T	T	377	29	ST18	2	2
TGS1	96764	broad.mit.edu	37	8	56723472	56723472	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:56723472G>T	uc003xsj.3	+	c.2176G>T	c.(2176-2178)GCC>TCC	p.A726S	TGS1_uc010lyh.2_Intron	NM_024831	NP_079107	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase homolog	726	Sufficient for catalytic activity.				cellular lipid metabolic process|ncRNA metabolic process|regulation of transcription, DNA-dependent|ribonucleoprotein complex import into nucleus|RNA capping|spliceosomal snRNP assembly|transcription, DNA-dependent	Cajal body|cytosol|small nuclear ribonucleoprotein complex	RNA trimethylguanosine synthase activity			ovary(1)|lung(1)|breast(1)	3		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			Esophageal Squamous(34;275 823 4842 34837 48447)				978				0.081633	1.552277	53.966469	24	270	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56723472	56723472	16365	8	G	T	T	T	598	46	TGS1	2	2
LYN	4067	broad.mit.edu	37	8	56866543	56866543	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:56866543G>A	uc003xsk.3	+	c.790G>A	c.(790-792)GGT>AGT	p.G264S	LYN_uc003xsl.3_Missense_Mutation_p.G243S	NM_002350	NP_002341	P07948	LYN_HUMAN	Yamaguchi sarcoma viral (v-yes-1) oncogene	264	Protein kinase.				erythrocyte differentiation|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of cellular component movement|positive regulation of stress-activated protein kinase signaling cascade|positive regulation of tyrosine phosphorylation of STAT protein|response to DNA damage stimulus|T cell costimulation	cytosol|Golgi apparatus|membrane raft|nucleus|perinuclear region of cytoplasm	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|receptor signaling protein tyrosine kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)							240				0.1125	20.15144	43.859847	18	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56866543	56866543	9484	8	G	A	A	A	559	43	LYN	2	2
CYP7A1	1581	broad.mit.edu	37	8	59404216	59404216	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:59404216G>T	uc003xtm.3	-	c.1333C>A	c.(1333-1335)CCT>ACT	p.P445T		NM_000780	NP_000771	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A,	445					bile acid biosynthetic process|cellular lipid metabolic process|cellular response to cholesterol|cellular response to glucose stimulus|cholesterol catabolic process|cholesterol homeostasis|oxidation-reduction process|regulation of bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	cholesterol 7-alpha-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)												0.109589	3.040613	14.07575	8	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59404216	59404216	4361	8	G	T	T	T	533	41	CYP7A1	2	2
CYP7B1	9420	broad.mit.edu	37	8	65537045	65537045	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:65537045C>A	uc003xvj.2	-	c.174G>T	c.(172-174)GTG>GTT	p.V58V		NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,	58					bile acid biosynthetic process|cell death|cholesterol metabolic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)												0.135294	33.540549	55.428192	23	147	KEEP	---	---	---	---	capture		Silent	SNP	65537045	65537045	4362	8	C	A	A	A	262	21	CYP7B1	2	2
SLCO5A1	81796	broad.mit.edu	37	8	70585465	70585465	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:70585465T>C	uc003xyl.2	-	c.2186A>G	c.(2185-2187)TAC>TGC	p.Y729C	SLCO5A1_uc010lzb.2_Missense_Mutation_p.Y674C|SLCO5A1_uc011lfa.1_Non-coding_Transcript|SLCO5A1_uc003xyk.2_3'UTR	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,	729	Extracellular (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)	3	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)											0.092664	21.019786	64.247699	24	235	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70585465	70585465	15228	8	T	C	C	C	741	57	SLCO5A1	4	4
EYA1	2138	broad.mit.edu	37	8	72184101	72184101	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:72184101G>T	uc003xys.3	-	c.858C>A	c.(856-858)CCC>CCA	p.P286P	EYA1_uc003xyr.3_Silent_p.P281P|EYA1_uc003xyt.3_Silent_p.P253P|EYA1_uc010lzf.2_Silent_p.P213P|EYA1_uc003xyu.2_Silent_p.P286P|EYA1_uc011lfe.1_Silent_p.P280P|EYA1_uc003xyv.2_Silent_p.P164P	NM_172058	NP_742055	Q99502	EYA1_HUMAN	eyes absent 1 isoform b	286					double-strand break repair|histone dephosphorylation|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|sensory perception of sound|transcription, DNA-dependent	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	5	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)											0.10951	35.578053	87.985515	38	309	KEEP	---	---	---	---	capture		Silent	SNP	72184101	72184101	5522	8	G	T	T	T	600	47	EYA1	2	2
TRPA1	8989	broad.mit.edu	37	8	72958754	72958754	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:72958754G>T	uc003xza.2	-	c.2055C>A	c.(2053-2055)GCC>GCA	p.A685A		NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	685	Cytoplasmic (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)									0.119048	8.182547	20.164908	10	74	KEEP	---	---	---	---	capture		Silent	SNP	72958754	72958754	17128	8	G	T	T	T	548	43	TRPA1	2	2
ZFHX4	79776	broad.mit.edu	37	8	77619978	77619978	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77619978C>G	uc003yav.2	+	c.2710C>G	c.(2710-2712)CTC>GTC	p.L904V	ZFHX4_uc003yat.1_Missense_Mutation_p.L904V|ZFHX4_uc003yau.1_Missense_Mutation_p.L930V|ZFHX4_uc003yaw.1_Missense_Mutation_p.L904V	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	904					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.121212	7.675266	12.315768	4	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77619978	77619978	18223	8	C	G	G	G	416	32	ZFHX4	3	3
ZFHX4	79776	broad.mit.edu	37	8	77763587	77763587	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77763587C>G	uc003yav.2	+	c.4295C>G	c.(4294-4296)TCC>TGC	p.S1432C	ZFHX4_uc003yau.1_Missense_Mutation_p.S1477C|ZFHX4_uc003yaw.1_Missense_Mutation_p.S1432C	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1432					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.125	9.745567	15.241429	5	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77763587	77763587	18223	8	C	G	G	G	390	30	ZFHX4	3	3
ZFHX4	79776	broad.mit.edu	37	8	77764096	77764096	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77764096C>A	uc003yav.2	+	c.4804C>A	c.(4804-4806)CAG>AAG	p.Q1602K	ZFHX4_uc003yau.1_Missense_Mutation_p.Q1647K|ZFHX4_uc003yaw.1_Missense_Mutation_p.Q1602K	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1602					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.121622	11.619413	22.001892	9	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77764096	77764096	18223	8	C	A	A	A	273	21	ZFHX4	2	2
RALYL	138046	broad.mit.edu	37	8	85799896	85799896	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:85799896C>A	uc003yct.3	+	c.782C>A	c.(781-783)TCA>TAA	p.S261*	RALYL_uc003ycq.3_Nonsense_Mutation_p.S248*|RALYL_uc003ycr.3_Nonsense_Mutation_p.S248*|RALYL_uc003ycs.3_Nonsense_Mutation_p.S248*|RALYL_uc010lzy.2_Nonsense_Mutation_p.S237*|RALYL_uc003ycu.3_Nonsense_Mutation_p.S175*|RALYL_uc003ycv.3_Intron	NM_001100391	NP_001093861	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like isoform 1	248	Potential.						identical protein binding|nucleotide binding|RNA binding			ovary(1)	1														0.119048	10.386795	22.361171	10	74	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	85799896	85799896	13480	8	C	A	A	A	377	29	RALYL	5	2
PSKH2	85481	broad.mit.edu	37	8	87076623	87076623	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:87076623G>T	uc011lfy.1	-	c.423C>A	c.(421-423)ACC>ACA	p.T141T		NM_033126	NP_149117	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	141	Protein kinase.				protein phosphorylation		ATP binding|protein serine/threonine kinase activity			lung(2)|ovary(1)	3			STAD - Stomach adenocarcinoma(118;0.129)							100				0.094118	3.731324	17.810959	8	77	KEEP	---	---	---	---	capture		Silent	SNP	87076623	87076623	13118	8	G	T	T	T	496	39	PSKH2	1	1
KIAA1429	25962	broad.mit.edu	37	8	95508630	95508630	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:95508630C>A	uc003ygo.1	-	c.4309G>T	c.(4309-4311)GAG>TAG	p.E1437*	KIAA1429_uc010maz.1_Non-coding_Transcript	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	1437					mRNA processing|RNA splicing	nucleus				ovary(1)	1	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)											0.158537	19.212055	28.341788	13	69	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	95508630	95508630	8540	8	C	A	A	A	416	32	KIAA1429	5	2
MATN2	4147	broad.mit.edu	37	8	99019735	99019735	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:99019735T>A	uc003yic.2	+	c.1479T>A	c.(1477-1479)CAT>CAA	p.H493Q	MATN2_uc010mbh.1_Missense_Mutation_p.H452Q|MATN2_uc003yid.2_Missense_Mutation_p.H493Q|MATN2_uc003yie.1_Missense_Mutation_p.H493Q|MATN2_uc010mbi.1_Missense_Mutation_p.H326Q|MATN2_uc010mbj.1_5'UTR	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor	493	EGF-like 7.					proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)											0.353448	123.148574	125.341633	41	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99019735	99019735	9718	8	T	A	A	A	660	51	MATN2	3	3
KIAA1529	57653	broad.mit.edu	37	9	100090327	100090327	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:100090327A>G	uc011lut.1	+	c.2236A>G	c.(2236-2238)ACA>GCA	p.T746A	KIAA1529_uc004axe.1_Missense_Mutation_p.T746A|KIAA1529_uc004axg.1_Missense_Mutation_p.T607A|KIAA1529_uc004axh.1_5'Flank|KIAA1529_uc011luw.1_5'Flank|KIAA1529_uc011lus.1_Missense_Mutation_p.T564A|KIAA1529_uc010msm.1_Intron|KIAA1529_uc004axf.2_Missense_Mutation_p.T607A|KIAA1529_uc011luv.1_Missense_Mutation_p.T604A	NM_020893	NP_065944			hypothetical protein LOC57653											ovary(4)|large_intestine(2)	6		Acute lymphoblastic leukemia(62;0.154)												0.12782	66.881053	102.775137	34	232	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100090327	100090327	8549	9	A	G	G	G	130	10	KIAA1529	4	4
ANKS6	203286	broad.mit.edu	37	9	101552507	101552507	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:101552507C>T	uc004ayu.2	-	c.741G>A	c.(739-741)AAG>AAA	p.K247K	ANKS6_uc004ayy.1_Non-coding_Transcript	NM_173551	NP_775822	Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain	247	ANK 6.									ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)												0.231707	46.378931	51.789514	19	63	KEEP	---	---	---	---	capture		Silent	SNP	101552507	101552507	700	9	C	T	T	T	311	24	ANKS6	2	2
ALG2	85365	broad.mit.edu	37	9	101980872	101980872	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:101980872G>A	uc004azf.2	-	c.595C>T	c.(595-597)CTC>TTC	p.L199F	ALG2_uc004azg.2_Missense_Mutation_p.L106F	NM_033087	NP_149078	Q9H553	ALG2_HUMAN	alpha-1,3-mannosyltransferase ALG2	199					dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in endoplasmic reticulum|protein N-linked glycosylation via asparagine|response to calcium ion	endoplasmic reticulum membrane|integral to membrane|membrane fraction|nucleus|perinuclear region of cytoplasm	alpha-1,3-mannosyltransferase activity|calcium-dependent protein binding|protein anchor|protein heterodimerization activity|protein N-terminus binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.0559)												0.086022	3.13775	19.281658	8	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101980872	101980872	522	9	G	A	A	A	455	35	ALG2	2	2
TEX10	54881	broad.mit.edu	37	9	103092305	103092305	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:103092305T>A	uc004bas.2	-	c.1397A>T	c.(1396-1398)GAG>GTG	p.E466V	TEX10_uc011lvf.1_Missense_Mutation_p.E305V|TEX10_uc011lvg.1_Missense_Mutation_p.E469V|TEX10_uc011lvh.1_Missense_Mutation_p.E401V	NM_017746	NP_060216	Q9NXF1	TEX10_HUMAN	testis expressed 10 isoform 1	466						integral to membrane|MLL1 complex|nuclear membrane|nucleolus	binding			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)										0.102041	10.512181	33.728506	15	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103092305	103092305	16299	9	T	A	A	A	702	54	TEX10	3	3
C9orf125	84302	broad.mit.edu	37	9	104238432	104238432	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:104238432C>A	uc004bbm.2	-	c.943G>T	c.(943-945)GAA>TAA	p.E315*		NM_032342	NP_115718	Q9BRR3	CI125_HUMAN	hypothetical protein LOC84302	315						integral to membrane					0		Acute lymphoblastic leukemia(62;0.0527)												0.081081	-5.124229	21.379581	12	136	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	104238432	104238432	2567	9	C	A	A	A	390	30	C9orf125	5	2
PPP3R2	5535	broad.mit.edu	37	9	104357038	104357038	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:104357038G>T	uc004bbr.2	-	c.175C>A	c.(175-177)CGG>AGG	p.R59R	GRIN3A_uc004bbp.1_Intron|GRIN3A_uc004bbq.1_Intron|PPP3R2_uc010mtf.1_Intron	NM_147180	NP_671709	Q96LZ3	CANB2_HUMAN	protein phosphatase 3 regulatory subunit B, beta	56	EF-hand 2.						calcium ion binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(62;0.0527)			Cyclosporine(DB00091)				p.R59W(RCHACV-Tumor)	16				0.149606	32.479304	47.402515	19	108	KEEP	---	---	---	---	capture		Silent	SNP	104357038	104357038	12837	9	G	T	T	T	493	38	PPP3R2	1	1
SMC2	10592	broad.mit.edu	37	9	106889740	106889740	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:106889740G>T	uc004bbv.2	+	c.2769G>T	c.(2767-2769)GAG>GAT	p.E923D	SMC2_uc004bbw.2_Missense_Mutation_p.E923D|SMC2_uc011lvl.1_Missense_Mutation_p.E923D|SMC2_uc004bbx.2_Missense_Mutation_p.E923D|SMC2_uc004bby.2_Non-coding_Transcript	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	923	Potential.				cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|lung(1)|breast(1)	8										1437				0.127451	15.689864	29.524363	13	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106889740	106889740	15281	9	G	T	T	T	451	35	SMC2	2	2
OR13C5	138799	broad.mit.edu	37	9	107360884	107360884	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107360884C>A	uc011lvp.1	-	c.811G>T	c.(811-813)GAT>TAT	p.D271Y		NM_001004482	NP_001004482	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C,	271	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)	3														0.079365	-0.877458	10.505824	5	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107360884	107360884	11343	9	C	A	A	A	416	32	OR13C5	2	2
OR13C2	392376	broad.mit.edu	37	9	107367473	107367473	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107367473C>T	uc011lvq.1	-	c.436G>A	c.(436-438)GCT>ACT	p.A146T		NM_001004481	NP_001004481	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C,	146	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.090909	2.794958	13.935041	6	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107367473	107367473	11340	9	C	T	T	T	364	28	OR13C2	2	2
ABCA1	19	broad.mit.edu	37	9	107591340	107591340	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107591340C>G	uc004bcl.2	-	c.1972G>C	c.(1972-1974)GGC>CGC	p.G658R		NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	658	Helical; (Potential).				Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol binding|cholesterol transporter activity|phospholipid binding|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|ovary(4)|central_nervous_system(1)|pancreas(1)	10				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)									0.107143	5.723066	18.673072	9	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107591340	107591340	29	9	C	G	G	G	286	22	ABCA1	3	3
ZNF462	58499	broad.mit.edu	37	9	109692040	109692040	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:109692040G>A	uc004bcz.2	+	c.5847G>A	c.(5845-5847)AGG>AGA	p.R1949R	ZNF462_uc010mto.2_Silent_p.R1797R|ZNF462_uc004bda.2_Silent_p.R1797R|ZNF462_uc011lvz.1_5'Flank	NM_021224	NP_067047	Q96JM2	ZN462_HUMAN	zinc finger protein 462	1949					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5														0.081081	1.406176	21.235861	9	102	KEEP	---	---	---	---	capture		Silent	SNP	109692040	109692040	18519	9	G	A	A	A	555	43	ZNF462	2	2
SVEP1	79987	broad.mit.edu	37	9	113148238	113148239	+	Missense_Mutation	DNP	GG	TT	TT	rs10817003	byFrequency;by1000genomes	TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:113148238_113148239GG>TT	uc010mtz.2	-	c.10176_10177CC>AA	c.(10174-10179)GGCCAC>GGAAAC	p.H3393N	SVEP1_uc010mty.2_Missense_Mutation_p.H1319N	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	3393	Sushi 33.				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7														0.140625	12.830309	20.811162	9	55	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	113148238	113148239	15940	9	GG	TT	TT	TT	611	47	SVEP1	2	2
SVEP1	79987	broad.mit.edu	37	9	113208289	113208289	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:113208289C>A	uc010mtz.2	-	c.4291G>T	c.(4291-4293)GAA>TAA	p.E1431*	SVEP1_uc010mua.1_Nonsense_Mutation_p.E1431*	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	1431	Pentaxin.				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7														0.222222	14.034326	15.951826	6	21	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	113208289	113208289	15940	9	C	A	A	A	377	29	SVEP1	5	2
SVEP1	79987	broad.mit.edu	37	9	113234499	113234499	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:113234499G>T	uc010mtz.2	-	c.2704C>A	c.(2704-2706)CGG>AGG	p.R902R	SVEP1_uc010mua.1_Silent_p.R902R	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	902					cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7														0.112195	30.170525	60.623806	23	182	KEEP	---	---	---	---	capture		Silent	SNP	113234499	113234499	15940	9	G	T	T	T	519	40	SVEP1	1	1
MUSK	4593	broad.mit.edu	37	9	113562997	113562997	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:113562997C>T	uc004bey.2	+	c.2339C>T	c.(2338-2340)ACT>ATT	p.T780I	MUSK_uc004bez.1_Missense_Mutation_p.T360I	NM_005592	NP_005583	O15146	MUSK_HUMAN	skeletal muscle receptor tyrosine kinase	780	Protein kinase.|Cytoplasmic (Potential).				protein phosphorylation	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			ovary(2)|lung(2)|central_nervous_system(1)	5										297				0.08547	0.952971	21.348637	10	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113562997	113562997	10383	9	C	T	T	T	260	20	MUSK	2	2
C9orf43	257169	broad.mit.edu	37	9	116191477	116191477	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:116191477C>A	uc004bho.3	+	c.1197C>A	c.(1195-1197)CCC>CCA	p.P399P	C9orf43_uc004bhp.2_Silent_p.P399P	NM_152786	NP_689999	Q8TAL5	CI043_HUMAN	hypothetical protein LOC257169	399											0														0.099057	14.269137	48.300259	21	191	KEEP	---	---	---	---	capture		Silent	SNP	116191477	116191477	2598	9	C	A	A	A	262	21	C9orf43	2	2
RGS3	5998	broad.mit.edu	37	9	116299126	116299126	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:116299126G>T	uc004bhq.2	+	c.1965G>T	c.(1963-1965)AAG>AAT	p.K655N	RGS3_uc004bhr.2_Missense_Mutation_p.K543N|RGS3_uc004bhs.2_Missense_Mutation_p.K545N|RGS3_uc004bht.2_Missense_Mutation_p.K374N|RGS3_uc010muy.2_Missense_Mutation_p.K374N|RGS3_uc004bhu.2_Missense_Mutation_p.K281N|RGS3_uc004bhv.2_5'UTR	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6	655					inactivation of MAPK activity|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3														0.098039	5.330597	38.358058	20	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	116299126	116299126	13780	9	G	T	T	T	425	33	RGS3	2	2
COL27A1	85301	broad.mit.edu	37	9	116931016	116931016	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:116931016C>G	uc011lxl.1	+	c.1181C>G	c.(1180-1182)TCT>TGT	p.S394C	COL27A1_uc004bii.2_Non-coding_Transcript|COL27A1_uc010mvd.1_Missense_Mutation_p.S244C	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor	394	Pro-rich.				cell adhesion		extracellular matrix structural constituent			ovary(3)	3														0.132716	85.088387	127.536848	43	281	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	116931016	116931016	3823	9	C	G	G	G	416	32	COL27A1	3	3
TRIM32	22954	broad.mit.edu	37	9	119460463	119460463	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:119460463G>T	uc004bjx.2	+	c.442G>T	c.(442-444)GAC>TAC	p.D148Y	ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjs.1_Intron|ASTN2_uc004bjt.1_Intron|TRIM32_uc004bjw.2_Missense_Mutation_p.D148Y	NM_001099679	NP_001093149	Q13049	TRI32_HUMAN	tripartite motif-containing 32	148	Potential.				fat cell differentiation|innate immune response|negative regulation of apoptosis|negative regulation of fibroblast proliferation|positive regulation of cell cycle|positive regulation of cell growth|positive regulation of cell migration|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein catabolic process|positive regulation of proteolysis|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to tumor necrosis factor|response to UV	nucleus	myosin binding|protein self-association|RNA binding|Tat protein binding|transcription coactivator activity|translation initiation factor binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(2)|kidney(1)	3						Esophageal Squamous(92;212 1916 19711 26951)								0.144828	27.970775	45.584407	21	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119460463	119460463	17050	9	G	T	T	T	533	41	TRIM32	2	2
TLR4	7099	broad.mit.edu	37	9	120474737	120474737	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:120474737G>T	uc004bjz.2	+	c.331G>T	c.(331-333)GGA>TGA	p.G111*	TLR4_uc004bka.2_Nonsense_Mutation_p.G71*|TLR4_uc004bkb.2_De_novo_Start_OutOfFrame	NM_138554	NP_612564	O00206	TLR4_HUMAN	toll-like receptor 4 precursor	111	LRR 3.|Extracellular (Potential).				activation of MAPK activity|cellular response to mechanical stimulus|defense response to Gram-negative bacterium|detection of fungus|detection of lipopolysaccharide|I-kappaB phosphorylation|innate immune response|intestinal epithelial structure maintenance|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-23 production|negative regulation of interleukin-6 production|negative regulation of osteoclast differentiation|negative regulation of tumor necrosis factor production|positive regulation of chemokine production|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of inflammatory response|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interferon-gamma production|positive regulation of interleukin-1 production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 biosynthetic process|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of platelet activation|positive regulation of tumor necrosis factor biosynthetic process|positive regulation of tumor necrosis factor production|T-helper 1 type immune response|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	external side of plasma membrane|integral to plasma membrane|lipopolysaccharide receptor complex|perinuclear region of cytoplasm	lipopolysaccharide receptor activity|transmembrane receptor activity			ovary(4)	4										157				0.089744	2.361244	15.616503	7	71	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	120474737	120474737	16483	9	G	T	T	T	455	35	TLR4	5	2
TLR4	7099	broad.mit.edu	37	9	120476443	120476443	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:120476443C>A	uc004bjz.2	+	c.2037C>A	c.(2035-2037)ATC>ATA	p.I679I	TLR4_uc004bka.2_Silent_p.I639I|TLR4_uc004bkb.2_Silent_p.I479I	NM_138554	NP_612564	O00206	TLR4_HUMAN	toll-like receptor 4 precursor	679	Cytoplasmic (Potential).|TIR.				activation of MAPK activity|cellular response to mechanical stimulus|defense response to Gram-negative bacterium|detection of fungus|detection of lipopolysaccharide|I-kappaB phosphorylation|innate immune response|intestinal epithelial structure maintenance|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of ERK1 and ERK2 cascade|negative regulation of interferon-gamma production|negative regulation of interleukin-17 production|negative regulation of interleukin-23 production|negative regulation of interleukin-6 production|negative regulation of osteoclast differentiation|negative regulation of tumor necrosis factor production|positive regulation of chemokine production|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of inflammatory response|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interferon-gamma production|positive regulation of interleukin-1 production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 biosynthetic process|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of platelet activation|positive regulation of tumor necrosis factor biosynthetic process|positive regulation of tumor necrosis factor production|T-helper 1 type immune response|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	external side of plasma membrane|integral to plasma membrane|lipopolysaccharide receptor complex|perinuclear region of cytoplasm	lipopolysaccharide receptor activity|transmembrane receptor activity			ovary(4)	4										157				0.109756	5.909029	18.282154	9	73	KEEP	---	---	---	---	capture		Silent	SNP	120476443	120476443	16483	9	C	A	A	A	408	32	TLR4	2	2
OR1J2	26740	broad.mit.edu	37	9	125273139	125273139	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125273139G>T	uc004bmj.1	+	c.59G>T	c.(58-60)CGG>CTG	p.R20L	OR1J2_uc011lyv.1_Missense_Mutation_p.R20L	NM_054107	NP_473448	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J,	20	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)|breast(1)|skin(1)	3														0.099099	16.489714	52.180652	22	200	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125273139	125273139	11366	9	G	T	T	T	507	39	OR1J2	1	1
OR1Q1	158131	broad.mit.edu	37	9	125377563	125377563	+	Missense_Mutation	SNP	G	T	T	rs116701890	by1000genomes	TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125377563G>T	uc011lyy.1	+	c.547G>T	c.(547-549)GCT>TCT	p.A183S		NM_012364	NP_036496	Q15612	OR1Q1_HUMAN	olfactory receptor, family 1, subfamily Q,	183	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.063694	-8.476889	22.620004	10	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125377563	125377563	11377	9	G	T	T	T	494	38	OR1Q1	1	1
RC3H2	54542	broad.mit.edu	37	9	125617621	125617621	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125617621C>A	uc010mwc.1	-	c.2657G>T	c.(2656-2658)AGG>ATG	p.R886M	RC3H2_uc004bnc.2_Non-coding_Transcript|RC3H2_uc004bnd.1_Missense_Mutation_p.R886M|RC3H2_uc004bne.3_Missense_Mutation_p.R886M	NM_001100588	NP_001094058	Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type zinc finger domains 2	886						cell surface|endomembrane system|membrane|membrane fraction|perinuclear region of cytoplasm	DNA binding|zinc ion binding			ovary(1)	1														0.099174	8.701682	28.144039	12	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125617621	125617621	13636	9	C	A	A	A	312	24	RC3H2	2	2
DENND1A	57706	broad.mit.edu	37	9	126146038	126146038	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:126146038G>C	uc011lzm.1	-	c.1765C>G	c.(1765-1767)CTG>GTG	p.L589V	DENND1A_uc011lzl.1_Missense_Mutation_p.L396V|DENND1A_uc004bny.1_Missense_Mutation_p.L360V|DENND1A_uc004bnz.1_Missense_Mutation_p.L578V|DENND1A_uc010mwh.1_5'UTR	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1	578						cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2														0.076923	-0.021961	21.42014	9	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126146038	126146038	4605	9	G	C	C	C	451	35	DENND1A	3	3
GOLGA1	2800	broad.mit.edu	37	9	127660853	127660853	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:127660853T>A	uc004bpc.2	-	c.1382A>T	c.(1381-1383)CAC>CTC	p.H461L	GOLGA1_uc010mws.2_Non-coding_Transcript	NM_002077	NP_002068	Q92805	GOGA1_HUMAN	golgin 97	461	Potential.|Gln-rich.					Golgi cisterna membrane				ovary(1)	1														0.115854	23.116116	46.935432	19	145	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	127660853	127660853	6820	9	T	A	A	A	767	59	GOLGA1	3	3
GAPVD1	26130	broad.mit.edu	37	9	128061359	128061359	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:128061359C>A	uc004bpp.2	+	c.159C>A	c.(157-159)ATC>ATA	p.I53I	GAPVD1_uc004bpo.2_Silent_p.I53I|GAPVD1_uc011lzs.1_Silent_p.I53I|GAPVD1_uc004bpq.2_Silent_p.I53I|GAPVD1_uc010mwx.2_Silent_p.I53I|GAPVD1_uc004bpr.2_Silent_p.I53I|GAPVD1_uc004bps.2_Silent_p.I53I|GAPVD1_uc010mwy.1_5'Flank	NM_015635	NP_056450	Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	53					endocytosis|regulation of protein transport|regulation of small GTPase mediated signal transduction|signal transduction	cytosol|endosome|membrane	GTPase activating protein binding|GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4														0.097087	4.864879	21.627032	10	93	KEEP	---	---	---	---	capture		Silent	SNP	128061359	128061359	6503	9	C	A	A	A	369	29	GAPVD1	2	2
CIZ1	25792	broad.mit.edu	37	9	130941553	130941553	+	Silent	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:130941553G>A	uc011mas.1	-	c.1023C>T	c.(1021-1023)TTC>TTT	p.F341F	CIZ1_uc004btr.2_Silent_p.F311F|CIZ1_uc004bts.2_Silent_p.F282F|CIZ1_uc011maq.1_Silent_p.F306F|CIZ1_uc004btu.2_Silent_p.F287F|CIZ1_uc004btt.2_Silent_p.F311F|CIZ1_uc011mar.1_Silent_p.F210F|CIZ1_uc004btw.2_Silent_p.F311F|CIZ1_uc004btv.2_Silent_p.F311F|CIZ1_uc004btx.2_Silent_p.F287F	NM_012127	NP_036259	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1 isoform	311	Gln-rich.					nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4														0.133333	23.649942	41.27537	18	117	KEEP	---	---	---	---	capture		Silent	SNP	130941553	130941553	3577	9	G	A	A	A	529	41	CIZ1	2	2
NUP188	23511	broad.mit.edu	37	9	131744890	131744890	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:131744890G>T	uc004bws.1	+	c.1579G>T	c.(1579-1581)GCA>TCA	p.A527S	NUP188_uc004bwu.2_5'Flank	NM_015354	NP_056169	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	527					carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|kidney(1)|breast(1)	6														0.111888	14.575179	35.920586	16	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131744890	131744890	11163	9	G	T	T	T	546	42	NUP188	2	2
ASB6	140459	broad.mit.edu	37	9	132400147	132400147	+	Silent	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:132400147G>C	uc004byf.1	-	c.1188C>G	c.(1186-1188)GTC>GTG	p.V396V	ASB6_uc004bye.1_Silent_p.V321V|ASB6_uc004byg.1_3'UTR|ASB6_uc011mbt.1_Silent_p.V317V|ASB6_uc010myx.1_Silent_p.V367V	NM_017873	NP_060343	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box-containing 6 isoform	396	SOCS box.				intracellular signal transduction	cytoplasm					0		Ovarian(14;0.00556)												0.119565	15.270189	28.332344	11	81	KEEP	---	---	---	---	capture		Silent	SNP	132400147	132400147	1045	9	G	C	C	C	574	45	ASB6	3	3
ASS1	445	broad.mit.edu	37	9	133342122	133342122	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:133342122C>G	uc010mza.2	+	c.659C>G	c.(658-660)CCC>CGC	p.P220R	ASS1_uc004bzm.2_Missense_Mutation_p.P144R|ASS1_uc004bzn.2_Missense_Mutation_p.P144R|ASS1_uc004bzo.2_Missense_Mutation_p.P125R|ASS1_uc010mzb.2_Missense_Mutation_p.P182R|ASS1_uc004bzp.2_Missense_Mutation_p.P144R|ASS1_uc010mzc.2_Missense_Mutation_p.P144R	NM_054012	NP_446464	P00966	ASSY_HUMAN	argininosuccinate synthetase 1	144					arginine biosynthetic process|urea cycle	cytosol	argininosuccinate synthase activity|ATP binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)									0.09375	3.363282	13.925598	6	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133342122	133342122	1080	9	C	G	G	G	286	22	ASS1	3	3
LAMC3	10319	broad.mit.edu	37	9	133928036	133928036	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:133928036G>T	uc004caa.1	+	c.1789G>T	c.(1789-1791)GCC>TCC	p.A597S		NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	597	Laminin IV type A.				cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)								OREG0019556	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.269231	18.71255	19.962581	7	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133928036	133928036	8939	9	G	T	T	T	598	46	LAMC3	2	2
BAT2L1	84726	broad.mit.edu	37	9	134353267	134353267	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:134353267G>T	uc004can.3	+	c.4543G>T	c.(4543-4545)GCC>TCC	p.A1515S	BAT2L1_uc004cao.3_Missense_Mutation_p.A873S	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like	1515							protein binding				0														0.201835	45.081794	54.093026	22	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134353267	134353267	1341	9	G	T	T	T	546	42	BAT2L1	2	2
POMT1	10585	broad.mit.edu	37	9	134394319	134394319	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:134394319C>T	uc004cav.2	+	c.1527C>T	c.(1525-1527)AAC>AAT	p.N509N	POMT1_uc004cax.2_Silent_p.N487N|POMT1_uc011mcj.1_Silent_p.N265N|POMT1_uc004cau.2_Silent_p.N487N|POMT1_uc004caw.2_Silent_p.N433N|POMT1_uc011mck.1_Silent_p.N370N|POMT1_uc011mcl.1_Silent_p.N335N|POMT1_uc011mcm.1_Silent_p.N457N|POMT1_uc011mcn.1_3'UTR	NM_007171	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1 isoform a	509	MIR 3.				multicellular organismal development|protein O-linked glycosylation	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity|metal ion binding				0		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)										0.135135	19.485224	33.780238	15	96	KEEP	---	---	---	---	capture		Silent	SNP	134394319	134394319	12674	9	C	T	T	T	246	19	POMT1	1	1
C9orf96	169436	broad.mit.edu	37	9	136260790	136260790	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:136260790C>A	uc004cdk.2	+	c.766C>A	c.(766-768)CTG>ATG	p.L256M	C9orf96_uc004cdl.2_Non-coding_Transcript	NM_153710	NP_714921	Q8NE28	SGK71_HUMAN	hypothetical protein LOC169436	256	Protein kinase.				protein phosphorylation		ATP binding|protein kinase activity			central_nervous_system(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)						527				0.139535	15.134504	25.943138	12	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136260790	136260790	2624	9	C	A	A	A	311	24	C9orf96	2	2
COL5A1	1289	broad.mit.edu	37	9	137664635	137664635	+	Splice_Site_SNP	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:137664635G>A	uc004cfe.2	+	c.2287_splice	c.e26-1	p.G763_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)										0.065789	-6.880403	22.865195	10	142	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	137664635	137664635	3834	9	G	A	A	A	455	35	COL5A1	5	2
COL5A1	1289	broad.mit.edu	37	9	137708881	137708882	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:137708881_137708882GG>TT	uc004cfe.2	+	c.4132_4133GG>TT	c.(4132-4134)GGC>TTC	p.G1378F		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	1378	Triple-helical region.				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)										0.134752	31.662408	49.868673	19	122	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	137708881	137708882	3834	9	GG	TT	TT	TT	507	39	COL5A1	1	1
FCN1	2219	broad.mit.edu	37	9	137801875	137801875	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:137801875G>T	uc004cfi.2	-	c.750C>A	c.(748-750)GGC>GGA	p.G250G		NM_002003	NP_001994	O00602	FCN1_HUMAN	ficolin 1 precursor	250	Fibrinogen C-terminal.				opsonization|signal transduction	collagen|extracellular space	antigen binding|calcium ion binding|receptor binding|sugar binding			large_intestine(1)|ovary(1)	2		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)										0.108696	34.940986	90.718158	40	328	KEEP	---	---	---	---	capture		Silent	SNP	137801875	137801875	6028	9	G	T	T	T	535	42	FCN1	2	2
FCN1	2219	broad.mit.edu	37	9	137809691	137809691	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:137809691G>T	uc004cfi.2	-	c.27C>A	c.(25-27)GCC>GCA	p.A9A		NM_002003	NP_001994	O00602	FCN1_HUMAN	ficolin 1 precursor	9					opsonization|signal transduction	collagen|extracellular space	antigen binding|calcium ion binding|receptor binding|sugar binding			large_intestine(1)|ovary(1)	2		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)										0.142857	20.485338	32.537225	14	84	KEEP	---	---	---	---	capture		Silent	SNP	137809691	137809691	6028	9	G	T	T	T	548	43	FCN1	2	2
PTGDS	5730	broad.mit.edu	37	9	139873716	139873716	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:139873716C>A	uc004cke.2	+	c.296C>A	c.(295-297)GCG>GAG	p.A99E	PTGDS_uc004ckd.2_Non-coding_Transcript|PTGDS_uc004ckf.2_Non-coding_Transcript	NM_000954	NP_000945	P41222	PTGDS_HUMAN	prostaglandin D2 synthase, brain	99					prostaglandin biosynthetic process|regulation of circadian sleep/wake cycle, sleep	Golgi apparatus|nuclear membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum	fatty acid binding|prostaglandin-D synthase activity|retinoid binding|transporter activity			ovary(1)	1	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)										0.097222	8.60594	31.954797	14	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139873716	139873716	13196	9	C	A	A	A	351	27	PTGDS	1	1
ABCA2	20	broad.mit.edu	37	9	139906938	139906938	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:139906938T>A	uc004ckm.1	-	c.5276A>T	c.(5275-5277)CAG>CTG	p.Q1759L	ABCA2_uc011mel.1_Missense_Mutation_p.Q1729L|ABCA2_uc011mem.1_Missense_Mutation_p.Q1728L|ABCA2_uc004ckl.1_Missense_Mutation_p.Q1659L|ABCA2_uc004ckn.1_Non-coding_Transcript	NM_212533	NP_997698	Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A, member 2	1728					cholesterol homeostasis|lipid metabolic process|regulation of intracellular cholesterol transport|regulation of transcription from RNA polymerase II promoter|response to drug|response to steroid hormone stimulus	ATP-binding cassette (ABC) transporter complex|cytoplasmic membrane-bounded vesicle|endosome|integral to membrane|lysosomal membrane|microtubule organizing center	ATP binding|ATPase activity, coupled to transmembrane movement of substances				0	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)										0.102564	4.255818	16.527593	8	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139906938	139906938	33	9	T	A	A	A	715	55	ABCA2	3	3
CACNA1B	774	broad.mit.edu	37	9	140811693	140811693	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:140811693A>T	uc004cog.2	+	c.776A>T	c.(775-777)GAT>GTT	p.D259V		NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	259	I.|Extracellular (Potential).				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)									0.11	9.953142	25.0066	11	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140811693	140811693	2655	9	A	T	T	T	156	12	CACNA1B	3	3
FREM1	158326	broad.mit.edu	37	9	14851592	14851592	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:14851592C>A	uc003zlm.2	-	c.842G>T	c.(841-843)TGG>TTG	p.W281L	FREM1_uc010mic.2_Non-coding_Transcript	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	281	CSPG 1.				cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)										0.341615	149.261532	152.837367	55	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14851592	14851592	6291	9	C	A	A	A	273	21	FREM1	2	2
FREM1	158326	broad.mit.edu	37	9	14868959	14868959	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:14868959C>T	uc003zlm.2	-	c.17G>A	c.(16-18)TGG>TAG	p.W6*	FREM1_uc010mic.2_Non-coding_Transcript	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	6					cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)										0.266667	9.892422	10.630669	4	11	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	14868959	14868959	6291	9	C	T	T	T	273	21	FREM1	5	2
HAUS6	54801	broad.mit.edu	37	9	19058167	19058167	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:19058167C>G	uc003znk.2	-	c.2598G>C	c.(2596-2598)TTG>TTC	p.L866F	HAUS6_uc011lmz.1_Missense_Mutation_p.L586F|HAUS6_uc003znl.1_Missense_Mutation_p.L730F	NM_017645	NP_060115	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	866					cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleus|spindle				ovary(2)	2														0.297619	254.738319	263.958191	75	177	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19058167	19058167	7252	9	C	G	G	G	376	29	HAUS6	3	3
SLC24A2	25769	broad.mit.edu	37	9	19516285	19516285	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:19516285T>A	uc003zoa.1	-	c.1852A>T	c.(1852-1854)ATC>TTC	p.I618F	SLC24A2_uc003zob.1_Missense_Mutation_p.I601F	NM_020344	NP_065077	Q9UI40	NCKX2_HUMAN	solute carrier family 24	618	Helical; (Potential).				visual perception	integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(3)	3				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)										0.19375	73.139688	87.136774	31	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19516285	19516285	14963	9	T	A	A	A	663	51	SLC24A2	3	3
TEK	7010	broad.mit.edu	37	9	27185502	27185502	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:27185502C>A	uc003zqi.3	+	c.1202C>A	c.(1201-1203)ACG>AAG	p.T401K	TEK_uc011lno.1_Missense_Mutation_p.T358K|TEK_uc011lnp.1_Missense_Mutation_p.T254K|TEK_uc003zqj.1_Missense_Mutation_p.T335K	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor	401	Extracellular (Potential).|Ig-like C2-type 2.				angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)						493				0.348387	165.052968	168.220052	54	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27185502	27185502	16278	9	C	A	A	A	247	19	TEK	1	1
PIGO	84720	broad.mit.edu	37	9	35092199	35092199	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:35092199G>C	uc003zwd.2	-	c.1685C>G	c.(1684-1686)TCT>TGT	p.S562C	PIGO_uc003zwc.1_3'UTR|PIGO_uc003zwe.2_Intron|PIGO_uc003zwf.2_Intron|PIGO_uc003zwg.1_Missense_Mutation_p.S125C	NM_032634	NP_116023	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	562					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	transferase activity			large_intestine(1)|ovary(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)											0.068966	-1.399418	20.877516	8	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35092199	35092199	12318	9	G	C	C	C	429	33	PIGO	3	3
GBA2	57704	broad.mit.edu	37	9	35738836	35738836	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:35738836C>T	uc011lpd.1	-	c.1878G>A	c.(1876-1878)CTG>CTA	p.L626L	GBA2_uc003zxx.1_5'Flank|GBA2_uc011lpb.1_Silent_p.L620L|GBA2_uc003zxw.2_Silent_p.L620L|GBA2_uc011lpc.1_Silent_p.L620L|GBA2_uc003zxy.1_Silent_p.L333L	NM_020944	NP_065995	Q9HCG7	GBA2_HUMAN	bile acid beta-glucosidase	620	Extracellular (Potential).				bile acid metabolic process|glucosylceramide catabolic process|O-glycoside catabolic process	integral to membrane|microsome|plasma membrane|smooth endoplasmic reticulum	beta-glucosidase activity|glucosylceramidase activity			ovary(2)	2	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)											0.071429	-4.948399	13.600117	7	91	KEEP	---	---	---	---	capture		Silent	SNP	35738836	35738836	6533	9	C	T	T	T	366	29	GBA2	2	2
GDA	9615	broad.mit.edu	37	9	74764488	74764488	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:74764488C>A	uc004air.2	+	c.13C>A	c.(13-15)CAG>AAG	p.Q5K	GDA_uc011lse.1_Intron|GDA_uc004aiq.2_Missense_Mutation_p.Q5K|GDA_uc011lsf.1_5'UTR|GDA_uc010mow.1_Non-coding_Transcript|GDA_uc004ais.2_5'UTR	NM_004293	NP_004284	Q9Y2T3	GUAD_HUMAN	guanine deaminase	5					nervous system development|purine base metabolic process|purine nucleotide catabolic process	cytosol	guanine deaminase activity|zinc ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)										0.12	5.515803	12.600193	6	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74764488	74764488	6573	9	C	A	A	A	377	29	GDA	2	2
PTPRD	5789	broad.mit.edu	37	9	8376609	8376609	+	Nonsense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:8376609T>A	uc003zkk.2	-	c.4504A>T	c.(4504-4506)AAG>TAG	p.K1502*	PTPRD_uc003zkp.2_Nonsense_Mutation_p.K1096*|PTPRD_uc003zkq.2_Nonsense_Mutation_p.K1095*|PTPRD_uc003zkr.2_Nonsense_Mutation_p.K1086*|PTPRD_uc003zks.2_Nonsense_Mutation_p.K1095*|PTPRD_uc003zkl.2_Nonsense_Mutation_p.K1493*|PTPRD_uc003zkm.2_Nonsense_Mutation_p.K1489*|PTPRD_uc003zkn.2_Nonsense_Mutation_p.K1091*|PTPRD_uc003zko.2_Nonsense_Mutation_p.K1092*	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1502	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 1.				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(10)|large_intestine(3)|ovary(2)|urinary_tract(1)	16		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)						1253	TSP Lung(15;0.13)			0.415385	81.114967	81.5208	27	38	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	8376609	8376609	13256	9	T	A	A	A	819	63	PTPRD	5	3
PTPRD	5789	broad.mit.edu	37	9	8460523	8460523	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:8460523G>T	uc003zkk.2	-	c.3763C>A	c.(3763-3765)CTG>ATG	p.L1255M	PTPRD_uc003zkp.2_Missense_Mutation_p.L844M|PTPRD_uc003zkq.2_Missense_Mutation_p.L844M|PTPRD_uc003zkr.2_Missense_Mutation_p.L839M|PTPRD_uc003zks.2_Missense_Mutation_p.L834M|PTPRD_uc003zkl.2_Missense_Mutation_p.L1246M|PTPRD_uc003zkm.2_Missense_Mutation_p.L1242M|PTPRD_uc003zkn.2_Missense_Mutation_p.L844M|PTPRD_uc003zko.2_Missense_Mutation_p.L841M	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1255	Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(10)|large_intestine(3)|ovary(2)|urinary_tract(1)	16		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)						1253	TSP Lung(15;0.13)			0.262626	57.700377	62.751603	26	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8460523	8460523	13256	9	G	T	T	T	425	33	PTPRD	2	2
FLJ46321	389763	broad.mit.edu	37	9	84609178	84609178	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:84609178C>A	uc004amn.2	+	c.3793C>A	c.(3793-3795)CGT>AGT	p.R1265S		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	1265						integral to membrane					0														0.121827	34.070648	61.659037	24	173	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84609178	84609178	6174	9	C	A	A	A	299	23	FLJ46321	1	1
DMRT1	1761	broad.mit.edu	37	9	847035	847035	+	Nonsense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:847035G>T	uc003zgv.2	+	c.430G>T	c.(430-432)GAG>TAG	p.E144*	DMRT1_uc003zgu.1_Nonsense_Mutation_p.E144*	NM_021951	NP_068770	Q9Y5R6	DMRT1_HUMAN	doublesex and mab-3 related transcription factor	144					cell differentiation|male gonad development|regulation of transcription, DNA-dependent|sex determination	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(10;2.66e-10)|Lung NSC(10;2.82e-10)|Breast(48;0.232)		Lung(218;0.037)										0.12037	14.196371	29.465524	13	95	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	847035	847035	4765	9	G	T	T	T	481	37	DMRT1	5	1
PTPRD	5789	broad.mit.edu	37	9	8524977	8524977	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:8524977G>T	uc003zkk.2	-	c.627C>A	c.(625-627)GCC>GCA	p.A209A	PTPRD_uc003zkp.2_Silent_p.A209A|PTPRD_uc003zkq.2_Silent_p.A209A|PTPRD_uc003zkr.2_Silent_p.A203A|PTPRD_uc003zks.2_Silent_p.A203A|PTPRD_uc003zkl.2_Silent_p.A209A|PTPRD_uc003zkm.2_Silent_p.A200A|PTPRD_uc003zkn.2_Silent_p.A209A|PTPRD_uc003zko.2_Silent_p.A206A	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	209	Extracellular (Potential).|Ig-like C2-type 2.				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(10)|large_intestine(3)|ovary(2)|urinary_tract(1)	16		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)						1253	TSP Lung(15;0.13)			0.084249	-2.35222	45.783439	23	250	KEEP	---	---	---	---	capture		Silent	SNP	8524977	8524977	13256	9	G	T	T	T	600	47	PTPRD	2	2
RASEF	158158	broad.mit.edu	37	9	85622420	85622420	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:85622420C>A	uc004amo.1	-	c.960G>T	c.(958-960)AGG>AGT	p.R320S		NM_152573	NP_689786	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	320	Potential.				protein transport|small GTPase mediated signal transduction	perinuclear region of cytoplasm	calcium ion binding|GTP binding			lung(1)|breast(1)	2														0.134615	26.9792	47.168109	21	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85622420	85622420	13529	9	C	A	A	A	285	22	RASEF	2	2
SECISBP2	79048	broad.mit.edu	37	9	91943595	91943595	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:91943595G>T	uc004aqj.1	+	c.595G>T	c.(595-597)GAC>TAC	p.D199Y	SECISBP2_uc010mqn.1_Missense_Mutation_p.D199Y|SECISBP2_uc004aqi.1_Missense_Mutation_p.D126Y|SECISBP2_uc011ltk.1_Missense_Mutation_p.D198Y|SECISBP2_uc004aqk.1_Missense_Mutation_p.D126Y|SECISBP2_uc010mqo.1_5'UTR|SECISBP2_uc011ltl.1_Missense_Mutation_p.D131Y	NM_024077	NP_076982	Q96T21	SEBP2_HUMAN	SECIS binding protein 2	199					translation	nucleus	mRNA 3'-UTR binding			ovary(2)	2														0.082192	-0.811694	12.162913	6	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91943595	91943595	14492	9	G	T	T	T	429	33	SECISBP2	2	2
SEMA4D	10507	broad.mit.edu	37	9	92006263	92006264	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:92006263_92006264CC>AA	uc004aqo.1	-	c.689_690GG>TT	c.(688-690)AGG>ATT	p.R230I	SEMA4D_uc011ltm.1_Missense_Mutation_p.R230I|SEMA4D_uc011ltn.1_Non-coding_Transcript|SEMA4D_uc011lto.1_Non-coding_Transcript|SEMA4D_uc004aqp.1_Missense_Mutation_p.R228I	NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1	230	Sema.|Extracellular (Potential).				anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2														0.151515	33.814512	49.166791	20	112	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	92006263	92006264	14520	9	CC	AA	AA	AA	285	22	SEMA4D	2	2
ROR2	4920	broad.mit.edu	37	9	94487066	94487066	+	Silent	SNP	C	A	A	rs41277837		TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:94487066C>A	uc004arj.1	-	c.1710G>T	c.(1708-1710)CCG>CCT	p.P570P	ROR2_uc004ari.1_Silent_p.P430P	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	570	Cytoplasmic (Potential).|Protein kinase.				negative regulation of cell proliferation|positive regulation of cell migration|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(6)|central_nervous_system(5)|ovary(3)|large_intestine(2)	16										461				0.109091	5.718291	14.035865	6	49	KEEP	---	---	---	---	capture		Silent	SNP	94487066	94487066	14006	9	C	A	A	A	340	27	ROR2	1	1
IARS	3376	broad.mit.edu	37	9	95004448	95004448	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:95004448T>A	uc004art.1	-	c.3165A>T	c.(3163-3165)CAA>CAT	p.Q1055H	IARS_uc004ars.1_Missense_Mutation_p.Q900H|IARS_uc004aru.3_Missense_Mutation_p.Q1055H|IARS_uc010mqr.2_Missense_Mutation_p.Q945H|IARS_uc010mqt.2_Missense_Mutation_p.Q278H	NM_013417	NP_038203	P41252	SYIC_HUMAN	isoleucine tRNA synthetase	1055					isoleucyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	ATP binding|isoleucine-tRNA ligase activity|protein binding			ovary(1)	1					L-Isoleucine(DB00167)									0.11039	15.05841	38.19253	17	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95004448	95004448	7773	9	T	A	A	A	725	56	IARS	3	3
CENPI	2491	broad.mit.edu	37	X	100417903	100417903	+	Missense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:100417903C>T	uc004egx.2	+	c.2218C>T	c.(2218-2220)CAT>TAT	p.H740Y	CENPI_uc011mrg.1_Missense_Mutation_p.H726Y	NM_006733	NP_006724	Q92674	CENPI_HUMAN	centromere protein I	740					CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm				skin(1)	1														0.19802	41.038225	49.618065	20	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100417903	100417903	3366	23	C	T	T	T	377	29	CENPI	2	2
DRP2	1821	broad.mit.edu	37	X	100503543	100503543	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:100503543G>C	uc004egz.2	+	c.1495G>C	c.(1495-1497)GGC>CGC	p.G499R	DRP2_uc011mrh.1_Missense_Mutation_p.G421R	NM_001939	NP_001930	Q13474	DRP2_HUMAN	dystrophin related protein 2	499					central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2														0.173375	122.797589	155.336947	56	267	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100503543	100503543	4948	23	G	C	C	C	611	47	DRP2	3	3
BTK	695	broad.mit.edu	37	X	100613310	100613310	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:100613310G>T	uc010nno.2	-	c.1192C>A	c.(1192-1194)CAC>AAC	p.H398N	BTK_uc004ehf.2_5'UTR|BTK_uc010nnh.2_Non-coding_Transcript|BTK_uc010nni.2_Non-coding_Transcript|BTK_uc004ehe.2_Non-coding_Transcript|BTK_uc010nnj.2_Non-coding_Transcript|BTK_uc010nnk.2_Non-coding_Transcript|BTK_uc010nnl.2_5'UTR|BTK_uc010nnm.2_5'UTR|BTK_uc004ehg.2_Missense_Mutation_p.H364N|BTK_uc010nnn.2_Intron|BTK_uc004ehh.1_Non-coding_Transcript|BTK_uc004ehi.2_Missense_Mutation_p.H364N	NM_000061	NP_000052	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	364	SH2.		H -> P (in XLA).		calcium-mediated signaling|induction of apoptosis by extracellular signals|mesoderm development	cytosol|membrane raft|nucleus|plasma membrane	ATP binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol-3,4,5-trisphosphate binding			central_nervous_system(2)|ovary(1)|lung(1)	4										247				0.107477	21.073824	53.776365	23	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100613310	100613310	1591	23	G	T	T	T	598	46	BTK	2	2
GLRA4	441509	broad.mit.edu	37	X	102978817	102978817	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:102978817C>A	uc011mse.1	-	c.544G>T	c.(544-546)GAC>TAC	p.D182Y	GLRA4_uc010nou.2_Missense_Mutation_p.D182Y	NM_001024452	NP_001019623	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4 precursor	182	Extracellular (Potential).					cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity				0														0.170732	12.997123	17.203302	7	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102978817	102978817	6725	23	C	A	A	A	390	30	GLRA4	2	2
IRS4	8471	broad.mit.edu	37	X	107977664	107977664	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:107977664G>T	uc004eoc.2	-	c.1911C>A	c.(1909-1911)CCC>CCA	p.P637P		NM_003604	NP_003595	O14654	IRS4_HUMAN	insulin receptor substrate 4	637	Pro-rich.					plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity			ovary(4)|large_intestine(2)|lung(1)|breast(1)|pancreas(1)	9														0.1125	29.855816	77.471113	36	284	KEEP	---	---	---	---	capture		Silent	SNP	107977664	107977664	8146	23	G	T	T	T	548	43	IRS4	2	2
AMMECR1	9949	broad.mit.edu	37	X	109507780	109507780	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:109507780C>A	uc004eoo.2	-	c.521G>T	c.(520-522)GGA>GTA	p.G174V	AMMECR1_uc004eop.2_Intron|AMMECR1_uc004eoq.2_Missense_Mutation_p.G51V	NM_015365	NP_056180	Q9Y4X0	AMER1_HUMAN	AMMECR1 protein isoform 1	174	AMMECR1.										0														0.115789	9.950132	23.767443	11	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109507780	109507780	581	23	C	A	A	A	390	30	AMMECR1	2	2
DCX	1641	broad.mit.edu	37	X	110574132	110574132	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:110574132C>A	uc011msv.1	-	c.1189G>T	c.(1189-1191)GCA>TCA	p.A397S	DCX_uc004epd.2_Intron|DCX_uc004epe.2_Intron|DCX_uc004epf.2_Missense_Mutation_p.A316S|DCX_uc004epg.2_Intron	NM_178152	NP_835365	O43602	DCX_HUMAN	doublecortin isoform b	392	Pro/Ser-rich.				axon guidance|central nervous system development|intracellular signal transduction	cytosol|microtubule associated complex	microtubule binding			central_nervous_system(2)|lung(1)|skin(1)	4														0.115385	20.336587	39.271414	15	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110574132	110574132	4489	23	C	A	A	A	299	23	DCX	1	1
LONRF3	79836	broad.mit.edu	37	X	118151596	118151596	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:118151596G>T	uc004eqw.2	+	c.2223G>T	c.(2221-2223)AAG>AAT	p.K741N	LONRF3_uc004eqx.2_Missense_Mutation_p.K700N|LONRF3_uc004eqy.2_Non-coding_Transcript|LONRF3_uc004eqz.2_Missense_Mutation_p.K485N	NM_001031855	NP_001027026	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger	741	Lon.				proteolysis		ATP-dependent peptidase activity|protein binding|zinc ion binding			breast(1)|central_nervous_system(1)	2														0.21519	33.796539	39.757133	17	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118151596	118151596	9268	23	G	T	T	T	451	35	LONRF3	2	2
DCAF12L1	139170	broad.mit.edu	37	X	125685886	125685886	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:125685886C>A	uc004eul.2	-	c.706G>T	c.(706-708)GAG>TAG	p.E236*		NM_178470	NP_848565	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	236										skin(3)	3														0.204082	18.241085	22.336847	10	39	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	125685886	125685886	4435	23	C	A	A	A	403	31	DCAF12L1	5	1
ACTRT1	139741	broad.mit.edu	37	X	127185556	127185556	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:127185556G>T	uc004eum.2	-	c.630C>A	c.(628-630)GCC>GCA	p.A210A		NM_138289	NP_612146	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	210						cytoplasm|cytoskeleton				ovary(2)|central_nervous_system(2)	4														0.121212	20.511564	39.071154	16	116	KEEP	---	---	---	---	capture		Silent	SNP	127185556	127185556	219	23	G	T	T	T	496	39	ACTRT1	1	1
TLR8	51311	broad.mit.edu	37	X	12939284	12939284	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:12939284G>A	uc004cvd.2	+	c.2179G>A	c.(2179-2181)GAC>AAC	p.D727N	TLR8_uc004cve.2_Missense_Mutation_p.D709N	NM_138636	NP_619542	Q9NR97	TLR8_HUMAN	toll-like receptor 8 precursor	709	LRR 21.|Extracellular (Potential).				cellular response to mechanical stimulus|defense response to virus|I-kappaB kinase/NF-kappaB cascade|immunoglobulin mediated immune response|inflammatory response|innate immune response|positive regulation of innate immune response|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process	endosome membrane|integral to membrane	DNA binding|double-stranded RNA binding|single-stranded RNA binding|transmembrane receptor activity			ovary(4)|large_intestine(1)	5														0.07619	-3.791885	15.54764	8	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12939284	12939284	16487	23	G	A	A	A	585	45	TLR8	2	2
ARHGAP36	158763	broad.mit.edu	37	X	130218249	130218249	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:130218249C>A	uc004evz.2	+	c.616C>A	c.(616-618)CTG>ATG	p.L206M	ARHGAP36_uc004ewa.2_Missense_Mutation_p.L194M|ARHGAP36_uc004ewb.2_Missense_Mutation_p.L175M|ARHGAP36_uc004ewc.2_Missense_Mutation_p.L70M	NM_144967	NP_659404	Q6ZRI8	RHG36_HUMAN	hypothetical protein LOC158763 precursor	206					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)	3														0.309524	34.459723	35.817275	13	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130218249	130218249	895	23	C	A	A	A	311	24	ARHGAP36	2	2
DDX26B	203522	broad.mit.edu	37	X	134703357	134703357	+	Splice_Site_SNP	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:134703357G>T	uc004eyw.3	+	c.1287_splice	c.e10+1	p.L429_splice	DDX26B_uc004eyx.3_Splice_Site_SNP	NM_182540	NP_872346			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide												0	Acute lymphoblastic leukemia(192;6.56e-05)													0.741071	289.271123	295.163787	83	29	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	134703357	134703357	4524	23	G	T	T	T	468	36	DDX26B	5	2
SLC9A6	10479	broad.mit.edu	37	X	135112295	135112295	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135112295G>T	uc004ezk.2	+	c.1621G>T	c.(1621-1623)GGT>TGT	p.G541C	SLC9A6_uc004ezj.2_Missense_Mutation_p.G509C	NM_001042537	NP_001036002	Q92581	SL9A6_HUMAN	solute carrier family 9 (sodium/hydrogen	509					regulation of pH	early endosome membrane|endoplasmic reticulum membrane|integral to membrane|microsome|plasma membrane|recycling endosome membrane	sodium:hydrogen antiporter activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)													0.653595	323.534873	326.71893	100	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135112295	135112295	15215	23	G	T	T	T	611	47	SLC9A6	2	2
GPR112	139378	broad.mit.edu	37	X	135427823	135427823	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135427823A>T	uc004ezu.1	+	c.1958A>T	c.(1957-1959)GAG>GTG	p.E653V	GPR112_uc010nsb.1_Missense_Mutation_p.E448V|GPR112_uc010nsc.1_Missense_Mutation_p.E420V	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	653	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	11	Acute lymphoblastic leukemia(192;0.000127)									487				0.115702	14.076922	31.664093	14	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135427823	135427823	6903	23	A	T	T	T	143	11	GPR112	3	3
GPR112	139378	broad.mit.edu	37	X	135455194	135455194	+	Missense_Mutation	SNP	C	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135455194C>G	uc004ezu.1	+	c.7747C>G	c.(7747-7749)CAC>GAC	p.H2583D	GPR112_uc010nsb.1_Missense_Mutation_p.H2378D	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	2583	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	11	Acute lymphoblastic leukemia(192;0.000127)									487				0.370036	683.331085	691.554806	205	349	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135455194	135455194	6903	23	C	G	G	G	377	29	GPR112	3	3
OFD1	8481	broad.mit.edu	37	X	13785314	13785314	+	Nonsense_Mutation	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:13785314C>T	uc004cvp.3	+	c.2668C>T	c.(2668-2670)CGA>TGA	p.R890*	OFD1_uc004cvr.3_Nonsense_Mutation_p.R420*|OFD1_uc011mil.1_Nonsense_Mutation_p.R457*|OFD1_uc004cvq.3_Nonsense_Mutation_p.R713*|OFD1_uc010nen.2_Nonsense_Mutation_p.R889*|OFD1_uc004cvs.3_Non-coding_Transcript|OFD1_uc004cvu.3_Nonsense_Mutation_p.R849*|OFD1_uc004cvv.3_Nonsense_Mutation_p.R849*	NM_003611	NP_003602	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	890	Mediates the interaction with SDCCAG8.|Potential.				cilium movement involved in determination of left/right asymmetry|G2/M transition of mitotic cell cycle	centriole|cilium|cytosol|microtubule basal body|nuclear membrane	alpha-tubulin binding|gamma-tubulin binding				0														0.107143	9.6153	26.772792	12	100	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	13785314	13785314	11243	23	C	T	T	T	243	19	OFD1	5	1
MAGEC3	139081	broad.mit.edu	37	X	140967167	140967167	+	Silent	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:140967167C>A	uc011mwp.1	+	c.465C>A	c.(463-465)TCC>TCA	p.S155S		NM_138702	NP_619647	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3 isoform 1	155										skin(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.4	10.296593	10.384427	4	6	KEEP	---	---	---	---	capture		Silent	SNP	140967167	140967167	9563	23	C	A	A	A	275	22	MAGEC3	2	2
MAGEC1	9947	broad.mit.edu	37	X	140995493	140995493	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:140995493A>T	uc004fbt.2	+	c.2303A>T	c.(2302-2304)GAG>GTG	p.E768V	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	768							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.144201	67.232744	106.120206	46	273	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140995493	140995493	9561	23	A	T	T	T	143	11	MAGEC1	3	3
SLITRK4	139065	broad.mit.edu	37	X	142717696	142717696	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:142717696C>A	uc004fbx.2	-	c.1229G>T	c.(1228-1230)AGC>ATC	p.S410I	SLITRK4_uc004fby.2_Missense_Mutation_p.S410I	NM_173078	NP_775101	Q8IW52	SLIK4_HUMAN	slit and trk like 4 protein precursor	410	Extracellular (Potential).|LRR 8.					integral to membrane				upper_aerodigestive_tract(1)|large_intestine(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.241758	53.900631	59.43863	22	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142717696	142717696	15243	23	C	A	A	A	364	28	SLITRK4	2	2
SLITRK4	139065	broad.mit.edu	37	X	142718102	142718102	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:142718102G>T	uc004fbx.2	-	c.823C>A	c.(823-825)CTG>ATG	p.L275M	SLITRK4_uc004fby.2_Missense_Mutation_p.L275M	NM_173078	NP_775101	Q8IW52	SLIK4_HUMAN	slit and trk like 4 protein precursor	275	Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|large_intestine(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.192661	44.40667	54.024984	21	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142718102	142718102	15243	23	G	T	T	T	451	35	SLITRK4	2	2
IL3RA	3563	broad.mit.edu	37	X	1471274	1471274	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:1471274G>C	uc004cps.2	+	c.491G>C	c.(490-492)GGG>GCG	p.G164A	IL3RA_uc011mhd.1_Missense_Mutation_p.G86A	NM_002183	NP_002174	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha precursor	164	Extracellular (Potential).					integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)									0.065672	-19.392984	46.224112	22	313	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1471274	1471274	7996	23	G	C	C	C	559	43	IL3RA	3	3
CXorf40A	91966	broad.mit.edu	37	X	148627288	148627288	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:148627288A>G	uc004fdi.2	+	c.163A>G	c.(163-165)ACC>GCC	p.T55A	CXorf40A_uc004fdb.2_Missense_Mutation_p.T38A|CXorf40A_uc011mxm.1_Missense_Mutation_p.T38A|CXorf40A_uc011mxn.1_Missense_Mutation_p.T38A|CXorf40A_uc004fdd.2_Missense_Mutation_p.T38A|CXorf40A_uc004fde.1_Missense_Mutation_p.T38A|CXorf40A_uc011mxo.1_Missense_Mutation_p.Y127C|CXorf40A_uc004fdg.2_Missense_Mutation_p.T38A|CXorf40A_uc004fdf.2_Missense_Mutation_p.T38A|CXorf40A_uc004fdh.2_Missense_Mutation_p.T38A|CXorf40A_uc010nsy.2_Missense_Mutation_p.T38A	NM_178124	NP_835225	Q8TE69	CX04A_HUMAN	chromosome X open reading frame 40	38							protein binding				0	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)													0.15873	22.616225	29.603385	10	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148627288	148627288	4269	23	A	G	G	G	182	14	CXorf40A	4	4
ZNF185	7739	broad.mit.edu	37	X	152083041	152083041	+	Missense_Mutation	SNP	T	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:152083041T>G	uc011myg.1	+	c.8T>G	c.(7-9)ATC>AGC	p.I3S	ZNF185_uc011myh.1_Missense_Mutation_p.I3S|ZNF185_uc011myi.1_Missense_Mutation_p.I3S|ZNF185_uc011myj.1_Missense_Mutation_p.I3S|ZNF185_uc010ntv.1_Missense_Mutation_p.I3S|ZNF185_uc011myk.1_Missense_Mutation_p.I3S	NM_007150	NP_009081	O15231	ZN185_HUMAN	zinc finger protein 185	3						cytoplasm|cytoskeleton|focal adhesion	zinc ion binding			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.8	47.509311	48.765331	12	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152083041	152083041	18343	23	T	G	G	G	650	50	ZNF185	4	4
SSR4	6748	broad.mit.edu	37	X	153062964	153062964	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153062964G>T	uc004fiv.2	+	c.271G>T	c.(271-273)GGC>TGC	p.G91C	IDH3G_uc004fip.2_5'Flank|IDH3G_uc004fiq.2_5'Flank|IDH3G_uc010num.2_5'Flank|IDH3G_uc004fir.2_5'Flank|IDH3G_uc004fit.1_5'Flank|IDH3G_uc004fis.2_5'Flank|SSR4_uc004fiw.2_Missense_Mutation_p.G80C	NM_006280	NP_006271	P51571	SSRD_HUMAN	signal sequence receptor, delta precursor	80	Lumenal (Potential).				intracellular protein transport	integral to membrane|Sec61 translocon complex	calcium ion binding|protein binding				0	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)													0.145161	14.430844	21.943558	9	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	153062964	153062964	15709	23	G	T	T	T	455	35	SSR4	2	2
L1CAM	3897	broad.mit.edu	37	X	153130872	153130872	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153130872G>T	uc004fjb.2	-	c.2631C>A	c.(2629-2631)ACC>ACA	p.T877T	L1CAM_uc004fjc.2_Silent_p.T877T|L1CAM_uc010nuo.2_Silent_p.T872T	NM_000425	NP_000416	P32004	L1CAM_HUMAN	L1 cell adhesion molecule isoform 1 precursor	877	Extracellular (Potential).|Fibronectin type-III 3.				axon guidance|blood coagulation|cell death|leukocyte migration	integral to membrane				ovary(8)|central_nervous_system(1)	9	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.150235	51.393904	76.350565	32	181	KEEP	---	---	---	---	capture		Silent	SNP	153130872	153130872	8911	23	G	T	T	T	600	47	L1CAM	2	2
MECP2	4204	broad.mit.edu	37	X	153297886	153297886	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153297886G>C	uc004fjw.2	-	c.185C>G	c.(184-186)GCC>GGC	p.A62G	MECP2_uc004fjv.2_Missense_Mutation_p.A50G	NM_001110792	NP_001104262	P51608	MECP2_HUMAN	methyl CpG binding protein 2 isoform 2	50					negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity|transcription repressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.111628	26.047127	58.118733	24	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	153297886	153297886	9812	23	G	C	C	C	546	42	MECP2	3	3
FIGF	2277	broad.mit.edu	37	X	15376214	15376214	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:15376214G>T	uc004cwt.1	-	c.403C>A	c.(403-405)CCT>ACT	p.P135T		NM_004469	NP_004460	O43915	VEGFD_HUMAN	vascular endothelial growth factor D	135					angiogenesis|cell differentiation|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of mast cell chemotaxis|vascular endothelial growth factor receptor signaling pathway	extracellular space|membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity|platelet-derived growth factor receptor binding	p.P135S(1)		ovary(1)|breast(1)|central_nervous_system(1)	3	Hepatocellular(33;0.183)									167				0.287356	122.203686	129.246833	50	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15376214	15376214	6127	23	G	T	T	T	559	43	FIGF	2	2
SPRY3	10251	broad.mit.edu	37	X	155004396	155004396	+	Missense_Mutation	SNP	T	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:155004396T>A	uc004fnq.1	+	c.863T>A	c.(862-864)GTA>GAA	p.V288E	SPRY3_uc010nvl.1_Missense_Mutation_p.V189E	NM_005840	NP_005831	O43610	SPY3_HUMAN	sprouty homolog 3	288					multicellular organismal development|regulation of signal transduction	cytoplasm|membrane					0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)													0.079096	-1.376034	30.633944	14	163	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155004396	155004396	15621	23	T	A	A	A	741	57	SPRY3	3	3
NHS	4810	broad.mit.edu	37	X	17744755	17744755	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:17744755G>T	uc011mix.1	+	c.2529G>T	c.(2527-2529)AGG>AGT	p.R843S	NHS_uc004cxx.2_Missense_Mutation_p.R822S|NHS_uc004cxy.2_Missense_Mutation_p.R666S|NHS_uc004cxz.2_Missense_Mutation_p.R645S|NHS_uc004cya.2_Missense_Mutation_p.R545S	NM_001136024	NP_001129496	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 2	822						nucleus				ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	6	Hepatocellular(33;0.183)													0.251799	78.710113	86.457314	35	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17744755	17744755	10811	23	G	T	T	T	529	41	NHS	2	2
NHS	4810	broad.mit.edu	37	X	17745107	17745107	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:17745107A>G	uc011mix.1	+	c.2881A>G	c.(2881-2883)AGA>GGA	p.R961G	NHS_uc004cxx.2_Missense_Mutation_p.R940G|NHS_uc004cxy.2_Missense_Mutation_p.R784G|NHS_uc004cxz.2_Missense_Mutation_p.R763G|NHS_uc004cya.2_Missense_Mutation_p.R663G	NM_001136024	NP_001129496	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 2	940						nucleus				ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	6	Hepatocellular(33;0.183)													0.113475	25.913614	46.682997	16	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17745107	17745107	10811	23	A	G	G	G	192	15	NHS	4	4
MAP3K15	389840	broad.mit.edu	37	X	19389161	19389161	+	Missense_Mutation	SNP	G	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:19389161G>A	uc004czk.1	-	c.1741C>T	c.(1741-1743)CAC>TAC	p.H581Y	MAP3K15_uc004czj.1_Missense_Mutation_p.H541Y|MAP3K15_uc004czi.1_Missense_Mutation_p.H40Y	NM_001001671	NP_001001671	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase	1106					protein phosphorylation		ATP binding|MAP kinase kinase kinase activity|metal ion binding			ovary(3)|lung(2)|skin(1)	6	Hepatocellular(33;0.183)													0.27451	38.027058	40.363245	14	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19389161	19389161	9632	23	G	A	A	A	611	47	MAP3K15	2	2
MAP7D2	256714	broad.mit.edu	37	X	20062499	20062499	+	Nonsense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:20062499C>A	uc010nfo.1	-	c.862G>T	c.(862-864)GGA>TGA	p.G288*	MAP7D2_uc004czq.1_Nonsense_Mutation_p.G132*|MAP7D2_uc011mji.1_Nonsense_Mutation_p.G195*|MAP7D2_uc004czr.1_Nonsense_Mutation_p.G247*|MAP7D2_uc011mjj.1_Nonsense_Mutation_p.G202*	NM_152780	NP_689993	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	247										ovary(2)|breast(1)	3														0.311321	83.952919	87.365506	33	73	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	20062499	20062499	9651	23	C	A	A	A	312	24	MAP7D2	5	2
PHEX	5251	broad.mit.edu	37	X	22237202	22237202	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:22237202C>A	uc004dah.2	+	c.1750C>A	c.(1750-1752)CAT>AAT	p.H584N	PHEX_uc011mjr.1_Missense_Mutation_p.H584N|PHEX_uc011mjs.1_Missense_Mutation_p.H487N	NM_000444	NP_000435	P78562	PHEX_HUMAN	phosphate-regulating neutral endopeptidase	584	Extracellular (Potential).	Zinc; catalytic (By similarity).			biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3														0.347826	72.077347	73.48853	24	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22237202	22237202	12242	23	C	A	A	A	221	17	PHEX	2	2
MAGEB6	158809	broad.mit.edu	37	X	26213127	26213127	+	Silent	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:26213127A>T	uc004dbr.2	+	c.1164A>T	c.(1162-1164)CCA>CCT	p.P388P	MAGEB6_uc010ngc.1_Silent_p.P168P	NM_173523	NP_775794	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	388	MAGE.									ovary(3)	3														0.342593	107.046313	109.40851	37	71	KEEP	---	---	---	---	capture		Silent	SNP	26213127	26213127	9560	23	A	T	T	T	67	6	MAGEB6	3	3
MXRA5	25878	broad.mit.edu	37	X	3228223	3228223	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:3228223G>T	uc004crg.3	-	c.8021C>A	c.(8020-8022)CCC>CAC	p.P2674H		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	2674	Ig-like C2-type 11.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.136986	11.69496	21.015485	10	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3228223	3228223	10397	23	G	T	T	T	559	43	MXRA5	2	2
MXRA5	25878	broad.mit.edu	37	X	3238801	3238801	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:3238801C>A	uc004crg.3	-	c.4925G>T	c.(4924-4926)TGG>TTG	p.W1642L		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	1642						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.117021	25.811607	52.936236	22	166	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3238801	3238801	10397	23	C	A	A	A	273	21	MXRA5	2	2
DMD	1756	broad.mit.edu	37	X	32398633	32398633	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:32398633C>A	uc004dda.1	-	c.4839G>T	c.(4837-4839)TGG>TGT	p.W1613C	DMD_uc004dcw.2_Missense_Mutation_p.W269C|DMD_uc004dcx.2_Missense_Mutation_p.W272C|DMD_uc004dcz.2_Missense_Mutation_p.W1490C|DMD_uc004dcy.1_Missense_Mutation_p.W1609C|DMD_uc004ddb.1_Missense_Mutation_p.W1605C|DMD_uc010ngo.1_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	1613	Spectrin 11.|Interaction with SYNM (By similarity).				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)												0.197531	35.250709	42.154122	16	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32398633	32398633	4760	23	C	A	A	A	286	22	DMD	2	2
DMD	1756	broad.mit.edu	37	X	32486670	32486670	+	Missense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:32486670A>T	uc004dda.1	-	c.3107T>A	c.(3106-3108)CTG>CAG	p.L1036Q	DMD_uc004dcz.2_Missense_Mutation_p.L913Q|DMD_uc004dcy.1_Missense_Mutation_p.L1032Q|DMD_uc004ddb.1_Missense_Mutation_p.L1028Q|DMD_uc010ngo.1_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	1036	Spectrin 6.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)												0.25	10.492341	11.401276	4	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32486670	32486670	4760	23	A	T	T	T	91	7	DMD	3	3
CXorf59	286464	broad.mit.edu	37	X	36122805	36122805	+	Nonsense_Mutation	SNP	A	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:36122805A>T	uc004ddk.1	+	c.1042A>T	c.(1042-1044)AAA>TAA	p.K348*		NM_173695	NP_775966	Q8N9S7	CX059_HUMAN	hypothetical protein LOC286464	348						integral to membrane				central_nervous_system(1)	1														0.37037	26.341576	26.740739	10	17	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	36122805	36122805	4279	23	A	T	T	T	65	5	CXorf59	5	3
FAM47C	442444	broad.mit.edu	37	X	37027144	37027144	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:37027144C>A	uc004ddl.1	+	c.661C>A	c.(661-663)CAT>AAT	p.H221N		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	221										ovary(3)	3														0.304348	35.428717	37.002262	14	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37027144	37027144	5792	23	C	A	A	A	273	21	FAM47C	2	2
FAM47C	442444	broad.mit.edu	37	X	37028190	37028190	+	Silent	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:37028190T>C	uc004ddl.1	+	c.1707T>C	c.(1705-1707)AGT>AGC	p.S569S		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	569										ovary(3)	3														0.155844	27.461463	36.15917	12	65	KEEP	---	---	---	---	capture		Silent	SNP	37028190	37028190	5792	23	T	C	C	C	751	58	FAM47C	4	4
FAM47C	442444	broad.mit.edu	37	X	37029325	37029325	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:37029325G>T	uc004ddl.1	+	c.2842G>T	c.(2842-2844)GGG>TGG	p.G948W		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	948										ovary(3)	3														0.113636	14.722914	34.168954	15	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37029325	37029325	5792	23	G	T	T	T	559	43	FAM47C	2	2
GPR82	27197	broad.mit.edu	37	X	41586498	41586498	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:41586498C>T	uc004dfs.1	+	c.219C>T	c.(217-219)ATC>ATT	p.I73I	CASK_uc004dfl.3_Intron|CASK_uc004dfm.3_Intron|CASK_uc004dfn.3_Intron|GPR82_uc004dft.2_Silent_p.I73I|GPR82_uc004dfu.1_Non-coding_Transcript	NM_080817	NP_543007	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	73	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2														0.172414	20.410998	26.293804	10	48	KEEP	---	---	---	---	capture		Silent	SNP	41586498	41586498	6987	23	C	T	T	T	408	32	GPR82	2	2
DUSP21	63904	broad.mit.edu	37	X	44703497	44703497	+	Missense_Mutation	SNP	A	G	G			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:44703497A>G	uc004dgd.2	+	c.119A>G	c.(118-120)AAA>AGA	p.K40R		NM_022076	NP_071359	Q9H596	DUS21_HUMAN	dual specificity phosphatase 21	40	Tyrosine-protein phosphatase.					cytoplasm|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			large_intestine(1)|lung(1)	2														0.325	84.170344	86.320116	26	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44703497	44703497	5005	23	A	G	G	G	13	1	DUSP21	4	4
CXorf36	79742	broad.mit.edu	37	X	45013396	45013397	+	Nonsense_Mutation	DNP	GG	TT	TT			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:45013396_45013397GG>TT	uc004dgg.2	-	c.719_720CC>AA	c.(718-720)TCC>TAA	p.S240*		NM_176819	NP_789789	Q9H7Y0	CX036_HUMAN	hypothetical protein LOC79742 isoform 1	240						extracellular region				lung(1)	1														0.4	44.142728	44.448967	14	21	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	45013396	45013397	4267	23	GG	TT	TT	TT	444	35	CXorf36	5	2
CXorf36	79742	broad.mit.edu	37	X	45051245	45051245	+	Silent	SNP	C	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:45051245C>T	uc004dgg.2	-	c.249G>A	c.(247-249)CTG>CTA	p.L83L	CXorf36_uc004dgi.3_Silent_p.L83L	NM_176819	NP_789789	Q9H7Y0	CX036_HUMAN	hypothetical protein LOC79742 isoform 1	83						extracellular region				lung(1)	1														0.264706	21.156919	22.860399	9	25	KEEP	---	---	---	---	capture		Silent	SNP	45051245	45051245	4267	23	C	T	T	T	262	21	CXorf36	2	2
USP11	8237	broad.mit.edu	37	X	47103906	47103906	+	Silent	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:47103906G>T	uc004dhp.2	+	c.1929G>T	c.(1927-1929)GTG>GTT	p.V643V	USP11_uc004dhq.2_Silent_p.V370V	NM_004651	NP_004642	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	643					protein deubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)|central_nervous_system(1)	2														0.104167	4.054755	11.524757	5	43	KEEP	---	---	---	---	capture		Silent	SNP	47103906	47103906	17604	23	G	T	T	T	574	45	USP11	2	2
PPP1R3F	89801	broad.mit.edu	37	X	49143232	49143232	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:49143232G>C	uc004dnh.1	+	c.2080G>C	c.(2080-2082)GCC>CCC	p.A694P	PPP1R3F_uc011mnd.1_Missense_Mutation_p.A365P|PPP1R3F_uc004dni.2_Missense_Mutation_p.A348P|PPP1R3F_uc004dnj.1_Missense_Mutation_p.A348P	NM_033215	NP_149992	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory (inhibitor)	694	Extracellular (Potential).					integral to membrane				ovary(2)	2	Ovarian(276;0.236)													0.4	20.1473	20.278384	6	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49143232	49143232	12810	23	G	C	C	C	442	34	PPP1R3F	3	3
TSPYL2	64061	broad.mit.edu	37	X	53111967	53111967	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:53111967G>T	uc004drw.2	+	c.287G>T	c.(286-288)GGC>GTC	p.G96V	TSPYL2_uc004drv.2_Missense_Mutation_p.G96V|TSPYL2_uc004drx.1_5'Flank	NM_022117	NP_071400	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	96					cell cycle|chromatin modification|negative regulation of cell cycle|negative regulation of cell growth|negative regulation of DNA replication|nucleosome assembly|regulation of protein kinase activity|regulation of signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|rDNA binding				0														0.5	10.19971	10.19971	4	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53111967	53111967	17213	23	G	T	T	T	546	42	TSPYL2	2	2
HUWE1	10075	broad.mit.edu	37	X	53574724	53574724	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:53574724C>A	uc004dsp.2	-	c.10546G>T	c.(10546-10548)GCC>TCC	p.A3516S	HUWE1_uc004dsn.2_Missense_Mutation_p.A2324S	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	3516	Thr-rich.				base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17														0.285714	10.694168	11.271075	4	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53574724	53574724	7761	23	C	A	A	A	364	28	HUWE1	2	2
HUWE1	10075	broad.mit.edu	37	X	53644083	53644083	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:53644083C>A	uc004dsp.2	-	c.1805G>T	c.(1804-1806)GGC>GTC	p.G602V		NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	602					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17														0.176471	5.714325	7.391715	3	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53644083	53644083	7761	23	C	A	A	A	338	26	HUWE1	2	2
MAGEH1	28986	broad.mit.edu	37	X	55479419	55479419	+	Missense_Mutation	SNP	G	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:55479419G>C	uc004dum.2	+	c.612G>C	c.(610-612)GAG>GAC	p.E204D		NM_014061	NP_054780	Q9H213	MAGH1_HUMAN	melanoma antigen, family H, 1 protein	204					apoptosis					ovary(1)|lung(1)|central_nervous_system(1)	3														0.289474	57.518312	60.538229	22	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55479419	55479419	9571	23	G	C	C	C	451	35	MAGEH1	3	3
MTMR8	55613	broad.mit.edu	37	X	63445161	63445161	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:63445161C>A	uc011mou.1	-	c.1495G>T	c.(1495-1497)GTG>TTG	p.V499L	ASB12_uc004dvp.1_Missense_Mutation_p.V115L|ASB12_uc004dvq.1_Missense_Mutation_p.V124L|ASB12_uc004dvr.1_Missense_Mutation_p.V124L	NM_017677	NP_060147	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	315	Myotubularin phosphatase.					nuclear envelope	protein tyrosine phosphatase activity			ovary(2)|breast(2)	4														0.322581	29.037989	29.905036	10	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63445161	63445161	10342	23	C	A	A	A	221	17	MTMR8	2	2
TBX22	50945	broad.mit.edu	37	X	79286474	79286474	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:79286474G>T	uc010nmg.1	+	c.1427G>T	c.(1426-1428)AGA>ATA	p.R476I	TBX22_uc004edi.1_Missense_Mutation_p.R356I|TBX22_uc004edj.1_Missense_Mutation_p.R476I	NM_001109878	NP_001103348	Q9Y458	TBX22_HUMAN	T-box 22 isoform 1	476					multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			large_intestine(3)|central_nervous_system(2)|lung(1)|ovary(1)	7										298				0.313725	41.879271	43.455427	16	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79286474	79286474	16184	23	G	T	T	T	429	33	TBX22	2	2
FAM46D	169966	broad.mit.edu	37	X	79698553	79698553	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:79698553G>T	uc004edl.1	+	c.515G>T	c.(514-516)AGT>ATT	p.S172I	FAM46D_uc004edm.1_Missense_Mutation_p.S172I	NM_152630	NP_689843	Q8NEK8	FA46D_HUMAN	hypothetical protein LOC169966	172										lung(2)	2														0.262295	45.10582	48.202391	16	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79698553	79698553	5789	23	G	T	T	T	468	36	FAM46D	2	2
PCDH11X	27328	broad.mit.edu	37	X	91134268	91134268	+	Missense_Mutation	SNP	G	T	T			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:91134268G>T	uc004efk.1	+	c.3029G>T	c.(3028-3030)AGA>ATA	p.R1010I	PCDH11X_uc004efl.1_Missense_Mutation_p.R1010I|PCDH11X_uc004efo.1_Missense_Mutation_p.R1010I|PCDH11X_uc010nmv.1_Missense_Mutation_p.R1010I|PCDH11X_uc004efm.1_Missense_Mutation_p.R1010I|PCDH11X_uc004efn.1_Missense_Mutation_p.R1010I|PCDH11X_uc004efh.1_Missense_Mutation_p.R1010I|PCDH11X_uc004efj.1_Missense_Mutation_p.R1010I	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	1010	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.314607	70.960871	73.686491	28	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91134268	91134268	11928	23	G	T	T	T	429	33	PCDH11X	2	2
NAP1L3	4675	broad.mit.edu	37	X	92927735	92927735	+	Missense_Mutation	SNP	C	A	A			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:92927735C>A	uc004efq.2	-	c.569G>T	c.(568-570)GGT>GTT	p.G190V	FAM133A_uc004efr.1_5'Flank	NM_004538	NP_004529	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	190	Glu-rich.				nucleosome assembly	chromatin assembly complex				ovary(1)|skin(1)	2														0.351351	106.09903	108.258999	39	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92927735	92927735	10554	23	C	A	A	A	234	18	NAP1L3	2	2
SRPX2	27286	broad.mit.edu	37	X	99921831	99921831	+	Missense_Mutation	SNP	T	C	C			TCGA-05-4382-01	TCGA-05-4382-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:99921831T>C	uc004egb.2	+	c.862T>C	c.(862-864)TGT>CGT	p.C288R		NM_014467	NP_055282	O60687	SRPX2_HUMAN	sushi-repeat-containing protein, X-linked 2	288	Sushi 3.				angiogenesis|cell motility|cell-cell adhesion|positive regulation of cell migration involved in sprouting angiogenesis|regulation of phosphorylation	cytoplasm|extracellular region	receptor binding			ovary(2)	2														0.243902	24.129777	26.580529	10	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99921831	99921831	15679	23	T	C	C	C	715	55	SRPX2	4	4
