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
CCDC7	221016	broad.mit.edu	37	10	32860802	32860802	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:32860802G>A	uc001iwj.2	+	c.1435G>A	c.(1435-1437)GGA>AGA	p.G479R	CCDC7_uc001iwk.2_Missense_Mutation_p.G479R|CCDC7_uc009xlv.2_Non-coding_Transcript|C10orf68_uc001iwl.1_5'UTR|C10orf68_uc001iwm.1_Intron|C10orf68_uc001iwn.3_Intron	NM_145023	NP_659460	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	479											0		Breast(68;0.000207)|Prostate(175;0.0107)												0.305556	31.812891	33.026118	11	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32860802	32860802	2965	10	G	A	A	A	507	39	CCDC7	1	1
ZNF32	7580	broad.mit.edu	37	10	44139741	44139741	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:44139741C>A	uc001jbb.2	-	c.579G>T	c.(577-579)CAG>CAT	p.Q193H	ZNF32_uc001jbc.2_Missense_Mutation_p.Q193H	NM_001005368	NP_001005368	P17041	ZNF32_HUMAN	zinc finger protein 32	193	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1		all_neural(218;0.0182)|Ovarian(717;0.0443)|Renal(717;0.157)		Lung(62;0.179)										0.32967	87.116641	89.458075	30	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44139741	44139741	18430	10	C	A	A	A	259	20	ZNF32	2	2
DDX21	9188	broad.mit.edu	37	10	70728878	70728878	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:70728878G>T	uc001jov.1	+	c.1236_splice	c.e7+1	p.E412_splice	DDX21_uc001jow.1_Splice_Site_SNP_p.E344_splice	NM_004728	NP_004719			DEAD (Asp-Glu-Ala-Asp) box polypeptide 21							nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)	3														0.183673	21.045166	25.646901	9	40	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	70728878	70728878	4520	10	G	T	T	T	572	44	DDX21	5	2
USH1C	10083	broad.mit.edu	37	11	17517186	17517186	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:17517186G>T	uc001mne.2	-	c.2585C>A	c.(2584-2586)CCG>CAG	p.P862Q	USH1C_uc001mnf.2_Intron|USH1C_uc009yhb.2_Intron|USH1C_uc001mng.2_Intron|USH1C_uc001mnd.2_Intron	NM_153676	NP_710142	Q9Y6N9	USH1C_HUMAN	harmonin isoform b3	Error:Variant_position_missing_in_Q9Y6N9_after_alignment					equilibrioception|G2/M transition of mitotic cell cycle|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	apical part of cell|cytoplasm|stereocilium	protein binding			ovary(1)	1														0.525547	225.257895	225.341935	72	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17517186	17517186	17596	11	G	T	T	T	507	39	USH1C	1	1
PTDSS2	81490	broad.mit.edu	37	11	460269	460269	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:460269A>T	uc001lpj.2	+	c.265A>T	c.(265-267)ACG>TCG	p.T89S	PTDSS2_uc009ybv.1_Missense_Mutation_p.T89S	NM_030783	NP_110410	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	89	Extracellular (Potential).					integral to membrane					0		all_cancers(49;1.59e-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;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)									0.388889	21.322384	21.516552	7	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	460269	460269	13191	11	A	T	T	T	78	6	PTDSS2	3	3
PRG3	10394	broad.mit.edu	37	11	57146264	57146264	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57146264C>T	uc001njv.1	-	c.397G>A	c.(397-399)GGA>AGA	p.G133R		NM_006093	NP_006084	Q9Y2Y8	PRG3_HUMAN	proteoglycan 3 precursor	133	C-type lectin.				basophil activation|histamine biosynthetic process|immune response|leukotriene biosynthetic process|negative regulation of translation|neutrophil activation|positive regulation of interleukin-8 biosynthetic process|superoxide anion generation		sugar binding				0						Melanoma(154;1456 2519 19358 45229)								0.5	38.375449	38.375449	13	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57146264	57146264	12923	11	C	T	T	T	299	23	PRG3	1	1
ATG2A	23130	broad.mit.edu	37	11	64670071	64670071	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64670071T>A	uc001obx.2	-	c.3694A>T	c.(3694-3696)AAC>TAC	p.N1232Y	ATG2A_uc001obw.2_5'UTR	NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1232							protein binding			ovary(1)|central_nervous_system(1)	2														0.583333	20.724652	20.797107	7	5	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64670071	64670071	1112	11	T	A	A	A	819	63	ATG2A	3	3
DNAH10	196385	broad.mit.edu	37	12	124408974	124408974	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:124408974C>A	uc001uft.3	+	c.11407C>A	c.(11407-11409)CAG>AAG	p.Q3803K	DNAH10_uc001ufu.3_5'Flank	NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3803	TPR 4.				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|central_nervous_system(1)|skin(1)	5	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)										0.615385	24.513864	24.672818	8	5	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124408974	124408974	4780	12	C	A	A	A	325	25	DNAH10	2	2
KRT8	3856	broad.mit.edu	37	12	53298675	53298675	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:53298675A>C	uc009zmk.1	-	c.175T>G	c.(175-177)TCC>GCC	p.S59A	KRT8_uc001sbd.2_Missense_Mutation_p.S31A|KRT8_uc009zmj.2_Missense_Mutation_p.S31A|KRT8_uc009zml.1_Missense_Mutation_p.S31A|KRT8_uc009zmm.1_Missense_Mutation_p.S31A	NM_002273	NP_002264	P05787	K2C8_HUMAN	keratin 8	31	Head.|Ser-rich.				cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)									0.166667	5.147261	6.407296	2	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53298675	53298675	8808	12	A	C	C	C	117	9	KRT8	4	4
CEP290	80184	broad.mit.edu	37	12	88457805	88457805	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:88457805G>T	uc001tar.2	-	c.6223C>A	c.(6223-6225)CTG>ATG	p.L2075M	CEP290_uc001taq.2_Missense_Mutation_p.L1135M	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	2075	Potential.				cell projection organization|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding|transcription activator activity			ovary(5)|breast(1)|pancreas(1)	7														0.176471	6.213918	7.891381	3	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88457805	88457805	3386	12	G	T	T	T	464	36	CEP290	2	2
KLHL1	57626	broad.mit.edu	37	13	70681530	70681530	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:70681530G>C	uc001vip.2	-	c.302C>G	c.(301-303)ACG>AGG	p.T101R	KLHL1_uc010thm.1_Missense_Mutation_p.T101R|ATXN8OS_uc010aej.1_Non-coding_Transcript	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein	101					actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)										0.25	31.406312	33.904516	11	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70681530	70681530	8677	13	G	C	C	C	520	40	KLHL1	3	3
FSCB	84075	broad.mit.edu	37	14	44974834	44974835	+	Missense_Mutation	DNP	CC	AG	AG			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:44974834_44974835CC>AG	uc001wvn.2	-	c.1356_1357GG>CT	c.(1354-1359)GAGGCT>GACTCT	p.452_453EA>DS		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	452_453						cilium				breast(3)|ovary(2)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(112;0.128)					p.E452E(BT20-Tumor)	151				0.5	66.942296	66.942296	22	22	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	44974834	44974835	6316	14	CC	AG	AG	AG	338	26	FSCB	2	2
RTN1	6252	broad.mit.edu	37	14	60074109	60074109	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:60074109C>A	uc001xen.1	-	c.1867G>T	c.(1867-1869)GTC>TTC	p.V623F	RTN1_uc001xem.1_Missense_Mutation_p.V203F|RTN1_uc001xek.1_Missense_Mutation_p.V55F|RTN1_uc001xel.1_Non-coding_Transcript|RTN1_uc010apl.1_Missense_Mutation_p.V40F	NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	623	Reticulon.|Helical; (Potential).				neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)										0.595238	84.881881	85.214991	25	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60074109	60074109	14205	14	C	A	A	A	247	19	RTN1	1	1
KCNK10	54207	broad.mit.edu	37	14	88652450	88652450	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:88652450G>T	uc001xwm.2	-	c.1061C>A	c.(1060-1062)GCT>GAT	p.A354D	KCNK10_uc001xwn.2_Missense_Mutation_p.A354D|KCNK10_uc001xwo.2_Missense_Mutation_p.A349D	NM_138318	NP_612191	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	349	Cytoplasmic (Potential).				signal transduction	integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|pancreas(1)	3														0.366667	26.900941	27.375741	11	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88652450	88652450	8364	14	G	T	T	T	442	34	KCNK10	2	2
SLC24A4	123041	broad.mit.edu	37	14	92909141	92909141	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:92909141G>A	uc001yak.2	+	c.512G>A	c.(511-513)TGC>TAC	p.C171Y	SLC24A4_uc001yai.2_Missense_Mutation_p.C124Y|SLC24A4_uc010twm.1_Missense_Mutation_p.C188Y|SLC24A4_uc001yaj.2_Missense_Mutation_p.C171Y|SLC24A4_uc010auj.2_Missense_Mutation_p.C79Y|SLC24A4_uc010twn.1_5'Flank	NM_153646	NP_705932	Q8NFF2	NCKX4_HUMAN	solute carrier family 24 member 4 isoform 1	171	Helical; (Potential).					integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			breast(2)|ovary(1)	3		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)		NSCLC(10;315 435 10383 28450 38798)								0.492754	195.996241	196.002381	68	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92909141	92909141	14965	14	G	A	A	A	598	46	SLC24A4	2	2
ADAMTS17	170691	broad.mit.edu	37	15	100801842	100801842	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:100801842C>A	uc002bvv.1	-	c.874_splice	c.e6-1	p.A292_splice	ADAMTS17_uc002bvx.1_Splice_Site_SNP_p.A49_splice	NM_139057	NP_620688			ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)										0.666667	69.456572	70.267089	22	11	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	100801842	100801842	263	15	C	A	A	A	312	24	ADAMTS17	5	2
SNRPA1	6627	broad.mit.edu	37	15	101833351	101833351	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:101833351G>C	uc002bww.2	-	c.109C>G	c.(109-111)CTA>GTA	p.L37V	SNRPA1_uc002bwx.2_Intron|SNRPA1_uc010bpc.2_Intron	NM_003090	NP_003081	P09661	RU2A_HUMAN	small nuclear ribonucleoprotein polypeptide A'	37	LRR 1.				nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nucleoplasm|U2 snRNP	protein binding|RNA binding			kidney(1)	1	Lung NSC(78;0.00156)|all_lung(78;0.00195)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00113)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)											0.583333	104.207689	104.498406	28	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101833351	101833351	15360	15	G	C	C	C	425	33	SNRPA1	3	3
MYO5A	4644	broad.mit.edu	37	15	52609419	52609419	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:52609419C>A	uc002aby.2	-	c.5160G>T	c.(5158-5160)AGG>AGT	p.R1720S	MYO5A_uc002abx.3_Missense_Mutation_p.R1693S|MYO5A_uc010ugd.1_Missense_Mutation_p.R442S	NM_000259	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA isoform 1	1720	Dilute.				actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)										1	129.388119	129.388119	35	0	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52609419	52609419	10473	15	C	A	A	A	233	18	MYO5A	2	2
FAM169B	283777	broad.mit.edu	37	15	98995157	98995157	+	Silent	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:98995157G>A	uc002buk.1	-	c.267C>T	c.(265-267)CAC>CAT	p.H89H		NM_182562	NP_872368	Q8N8A8	F169B_HUMAN	hypothetical protein LOC283777	89											0														0.543478	71.166002	71.241302	25	21	KEEP	---	---	---	---	capture		Silent	SNP	98995157	98995157	5692	15	G	A	A	A	568	44	FAM169B	2	2
TELO2	9894	broad.mit.edu	37	16	1545620	1545620	+	Silent	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1545620C>T	uc002cly.2	+	c.609C>T	c.(607-609)CTC>CTT	p.L203L	TELO2_uc010uvg.1_Silent_p.L203L	NM_016111	NP_057195	Q9Y4R8	TELO2_HUMAN	TEL2, telomere maintenance 2, homolog	203						chromosome, telomeric region|cytoplasm|membrane|nucleus	protein binding				0		Hepatocellular(780;0.219)												0.444444	35.4011	35.472715	12	15	KEEP	---	---	---	---	capture		Silent	SNP	1545620	1545620	16284	16	C	T	T	T	379	30	TELO2	2	2
ZNF629	23361	broad.mit.edu	37	16	30793474	30793474	+	Silent	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30793474G>A	uc002dzs.1	-	c.2175C>T	c.(2173-2175)CTC>CTT	p.L725L		NM_001080417	NP_001073886	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	725	C2H2-type 17.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			Colorectal(24;0.198)											0.5	46.75424	46.75424	17	17	KEEP	---	---	---	---	capture		Silent	SNP	30793474	30793474	18648	16	G	A	A	A	574	45	ZNF629	2	2
ZNF423	23090	broad.mit.edu	37	16	49823452	49823452	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:49823452C>A	uc002efs.2	-	c.22G>T	c.(22-24)GAG>TAG	p.E8*		NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	8					cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	transcription activator activity|transcription repressor activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)								386				0.491525	85.767292	85.771073	29	30	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	49823452	49823452	18491	16	C	A	A	A	416	32	ZNF423	5	2
IRX5	10265	broad.mit.edu	37	16	54966629	54966629	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:54966629C>G	uc002ehv.2	+	c.469C>G	c.(469-471)CTC>GTC	p.L157V	IRX5_uc010cca.1_Missense_Mutation_p.L209V|IRX5_uc002ehw.2_Missense_Mutation_p.L91V	NM_005853	NP_005844	P78411	IRX5_HUMAN	iroquois homeobox protein 5	157	Homeobox; TALE-type.				regulation of transcription, DNA-dependent|response to stimulus|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|vitamin D binding				0														0.434579	273.641919	274.438946	93	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54966629	54966629	8151	16	C	G	G	G	312	24	IRX5	3	3
CDH16	1014	broad.mit.edu	37	16	66945908	66945908	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:66945908G>T	uc002eql.2	-	c.1684C>A	c.(1684-1686)CCC>ACC	p.P562T	CDH16_uc010cdy.2_Missense_Mutation_p.P562T|CDH16_uc002eqm.2_Missense_Mutation_p.P465T	NM_004062	NP_004053	O75309	CAD16_HUMAN	cadherin 16 precursor	562	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)										0.378378	74.519077	75.498849	28	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66945908	66945908	3230	16	G	T	T	T	559	43	CDH16	2	2
HAS3	3038	broad.mit.edu	37	16	69143594	69143594	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:69143594A>C	uc010cfh.2	+	c.296A>C	c.(295-297)GAC>GCC	p.D99A	HAS3_uc002ewk.2_Missense_Mutation_p.D99A|HAS3_uc010vlk.1_Missense_Mutation_p.D99A|HAS3_uc002ewl.2_Missense_Mutation_p.D99A	NM_005329	NP_005320	O00219	HAS3_HUMAN	hyaluronan synthase 3 isoform a	99	Cytoplasmic (Potential).				carbohydrate metabolic process	integral to plasma membrane	hyaluronan synthase activity				0		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)										0.444444	39.297543	39.369954	12	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69143594	69143594	7245	16	A	C	C	C	130	10	HAS3	4	4
NQO1	1728	broad.mit.edu	37	16	69744936	69744936	+	Silent	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:69744936C>T	uc002exp.2	-	c.768G>A	c.(766-768)GTG>GTA	p.V256V	NQO1_uc010cfm.2_Silent_p.V235V|NQO1_uc002exq.2_Silent_p.V222V|NQO1_uc002exr.2_Silent_p.V218V|NQO1_uc010vll.1_Silent_p.V184V	NM_000903	NP_000894	P15559	NQO1_HUMAN	NAD(P)H menadione oxidoreductase 1,	256					nitric oxide biosynthetic process|oxidation-reduction process|regulation of cellular amino acid metabolic process|response to toxin|synaptic transmission, cholinergic|xenobiotic metabolic process	cytosol	coenzyme binding|cytochrome-b5 reductase activity|electron carrier activity|NAD(P)H dehydrogenase (quinone) activity				0					Dicumarol(DB00266)|Menadione(DB00170)									0.076142	-0.457336	35.737219	15	182	KEEP	---	---	---	---	capture		Silent	SNP	69744936	69744936	11016	16	C	T	T	T	262	21	NQO1	2	2
LGALS9B	284194	broad.mit.edu	37	17	20361582	20361582	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:20361582C>T	uc002gxa.1	-	c.247G>A	c.(247-249)GGG>AGG	p.G83R	LGALS9B_uc002gwz.1_Missense_Mutation_p.G83R|LGALS9B_uc010vzh.1_5'UTR	NM_001042685	NP_001036150	Q3B8N2	LEG9B_HUMAN	galectin-9 like	83	Beta-galactoside binding 1 (By similarity).|Galectin 1.						sugar binding				0														0.131222	43.689212	72.855836	29	192	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20361582	20361582	9075	17	C	T	T	T	286	22	LGALS9B	2	2
DNAJC7	7266	broad.mit.edu	37	17	40134023	40134023	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40134023G>A	uc002hyo.2	-	c.1234C>T	c.(1234-1236)CGG>TGG	p.R412W	DNAJC7_uc010cxu.2_Missense_Mutation_p.R359W|DNAJC7_uc010cxv.2_Intron|DNAJC7_uc010wgb.1_Missense_Mutation_p.R356W|DNAJC7_uc010wgc.1_Missense_Mutation_p.R270W|DNAJC7_uc002hyp.2_Missense_Mutation_p.R356W	NM_003315	NP_003306	Q99615	DNJC7_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 7	412	J.				chaperone cofactor-dependent protein refolding	cytoplasm|cytoskeleton|nucleus	heat shock protein binding|unfolded protein binding			ovary(1)	1		all_cancers(22;0.00273)|Breast(137;0.00104)|all_epithelial(22;0.0305)				Colon(63;618 1117 8600 10857 19751)								0.285714	44.417985	47.021151	18	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40134023	40134023	4837	17	G	A	A	A	480	37	DNAJC7	1	1
AOC3	8639	broad.mit.edu	37	17	41004563	41004563	+	Silent	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:41004563G>T	uc002ibv.2	+	c.1203G>T	c.(1201-1203)GGG>GGT	p.G401G		NM_003734	NP_003725	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3 precursor	401	Extracellular (Potential).				amine metabolic process|cell adhesion|inflammatory response|oxidation-reduction process	cell surface|integral to membrane|plasma membrane	aliphatic-amine oxidase activity|aminoacetone:oxygen oxidoreductase(deaminating) activity|copper ion binding|phenethylamine:oxygen oxidoreductase (deaminating) activity|primary amine oxidase activity|protein homodimerization activity|quinone binding|tryptamine:oxygen oxidoreductase (deaminating) activity			central_nervous_system(2)|ovary(1)	3		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	NSCLC(3;192 220 10664 11501 16477)								0.254237	71.752042	78.119561	30	88	KEEP	---	---	---	---	capture		Silent	SNP	41004563	41004563	738	17	G	T	T	T	548	43	AOC3	2	2
SLC4A1	6521	broad.mit.edu	37	17	42340032	42340032	+	Silent	SNP	G	T	T	rs55900479		TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:42340032G>T	uc002igf.3	-	c.78C>A	c.(76-78)ATC>ATA	p.I26I	SLC4A1_uc002igg.3_Silent_p.I26I	NM_000342	NP_000333	P02730	B3AT_HUMAN	solute carrier family 4, anion exchanger, member	26	Cytoplasmic.				bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)										0.695652	43.188306	43.969769	16	7	KEEP	---	---	---	---	capture		Silent	SNP	42340032	42340032	15147	17	G	T	T	T	525	41	SLC4A1	2	2
UNC13D	201294	broad.mit.edu	37	17	73830750	73830750	+	Silent	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:73830750C>A	uc002jpp.2	-	c.2040G>T	c.(2038-2040)CGG>CGT	p.R680R	UNC13D_uc010wsk.1_Silent_p.R680R|UNC13D_uc002jpq.1_Silent_p.R330R	NM_199242	NP_954712	Q70J99	UN13D_HUMAN	unc-13 homolog D	680					positive regulation of exocytosis|regulation of mast cell degranulation	exocytic vesicle|late endosome|lysosome|membrane|recycling endosome	protein binding				0			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)											0.3	6.818606	7.177621	3	7	KEEP	---	---	---	---	capture		Silent	SNP	73830750	73830750	17545	17	C	A	A	A	275	22	UNC13D	2	2
ST6GALNAC1	55808	broad.mit.edu	37	17	74623576	74623577	+	Nonsense_Mutation	DNP	GG	TT	TT			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:74623576_74623577GG>TT	uc002jsh.2	-	c.920_921CC>AA	c.(919-921)TCC>TAA	p.S307*	ST6GALNAC1_uc002jsi.2_Nonsense_Mutation_p.S175*|ST6GALNAC1_uc002jsj.2_Non-coding_Transcript	NM_018414	NP_060884	Q9NSC7	SIA7A_HUMAN	sialyltransferase 7A	307	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity				0														0.214286	91.855792	105.554454	39	143	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	74623576	74623577	15741	17	GG	TT	TT	TT	600	47	ST6GALNAC1	5	2
RPTOR	57521	broad.mit.edu	37	17	78858847	78858847	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:78858847G>T	uc002jyt.1	+	c.1882G>T	c.(1882-1884)GGC>TGC	p.G628C	RPTOR_uc010wug.1_Intron	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1	628					cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)	5										1368				0.6	19.451833	19.53934	6	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78858847	78858847	14145	17	G	T	T	T	559	43	RPTOR	2	2
UPF1	5976	broad.mit.edu	37	19	18956882	18956882	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:18956882G>A	uc002nkg.2	+	c.325G>A	c.(325-327)GAA>AAA	p.E109K	UPF1_uc002nkf.2_Missense_Mutation_p.E109K	NM_002911	NP_002902	Q92900	RENT1_HUMAN	regulator of nonsense transcripts 1	109	Sufficient for interaction with RENT2.				cell cycle|DNA repair|DNA replication|histone mRNA catabolic process|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational termination	chromatin|cytoplasmic mRNA processing body|exon-exon junction complex	ATP binding|ATP-dependent RNA helicase activity|chromatin binding|DNA binding|protein binding|protein binding|RNA binding|zinc ion binding			ovary(1)	1														0.408163	56.084999	56.447453	20	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18956882	18956882	17563	19	G	A	A	A	585	45	UPF1	2	2
RYR1	6261	broad.mit.edu	37	19	39058536	39058536	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:39058536G>C	uc002oit.2	+	c.13638G>C	c.(13636-13638)GAG>GAC	p.E4546D	RYR1_uc002oiu.2_Missense_Mutation_p.E4541D	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	4546					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)	10	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)									0.363636	63.497602	64.610937	24	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39058536	39058536	14248	19	G	C	C	C	451	35	RYR1	3	3
LIPE	3991	broad.mit.edu	37	19	42909604	42909604	+	Silent	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42909604G>T	uc002otr.2	-	c.2475C>A	c.(2473-2475)TCC>TCA	p.S825S		NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase	825					cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)												0.474576	85.294503	85.327786	28	31	KEEP	---	---	---	---	capture		Silent	SNP	42909604	42909604	9148	19	G	T	T	T	444	35	LIPE	2	2
TSKS	60385	broad.mit.edu	37	19	50245223	50245223	+	Silent	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:50245223C>T	uc002ppm.2	-	c.1416G>A	c.(1414-1416)CTG>CTA	p.L472L		NM_021733	NP_068379	Q9UJT2	TSKS_HUMAN	testis-specific kinase substrate	472							protein binding			large_intestine(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)										0.51145	185.181101	185.195057	67	64	KEEP	---	---	---	---	capture		Silent	SNP	50245223	50245223	17177	19	C	T	T	T	366	29	TSKS	2	2
KDM4B	23030	broad.mit.edu	37	19	5082484	5082484	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:5082484G>T	uc010xim.1	+	c.887G>T	c.(886-888)CGG>CTG	p.R296L	KDM4B_uc010xil.1_Missense_Mutation_p.R296L|KDM4B_uc002mbq.3_Missense_Mutation_p.R296L|KDM4B_uc002mbr.3_Missense_Mutation_p.R54L	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B	296	JmjC.				chromatin modification|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1														0.6	10.025909	10.069624	3	2	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5082484	5082484	8435	19	G	T	T	T	507	39	KDM4B	1	1
SHANK1	50944	broad.mit.edu	37	19	51165647	51165647	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51165647G>A	uc002psx.1	-	c.6061C>T	c.(6061-6063)CCC>TCC	p.P2021S	SHANK1_uc002psw.1_Missense_Mutation_p.P1405S	NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	2021					cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)										0.5625	26.476257	26.530803	9	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51165647	51165647	14756	19	G	A	A	A	546	42	SHANK1	2	2
LILRB2	10288	broad.mit.edu	37	19	54782759	54782759	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54782759C>T	uc002qfb.2	-	c.863G>A	c.(862-864)CGC>CAC	p.R288H	LILRA6_uc002qew.1_Intron|LILRB2_uc010eri.2_Missense_Mutation_p.R288H|LILRB2_uc010erj.2_Non-coding_Transcript|LILRB2_uc002qfc.2_Missense_Mutation_p.R288H|LILRB2_uc010yet.1_Missense_Mutation_p.R172H|LILRB2_uc010yeu.1_Non-coding_Transcript	NM_005874	NP_005865	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor,	288	Extracellular (Potential).|Ig-like C2-type 3.				cell surface receptor linked signaling pathway|cell-cell signaling|cellular defense response|immune response|regulation of immune response	integral to plasma membrane|membrane fraction	receptor activity				0	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)										0.4	31.236161	31.484465	12	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54782759	54782759	9117	19	C	T	T	T	351	27	LILRB2	1	1
ZNF550	162972	broad.mit.edu	37	19	58058537	58058537	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:58058537T>C	uc002qpe.1	-	c.952A>G	c.(952-954)ATA>GTA	p.I318V	ZNF547_uc002qpm.3_Intron|ZNF549_uc010eud.1_Intron|ZNF550_uc002qpc.2_Non-coding_Transcript|ZNF550_uc010eue.1_Non-coding_Transcript|ZNF550_uc002qpd.2_Non-coding_Transcript	NM_001039654	NP_001034743	Q7Z398	ZN550_HUMAN	zinc finger protein 550	359	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)										0.268657	46.926355	50.159366	18	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58058537	58058537	18577	19	T	C	C	C	663	51	ZNF550	4	4
ZNF256	10172	broad.mit.edu	37	19	58452773	58452773	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:58452773C>T	uc002qqu.2	-	c.1403G>A	c.(1402-1404)TGT>TAT	p.C468Y	ZNF256_uc010euj.2_Missense_Mutation_p.C315Y	NM_005773	NP_005764	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	468	C2H2-type 10.				multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	DNA binding|general transcriptional repressor activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		NSCLC(55;1313 1552 8040 11996)								0.12963	37.551182	66.392733	28	188	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58452773	58452773	18390	19	C	T	T	T	221	17	ZNF256	2	2
TBX15	6913	broad.mit.edu	37	1	119441650	119441651	+	Splice_Site_DNP	DNP	CC	AA	AA			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:119441650_119441651CC>AA	uc001ehl.1	-	c.706_splice	c.e7+1	p.G236_splice	TBX15_uc009whj.1_Splice_Site_DNP_p.A27_splice	NM_152380	NP_689593			T-box 15						regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|pancreas(1)	2	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)										0.104167	17.993793	47.905261	20	172	KEEP	---	---	---	---	capture		Splice_Site_DNP	DNP	119441650	119441651	16178	1	CC	AA	AA	AA	234	18	TBX15	5	2
NOTCH2	4853	broad.mit.edu	37	1	120458798	120458798	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:120458798T>C	uc001eik.2	-	c.6547A>G	c.(6547-6549)ATG>GTG	p.M2183V		NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	2183	Cytoplasmic (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				0.176744	75.950653	97.280716	38	177	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120458798	120458798	10951	1	T	C	C	C	637	49	NOTCH2	4	4
FLG2	388698	broad.mit.edu	37	1	152325391	152325391	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152325391A>C	uc001ezw.3	-	c.4871T>G	c.(4870-4872)ATA>AGA	p.I1624R		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1624	Filaggrin 6.						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)											0.028961	-105.969799	37.232235	17	570	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152325391	152325391	6161	1	A	C	C	C	208	16	FLG2	4	4
CLCNKA	1187	broad.mit.edu	37	1	16358322	16358322	+	Silent	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:16358322C>T	uc001axu.2	+	c.1740C>T	c.(1738-1740)CCC>CCT	p.P580P	CLCNKA_uc001axt.2_Non-coding_Transcript|CLCNKA_uc001axv.2_Silent_p.P580P|CLCNKA_uc010obw.1_Silent_p.P537P|CLCNKB_uc001axw.3_Intron|CLCNKA_uc010oby.1_Intron	NM_004070	NP_004061	P51800	CLCKA_HUMAN	chloride channel Ka isoform 1	580	CBS 1.				excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)									0.875	49.058507	51.254887	14	2	KEEP	---	---	---	---	capture		Silent	SNP	16358322	16358322	3605	1	C	T	T	T	275	22	CLCNKA	2	2
PADI2	11240	broad.mit.edu	37	1	17420155	17420155	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:17420155C>A	uc001baf.2	-	c.436G>T	c.(436-438)GGC>TGC	p.G146C	PADI2_uc010ocm.1_Intron|PADI2_uc001bag.1_Missense_Mutation_p.G146C	NM_007365	NP_031391	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	146					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity			ovary(3)|pancreas(1)|central_nervous_system(1)|skin(1)	6		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)									0.125	9.676495	21.694352	11	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17420155	17420155	11794	1	C	A	A	A	286	22	PADI2	2	2
KIAA1751	85452	broad.mit.edu	37	1	1903428	1903428	+	Silent	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:1903428G>T	uc009vkz.1	-	c.879C>A	c.(877-879)TCC>TCA	p.S293S	KIAA1751_uc001aim.1_Silent_p.S293S	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452	293										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)										0.25	13.730039	15.103965	6	18	KEEP	---	---	---	---	capture		Silent	SNP	1903428	1903428	8567	1	G	T	T	T	496	39	KIAA1751	1	1
OBSCN	84033	broad.mit.edu	37	1	228527676	228527676	+	Silent	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228527676G>T	uc009xez.1	+	c.17289G>T	c.(17287-17289)ACG>ACT	p.T5763T	OBSCN_uc001hsn.2_Silent_p.T5763T|OBSCN_uc001hsr.1_Silent_p.T392T	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	5763	DH.				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				0.181818	15.975491	20.160022	8	36	KEEP	---	---	---	---	capture		Silent	SNP	228527676	228527676	11217	1	G	T	T	T	496	39	OBSCN	1	1
RYR2	6262	broad.mit.edu	37	1	237823355	237823355	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237823355A>G	uc001hyl.1	+	c.8279A>G	c.(8278-8280)TAT>TGT	p.Y2760C		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2760	Modulator (Potential).|Cytoplasmic (By similarity).|3.|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.588235	33.405128	33.513093	10	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237823355	237823355	14249	1	A	G	G	G	208	16	RYR2	4	4
TP73	7161	broad.mit.edu	37	1	3599745	3599745	+	Splice_Site_SNP	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:3599745G>A	uc001akp.2	+	c.186_splice	c.e3+1	p.M62_splice	TP73_uc001akq.2_Splice_Site_SNP_p.M62_splice	NM_005427	NP_005418			tumor protein p73 isoform a						cellular response to UV|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|mismatch repair|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of JUN kinase activity|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription from RNA polymerase II promoter|protein tetramerization|response to gamma radiation|response to X-ray	chromatin|cytosol|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|metal ion binding|p53 binding|promoter binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription factor binding|transcription repressor activity			ovary(1)|lung(1)	2	all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198)	all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127)		Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226)						1049				0.434783	27.931655	28.019228	10	13	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	3599745	3599745	16937	1	G	A	A	A	572	44	TP73	5	2
C1orf175	374977	broad.mit.edu	37	1	55167778	55167778	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:55167778C>T	uc010ooe.1	+	c.3301C>T	c.(3301-3303)CGC>TGC	p.R1101C	C1orf175_uc001cxq.2_Non-coding_Transcript|C1orf175_uc001cxs.2_Non-coding_Transcript|C1orf175_uc010ood.1_Missense_Mutation_p.R619C|C1orf175_uc010oof.1_Non-coding_Transcript|C1orf175_uc001cxr.1_Non-coding_Transcript|C1orf175_uc009vzq.1_Non-coding_Transcript|C1orf175_uc001cxt.1_Non-coding_Transcript|C1orf175_uc009vzr.1_Missense_Mutation_p.R303C	NM_001039464	NP_001034553	Q68CQ1	HEAT8_HUMAN	hypothetical protein LOC374977	1101	HEAT 3.					integral to membrane	binding				0														0.708333	103.036432	104.894799	34	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55167778	55167778	2083	1	C	T	T	T	351	27	C1orf175	1	1
RABGGTB	5876	broad.mit.edu	37	1	76253196	76253196	+	Silent	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:76253196G>A	uc001dgy.1	+	c.18G>A	c.(16-18)AAG>AAA	p.K6K	RABGGTB_uc009wbt.1_Non-coding_Transcript|RABGGTB_uc001dha.1_5'UTR|SNORD45A_uc009wbu.1_5'Flank|SNORD45B_uc009wbv.1_5'Flank	NM_004582	NP_004573	P53611	PGTB2_HUMAN	RAB geranylgeranyltransferase, beta subunit	6					protein modification process|visual perception		metal ion binding|protein binding|Rab geranylgeranyltransferase activity			ovary(1)	1														0.151376	65.434451	90.810653	33	185	KEEP	---	---	---	---	capture		Silent	SNP	76253196	76253196	13427	1	G	A	A	A	451	35	RABGGTB	2	2
CST1	1469	broad.mit.edu	37	20	23728528	23728528	+	Silent	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:23728528C>T	uc002wtp.2	-	c.351G>A	c.(349-351)TTG>TTA	p.L117L		NM_001898	NP_001889	P01037	CYTN_HUMAN	cystatin SN precursor	117						extracellular region	cysteine-type endopeptidase inhibitor activity			ovary(1)	1	Lung NSC(19;0.0676)|all_lung(19;0.148)													0.105263	2.669526	8.55855	4	34	KEEP	---	---	---	---	capture		Silent	SNP	23728528	23728528	4111	20	C	T	T	T	220	17	CST1	2	2
DDX27	55661	broad.mit.edu	37	20	47838010	47838010	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:47838010C>T	uc002xuh.2	+	c.208C>T	c.(208-210)CGA>TGA	p.R70*		NM_017895	NP_060365	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	70	Asp/Glu/Lys-rich.					nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)											0.25	23.930051	26.203619	10	30	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	47838010	47838010	4525	20	C	T	T	T	243	19	DDX27	5	1
ZNF831	128611	broad.mit.edu	37	20	57768130	57768130	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:57768130G>T	uc002yan.2	+	c.2056G>T	c.(2056-2058)GCA>TCA	p.A686S		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	686						intracellular	nucleic acid binding|zinc ion binding			ovary(1)|skin(1)	2	all_lung(29;0.0085)													0.294118	14.069717	14.713756	5	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57768130	57768130	18784	20	G	T	T	T	494	38	ZNF831	1	1
CHGB	1114	broad.mit.edu	37	20	5903537	5903537	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:5903537C>A	uc002wmg.2	+	c.747C>A	c.(745-747)CAC>CAA	p.H249Q	CHGB_uc010zqz.1_5'UTR	NM_001819	NP_001810	P05060	SCG1_HUMAN	chromogranin B precursor	249						extracellular space	hormone activity			breast(3)|ovary(1)	4														0.569444	122.172485	122.473759	41	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5903537	5903537	3473	20	C	A	A	A	233	18	CHGB	2	2
MYH9	4627	broad.mit.edu	37	22	36691012	36691012	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:36691012T>A	uc003apg.2	-	c.3596A>T	c.(3595-3597)GAG>GTG	p.E1199V		NM_002473	NP_002464	P35579	MYH9_HUMAN	myosin, heavy polypeptide 9, non-muscle	1199	Potential.				actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	10										1624				0.32	38.743379	40.204904	16	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36691012	36691012	10437	22	T	A	A	A	702	54	MYH9	3	3
IL1RL1	9173	broad.mit.edu	37	2	102968257	102968257	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:102968257A>T	uc002tbu.1	+	c.1547A>T	c.(1546-1548)CAC>CTC	p.H516L	IL18R1_uc002tbw.3_Intron	NM_016232	NP_057316	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1 isoform 1	516	TIR.|Cytoplasmic (Potential).				innate immune response	integral to membrane	interleukin-1 receptor activity|receptor signaling protein activity			ovary(1)|central_nervous_system(1)|skin(1)	3														0.211268	34.293414	39.763336	15	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102968257	102968257	7964	2	A	T	T	T	78	6	IL1RL1	3	3
ANAPC1	64682	broad.mit.edu	37	2	112545863	112545863	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:112545863C>T	uc002thi.2	-	c.4747G>A	c.(4747-4749)GCT>ACT	p.A1583T		NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	1583					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|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|cytosol|nucleoplasm					0														0.092105	3.671267	16.398829	7	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112545863	112545863	601	2	C	T	T	T	351	27	ANAPC1	1	1
ATF2	1386	broad.mit.edu	37	2	175962264	175962264	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:175962264T>C	uc002ujl.2	-	c.886A>G	c.(886-888)AAA>GAA	p.K296E	ATF2_uc010fqv.2_Missense_Mutation_p.K247E|ATF2_uc002ujv.2_Missense_Mutation_p.K43E|ATF2_uc002ujm.2_Missense_Mutation_p.K238E|ATF2_uc002ujn.2_Non-coding_Transcript|ATF2_uc002ujo.2_Intron|ATF2_uc002ujp.2_Non-coding_Transcript|ATF2_uc002ujq.2_Missense_Mutation_p.K296E|ATF2_uc002ujr.2_Non-coding_Transcript|ATF2_uc010fqu.2_Missense_Mutation_p.K278E|ATF2_uc002ujs.2_Missense_Mutation_p.K238E|ATF2_uc002ujt.2_Non-coding_Transcript|ATF2_uc002uju.2_Non-coding_Transcript|ATF2_uc002ujw.1_Missense_Mutation_p.K238E|ATF2_uc002ujx.1_Non-coding_Transcript	NM_001880	NP_001871	P15336	ATF2_HUMAN	activating transcription factor 2	296					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				0.063492	-9.099441	15.894097	8	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	175962264	175962264	1099	2	T	C	C	C	819	63	ATF2	4	4
COL3A1	1281	broad.mit.edu	37	2	189851866	189851866	+	Splice_Site_SNP	SNP	G	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:189851866G>C	uc002uqj.1	+	c.528_splice	c.e5+1	p.A176_splice		NM_000090	NP_000081			collagen type III alpha 1 preproprotein						axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)					1079				0.47	168.220217	168.298405	47	53	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	189851866	189851866	3826	2	G	C	C	C	624	48	COL3A1	5	3
SPEG	10290	broad.mit.edu	37	2	220353792	220353792	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220353792C>A	uc010fwg.2	+	c.8166C>A	c.(8164-8166)CAC>CAA	p.H2722Q		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	2722	Fibronectin type-III 2.				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				0.388889	64.062591	64.646638	21	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220353792	220353792	15548	2	C	A	A	A	233	18	SPEG	2	2
COL4A3	1285	broad.mit.edu	37	2	228175633	228175633	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228175633C>A	uc002vom.1	+	c.4897C>A	c.(4897-4899)CTG>ATG	p.L1633M	COL4A3_uc002von.1_Intron|COL4A3_uc002voo.1_Intron|COL4A3_uc002vop.1_Intron|COL4A3_uc010fxf.1_Missense_Mutation_p.L49M	NM_000091	NP_000082	Q01955	CO4A3_HUMAN	alpha 3 type IV collagen isoform 1 precursor	1633	Collagen IV NC1.				activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound	collagen type IV	extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity			skin(2)|ovary(1)	3		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)										0.048387	-16.254654	10.646575	6	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228175633	228175633	3829	2	C	A	A	A	363	28	COL4A3	2	2
HDAC4	9759	broad.mit.edu	37	2	239975263	239975263	+	Silent	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:239975263G>A	uc002vyk.3	-	c.3108C>T	c.(3106-3108)TCC>TCT	p.S1036S	HDAC4_uc010fyy.2_Silent_p.S993S	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4	1036	Histone deacetylase.				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				0.363636	24.395103	24.75457	8	14	KEEP	---	---	---	---	capture		Silent	SNP	239975263	239975263	7292	2	G	A	A	A	600	47	HDAC4	2	2
CD8B	926	broad.mit.edu	37	2	87073892	87073892	+	Silent	SNP	T	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:87073892T>A	uc002ssa.2	-	c.498A>T	c.(496-498)CCA>CCT	p.P166P	RMND5A_uc002srs.3_Intron|CD8B_uc002srw.2_Silent_p.P166P|CD8B_uc002srx.2_Silent_p.P166P|CD8B_uc002sry.2_Intron|CD8B_uc010fgt.2_Intron|CD8B_uc002srz.2_Silent_p.P166P|CD8B_uc010yto.1_Silent_p.P166P	NM_172099	NP_742097	P10966	CD8B_HUMAN	CD8b antigen isoform 1 precursor	166	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														0.4	13.498611	13.585893	4	6	KEEP	---	---	---	---	capture		Silent	SNP	87073892	87073892	3173	2	T	A	A	A	756	59	CD8B	3	3
LSAMP	4045	broad.mit.edu	37	3	115529219	115529219	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:115529219G>A	uc011bis.1	-	c.1031C>T	c.(1030-1032)GCC>GTC	p.A344V	LSAMP_uc003ebt.2_Missense_Mutation_p.A321V	NM_002338	NP_002329	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein	321					cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)										0.432432	48.794902	48.94208	16	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115529219	115529219	9424	3	G	A	A	A	546	42	LSAMP	2	2
KALRN	8997	broad.mit.edu	37	3	123953741	123953741	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:123953741A>G	uc003ehg.2	+	c.208A>G	c.(208-210)AGA>GGA	p.R70G	KALRN_uc010hrv.1_Missense_Mutation_p.R70G|KALRN_uc003ehf.1_Missense_Mutation_p.R70G|KALRN_uc011bjy.1_Missense_Mutation_p.R70G	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	70	CRAL-TRIO.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)	5										1865				0.65	45.578468	45.974828	13	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123953741	123953741	8279	3	A	G	G	G	36	3	KALRN	4	4
H1FX	8971	broad.mit.edu	37	3	129034608	129034608	+	Silent	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:129034608G>T	uc003elx.2	-	c.138C>A	c.(136-138)GGC>GGA	p.G46G	C3orf47_uc011bkv.1_5'Flank	NM_006026	NP_006017	Q92522	H1X_HUMAN	H1 histone family, member X	46	H15.				nucleosome assembly	nucleosome|nucleus	DNA binding				0														0.5	9.626023	9.626023	3	3	KEEP	---	---	---	---	capture		Silent	SNP	129034608	129034608	7203	3	G	T	T	T	587	46	H1FX	2	2
CACNA1D	776	broad.mit.edu	37	3	53779849	53779849	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:53779849G>T	uc003dgu.3	+	c.3175_splice	c.e26-1	p.G1059_splice	CACNA1D_uc003dgv.3_Splice_Site_SNP_p.G1039_splice|CACNA1D_uc003dgy.3_Splice_Site_SNP_p.G1039_splice|CACNA1D_uc003dgw.3_Splice_Site_SNP_p.G706_splice|CACNA1D_uc003dgx.1_Splice_Site_SNP_p.G187_splice	NM_000720	NP_000711			calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|liver(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)									1	79.987524	79.987524	22	0	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	53779849	53779849	2657	3	G	T	T	T	455	35	CACNA1D	5	2
DAPP1	27071	broad.mit.edu	37	4	100784205	100784205	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:100784205A>T	uc003hvf.3	+	c.576A>T	c.(574-576)GAA>GAT	p.E192D	DAPP1_uc011cek.1_3'UTR|DAPP1_uc010ilh.2_Missense_Mutation_p.E192D	NM_014395	NP_055210	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and	192	PH.				signal transduction	cytoplasm|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|protein tyrosine phosphatase activity				0				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)										0.92	78.713327	83.040274	23	2	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100784205	100784205	4406	4	A	T	T	T	24	2	DAPP1	3	3
MAEA	10296	broad.mit.edu	37	4	1305800	1305800	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:1305800G>A	uc003gda.2	+	c.103G>A	c.(103-105)GCC>ACC	p.A35T	MAEA_uc010ibs.1_Missense_Mutation_p.A35T|MAEA_uc003gdb.2_Missense_Mutation_p.A35T|MAEA_uc011bvb.1_Missense_Mutation_p.A35T|MAEA_uc003gdc.2_Missense_Mutation_p.A35T|MAEA_uc003gdd.2_Non-coding_Transcript|MAEA_uc011bvc.1_Missense_Mutation_p.A34T|MAEA_uc011bvd.1_5'UTR	NM_001017405	NP_001017405	Q7L5Y9	MAEA_HUMAN	macrophage erythroblast attacher isoform 1	35	Extracellular and involved in cell to cell contact.				cell adhesion|cell cycle|cell division|erythrocyte maturation|negative regulation of myeloid cell apoptosis|regulation of mitotic cell cycle	actomyosin contractile ring|integral to plasma membrane|membrane fraction|nuclear matrix|spindle	actin binding			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(23;0.0201)											1	83.064108	83.064108	23	0	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1305800	1305800	9530	4	G	A	A	A	494	38	MAEA	1	1
NAA11	84779	broad.mit.edu	37	4	80246396	80246396	+	Silent	SNP	A	G	G			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:80246396A>G	uc003hlt.3	-	c.636T>C	c.(634-636)TCT>TCC	p.S212S		NM_032693	NP_116082	Q9BSU3	NAA11_HUMAN	alpha-N-acetyltransferase 1B	212						cytoplasm|nucleus	peptide alpha-N-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2														0.956522	72.105035	74.096605	22	1	KEEP	---	---	---	---	capture		Silent	SNP	80246396	80246396	10512	4	A	G	G	G	80	7	NAA11	4	4
SLIT3	6586	broad.mit.edu	37	5	168151488	168151488	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:168151488A>G	uc010jjg.2	-	c.2272T>C	c.(2272-2274)TAC>CAC	p.Y758H	SLIT3_uc003mab.2_Missense_Mutation_p.Y758H	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	758	LRR 17.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)	3	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			Ovarian(29;311 847 10864 17279 24903)								1	8.777257	8.55409	2	0	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168151488	168151488	15239	5	A	G	G	G	182	14	SLIT3	4	4
MTMR12	54545	broad.mit.edu	37	5	32229893	32229893	+	Silent	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:32229893C>T	uc003jhq.2	-	c.2235G>A	c.(2233-2235)GGG>GGA	p.G745G	MTMR12_uc010iuk.2_Silent_p.G691G|MTMR12_uc010iul.2_Silent_p.G635G	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12	745						cytoplasm	phosphatase activity			ovary(1)	1														0.653846	179.149308	180.780472	51	27	KEEP	---	---	---	---	capture		Silent	SNP	32229893	32229893	10334	5	C	T	T	T	275	22	MTMR12	2	2
FOXO3	2309	broad.mit.edu	37	6	108985148	108985148	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:108985148A>T	uc003psk.2	+	c.1112A>T	c.(1111-1113)GAT>GTT	p.D371V	FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_Missense_Mutation_p.D371V|FOXO3_uc011ean.1_Missense_Mutation_p.D151V|FOXO3_uc010kdj.1_Missense_Mutation_p.D151V	NM_201559	NP_963853	O43524	FOXO3_HUMAN	forkhead box O3A	371				D -> E (in Ref. 5; CAA04860).	antral ovarian follicle growth|apoptosis|embryo development|glucose homeostasis|induction of apoptosis|initiation of primordial ovarian follicle growth|insulin receptor signaling pathway|negative regulation of gene-specific transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|oocyte maturation|ovulation from ovarian follicle|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			central_nervous_system(4)|lung(2)	6		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)						42				0.184211	14.80233	18.358003	7	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108985148	108985148	6270	6	A	T	T	T	156	12	FOXO3	3	3
FNDC1	84624	broad.mit.edu	37	6	159653451	159653451	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:159653451C>A	uc010kjv.2	+	c.1907C>A	c.(1906-1908)CCT>CAT	p.P636H	FNDC1_uc010kjw.1_Missense_Mutation_p.P521H	NM_032532	NP_115921	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	636						extracellular region				large_intestine(4)|ovary(3)|central_nervous_system(1)	8		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)										0.434783	58.901317	59.06981	20	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	159653451	159653451	6210	6	C	A	A	A	312	24	FNDC1	2	2
SCIN	85477	broad.mit.edu	37	7	12684300	12684300	+	Silent	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:12684300C>T	uc003ssn.3	+	c.1851C>T	c.(1849-1851)TAC>TAT	p.Y617Y	SCIN_uc010ktt.2_Non-coding_Transcript|SCIN_uc003sso.3_Silent_p.Y370Y	NM_001112706	NP_001106177	Q9Y6U3	ADSV_HUMAN	scinderin isoform 1	617	Ca(2+)-dependent actin binding.				actin filament capping|actin filament severing|actin nucleation|calcium ion-dependent exocytosis|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of megakaryocyte differentiation|positive regulation of secretion|regulation of chondrocyte differentiation	cell cortex|cytoskeleton	1-phosphatidylinositol binding|actin filament binding|calcium ion binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)										0.318182	20.418225	21.064123	7	15	KEEP	---	---	---	---	capture		Silent	SNP	12684300	12684300	14387	7	C	T	T	T	246	19	SCIN	1	1
UNCX	340260	broad.mit.edu	37	7	1273269	1273269	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:1273269C>T	uc011jvw.1	+	c.388C>T	c.(388-390)CCC>TCC	p.P130S		NM_001080461	NP_001073930	A6NJT0	UNC4_HUMAN	UNC homeobox	130	Homeobox.				cell differentiation|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)										0.354839	30.51562	31.091506	11	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1273269	1273269	17557	7	C	T	T	T	390	30	UNCX	2	2
CARD11	84433	broad.mit.edu	37	7	2954949	2954949	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:2954949T>C	uc003smv.2	-	c.2761A>G	c.(2761-2763)ATC>GTC	p.I921V		NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	921					positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|central_nervous_system(1)	48		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)						1492				0.423077	29.220303	29.354253	11	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2954949	2954949	2764	7	T	C	C	C	663	51	CARD11	4	4
PKD1L1	168507	broad.mit.edu	37	7	47969029	47969029	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:47969029G>A	uc003tny.1	-	c.832C>T	c.(832-834)CCT>TCT	p.P278S		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	278	Extracellular (Potential).				cell-cell adhesion	integral to membrane				ovary(7)|breast(1)	8														0.381818	123.621516	124.969704	42	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47969029	47969029	12388	7	G	A	A	A	533	41	PKD1L1	2	2
ZFPM2	23414	broad.mit.edu	37	8	106814171	106814171	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:106814171C>A	uc003ymd.2	+	c.1861C>A	c.(1861-1863)CTT>ATT	p.L621I	ZFPM2_uc011lhs.1_Missense_Mutation_p.L352I	NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2	621					blood coagulation|transcription, DNA-dependent	nucleoplasm	DNA binding|RNA polymerase II transcription factor activity|transcription corepressor activity|transcription repressor activity|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)											0.25	57.427018	63.110228	25	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106814171	106814171	18248	8	C	A	A	A	416	32	ZFPM2	2	2
BLK	640	broad.mit.edu	37	8	11412989	11412989	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:11412989G>T	uc003wty.2	+	c.768G>T	c.(766-768)TGG>TGT	p.W256C	BLK_uc003wtz.2_Missense_Mutation_p.W185C	NM_001715	NP_001706	P51451	BLK_HUMAN	B lymphoid tyrosine kinase	256	Protein kinase.				intracellular protein kinase cascade|positive regulation of insulin secretion|protein phosphorylation		ATP binding|non-membrane spanning protein tyrosine kinase activity			large_intestine(1)|ovary(1)	2			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)						676				0.717391	100.166173	102.111911	33	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11412989	11412989	1469	8	G	T	T	T	533	41	BLK	2	2
TM2D2	83877	broad.mit.edu	37	8	38853916	38853916	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:38853916C>T	uc003xmk.2	-	c.43G>A	c.(43-45)GGC>AGC	p.G15S	ADAM9_uc011lcf.1_5'Flank|ADAM9_uc003xmr.2_5'Flank|ADAM9_uc011lcg.1_5'Flank|ADAM9_uc010lwr.2_5'Flank|TM2D2_uc003xml.2_5'UTR|TM2D2_uc003xmm.2_Intron|TM2D2_uc003xmn.2_Intron|ADAM9_uc003xmo.1_5'Flank|ADAM9_uc003xmp.2_5'Flank	NM_078473	NP_510882	Q9BX73	TM2D2_HUMAN	TM2 domain containing 2 isoform a	15						integral to membrane					0		all_lung(54;0.00338)|Lung NSC(58;0.0133)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)											0.214286	12.140109	14.247992	6	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38853916	38853916	16494	8	C	T	T	T	299	23	TM2D2	1	1
ARFGEF1	10565	broad.mit.edu	37	8	68165702	68165702	+	Silent	SNP	T	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:68165702T>C	uc003xxo.1	-	c.2682A>G	c.(2680-2682)ACA>ACG	p.T894T	ARFGEF1_uc003xxl.1_Silent_p.T348T	NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine	894					exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)							932				0.275	28.905158	30.730893	11	29	KEEP	---	---	---	---	capture		Silent	SNP	68165702	68165702	863	8	T	C	C	C	808	63	ARFGEF1	4	4
TERF1	7013	broad.mit.edu	37	8	73951377	73951377	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:73951377A>G	uc003xzd.2	+	c.1066A>G	c.(1066-1068)AGA>GGA	p.R356G	TERF1_uc003xze.2_Missense_Mutation_p.R336G	NM_017489	NP_059523	P54274	TERF1_HUMAN	telomeric repeat binding factor 1 isoform 1	356	Interaction with RLIM.|Nuclear localization signal (Potential).				activation of caspase activity|age-dependent telomere shortening|cell division|G2/M transition of mitotic cell cycle|induction of apoptosis|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of telomere maintenance via semi-conservative replication|negative regulation of telomere maintenance via telomerase|positive regulation of microtubule polymerization|positive regulation of mitosis|positive regulation of mitotic cell cycle|protein homooligomerization|telomere maintenance via telomerase|telomere maintenance via telomerase|telomere maintenance via telomere shortening	chromosome, telomeric region|cytoplasm|nuclear telomere cap complex|nucleoplasm|nucleus|spindle	caspase activator activity|DNA bending activity|double-stranded telomeric DNA binding|identical protein binding|microtubule binding|protein heterodimerization activity|protein homodimerization activity|telomerase inhibitor activity|telomeric DNA binding			ovary(1)|lung(1)|skin(1)	3	Breast(64;0.218)		Epithelial(68;0.0984)											0.458333	40.224518	40.260571	11	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73951377	73951377	16288	8	A	G	G	G	36	3	TERF1	4	4
WWP1	11059	broad.mit.edu	37	8	87423913	87423913	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:87423913G>A	uc003ydt.2	+	c.871G>A	c.(871-873)GAA>AAA	p.E291K	WWP1_uc010mai.2_Missense_Mutation_p.E67K	NM_007013	NP_008944	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase	291					central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction	cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			liver(1)	1														0.11236	12.293039	25.492675	10	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87423913	87423913	17989	8	G	A	A	A	429	33	WWP1	2	2
SLC26A7	115111	broad.mit.edu	37	8	92307916	92307916	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:92307916G>C	uc003yez.2	+	c.462G>C	c.(460-462)TTG>TTC	p.L154F	SLC26A7_uc003yex.2_Missense_Mutation_p.L154F|SLC26A7_uc003yey.2_Non-coding_Transcript|SLC26A7_uc003yfa.2_Missense_Mutation_p.L154F	NM_134266	NP_599028	Q8TE54	S26A7_HUMAN	solute carrier family 26, member 7 isoform b	154	Helical; (Potential).					basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)											0.308411	82.630184	86.198976	33	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92307916	92307916	15019	8	G	C	C	C	607	47	SLC26A7	3	3
PPAN-P2RY11	692312	broad.mit.edu	37	19	10218222	10218223	+	Frame_Shift_Ins	INS	-	G	G			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10218222_10218223insG	uc002mna.2	+	c.231_232insG	c.(229-234)GCTGGGfs	p.A77fs	PPAN-P2RY11_uc010xla.1_Frame_Shift_Ins_p.A77fs|PPAN_uc002mmz.1_Frame_Shift_Ins_p.A77fs|PPAN_uc002mnb.1_Frame_Shift_Ins_p.A24fs|SNORD105_uc010dwy.1_5'Flank|SNORD105B_uc010dwz.1_5'Flank	NM_001040664	NP_001035754	Q9NQ55	SSF1_HUMAN	PPAN-P2RY11 protein	77_78	Brix.				RNA splicing	nucleolus	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)											0.34			30	57		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	10218222	10218223	12719	19	-	G	G	G	704	55	PPAN-P2RY11	5	5
FBN3	84467	broad.mit.edu	37	19	8182044	8182052	+	Splice_Site_Del	DEL	CCCACCTAC	-	-			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:8182044_8182052delCCCACCTAC	uc002mjf.2	-	c.3586_splice	c.e27+1	p.D1196_splice		NM_032447	NP_115823			fibrillin 3 precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|central_nervous_system(1)|pancreas(1)	8														0.31			23	51		---	---	---	---	capture_indel		Splice_Site_Del	DEL	8182044	8182052	5940	19	CCCACCTAC	-	-	-	326	26	FBN3	5	5
CD207	50489	broad.mit.edu	37	2	71060984	71060984	+	Frame_Shift_Del	DEL	G	-	-			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:71060984_71060984delG	uc002shg.2	-	c.358_358delC	c.(358-360)CGTfs	p.R120fs		NM_015717	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 antigen, langerin	120	Extracellular (Potential).				defense response to virus	endocytic vesicle|integral to membrane	mannose binding			ovary(1)|lung(1)	2														0.42			37	51		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	71060984	71060984	3110	2	G	-	-	-	494	38	CD207	5	5
TNRC18	84629	broad.mit.edu	37	7	5401258	5401259	+	Frame_Shift_Ins	INS	-	GG	GG			TCGA-17-Z058-01	TCGA-17-Z058-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:5401258_5401259insGG	uc003soi.3	-	c.4627_4628insCC	c.(4627-4629)CGCfs	p.R1543fs		NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1543							DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)										0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	5401258	5401259	16880	7	-	GG	GG	GG	351	27	TNRC18	5	5
