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
CALHM1	255022	broad.mit.edu	37	10	105218098	105218098	+	Silent	SNP	T	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:105218098T>G	uc001kxe.2	-	c.411A>C	c.(409-411)GCA>GCC	p.A137A		NM_001001412	NP_001001412	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	137						endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel activity|identical protein binding			ovary(1)	1														0.28125	26.360741	27.737473	9	23	KEEP	---	---	---	---	capture		Silent	SNP	105218098	105218098	2698	10	T	G	G	G	756	59	CALHM1	4	4
C10orf79	80217	broad.mit.edu	37	10	105890011	105890011	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:105890011C>T	uc001kxw.2	-	c.4884G>A	c.(4882-4884)ATG>ATA	p.M1628I	C10orf79_uc009xxq.2_Missense_Mutation_p.M907I	NM_025145	NP_079421	Q8NDM7	WDR96_HUMAN	hypothetical protein LOC80217	1628											0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)										0.186441	22.586581	28.026169	11	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105890011	105890011	1655	10	C	T	T	T	325	25	C10orf79	2	2
ATRNL1	26033	broad.mit.edu	37	10	117093795	117093795	+	Missense_Mutation	SNP	G	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:117093795G>C	uc001lcg.2	+	c.3041G>C	c.(3040-3042)TGC>TCC	p.C1014S	ATRNL1_uc010qsm.1_Intron|ATRNL1_uc010qsn.1_Intron	NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor	1014	Laminin EGF-like 1.|Extracellular (Potential).					integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)										0.066667	-2.21172	6.548637	3	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117093795	117093795	1226	10	G	C	C	C	598	46	ATRNL1	3	3
ITGA8	8516	broad.mit.edu	37	10	15714661	15714661	+	Missense_Mutation	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:15714661G>T	uc001ioc.1	-	c.764C>A	c.(763-765)ACG>AAG	p.T255K	ITGA8_uc010qcb.1_Missense_Mutation_p.T255K	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor	255	Extracellular (Potential).|FG-GAP 4.				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6														0.176471	57.884455	71.244819	24	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15714661	15714661	8186	10	G	T	T	T	520	40	ITGA8	1	1
C10orf68	79741	broad.mit.edu	37	10	33015700	33015700	+	Missense_Mutation	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:33015700G>T	uc001iwm.1	+	c.457G>T	c.(457-459)GTG>TTG	p.V153L	C10orf68_uc001iwl.1_Missense_Mutation_p.V185L|C10orf68_uc001iwn.3_Missense_Mutation_p.V177L|C10orf68_uc010qei.1_Missense_Mutation_p.V104L|C10orf68_uc001iwo.3_5'Flank	NM_024688	NP_078964	Q9H943	CJ068_HUMAN	chromosome 10 open reading frame 68	177										ovary(1)	1														0.3	15.321533	16.050445	6	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33015700	33015700	1650	10	G	T	T	T	468	36	C10orf68	2	2
ANKRD30A	91074	broad.mit.edu	37	10	37438705	37438705	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:37438705C>A	uc001iza.1	+	c.1405C>A	c.(1405-1407)CCT>ACT	p.P469T		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	525					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)	8														0.133333	11.545731	21.460588	10	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37438705	37438705	663	10	C	A	A	A	338	26	ANKRD30A	2	2
P4HA1	5033	broad.mit.edu	37	10	74810876	74810876	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:74810876C>A	uc010qka.1	-	c.835G>T	c.(835-837)GCT>TCT	p.A279S	P4HA1_uc001jtg.2_Missense_Mutation_p.A279S|P4HA1_uc001jth.2_Missense_Mutation_p.A279S|P4HA1_uc010qkb.1_Missense_Mutation_p.A279S|P4HA1_uc001jti.2_Non-coding_Transcript	NM_001142595	NP_001136067	P13674	P4HA1_HUMAN	prolyl 4-hydroxylase, alpha I subunit isoform 2	279					oxidation-reduction process	endoplasmic reticulum lumen|mitochondrion	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity			ovary(1)	1	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	Colon(147;367 2405 2662 52127)								0.155963	60.020413	84.65866	34	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74810876	74810876	11769	10	C	A	A	A	325	25	P4HA1	2	2
ATP5C1	509	broad.mit.edu	37	10	7842009	7842009	+	Missense_Mutation	SNP	A	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:7842009A>T	uc001iju.2	+	c.592A>T	c.(592-594)ACA>TCA	p.T198S	ATP5C1_uc009xiq.1_Missense_Mutation_p.T198S|ATP5C1_uc010qbc.1_Missense_Mutation_p.T149S|ATP5C1_uc001ijv.2_Missense_Mutation_p.T198S	NM_001001973	NP_001001973	P36542	ATPG_HUMAN	ATP synthase, H+ transporting, mitochondrial F1	198					mitochondrial ATP synthesis coupled proton transport|oxidative phosphorylation|respiratory electron transport chain	mitochondrial matrix|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1)	hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism				0						Melanoma(143;1012 1820 16249 30920 33158)								0.176101	54.906328	70.640022	28	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7842009	7842009	1168	10	A	T	T	T	130	10	ATP5C1	3	3
LRIT1	26103	broad.mit.edu	37	10	85993891	85993891	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:85993891G>A	uc001kcz.1	-	c.833C>T	c.(832-834)ACT>ATT	p.T278I		NM_015613	NP_056428	Q9P2V4	LRIT1_HUMAN	retina specific protein PAL	278	Lumenal (Potential).|Ig-like C2-type.					integral to endoplasmic reticulum membrane					0														0.148148	18.884683	28.645603	12	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85993891	85993891	9320	10	G	A	A	A	468	36	LRIT1	2	2
ACCSL	390110	broad.mit.edu	37	11	44080129	44080129	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:44080129C>T	uc001mxw.1	+	c.1504C>T	c.(1504-1506)CTC>TTC	p.L502F	ACCSL_uc009ykr.2_Missense_Mutation_p.L321F	NM_001031854	NP_001027025	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase	502							1-aminocyclopropane-1-carboxylate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(5)	5														0.148437	31.957694	47.049774	19	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44080129	44080129	135	11	C	T	T	T	364	28	ACCSL	2	2
PRDM11	56981	broad.mit.edu	37	11	45246107	45246107	+	Missense_Mutation	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:45246107G>T	uc001myo.2	+	c.1184G>T	c.(1183-1185)GGG>GTG	p.G395V		NM_020229	NP_064614	Q9NQV5	PRD11_HUMAN	PR domain containing 11	395											0						NSCLC(118;1511 1736 6472 36603 43224)								0.185185	44.285879	57.019372	25	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45246107	45246107	12894	11	G	T	T	T	559	43	PRDM11	2	2
OR52N2	390077	broad.mit.edu	37	11	5842280	5842280	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5842280G>A	uc010qzp.1	+	c.715G>A	c.(715-717)GCC>ACC	p.A239T	TRIM5_uc001mbq.1_Intron	NM_001005174	NP_001005174	Q8NGI0	O52N2_HUMAN	olfactory receptor, family 52, subfamily N,	239	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.49e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.074627	-6.086579	18.788096	10	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5842280	5842280	11538	11	G	A	A	A	442	34	OR52N2	2	2
C11orf9	745	broad.mit.edu	37	11	61548502	61548502	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:61548502C>A	uc001nsc.1	+	c.2557C>A	c.(2557-2559)CCC>ACC	p.P853T	C11orf9_uc001nse.1_Missense_Mutation_p.P818T|C11orf9_uc010rll.1_Missense_Mutation_p.P244T	NM_001127392	NP_001120864	Q9Y2G1	MRF_HUMAN	myelin gene regulatory factor isoform 2	853					central nervous system myelination|positive regulation of myelination|positive regulation of transcription, DNA-dependent	integral to membrane|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1														0.27451	35.251475	37.573088	14	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61548502	61548502	1711	11	C	A	A	A	338	26	C11orf9	2	2
CNGA4	1262	broad.mit.edu	37	11	6262815	6262815	+	Nonsense_Mutation	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6262815G>T	uc001mco.2	+	c.1072G>T	c.(1072-1074)GAG>TAG	p.E358*	CNGA4_uc010raa.1_Nonsense_Mutation_p.E127*|CNGA4_uc001mcn.2_Nonsense_Mutation_p.E318*	NM_001037329	NP_001032406	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	358	cNMP.|Cytoplasmic (Potential).				response to stimulus|sensory perception of smell		cAMP binding				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.128205	13.396257	23.903051	10	68	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	6262815	6262815	3737	11	G	T	T	T	533	41	CNGA4	5	2
FOLR1	2348	broad.mit.edu	37	11	71906939	71906939	+	Splice_Site_SNP	SNP	A	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:71906939A>C	uc001orz.1	+	c.494_splice	c.e6-2	p.G165_splice	FOLR1_uc001osa.1_Splice_Site_SNP_p.G165_splice|FOLR1_uc001osb.1_Splice_Site_SNP_p.G165_splice|FOLR1_uc001osc.1_Splice_Site_SNP_p.G165_splice|FOLR1_uc001osd.1_Splice_Site_SNP_p.G165_splice	NM_016724	NP_057936			folate receptor 1 precursor						cell death|folic acid transport|receptor-mediated endocytosis	anchored to membrane|extracellular region|integral to plasma membrane|membrane fraction	folic acid binding|receptor activity			ovary(1)	1														0.188889	37.444685	45.579886	17	73	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	71906939	71906939	6223	11	A	C	C	C	91	7	FOLR1	5	4
ME3	10873	broad.mit.edu	37	11	86267641	86267641	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:86267641C>T	uc001pbz.2	-	c.421G>A	c.(421-423)GTG>ATG	p.V141M	ME3_uc001pca.2_Missense_Mutation_p.V141M|ME3_uc009yvk.2_Missense_Mutation_p.V141M|ME3_uc010rtr.1_Non-coding_Transcript	NM_001014811	NP_001014811	Q16798	MAON_HUMAN	mitochondrial malic enzyme 3 precursor	141					aerobic respiration|malate metabolic process|oxygen metabolic process|pyruvate metabolic process	mitochondrial matrix	malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|metal ion binding|NAD binding			ovary(1)	1		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)			NADH(DB00157)									0.147059	8.262373	12.32335	5	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86267641	86267641	9808	11	C	T	T	T	247	19	ME3	1	1
SBNO1	55206	broad.mit.edu	37	12	123801796	123801796	+	Missense_Mutation	SNP	C	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:123801796C>G	uc010tap.1	-	c.2907G>C	c.(2905-2907)TGG>TGC	p.W969C	SBNO1_uc010tao.1_Missense_Mutation_p.W968C|SBNO1_uc010taq.1_Intron|SBNO1_uc001ues.1_5'Flank	NM_018183	NP_060653	A3KN83	SBNO1_HUMAN	sno, strawberry notch homolog 1	969							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)										0.205479	39.283818	45.15669	15	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123801796	123801796	14343	12	C	G	G	G	390	30	SBNO1	3	3
OVCH1	341350	broad.mit.edu	37	12	29624866	29624866	+	Silent	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:29624866G>T	uc001rix.1	-	c.1725C>A	c.(1723-1725)ATC>ATA	p.I575I		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	575	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)													0.461538	17.84934	17.86579	6	7	KEEP	---	---	---	---	capture		Silent	SNP	29624866	29624866	11736	12	G	T	T	T	473	37	OVCH1	1	1
KCNA1	3736	broad.mit.edu	37	12	5021088	5021088	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5021088G>A	uc001qnh.2	+	c.544G>A	c.(544-546)GTC>ATC	p.V182I		NM_000217	NP_000208	Q09470	KCNA1_HUMAN	potassium voltage-gated channel subfamily A	182	Helical; Name=Segment S1; (Potential).				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)									0.178571	19.323747	24.764356	10	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5021088	5021088	8306	12	G	A	A	A	520	40	KCNA1	1	1
KRT80	144501	broad.mit.edu	37	12	52567409	52567409	+	Missense_Mutation	SNP	T	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52567409T>G	uc001rzw.2	-	c.911A>C	c.(910-912)GAG>GCG	p.E304A	KRT80_uc001rzx.2_Missense_Mutation_p.E269A|KRT80_uc001rzy.2_Missense_Mutation_p.E269A	NM_182507	NP_872313	Q6KB66	K2C80_HUMAN	keratin 80 isoform a	269	Rod.|Coil 2.					keratin filament	structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.108)		GBM(178;2309 2916 15678 35873)								0.190476	21.424822	27.033837	12	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52567409	52567409	8809	12	T	G	G	G	702	54	KRT80	4	4
KCNC2	3747	broad.mit.edu	37	12	75444672	75444672	+	Silent	SNP	A	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:75444672A>C	uc001sxg.1	-	c.1113T>G	c.(1111-1113)CTT>CTG	p.L371L	KCNC2_uc009zry.2_Silent_p.L371L|KCNC2_uc001sxe.2_Silent_p.L371L|KCNC2_uc001sxf.2_Silent_p.L371L|KCNC2_uc010stw.1_Silent_p.L371L	NM_139137	NP_631875	Q96PR1	KCNC2_HUMAN	Shaw-related voltage-gated potassium channel	371	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(2)|pancreas(2)|skin(1)|lung(1)	6														0.2	21.995178	25.329306	8	32	KEEP	---	---	---	---	capture		Silent	SNP	75444672	75444672	8320	12	A	C	C	C	54	5	KCNC2	4	4
NAV3	89795	broad.mit.edu	37	12	78513025	78513025	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:78513025G>A	uc001syp.2	+	c.3049G>A	c.(3049-3051)GAT>AAT	p.D1017N	NAV3_uc001syo.2_Missense_Mutation_p.D1017N|NAV3_uc010sub.1_Missense_Mutation_p.D517N|NAV3_uc009zsf.2_Missense_Mutation_p.D25N	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	1017						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|kidney(1)|pancreas(1)	16										1091				0.234783	65.946708	73.29417	27	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78513025	78513025	10581	12	G	A	A	A	481	37	NAV3	1	1
LUM	4060	broad.mit.edu	37	12	91502247	91502247	+	Silent	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:91502247C>T	uc001tbm.2	-	c.510G>A	c.(508-510)CGG>CGA	p.R170R	LUM_uc001tbn.2_Intron	NM_002345	NP_002336	P51884	LUM_HUMAN	lumican precursor	170	LRR 5.				collagen fibril organization|visual perception	extracellular space|fibrillar collagen	collagen binding|extracellular matrix structural constituent			central_nervous_system(2)	2														0.061728	-6.174637	10.043499	5	76	KEEP	---	---	---	---	capture		Silent	SNP	91502247	91502247	9461	12	C	T	T	T	327	26	LUM	2	2
SERPINA5	5104	broad.mit.edu	37	14	95056618	95056618	+	Missense_Mutation	SNP	T	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:95056618T>A	uc001ydm.2	+	c.860T>A	c.(859-861)CTG>CAG	p.L287Q	SERPINA5_uc010ave.2_Missense_Mutation_p.L287Q|SERPINA3_uc001ydo.3_5'Flank	NM_000624	NP_000615	P05154	IPSP_HUMAN	serine (or cysteine) proteinase inhibitor, clade	287					fusion of sperm to egg plasma membrane|regulation of proteolysis|spermatogenesis	extracellular region|membrane|protein complex	acrosin binding|heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(2)	2				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)									0.4	19.046706	19.177963	6	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95056618	95056618	14580	14	T	A	A	A	715	55	SERPINA5	3	3
SPPL2A	84888	broad.mit.edu	37	15	51040396	51040396	+	Missense_Mutation	SNP	G	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:51040396G>C	uc001zyv.2	-	c.364C>G	c.(364-366)CCT>GCT	p.P122A		NM_032802	NP_116191	Q8TCT8	PSL2_HUMAN	signal peptide peptidase-like 2A	122	Cytoplasmic (Potential).|PA.					integral to membrane	aspartic-type endopeptidase activity				0				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		Melanoma(50;790 1209 4069 22965 33125)								0.25	8.418885	9.100818	3	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51040396	51040396	15601	15	G	C	C	C	533	41	SPPL2A	3	3
FAM154B	283726	broad.mit.edu	37	15	82574861	82574861	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:82574861C>A	uc002bgv.2	+	c.655C>A	c.(655-657)CGT>AGT	p.R219S	FAM154B_uc010unr.1_Missense_Mutation_p.R204S|FAM154B_uc010uns.1_Non-coding_Transcript	NM_001008226	NP_001008227	Q658L1	F154B_HUMAN	hypothetical protein LOC283726	219											0														0.2	18.279485	21.626085	8	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82574861	82574861	5662	15	C	A	A	A	299	23	FAM154B	1	1
SLC5A2	6524	broad.mit.edu	37	16	31500054	31500054	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:31500054G>A	uc002ecf.3	+	c.1241G>A	c.(1240-1242)CGG>CAG	p.R414Q	SLC5A2_uc010car.2_Intron|C16orf58_uc002ecg.2_Non-coding_Transcript	NM_003041	NP_003032	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose	414	Extracellular (Potential).				carbohydrate metabolic process	integral to membrane	low-affinity glucose:sodium symporter activity			ovary(1)	1														0.375	17.949049	18.167329	6	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31500054	31500054	15162	16	G	A	A	A	507	39	SLC5A2	1	1
MYH2	4620	broad.mit.edu	37	17	10428126	10428126	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10428126C>A	uc010coi.2	-	c.4919G>T	c.(4918-4920)CGC>CTC	p.R1640L	MYH2_uc002gmp.3_Missense_Mutation_p.R1640L|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1640	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|lung(1)|kidney(1)	11														0.197802	43.3121	51.038867	18	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10428126	10428126	10430	17	C	A	A	A	351	27	MYH2	1	1
TP53	7157	broad.mit.edu	37	17	7578203	7578203	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7578203C>T	uc002gim.2	-	c.646G>A	c.(646-648)GTG>ATG	p.V216M	TP53_uc002gig.1_Missense_Mutation_p.V216M|TP53_uc002gih.2_Missense_Mutation_p.V216M|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.V84M|TP53_uc010cng.1_Missense_Mutation_p.V84M|TP53_uc002gii.1_Missense_Mutation_p.V84M|TP53_uc010cnh.1_Missense_Mutation_p.V216M|TP53_uc010cni.1_Missense_Mutation_p.V216M|TP53_uc002gij.2_Missense_Mutation_p.V216M|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Missense_Mutation_p.V123M|TP53_uc002gio.2_Missense_Mutation_p.V84M|TP53_uc010vug.1_Missense_Mutation_p.V177M	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	216	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		V -> A (in sporadic cancers; somatic mutation).|V -> E (in sporadic cancers; somatic mutation).|V -> W (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|V -> M (in sporadic cancers; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).|V -> G (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.V216M(46)|p.V216del(8)|p.V216L(7)|p.0?(6)|p.H214fs*5(2)|p.V216fs*6(2)|p.D208fs*1(1)|p.S215_V216insX(1)|p.S215fs*31(1)|p.S215_V218>R(1)|p.T211fs*28(1)|p.V216fs*5(1)|p.V216fs*32(1)|p.D207_V216del10(1)|p.S215fs*27(1)|p.V216fs*33(1)|p.V216_Y220delVVVPY(1)|p.S215fs*29(1)|p.D208_V216delDRNTFRHSV(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	p.V216M(ECC12-Tumor)|p.V216L(LCLC103H-Tumor)|p.V216M(HT-Tumor)|p.V216M(SNU216-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.157895	4.310412	6.435621	3	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7578203	7578203	16923	17	C	T	T	T	221	17	TP53	2	2
ENPP7	339221	broad.mit.edu	37	17	77709193	77709193	+	Missense_Mutation	SNP	A	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:77709193A>T	uc002jxa.2	+	c.751A>T	c.(751-753)ACC>TCC	p.T251S		NM_178543	NP_848638	Q6UWV6	ENPP7_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	251					negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity			central_nervous_system(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)											0.404762	97.021859	97.690497	34	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77709193	77709193	5328	17	A	T	T	T	130	10	ENPP7	3	3
DSG2	1829	broad.mit.edu	37	18	29126289	29126289	+	Silent	SNP	T	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:29126289T>C	uc002kwu.3	+	c.2940T>C	c.(2938-2940)GCT>GCC	p.A980A		NM_001943	NP_001934	Q14126	DSG2_HUMAN	desmoglein 2 preproprotein	980	Desmoglein repeat 4.|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)											0.333333	57.08032	58.385203	18	36	KEEP	---	---	---	---	capture		Silent	SNP	29126289	29126289	4961	18	T	C	C	C	678	53	DSG2	4	4
NETO1	81832	broad.mit.edu	37	18	70461611	70461611	+	Missense_Mutation	SNP	C	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:70461611C>G	uc002lkw.2	-	c.498G>C	c.(496-498)TTG>TTC	p.L166F	NETO1_uc002lkx.1_Missense_Mutation_p.L165F|NETO1_uc002lky.1_Missense_Mutation_p.L166F	NM_138966	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin- and tolloid-like protein 1 isoform 3	166	Extracellular (Potential).				memory|regulation of long-term neuronal synaptic plasticity|visual learning	cell junction|excitatory synapse|extracellular region|integral to membrane|postsynaptic density|postsynaptic membrane	receptor activity			ovary(2)	2		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)										0.163265	33.417827	44.016042	16	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70461611	70461611	10738	18	C	G	G	G	376	29	NETO1	3	3
KEAP1	9817	broad.mit.edu	37	19	10602310	10602310	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10602310C>A	uc002moq.1	-	c.1268G>T	c.(1267-1269)GGC>GTC	p.G423V	KEAP1_uc002mop.1_Missense_Mutation_p.G141V|KEAP1_uc002mor.1_Missense_Mutation_p.G423V	NM_012289	NP_036421	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	423	Kelch 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|midbody|nucleus	protein binding			breast(2)|ovary(1)|pancreas(1)	4			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)											0.166667	7.212593	9.719958	4	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10602310	10602310	8447	19	C	A	A	A	338	26	KEAP1	2	2
ZNF709	163051	broad.mit.edu	37	19	12575444	12575444	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:12575444C>A	uc002mtv.3	-	c.1292G>T	c.(1291-1293)TGT>TTT	p.C431F	ZNF709_uc002mtw.3_Missense_Mutation_p.C399F|ZNF709_uc002mtx.3_Missense_Mutation_p.C431F	NM_152601	NP_689814	Q8N972	ZN709_HUMAN	zinc finger protein 709 isoform a	431	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GBM(33;565 669 12371 29134 51667)								0.107143	19.647091	45.355442	18	150	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12575444	12575444	18709	19	C	A	A	A	221	17	ZNF709	2	2
FFAR3	2865	broad.mit.edu	37	19	35849909	35849909	+	Silent	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:35849909C>T	uc002nzd.2	+	c.117C>T	c.(115-117)TTC>TTT	p.F39F	FFAR3_uc010xsu.1_Non-coding_Transcript	NM_005304	NP_005295	O14843	FFAR3_HUMAN	free fatty acid receptor 3	39	Helical; Name=1; (Potential).					integral to plasma membrane	G-protein coupled receptor activity|lipid binding				0	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)			Esophageal Squamous(185;1742 2042 21963 24215 27871)								0.085714	-0.565473	17.755198	9	96	KEEP	---	---	---	---	capture		Silent	SNP	35849909	35849909	6066	19	C	T	T	T	402	31	FFAR3	1	1
RYR1	6261	broad.mit.edu	37	19	38934235	38934235	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:38934235G>A	uc002oit.2	+	c.308G>A	c.(307-309)GGC>GAC	p.G103D	RYR1_uc002oiu.2_Missense_Mutation_p.G103D	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	103	Cytoplasmic.|MIR 1.				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)									0.138889	8.160651	12.689171	5	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38934235	38934235	14248	19	G	A	A	A	546	42	RYR1	2	2
KLK12	43849	broad.mit.edu	37	19	51532662	51532662	+	Missense_Mutation	SNP	A	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51532662A>G	uc002pvh.1	-	c.643T>C	c.(643-645)TCC>CCC	p.S215P	KLK11_uc002pvd.1_5'Flank|KLK11_uc002pve.1_5'Flank|KLK11_uc002pvf.1_5'Flank|KLK11_uc002pvc.3_5'Flank|KLK11_uc010eom.2_5'Flank|KLK12_uc002pvg.1_Missense_Mutation_p.S215P|KLK12_uc010ycp.1_Non-coding_Transcript|KLK12_uc010ycq.1_Missense_Mutation_p.S105P|KLK12_uc010ycr.1_Missense_Mutation_p.S105P|KLK12_uc010ycs.1_Missense_Mutation_p.S105P|KLK12_uc002pvi.1_Missense_Mutation_p.S215P|KLK12_uc002pvj.1_3'UTR	NM_019598	NP_062544	Q9UKR0	KLK12_HUMAN	kallikrein 12 isoform 1	215	Peptidase S1.				proteolysis	extracellular region|soluble fraction	serine-type endopeptidase activity			ovary(1)	1		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)										0.09375	3.41765	14.028126	6	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51532662	51532662	8714	19	A	G	G	G	130	10	KLK12	4	4
ZNF813	126017	broad.mit.edu	37	19	53994017	53994017	+	Silent	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53994017C>T	uc002qbu.2	+	c.531C>T	c.(529-531)TCC>TCT	p.S177S	ZNF813_uc010eqq.1_Intron	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	177					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)										0.183099	58.827057	72.167132	26	116	KEEP	---	---	---	---	capture		Silent	SNP	53994017	53994017	18773	19	C	T	T	T	275	22	ZNF813	2	2
ZIM2	23619	broad.mit.edu	37	19	57286129	57286129	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57286129C>A	uc002qnr.2	-	c.1511G>T	c.(1510-1512)GGC>GTC	p.G504V	ZIM2_uc010ygq.1_Missense_Mutation_p.G300V|ZIM2_uc010ygr.1_Missense_Mutation_p.G300V|ZIM2_uc002qnq.2_Missense_Mutation_p.G504V|ZIM2_uc010etp.2_Missense_Mutation_p.G504V|ZIM2_uc010ygs.1_Missense_Mutation_p.G504V	NM_015363	NP_056178	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	504	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)										0.148148	14.175205	20.583452	8	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57286129	57286129	18275	19	C	A	A	A	338	26	ZIM2	2	2
PTBP1	5725	broad.mit.edu	37	19	803637	803637	+	Splice_Site_SNP	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:803637G>T	uc002lpp.2	+	c.115_splice	c.e3+1	p.A39_splice	PTBP1_uc002lpq.2_Splice_Site_SNP_p.A39_splice|PTBP1_uc002lpr.2_Splice_Site_SNP_p.A39_splice|PTBP1_uc002lps.2_Intron|PTBP1_uc002lpt.2_Splice_Site_SNP|PTBP1_uc002lpu.1_Splice_Site_SNP_p.A9_splice	NM_002819	NP_002810			polypyrimidine tract-binding protein 1 isoform						nuclear mRNA splicing, via spliceosome	heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	nucleotide binding|poly-pyrimidine tract binding|protein binding			kidney(1)	1		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.069767	-4.567927	12.10388	6	80	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	803637	803637	13179	19	G	T	T	T	572	44	PTBP1	5	2
AADACL3	126767	broad.mit.edu	37	1	12785337	12785337	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:12785337G>A	uc009vnn.1	+	c.427G>A	c.(427-429)GCA>ACA	p.A143T	AADACL3_uc001aug.1_Missense_Mutation_p.A73T	NM_001103170	NP_001096640	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3 isoform 1	143							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)										0.092784	1.079616	17.422994	9	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12785337	12785337	13	1	G	A	A	A	494	38	AADACL3	1	1
LOC649330	649330	broad.mit.edu	37	1	12907473	12907473	+	Missense_Mutation	SNP	G	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:12907473G>C	uc009vno.2	-	c.670C>G	c.(670-672)CAG>GAG	p.Q224E	HNRNPCL1_uc010obf.1_Missense_Mutation_p.Q224E	NM_001146181	NP_001139653	B7ZW38	B7ZW38_HUMAN	heterogeneous nuclear ribonucleoprotein C-like	224							nucleic acid binding|nucleotide binding				0														0.10828	16.149122	40.112096	17	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12907473	12907473	9249	1	G	C	C	C	598	46	LOC649330	3	3
BCL9	607	broad.mit.edu	37	1	147096156	147096156	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:147096156C>A	uc001epq.2	+	c.3677C>A	c.(3676-3678)CCT>CAT	p.P1226H	BCL9_uc010ozr.1_Missense_Mutation_p.P1140H	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	1226	Pro-rich.				Wnt receptor signaling pathway	nucleus	protein binding			large_intestine(2)|ovary(2)	4	all_hematologic(923;0.115)									202				0.097826	5.703075	20.60842	9	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	147096156	147096156	1402	1	C	A	A	A	312	24	BCL9	2	2
CASP9	842	broad.mit.edu	37	1	15834374	15834374	+	Silent	SNP	T	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:15834374T>A	uc001awn.2	-	c.447A>T	c.(445-447)GCA>GCT	p.A149A	CASP9_uc001awm.1_Silent_p.A149A|CASP9_uc001awo.2_Intron|CASP9_uc001awp.2_5'UTR|CASP9_uc009voi.2_5'UTR|CASP9_uc010obm.1_Silent_p.A66A|CASP9_uc001awq.2_Silent_p.A66A	NM_001229	NP_001220	P55211	CASP9_HUMAN	caspase 9 isoform alpha preproprotein	149					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				0.081081	1.998751	15.223822	6	68	KEEP	---	---	---	---	capture		Silent	SNP	15834374	15834374	2798	1	T	A	A	A	704	55	CASP9	3	3
RXRG	6258	broad.mit.edu	37	1	165389184	165389184	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:165389184C>T	uc001gda.2	-	c.365G>A	c.(364-366)GGA>GAA	p.G122E		NM_006917	NP_008848	P48443	RXRG_HUMAN	retinoid X receptor, gamma isoform a	122	Modulating (By similarity).				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)									0.262295	42.886176	45.995257	16	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165389184	165389184	14245	1	C	T	T	T	390	30	RXRG	2	2
TBX19	9095	broad.mit.edu	37	1	168260408	168260408	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:168260408C>T	uc001gfl.2	+	c.214C>T	c.(214-216)CCA>TCA	p.P72S	TBX19_uc001gfj.3_Missense_Mutation_p.P3S	NM_005149	NP_005140	O60806	TBX19_HUMAN	T-box 19	72	T-box.				anatomical structure morphogenesis	nucleus	DNA binding|RNA polymerase II transcription factor activity				0	all_hematologic(923;0.215)													0.164835	59.141296	78.543709	30	152	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168260408	168260408	16180	1	C	T	T	T	390	30	TBX19	2	2
METTL13	51603	broad.mit.edu	37	1	171753362	171753362	+	Silent	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:171753362C>T	uc001ghz.2	+	c.636C>T	c.(634-636)TTC>TTT	p.F212F	METTL13_uc001gia.2_Silent_p.F126F|METTL13_uc001gib.2_Intron|METTL13_uc010pml.1_Silent_p.F211F	NM_015935	NP_057019	Q8N6R0	MTL13_HUMAN	CGI-01 protein isoform 1	212							methyltransferase activity|protein binding			kidney(1)	1														0.207921	47.488771	55.420404	21	80	KEEP	---	---	---	---	capture		Silent	SNP	171753362	171753362	9887	1	C	T	T	T	376	29	METTL13	2	2
KLHL20	27252	broad.mit.edu	37	1	173751319	173751319	+	Missense_Mutation	SNP	A	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:173751319A>G	uc001gjc.2	+	c.1696A>G	c.(1696-1698)ACA>GCA	p.T566A	KLHL20_uc010pmr.1_Missense_Mutation_p.T377A|KLHL20_uc009wwf.2_Missense_Mutation_p.T548A	NM_014458	NP_055273	Q9Y2M5	KLH20_HUMAN	kelch-like 20	566	Kelch 6.				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)								0.033898	-20.186038	7.729574	4	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	173751319	173751319	8687	1	A	G	G	G	26	2	KLHL20	4	4
RC3H1	149041	broad.mit.edu	37	1	173931109	173931109	+	Silent	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:173931109G>A	uc010pmt.1	-	c.1956C>T	c.(1954-1956)AAC>AAT	p.N652N	RC3H1_uc001gju.3_Silent_p.N652N|RC3H1_uc010pms.1_Silent_p.N652N|RC3H1_uc001gjv.2_Silent_p.N652N	NM_172071	NP_742068	Q5TC82	RC3H1_HUMAN	roquin	652	Pro-rich.					cytoplasm	RNA binding|zinc ion binding			ovary(2)	2														0.05814	-7.692117	9.908398	5	81	KEEP	---	---	---	---	capture		Silent	SNP	173931109	173931109	13635	1	G	A	A	A	464	36	RC3H1	2	2
PPP1R15B	84919	broad.mit.edu	37	1	204379080	204379080	+	Missense_Mutation	SNP	T	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:204379080T>C	uc001hav.3	-	c.1460A>G	c.(1459-1461)TAT>TGT	p.Y487C		NM_032833	NP_116222	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	487					regulation of translation					ovary(1)|pancreas(1)	2	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)											0.215686	58.702545	66.304086	22	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	204379080	204379080	12799	1	T	C	C	C	637	49	PPP1R15B	4	4
KCNK2	3776	broad.mit.edu	37	1	215259895	215259895	+	Silent	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:215259895C>A	uc001hkq.2	+	c.231C>A	c.(229-231)GCC>GCA	p.A77A	KCNK2_uc001hko.2_Silent_p.A73A|KCNK2_uc009xdm.2_Non-coding_Transcript|KCNK2_uc001hkp.2_Non-coding_Transcript|KCNK2_uc010pua.1_Non-coding_Transcript|KCNK2_uc001hkr.3_Silent_p.A62A	NM_001017425	NP_001017425	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2 isoform	77	Helical; (Potential).						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)									0.148148	19.262282	28.878074	12	69	KEEP	---	---	---	---	capture		Silent	SNP	215259895	215259895	8371	1	C	A	A	A	262	21	KCNK2	2	2
CAPN9	10753	broad.mit.edu	37	1	230895275	230895275	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:230895275G>A	uc001htz.1	+	c.301G>A	c.(301-303)GCC>ACC	p.A101T	CAPN9_uc009xfg.1_Intron|CAPN9_uc001hua.1_Missense_Mutation_p.A101T	NM_006615	NP_006606	O14815	CAN9_HUMAN	calpain 9 isoform 1	101	Calpain catalytic.				digestion|proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)												0.134615	5.866804	12.569684	7	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	230895275	230895275	2751	1	G	A	A	A	442	34	CAPN9	2	2
EPHB2	2048	broad.mit.edu	37	1	23219500	23219500	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:23219500C>T	uc009vqj.1	+	c.1552C>T	c.(1552-1554)CGC>TGC	p.R518C	EPHB2_uc001bge.2_Missense_Mutation_p.R518C|EPHB2_uc001bgf.2_Missense_Mutation_p.R518C|EPHB2_uc010odu.1_Missense_Mutation_p.R518C	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	518	Fibronectin type-III 2.|Extracellular (Potential).				axon guidance|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)						437				0.224138	26.292569	30.321393	13	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23219500	23219500	5368	1	C	T	T	T	351	27	EPHB2	1	1
RBM34	23029	broad.mit.edu	37	1	235295187	235295187	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:235295187C>A	uc001hwn.2	-	c.1134G>T	c.(1132-1134)AAG>AAT	p.K378N	TOMM20_uc001hwl.2_5'Flank|RBM34_uc001hwo.2_Non-coding_Transcript|ARID4B_uc001hwp.2_Non-coding_Transcript	NM_015014	NP_055829	P42696	RBM34_HUMAN	RNA binding motif protein 34 isoform 1	378						nucleolus	nucleotide binding|RNA binding			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)											0.191781	25.663313	32.211097	14	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	235295187	235295187	13593	1	C	A	A	A	415	32	RBM34	2	2
NLRP3	114548	broad.mit.edu	37	1	247588207	247588207	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247588207G>A	uc001icr.2	+	c.1462G>A	c.(1462-1464)GAC>AAC	p.D488N	NLRP3_uc001ics.2_Missense_Mutation_p.D488N|NLRP3_uc001icu.2_Missense_Mutation_p.D488N|NLRP3_uc001icw.2_Missense_Mutation_p.D488N|NLRP3_uc001icv.2_Missense_Mutation_p.D488N|NLRP3_uc010pyw.1_Missense_Mutation_p.D486N|NLRP3_uc001ict.1_Missense_Mutation_p.D486N	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	488	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				0.166667	9.095607	12.225548	5	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247588207	247588207	10881	1	G	A	A	A	481	37	NLRP3	1	1
EIF3I	8668	broad.mit.edu	37	1	32694336	32694336	+	Silent	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:32694336C>T	uc001bur.3	+	c.648C>T	c.(646-648)GAC>GAT	p.D216D	EIF3I_uc009vuc.2_Silent_p.D216D|EIF3I_uc001bus.2_Silent_p.D168D	NM_003757	NP_003748	Q13347	EIF3I_HUMAN	eukaryotic translation initiation factor 3,	216	WD 4.					cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)				Colon(102;1138 2140 2180 17876)								0.041791	-47.000844	28.548814	14	321	KEEP	---	---	---	---	capture		Silent	SNP	32694336	32694336	5210	1	C	T	T	T	259	20	EIF3I	2	2
DOCK7	85440	broad.mit.edu	37	1	62941485	62941485	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:62941485G>A	uc001daq.2	-	c.5821C>T	c.(5821-5823)CGT>TGT	p.R1941C	DOCK7_uc001dan.2_Missense_Mutation_p.R1804C|DOCK7_uc001dao.2_Missense_Mutation_p.R1802C|DOCK7_uc001dap.2_Missense_Mutation_p.R1921C|DOCK7_uc001dam.2_Missense_Mutation_p.R1123C|DOCK7_uc010oov.1_Missense_Mutation_p.R682C|DOCK7_uc001dar.1_Missense_Mutation_p.R115C	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1952	DHR-2.				activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2														0.18797	57.932638	70.0273	25	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62941485	62941485	4876	1	G	A	A	A	507	39	DOCK7	1	1
ST6GALNAC5	81849	broad.mit.edu	37	1	77510030	77510030	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:77510030G>A	uc001dhi.2	+	c.403G>A	c.(403-405)GTG>ATG	p.V135M	ST6GALNAC5_uc010ori.1_Intron|ST6GALNAC5_uc009wbw.2_Non-coding_Transcript	NM_030965	NP_112227	Q9BVH7	SIA7E_HUMAN	sialyltransferase 7E	135	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	sialyltransferase activity			pancreas(1)	1														0.138889	15.222305	24.281131	10	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77510030	77510030	15745	1	G	A	A	A	520	40	ST6GALNAC5	1	1
SLC2A7	155184	broad.mit.edu	37	1	9064913	9064913	+	Silent	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:9064913G>T	uc009vmo.1	-	c.1218C>A	c.(1216-1218)ACC>ACA	p.T406T		NM_207420	NP_997303	Q6PXP3	GTR7_HUMAN	intestinal facilitative glucose transporter 7	406	Cytoplasmic (Potential).					integral to membrane|plasma membrane	sugar transmembrane transporter activity				0	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)										0.217391	11.761856	13.456238	5	18	KEEP	---	---	---	---	capture		Silent	SNP	9064913	9064913	15047	1	G	T	T	T	496	39	SLC2A7	1	1
DEFB123	245936	broad.mit.edu	37	20	30037860	30037860	+	Silent	SNP	T	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:30037860T>C	uc002wvy.2	+	c.87T>C	c.(85-87)TAT>TAC	p.Y29Y		NM_153324	NP_697019	Q8N688	DB123_HUMAN	defensin, beta 123 precursor	29					defense response to bacterium	extracellular region					0	Lung NSC(7;0.000139)|all_lung(7;0.000197)|all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)											0.132075	18.373747	32.323636	14	92	KEEP	---	---	---	---	capture		Silent	SNP	30037860	30037860	4586	20	T	C	C	C	660	51	DEFB123	4	4
TOP1	7150	broad.mit.edu	37	20	39741460	39741460	+	Silent	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:39741460G>A	uc002xjl.2	+	c.1347G>A	c.(1345-1347)CGG>CGA	p.R449R		NM_003286	NP_003277	P11387	TOP1_HUMAN	DNA topoisomerase I	449					DNA topological change|DNA unwinding involved in replication|interspecies interaction between organisms|phosphorylation|programmed cell death|response to drug	chromosome|nucleolus|nucleoplasm	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity|protein binding			breast(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Topotecan(DB01030)					252				0.157895	5.21411	7.333661	3	16	KEEP	---	---	---	---	capture		Silent	SNP	39741460	39741460	16905	20	G	A	A	A	535	42	TOP1	2	2
SULF2	55959	broad.mit.edu	37	20	46307439	46307439	+	Missense_Mutation	SNP	T	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:46307439T>G	uc002xto.2	-	c.1174A>C	c.(1174-1176)ACG>CCG	p.T392P	SULF2_uc002xtr.2_Missense_Mutation_p.T392P|SULF2_uc002xtq.2_Missense_Mutation_p.T392P	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor	392					bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)	5										709				0.16	47.017423	63.522272	24	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46307439	46307439	15891	20	T	G	G	G	767	59	SULF2	4	4
ZNF831	128611	broad.mit.edu	37	20	57771017	57771017	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:57771017C>T	uc002yan.2	+	c.3832C>T	c.(3832-3834)CGT>TGT	p.R1278C		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1278						intracellular	nucleic acid binding|zinc ion binding			ovary(1)|skin(1)	2	all_lung(29;0.0085)													0.118644	17.880069	34.722967	14	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57771017	57771017	18784	20	C	T	T	T	403	31	ZNF831	1	1
C20orf196	149840	broad.mit.edu	37	20	5843983	5843983	+	Silent	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:5843983C>A	uc002wmf.2	+	c.492C>A	c.(490-492)TCC>TCA	p.S164S		NM_152504	NP_689717	Q8IYI0	CT196_HUMAN	hypothetical protein LOC149840	164											0														0.155844	20.772585	29.465201	12	65	KEEP	---	---	---	---	capture		Silent	SNP	5843983	5843983	2179	20	C	A	A	A	262	21	C20orf196	2	2
PRPF6	24148	broad.mit.edu	37	20	62664298	62664298	+	Silent	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62664298C>T	uc002yho.2	+	c.2778C>T	c.(2776-2778)ATC>ATT	p.I926I	PRPF6_uc002yhp.2_Silent_p.I886I|NCRNA00176_uc002yhq.2_5'Flank|NCRNA00176_uc011abq.1_5'Flank	NM_012469	NP_036601	O94906	PRP6_HUMAN	PRP6 pre-mRNA processing factor 6 homolog	926					assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)													0.083333	0.811098	9.236357	4	44	KEEP	---	---	---	---	capture		Silent	SNP	62664298	62664298	13017	20	C	T	T	T	395	31	PRPF6	1	1
USP25	29761	broad.mit.edu	37	21	17205774	17205774	+	Missense_Mutation	SNP	G	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:17205774G>C	uc011aby.1	+	c.2101G>C	c.(2101-2103)GAA>CAA	p.E701Q	USP25_uc002yjy.1_Missense_Mutation_p.E701Q|USP25_uc002yjz.1_Missense_Mutation_p.E701Q|USP25_uc010gla.1_Intron	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	686	Potential.				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)										0.156863	17.467438	23.196197	8	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17205774	17205774	17619	21	G	C	C	C	429	33	USP25	3	3
CECR2	27443	broad.mit.edu	37	22	18022446	18022446	+	Missense_Mutation	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:18022446G>T	uc010gqw.1	+	c.2548G>T	c.(2548-2550)GGG>TGG	p.G850W	CECR2_uc010gqv.1_Missense_Mutation_p.G709W|CECR2_uc002zml.2_Missense_Mutation_p.G709W	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	892					chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)										0.211538	24.531855	28.507544	11	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18022446	18022446	3339	22	G	T	T	T	559	43	CECR2	2	2
IL18RAP	8807	broad.mit.edu	37	2	103061650	103061650	+	Missense_Mutation	SNP	A	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:103061650A>G	uc002tbx.2	+	c.922A>G	c.(922-924)ATT>GTT	p.I308V	IL18RAP_uc010fiz.2_Missense_Mutation_p.I166V	NM_003853	NP_003844	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	308	Ig-like C2-type 2.|Extracellular (Potential).				cell surface receptor linked signaling pathway|inflammatory response|innate immune response	integral to membrane	transmembrane receptor activity			ovary(2)	2														0.166667	11.827404	15.621322	6	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103061650	103061650	7949	2	A	G	G	G	208	16	IL18RAP	4	4
CKAP2L	150468	broad.mit.edu	37	2	113500284	113500284	+	Missense_Mutation	SNP	T	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:113500284T>A	uc002tie.2	-	c.1821A>T	c.(1819-1821)GAA>GAT	p.E607D	CKAP2L_uc002tif.2_Missense_Mutation_p.E196D|CKAP2L_uc010yxp.1_Missense_Mutation_p.E442D	NM_152515	NP_689728	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	607											0														0.333333	36.461041	37.420949	13	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113500284	113500284	3579	2	T	A	A	A	725	56	CKAP2L	3	3
FAM123C	205147	broad.mit.edu	37	2	131520541	131520541	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:131520541C>T	uc002trw.2	+	c.896C>T	c.(895-897)GCC>GTC	p.A299V	FAM123C_uc010fmv.2_Missense_Mutation_p.A299V|FAM123C_uc010fms.1_Missense_Mutation_p.A299V|FAM123C_uc010fmt.1_Missense_Mutation_p.A299V|FAM123C_uc010fmu.1_Missense_Mutation_p.A299V	NM_152698	NP_689911	Q8N944	F123C_HUMAN	hypothetical protein LOC205147	299										pancreas(2)|ovary(1)	3	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.13)										0.188679	20.218391	25.027554	10	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131520541	131520541	5621	2	C	T	T	T	338	26	FAM123C	2	2
THSD7B	80731	broad.mit.edu	37	2	138414680	138414680	+	Missense_Mutation	SNP	A	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:138414680A>G	uc002tva.1	+	c.4238A>G	c.(4237-4239)AAT>AGT	p.N1413S	THSD7B_uc010zbj.1_Non-coding_Transcript	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)										0.140351	14.06792	21.188932	8	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	138414680	138414680	16408	2	A	G	G	G	52	4	THSD7B	4	4
LRP1B	53353	broad.mit.edu	37	2	141259382	141259382	+	Silent	SNP	A	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141259382A>C	uc002tvj.1	-	c.8724T>G	c.(8722-8724)GGT>GGG	p.G2908G		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2908	Extracellular (Potential).|LDL-receptor class A 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)			0.1	0.091897	6.477088	4	36	KEEP	---	---	---	---	capture		Silent	SNP	141259382	141259382	9328	2	A	C	C	C	119	10	LRP1B	4	4
XIRP2	129446	broad.mit.edu	37	2	168103381	168103381	+	Missense_Mutation	SNP	A	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168103381A>G	uc002udx.2	+	c.5479A>G	c.(5479-5481)ACA>GCA	p.T1827A	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.T1652A|XIRP2_uc010fpq.2_Missense_Mutation_p.T1605A|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1652					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.073529	0.452089	13.133047	5	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168103381	168103381	18011	2	A	G	G	G	182	14	XIRP2	4	4
XIRP2	129446	broad.mit.edu	37	2	168104724	168104724	+	Missense_Mutation	SNP	C	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168104724C>G	uc002udx.2	+	c.6822C>G	c.(6820-6822)ATC>ATG	p.I2274M	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.I2099M|XIRP2_uc010fpq.2_Missense_Mutation_p.I2052M|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	2099					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.208333	24.919766	28.705777	10	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168104724	168104724	18011	2	C	G	G	G	369	29	XIRP2	3	3
EPHA4	2043	broad.mit.edu	37	2	222307631	222307631	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:222307631C>A	uc002vmq.2	-	c.1992G>T	c.(1990-1992)AGG>AGT	p.R664S	EPHA4_uc002vmr.2_Missense_Mutation_p.R664S|EPHA4_uc010zlm.1_Missense_Mutation_p.R605S|EPHA4_uc010zln.1_Missense_Mutation_p.R664S	NM_004438	NP_004429	P54764	EPHA4_HUMAN	ephrin receptor EphA4 precursor	664	Protein kinase.|Cytoplasmic (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			lung(3)|large_intestine(2)|central_nervous_system(2)|urinary_tract(1)|skin(1)	9		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)						395				0.066667	-9.160735	11.36748	7	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	222307631	222307631	5362	2	C	A	A	A	389	30	EPHA4	2	2
LTBP1	4052	broad.mit.edu	37	2	33246130	33246130	+	Silent	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:33246130C>A	uc002ros.2	+	c.720C>A	c.(718-720)TCC>TCA	p.S240S		NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	240					negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|lung(1)|central_nervous_system(1)	7	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)												0.09697	5.676089	32.767086	16	149	KEEP	---	---	---	---	capture		Silent	SNP	33246130	33246130	9449	2	C	A	A	A	301	24	LTBP1	2	2
SOS1	6654	broad.mit.edu	37	2	39281778	39281778	+	Missense_Mutation	SNP	T	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:39281778T>A	uc002rrk.3	-	c.697A>T	c.(697-699)AAT>TAT	p.N233Y	SOS1_uc010ynr.1_Non-coding_Transcript|SOS1_uc002rrl.2_5'Flank	NM_005633	NP_005624	Q07889	SOS1_HUMAN	son of sevenless homolog 1	233	DH.				apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|lung(1)|central_nervous_system(1)	6		all_hematologic(82;0.21)							p.N233Y(OCIAML5-Tumor)|p.N233Y(LXF289-Tumor)	444				0.071429	-1.842835	8.754033	4	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39281778	39281778	15436	2	T	A	A	A	819	63	SOS1	3	3
KIDINS220	57498	broad.mit.edu	37	2	8890421	8890421	+	Missense_Mutation	SNP	A	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:8890421A>T	uc002qzc.2	-	c.3235T>A	c.(3235-3237)TAC>AAC	p.Y1079N	KIDINS220_uc010yiv.1_Missense_Mutation_p.Y845N|KIDINS220_uc002qzd.2_Missense_Mutation_p.Y1037N|KIDINS220_uc010yiw.1_Missense_Mutation_p.Y1080N|KIDINS220_uc002qzb.2_5'UTR|KIDINS220_uc002qze.2_Missense_Mutation_p.Y84N	NM_020738	NP_065789	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate of 220 kDa	1079	Cytoplasmic (Potential).				activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)													0.232143	33.860176	37.529747	13	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8890421	8890421	8582	2	A	T	T	T	182	14	KIDINS220	3	3
SEMA4C	54910	broad.mit.edu	37	2	97529783	97529783	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:97529783C>A	uc002sxg.3	-	c.1369G>T	c.(1369-1371)GTG>TTG	p.V457L	SEMA4C_uc002sxf.3_5'Flank|SEMA4C_uc002sxe.2_5'Flank|SEMA4C_uc002sxh.3_Missense_Mutation_p.V404L	NM_017789	NP_060259	Q9C0C4	SEM4C_HUMAN	semaphorin 4C precursor	404	Extracellular (Potential).|Dominant negative effect on myogenic differentiation (By similarity).|Sema.				muscle cell differentiation|nervous system development|positive regulation of stress-activated MAPK cascade	cell junction|integral to membrane|postsynaptic density|postsynaptic membrane|synaptic vesicle membrane	receptor activity			skin(1)	1														0.324324	34.788528	35.801273	12	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97529783	97529783	14519	2	C	A	A	A	234	18	SEMA4C	2	2
CNTN4	152330	broad.mit.edu	37	3	2908581	2908581	+	Silent	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:2908581G>T	uc003bpc.2	+	c.600G>T	c.(598-600)GTG>GTT	p.V200V	CNTN4_uc003bpb.1_5'UTR|CNTN4_uc003bpd.1_Silent_p.V200V	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	200	Ig-like C2-type 2.				axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)										0.104478	2.877969	13.321525	7	60	KEEP	---	---	---	---	capture		Silent	SNP	2908581	2908581	3781	3	G	T	T	T	574	45	CNTN4	2	2
RBM5	10181	broad.mit.edu	37	3	50145581	50145581	+	Splice_Site_SNP	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:50145581G>A	uc003cyg.2	+	c.1119_splice	c.e13+1	p.Q373_splice	RBM5_uc011bdj.1_Splice_Site_SNP_p.Q317_splice|RBM5_uc011bdk.1_Splice_Site_SNP_p.Q201_splice	NM_005778	NP_005769			RNA binding motif protein 5						apoptosis|negative regulation of cell proliferation|positive regulation of apoptosis|regulation of alternative nuclear mRNA splicing, via spliceosome|spliceosome assembly	nucleoplasm|spliceosomal complex	DNA binding|mRNA binding|nucleotide binding|protein binding|zinc ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)										0.142857	15.068003	22.78215	9	54	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	50145581	50145581	13605	3	G	A	A	A	572	44	RBM5	5	2
RBM5	10181	broad.mit.edu	37	3	50154766	50154766	+	Missense_Mutation	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:50154766G>T	uc003cyg.2	+	c.2276G>T	c.(2275-2277)GGC>GTC	p.G759V	RBM5_uc011bdj.1_Missense_Mutation_p.G703V|RBM5_uc011bdk.1_Missense_Mutation_p.G587V|RBM5_uc003cyh.2_Missense_Mutation_p.G216V	NM_005778	NP_005769	P52756	RBM5_HUMAN	RNA binding motif protein 5	759	G-patch.|Required for interaction with U2AF2.				apoptosis|negative regulation of cell proliferation|positive regulation of apoptosis|regulation of alternative nuclear mRNA splicing, via spliceosome|spliceosome assembly	nucleoplasm|spliceosomal complex	DNA binding|mRNA binding|nucleotide binding|protein binding|zinc ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)										0.066667	-6.589402	10.910726	6	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50154766	50154766	13605	3	G	T	T	T	546	42	RBM5	2	2
GUCY1A3	2982	broad.mit.edu	37	4	156631937	156631937	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:156631937C>T	uc003iov.2	+	c.620C>T	c.(619-621)CCT>CTT	p.P207L	GUCY1A3_uc003iou.2_Missense_Mutation_p.P207L|GUCY1A3_uc010iqc.2_Missense_Mutation_p.P207L|GUCY1A3_uc003iow.2_Missense_Mutation_p.P207L|GUCY1A3_uc010iqd.2_Missense_Mutation_p.P206L|GUCY1A3_uc003iox.2_Missense_Mutation_p.P207L|GUCY1A3_uc003ioz.2_5'UTR|GUCY1A3_uc003ioy.2_Missense_Mutation_p.P207L|GUCY1A3_uc010iqe.2_5'UTR|GUCY1A3_uc003ipa.2_Intron|GUCY1A3_uc003ipb.2_Missense_Mutation_p.P207L	NM_000856	NP_000847	Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3 isoform A	207					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)										0.079365	1.623492	13.002545	5	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156631937	156631937	7174	4	C	T	T	T	312	24	GUCY1A3	2	2
AMBN	258	broad.mit.edu	37	4	71464085	71464085	+	Silent	SNP	T	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:71464085T>C	uc003hfl.2	+	c.148T>C	c.(148-150)TTG>CTG	p.L50L		NM_016519	NP_057603	Q9NP70	AMBN_HUMAN	ameloblastin precursor	50					bone mineralization|cell adhesion|cell proliferation|odontogenesis of dentine-containing tooth	proteinaceous extracellular matrix	growth factor activity|structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)											0.076923	0.959657	12.835713	5	60	KEEP	---	---	---	---	capture		Silent	SNP	71464085	71464085	566	4	T	C	C	C	777	60	AMBN	4	4
CDH10	1008	broad.mit.edu	37	5	24491685	24491685	+	Missense_Mutation	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:24491685C>A	uc003jgr.1	-	c.1876G>T	c.(1876-1878)GTT>TTT	p.V626F	CDH10_uc011cnu.1_Non-coding_Transcript	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	626	Helical; (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)										0.223684	41.134579	46.469434	17	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24491685	24491685	3225	5	C	A	A	A	286	22	CDH10	2	2
HCN1	348980	broad.mit.edu	37	5	45396782	45396782	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:45396782C>T	uc003jok.2	-	c.1042G>A	c.(1042-1044)GCA>ACA	p.A348T		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	348						integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1														0.130952	14.181482	25.219333	11	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45396782	45396782	7278	5	C	T	T	T	351	27	HCN1	1	1
ADCY2	108	broad.mit.edu	37	5	7520955	7520955	+	Silent	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:7520955C>T	uc003jdz.1	+	c.513C>T	c.(511-513)ATC>ATT	p.I171I		NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	171	Helical; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)	6														0.074468	-1.941155	15.526761	7	87	KEEP	---	---	---	---	capture		Silent	SNP	7520955	7520955	295	5	C	T	T	T	395	31	ADCY2	1	1
VCAN	1462	broad.mit.edu	37	5	82834850	82834850	+	Missense_Mutation	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82834850G>T	uc003kii.3	+	c.6028G>T	c.(6028-6030)GGC>TGC	p.G2010C	VCAN_uc003kij.3_Missense_Mutation_p.G1023C|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Missense_Mutation_p.G674C	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	2010	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)										0.147059	8.614406	12.63273	5	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82834850	82834850	17703	5	G	T	T	T	559	43	VCAN	2	2
VCAN	1462	broad.mit.edu	37	5	82835757	82835757	+	Missense_Mutation	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82835757G>T	uc003kii.3	+	c.6935G>T	c.(6934-6936)GGA>GTA	p.G2312V	VCAN_uc003kij.3_Missense_Mutation_p.G1325V|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Missense_Mutation_p.G976V	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	2312	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)										0.186441	18.599456	24.031218	11	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82835757	82835757	17703	5	G	T	T	T	533	41	VCAN	2	2
SYNE1	23345	broad.mit.edu	37	6	152615182	152615182	+	Silent	SNP	G	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:152615182G>C	uc010kiw.2	-	c.17763C>G	c.(17761-17763)TCC>TCG	p.S5921S	SYNE1_uc010kiv.2_Silent_p.S445S|SYNE1_uc003qos.3_Silent_p.S445S|SYNE1_uc003qot.3_Silent_p.S5850S|SYNE1_uc003qou.3_Silent_p.S5921S|SYNE1_uc010kiy.1_Silent_p.S96S	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5921	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|ovary(8)|large_intestine(5)|pancreas(2)	30		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)										0.27451	36.425183	38.762936	14	37	KEEP	---	---	---	---	capture		Silent	SNP	152615182	152615182	15966	6	G	C	C	C	548	43	SYNE1	3	3
PGK2	5232	broad.mit.edu	37	6	49754110	49754110	+	Missense_Mutation	SNP	T	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:49754110T>G	uc003ozu.2	-	c.791A>C	c.(790-792)AAG>ACG	p.K264T		NM_138733	NP_620061	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	264					glycolysis	cytosol	ATP binding|phosphoglycerate kinase activity			ovary(1)	1	Lung NSC(77;0.0402)													0.051724	-15.03318	9.703913	6	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49754110	49754110	12214	6	T	G	G	G	728	56	PGK2	4	4
COL19A1	1310	broad.mit.edu	37	6	70881870	70881870	+	Silent	SNP	A	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:70881870A>C	uc003pfc.1	+	c.2583A>C	c.(2581-2583)GCA>GCC	p.A861A		NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	861	Triple-helical region 5 (COL5).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4														0.222222	23.783497	26.33645	8	28	KEEP	---	---	---	---	capture		Silent	SNP	70881870	70881870	3814	6	A	C	C	C	54	5	COL19A1	4	4
MUC17	140453	broad.mit.edu	37	7	100680433	100680433	+	Silent	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100680433C>T	uc003uxp.1	+	c.5736C>T	c.(5734-5736)GAC>GAT	p.D1912D	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1912	Extracellular (Potential).|30.|59 X approximate tandem repeats.|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)													0.047393	-24.958775	21.006571	10	201	KEEP	---	---	---	---	capture		Silent	SNP	100680433	100680433	10368	7	C	T	T	T	246	19	MUC17	1	1
PIK3CG	5294	broad.mit.edu	37	7	106508507	106508507	+	Silent	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:106508507C>T	uc003vdv.3	+	c.501C>T	c.(499-501)AAC>AAT	p.N167N	PIK3CG_uc003vdu.2_Silent_p.N167N|PIK3CG_uc003vdw.2_Silent_p.N167N	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	167					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				0.121212	4.581053	9.218805	4	29	KEEP	---	---	---	---	capture		Silent	SNP	106508507	106508507	12340	7	C	T	T	T	246	19	PIK3CG	1	1
RNF148	378925	broad.mit.edu	37	7	122342159	122342159	+	Nonsense_Mutation	SNP	T	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:122342159T>A	uc003vkk.1	-	c.646A>T	c.(646-648)AGA>TGA	p.R216*	CADPS2_uc010lkp.2_Intron|CADPS2_uc010lkq.2_Intron|RNF133_uc003vkj.1_5'Flank|RNF148_uc010lkr.1_Intron	NM_198085	NP_932351	Q8N7C7	RN148_HUMAN	ring finger protein 148 precursor	216						integral to membrane	zinc ion binding				0														0.05	-8.368515	8.814971	4	76	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	122342159	122342159	13926	7	T	A	A	A	687	53	RNF148	5	3
MGAM	8972	broad.mit.edu	37	7	141740570	141740570	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:141740570G>A	uc003vwy.2	+	c.2422G>A	c.(2422-2424)GGA>AGA	p.G808R		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	808	Lumenal (Potential).|Maltase.				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)									0.166667	11.426388	15.219881	6	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141740570	141740570	9931	7	G	A	A	A	611	47	MGAM	2	2
OR9A2	135924	broad.mit.edu	37	7	142723355	142723355	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142723355G>A	uc003wcc.1	-	c.865C>T	c.(865-867)CGG>TGG	p.R289W		NM_001001658	NP_001001658	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A,	289	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Melanoma(164;0.059)													0.2	22.032138	26.210275	10	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142723355	142723355	11659	7	G	A	A	A	480	37	OR9A2	1	1
PKD1L1	168507	broad.mit.edu	37	7	47942012	47942012	+	Silent	SNP	T	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:47942012T>G	uc003tny.1	-	c.2028A>C	c.(2026-2028)CCA>CCC	p.P676P		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	676	Extracellular (Potential).|REJ.				cell-cell adhesion	integral to membrane				ovary(7)|breast(1)	8														0.16129	3.158269	6.572654	5	26	KEEP	---	---	---	---	capture		Silent	SNP	47942012	47942012	12388	7	T	G	G	G	756	59	PKD1L1	4	4
CSMD3	114788	broad.mit.edu	37	8	114326834	114326834	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:114326834C>T	uc003ynu.2	-	c.367G>A	c.(367-369)GAT>AAT	p.D123N	CSMD3_uc003ynt.2_Missense_Mutation_p.D83N|CSMD3_uc011lhx.1_Missense_Mutation_p.D123N|CSMD3_uc010mcx.1_Missense_Mutation_p.D123N|CSMD3_uc003ynx.3_Missense_Mutation_p.D123N	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	123	Extracellular (Potential).|CUB 1.					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)			0.169231	22.889295	29.616776	11	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114326834	114326834	4087	8	C	T	T	T	377	29	CSMD3	2	2
CSMD3	114788	broad.mit.edu	37	8	114326898	114326898	+	Silent	SNP	A	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:114326898A>G	uc003ynu.2	-	c.303T>C	c.(301-303)AAT>AAC	p.N101N	CSMD3_uc003ynt.2_Silent_p.N61N|CSMD3_uc011lhx.1_Silent_p.N101N|CSMD3_uc010mcx.1_Silent_p.N101N|CSMD3_uc003ynx.3_Silent_p.N101N	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	101	Extracellular (Potential).|CUB 1.					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)			0.133333	28.128185	43.813275	16	104	KEEP	---	---	---	---	capture		Silent	SNP	114326898	114326898	4087	8	A	G	G	G	206	16	CSMD3	4	4
FER1L6	654463	broad.mit.edu	37	8	124998366	124998366	+	Missense_Mutation	SNP	T	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:124998366T>C	uc003yqw.2	+	c.1469T>C	c.(1468-1470)ATG>ACG	p.M490T		NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	490	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)											0.155844	19.396381	28.094188	12	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124998366	124998366	6052	8	T	C	C	C	663	51	FER1L6	4	4
EXTL3	2137	broad.mit.edu	37	8	28574075	28574075	+	Missense_Mutation	SNP	G	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:28574075G>A	uc003xgz.1	+	c.499G>A	c.(499-501)GGC>AGC	p.G167S		NM_001440	NP_001431	O43909	EXTL3_HUMAN	exostoses-like 3	167	Lumenal (Potential).					integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding|protein binding				0		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)										0.216667	30.0559	34.489944	13	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28574075	28574075	5521	8	G	A	A	A	507	39	EXTL3	1	1
TLR4	7099	broad.mit.edu	37	9	120476501	120476501	+	Missense_Mutation	SNP	G	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:120476501G>C	uc004bjz.2	+	c.2095G>C	c.(2095-2097)GGG>CGG	p.G699R	TLR4_uc004bka.2_Missense_Mutation_p.G659R|TLR4_uc004bkb.2_Missense_Mutation_p.G499R	NM_138554	NP_612564	O00206	TLR4_HUMAN	toll-like receptor 4 precursor	699	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				0.169811	18.541367	24.00987	9	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120476501	120476501	16483	9	G	C	C	C	455	35	TLR4	3	3
OR1L8	138881	broad.mit.edu	37	9	125330105	125330105	+	Missense_Mutation	SNP	A	G	G			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125330105A>G	uc004bmp.1	-	c.652T>C	c.(652-654)TCT>CCT	p.S218P		NM_001004454	NP_001004454	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L,	218	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3														0.263158	14.466327	15.430148	5	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125330105	125330105	11373	9	A	G	G	G	143	11	OR1L8	4	4
TIMM8A	1678	broad.mit.edu	37	X	100601582	100601582	+	Missense_Mutation	SNP	C	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:100601582C>T	uc004ehd.2	-	c.199G>A	c.(199-201)GTT>ATT	p.V67I		NM_004085	NP_004076	O60220	TIM8A_HUMAN	translocase of inner mitochondrial membrane 8	67					nervous system development|protein import into mitochondrial inner membrane|transmembrane transport	mitochondrial inner membrane|mitochondrial intermembrane space protein transporter complex	protein binding				0														0.201299	67.874735	80.639509	31	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100601582	100601582	16443	23	C	T	T	T	247	19	TIMM8A	1	1
FRMPD4	9758	broad.mit.edu	37	X	12736241	12736241	+	Missense_Mutation	SNP	G	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:12736241G>T	uc004cuz.1	+	c.3296G>T	c.(3295-3297)GGT>GTT	p.G1099V	FRMPD4_uc011mij.1_Missense_Mutation_p.G1091V	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	1099					positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13														0.176471	35.594686	45.665627	18	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12736241	12736241	6309	23	G	T	T	T	572	44	FRMPD4	2	2
USP26	83844	broad.mit.edu	37	X	132161641	132161641	+	Missense_Mutation	SNP	T	C	C			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:132161641T>C	uc010nrm.1	-	c.608A>G	c.(607-609)TAC>TGC	p.Y203C	USP26_uc011mvf.1_Missense_Mutation_p.Y203C	NM_031907	NP_114113	Q9BXU7	UBP26_HUMAN	ubiquitin-specific protease 26	203					protein deubiquitination|ubiquitin-dependent protein catabolic process	nucleus	cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity			central_nervous_system(3)|kidney(1)|liver(1)	5	Acute lymphoblastic leukemia(192;0.000127)					NSCLC(104;342 1621 36940 47097 52632)								0.236111	47.946854	52.524703	17	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132161641	132161641	17620	23	T	C	C	C	741	57	USP26	4	4
ABCB7	22	broad.mit.edu	37	X	74288884	74288884	+	Silent	SNP	C	A	A			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:74288884C>A	uc004ebz.2	-	c.1620G>T	c.(1618-1620)GTG>GTT	p.V540V	ABCB7_uc004eca.2_Silent_p.V539V|ABCB7_uc011mqn.1_Silent_p.V513V|ABCB7_uc010nls.2_Silent_p.V500V|ABCB7_uc010nlt.2_Silent_p.V499V	NM_004299	NP_004290	O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B, member 7	539	ABC transporter.				cellular iron ion homeostasis	integral to membrane|mitochondrial inner membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|heme transporter activity			ovary(1)	1														0.189781	53.598471	65.95622	26	111	KEEP	---	---	---	---	capture		Silent	SNP	74288884	74288884	47	23	C	A	A	A	366	29	ABCB7	2	2
PIGB	9488	broad.mit.edu	37	15	55631502	55631503	+	Frame_Shift_Ins	INS	-	T	T			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:55631502_55631503insT	uc002act.2	+	c.832_833insT	c.(832-834)ATTfs	p.I278fs	PIGB_uc010ugg.1_Frame_Shift_Ins_p.I83fs	NM_004855	NP_004846	Q92521	PIGB_HUMAN	phosphatidylinositol glycan, class B	278					C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	integral to membrane|intrinsic to endoplasmic reticulum membrane	glycolipid mannosyltransferase activity				0				all cancers(107;0.0255)										0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	55631502	55631503	12309	15	-	T	T	T	208	16	PIGB	5	5
NFKBIB	4793	broad.mit.edu	37	19	39390759	39390759	+	Frame_Shift_Del	DEL	G	-	-			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:39390759_39390759delG	uc002ojw.2	+	c.87_87delG	c.(85-87)GCGfs	p.A29fs	SIRT2_uc002oju.1_5'Flank|SIRT2_uc010egj.1_5'Flank|SIRT2_uc002ojv.1_5'Flank|SIRT2_uc002ojt.1_5'Flank|NFKBIB_uc010egk.1_Intron|NFKBIB_uc002ojx.2_Frame_Shift_Del_p.R16fs|NFKBIB_uc002ojy.2_Frame_Shift_Del_p.A29fs	NM_002503	NP_002494	Q15653	IKBB_HUMAN	nuclear factor of kappa light polypeptide gene	29					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|transcription, DNA-dependent	cytosol|nucleus	protein binding|signal transducer activity|transcription coactivator activity			kidney(1)	1	all_cancers(60;4.39e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			Pancreas(165;1492 2005 6979 7739 34483)						OREG0032100	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)	0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	39390759	39390759	10778	19	G	-	-	-	507	39	NFKBIB	5	5
ETV7	51513	broad.mit.edu	37	6	36341285	36341285	+	Frame_Shift_Del	DEL	A	-	-			TCGA-50-5068-01	TCGA-50-5068-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:36341285_36341285delA	uc003omb.2	-	c.378_378delT	c.(376-378)TTTfs	p.F126fs	ETV7_uc003olz.1_Frame_Shift_Del_p.F126fs|ETV7_uc003oma.1_Frame_Shift_Del_p.F71fs|ETV7_uc010jwg.2_Non-coding_Transcript|ETV7_uc003omc.2_Frame_Shift_Del_p.F71fs|ETV7_uc010jwj.2_Frame_Shift_Del_p.F67fs|ETV7_uc010jwh.2_Frame_Shift_Del_p.F45fs|ETV7_uc010jwi.2_Frame_Shift_Del_p.F126fs|ETV7_uc011dtl.1_5'UTR	NM_016135	NP_057219	Q9Y603	ETV7_HUMAN	ets variant 7	126					organ morphogenesis|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|specific RNA polymerase II transcription factor activity			ovary(1)|skin(1)	2														0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	36341285	36341285	5477	6	A	-	-	-	63	5	ETV7	5	5
