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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	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	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
NPHP4	261734	broad.mit.edu	37	1	5964828	5964828	+	Silent	SNP	C	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:5964828C>T	uc001alq.1	-	16	2258	c.1992G>A	c.(1990-1992)AAG>AAA	p.K664K	NPHP4_uc001als.1_RNA|NPHP4_uc009vlt.1_RNA|NPHP4_uc001alt.1_RNA|NPHP4_uc009vlu.1_RNA	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	664					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		AATACACAGTCTTTGGCCATG	0.577													18	124	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	13634777	13634777	+	RNA	SNP	G	T	T	rs140981411	by1000genomes	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:13634777G>T	uc001auz.3	+	4		c.990G>T								Homo sapiens PRAME family member 10, mRNA (cDNA clone MGC:138413 IMAGE:8327676), complete cds.																		CTAGCTGATCGGGACATGGAG	0.507													3	57	---	---	---	---	PASS
C1orf89	79363	broad.mit.edu	37	1	16559013	16559013	+	Silent	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:16559013G>T	uc001ayd.2	-	4	941	c.519C>A	c.(517-519)ATC>ATA	p.I173I		NM_030907	NP_112169	Q9BU20	RSG1_HUMAN	hypothetical protein LOC79363	173	Small GTPase-like.				cellular protein localization|cilium assembly|exocytosis|protein transport|regulation of exocytosis|regulation of vesicle fusion|small GTPase mediated signal transduction	cilium|microtubule basal body	GTP binding				0		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;3.2e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0114)|READ - Rectum adenocarcinoma(331;0.0649)		ACTTGGAGCCGATGACCATCC	0.592													3	50	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16918794	16918794	+	Translation_Start_Site	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:16918794G>A	uc009vos.1	-	6	713	c.-175C>T	c.(-177--173)CACGC>CATGC		NBPF1_uc010oce.1_Translation_Start_Site	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TGTGGCCAGCGTGCCAGGTAA	0.502													3	16	---	---	---	---	PASS
MST1P9	11223	broad.mit.edu	37	1	17085872	17085872	+	Missense_Mutation	SNP	A	G	G	rs1806514	by1000genomes	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:17085872A>G	uc010ock.1	-	8	949	c.949T>C	c.(949-951)TGG>CGG	p.W317R	CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_5'UTR	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						TCGAGGTTCCAGCAGAAGTTC	0.662													3	42	---	---	---	---	PASS
HP1BP3	50809	broad.mit.edu	37	1	21103089	21103089	+	Splice_Site	SNP	C	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:21103089C>G	uc001bdw.1	-	4	490	c.350_splice	c.e4+1	p.D117_splice	HP1BP3_uc001bdv.1_Splice_Site_p.D79_splice|HP1BP3_uc010odh.1_Splice_Site_p.D79_splice|HP1BP3_uc001bdy.1_Splice_Site_p.D117_splice|HP1BP3_uc001bdz.2_Splice_Site|HP1BP3_uc001bea.2_Splice_Site_p.D116_splice|HP1BP3_uc001beb.2_Splice_Site_p.E117_splice	NM_016287	NP_057371	Q5SSJ5	HP1B3_HUMAN	HP1-BP74						nucleosome assembly	nucleosome|nucleus	DNA binding			central_nervous_system(1)|skin(1)	2		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		TAACTCCTTACTCCTTTTTGG	0.368													46	243	---	---	---	---	PASS
HSPG2	3339	broad.mit.edu	37	1	22216543	22216543	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:22216543T>A	uc001bfj.2	-	6	545	c.505A>T	c.(505-507)ATC>TTC	p.I169F	HSPG2_uc009vqd.2_Missense_Mutation_p.I169F|HSPG2_uc009vqe.1_Silent_p.S67S	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	169	SEA.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)	CCGCTGGAGATGACCCTGAGC	0.617													18	147	---	---	---	---	PASS
SLC22A15	55356	broad.mit.edu	37	1	116519322	116519322	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:116519322C>A	uc001egb.3	+	1	204	c.74C>A	c.(73-75)GCC>GAC	p.A25D	SLC22A15_uc001ega.2_Missense_Mutation_p.A25D	NM_018420	NP_060890	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	25	Helical; (Potential).				ion transport	integral to membrane	transmembrane transporter activity			large_intestine(2)	2	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TTCCTGCTGGCCGTGCTGCTG	0.716													3	36	---	---	---	---	PASS
MTX1	4580	broad.mit.edu	37	1	155178660	155178660	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:155178660G>A	uc001fjb.2	+	1	171	c.65G>A	c.(64-66)AGT>AAT	p.S22N	RAG1AP1_uc010pey.1_Intron|THBS3_uc001fix.2_5'Flank|THBS3_uc009wqi.2_5'Flank|THBS3_uc001fiz.2_5'Flank|THBS3_uc001fiy.2_5'Flank|THBS3_uc010pfu.1_5'Flank|THBS3_uc010pfv.1_5'Flank|THBS3_uc001fja.2_Intron|THBS3_uc009wqj.1_Intron|MTX1_uc001fjc.2_Missense_Mutation_p.S22N	NM_002455	NP_002446	Q13505	MTX1_HUMAN	metaxin 1 isoform 1	22					protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane	protein binding			skin(1)	1	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CCCTGGAGCAGTACAGGCCAC	0.697													5	26	---	---	---	---	PASS
ASH1L	55870	broad.mit.edu	37	1	155448258	155448258	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:155448258C>A	uc009wqq.2	-	3	4883	c.4403G>T	c.(4402-4404)AGT>ATT	p.S1468I	ASH1L_uc001fkt.2_Missense_Mutation_p.S1468I|ASH1L_uc009wqr.1_Missense_Mutation_p.S1468I	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	1468					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			AGGAGGAACACTGGGGTAGGT	0.488													35	175	---	---	---	---	PASS
OR6N1	128372	broad.mit.edu	37	1	158735740	158735740	+	Missense_Mutation	SNP	A	G	G	rs857826	byFrequency	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:158735740A>G	uc010piq.1	-	1	733	c.733T>C	c.(733-735)TTC>CTC	p.F245L		NM_001005185	NP_001005185	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N,	245	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)					ACCACAGTGAAGTGGGAGGCA	0.537													7	294	---	---	---	---	PASS
FASLG	356	broad.mit.edu	37	1	172635069	172635069	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:172635069T>G	uc001gis.2	+	4	916	c.759T>G	c.(757-759)AGT>AGG	p.S253R	FASLG_uc001git.2_3'UTR	NM_000639	NP_000630	P48023	TNFL6_HUMAN	fas ligand	253	Extracellular (Potential).				activation of caspase activity|activation of pro-apoptotic gene products|cell-cell signaling|immune response|induction of necroptosis by extracellular signals|induction of necroptosis of activated-T cells|necrotic cell death|negative regulation of angiogenesis|positive regulation of I-kappaB kinase/NF-kappaB cascade|signal transduction	extracellular space|integral to plasma membrane	cytokine activity			lung(2)|breast(1)	3						ATCTTACCAGTGCTGATCATT	0.473													37	208	---	---	---	---	PASS
PRG4	10216	broad.mit.edu	37	1	186276291	186276291	+	Silent	SNP	A	G	G	rs151267614	byFrequency	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:186276291A>G	uc001gru.3	+	7	1491	c.1440A>G	c.(1438-1440)AAA>AAG	p.K480K	PRG4_uc001grt.3_Silent_p.K439K|PRG4_uc009wyl.2_Silent_p.K387K|PRG4_uc009wym.2_Silent_p.K346K|PRG4_uc010poo.1_Intron	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	480	59 X 8 AA repeats of K-X-P-X-P-T-T-X.|18; approximate.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						CCACTCCCAAAGAGCCTGCAC	0.662													6	85	---	---	---	---	PASS
PLXNA2	5362	broad.mit.edu	37	1	208390820	208390820	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:208390820C>T	uc001hgz.2	-	2	1206	c.448G>A	c.(448-450)GAG>AAG	p.E150K	PLXNA2_uc001hha.3_Missense_Mutation_p.E204K	NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor	150	Extracellular (Potential).|Sema.				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TGGGATGGCTCCACCAGGATG	0.582													8	274	---	---	---	---	PASS
MIA3	375056	broad.mit.edu	37	1	222802376	222802376	+	Missense_Mutation	SNP	A	G	G	rs2936052	by1000genomes	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:222802376A>G	uc001hnl.2	+	4	1823	c.1814A>G	c.(1813-1815)AAA>AGA	p.K605R	MIA3_uc009xea.1_Missense_Mutation_p.K441R	NM_198551	NP_940953	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	605	Extracellular (Potential).				exocytosis|negative regulation of cell adhesion|negative regulation of cell migration|positive regulation of leukocyte migration|protein transport|wound healing	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(131;0.0199)		AATGGGGCCAAACTGCACACG	0.473													5	210	---	---	---	---	PASS
SNTG2	54221	broad.mit.edu	37	2	1168808	1168808	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr2:1168808G>T	uc002qwq.2	+	8	658	c.530G>T	c.(529-531)AGT>ATT	p.S177I	SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	177					central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		GACCACAGCAGTGGGGCCTCC	0.488													47	335	---	---	---	---	PASS
PROKR1	10887	broad.mit.edu	37	2	68873392	68873392	+	Missense_Mutation	SNP	T	A	A	rs35335568		TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr2:68873392T>A	uc010yqj.1	+	1	439	c.439T>A	c.(439-441)TCT>ACT	p.S147T	PROKR1_uc002ses.2_RNA	NM_138964	NP_620414	Q8TCW9	PKR1_HUMAN	G protein-coupled receptor 73	147	Helical; Name=3; (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(1)	1						GCGCACTGTCTCTCTCTATGT	0.592													8	213	---	---	---	---	PASS
MRPS9	64965	broad.mit.edu	37	2	105706377	105706377	+	Splice_Site	SNP	G	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr2:105706377G>C	uc002tcn.3	+	7	644	c.576_splice	c.e7-1	p.R192_splice		NM_182640	NP_872578	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9 precursor						DNA damage response, detection of DNA damage|translation	mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome				0						TATTTTAACAGAGACGTGATT	0.303													17	56	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179438165	179438165	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr2:179438165T>C	uc010zfg.1	-	275	65214	c.64990A>G	c.(64990-64992)ACA>GCA	p.T21664A	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.T15359A|TTN_uc010zfi.1_Missense_Mutation_p.T15292A|TTN_uc010zfj.1_Missense_Mutation_p.T15167A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	22591							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTAATAGTTGTCACTTCAGGG	0.458													38	183	---	---	---	---	PASS
NGLY1	55768	broad.mit.edu	37	3	25792603	25792603	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr3:25792603C>G	uc003cdl.2	-	4	752	c.644G>C	c.(643-645)AGA>ACA	p.R215T	NGLY1_uc010hfg.2_Missense_Mutation_p.R215T|NGLY1_uc003cdm.2_Missense_Mutation_p.R215T|NGLY1_uc011awo.1_Missense_Mutation_p.R173T|NGLY1_uc003cdk.2_RNA	NM_018297	NP_060767	Q96IV0	NGLY1_HUMAN	N-glycanase 1 isoform 1	215					glycoprotein catabolic process	cytoplasm	metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding			breast(1)	1						ATCCAATTTTCTAGCTCTCGA	0.308													15	82	---	---	---	---	PASS
XCR1	2829	broad.mit.edu	37	3	46063159	46063159	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr3:46063159C>G	uc003cpe.2	-	3	505	c.281G>C	c.(280-282)GGC>GCC	p.G94A	uc003cpd.1_5'Flank|XCR1_uc003cpf.2_Missense_Mutation_p.G94A	NM_005283	NP_005274	P46094	XCR1_HUMAN	XC chemokine receptor 1	94	Extracellular (Potential).				chemotaxis|G-protein signaling, coupled to cyclic nucleotide second messenger|inflammatory response	integral to plasma membrane	chemokine receptor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CAGCACCCAGCCCCAGTGGTA	0.547													10	60	---	---	---	---	PASS
ITIH3	3699	broad.mit.edu	37	3	52836783	52836783	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr3:52836783T>A	uc003dfv.2	+	13	1706	c.1670T>A	c.(1669-1671)CTC>CAC	p.L557H	ITIH3_uc011bek.1_Intron	NM_002217	NP_002208	Q06033	ITIH3_HUMAN	inter-alpha (globulin) inhibitor H3	557					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|liver(1)	3				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		ATTGAGCGGCTCTGGGCCTAC	0.607													10	48	---	---	---	---	PASS
EAF2	55840	broad.mit.edu	37	3	121563355	121563355	+	Silent	SNP	T	C	C	rs9884018	byFrequency	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr3:121563355T>C	uc003een.2	+	2	261	c.162T>C	c.(160-162)GGT>GGC	p.G54G	EAF2_uc003eeo.2_5'UTR	NM_018456	NP_060926	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	54	Necessary for interaction with ELL.				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	protein binding				0				GBM - Glioblastoma multiforme(114;0.0972)		TTGAGGTTGGTGAAGGTGAAC	0.323													7	183	---	---	---	---	PASS
BOD1L	259282	broad.mit.edu	37	4	13601501	13601501	+	Silent	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr4:13601501G>A	uc003gmz.1	-	10	7140	c.7023C>T	c.(7021-7023)TCC>TCT	p.S2341S	BOD1L_uc010idr.1_Silent_p.S1678S	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	2341							DNA binding			ovary(5)|breast(1)	6						CAATGCTGGCGGAAATTGGCA	0.522													10	53	---	---	---	---	PASS
NDST3	9348	broad.mit.edu	37	4	119161795	119161795	+	Silent	SNP	G	A	A	rs617430	byFrequency	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr4:119161795G>A	uc003ibx.2	+	11	2638	c.2235G>A	c.(2233-2235)CCG>CCA	p.P745P		NM_004784	NP_004775	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan	745	Lumenal (Potential).|Heparan sulfate N-sulfotransferase 3.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1						GTTTGGTCCCGGGGTGGTATG	0.488													4	118	---	---	---	---	PASS
ADAM29	11086	broad.mit.edu	37	4	175897499	175897499	+	Nonsense_Mutation	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr4:175897499G>T	uc003iuc.2	+	5	1493	c.823G>T	c.(823-825)GAG>TAG	p.E275*	ADAM29_uc003iud.2_Nonsense_Mutation_p.E275*|ADAM29_uc010irr.2_Nonsense_Mutation_p.E275*|ADAM29_uc011cki.1_Nonsense_Mutation_p.E275*	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	275	Peptidase M12B.|Extracellular (Potential).				proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		GTGGAAGTCGGAGAACATTAC	0.413													10	373	---	---	---	---	PASS
LOC285501	285501	broad.mit.edu	37	4	178897079	178897079	+	RNA	SNP	T	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr4:178897079T>A	uc010iru.2	+	5		c.748T>A				NR_028342				Homo sapiens cDNA clone IMAGE:4828874.												0		all_lung(41;6.03e-08)|Lung NSC(41;4.26e-07)|Breast(14;0.00066)|Melanoma(52;0.00168)|Prostate(90;0.0129)|all_hematologic(60;0.0202)|Renal(120;0.0246)|Colorectal(36;0.0508)|Hepatocellular(41;0.236)		all cancers(43;9.24e-25)|Epithelial(43;6.28e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.29e-10)|LUSC - Lung squamous cell carcinoma(1;2.61e-05)|Lung(1;3.22e-05)|GBM - Glioblastoma multiforme(59;0.000185)|Colorectal(24;0.000244)|STAD - Stomach adenocarcinoma(60;0.000777)|COAD - Colon adenocarcinoma(29;0.000884)		CTCTGAAGTATATTTTTTCTA	0.363													13	303	---	---	---	---	PASS
CDH6	1004	broad.mit.edu	37	5	31267702	31267702	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr5:31267702C>G	uc003jhe.1	+	2	448	c.122C>G	c.(121-123)TCT>TGT	p.S41C	CDH6_uc003jhd.1_Missense_Mutation_p.S41C	NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein	41					adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|skin(2)|large_intestine(1)	7						CTGGAGCTCTCTGGAAACAGC	0.483													23	164	---	---	---	---	PASS
CRHBP	1393	broad.mit.edu	37	5	76259198	76259198	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr5:76259198G>T	uc003ker.2	+	6	1004	c.724G>T	c.(724-726)GAC>TAC	p.D242Y		NM_001882	NP_001873	P24387	CRHBP_HUMAN	corticotropin releasing hormone binding protein	242					female pregnancy|learning or memory|signal transduction	soluble fraction					0		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-51)|Epithelial(54;8.79e-46)|all cancers(79;2.49e-41)		GGGAATAGGAGACTTTGTGGA	0.473													64	307	---	---	---	---	PASS
CMYA5	202333	broad.mit.edu	37	5	79041206	79041206	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr5:79041206G>A	uc003kgc.2	+	4	10968	c.10896G>A	c.(10894-10896)ATG>ATA	p.M3632I		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3632	B-box coiled-coil; BBC.|Potential.|Amphipathic helix H2.					perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TGCAGAGCATGGACACTGCCA	0.488													19	104	---	---	---	---	PASS
LOX	4015	broad.mit.edu	37	5	121413182	121413182	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr5:121413182C>T	uc003ksu.2	-	1	874	c.499G>A	c.(499-501)GTG>ATG	p.V167M	LOX_uc010jcq.2_5'Flank|LOX_uc011cwk.1_5'Flank|LOX_uc010jcr.2_5'Flank	NM_002317	NP_002308	P28300	LYOX_HUMAN	lysyl oxidase preproprotein	167					protein modification process	extracellular space	copper ion binding|protein-lysine 6-oxidase activity			lung(1)	1		all_cancers(142;0.0124)|Prostate(80;0.0322)|Ovarian(225;0.0814)|Breast(839;0.143)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;2.14e-11)|OV - Ovarian serous cystadenocarcinoma(64;7.87e-10)|all cancers(49;2.49e-09)|COAD - Colon adenocarcinoma(49;0.02)		TCGTCGCCCACCATGCCGTCC	0.622													26	133	---	---	---	---	PASS
C6orf218	221718	broad.mit.edu	37	6	10430136	10430136	+	RNA	SNP	T	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr6:10430136T>G	uc003myz.2	-	3		c.900A>C				NR_027793				Homo sapiens chromosome 6 open reading frame 218, mRNA (cDNA clone IMAGE:3917693).												0	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.124)				TACGCTTAAGTGTGATCACAG	0.483											OREG0017184	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	58	330	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12124855	12124855	+	Missense_Mutation	SNP	G	A	A	rs2228213	by1000genomes	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr6:12124855G>A	uc003nac.2	+	4	5006	c.4827G>A	c.(4825-4827)ATG>ATA	p.M1609I	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	1609					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TTGACAGCATGTCTAATTCGC	0.458													7	268	---	---	---	---	PASS
TNXB	7148	broad.mit.edu	37	6	32023935	32023935	+	Silent	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr6:32023935G>T	uc003nzl.2	-	24	8362	c.8160C>A	c.(8158-8160)ACC>ACA	p.T2720T		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	2778					actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0						TGGGGCTGGGGGTCTCTTCCT	0.627													9	66	---	---	---	---	PASS
MDGA1	266727	broad.mit.edu	37	6	37622688	37622688	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr6:37622688C>G	uc003onu.1	-	5	1779	c.600G>C	c.(598-600)AAG>AAC	p.K200N	MDGA1_uc003onw.3_5'Flank	NM_153487	NP_705691	Q8NFP4	MDGA1_HUMAN	MAM domain containing	200	Ig-like 2.				brain development|neuron migration|spinal cord association neuron differentiation	anchored to plasma membrane				central_nervous_system(2)	2						GGTTCTTCAGCTTCAGGACCT	0.612													15	82	---	---	---	---	PASS
FAM83B	222584	broad.mit.edu	37	6	54735287	54735287	+	Silent	SNP	T	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr6:54735287T>C	uc003pck.2	+	2	359	c.243T>C	c.(241-243)GAT>GAC	p.D81D		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	81										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)					GTACTGATGATTCCTGTGATG	0.433													53	329	---	---	---	---	PASS
FUT9	10690	broad.mit.edu	37	6	96651187	96651187	+	Silent	SNP	C	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr6:96651187C>T	uc003pop.3	+	3	497	c.156C>T	c.(154-156)AAC>AAT	p.N52N		NM_006581	NP_006572	Q9Y231	FUT9_HUMAN	fucosyltransferase 9 (alpha (1,3)	52	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			skin(4)|ovary(1)	5		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)		AAATGAAAAACTTCTTTTCCA	0.423													33	163	---	---	---	---	PASS
TIAM2	26230	broad.mit.edu	37	6	155451342	155451342	+	Silent	SNP	C	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr6:155451342C>T	uc003qqb.2	+	6	2258	c.985C>T	c.(985-987)CTG>TTG	p.L329L	TIAM2_uc003qqe.2_Silent_p.L329L	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	329					apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		GCATGCCAGCCTGAGCAACCG	0.577													15	88	---	---	---	---	PASS
SLC22A3	6581	broad.mit.edu	37	6	160864677	160864677	+	Silent	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr6:160864677G>A	uc003qti.2	+	9	1440	c.1413G>A	c.(1411-1413)TCG>TCA	p.S471S	SLC22A3_uc011efx.1_RNA	NM_021977	NP_068812	O75751	S22A3_HUMAN	solute carrier family 22 member 3	471	Helical; (Potential).					integral to plasma membrane|membrane fraction	protein binding|quaternary ammonium group transmembrane transporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)		TCGGAGTTTCGCTCTGTTCAG	0.378													5	139	---	---	---	---	PASS
UNC93A	54346	broad.mit.edu	37	6	167709633	167709633	+	Missense_Mutation	SNP	A	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr6:167709633A>T	uc003qvq.2	+	3	558	c.383A>T	c.(382-384)AAG>ATG	p.K128M	UNC93A_uc003qvr.2_Missense_Mutation_p.K128M	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1	128						integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		AAGGCGGGAAAGCGTGGCAAA	0.552													30	219	---	---	---	---	PASS
SDK1	221935	broad.mit.edu	37	7	3681627	3681627	+	Silent	SNP	A	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr7:3681627A>T	uc003smx.2	+	4	742	c.603A>T	c.(601-603)ACA>ACT	p.T201T		NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	201	Ig-like C2-type 2.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		AGAGGAAAACAGTTTCTCAAG	0.463													7	203	---	---	---	---	PASS
EGFR	1956	broad.mit.edu	37	7	55273231	55273231	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr7:55273231G>T	uc003tqk.2	+	28	3800	c.3554G>T	c.(3553-3555)GGC>GTC	p.G1185V	EGFR_uc011kco.1_Missense_Mutation_p.G1132V	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	1185	Cytoplasmic (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)	AAGCCAAATGGCATCTTTAAG	0.527		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			9	74	---	---	---	---	PASS
CTTNBP2	83992	broad.mit.edu	37	7	117432054	117432054	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr7:117432054G>A	uc003vjf.2	-	4	1288	c.1196C>T	c.(1195-1197)CCC>CTC	p.P399L		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	399	Pro-rich.									ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		GGGAAGTGGGGGTGTGCTACT	0.527													92	272	---	---	---	---	PASS
ARHGEF10	9639	broad.mit.edu	37	8	1851472	1851472	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr8:1851472G>A	uc003wpr.2	+	16	1854	c.1676G>A	c.(1675-1677)GGC>GAC	p.G559D	ARHGEF10_uc003wpq.1_Missense_Mutation_p.G583D|ARHGEF10_uc003wps.2_Missense_Mutation_p.G521D|ARHGEF10_uc003wpt.2_Missense_Mutation_p.G435D|ARHGEF10_uc003wpv.2_Missense_Mutation_p.G292D|ARHGEF10_uc010lre.2_Missense_Mutation_p.G239D	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10	584	DH.				centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		ACCTCCAAAGGCCACCCCGAC	0.537													43	221	---	---	---	---	PASS
FLJ10661	286042	broad.mit.edu	37	8	8096026	8096026	+	RNA	SNP	T	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr8:8096026T>G	uc011kwt.1	+	8		c.1221T>G			FLJ10661_uc010lrq.2_Intron|FLJ10661_uc003wsf.3_Intron	NR_024362				Homo sapiens cDNA FLJ60033 complete cds, highly similar to Protein FAM86A.												0						TGACCCCTGATGCATAGCCCT	0.667													4	4	---	---	---	---	PASS
KCNS2	3788	broad.mit.edu	37	8	99440309	99440309	+	Silent	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr8:99440309G>T	uc003yin.2	+	2	452	c.102G>T	c.(100-102)ACG>ACT	p.T34T		NM_020697	NP_065748	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel,	34	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			GCTCGCACACGCTGCTGCGCT	0.672													3	71	---	---	---	---	PASS
TOPORS	10210	broad.mit.edu	37	9	32541532	32541532	+	Silent	SNP	A	G	G	rs12348918	byFrequency	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr9:32541532A>G	uc003zrb.2	-	3	3158	c.2991T>C	c.(2989-2991)GAT>GAC	p.D997D	TOPORS_uc003zrc.2_Silent_p.D930D	NM_005802	NP_005793	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich	997					DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		CTTCTCTTACATCGAGAGTTT	0.423													8	363	---	---	---	---	PASS
ZCCHC7	84186	broad.mit.edu	37	9	37126633	37126633	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr9:37126633A>G	uc003zzq.2	+	2	477	c.304A>G	c.(304-306)AGA>GGA	p.R102G	ZCCHC7_uc011lqh.1_Intron|ZCCHC7_uc011lqi.1_Missense_Mutation_p.R101G|ZCCHC7_uc010mlt.2_Missense_Mutation_p.R101G|ZCCHC7_uc003zzs.1_Missense_Mutation_p.R101G	NM_032226	NP_115602	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	102							nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(29;0.0137)		CAGTATTTATAGATGTAAAGG	0.393													13	448	---	---	---	---	PASS
HSDL2	84263	broad.mit.edu	37	9	115200783	115200783	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr9:115200783T>C	uc004bga.1	+	7	764	c.671T>C	c.(670-672)ATT>ACT	p.I224T	HSDL2_uc011lwv.1_Missense_Mutation_p.I103T|HSDL2_uc004bgb.1_Intron|HSDL2_uc004bgc.1_Missense_Mutation_p.I151T|HSDL2_uc011lww.1_Missense_Mutation_p.I19T	NM_032303	NP_115679	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	224						peroxisome	oxidoreductase activity|sterol binding				0						GTTGATATCATTGCAGATGCA	0.368													21	126	---	---	---	---	PASS
C9orf117	286207	broad.mit.edu	37	9	130473624	130473624	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr9:130473624C>A	uc004brn.1	+	4	744	c.704C>A	c.(703-705)ACC>AAC	p.T235N	PTRH1_uc004brm.2_Intron|C9orf117_uc010mxl.1_RNA	NM_001012502	NP_001012520	Q5JU67	CI117_HUMAN	hypothetical protein LOC286207	235											0						AACGGCATTACCCTGCAGATG	0.557													11	93	---	---	---	---	PASS
LCN2	3934	broad.mit.edu	37	9	130913928	130913928	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr9:130913928G>A	uc004bto.1	+	3	360	c.287G>A	c.(286-288)TGT>TAT	p.C96Y	LCN2_uc011map.1_Missense_Mutation_p.C96Y	NM_005564	NP_005555	P80188	NGAL_HUMAN	lipocalin 2 precursor	96					apoptosis|innate immune response|regulation of apoptosis|siderophore transport		iron ion binding|transporter activity				0						AAAAAGAAGTGTGACTACTGG	0.582													21	117	---	---	---	---	PASS
RAPGEF1	2889	broad.mit.edu	37	9	134501446	134501446	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr9:134501446G>C	uc004cbc.2	-	10	1644	c.1514C>G	c.(1513-1515)GCG>GGG	p.A505G	RAPGEF1_uc004cbb.2_Missense_Mutation_p.A523G|RAPGEF1_uc010mzm.2_RNA|RAPGEF1_uc010mzn.2_Missense_Mutation_p.A510G|RAPGEF1_uc004cbd.2_Missense_Mutation_p.A510G	NM_005312	NP_005303	Q13905	RPGF1_HUMAN	guanine nucleotide-releasing factor 2 isoform a	505					activation of MAPKK activity|nerve growth factor receptor signaling pathway|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome	guanyl-nucleotide exchange factor activity|SH3 domain binding			lung(3)|ovary(2)|breast(1)|skin(1)	7		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		AGCAAAGGGCGCGTAGGGGAC	0.582													17	92	---	---	---	---	PASS
C10orf47	254427	broad.mit.edu	37	10	11908743	11908743	+	Missense_Mutation	SNP	G	A	A	rs142957936		TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr10:11908743G>A	uc001ikx.2	+	3	506	c.352G>A	c.(352-354)GGG>AGG	p.G118R	uc001iky.1_Intron	NM_153256	NP_694988	Q86WR7	CJ047_HUMAN	hypothetical protein LOC254427	118										central_nervous_system(1)	1						ACCTGGCGCCGGGGAAGCCGA	0.637													20	64	---	---	---	---	PASS
RBP3	5949	broad.mit.edu	37	10	48389852	48389852	+	Silent	SNP	C	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr10:48389852C>T	uc001jez.2	-	1	1140	c.1026G>A	c.(1024-1026)ACG>ACA	p.T342T		NM_002900	NP_002891	P10745	RET3_HUMAN	retinol-binding protein 3 precursor	342	4 X approximate tandem repeats.|2.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			large_intestine(1)|central_nervous_system(1)	2					Vitamin A(DB00162)	GGTCCACCAGCGTGTAGTAGT	0.637													17	82	---	---	---	---	PASS
SUPV3L1	6832	broad.mit.edu	37	10	70954956	70954956	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr10:70954956T>G	uc001jpe.1	+	7	921	c.866T>G	c.(865-867)GTA>GGA	p.V289G	SUPV3L1_uc010qjd.1_Missense_Mutation_p.V158G	NM_003171	NP_003162	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 precursor	289	Helicase ATP-binding.				DNA duplex unwinding	mitochondrial nucleoid|nucleus	ATP binding|DNA binding|DNA helicase activity|RNA binding			urinary_tract(1)|ovary(1)	2						GAAGTGGCTGTAATTGATGAA	0.363													12	60	---	---	---	---	PASS
NEUROG3	50674	broad.mit.edu	37	10	71332506	71332506	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr10:71332506G>T	uc001jpp.2	-	2	452	c.294C>A	c.(292-294)AAC>AAA	p.N98K		NM_020999	NP_066279	Q9Y4Z2	NGN3_HUMAN	neurogenin 3	98	Helix-loop-helix motif.			N -> D (in Ref. 1; CAB45384).	central nervous system development|endocrine pancreas development|peripheral nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity	nucleus	transcription coactivator activity				0						CCGAGTTGAGGTTGTGCATTC	0.642													7	44	---	---	---	---	PASS
CSNK2A1P	283106	broad.mit.edu	37	11	11374269	11374269	+	Missense_Mutation	SNP	A	G	G	rs2071460	by1000genomes	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr11:11374269A>G	uc001mjp.2	-	1	636	c.398T>C	c.(397-399)ATT>ACT	p.I133T	GALNTL4_uc001mjo.2_Intron	NM_177559	NP_808227			casein kinase II alpha 1 subunit isoform a												0						GTAAAATCGAATATCATAGTC	0.408													5	253	---	---	---	---	PASS
SLC43A3	29015	broad.mit.edu	37	11	57182087	57182087	+	Splice_Site	SNP	C	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr11:57182087C>A	uc001nkg.2	-	11	1470	c.1060_splice	c.e11+1	p.G354_splice	PRG2_uc001nke.2_Splice_Site_p.G253_splice|SLC43A3_uc001nkh.2_Splice_Site_p.G354_splice|SLC43A3_uc010rjr.1_Splice_Site_p.G367_splice|SLC43A3_uc009yme.2_Splice_Site_p.G354_splice|SLC43A3_uc001nki.2_Splice_Site_p.G354_splice	NM_014096	NP_054815	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3						transmembrane transport	integral to membrane				central_nervous_system(1)	1						CCGCATCTCACCTGTCTTTCT	0.512													19	253	---	---	---	---	PASS
MPEG1	219972	broad.mit.edu	37	11	58979678	58979678	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr11:58979678G>A	uc001nnu.3	-	1	817	c.661C>T	c.(661-663)CTC>TTC	p.L221F		NM_001039396	NP_001034485	Q2M385	MPEG1_HUMAN	macrophage expressed gene 1 precursor	221	MACPF.|Extracellular (Potential).					integral to membrane				ovary(1)|skin(1)	2		all_epithelial(135;0.125)				GAGGCCCTGAGGTGGTCCTCC	0.572													12	98	---	---	---	---	PASS
MALAT1	378938	broad.mit.edu	37	11	65271551	65271551	+	RNA	SNP	A	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr11:65271551A>G	uc010roh.1	+	1		c.6319A>G			uc001ody.2_5'Flank	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0						TATTGACCTTATATAGGGAAG	0.368													7	45	---	---	---	---	PASS
ART4	420	broad.mit.edu	37	12	14993378	14993378	+	Splice_Site	SNP	C	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr12:14993378C>A	uc001rcl.1	-	2	1219	c.853_splice	c.e2+1	p.A285_splice	ART4_uc009zid.1_Intron|ART4_uc009zie.1_Intron|ART4_uc001rcm.1_Missense_Mutation_p.G285V	NM_021071	NP_066549	Q93070	NAR4_HUMAN	ADP-ribosyltransferase 4 precursor						arginine metabolic process|protein ADP-ribosylation	anchored to membrane|plasma membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity				0						ATAAAGAATACCTTTTAGCAG	0.388													17	109	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49443872	49443872	+	Nonsense_Mutation	SNP	C	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr12:49443872C>A	uc001rta.3	-	11	3499	c.3499G>T	c.(3499-3501)GAG>TAG	p.E1167*		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1167	Pro-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						GGGTAGACCTCCATAGGGGTC	0.617			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			28	148	---	---	---	---	PASS
MON2	23041	broad.mit.edu	37	12	62946846	62946846	+	Silent	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr12:62946846G>A	uc001sre.2	+	24	3493	c.3102G>A	c.(3100-3102)GTG>GTA	p.V1034V	MON2_uc009zqj.2_Silent_p.V1034V|MON2_uc010ssl.1_Silent_p.V962V|MON2_uc010ssm.1_Silent_p.V1011V|MON2_uc010ssn.1_Silent_p.V1034V|MON2_uc001srf.2_Silent_p.V797V	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog	1035					Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		AACTATGTGTGGATCCCCGTC	0.453													8	326	---	---	---	---	PASS
HELB	92797	broad.mit.edu	37	12	66725338	66725338	+	Silent	SNP	A	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr12:66725338A>G	uc001sti.2	+	12	3103	c.3075A>G	c.(3073-3075)GTA>GTG	p.V1025V	HELB_uc010ssz.1_RNA|HELB_uc009zqt.1_RNA	NM_033647	NP_387467	Q8NG08	HELB_HUMAN	helicase (DNA) B	1025					DNA replication, synthesis of RNA primer		ATP binding|ATP-dependent 5'-3' DNA helicase activity|single-stranded DNA-dependent ATP-dependent DNA helicase activity			central_nervous_system(1)|pancreas(1)	2			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		CTGATGGAGTAGATACAGATG	0.438													26	133	---	---	---	---	PASS
GRIP1	23426	broad.mit.edu	37	12	66765694	66765694	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr12:66765694G>A	uc001stk.2	-	22	2877	c.2636C>T	c.(2635-2637)TCG>TTG	p.S879L	GRIP1_uc010sta.1_Missense_Mutation_p.S823L|GRIP1_uc001stj.2_Missense_Mutation_p.S646L|GRIP1_uc001stl.1_Missense_Mutation_p.S756L|GRIP1_uc001stm.2_Missense_Mutation_p.S864L	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	931					androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		CGTGCTCCCCGACATGATTGT	0.517													24	110	---	---	---	---	PASS
TBX5	6910	broad.mit.edu	37	12	114804033	114804033	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr12:114804033G>T	uc001tvo.2	-	8	1414	c.919C>A	c.(919-921)CCA>ACA	p.P307T	TBX5_uc001tvp.2_Missense_Mutation_p.P307T|TBX5_uc001tvq.2_Missense_Mutation_p.P257T|TBX5_uc010syv.1_Missense_Mutation_p.P307T	NM_181486	NP_852259	Q99593	TBX5_HUMAN	T-box 5 isoform 1	307					cardiac left ventricle formation|cell migration involved in coronary vasculogenesis|cell-cell signaling|embryonic arm morphogenesis|induction of apoptosis|negative regulation of cardiac muscle cell proliferation|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|pericardium development|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|ventricular septum development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(6)|pancreas(1)|skin(1)	8	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		GGGTTGGGTGGAGGCAGGAGG	0.532													25	109	---	---	---	---	PASS
XPO4	64328	broad.mit.edu	37	13	21417991	21417991	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr13:21417991A>C	uc001unq.3	-	5	527	c.491T>G	c.(490-492)TTG>TGG	p.L164W	XPO4_uc010tcr.1_Missense_Mutation_p.L90W	NM_022459	NP_071904	Q9C0E2	XPO4_HUMAN	exportin 4	164					protein transport	cytoplasm|nucleus	protein binding			large_intestine(1)|ovary(1)|kidney(1)	3		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)		AAATTCACTCAATAGCGCAGT	0.348													32	165	---	---	---	---	PASS
TPTE2P3	220115	broad.mit.edu	37	13	53151292	53151292	+	RNA	SNP	A	C	C	rs146809843	by1000genomes	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr13:53151292A>C	uc001vgw.2	+	20		c.2057A>C				NR_002793				Homo sapiens TPTE and PTEN homologous inositol lipid phosphatase pseudogene, mRNA (cDNA clone IMAGE:5298506), with apparent retained intron.												0						TAAAAAGATTAGTTATTTATT	0.358													3	5	---	---	---	---	PASS
TPTE2P3	220115	broad.mit.edu	37	13	53151293	53151293	+	RNA	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr13:53151293G>A	uc001vgw.2	+	20		c.2058G>A				NR_002793				Homo sapiens TPTE and PTEN homologous inositol lipid phosphatase pseudogene, mRNA (cDNA clone IMAGE:5298506), with apparent retained intron.												0						AAAAAGATTAGTTATTTATTC	0.358													3	5	---	---	---	---	PASS
C14orf166B	145497	broad.mit.edu	37	14	77302633	77302633	+	Missense_Mutation	SNP	A	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr14:77302633A>T	uc001xsx.2	+	4	588	c.474A>T	c.(472-474)CAA>CAT	p.Q158H	C14orf166B_uc010asn.1_Translation_Start_Site|C14orf166B_uc001xsw.2_RNA|C14orf166B_uc010aso.1_RNA|C14orf166B_uc010tvg.1_RNA|C14orf166B_uc010tvh.1_RNA	NM_194287	NP_919263	Q0VAA2	CN16B_HUMAN	hypothetical protein LOC145497	158											0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)		AGATGCTACAAGAGAACTACT	0.552													8	20	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102505453	102505453	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr14:102505453G>T	uc001yks.2	+	60	11486	c.11322G>T	c.(11320-11322)AAG>AAT	p.K3774N		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	3774	Potential.|AAA 5 (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						AGAACCTGAAGAGAGAGGCTG	0.537													21	130	---	---	---	---	PASS
OR4M2	390538	broad.mit.edu	37	15	22369362	22369362	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr15:22369362C>A	uc010tzu.1	+	1	787	c.787C>A	c.(787-789)CCA>ACA	p.P263T	LOC727924_uc001yua.2_Intron|LOC727924_uc001yub.1_Intron|OR4N4_uc001yuc.1_Intron	NM_001004719	NP_001004719	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M,	263	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		TTATGCTCGCCCATTTGACTC	0.418													39	616	---	---	---	---	PASS
RAB11A	8766	broad.mit.edu	37	15	66169865	66169865	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr15:66169865C>A	uc002apk.2	+	2	364	c.236C>A	c.(235-237)GCA>GAA	p.A79E	RAB11A_uc010ujk.1_Missense_Mutation_p.A79E	NM_004663	NP_004654	P62491	RB11A_HUMAN	Ras-related protein Rab-11A	79					cell cycle|cytokinesis|neuron projection development|plasma membrane to endosome transport|protein localization in plasma membrane|small GTPase mediated signal transduction|vesicle-mediated transport	cleavage furrow|plasma membrane|recycling endosome membrane|trans-Golgi network	GTP binding|GTPase activity|syntaxin binding				0						ATAACATCAGCGTAAGTCTCA	0.393													4	69	---	---	---	---	PASS
GOLGA6L5	374650	broad.mit.edu	37	15	85055915	85055915	+	RNA	SNP	T	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr15:85055915T>C	uc002bkm.2	-	6		c.645A>G				NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						TCCTGTCTCCTGTTCAGGAGA	0.527													3	19	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	15023280	15023280	+	Splice_Site	SNP	T	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr16:15023280T>C	uc010uzk.1	+	6	1123	c.847_splice	c.e6+2	p.G283_splice	NPIP_uc002dcx.3_Splice_Site					SubName: Full=cDNA FLJ57488, highly similar to Polycystin-1;																		CGCTGGCGGGTGAGGAGATCG	0.701													4	20	---	---	---	---	PASS
GPR139	124274	broad.mit.edu	37	16	20043984	20043984	+	Silent	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr16:20043984G>T	uc002dgu.1	-	2	297	c.135C>A	c.(133-135)ATC>ATA	p.I45I	GPR139_uc010vaw.1_5'UTR	NM_001002911	NP_001002911	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	45	Helical; Name=1; (Potential).					integral to membrane|plasma membrane				ovary(2)	2						TCACTGTCAAGATATTTGCTG	0.478													4	48	---	---	---	---	PASS
GSG1L	146395	broad.mit.edu	37	16	27802719	27802719	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr16:27802719T>G	uc002doz.2	-	7	1053	c.968A>C	c.(967-969)CAG>CCG	p.Q323P	GSG1L_uc010bya.1_Missense_Mutation_p.Q272P|GSG1L_uc010bxz.1_Missense_Mutation_p.Q186P|GSG1L_uc002doy.2_Missense_Mutation_p.Q168P	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1	323						integral to membrane				ovary(1)	1						GACCCAGCACTGTCGGTTCAG	0.642													14	96	---	---	---	---	PASS
GSG1L	146395	broad.mit.edu	37	16	27802748	27802748	+	Silent	SNP	G	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr16:27802748G>C	uc002doz.2	-	7	1024	c.939C>G	c.(937-939)TCC>TCG	p.S313S	GSG1L_uc010bya.1_Silent_p.S262S|GSG1L_uc010bxz.1_Silent_p.S176S|GSG1L_uc002doy.2_Silent_p.S158S	NM_001109763	NP_001103233	Q6UXU4	GSG1L_HUMAN	GSG1-like isoform 1	313						integral to membrane				ovary(1)	1						CTTCCTGTGCGGAGCTCCGGG	0.637													9	72	---	---	---	---	PASS
VPS35	55737	broad.mit.edu	37	16	46712857	46712857	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr16:46712857G>C	uc002eef.3	-	6	817	c.718C>G	c.(718-720)CAG>GAG	p.Q240E	VPS35_uc002eed.2_Missense_Mutation_p.Q61E|VPS35_uc002eee.2_Missense_Mutation_p.Q201E	NM_018206	NP_060676	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35	240					protein transport|retrograde transport, endosome to Golgi	cytosol|endosome|membrane	protein binding				0		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				ATATAAACCTGTTTGTAACGT	0.308													39	188	---	---	---	---	PASS
CDH5	1003	broad.mit.edu	37	16	66432423	66432423	+	Missense_Mutation	SNP	T	C	C	rs1049970	byFrequency	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr16:66432423T>C	uc002eom.3	+	10	1706	c.1550T>C	c.(1549-1551)ATC>ACC	p.I517T		NM_001795	NP_001786	P33151	CADH5_HUMAN	cadherin 5, type 2 preproprotein	517	Cadherin 5.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|regulation of establishment of cell polarity	integral to membrane|membrane fraction	beta-catenin binding|calcium ion binding|ion channel binding|receptor binding			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)		TTCAAATTCATCTTGAATACT	0.368													3	87	---	---	---	---	PASS
GLOD4	51031	broad.mit.edu	37	17	674590	674590	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr17:674590G>A	uc002frv.2	-	6	639	c.563C>T	c.(562-564)GCT>GTT	p.A188V	GLOD4_uc002frt.2_Missense_Mutation_p.A117V|GLOD4_uc002fru.2_Missense_Mutation_p.A173V|GLOD4_uc010vqc.1_Missense_Mutation_p.A164V	NM_016080	NP_057164	Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4	188						mitochondrion					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		GCCCAGCAAAGCCCTTTGCTT	0.343													51	396	---	---	---	---	PASS
DNAH2	146754	broad.mit.edu	37	17	7673934	7673934	+	Silent	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr17:7673934G>A	uc002giu.1	+	25	4172	c.4158G>A	c.(4156-4158)AAG>AAA	p.K1386K		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	1386	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TACCCTACAAGGATAAGGGCC	0.552													42	182	---	---	---	---	PASS
CCDC144B	284047	broad.mit.edu	37	17	18528456	18528456	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr17:18528456G>T	uc002gub.1	-	1	390	c.305C>A	c.(304-306)CCT>CAT	p.P102H	CCDC144B_uc002gua.3_RNA|CCDC144B_uc010vyc.1_RNA|CCDC144B_uc002guc.1_Missense_Mutation_p.P102H	NM_182568	NP_872374			coiled-coil domain containing 144B											ovary(1)|skin(1)	2						AGTGTCTCCAGGAGCCAAGAC	0.637													23	272	---	---	---	---	PASS
CCDC144B	284047	broad.mit.edu	37	17	18528457	18528457	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr17:18528457G>T	uc002gub.1	-	1	389	c.304C>A	c.(304-306)CCT>ACT	p.P102T	CCDC144B_uc002gua.3_RNA|CCDC144B_uc010vyc.1_RNA|CCDC144B_uc002guc.1_Missense_Mutation_p.P102T	NM_182568	NP_872374			coiled-coil domain containing 144B											ovary(1)|skin(1)	2						GTGTCTCCAGGAGCCAAGACG	0.637													21	272	---	---	---	---	PASS
FAM27L	284123	broad.mit.edu	37	17	21826233	21826233	+	RNA	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr17:21826233G>T	uc002gyz.2	+	2		c.343G>T				NR_028336				Homo sapiens family with sequence similarity 27-like, mRNA (cDNA clone MGC:35151 IMAGE:5169482), complete cds.												0				UCEC - Uterine corpus endometrioid carcinoma (53;0.11)|BRCA - Breast invasive adenocarcinoma(1;0.00463)		GCCACACCACGATACAGTCTT	0.542													14	85	---	---	---	---	PASS
ANKRD13B	124930	broad.mit.edu	37	17	27934857	27934857	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr17:27934857G>A	uc002hei.2	+	2	325	c.212G>A	c.(211-213)GGC>GAC	p.G71D	ANKRD13B_uc002heh.2_5'UTR|ANKRD13B_uc002hej.2_RNA	NM_152345	NP_689558	Q86YJ7	AN13B_HUMAN	ankyrin repeat domain 13B	71	ANK 1.										0						CTGGCGCACGGCGCAGACGTG	0.701													16	72	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	39565994	39565994	+	RNA	SNP	T	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr17:39565994T>G	uc002hwo.1	+	2		c.1415T>G								Homo sapiens cDNA FLJ41849 fis, clone NT2RI3003409.																		GGGGTCTGGGTCAATGACATC	0.458													2	6	---	---	---	---	PASS
MAPT	4137	broad.mit.edu	37	17	44067382	44067382	+	Missense_Mutation	SNP	T	C	C	rs2258689		TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr17:44067382T>C	uc002ijr.3	+	8	1641	c.1321T>C	c.(1321-1323)TAC>CAC	p.Y441H	MAPT_uc010dau.2_Missense_Mutation_p.Y441H|MAPT_uc002ijs.3_Intron|MAPT_uc002ijx.3_Intron|MAPT_uc002ijt.3_Intron|MAPT_uc002iju.3_Intron|MAPT_uc002ijv.3_Intron	NM_016835	NP_058519	P10636	TAU_HUMAN	microtubule-associated protein tau isoform 1	441					cellular component disassembly involved in apoptosis|microtubule cytoskeleton organization|negative regulation of microtubule depolymerization|positive regulation of axon extension|positive regulation of microtubule polymerization|regulation of autophagy	axon|cytosol|growth cone|microtubule|microtubule associated complex|nuclear periphery|plasma membrane|tubulin complex	apolipoprotein E binding|enzyme binding|identical protein binding|lipoprotein particle binding|microtubule binding|protein binding|SH3 domain binding|structural constituent of cytoskeleton			pancreas(1)	1		Melanoma(429;0.216)				CTCTCCTAAATACGTCTCTTC	0.542													8	418	---	---	---	---	PASS
MED13	9969	broad.mit.edu	37	17	60140573	60140573	+	Silent	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr17:60140573G>A	uc002izo.2	-	2	233	c.156C>T	c.(154-156)CCC>CCT	p.P52P		NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	52					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						TGCTCAAAATGGGGTCTTCTT	0.453													67	287	---	---	---	---	PASS
SSTR2	6752	broad.mit.edu	37	17	71165834	71165834	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr17:71165834C>G	uc002jje.2	+	2	736	c.376C>G	c.(376-378)CAG>GAG	p.Q126E		NM_001050	NP_001041	P30874	SSR2_HUMAN	somatostatin receptor 2	126	Helical; Name=3; (Potential).				digestion|negative regulation of cell proliferation|response to nutrient	integral to plasma membrane	PDZ domain binding|somatostatin receptor activity				0			LUSC - Lung squamous cell carcinoma(166;0.197)			TGGCATCAATCAGTTCACCAG	0.587													25	104	---	---	---	---	PASS
NPTX1	4884	broad.mit.edu	37	17	78449346	78449346	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr17:78449346G>T	uc002jyp.1	-	2	775	c.617C>A	c.(616-618)ACC>AAC	p.T206N		NM_002522	NP_002513	Q15818	NPTX1_HUMAN	neuronal pentraxin I precursor	206					central nervous system development|synaptic transmission|transport	transport vesicle	metal ion binding				0	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			GTGCAGGGAGGTCAGGGCGGT	0.687													6	46	---	---	---	---	PASS
EPB41L3	23136	broad.mit.edu	37	18	5445182	5445182	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr18:5445182T>G	uc002kmt.1	-	4	529	c.443A>C	c.(442-444)AAA>ACA	p.K148T	EPB41L3_uc010wzh.1_Missense_Mutation_p.K148T|EPB41L3_uc002kmu.1_Missense_Mutation_p.K148T|EPB41L3_uc010dkq.1_Missense_Mutation_p.K39T|EPB41L3_uc010dks.1_Missense_Mutation_p.K170T|EPB41L3_uc002kmv.1_Missense_Mutation_p.K39T	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	148	FERM.				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5						AAAGTAGTCTTTCTCTAGCAA	0.408													48	278	---	---	---	---	PASS
SETBP1	26040	broad.mit.edu	37	18	42530401	42530401	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr18:42530401G>A	uc010dni.2	+	4	1392	c.1096G>A	c.(1096-1098)GAA>AAA	p.E366K		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	366						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		TGACAATACAGAAGGGAAAAG	0.453									Schinzel-Giedion_syndrome				33	149	---	---	---	---	PASS
MRO	83876	broad.mit.edu	37	18	48327815	48327815	+	Silent	SNP	G	A	A	rs2276186	byFrequency	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr18:48327815G>A	uc002lew.3	-	6	783	c.489C>T	c.(487-489)GCC>GCT	p.A163A	MRO_uc010xdn.1_Intron|MRO_uc010dpa.2_Silent_p.A177A|MRO_uc010dpb.2_Intron|MRO_uc010dpc.2_Intron|MRO_uc002lex.3_Silent_p.A163A	NM_031939	NP_114145	Q9BYG7	MSTRO_HUMAN	maestro isoform a	163	HEAT.					nucleolus	binding				0		Colorectal(6;0.0596)		Colorectal(21;0.082)		ATTTCCTCCCGGCAAAGGCAG	0.463													10	350	---	---	---	---	PASS
PIP5K1C	23396	broad.mit.edu	37	19	3643243	3643243	+	Silent	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:3643243G>A	uc002lyj.1	-	13	1704	c.1647C>T	c.(1645-1647)TAC>TAT	p.Y549Y	PIP5K1C_uc010xhq.1_Silent_p.Y549Y|PIP5K1C_uc010xhr.1_Silent_p.Y549Y	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type	549					axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		TCGCCCACCTGTACCGCGGCT	0.657													14	64	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8212299	8212299	+	Silent	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:8212299G>A	uc002mjf.2	-	1	87	c.66C>T	c.(64-66)GCC>GCT	p.A22A		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	22						proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						TGCACAACAGGGCCGACCAGG	0.692													4	16	---	---	---	---	PASS
ZNF85	7639	broad.mit.edu	37	19	21132414	21132414	+	Missense_Mutation	SNP	C	A	A	rs144723751	by1000genomes	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:21132414C>A	uc002npg.3	+	4	1221	c.1094C>A	c.(1093-1095)ACT>AAT	p.T365N	ZNF85_uc010ecn.2_Missense_Mutation_p.T300N|ZNF85_uc010eco.2_Missense_Mutation_p.T313N|ZNF85_uc002npi.2_Missense_Mutation_p.T306N	NM_003429	NP_003420	Q03923	ZNF85_HUMAN	zinc finger protein 85	365						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			central_nervous_system(1)	1						GTAATTCATACTGGAGAGAAA	0.358													4	106	---	---	---	---	PASS
CLIP3	25999	broad.mit.edu	37	19	36508303	36508303	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:36508303C>T	uc010eeq.1	-	11	1783	c.1501G>A	c.(1501-1503)GTG>ATG	p.V501M	uc002ocy.2_Intron|CLIP3_uc002ocz.1_Missense_Mutation_p.V501M	NM_015526	NP_056341	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	501	GoLD.				chaperone-mediated protein transport|fat cell differentiation|membrane biogenesis|negative regulation of microtubule polymerization|peptidyl-L-cysteine S-palmitoylation|positive regulation of apoptosis|positive regulation of endocytosis|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose transport|positive regulation of protein phosphorylation	early endosome membrane|Golgi stack|membrane raft|microsome|plasma membrane|recycling endosome membrane|trans-Golgi network membrane	ganglioside binding|microtubule binding			ovary(2)|pancreas(1)|skin(1)	4	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			ACTTGATGCACTTTTTTGGCT	0.547													3	79	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40384050	40384050	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:40384050C>G	uc002omp.3	-	21	9568	c.9560G>C	c.(9559-9561)GGC>GCC	p.G3187A		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	3187	TIL 7.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCACTGGCAGCCCTCCACACA	0.662													22	48	---	---	---	---	PASS
BCKDHA	593	broad.mit.edu	37	19	41903833	41903833	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:41903833C>A	uc002oqq.2	+	1	130	c.101C>A	c.(100-102)GCT>GAT	p.A34D	CYP2F1_uc010xvw.1_Intron|BCKDHA_uc002oqm.3_Intron|EXOSC5_uc002oqo.2_5'Flank|BCKDHA_uc002oqp.1_5'UTR|BCKDHA_uc002oqr.2_Missense_Mutation_p.A34D|BCKDHA_uc010xvz.1_Intron	NM_000709	NP_000700	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha	34					branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|alpha-ketoacid dehydrogenase activity|carboxy-lyase activity|metal ion binding|protein binding				0						CGGGGACTGGCTAGATCTGTG	0.602													6	57	---	---	---	---	PASS
DMRTC2	63946	broad.mit.edu	37	19	42354650	42354650	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:42354650G>C	uc002ors.2	+	8	956	c.873G>C	c.(871-873)CAG>CAC	p.Q291H	DMRTC2_uc002orr.1_Missense_Mutation_p.Q219H|DMRTC2_uc010xwe.1_Missense_Mutation_p.Q342H	NM_001040283	NP_001035373	Q8IXT2	DMRTD_HUMAN	DMRT-like family C2	291	Pro-rich.				cell differentiation|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0						GGCAGCTGCAGCAAGAGGCAG	0.632													8	94	---	---	---	---	PASS
ATP1A3	478	broad.mit.edu	37	19	42492276	42492276	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:42492276T>C	uc002osg.2	-	4	323	c.169A>G	c.(169-171)AAA>GAA	p.K57E	ATP1A3_uc010xwf.1_Missense_Mutation_p.K68E|ATP1A3_uc010xwg.1_Missense_Mutation_p.K27E|ATP1A3_uc010xwh.1_Missense_Mutation_p.K70E|ATP1A3_uc002osh.2_Missense_Mutation_p.K57E	NM_152296	NP_689509	P13637	AT1A3_HUMAN	Na+/K+ -ATPase alpha 3 subunit	57	Cytoplasmic (Potential).				ATP biosynthetic process	endoplasmic reticulum|Golgi apparatus	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(1)|pancreas(1)	2						TCCTGGGCTTTGCTGTGGGTC	0.627													20	113	---	---	---	---	PASS
BCAM	4059	broad.mit.edu	37	19	45316807	45316807	+	Silent	SNP	C	T	T	rs3810140	byFrequency	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:45316807C>T	uc002ozu.2	+	6	758	c.714C>T	c.(712-714)GCC>GCT	p.A238A	BCAM_uc002ozt.1_Silent_p.A238A	NM_005581	NP_005572	P50895	BCAM_HUMAN	basal cell adhesion molecule isoform 1	238	Extracellular (Potential).|Ig-like V-type 2.				cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			skin(1)	1	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				TCCACTGCGCCGCCCACTACA	0.697													4	93	---	---	---	---	PASS
GLTSCR1	29998	broad.mit.edu	37	19	48176998	48176998	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:48176998C>A	uc002phh.3	+	4	257	c.63C>A	c.(61-63)GAC>GAA	p.D21E		NM_015711	NP_056526	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	21							protein binding			pancreas(3)	3		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		CCCTCAATGACTTCTTGCATG	0.353													28	132	---	---	---	---	PASS
ZNF616	90317	broad.mit.edu	37	19	52619794	52619794	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:52619794G>C	uc002pym.2	-	4	906	c.623C>G	c.(622-624)ACT>AGT	p.T208S	ZNF616_uc002pyn.2_RNA	NM_178523	NP_848618	Q08AN1	ZN616_HUMAN	zinc finger protein 616	208					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		TTTCTCTGTAGTATGTATCCT	0.393													6	294	---	---	---	---	PASS
LILRB3	11025	broad.mit.edu	37	19	54725995	54725995	+	Silent	SNP	G	A	A	rs61187720	by1000genomes	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:54725995G>A	uc002qef.1	-	4	474	c.363C>T	c.(361-363)TAC>TAT	p.Y121Y	LILRB3_uc002qee.1_Silent_p.Y121Y|LILRB3_uc002qeh.1_Silent_p.Y121Y|LILRB3_uc002qeg.1_RNA|LILRB3_uc002qei.1_Intron|LILRA6_uc002qek.1_Intron|LILRB3_uc010erh.1_Silent_p.Y121Y|LILRB3_uc002qej.1_Intron|LILRA6_uc002qel.1_Intron|LILRA6_uc002qem.1_Intron|LILRB3_uc002qen.1_Intron|LILRB3_uc002qeo.1_Intron|LILRB3_uc002qep.1_Silent_p.Y121Y|LILRB3_uc002qeq.1_Intron|LILRB3_uc002qer.1_Intron|LILRB3_uc002qes.1_Intron|LILRA6_uc010yep.1_Intron|LILRA6_uc010yeq.1_Intron	NM_006864	NP_006855	O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor,	121	Extracellular (Potential).|Ig-like C2-type 2.				cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	transmembrane receptor activity			skin(2)|ovary(1)	3	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGGTTTGCTGTAGGCTCCTA	0.602													4	8	---	---	---	---	PASS
ZNF17	7565	broad.mit.edu	37	19	57931923	57931923	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr19:57931923G>A	uc002qoo.1	+	3	1294	c.1063G>A	c.(1063-1065)GAA>AAA	p.E355K	ZNF547_uc002qpm.3_Intron|ZNF17_uc002qop.1_Missense_Mutation_p.E357K	NM_006959	NP_008890	P17021	ZNF17_HUMAN	zinc finger protein 17	355					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		TCACACTGGAGAAAGGCCTTT	0.388													42	187	---	---	---	---	PASS
STK35	140901	broad.mit.edu	37	20	2083973	2083973	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr20:2083973C>T	uc010gak.2	+	2	854	c.854C>T	c.(853-855)TCG>TTG	p.S285L	STK35_uc010zpu.1_Missense_Mutation_p.S152L|STK35_uc002wfw.3_Missense_Mutation_p.S152L	NM_080836	NP_543026	Q8TDR2	STK35_HUMAN	serine/threonine kinase 35	285	Protein kinase.					cytoplasm|nucleolus	ATP binding|protein serine/threonine kinase activity			ovary(1)	1						AACAAGAGCTCGCAGCTTTAC	0.647													6	63	---	---	---	---	PASS
ZNF341	84905	broad.mit.edu	37	20	32379198	32379198	+	Nonsense_Mutation	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr20:32379198G>T	uc002wzy.2	+	15	2460	c.2440G>T	c.(2440-2442)GAG>TAG	p.E814*	ZNF341_uc002wzx.2_Nonsense_Mutation_p.E807*|ZNF341_uc010geq.2_Nonsense_Mutation_p.E724*|ZNF341_uc010ger.2_RNA|ZNF341_uc002wzz.2_Nonsense_Mutation_p.E241*	NM_032819	NP_116208	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	814					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						CGCGGAAACTGAGCTGGTGGT	0.711													7	69	---	---	---	---	PASS
CYYR1	116159	broad.mit.edu	37	21	27840880	27840880	+	Silent	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr21:27840880G>T	uc002ymd.2	-	4	727	c.405C>A	c.(403-405)ACC>ACA	p.T135T	CYYR1_uc011ack.1_RNA|CYYR1_uc002yme.2_Silent_p.T136T	NM_052954	NP_443186	Q96J86	CYYR1_HUMAN	cysteine and tyrosine-rich 1 protein precursor	135	Cytoplasmic (Potential).					integral to membrane					0						GACCCTGTGGGGTGGGGGAGT	0.532													20	101	---	---	---	---	PASS
GGT5	2687	broad.mit.edu	37	22	24621251	24621251	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr22:24621251C>T	uc002zzo.3	-	10	1882	c.1465G>A	c.(1465-1467)GGG>AGG	p.G489R	GGT5_uc002zzp.3_Missense_Mutation_p.G490R|GGT5_uc002zzr.3_Missense_Mutation_p.G457R|GGT5_uc002zzq.3_Missense_Mutation_p.G457R|GGT5_uc011ajm.1_Missense_Mutation_p.G413R	NM_004121	NP_004112	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5 isoform b	489	Extracellular (Potential).				glutathione biosynthetic process|hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	integral to membrane|plasma membrane	acyltransferase activity|gamma-glutamyltransferase activity			ovary(2)|skin(1)	3						CCGCCAGCCCCGCCAATCACT	0.622													26	92	---	---	---	---	PASS
TOM1	10043	broad.mit.edu	37	22	35742925	35742925	+	Silent	SNP	T	G	G	rs743810	byFrequency	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr22:35742925T>G	uc003ann.2	+	14	1412	c.1287T>G	c.(1285-1287)GGT>GGG	p.G429G	TOM1_uc011ami.1_Silent_p.G396G|TOM1_uc011amj.1_Silent_p.G272G|TOM1_uc003ans.2_Silent_p.G272G|TOM1_uc011amk.1_Silent_p.G391G|TOM1_uc003anp.2_Silent_p.G429G|TOM1_uc011aml.1_Silent_p.G384G|TOM1_uc003ano.2_RNA|TOM1_uc003anq.2_Silent_p.G423G|TOM1_uc003anr.2_Silent_p.G272G	NM_005488	NP_005479	O60784	TOM1_HUMAN	target of myb1 isoform 1	429					endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1						CTTCCCAGGGTAATGATGCGG	0.662													5	224	---	---	---	---	PASS
APOL1	8542	broad.mit.edu	37	22	36661373	36661373	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr22:36661373G>T	uc003apf.2	+	6	659	c.491G>T	c.(490-492)GGG>GTG	p.G164V	APOL1_uc011amn.1_Missense_Mutation_p.G41V|APOL1_uc003apc.2_RNA|APOL1_uc003ape.2_Missense_Mutation_p.G180V|APOL1_uc011amo.1_Missense_Mutation_p.G41V|APOL1_uc011amp.1_Missense_Mutation_p.G164V|APOL1_uc011amq.1_Missense_Mutation_p.G146V|APOL1_uc010gwx.2_Missense_Mutation_p.G41V	NM_003661	NP_003652	O14791	APOL1_HUMAN	apolipoprotein L1 isoform a precursor	164					cholesterol metabolic process|cytolysis|innate immune response|killing of cells of other organism|lipid transport|lipoprotein metabolic process	high-density lipoprotein particle|very-low-density lipoprotein particle	chloride channel activity|lipid binding|protein binding			breast(2)|ovary(1)	3						CTTGCAGATGGGGTTCAGAAG	0.522													39	215	---	---	---	---	PASS
TBC1D22A	25771	broad.mit.edu	37	22	47432981	47432981	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr22:47432981C>T	uc003bib.2	+	11	1351	c.1216C>T	c.(1216-1218)CAC>TAC	p.H406Y	TBC1D22A_uc010haf.2_Missense_Mutation_p.H376Y|TBC1D22A_uc003bic.2_Missense_Mutation_p.H347Y|TBC1D22A_uc003bie.2_Missense_Mutation_p.H328Y|TBC1D22A_uc003bid.2_RNA|TBC1D22A_uc010hag.2_RNA|TBC1D22A_uc003bif.2_Missense_Mutation_p.H359Y	NM_014346	NP_055161	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	406	Rab-GAP TBC.					intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		AGTGCACCGGCACCTGGACCA	0.597													17	110	---	---	---	---	PASS
SSX8	280659	broad.mit.edu	37	X	52662529	52662529	+	RNA	SNP	A	G	G	rs150583046	by1000genomes	TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chrX:52662529A>G	uc011mob.1	+	8		c.978A>G				NR_027250				Homo sapiens cDNA FLJ56587 complete cds, highly similar to Protein SSX8.												0						TGTTCACAACAGTGAAAAGTT	0.438													3	31	---	---	---	---	PASS
TSIX	9383	broad.mit.edu	37	X	73046744	73046744	+	RNA	SNP	T	C	C			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chrX:73046744T>C	uc004ebn.2	+	1		c.34705T>C			XIST_uc004ebm.1_RNA	NR_003255				Homo sapiens XIST antisense RNA (non-protein coding) (TSIX), non-coding RNA.												0						TCTTAAGACTTCTAACTCAAG	0.502													43	70	---	---	---	---	PASS
TSIX	9383	broad.mit.edu	37	X	73046745	73046745	+	RNA	SNP	C	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chrX:73046745C>T	uc004ebn.2	+	1		c.34706C>T			XIST_uc004ebm.1_RNA	NR_003255				Homo sapiens XIST antisense RNA (non-protein coding) (TSIX), non-coding RNA.												0						CTTAAGACTTCTAACTCAAGC	0.502													46	68	---	---	---	---	PASS
MAGEA11	4110	broad.mit.edu	37	X	148798036	148798036	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chrX:148798036T>A	uc004fdq.2	+	5	992	c.890T>A	c.(889-891)CTC>CAC	p.L297H	HSFX2_uc004fdl.2_Intron|HSFX1_uc004fdm.2_Intron|MAGEA11_uc004fdr.2_Missense_Mutation_p.L268H	NM_005366	NP_005357	P43364	MAGAB_HUMAN	melanoma antigen family A, 11 isoform a	297	MAGE.					cytoplasm|nucleus	protein binding			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					TCCCTCAACCTCTCTTATGAT	0.498													56	78	---	---	---	---	PASS
TTC4	7268	broad.mit.edu	37	1	55186887	55186893	+	Frame_Shift_Del	DEL	CCTGCCA	-	-			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:55186887_55186893delCCTGCCA	uc001cxx.3	+	4	496_502	c.443_449delCCTGCCA	c.(442-450)CCCTGCCACfs	p.P148fs	C1orf175_uc001cxq.2_RNA|TTC4_uc001cxw.3_Frame_Shift_Del_p.P148fs|TTC4_uc001cxv.2_Frame_Shift_Del_p.P159fs	NM_004623	NP_004614	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	148_150	TPR 2.						binding				0						AAGCTAAAACCCTGCCACCTCAAAGCA	0.357													85	8	---	---	---	---	
RASAL2	9462	broad.mit.edu	37	1	178433459	178433461	+	In_Frame_Del	DEL	CAG	-	-			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr1:178433459_178433461delCAG	uc001glr.2	+	13	3001_3003	c.2876_2878delCAG	c.(2875-2880)ACAGCA>ACA	p.A961del	RASAL2_uc001glq.2_In_Frame_Del_p.A1102del|RASAL2_uc009wxc.2_In_Frame_Del_p.A475del	NM_004841	NP_004832	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 1	961					negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5						GTAGAGAGGACAGCAGCCTGGGT	0.483													103	14	---	---	---	---	
REV1	51455	broad.mit.edu	37	2	100055101	100055102	+	Frame_Shift_Ins	INS	-	T	T			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr2:100055101_100055102insT	uc002tad.2	-	6	1386_1387	c.1174_1175insA	c.(1174-1176)ATGfs	p.M392fs	REV1_uc002tac.2_Frame_Shift_Ins_p.M392fs|REV1_uc002tae.1_Frame_Shift_Ins_p.M371fs	NM_016316	NP_057400	Q9UBZ9	REV1_HUMAN	REV1-like isoform 1	392					DNA replication|error-prone translesion synthesis|response to UV	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding			ovary(2)	2						GCCTGTTTTCATTTTTTTTAAC	0.351								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					263	9	---	---	---	---	
SDAD1	55153	broad.mit.edu	37	4	76888458	76888458	+	Frame_Shift_Del	DEL	C	-	-			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr4:76888458delC	uc003hje.3	-	12	1136	c.1017delG	c.(1015-1017)TTGfs	p.L339fs	SDAD1_uc003hjf.3_Frame_Shift_Del_p.L242fs|SDAD1_uc011cbr.1_Frame_Shift_Del_p.L302fs	NM_018115	NP_060585	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	339					protein transport|ribosomal large subunit biogenesis	nucleolus	protein binding			ovary(1)	1			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GAAACCTTTGCAAAAAGGGAT	0.418													60	15	---	---	---	---	
GAPVD1	26130	broad.mit.edu	37	9	128113082	128113086	+	Frame_Shift_Del	DEL	TGCGC	-	-			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr9:128113082_128113086delTGCGC	uc010mwx.2	+	23	3880_3884	c.3554_3558delTGCGC	c.(3553-3558)ATGCGCfs	p.M1185fs	GAPVD1_uc004bpp.2_Frame_Shift_Del_p.M1194fs|GAPVD1_uc004bpq.2_Frame_Shift_Del_p.M1167fs|GAPVD1_uc004bpr.2_Frame_Shift_Del_p.M1146fs|GAPVD1_uc004bps.2_Frame_Shift_Del_p.M1140fs|GAPVD1_uc004bpt.2_Frame_Shift_Del_p.M200fs	NM_015635	NP_056450	Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1185_1186					endocytosis|regulation of protein transport|regulation of small GTPase mediated signal transduction|signal transduction	cytosol|endosome|membrane	GTPase activating protein binding|GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4						CAAGAAACAATGCGCTGTGTGTGCC	0.361													264	32	---	---	---	---	
BRCA2	675	broad.mit.edu	37	13	32910661	32910662	+	Frame_Shift_Ins	INS	-	A	A			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr13:32910661_32910662insA	uc001uub.1	+	11	2396_2397	c.2169_2170insA	c.(2167-2172)AGCAAAfs	p.S723fs		NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	723_724	Interaction with NPM1.				cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		ATCCAAAAAGCAAAAAAGTTTC	0.376			D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			87	25	---	---	---	---	
SGK269	79834	broad.mit.edu	37	15	77407550	77407566	+	Frame_Shift_Del	DEL	CAGCAAGGAAATGACCA	-	-			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr15:77407550_77407566delCAGCAAGGAAATGACCA	uc002bcm.2	-	6	4481_4497	c.4173_4189delTGGTCATTTCCTTGCTG	c.(4171-4191)TGTGGTCATTTCCTTGCTGAAfs	p.C1391fs		NM_024776	NP_079052	Q9H792	PEAK1_HUMAN	NKF3 kinase family member	1391_1397	Protein kinase.				cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading	actin cytoskeleton|cytoplasm|focal adhesion	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding				0				STAD - Stomach adenocarcinoma(199;0.124)		TTAGGGACTTCAGCAAGGAAATGACCACAGTCCTGCT	0.479													218	16	---	---	---	---	
DSCAM	1826	broad.mit.edu	37	21	41424003	41424003	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EJ-5495-01A-01D-1576-08	TCGA-EJ-5495-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	29a06cd9-5e37-41b7-954f-173a2ab44179	695fd2d7-9426-45e1-81f0-79fbdf6ba0bf	g.chr21:41424003delA	uc002yyq.1	-	30	5519	c.5067delT	c.(5065-5067)GCTfs	p.A1689fs	DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1689	Cytoplasmic (Potential).				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CTCCAAAGTCAGCATCCGTCA	0.532													168	19	---	---	---	---	
