Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	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
KLHL17	339451	broad.mit.edu	37	1	898253	898253	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:898253G>A	uc001aca.1	+	6	1105	c.998G>A	c.(997-999)CGT>CAT	p.R333H	KLHL17_uc001acc.1_RNA|KLHL17_uc010nyb.1_Missense_Mutation_p.R56H	NM_198317	NP_938073	Q6TDP4	KLH17_HUMAN	kelch-like 17	333	Interaction with F-actin (By similarity).				actin cytoskeleton organization	actin cytoskeleton|cell junction|postsynaptic density|postsynaptic membrane	protein complex scaffold				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AGCCGCACACGTCCCCGGCGC	0.672													17	42	---	---	---	---	PASS
B3GALT6	126792	broad.mit.edu	37	1	1168415	1168415	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1168415G>A	uc001adk.2	+	1	787	c.757G>A	c.(757-759)GAC>AAC	p.D253N	SDF4_uc001adh.3_5'Flank|SDF4_uc001adi.3_5'Flank|SDF4_uc009vjv.2_5'Flank|SDF4_uc009vjw.2_5'Flank	NM_080605	NP_542172	Q96L58	B3GT6_HUMAN	beta-1,3-galactosyltransferase 6	253	Lumenal (Potential).				glycosaminoglycan biosynthetic process|protein glycosylation	Golgi cisterna membrane|Golgi medial cisterna|integral to membrane	galactosylxylosylprotein 3-beta-galactosyltransferase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.22e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GGCGCCGGTGGACGTCCAGCG	0.692													11	7	---	---	---	---	PASS
ACAP3	116983	broad.mit.edu	37	1	1235529	1235529	+	Intron	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1235529C>A	uc001aeb.2	-						ACAP3_uc001ady.2_5'Flank|ACAP3_uc001aea.2_Intron|ACAP3_uc001aec.1_Intron	NM_030649	NP_085152	Q96P50	ACAP3_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH						filopodium assembly|regulation of ARF GTPase activity|signal transduction		ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding				0						GCAGCCCCCACGCACTCACAG	0.642													30	56	---	---	---	---	PASS
PUSL1	126789	broad.mit.edu	37	1	1245137	1245137	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1245137G>A	uc001aed.2	+	5	580	c.550G>A	c.(550-552)GCT>ACT	p.A184T	ACAP3_uc001aeb.2_5'Flank|ACAP3_uc001aec.1_5'Flank|PUSL1_uc010nyi.1_Missense_Mutation_p.A23T|PUSL1_uc009vjx.2_5'UTR	NM_153339	NP_699170	Q8N0Z8	PUSL1_HUMAN	pseudouridylate synthase-like 1	184					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			skin(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;4.95e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CTTCCAGTCCGCTGGCAGCCC	0.687													4	14	---	---	---	---	PASS
PIK3CD	5293	broad.mit.edu	37	1	9777668	9777668	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9777668C>T	uc001aqb.3	+	8	1212	c.1004C>T	c.(1003-1005)GCC>GTC	p.A335V	PIK3CD_uc010oaf.1_Missense_Mutation_p.A335V|PIK3CD_uc001aqe.3_Missense_Mutation_p.A300V	NM_005026	NP_005017	O00329	PK3CD_HUMAN	catalytic phosphatidylinositol 3-kinase delta	335					phosphatidylinositol-mediated signaling|protein phosphorylation	phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(4)|skin(2)|central_nervous_system(1)	7	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)		AAAGTGAACGCCGACGAGCGG	0.602													19	50	---	---	---	---	PASS
PIK3CD	5293	broad.mit.edu	37	1	9777694	9777694	+	Intron	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9777694C>T	uc001aqb.3	+						PIK3CD_uc010oaf.1_Intron|PIK3CD_uc001aqe.3_Intron	NM_005026	NP_005017	O00329	PK3CD_HUMAN	catalytic phosphatidylinositol 3-kinase delta						phosphatidylinositol-mediated signaling|protein phosphorylation	phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(4)|skin(2)|central_nervous_system(1)	7	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)		GGTGGGGCTCCTGGGATAGGT	0.582													28	28	---	---	---	---	PASS
PIK3CD	5293	broad.mit.edu	37	1	9787039	9787039	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9787039C>T	uc001aqb.3	+	24	3278	c.3070C>T	c.(3070-3072)CGT>TGT	p.R1024C	PIK3CD_uc010oaf.1_Missense_Mutation_p.R1023C|PIK3CD_uc001aqe.3_Missense_Mutation_p.R1048C	NM_005026	NP_005017	O00329	PK3CD_HUMAN	catalytic phosphatidylinositol 3-kinase delta	1024	PI3K/PI4K.				phosphatidylinositol-mediated signaling|protein phosphorylation	phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(4)|skin(2)|central_nervous_system(1)	7	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)		CGAAGCCCTCCGTGAGAGCTG	0.577													9	65	---	---	---	---	PASS
CASZ1	54897	broad.mit.edu	37	1	10715863	10715863	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10715863G>A	uc001aro.2	-	9	1828	c.1508C>T	c.(1507-1509)ACG>ATG	p.T503M	CASZ1_uc001arp.1_Missense_Mutation_p.T503M|CASZ1_uc009vmx.2_Missense_Mutation_p.T527M	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a	503					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		CTGCTTACTCGTGAACCTCTG	0.632													21	94	---	---	---	---	PASS
UBXN11	91544	broad.mit.edu	37	1	26608936	26608936	+	Nonsense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26608936G>A	uc001blw.2	-	16	1690	c.1417C>T	c.(1417-1419)CGA>TGA	p.R473*	UBXN11_uc001blz.1_Nonsense_Mutation_p.R440*|UBXN11_uc001blv.2_Nonsense_Mutation_p.R435*|UBXN11_uc001bly.2_Nonsense_Mutation_p.R353*|UBXN11_uc001blx.2_Nonsense_Mutation_p.R231*|UBXN11_uc001bma.2_Nonsense_Mutation_p.R440*|UBXN11_uc001bmb.1_Nonsense_Mutation_p.R473*	NM_183008	NP_892120	Q5T124	UBX11_HUMAN	socius isoform 2	473						cytoplasm|cytoskeleton				ovary(1)	1						TTCGGGGCTCGGCGTGCCCGC	0.388													71	92	---	---	---	---	PASS
SF3A3	10946	broad.mit.edu	37	1	38435242	38435242	+	Splice_Site	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38435242C>G	uc001cci.2	-	13	1294	c.1170_splice	c.e13+1	p.K390_splice	SF3A3_uc010oik.1_Splice_Site_p.K337_splice	NM_006802	NP_006793	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3						nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nuclear speck	nucleic acid binding|protein binding|zinc ion binding				0	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CTGAGACTTACTTTGCCATCC	0.418													34	85	---	---	---	---	PASS
FOXJ3	22887	broad.mit.edu	37	1	42654556	42654556	+	Silent	SNP	A	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42654556A>C	uc001che.2	-	13	1809	c.1497T>G	c.(1495-1497)TCT>TCG	p.S499S	FOXJ3_uc001chf.2_Silent_p.S499S|FOXJ3_uc001chg.2_Silent_p.S499S	NM_014947	NP_055762	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	499					embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CCTGGTCTAAAGACCAGTTCT	0.368													39	53	---	---	---	---	PASS
CC2D1B	200014	broad.mit.edu	37	1	52824024	52824024	+	Silent	SNP	C	A	A	rs140467530	byFrequency	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52824024C>A	uc001ctq.1	-	13	1578	c.1440G>T	c.(1438-1440)CCG>CCT	p.P480P	CC2D1B_uc001ctr.2_Silent_p.P26P|CC2D1B_uc001cts.2_Silent_p.P171P	NM_032449	NP_115825	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	480										ovary(2)	2						CTTTATCAGCCGGGGCTGAAT	0.567													30	61	---	---	---	---	PASS
SGIP1	84251	broad.mit.edu	37	1	67109263	67109263	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67109263C>T	uc001dcr.2	+	7	537	c.320C>T	c.(319-321)TCG>TTG	p.S107L	SGIP1_uc010opd.1_5'UTR|SGIP1_uc001dcs.2_5'UTR|SGIP1_uc001dct.2_5'UTR	NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting	107	Poly-Glu.				positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3						TCAAGTGAATCGGAAGAAGAA	0.343													14	128	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144886204	144886204	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144886204C>A	uc001elw.3	-	23	3321	c.3030G>T	c.(3028-3030)AGG>AGT	p.R1010S	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.R1076S|PDE4DIP_uc001elv.3_Missense_Mutation_p.R17S	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1010	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GGAACTCAGCCCTCAGGTGGA	0.522			T	PDGFRB	MPD								61	321	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144886205	144886205	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144886205C>T	uc001elw.3	-	23	3320	c.3029G>A	c.(3028-3030)AGG>AAG	p.R1010K	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.R1076K|PDE4DIP_uc001elv.3_Missense_Mutation_p.R17K	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1010	Potential.				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GAACTCAGCCCTCAGGTGGAG	0.517			T	PDGFRB	MPD								62	323	---	---	---	---	PASS
GPR89B	51463	broad.mit.edu	37	1	147408812	147408812	+	Intron	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147408812T>G	uc001epv.3	+						GPR89B_uc010ozs.1_Intron|GPR89B_uc010ozt.1_Intron|GPR89B_uc010ozu.1_Intron|GPR89B_uc001epw.3_Intron|GPR89B_uc010ozv.1_Intron	NM_016334	NP_057418	B7ZAQ6	GPHRA_HUMAN	G protein-coupled receptor 89B						intracellular pH reduction|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein transport	Golgi cisterna membrane|Golgi-associated vesicle membrane|integral to membrane	signal transducer activity|voltage-gated anion channel activity				0	all_hematologic(923;0.0276)					TGAGAAGAAATCATTTTGTCA	0.318													46	89	---	---	---	---	PASS
SETDB1	9869	broad.mit.edu	37	1	150919447	150919447	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150919447T>C	uc001evu.2	+	10	1416	c.1226T>C	c.(1225-1227)CTG>CCG	p.L409P	SETDB1_uc009wmf.2_Missense_Mutation_p.L409P|SETDB1_uc001evv.2_Missense_Mutation_p.L409P|SETDB1_uc009wmg.1_Missense_Mutation_p.L409P	NM_001145415	NP_001138887	Q15047	SETB1_HUMAN	SET domain, bifurcated 1 isoform 1	409					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|Golgi apparatus|nucleus|plasma membrane	DNA binding|histone-lysine N-methyltransferase activity|protein binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			GCCTCTGCACTGGAGAAGAAG	0.493													46	100	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	151739754	151739754	+	IGR	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151739754C>G								OAZ3 (-4051 upstream) : OAZ3 (-4309 downstream)																							GTAACCACGACCAGCTTAAAG	0.542													59	128	---	---	---	---	PASS
SLC27A3	11000	broad.mit.edu	37	1	153752486	153752486	+	3'UTR	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153752486C>G	uc001fcz.2	+	10					SLC27A3_uc009won.2_RNA	NM_024330	NP_077306	Q5K4L6	S27A3_HUMAN	solute carrier family 27 member 3						fatty acid metabolic process	integral to membrane|mitochondrial membrane	ligase activity|nucleotide binding			ovary(1)	1	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TGAGAACTTCCACACCTGAGG	0.577													9	21	---	---	---	---	PASS
CD1E	913	broad.mit.edu	37	1	158325727	158325727	+	Silent	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158325727C>A	uc001fse.2	+	4	975	c.736C>A	c.(736-738)CGG>AGG	p.R246R	CD1E_uc010pid.1_Silent_p.R244R|CD1E_uc010pie.1_Silent_p.R147R|CD1E_uc010pif.1_Silent_p.R57R|CD1E_uc001fsd.2_Silent_p.R246R|CD1E_uc001fsk.2_Silent_p.R156R|CD1E_uc001fsj.2_Silent_p.R156R|CD1E_uc001fsc.2_Silent_p.R57R|CD1E_uc010pig.1_RNA|CD1E_uc001fsa.2_Silent_p.R57R|CD1E_uc001fsf.2_Silent_p.R246R|CD1E_uc001fry.2_Silent_p.R246R|CD1E_uc001fsg.2_Silent_p.R57R|CD1E_uc001fsh.2_Silent_p.R57R|CD1E_uc001fsi.2_Silent_p.R246R|CD1E_uc009wsv.2_Silent_p.R147R|CD1E_uc001frz.2_Silent_p.R156R|CD1E_uc009wsw.2_Silent_p.R4R	NM_030893	NP_112155	P15812	CD1E_HUMAN	CD1E antigen isoform a precursor	246	Ig-like.				antigen processing and presentation|immune response	early endosome|Golgi membrane|integral to plasma membrane|late endosome|lysosomal lumen				skin(3)	3	all_hematologic(112;0.0378)					GATGTGGATGCGGGGTGAGCA	0.642													55	136	---	---	---	---	PASS
OR6K3	391114	broad.mit.edu	37	1	158687805	158687805	+	Missense_Mutation	SNP	A	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158687805A>T	uc010pip.1	-	1	149	c.149T>A	c.(148-150)ATC>AAC	p.I50N		NM_001005327	NP_001005327	Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K,	50	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	all_hematologic(112;0.0378)					AAAAGTATAGATGAAAAGTAA	0.373													63	160	---	---	---	---	PASS
OR6K6	128371	broad.mit.edu	37	1	158725617	158725617	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158725617G>T	uc001fsw.1	+	1	1012	c.1012G>T	c.(1012-1014)GCT>TCT	p.A338S		NM_001005184	NP_001005184	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K,	338	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_hematologic(112;0.0378)					TCAGAAGAGGGCTGGTTGGGC	0.408													56	111	---	---	---	---	PASS
APCS	325	broad.mit.edu	37	1	159558188	159558188	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159558188C>T	uc001ftv.2	+	2	458	c.362C>T	c.(361-363)TCA>TTA	p.S121L		NM_001639	NP_001630	P02743	SAMP_HUMAN	serum amyloid P component precursor	121	Pentaxin.				acute-phase response|chaperone-mediated protein complex assembly|protein folding	extracellular space	metal ion binding|sugar binding|unfolded protein binding			ovary(1)|breast(1)	2	all_hematologic(112;0.0429)					GAGTCCTCATCAGGTATTGCT	0.468													51	88	---	---	---	---	PASS
RFWD2	64326	broad.mit.edu	37	1	175937610	175937610	+	Intron	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175937610C>A	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc009wwv.2_Intron|RFWD2_uc001gkt.1_Intron|SCARNA3_uc001gkx.1_RNA	NM_022457	NP_071902	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2 isoform a						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0						TATGTAGGATCGCTGCAATCT	0.428													64	131	---	---	---	---	PASS
TDRD5	163589	broad.mit.edu	37	1	179660053	179660053	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179660053C>A	uc001gnf.1	+	17	3171	c.2921C>A	c.(2920-2922)CCC>CAC	p.P974H	TDRD5_uc010pnp.1_Missense_Mutation_p.P1028H|TDRD5_uc001gnh.1_Missense_Mutation_p.P529H	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	974					DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5						CACTGGTACCCCAGTGTGAAA	0.532													33	55	---	---	---	---	PASS
ATP2B4	493	broad.mit.edu	37	1	203670058	203670058	+	Intron	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203670058G>A	uc001gzw.2	+						ATP2B4_uc001gzv.2_Intron|ATP2B4_uc009xaq.2_Intron	NM_001684	NP_001675	P23634	AT2B4_HUMAN	plasma membrane calcium ATPase 4 isoform 4b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|skin(1)	3	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			AAAGGTAAGGGGCATCTGGAA	0.488													14	46	---	---	---	---	PASS
KCNK2	3776	broad.mit.edu	37	1	215408273	215408273	+	Nonsense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215408273C>T	uc001hkq.2	+	7	1235	c.1066C>T	c.(1066-1068)CAG>TAG	p.Q356*	KCNK2_uc001hko.2_Nonsense_Mutation_p.Q352*|KCNK2_uc009xdm.2_RNA|KCNK2_uc001hkp.2_RNA|KCNK2_uc001hkr.3_Nonsense_Mutation_p.Q341*	NM_001017425	NP_001017425	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2 isoform	356	Cytoplasmic (Potential).|Required for basal channel activity (By similarity).						outward rectifier potassium channel activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)	TGACAAGTTCCAGCGGGCCAC	0.552													24	144	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216270496	216270496	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216270496G>T	uc001hku.1	-	22	5074	c.4687C>A	c.(4687-4689)CCT>ACT	p.P1563T		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1563	Laminin G-like 1.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TGATTGCCAGGTGATGCTGCA	0.383										HNSCC(13;0.011)			30	52	---	---	---	---	PASS
FBXO28	23219	broad.mit.edu	37	1	224345054	224345054	+	Missense_Mutation	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224345054T>G	uc001hoh.2	+	5	754	c.713T>G	c.(712-714)GTT>GGT	p.V238G	FBXO28_uc009xef.2_Missense_Mutation_p.F173V|FBXO28_uc010pvc.1_Missense_Mutation_p.V33G	NM_015176	NP_055991	Q9NVF7	FBX28_HUMAN	F-box protein 28 isoform a	238										ovary(2)|kidney(2)|lung(1)	5	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)		TCCTCCACAGTTCCAGGACCG	0.398													70	132	---	---	---	---	PASS
ZNF496	84838	broad.mit.edu	37	1	247492835	247492835	+	Nonsense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247492835C>A	uc001ico.2	-	3	511	c.46G>T	c.(46-48)GAG>TAG	p.E16*	ZNF496_uc009xgv.2_Nonsense_Mutation_p.E16*|ZNF496_uc001icp.2_Nonsense_Mutation_p.E16*|ZNF496_uc010pyv.1_Nonsense_Mutation_p.E16*	NM_032752	NP_116141	Q96IT1	ZN496_HUMAN	zinc finger protein 496	16					positive regulation of transcription, DNA-dependent|viral reproduction		DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			CTGGGCTCCTCACTTTCCTTC	0.602													39	141	---	---	---	---	PASS
OR2L2	26246	broad.mit.edu	37	1	248202133	248202133	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248202133C>T	uc001idw.2	+	1	660	c.564C>T	c.(562-564)TGC>TGT	p.C188C	OR2L13_uc001ids.2_Intron	NM_001004686	NP_001004686	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L,	188	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			CGCTAGCCTGCACAGACACTT	0.463													62	325	---	---	---	---	PASS
TMEM18	129787	broad.mit.edu	37	2	675626	675626	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:675626G>A	uc002qwl.2	-	2	156	c.62C>T	c.(61-63)ACG>ATG	p.T21M	TMEM18_uc002qwk.2_RNA|uc002qwm.1_5'Flank	NM_152834	NP_690047	Q96B42	TMM18_HUMAN	transmembrane protein 18	21					cell migration	integral to membrane|nuclear membrane				ovary(1)	1	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;5.27e-05)|all_epithelial(98;2.11e-06)|Ovarian(717;0.0253)		all cancers(51;1.95e-21)|Epithelial(75;9.47e-21)|OV - Ovarian serous cystadenocarcinoma(76;8.15e-18)|GBM - Glioblastoma multiforme(21;0.0285)		AGTCCAGTCCGTCTGCTGTAG	0.647													20	19	---	---	---	---	PASS
MYT1L	23040	broad.mit.edu	37	2	1926397	1926397	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1926397G>T	uc002qxe.2	-	10	1971	c.1144C>A	c.(1144-1146)CTC>ATC	p.L382I	MYT1L_uc002qxd.2_Missense_Mutation_p.L382I|MYT1L_uc010ewl.1_RNA	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	382					cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		AGCCGCATGAGGTTCAGCATG	0.592													8	52	---	---	---	---	PASS
C2orf71	388939	broad.mit.edu	37	2	29295558	29295558	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29295558G>T	uc002rmt.1	-	1	1570	c.1570C>A	c.(1570-1572)CCA>ACA	p.P524T		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	524					response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1						GCCTGAAATGGGCTTTCCCGG	0.522													42	179	---	---	---	---	PASS
CRIM1	51232	broad.mit.edu	37	2	36771551	36771551	+	Missense_Mutation	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36771551A>G	uc002rpd.2	+	15	2695	c.2656A>G	c.(2656-2658)ATT>GTT	p.I886V		NM_016441	NP_057525	Q9NZV1	CRIM1_HUMAN	cysteine-rich motor neuron 1 precursor	886	Extracellular (Potential).				nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				CAATATACCCATTGAGAAGAC	0.438													44	53	---	---	---	---	PASS
EML4	27436	broad.mit.edu	37	2	42511812	42511812	+	Missense_Mutation	SNP	G	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42511812G>C	uc002rsi.2	+	9	1242	c.980G>C	c.(979-981)GGA>GCA	p.G327A	EML4_uc010fap.2_Missense_Mutation_p.G269A|EML4_uc002rsj.2_5'Flank	NM_019063	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	327	WD 1.				microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250						ATTGCAACTGGACAGATAGCT	0.378			T	ALK	NSCLC								31	88	---	---	---	---	PASS
EML4	27436	broad.mit.edu	37	2	42511825	42511825	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42511825C>T	uc002rsi.2	+	9	1255	c.993C>T	c.(991-993)GGC>GGT	p.G331G	EML4_uc010fap.2_Silent_p.G273G|EML4_uc002rsj.2_5'Flank	NM_019063	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	331	WD 1.				microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250						AGATAGCTGGCGTGGATAAAG	0.378			T	ALK	NSCLC								31	93	---	---	---	---	PASS
CCDC85A	114800	broad.mit.edu	37	2	56570097	56570097	+	Intron	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56570097G>A	uc002rzn.2	+							NM_001080433	NP_001073902	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A											breast(3)|ovary(2)	5			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CCAGGTGGGTGACTTCCAGAA	0.383													10	11	---	---	---	---	PASS
ANXA4	307	broad.mit.edu	37	2	70052638	70052638	+	Silent	SNP	A	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70052638A>T	uc002sfr.3	+	13	1184	c.957A>T	c.(955-957)GGA>GGT	p.G319G	ANXA4_uc002sfs.3_Silent_p.G297G|ANXA4_uc010yqo.1_Silent_p.G235G	NM_001153	NP_001144	P09525	ANXA4_HUMAN	annexin IV	317					anti-apoptosis|signal transduction	cytoplasm	calcium ion binding|calcium-dependent phospholipid binding|phospholipase inhibitor activity				0						TCTGTGGAGGAGATGATTAAA	0.343													4	98	---	---	---	---	PASS
SEMA4F	10505	broad.mit.edu	37	2	74900824	74900824	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74900824G>T	uc002sna.1	+	7	802	c.691G>T	c.(691-693)GTG>TTG	p.V231L	SEMA4F_uc010ysb.1_3'UTR|SEMA4F_uc010ffq.1_Missense_Mutation_p.V198L|SEMA4F_uc010ffr.1_Intron|SEMA4F_uc002snb.1_5'UTR|SEMA4F_uc002snc.1_Intron	NM_004263	NP_004254	O95754	SEM4F_HUMAN	semaphorin W precursor	231	Sema.|Extracellular (Potential).				cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			ovary(2)|pancreas(1)|skin(1)	4						TGTCGCAGCCGTGGCCTTGAG	0.567													53	74	---	---	---	---	PASS
SEMA4F	10505	broad.mit.edu	37	2	74900882	74900882	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74900882T>C	uc002sna.1	+	7	860	c.749T>C	c.(748-750)TTC>TCC	p.F250S	SEMA4F_uc010ysb.1_3'UTR|SEMA4F_uc010ffq.1_Missense_Mutation_p.F217S|SEMA4F_uc010ffr.1_Intron|SEMA4F_uc002snb.1_5'UTR|SEMA4F_uc002snc.1_Intron	NM_004263	NP_004254	O95754	SEM4F_HUMAN	semaphorin W precursor	250	Sema.|Extracellular (Potential).				cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			ovary(2)|pancreas(1)|skin(1)	4						ATCTACTTCTTCTTTACGGAG	0.577													50	178	---	---	---	---	PASS
EIF2AK3	9451	broad.mit.edu	37	2	88888334	88888334	+	Silent	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88888334G>T	uc002stc.3	-	7	1453	c.1251C>A	c.(1249-1251)GTC>GTA	p.V417V		NM_004836	NP_004827	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha	417	Lumenal (Potential).				activation of caspase activity|bone mineralization|calcium-mediated signaling|chondrocyte development|endocrine pancreas development|endoplasmic reticulum organization|endoplasmic reticulum unfolded protein response|ER overload response|insulin secretion|insulin-like growth factor receptor signaling pathway|negative regulation of myelination|negative regulation of translational initiation in response to stress|protein autophosphorylation|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|identical protein binding			ovary(3)	3						TTTCATTAGTGACAGATTCCA	0.363													33	138	---	---	---	---	PASS
TMEM131	23505	broad.mit.edu	37	2	98429176	98429176	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98429176T>C	uc002syh.3	-	16	1883	c.1654A>G	c.(1654-1656)ATA>GTA	p.I552V		NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein	552						integral to membrane				ovary(4)|central_nervous_system(2)	6						CCAAAATCTATGAAACGTTCC	0.303													21	76	---	---	---	---	PASS
CCDC115	84317	broad.mit.edu	37	2	131098603	131098603	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131098603C>A	uc002tqy.1	-	4	532	c.308G>T	c.(307-309)AGG>ATG	p.R103M	CCDC115_uc002tqw.1_Missense_Mutation_p.R95M|CCDC115_uc010zaf.1_Missense_Mutation_p.R98M|CCDC115_uc002tqx.2_Missense_Mutation_p.R98M|CCDC115_uc002tqz.1_Missense_Mutation_p.R103M|IMP4_uc002tra.1_5'Flank	NM_032357	NP_115733	Q96NT0	CC115_HUMAN	coiled-coil domain containing 115	103						endosome|lysosome					0	Colorectal(110;0.1)					GCCCTTGCGCCTCCGCAGACC	0.478													11	21	---	---	---	---	PASS
UBXN4	23190	broad.mit.edu	37	2	136527327	136527327	+	Intron	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136527327T>G	uc002tur.2	+						UBXN4_uc002tus.2_Intron	NM_014607	NP_055422	Q92575	UBXN4_HUMAN	UBX domain containing 2						response to unfolded protein	endoplasmic reticulum membrane|nuclear envelope	protein binding			skin(2)	2						GGTTTTTTTTTTTTTAATACA	0.259													13	44	---	---	---	---	PASS
CXCR4	7852	broad.mit.edu	37	2	136872656	136872656	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136872656T>C	uc002tuz.2	-	2	937	c.842A>G	c.(841-843)CAC>CGC	p.H281R	CXCR4_uc002tuy.2_Missense_Mutation_p.H285R|CXCR4_uc010fnk.2_Missense_Mutation_p.H266R	NM_003467	NP_003458	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4 isoform b	281	Extracellular.				activation of MAPK activity|apoptosis|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|inflammatory response|initiation of viral infection|regulation of chemotaxis|response to hypoxia|response to virus	cell leading edge|cell surface|cytoplasmic membrane-bounded vesicle|integral to membrane|plasma membrane	actin binding|C-X-C chemokine receptor activity|coreceptor activity|myosin light chain binding|ubiquitin binding|ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)	AATCCACTTGTGCACAGTGTT	0.488													154	585	---	---	---	---	PASS
KCNH7	90134	broad.mit.edu	37	2	163393587	163393587	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163393587G>A	uc002uch.1	-	3	523	c.311C>T	c.(310-312)TCC>TTC	p.S104F	KCNH7_uc002uci.2_Missense_Mutation_p.S104F	NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,	104	Cytoplasmic (Potential).|PAC.				regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)	AATAAAAGTGGACCCTAAGGA	0.299													41	70	---	---	---	---	PASS
SCN9A	6335	broad.mit.edu	37	2	167141224	167141224	+	Silent	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167141224G>A	uc010fpl.2	-	12	2054	c.1713C>T	c.(1711-1713)GCC>GCT	p.A571A	uc002udp.2_Intron|SCN9A_uc002udr.1_Silent_p.A442A|SCN9A_uc002uds.1_Silent_p.A442A|SCN9A_uc002udt.1_Silent_p.A442A	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	571						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)	GCTCATCATCGGCAAATTCAG	0.493													29	91	---	---	---	---	PASS
GAD1	2571	broad.mit.edu	37	2	171693312	171693312	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171693312G>A	uc002ugi.2	+	6	979	c.557G>A	c.(556-558)CGA>CAA	p.R186Q	GAD1_uc002ugh.2_Missense_Mutation_p.R186Q	NM_000817	NP_000808	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 isoform GAD67	186					glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion|protein-pyridoxal-5-phosphate linkage	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|plasma membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			ovary(1)	1					L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	GGTCATCCTCGATTTTTCAAC	0.453													26	37	---	---	---	---	PASS
HNRNPA3	220988	broad.mit.edu	37	2	178080348	178080348	+	Nonsense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178080348C>T	uc002ulb.1	+	2	260	c.154C>T	c.(154-156)CGA>TGA	p.R52*	HNRNPA3_uc002ulc.1_Nonsense_Mutation_p.R52*|HNRNPA3_uc002uld.2_Nonsense_Mutation_p.R30*|HNRNPA3_uc002ule.2_5'Flank	NM_194247	NP_919223	P51991	ROA3_HUMAN	heterogeneous nuclear ribonucleoprotein A3	52	RRM 1.					catalytic step 2 spliceosome|nucleolus|nucleoplasm	nucleotide binding|protein binding|RNA binding			ovary(2)	2						TGATAGTTTACGAGAACATTT	0.428													31	104	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179396364	179396364	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179396364G>A	uc010zfg.1	-	307	97498	c.97274C>T	c.(97273-97275)ACG>ATG	p.T32425M	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.T26120M|TTN_uc010zfi.1_Missense_Mutation_p.T26053M|TTN_uc010zfj.1_Missense_Mutation_p.T25928M|TTN_uc002umq.2_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	33352							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)			GACTCCACTCGTGTTGGTGTA	0.453													55	75	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179435080	179435080	+	Missense_Mutation	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179435080T>G	uc010zfg.1	-	275	68299	c.68075A>C	c.(68074-68076)CAG>CCG	p.Q22692P	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.Q16387P|TTN_uc010zfi.1_Missense_Mutation_p.Q16320P|TTN_uc010zfj.1_Missense_Mutation_p.Q16195P	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	23619							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)			GCTGAGAGTCTGCACATTGGC	0.423													9	53	---	---	---	---	PASS
WDR75	84128	broad.mit.edu	37	2	190335583	190335583	+	Missense_Mutation	SNP	A	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190335583A>C	uc002uql.1	+	18	2088	c.2028A>C	c.(2026-2028)AAA>AAC	p.K676N	WDR75_uc002uqm.1_Missense_Mutation_p.K612N|WDR75_uc002uqn.1_Missense_Mutation_p.K454N|WDR75_uc002uqo.1_Missense_Mutation_p.K454N	NM_032168	NP_115544	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	676						nucleolus				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)			CAGAAGAAAAACTCACACCAA	0.348													11	30	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196892735	196892735	+	Silent	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196892735A>G	uc002utj.3	-	6	536	c.435T>C	c.(433-435)GAT>GAC	p.D145D		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	145	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						TTGTGCTTCCATCAGGGACAG	0.378													99	169	---	---	---	---	PASS
CPS1	1373	broad.mit.edu	37	2	211525340	211525340	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211525340G>T	uc002vee.3	+	32	4020	c.3888G>T	c.(3886-3888)TTG>TTT	p.L1296F	CPS1_uc010fur.2_Missense_Mutation_p.L1302F|CPS1_uc010fus.2_Missense_Mutation_p.L845F	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b	1296					carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)		TTCCAACATTGGACCATCCCA	0.363													43	179	---	---	---	---	PASS
SPAG16	79582	broad.mit.edu	37	2	214794767	214794767	+	Missense_Mutation	SNP	A	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214794767A>T	uc002veq.2	+	12	1390	c.1298A>T	c.(1297-1299)GAA>GTA	p.E433V	SPAG16_uc010fuz.1_Missense_Mutation_p.E284V|SPAG16_uc002ver.2_Missense_Mutation_p.E379V|SPAG16_uc010zjk.1_Missense_Mutation_p.E339V	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1	433					cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		TTGACCTTTGAAGGACACAGC	0.433													32	138	---	---	---	---	PASS
DOCK10	55619	broad.mit.edu	37	2	225669817	225669817	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225669817C>T	uc010fwz.1	-	37	4315	c.4076G>A	c.(4075-4077)AGA>AAA	p.R1359K	DOCK10_uc002vob.2_Missense_Mutation_p.R1353K|DOCK10_uc002voa.2_Missense_Mutation_p.R15K|DOCK10_uc002voc.2_Missense_Mutation_p.R213K	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1359							GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GCTGGGAGCTCTCTGCCAGTA	0.378													18	29	---	---	---	---	PASS
BRPF1	7862	broad.mit.edu	37	3	9786059	9786059	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9786059C>T	uc003bse.2	+	9	3168	c.2769C>T	c.(2767-2769)CAC>CAT	p.H923H	BRPF1_uc003bsf.2_Silent_p.H929H|BRPF1_uc003bsg.2_Silent_p.H922H|BRPF1_uc011ati.1_Intron	NM_004634	NP_004625	P55201	BRPF1_HUMAN	bromodomain and PHD finger-containing protein 1	923	Required for RUNX1 and RUNX2 transcriptional activation.				histone H3 acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|MOZ/MORF histone acetyltransferase complex|plasma membrane	DNA binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Medulloblastoma(99;0.227)					CCCCCAGCCACGGAGGCAGTC	0.667													23	13	---	---	---	---	PASS
ULK4	54986	broad.mit.edu	37	3	41979618	41979618	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41979618G>T	uc003ckv.3	-	3	411	c.210C>A	c.(208-210)CAC>CAA	p.H70Q	ULK4_uc003ckw.2_Missense_Mutation_p.H70Q|ULK4_uc003ckx.1_Missense_Mutation_p.H70Q	NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4	70	Protein kinase.						ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CTAGCCAGAGGTGGTTGCTTG	0.348													35	30	---	---	---	---	PASS
TRAK1	22906	broad.mit.edu	37	3	42251744	42251744	+	Intron	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42251744G>A	uc003cky.2	+						TRAK1_uc011azh.1_Missense_Mutation_p.G744R|TRAK1_uc011azi.1_Intron|TRAK1_uc011azj.1_Missense_Mutation_p.G670R|TRAK1_uc003cla.2_Missense_Mutation_p.G686R	NM_001042646	NP_001036111	Q9UPV9	TRAK1_HUMAN	OGT(O-Glc-NAc transferase)-interacting protein						endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1						TCGTCTGTGTGGGTGATGATT	0.493													206	194	---	---	---	---	PASS
KIF9	64147	broad.mit.edu	37	3	47316827	47316827	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47316827C>T	uc010hjp.2	-	4	851	c.247G>A	c.(247-249)GAT>AAT	p.D83N	KIF9_uc003cqx.2_Missense_Mutation_p.D83N|KIF9_uc003cqy.2_Missense_Mutation_p.D83N|KIF9_uc011bat.1_RNA|KIF9_uc011bau.1_RNA|KIF9_uc003cra.3_RNA	NM_001134878	NP_001128350	Q9HAQ2	KIF9_HUMAN	kinesin family member 9 isoform 2	83	Kinesin-motor.				blood coagulation|microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(1)	1		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		TTATAGCCATCGAGGGCCTGA	0.388													35	31	---	---	---	---	PASS
CNTN3	5067	broad.mit.edu	37	3	74334634	74334634	+	Silent	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74334634G>A	uc003dpm.1	-	19	2606	c.2526C>T	c.(2524-2526)TAC>TAT	p.Y842Y		NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor	842	Fibronectin type-III 3.				cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CCCCATTCCAGTACCGCACCT	0.463													111	93	---	---	---	---	PASS
OR5H14	403273	broad.mit.edu	37	3	97869132	97869132	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97869132C>A	uc003dsg.1	+	1	903	c.903C>A	c.(901-903)TTC>TTA	p.F301L		NM_001005514	NP_001005514	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H,	301	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						TAGCTTCATTCACAAAAATGT	0.303													9	119	---	---	---	---	PASS
OR5H6	79295	broad.mit.edu	37	3	97984036	97984036	+	Missense_Mutation	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97984036C>G	uc003dsi.1	+	1	908	c.908C>G	c.(907-909)CCC>CGC	p.P303R		NM_001005479	NP_001005479	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H,	303	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|large_intestine(1)	3						TTATTAAATCCCATGATCTAC	0.378													13	130	---	---	---	---	PASS
TOMM70A	9868	broad.mit.edu	37	3	100105680	100105680	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100105680T>C	uc003dtw.2	-	2	899	c.467A>G	c.(466-468)TAT>TGT	p.Y156C		NM_014820	NP_055635	O94826	TOM70_HUMAN	translocase of outer mitochondrial membrane 70	156	Cytoplasmic (Potential).|TPR 2.				protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane translocase complex	protein binding|protein transmembrane transporter activity			ovary(1)	1						TCTGTTTTGATAAAATGTAGA	0.348													45	145	---	---	---	---	PASS
RG9MTD1	54931	broad.mit.edu	37	3	101284244	101284244	+	Missense_Mutation	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101284244T>G	uc003duz.2	+	2	767	c.619T>G	c.(619-621)TTT>GTT	p.F207V		NM_017819	NP_060289	Q7L0Y3	MRRP1_HUMAN	RNA (guanine-9-) methyltransferase domain	207					tRNA processing	mitochondrion	methyltransferase activity|protein binding			ovary(1)	1						ACCTTTGGTTTTTGACATGGC	0.393													31	288	---	---	---	---	PASS
ZPLD1	131368	broad.mit.edu	37	3	102181156	102181156	+	Missense_Mutation	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102181156C>G	uc003dvs.1	+	13	1496	c.614C>G	c.(613-615)CCC>CGC	p.P205R	ZPLD1_uc003dvt.1_Missense_Mutation_p.P221R|ZPLD1_uc011bhg.1_Missense_Mutation_p.P205R	NM_175056	NP_778226	Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	205	ZP.|Extracellular (Potential).					integral to membrane				ovary(2)|skin(2)|central_nervous_system(1)	5						TTAATTATCCCCAGTATAGGA	0.343													12	106	---	---	---	---	PASS
IFT122	55764	broad.mit.edu	37	3	129237946	129237946	+	Intron	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129237946C>G	uc003emm.2	+						IFT122_uc003eml.2_Intron|IFT122_uc003emn.2_Intron|IFT122_uc003emo.2_Intron|IFT122_uc003emp.2_Intron|IFT122_uc010htc.2_Intron|IFT122_uc011bky.1_Intron|IFT122_uc003emq.2_Intron|IFT122_uc003emr.2_Intron|IFT122_uc011bla.1_Intron|IFT122_uc010hte.2_Intron|IFT122_uc003ems.2_Intron	NM_052989	NP_443715	Q9HBG6	IF122_HUMAN	WD repeat domain 10 isoform 2						camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2						CCAGATCCCTCCAGGCTCCCA	0.572													17	425	---	---	---	---	PASS
AMOTL2	51421	broad.mit.edu	37	3	134089920	134089920	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134089920G>A	uc003eqf.2	-	2	647	c.530C>T	c.(529-531)GCC>GTC	p.A177V	AMOTL2_uc003eqg.1_Missense_Mutation_p.A119V|AMOTL2_uc003eqh.1_Missense_Mutation_p.A119V	NM_016201	NP_057285	Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	119										large_intestine(1)	1						TGCCTGCTGGGCCGCATAGTA	0.687													12	42	---	---	---	---	PASS
HLTF	6596	broad.mit.edu	37	3	148757868	148757868	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148757868C>T	uc003ewq.1	-	21	2670	c.2452G>A	c.(2452-2454)GCA>ACA	p.A818T	HLTF_uc003ewr.1_Missense_Mutation_p.A818T|HLTF_uc003ews.1_Missense_Mutation_p.A817T|HLTF_uc010hve.1_Missense_Mutation_p.A817T	NM_139048	NP_620636	Q14527	HLTF_HUMAN	helicase-like transcription factor	818					chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CTGTCACGTGCTAATTCTTCT	0.323													23	108	---	---	---	---	PASS
NLGN1	22871	broad.mit.edu	37	3	173993266	173993266	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173993266C>A	uc003fio.1	+	5	1231	c.808C>A	c.(808-810)CTG>ATG	p.L270M	NLGN1_uc010hww.1_Missense_Mutation_p.L310M|NLGN1_uc003fip.1_Missense_Mutation_p.L270M	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	287	Extracellular (Potential).				calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			TGTCAACCTGCTGACTTTATC	0.418													67	138	---	---	---	---	PASS
CCDC39	339829	broad.mit.edu	37	3	180364958	180364958	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180364958G>A	uc010hxe.2	-	11	1551	c.1436C>T	c.(1435-1437)GCG>GTG	p.A479V	CCDC39_uc003fkn.2_RNA	NM_181426	NP_852091	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	479	Potential.				axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium axoneme|cytoplasm|cytoskeleton				ovary(4)	4	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TGCTTCAAGCGCTTGTTTTTC	0.343													14	65	---	---	---	---	PASS
PSMD2	5708	broad.mit.edu	37	3	184024268	184024268	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184024268C>T	uc003fnn.1	+	15	1968	c.1935C>T	c.(1933-1935)GAC>GAT	p.D645D	PSMD2_uc011brj.1_Silent_p.D486D|PSMD2_uc011brk.1_Silent_p.D515D	NM_002808	NP_002799	Q13200	PSMD2_HUMAN	proteasome 26S non-ATPase subunit 2	645					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding				0	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)	CCCCTGCTGACATGGGAGCAC	0.363													16	170	---	---	---	---	PASS
RTP4	64108	broad.mit.edu	37	3	187089076	187089076	+	Missense_Mutation	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187089076C>G	uc003frm.2	+	2	718	c.656C>G	c.(655-657)CCC>CGC	p.P219R		NM_022147	NP_071430	Q96DX8	RTP4_HUMAN	28kD interferon responsive protein	219	Cytoplasmic (Potential).				detection of chemical stimulus involved in sensory perception of bitter taste|protein targeting to membrane	cytoplasm|integral to membrane	protein binding				0	all_cancers(143;4.66e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		AAATTAGGGCCCAGTCGAGAC	0.453													9	101	---	---	---	---	PASS
PPP2R2C	5522	broad.mit.edu	37	4	6325261	6325261	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6325261C>T	uc003gjc.2	-	9	1482	c.1112G>A	c.(1111-1113)CGG>CAG	p.R371Q	PPP2R2C_uc003gjb.2_Missense_Mutation_p.R354Q|PPP2R2C_uc011bwd.1_Missense_Mutation_p.R364Q|PPP2R2C_uc011bwe.1_Missense_Mutation_p.R364Q|PPP2R2C_uc003gja.2_Missense_Mutation_p.R371Q	NM_020416	NP_065149	Q9Y2T4	2ABG_HUMAN	gamma isoform of regulatory subunit B55, protein	371	WD 6.				signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4						GGTCACGTCCCGCTTGGTGTT	0.632													14	47	---	---	---	---	PASS
KIAA0232	9778	broad.mit.edu	37	4	6843887	6843887	+	Missense_Mutation	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6843887A>G	uc003gjr.3	+	4	788	c.325A>G	c.(325-327)AAA>GAA	p.K109E	KIAA0232_uc003gjq.3_Missense_Mutation_p.K109E	NM_014743	NP_055558	Q92628	K0232_HUMAN	hypothetical protein LOC9778	109							ATP binding			ovary(2)	2						AGAAGAAATGAAAAAACAGGC	0.368													56	58	---	---	---	---	PASS
GABRA2	2555	broad.mit.edu	37	4	46252458	46252458	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46252458T>C	uc003gxc.3	-	9	1896	c.1223A>G	c.(1222-1224)AAG>AGG	p.K408R	GABRA2_uc010igc.2_Missense_Mutation_p.K408R|GABRA2_uc011bzc.1_Missense_Mutation_p.K413R	NM_001114175	NP_001107647	P47869	GBRA2_HUMAN	gamma-aminobutyric acid A receptor, alpha 2	408	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels	cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity	p.K408K(1)		ovary(2)|skin(2)	4					Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	GAAAGTTTTCTTTGCTTCAGC	0.403													115	116	---	---	---	---	PASS
PDGFRA	5156	broad.mit.edu	37	4	55140744	55140744	+	Silent	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55140744G>A	uc003han.3	+	11	1936	c.1605G>A	c.(1603-1605)TTG>TTA	p.L535L	PDGFRA_uc003haa.2_Intron|PDGFRA_uc010igq.1_Silent_p.L429L|PDGFRA_uc003ham.2_RNA|PDGFRA_uc003hao.1_5'Flank	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	535	Helical; (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	TGGTGCTGTTGGTGATTGTGA	0.448			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			64	81	---	---	---	---	PASS
RXFP1	59350	broad.mit.edu	37	4	159568269	159568269	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159568269G>T	uc003ipz.2	+	16	1754	c.1672G>T	c.(1672-1674)GGC>TGC	p.G558C	RXFP1_uc011cja.1_Missense_Mutation_p.G453C|RXFP1_uc010iqo.2_Missense_Mutation_p.G510C|RXFP1_uc011cjb.1_Missense_Mutation_p.G456C|RXFP1_uc010iqk.2_Missense_Mutation_p.G426C|RXFP1_uc011cjc.1_Missense_Mutation_p.G477C|RXFP1_uc011cjd.1_Missense_Mutation_p.G477C|RXFP1_uc010iql.2_Missense_Mutation_p.G402C|RXFP1_uc011cje.1_Missense_Mutation_p.G585C|RXFP1_uc010iqm.2_Missense_Mutation_p.G525C|RXFP1_uc011cjf.1_Missense_Mutation_p.G427C|RXFP1_uc010iqn.2_Missense_Mutation_p.G503C	NM_021634	NP_067647	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	558	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		AAACTACTATGGCACCAATGG	0.343													41	41	---	---	---	---	PASS
FNIP2	57600	broad.mit.edu	37	4	159791564	159791564	+	Silent	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159791564C>G	uc003iqe.3	+	14	3075	c.2892C>G	c.(2890-2892)ACC>ACG	p.T964T		NM_020840	NP_065891	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	964					DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		TTCATGGGACCGGCAGTGATG	0.552													21	47	---	---	---	---	PASS
ODZ3	55714	broad.mit.edu	37	4	183602986	183602986	+	Silent	SNP	G	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183602986G>C	uc003ivd.1	+	10	1891	c.1854G>C	c.(1852-1854)GGG>GGC	p.G618G	ODZ3_uc003ive.1_Silent_p.G24G	NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	618	EGF-like 4.|Extracellular (Potential).				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		TAGACCCTGGGTGTTCTAATC	0.403													10	23	---	---	---	---	PASS
CCDC111	201973	broad.mit.edu	37	4	185612647	185612647	+	Intron	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185612647A>G	uc003iwk.2	+						CCDC111_uc003iwj.2_Intron|CCDC111_uc003iwl.2_Intron|CCDC111_uc003iwm.2_Intron|CCDC111_uc003iwn.2_Intron	NM_152683	NP_689896	Q96LW4	CC111_HUMAN	coiled-coil domain containing 111						DNA replication, synthesis of RNA primer		DNA primase activity			central_nervous_system(1)	1		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.00531)|Hepatocellular(41;0.00932)|Renal(120;0.0246)|Prostate(90;0.0283)|all_hematologic(60;0.0749)|all_neural(102;0.131)		all cancers(43;5.84e-27)|Epithelial(43;2.2e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.28e-11)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.03e-05)|Colorectal(24;7.57e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000249)|COAD - Colon adenocarcinoma(29;0.000502)|LUSC - Lung squamous cell carcinoma(40;0.00995)|READ - Rectum adenocarcinoma(43;0.173)		TTTTTTAAACATAAAGGATTC	0.179													16	15	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187540801	187540801	+	Missense_Mutation	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187540801T>G	uc003izf.2	-	10	7127	c.6939A>C	c.(6937-6939)GAA>GAC	p.E2313D		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	2313	Extracellular (Potential).|Cadherin 21.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						CTCTATTTGGTTCTGAATCAG	0.453										HNSCC(5;0.00058)			74	73	---	---	---	---	PASS
CLPTM1L	81037	broad.mit.edu	37	5	1323906	1323906	+	Nonsense_Mutation	SNP	T	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1323906T>A	uc003jch.2	-	12	1322	c.1276A>T	c.(1276-1278)AAG>TAG	p.K426*	CLPTM1L_uc003jcg.2_Nonsense_Mutation_p.K257*	NM_030782	NP_110409	Q96KA5	CLP1L_HUMAN	CLPTM1-like	426	Extracellular (Potential).				apoptosis	integral to membrane				breast(1)|central_nervous_system(1)	2	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		TCCTACCTCTTATATTTGATA	0.537													47	62	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19483468	19483468	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19483468C>T	uc003jgc.2	-	11	2201	c.1824G>A	c.(1822-1824)TCG>TCA	p.S608S	CDH18_uc003jgd.2_Silent_p.S608S|CDH18_uc011cnm.1_Missense_Mutation_p.R572Q	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	608	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TCAAACCAGCCGAGGACAGGA	0.522													29	52	---	---	---	---	PASS
UGT3A2	167127	broad.mit.edu	37	5	36049404	36049404	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36049404C>A	uc003jjz.1	-	4	523	c.430G>T	c.(430-432)GTT>TTT	p.V144F	UGT3A2_uc011cos.1_Missense_Mutation_p.V110F|UGT3A2_uc011cot.1_Intron	NM_174914	NP_777574	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	144	Extracellular (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AAAGTTTCAACTATCACCATG	0.388													43	94	---	---	---	---	PASS
ZNF608	57507	broad.mit.edu	37	5	123980279	123980279	+	Missense_Mutation	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123980279C>G	uc003ktq.1	-	5	3904	c.3781G>C	c.(3781-3783)GAT>CAT	p.D1261H	ZNF608_uc003ktr.1_RNA|ZNF608_uc003ktp.1_5'UTR	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	1261						intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		TTCTCTCTATCAAGTTCTTCT	0.373													70	64	---	---	---	---	PASS
ADAMTS19	171019	broad.mit.edu	37	5	128957974	128957974	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128957974C>A	uc003kvb.1	+	10	1685	c.1685C>A	c.(1684-1686)ACA>AAA	p.T562K	ADAMTS19_uc010jdh.1_RNA	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	562	Disintegrin.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		CCAGGGATGACATACACTGCT	0.478													49	32	---	---	---	---	PASS
LARS	51520	broad.mit.edu	37	5	145493753	145493753	+	Silent	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145493753C>A	uc003lnx.1	-	32	3685	c.3447G>T	c.(3445-3447)GTG>GTT	p.V1149V	LARS_uc003lnw.1_Silent_p.V307V|LARS_uc011dbq.1_Silent_p.V1103V|LARS_uc011dbr.1_Silent_p.V1095V|LARS_uc011dbs.1_Silent_p.V1122V	NM_020117	NP_064502	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	1149					leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	TCATGAGGTCCACATTGAAAA	0.448													100	96	---	---	---	---	PASS
UNC5A	90249	broad.mit.edu	37	5	176295277	176295277	+	Intron	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176295277G>A	uc003mey.2	+						UNC5A_uc003mex.1_Intron|UNC5A_uc010jkg.1_Intron	NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	netrin receptor Unc5h1 precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CATAGCCTGTGAGTCTAGGGC	0.637													68	65	---	---	---	---	PASS
MGAT1	4245	broad.mit.edu	37	5	180219325	180219325	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180219325G>A	uc003mmg.3	-	2	1142	c.647C>T	c.(646-648)CCG>CTG	p.P216L	MGAT1_uc010jlf.2_Missense_Mutation_p.P216L|MGAT1_uc010jlg.2_Missense_Mutation_p.P216L|MGAT1_uc003mmh.3_Missense_Mutation_p.P216L|MGAT1_uc010jlh.2_Missense_Mutation_p.P216L|MGAT1_uc003mmi.3_Missense_Mutation_p.P216L	NM_002406	NP_002397	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein	216	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(1)	1	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAAGAAGTCCGGGGCCACCTC	0.652													29	29	---	---	---	---	PASS
GCM2	9247	broad.mit.edu	37	6	10875151	10875151	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10875151C>A	uc003mzn.3	-	5	670	c.598G>T	c.(598-600)GAC>TAC	p.D200Y	SYCP2L_uc011dim.1_Intron	NM_004752	NP_004743	O75603	GCM2_HUMAN	glial cells missing homolog 2	200					cellular calcium ion homeostasis|cellular phosphate ion homeostasis|parathyroid gland development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|sequence-specific DNA binding			ovary(2)|central_nervous_system(1)	3	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)				CCACTGCTGTCTTGATTTTCT	0.423													27	124	---	---	---	---	PASS
ZNF311	282890	broad.mit.edu	37	6	28966578	28966578	+	Silent	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28966578C>G	uc003nlu.2	-	6	861	c.348G>C	c.(346-348)CTG>CTC	p.L116L	ZNF311_uc011dlk.1_Silent_p.L24L|ZNF311_uc003nlv.2_Silent_p.L24L	NM_001010877	NP_001010877	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	116					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding				0						CTTCTCGCTCCAGATGAGAGA	0.428													69	188	---	---	---	---	PASS
ATP6V1G2	534	broad.mit.edu	37	6	31513318	31513318	+	Missense_Mutation	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31513318T>G	uc003nua.2	-	3	515	c.224A>C	c.(223-225)CAG>CCG	p.Q75P	BAT1_uc003ntv.2_Intron|ATP6V1G2_uc003ntz.2_Missense_Mutation_p.Q34P|NFKBIL1_uc011dnr.1_5'Flank|NFKBIL1_uc011dns.1_5'Flank|NFKBIL1_uc011dnt.1_5'Flank|NFKBIL1_uc003nuc.2_5'Flank|NFKBIL1_uc003nub.2_5'Flank	NM_130463	NP_569730	O95670	VATG2_HUMAN	ATPase, H+ transporting, lysosomal, V1 subunit	75					cellular iron ion homeostasis|insulin receptor signaling pathway|proton transport|transferrin transport	cytosol|melanosome|vacuolar proton-transporting V-type ATPase complex	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances|protein binding				0						CCTTGTAGCCTGCTCCACCTC	0.627													4	90	---	---	---	---	PASS
C6orf25	80739	broad.mit.edu	37	6	31691947	31691947	+	Silent	SNP	G	A	A	rs140027534		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31691947G>A	uc011doc.1	+	3	438	c.438G>A	c.(436-438)CCG>CCA	p.P146P	LY6G6C_uc003nwh.2_5'Flank|LY6G6C_uc010jtd.2_5'Flank|C6orf25_uc003nwk.2_Silent_p.P146P|C6orf25_uc011dod.1_Intron|C6orf25_uc011doe.1_Intron|C6orf25_uc003nwo.2_Intron|C6orf25_uc003nwn.2_Silent_p.P146P	NM_138272	NP_612116	O95866	G6B_HUMAN	G6B protein isoform G6b-B precursor	146	Helical; (Potential).					endoplasmic reticulum|Golgi apparatus|integral to membrane|plasma membrane	heparin binding|receptor activity				0						TCCTGATCCCGCTGCTGGGCG	0.667													19	41	---	---	---	---	PASS
EGFL8	80864	broad.mit.edu	37	6	32135181	32135181	+	Missense_Mutation	SNP	G	C	C	rs138835391		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32135181G>C	uc003oab.1	+	7	714	c.656G>C	c.(655-657)CGA>CCA	p.R219P	PPT2_uc003nzy.1_RNA|EGFL8_uc003oac.1_Missense_Mutation_p.R219P	NM_030652	NP_085155	Q99944	EGFL8_HUMAN	NG3 protein precursor	219	Potential.					extracellular region|integral to membrane	calcium ion binding				0						CACGAGCTGCGAGGGCGCCTG	0.607													13	59	---	---	---	---	PASS
CDKN1A	1026	broad.mit.edu	37	6	36652134	36652134	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36652134C>T	uc003omm.3	+	2	378	c.256C>T	c.(256-258)CGG>TGG	p.R86W	CDKN1A_uc011dtq.1_Missense_Mutation_p.R120W|CDKN1A_uc003oml.2_Missense_Mutation_p.R86W|CDKN1A_uc003omn.2_Missense_Mutation_p.R86W	NM_000389	NP_000380	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A	86					cell cycle arrest|cellular response to extracellular stimulus|cellular response to ionizing radiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|induction of apoptosis by intracellular signals|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of fibroblast proliferation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|S phase of mitotic cell cycle|stress-induced premature senescence	cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleoplasm|PCNA-p21 complex	cyclin-dependent protein kinase activating kinase activity|cyclin-dependent protein kinase inhibitor activity|metal ion binding			ovary(1)|breast(1)	2						CCGGCGAGGCCGGGATGAGTT	0.657									Multiple_Endocrine_Neoplasia_type_1				10	33	---	---	---	---	PASS
DNAH8	1769	broad.mit.edu	37	6	38891855	38891855	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38891855C>A	uc003ooe.1	+	71	10828	c.10228C>A	c.(10228-10230)CAA>AAA	p.Q3410K	uc003oof.1_Intron	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						GCTTAAAGATCAATGGGAAAT	0.388													80	61	---	---	---	---	PASS
RHAG	6005	broad.mit.edu	37	6	49582418	49582418	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49582418G>T	uc003ozk.3	-	5	851	c.789C>A	c.(787-789)CAC>CAA	p.H263Q	RHAG_uc010jzl.2_Missense_Mutation_p.H263Q|RHAG_uc010jzm.2_Missense_Mutation_p.H263Q	NM_000324	NP_000315	Q02094	RHAG_HUMAN	Rh-associated glycoprotein	263	Cytoplasmic (Potential).				carbon dioxide transport|cellular ion homeostasis	integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			breast(1)|skin(1)	2	Lung NSC(77;0.0255)					GCTTGCCTCGGTGCTCCACTA	0.498													117	161	---	---	---	---	PASS
HCRTR2	3062	broad.mit.edu	37	6	55128622	55128622	+	Splice_Site	SNP	T	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55128622T>A	uc003pcl.2	+	4	1077	c.762_splice	c.e4+2	p.Q254_splice	HCRTR2_uc010jzv.2_Splice_Site|HCRTR2_uc010jzw.1_Missense_Mutation_p.V190E	NM_001526	NP_001517	O43614	OX2R_HUMAN	orexin receptor 2						feeding behavior	integral to plasma membrane	neuropeptide receptor activity			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|breast(1)	6	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			TGTCGACAGGTATATAGTTTC	0.363													23	35	---	---	---	---	PASS
LCA5	167691	broad.mit.edu	37	6	80223280	80223280	+	Missense_Mutation	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80223280C>G	uc003pix.2	-	3	804	c.369G>C	c.(367-369)CAG>CAC	p.Q123H	LCA5_uc003piy.2_Missense_Mutation_p.Q123H|LCA5_uc011dyq.1_RNA|LCA5_uc011dyr.1_Missense_Mutation_p.Q123H	NM_001122769	NP_001116241	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	123	Potential.				protein transport	cilium axoneme|microtubule basal body	protein binding				0		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		CTAACTTGACCTGGAGTTCAG	0.388													97	115	---	---	---	---	PASS
NR2E1	7101	broad.mit.edu	37	6	108492769	108492769	+	Nonsense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108492769C>T	uc003psg.2	+	2	888	c.133C>T	c.(133-135)CGA>TGA	p.R45*		NM_003269	NP_003260	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	45	Nuclear receptor.				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)		ACGGAGCATCCGAAGGAATAG	0.552													128	124	---	---	---	---	PASS
C6orf174	387104	broad.mit.edu	37	6	127796683	127796683	+	Missense_Mutation	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127796683C>G	uc003qbd.2	-	6	3353	c.2488G>C	c.(2488-2490)GAC>CAC	p.D830H	C6orf174_uc003qbc.2_5'UTR	NM_001012279	NP_001012279	Q5TF21	CF174_HUMAN	hypothetical protein LOC387104 precursor	830	Potential.					integral to membrane				breast(3)|ovary(2)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.161)		ATGAGCCGGTCGATGGTCTTG	0.667													84	72	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152560753	152560753	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152560753T>C	uc010kiw.2	-	108	20584	c.19982A>G	c.(19981-19983)CAG>CGG	p.Q6661R	SYNE1_uc010kiv.2_Missense_Mutation_p.Q1185R|SYNE1_uc003qos.3_Missense_Mutation_p.Q1185R|SYNE1_uc003qot.3_Missense_Mutation_p.Q6590R|SYNE1_uc003qou.3_Missense_Mutation_p.Q6661R	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6661	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TGTATGGAACTGGGTTTCCTT	0.458										HNSCC(10;0.0054)			55	63	---	---	---	---	PASS
ZDHHC14	79683	broad.mit.edu	37	6	158014086	158014086	+	Missense_Mutation	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158014086A>G	uc003qqt.2	+	3	970	c.473A>G	c.(472-474)AAT>AGT	p.N158S	ZDHHC14_uc003qqs.2_Missense_Mutation_p.N158S|ZDHHC14_uc010kjm.1_Missense_Mutation_p.N53S	NM_024630	NP_078906	Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14 isoform 1	158						integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)|skin(1)	2		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)		GTCATCATCAATGGCCAGACC	0.522													34	97	---	---	---	---	PASS
PARK2	5071	broad.mit.edu	37	6	162475142	162475142	+	Missense_Mutation	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162475142T>G	uc003qtx.3	-	5	733	c.599A>C	c.(598-600)CAC>CCC	p.H200P	PARK2_uc003qtv.3_RNA|PARK2_uc010kkd.2_Missense_Mutation_p.H9P|PARK2_uc003qtw.3_Missense_Mutation_p.H9P|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Missense_Mutation_p.H200P	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1	200					aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		CCCAGGGCAGTGTGGGGATTG	0.413													34	88	---	---	---	---	PASS
INTS1	26173	broad.mit.edu	37	7	1539535	1539535	+	Silent	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1539535G>A	uc003skn.2	-	5	770	c.669C>T	c.(667-669)CCC>CCT	p.P223P	INTS1_uc003skq.2_Silent_p.P223P	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	223					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		CAAAGATCTCGGGCCAGTTCT	0.612													16	38	---	---	---	---	PASS
IQCE	23288	broad.mit.edu	37	7	2641070	2641070	+	Intron	SNP	T	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2641070T>A	uc003smo.3	+						IQCE_uc010ksm.1_Intron|IQCE_uc003sml.1_Intron|IQCE_uc011jvy.1_Intron|IQCE_uc011jvz.1_Intron|IQCE_uc003smk.3_Intron|IQCE_uc003smn.3_Intron	NM_152558	NP_689771	Q6IPM2	IQCE_HUMAN	IQ motif containing E isoform 1												0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		TTTTTTTTTTTCCAGAAAAAA	0.343													33	57	---	---	---	---	PASS
TNRC18	84629	broad.mit.edu	37	7	5353167	5353167	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5353167C>T	uc003soi.3	-	27	7704	c.7355G>A	c.(7354-7356)CGG>CAG	p.R2452Q		NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2452							DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CCCCGGCCTCCGAGGGCCCTT	0.677													10	24	---	---	---	---	PASS
THSD7A	221981	broad.mit.edu	37	7	11676275	11676275	+	Silent	SNP	A	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11676275A>T	uc003ssf.3	-	2	756	c.504T>A	c.(502-504)CCT>CCA	p.P168P		NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	168	Extracellular (Potential).					integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TATCCTCCGCAGGAATGTCTT	0.473										HNSCC(18;0.044)			24	67	---	---	---	---	PASS
ITGB8	3696	broad.mit.edu	37	7	20418789	20418789	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20418789C>T	uc003suu.2	+	4	1209	c.504C>T	c.(502-504)TCC>TCT	p.S168S	ITGB8_uc011jyh.1_Silent_p.S33S|ITGB8_uc003sut.2_Silent_p.S168S	NM_002214	NP_002205	P26012	ITB8_HUMAN	integrin, beta 8 precursor	168	VWFA.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development	integrin complex	protein binding|receptor activity			skin(3)	3						AATTAAATTCCGTTGGAAACG	0.338													22	117	---	---	---	---	PASS
EVX1	2128	broad.mit.edu	37	7	27284804	27284804	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27284804G>A	uc003szd.1	+	2	1051	c.565G>A	c.(565-567)GCC>ACC	p.A189T	EVX1_uc011jzn.1_Missense_Mutation_p.A7T|EVX1_uc010kuy.1_Silent_p.P170P	NM_001989	NP_001980	P49640	EVX1_HUMAN	even-skipped homeobox 1	189	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1						TTACCGCACCGCCTTCACCCG	0.657													40	87	---	---	---	---	PASS
CPVL	54504	broad.mit.edu	37	7	29152366	29152366	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29152366T>C	uc003szv.2	-	3	361	c.242A>G	c.(241-243)AAT>AGT	p.N81S	CPVL_uc003szw.2_Missense_Mutation_p.N81S|CPVL_uc003szx.2_Missense_Mutation_p.N81S	NM_031311	NP_112601	Q9H3G5	CPVL_HUMAN	serine carboxypeptidase vitellogenic-like	81					proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2						GTAAGTCTTATTCACGGTGAG	0.483													10	106	---	---	---	---	PASS
ZNF479	90827	broad.mit.edu	37	7	57194316	57194316	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57194316C>A	uc010kzo.2	-	3	420	c.149G>T	c.(148-150)AGA>ATA	p.R50I		NM_033273	NP_150376	Q96JC4	ZN479_HUMAN	zinc finger protein 479	50	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(1)	4			GBM - Glioblastoma multiforme(1;9.18e-12)			GACCAGGTTTCTGTAGTTCTC	0.378													53	210	---	---	---	---	PASS
GUSB	2990	broad.mit.edu	37	7	65426044	65426044	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65426044G>A	uc003tun.2	-	12	1872	c.1796C>T	c.(1795-1797)ACG>ATG	p.T599M	GUSB_uc011kdt.1_Missense_Mutation_p.T453M	NM_000181	NP_000172	P08236	BGLR_HUMAN	glucuronidase, beta precursor	599					glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0						CAGCACTCTCGTCGGTGCTAC	0.433													96	256	---	---	---	---	PASS
CALN1	83698	broad.mit.edu	37	7	71571125	71571125	+	Intron	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71571125C>G	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				AGCTGCTTGTCCGGGTCTTAC	0.552													19	40	---	---	---	---	PASS
CALN1	83698	broad.mit.edu	37	7	71868307	71868307	+	Missense_Mutation	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71868307T>G	uc003twb.3	-	2	439	c.48A>C	c.(46-48)AAA>AAC	p.K16N	CALN1_uc003twc.3_Intron	NM_031468	NP_113656	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 1	Error:Variant_position_missing_in_Q9BXU9_after_alignment						Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				CGTCCCCCTTTTTCTCATTCT	0.632													2	1	---	---	---	---	PASS
SEMA3C	10512	broad.mit.edu	37	7	80427490	80427490	+	Missense_Mutation	SNP	T	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80427490T>A	uc003uhj.2	-	11	1611	c.1049A>T	c.(1048-1050)AAT>ATT	p.N350I	SEMA3C_uc011kgw.1_Missense_Mutation_p.N368I|SEMA3C_uc011kgx.1_Missense_Mutation_p.N202I	NM_006379	NP_006370	Q99985	SEM3C_HUMAN	semaphorin 3C precursor	350	Sema.				immune response|response to drug	membrane	receptor activity			ovary(1)	1						AAAAGGCCCATTAAACACAGT	0.398													6	137	---	---	---	---	PASS
SEMA3E	9723	broad.mit.edu	37	7	83119461	83119461	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83119461C>A	uc003uhy.1	-	2	711	c.245G>T	c.(244-246)AGC>ATC	p.S82I		NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E precursor	82	Sema.				axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)				TCTCTCCAAGCTGAGGGAATA	0.413													40	80	---	---	---	---	PASS
STEAP2	261729	broad.mit.edu	37	7	89861917	89861917	+	Silent	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89861917G>A	uc003ujz.2	+	5	1845	c.1452G>A	c.(1450-1452)CCG>CCA	p.P484P	STEAP2_uc010len.2_Silent_p.P484P|STEAP2_uc003uka.2_Intron|STEAP2_uc003ukb.2_Silent_p.P484P|STEAP2_uc003ukc.2_Intron|STEAP2_uc003ukd.2_Intron	NM_152999	NP_694544	Q8NFT2	STEA2_HUMAN	six transmembrane epithelial antigen of the	484					electron transport chain|endocytosis|Golgi to plasma membrane transport|ion transport|iron ion homeostasis|regulated secretory pathway|response to hormone stimulus	cytosol|early endosome|endosome membrane|integral to Golgi membrane|plasma membrane|trans-Golgi network transport vesicle|vesicular fraction	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity|transporter activity			ovary(2)	2	all_hematologic(106;0.112)					ATGTCTCCCCGGAGAGGGTCA	0.403													28	42	---	---	---	---	PASS
CDK14	5218	broad.mit.edu	37	7	90356022	90356022	+	Missense_Mutation	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90356022C>G	uc003uky.2	+	3	487	c.265C>G	c.(265-267)CAA>GAA	p.Q89E	CDK14_uc003ukt.1_Missense_Mutation_p.Q43E|CDK14_uc003ukv.1_Missense_Mutation_p.Q43E|CDK14_uc003uku.1_Missense_Mutation_p.Q43E|CDK14_uc003ukx.1_Intron|CDK14_uc003ukz.1_Missense_Mutation_p.Q71E|CDK14_uc010les.1_Missense_Mutation_p.Q43E|CDK14_uc011khl.1_Translation_Start_Site	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1	89					cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						ACCAGCTAATCAAGTAAAGAG	0.463													81	95	---	---	---	---	PASS
TRRAP	8295	broad.mit.edu	37	7	98535291	98535291	+	Missense_Mutation	SNP	A	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98535291A>C	uc003upp.2	+	30	4461	c.4252A>C	c.(4252-4254)ATA>CTA	p.I1418L	TRRAP_uc011kis.1_Missense_Mutation_p.I1418L|TRRAP_uc003upr.2_Missense_Mutation_p.I1110L	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	1418					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AGGTGCTACCATAGAAGTCGA	0.398													8	151	---	---	---	---	PASS
CUX1	1523	broad.mit.edu	37	7	101845426	101845426	+	Missense_Mutation	SNP	G	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101845426G>C	uc003uyx.3	+	18	2887	c.2849G>C	c.(2848-2850)CGG>CCG	p.R950P	CUX1_uc003uys.3_Missense_Mutation_p.R961P|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform a	950	CUT 2.				negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						GAGCTCACCCGGCAGGTTAAG	0.597													82	189	---	---	---	---	PASS
DOCK4	9732	broad.mit.edu	37	7	111409709	111409709	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111409709T>C	uc003vfx.2	-	36	3946	c.3677A>G	c.(3676-3678)TAT>TGT	p.Y1226C	DOCK4_uc011kml.1_Missense_Mutation_p.Y107C|DOCK4_uc011kmm.1_Missense_Mutation_p.Y133C|DOCK4_uc003vfw.2_Missense_Mutation_p.Y676C|DOCK4_uc003vfy.2_Missense_Mutation_p.Y1271C	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1226	DHR-2.				cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)				TAGCTCGTCATATAAGAGGAG	0.527													30	42	---	---	---	---	PASS
PPP1R3A	5506	broad.mit.edu	37	7	113558772	113558772	+	Missense_Mutation	SNP	A	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113558772A>T	uc010ljy.1	-	1	311	c.280T>A	c.(280-282)TTA>ATA	p.L94I		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	94					glycogen metabolic process	integral to membrane				lung(9)|ovary(9)|pancreas(7)|skin(6)|breast(2)|prostate(1)	34						TCCGTCCCTAAGTCAAAAGTG	0.378													18	204	---	---	---	---	PASS
FLNC	2318	broad.mit.edu	37	7	128494544	128494544	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128494544G>A	uc003vnz.3	+	41	7014	c.6805G>A	c.(6805-6807)GGC>AGC	p.G2269S	FLNC_uc003voa.3_Missense_Mutation_p.G2236S	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	2269	Filamin 20.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12						GATCGTCGAGGGCGAGGACAG	0.647													4	16	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131853184	131853184	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131853184G>A	uc003vra.3	-	22	4394	c.4165C>T	c.(4165-4167)CTC>TTC	p.L1389F		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1389	Cytoplasmic (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1						GTCATGATGAGTGAGGCCACG	0.577													15	73	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131912348	131912348	+	Missense_Mutation	SNP	A	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131912348A>T	uc003vra.3	-	7	1973	c.1744T>A	c.(1744-1746)TAC>AAC	p.Y582N		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	582	Extracellular (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1						GGGACATTGTACGTCTCCAGG	0.552													29	77	---	---	---	---	PASS
OR9A2	135924	broad.mit.edu	37	7	142723568	142723568	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142723568T>C	uc003wcc.1	-	1	652	c.652A>G	c.(652-654)ATC>GTC	p.I218V		NM_001001658	NP_001001658	Q8NGT5	OR9A2_HUMAN	olfactory receptor, family 9, subfamily A,	218	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	Melanoma(164;0.059)					ATGGTGGAGATAATGTAGGTG	0.468													23	66	---	---	---	---	PASS
GIMAP1	170575	broad.mit.edu	37	7	150417223	150417223	+	Missense_Mutation	SNP	G	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150417223G>C	uc003whq.2	+	3	218	c.131G>C	c.(130-132)GGG>GCG	p.G44A	GIMAP1_uc003whp.2_Missense_Mutation_p.G52A	NM_130759	NP_570115	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	44	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGCGCCACTGGGAACAGCATC	0.642													55	197	---	---	---	---	PASS
FNTA	2339	broad.mit.edu	37	8	42940421	42940421	+	Missense_Mutation	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42940421A>G	uc003xps.2	+	9	1184	c.1136A>G	c.(1135-1137)CAA>CGA	p.Q379R	FNTA_uc003xpt.2_Missense_Mutation_p.Q288R|FNTA_uc003xpu.2_Missense_Mutation_p.Q312R|FNTA_uc003xpv.2_RNA	NM_002027	NP_002018	P49354	FNTA_HUMAN	farnesyltransferase, CAAX box, alpha isoform a	379					cellular component disassembly involved in apoptosis|positive regulation of deacetylase activity|positive regulation of tubulin deacetylation|protein farnesylation|protein geranylgeranylation|transforming growth factor beta receptor signaling pathway	cytosol|microtubule associated complex	alpha-tubulin binding|CAAX-protein geranylgeranyltransferase activity|microtubule binding|protein farnesyltransferase activity			ovary(1)	1	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			AATGTACAGCAATAACACCAT	0.403													6	98	---	---	---	---	PASS
PXDNL	137902	broad.mit.edu	37	8	52359584	52359584	+	Missense_Mutation	SNP	T	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52359584T>A	uc003xqu.3	-	12	1606	c.1505A>T	c.(1504-1506)CAG>CTG	p.Q502L		NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	502	Ig-like C2-type 3.				hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TACAGTCAGCTGCACAGACAC	0.448													49	244	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55538412	55538412	+	Missense_Mutation	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55538412T>G	uc003xsd.1	+	4	2118	c.1970T>G	c.(1969-1971)CTT>CGT	p.L657R	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	657					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			TTAACAAAACTTCCAAAAAAT	0.358													26	66	---	---	---	---	PASS
VCPIP1	80124	broad.mit.edu	37	8	67547217	67547217	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67547217C>A	uc003xwn.2	-	3	3447	c.3188G>T	c.(3187-3189)AGT>ATT	p.S1063I		NM_025054	NP_079330	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex	1063					protein ubiquitination	endoplasmic reticulum|Golgi stack	ubiquitin-specific protease activity			lung(2)|ovary(2)|central_nervous_system(1)|breast(1)|skin(1)|kidney(1)	8		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			TTTAGTGGAACTATTACTAAA	0.418													38	260	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77767456	77767456	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77767456C>A	uc003yav.2	+	10	8551	c.8164C>A	c.(8164-8166)CTT>ATT	p.L2722I	ZFHX4_uc003yau.1_Missense_Mutation_p.L2767I|ZFHX4_uc003yaw.1_Missense_Mutation_p.L2722I	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2722						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ACCGAAGAATCTTTTAAGCCC	0.383										HNSCC(33;0.089)			28	54	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77768504	77768504	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77768504C>A	uc003yav.2	+	10	9599	c.9212C>A	c.(9211-9213)TCC>TAC	p.S3071Y	ZFHX4_uc003yau.1_Missense_Mutation_p.S3116Y|ZFHX4_uc003yaw.1_Missense_Mutation_p.S3071Y	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	3071	Pro-rich.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AACGGTCCATCCTCCTTGCCG	0.502										HNSCC(33;0.089)			33	54	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	8	81471452	81471452	+	IGR	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81471452C>A								ZBTB10 (36844 upstream) : ZNF704 (79317 downstream)																							AGGCAGCCTTCCAGGAGCCAC	0.542													40	76	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	8	81471453	81471453	+	IGR	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81471453C>A								ZBTB10 (36845 upstream) : ZNF704 (79316 downstream)																							GGCAGCCTTCCAGGAGCCACG	0.542													38	77	---	---	---	---	PASS
PSKH2	85481	broad.mit.edu	37	8	87081659	87081659	+	Intron	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87081659C>T	uc011lfy.1	-							NM_033126	NP_149117	Q96QS6	KPSH2_HUMAN	protein serine kinase H2								ATP binding|protein serine/threonine kinase activity			stomach(2)|lung(2)|ovary(1)	5			STAD - Stomach adenocarcinoma(118;0.129)			CCTCACGTGGCGCTTTACCTG	0.502													11	45	---	---	---	---	PASS
SLC26A7	115111	broad.mit.edu	37	8	92346641	92346641	+	Missense_Mutation	SNP	A	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92346641A>C	uc003yex.2	+	7	1039	c.761A>C	c.(760-762)AAA>ACA	p.K254T	SLC26A7_uc003yey.2_RNA|SLC26A7_uc003yez.2_Missense_Mutation_p.K254T|SLC26A7_uc003yfa.2_Missense_Mutation_p.K254T	NM_052832	NP_439897	Q8TE54	S26A7_HUMAN	solute carrier family 26, member 7 isoform a	254	Extracellular (Potential).					basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)			TTTAAAAGGAAAATTAAAGTT	0.368													40	64	---	---	---	---	PASS
OSR2	116039	broad.mit.edu	37	8	99961551	99961551	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99961551C>A	uc003yir.2	+	2	906	c.371C>A	c.(370-372)GCT>GAT	p.A124D	OSR2_uc010mbn.2_Missense_Mutation_p.A124D|OSR2_uc003yiq.2_Missense_Mutation_p.A124D|OSR2_uc011lgx.1_Missense_Mutation_p.A245D	NM_001142462	NP_001135934	Q8N2R0	OSR2_HUMAN	odd-skipped related 2 isoform a	124					bone morphogenesis|chondrocyte differentiation|embryonic digit morphogenesis|embryonic forelimb morphogenesis|embryonic hindlimb morphogenesis|embryonic leg joint morphogenesis|embryonic skeletal joint morphogenesis|eyelid development in camera-type eye|head development|mesonephros development|metanephros development|middle ear morphogenesis|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|osteoblast proliferation|palate development|positive regulation of bone mineralization|positive regulation of epithelial cell proliferation|positive regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|zinc ion binding			central_nervous_system(1)	1	Breast(36;4.14e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.0136)			TTGGCGGTGGCTGCCACGCAA	0.612													107	192	---	---	---	---	PASS
SNX31	169166	broad.mit.edu	37	8	101661695	101661695	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101661695C>T	uc003yjr.2	-	1	199	c.48G>A	c.(46-48)GCG>GCA	p.A16A		NM_152628	NP_689841	Q8N9S9	SNX31_HUMAN	sorting nexin 31	16	PX.				cell communication|protein transport		phosphatidylinositol binding				0	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)			GGCCCCCCAGCGCGTCGGACC	0.697													8	12	---	---	---	---	PASS
MTBP	27085	broad.mit.edu	37	8	121519088	121519088	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121519088C>T	uc003ypc.1	+	16	1915	c.1870C>T	c.(1870-1872)CCG>TCG	p.P624S		NM_022045	NP_071328	Q96DY7	MTBP_HUMAN	Mdm2, transformed 3T3 cell double minute 2, p53	624	Interaction with MDM2 (By similarity).				cell cycle arrest					skin(2)|ovary(1)	3	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			TCAACCTTTACCGATTCAAAA	0.328													23	109	---	---	---	---	PASS
OC90	729330	broad.mit.edu	37	8	133044286	133044286	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133044286G>T	uc003ytg.2	-	11	873	c.873C>A	c.(871-873)TTC>TTA	p.F291L	OC90_uc011lix.1_Missense_Mutation_p.F291L	NM_001080399	NP_001073868	Q02509	OC90_HUMAN	otoconin 90	307					lipid catabolic process|phospholipid metabolic process		calcium ion binding|phospholipase A2 activity			ovary(2)|skin(1)	3	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			GCAGGAAGGTGAATCTGTCAC	0.547													33	112	---	---	---	---	PASS
SLA	6503	broad.mit.edu	37	8	134062194	134062194	+	Silent	SNP	A	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134062194A>C	uc003ytz.2	-	5	1033	c.201T>G	c.(199-201)GGT>GGG	p.G67G	TG_uc003ytw.2_Intron|TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron|SLA_uc011lje.1_Silent_p.G84G|SLA_uc011ljf.1_5'UTR|SLA_uc011ljg.1_Silent_p.G84G|SLA_uc010mdy.1_Silent_p.G67G|SLA_uc010mdz.1_Silent_p.G67G|SLA_uc010mea.2_RNA|SLA_uc011ljd.1_Silent_p.G107G	NM_001045556	NP_001039021	Q13239	SLAP1_HUMAN	Src-like-adaptor isoform a	67	SH3.					endosome	SH3/SH2 adaptor activity			lung(1)|liver(1)	2	all_epithelial(106;3.51e-21)|Lung NSC(106;4.24e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0279)|Breast(495;0.037)	BRCA - Breast invasive adenocarcinoma(115;0.000701)			AACTCTCTCGACCAGTGCTAA	0.438													25	117	---	---	---	---	PASS
FOXH1	8928	broad.mit.edu	37	8	145699868	145699868	+	Missense_Mutation	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145699868A>G	uc003zdc.2	-	3	1430	c.851T>C	c.(850-852)ATC>ACC	p.I284T		NM_003923	NP_003914	O75593	FOXH1_HUMAN	forkhead box H1	284	SMAD-interaction domain (SID).				axial mesoderm development|blood vessel development|cell migration involved in gastrulation|embryonic heart tube anterior/posterior pattern formation|floor plate formation|heart looping|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|specification of organ position|transforming growth factor beta receptor signaling pathway	activin responsive factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|R-SMAD binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding				0	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.76e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GGGAGTGTAGATAGGCAAGTA	0.652													22	87	---	---	---	---	PASS
ARHGAP39	80728	broad.mit.edu	37	8	145773569	145773569	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145773569G>A	uc003zdt.1	-	6	1456	c.901C>T	c.(901-903)CCC>TCC	p.P301S	ARHGAP39_uc011llk.1_Missense_Mutation_p.P301S|ARHGAP39_uc003zds.1_Missense_Mutation_p.P301S	NM_025251	NP_079527	Q9C0H5	RHG39_HUMAN	KIAA1688 protein	301	Pro-rich.				axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|nucleus	GTPase activator activity				0						GGGGAGGAGGGCTGCGAGTCC	0.682													26	47	---	---	---	---	PASS
TAF1L	138474	broad.mit.edu	37	9	32631226	32631226	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32631226T>C	uc003zrg.1	-	1	4442	c.4352A>G	c.(4351-4353)GAA>GGA	p.E1451G	uc003zrh.1_5'Flank	NM_153809	NP_722516	Q8IZX4	TAF1L_HUMAN	TBP-associated factor RNA polymerase 1-like	1451	Bromo 1.				male meiosis|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	transcription factor TFIID complex	DNA binding|histone acetyltransferase activity|protein serine/threonine kinase activity|TBP-class protein binding			lung(8)|skin(6)|central_nervous_system(4)|large_intestine(3)|ovary(2)|stomach(1)|breast(1)|pancreas(1)	26			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		ACGCACATTTTCACGGAGTGT	0.448													72	214	---	---	---	---	PASS
XPA	7507	broad.mit.edu	37	9	100459559	100459559	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100459559C>A	uc004axr.3	-	1	133	c.16G>T	c.(16-18)GGG>TGG	p.G6W	XPA_uc004axs.3_RNA	NM_000380	NP_000371	P23025	XPA_HUMAN	xeroderma pigmentosum, complementation group A	6	Interaction with CEP164 and required for UV resistance.				nucleotide-excision repair, DNA damage removal	nucleoplasm	damaged DNA binding|metal ion binding|nucleotide binding|protein domain specific binding|protein homodimerization activity			breast(1)	1		Acute lymphoblastic leukemia(62;0.158)				GGCAAAGCCCCGTCGGCCGCC	0.726			Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		NER	Xeroderma_Pigmentosum				16	13	---	---	---	---	PASS
DBC1	1620	broad.mit.edu	37	9	122075418	122075418	+	Nonsense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122075418G>T	uc004bkc.2	-	2	672	c.216C>A	c.(214-216)TAC>TAA	p.Y72*	DBC1_uc004bkd.2_Nonsense_Mutation_p.Y72*	NM_014618	NP_055433	O60477	DBC1_HUMAN	deleted in bladder cancer 1 precursor	72	MACPF.				cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8						GGTCTTACCTGTATATTTTAT	0.453													20	30	---	---	---	---	PASS
PTGS1	5742	broad.mit.edu	37	9	125133373	125133373	+	Intron	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125133373G>A	uc004bmg.1	+						PTGS1_uc011lys.1_Intron|PTGS1_uc010mwb.1_Intron|PTGS1_uc004bmf.1_Intron|PTGS1_uc004bmh.1_5'UTR	NM_000962	NP_000953	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 isoform 1						cyclooxygenase pathway|hormone biosynthetic process|regulation of blood pressure|response to oxidative stress|xenobiotic metabolic process	endoplasmic reticulum membrane|Golgi apparatus|microsome|plasma membrane	heme binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peroxidase activity|prostaglandin-endoperoxide synthase activity			ovary(1)|skin(1)	2					Acetaminophen(DB00316)|Aspirin(DB00945)|Balsalazide(DB01014)|Bromfenac(DB00963)|Ciclopirox(DB01188)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dipyrone(DB04817)|Etodolac(DB00749)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|gamma-Homolinolenic acid(DB00154)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lumiracoxib(DB01283)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Mesalazine(DB00244)|Minoxidil(DB00350)|Nabumetone(DB00461)|Naproxen(DB00788)|Phenacetin(DB03783)|Piroxicam(DB00554)|Rofecoxib(DB00533)|Salicyclic acid(DB00936)|Salsalate(DB01399)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Tolmetin(DB00500)	CATGAGCCGTGAGTGCGACCC	0.677													16	15	---	---	---	---	PASS
PHYH	5264	broad.mit.edu	37	10	13330441	13330441	+	Missense_Mutation	SNP	G	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13330441G>C	uc001imf.2	-	6	685	c.597C>G	c.(595-597)ATC>ATG	p.I199M	PHYH_uc001ime.2_Missense_Mutation_p.I99M|PHYH_uc001img.2_Missense_Mutation_p.I182M	NM_006214	NP_006205	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase isoform a precursor	199			I -> F (in RD).		fatty acid alpha-oxidation|nervous system development	peroxisomal matrix	electron carrier activity|L-ascorbic acid binding|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|phytanoyl-CoA dioxygenase activity|protein binding				0		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	TGTTCCGGCTGATGTGCTCCA	0.627													45	44	---	---	---	---	PASS
MYPN	84665	broad.mit.edu	37	10	69935098	69935098	+	Silent	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69935098G>A	uc001jnm.3	+	13	2768	c.2583G>A	c.(2581-2583)GCG>GCA	p.A861A	MYPN_uc001jnn.3_Silent_p.A586A|MYPN_uc001jno.3_Silent_p.A861A|MYPN_uc009xpt.2_Silent_p.A861A|MYPN_uc010qit.1_Silent_p.A567A|MYPN_uc010qiu.1_Intron	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin	861						nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5						AGGGATTAGCGAAGAAAAATA	0.418													25	27	---	---	---	---	PASS
BLNK	29760	broad.mit.edu	37	10	97969612	97969612	+	Missense_Mutation	SNP	G	C	C	rs35461367		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97969612G>C	uc001kls.3	-	9	906	c.728C>G	c.(727-729)TCC>TGC	p.S243C	BLNK_uc001kme.3_Missense_Mutation_p.S138C|BLNK_uc001klt.3_Missense_Mutation_p.S134C|BLNK_uc009xvc.2_RNA|BLNK_uc001klu.3_Missense_Mutation_p.S161C|BLNK_uc001klv.3_Missense_Mutation_p.S138C|BLNK_uc001klw.3_Intron|BLNK_uc001klx.3_Missense_Mutation_p.S220C|BLNK_uc001kly.3_Missense_Mutation_p.S243C|BLNK_uc001klz.3_RNA|BLNK_uc001kma.3_Missense_Mutation_p.S220C|BLNK_uc001kmb.3_Missense_Mutation_p.S39C|BLNK_uc001kmc.3_Intron|BLNK_uc001kmd.3_Missense_Mutation_p.S161C|BLNK_uc009xvd.2_RNA	NM_013314	NP_037446	Q8WV28	BLNK_HUMAN	B-cell linker isoform 1	243	Pro-rich.				B cell differentiation|humoral immune response|inflammatory response|intracellular signal transduction	cytoplasm|plasma membrane	SH3/SH2 adaptor activity|transmembrane receptor protein tyrosine kinase adaptor activity			skin(2)	2		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)		TGGCAACGGGGATGGTGCAGC	0.567													54	201	---	---	---	---	PASS
EIF3A	8661	broad.mit.edu	37	10	120796677	120796677	+	Silent	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120796677G>A	uc001ldu.2	-	21	4019	c.3873C>T	c.(3871-3873)GAC>GAT	p.D1291D	EIF3A_uc010qsu.1_Silent_p.D1257D	NM_003750	NP_003741	Q14152	EIF3A_HUMAN	eukaryotic translation initiation factor 3,	1291	Asp-rich.				formation of translation initiation complex	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|structural molecule activity|translation initiation factor activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		GGTCCCTGTCGTCTCTTAGAT	0.532													53	243	---	---	---	---	PASS
C10orf88	80007	broad.mit.edu	37	10	124697585	124697585	+	Nonsense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124697585C>A	uc001lgw.2	-	5	964	c.739G>T	c.(739-741)GGA>TGA	p.G247*	C10orf88_uc001lgx.2_Nonsense_Mutation_p.G149*	NM_024942	NP_079218	Q9H8K7	CJ088_HUMAN	hypothetical protein LOC80007	247											0		all_neural(114;0.0765)|Lung NSC(174;0.163)|all_lung(145;0.205)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0735)		TTTAAGGTTCCTAAGGTAGAT	0.403													60	72	---	---	---	---	PASS
CYP2E1	1571	broad.mit.edu	37	10	135345078	135345078	+	Intron	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135345078C>G	uc001lnj.1	+						CYP2E1_uc001lnk.1_Intron|CYP2E1_uc009ybl.1_Intron|CYP2E1_uc009ybm.1_Intron|CYP2E1_uc001lnl.1_5'Flank	NM_000773	NP_000764	P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E,						drug metabolic process|heterocycle metabolic process|monoterpenoid metabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding			central_nervous_system(3)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Clofibrate(DB00636)|Dacarbazine(DB00851)|Dapsone(DB00250)|Enflurane(DB00228)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethosuximide(DB00593)|Fomepizole(DB01213)|Glutathione(DB00143)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Isoniazid(DB00951)|Menadione(DB00170)|Mephenytoin(DB00532)|Methoxyflurane(DB01028)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitrofurantoin(DB00698)|Orphenadrine(DB01173)|Phenelzine(DB00780)|Quinidine(DB00908)|S-Adenosylmethionine(DB00118)|Sevoflurane(DB01236)|Theophylline(DB00277)|Tolbutamide(DB01124)	CTGCTGGCCCCTCTGCCTTAG	0.498									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				75	92	---	---	---	---	PASS
SIRT3	23410	broad.mit.edu	37	11	233040	233040	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:233040G>T	uc001lok.3	-	3	683	c.649C>A	c.(649-651)CAT>AAT	p.H217N	SIRT3_uc001loj.3_Missense_Mutation_p.H75N|SIRT3_uc010qvm.1_Missense_Mutation_p.H153N|SIRT3_uc010qvn.1_Missense_Mutation_p.H136N|SIRT3_uc010qvo.1_Missense_Mutation_p.H217N|SIRT3_uc010qvp.1_Missense_Mutation_p.H217N|SIRT3_uc010qvq.1_Missense_Mutation_p.H75N|SIRT3_uc009ybt.1_RNA	NM_012239	NP_036371	Q9NTG7	SIRT3_HUMAN	sirtuin 3 isoform a	217	Deacetylase sirtuin-type.				chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding			urinary_tract(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		CCCTTGTCATGAAGCAGCCGG	0.522													39	31	---	---	---	---	PASS
KCNQ1	3784	broad.mit.edu	37	11	2610087	2610087	+	Intron	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2610087G>A	uc001lwn.2	+						KCNQ1_uc009ydp.1_Intron|KCNQ1_uc001lwo.2_Intron	NM_000218	NP_000209	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like						blood circulation|membrane depolarization|muscle contraction|sensory perception of sound		delayed rectifier potassium channel activity|protein binding			ovary(1)	1		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	CAGTTCTGGTGAGAACCCCTC	0.617													17	17	---	---	---	---	PASS
OR52B4	143496	broad.mit.edu	37	11	4389372	4389372	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4389372G>T	uc010qye.1	-	1	154	c.154C>A	c.(154-156)CTC>ATC	p.L52I		NM_001005161	NP_001005161	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B,	52	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		CGCTTTGTGAGGATAATGAAG	0.527													20	25	---	---	---	---	PASS
SCUBE2	57758	broad.mit.edu	37	11	9072263	9072263	+	Intron	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9072263G>A	uc001mhh.1	-						SCUBE2_uc001mhi.1_Intron|SCUBE2_uc001mhj.1_Intron	NM_020974	NP_066025	Q9NQ36	SCUB2_HUMAN	CEGP1 protein precursor							extracellular region	calcium ion binding			ovary(1)|skin(1)	2				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		GACATCTTCAGAAAGAAACAA	0.473													45	49	---	---	---	---	PASS
OR4C11	219429	broad.mit.edu	37	11	55371668	55371668	+	Missense_Mutation	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55371668A>G	uc010rii.1	-	1	182	c.182T>C	c.(181-183)CTA>CCA	p.L61P		NM_001004700	NP_001004700	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C,	61	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						CAAATAAAATAGAAAGAAGTA	0.388													58	62	---	---	---	---	PASS
OR4C6	219432	broad.mit.edu	37	11	55432931	55432931	+	Missense_Mutation	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55432931A>G	uc001nht.3	+	3	554	c.289A>G	c.(289-291)ACC>GCC	p.T97A	OR4C6_uc010rik.1_Missense_Mutation_p.T97A	NM_001004704	NP_001004704	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C,	97	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2						AGGCTGCCTCACCCAGCTGTT	0.527													30	115	---	---	---	---	PASS
TNKS1BP1	85456	broad.mit.edu	37	11	57080646	57080646	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57080646C>A	uc001njr.2	-	4	1828	c.1516G>T	c.(1516-1518)GCC>TCC	p.A506S	TNKS1BP1_uc001njs.2_Missense_Mutation_p.A506S|TNKS1BP1_uc009ymd.1_5'UTR	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	506	Pro-rich.|Acidic.				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)				GCCTCGGCGGCCTCACTGGCT	0.657													5	22	---	---	---	---	PASS
TNKS1BP1	85456	broad.mit.edu	37	11	57080648	57080648	+	Missense_Mutation	SNP	T	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57080648T>A	uc001njr.2	-	4	1826	c.1514A>T	c.(1513-1515)GAG>GTG	p.E505V	TNKS1BP1_uc001njs.2_Missense_Mutation_p.E505V|TNKS1BP1_uc009ymd.1_5'UTR	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	505	Pro-rich.|Acidic.				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)				CTCGGCGGCCTCACTGGCTTC	0.647													5	19	---	---	---	---	PASS
STX5	6811	broad.mit.edu	37	11	62595044	62595044	+	Silent	SNP	G	A	A	rs149057421	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62595044G>A	uc001nvh.2	-	3	439	c.285C>T	c.(283-285)ACC>ACT	p.T95T	STX5_uc010rmi.1_5'UTR|STX5_uc009yoh.2_RNA|STX5_uc001nvi.2_Silent_p.T41T|STX5_uc010rmj.1_Silent_p.T95T|STX5_uc001nvj.2_Intron	NM_003164	NP_003155	Q13190	STX5_HUMAN	syntaxin 5	95	Cytoplasmic (Potential).				intracellular protein transport|retrograde transport, endosome to Golgi|vesicle targeting	ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane|nucleus|SNARE complex	protein N-terminus binding|SNAP receptor activity			ovary(1)|breast(1)	2						TGGCCATGAGGGTGAATTCAC	0.483													41	44	---	---	---	---	PASS
TECTA	7007	broad.mit.edu	37	11	121008472	121008472	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121008472G>T	uc010rzo.1	+	10	3284	c.3284G>T	c.(3283-3285)CGC>CTC	p.R1095L		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	1095					cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TGCCAAGCCCGCACCGACGCC	0.577													20	30	---	---	---	---	PASS
PKNOX2	63876	broad.mit.edu	37	11	125267941	125267941	+	Missense_Mutation	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125267941A>G	uc001qbu.2	+	7	885	c.571A>G	c.(571-573)ATC>GTC	p.I191V	PKNOX2_uc010saz.1_Missense_Mutation_p.I162V|PKNOX2_uc010sba.1_Missense_Mutation_p.I162V|PKNOX2_uc010sbb.1_Missense_Mutation_p.I127V	NM_022062	NP_071345	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	191						nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		CCAGCCCTCCATCAACCTTCA	0.572													59	47	---	---	---	---	PASS
KDM5A	5927	broad.mit.edu	37	12	441100	441100	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:441100T>C	uc001qif.1	-	13	2021	c.1658A>G	c.(1657-1659)TAC>TGC	p.Y553C	KDM5A_uc001qie.1_Missense_Mutation_p.Y553C|KDM5A_uc010sdn.1_Missense_Mutation_p.Y512C|KDM5A_uc010sdo.1_Missense_Mutation_p.Y172C	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1	553	JmjC.				chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3						ATTGGTCCTGTACACCTAAAT	0.373			T 	NUP98	AML								27	46	---	---	---	---	PASS
CCND2	894	broad.mit.edu	37	12	4409186	4409186	+	3'UTR	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4409186T>G	uc001qmo.2	+	5						NM_001759	NP_001750	P30279	CCND2_HUMAN	cyclin D2						cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation	cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus	protein kinase binding			haematopoietic_and_lymphoid_tissue(1)|breast(1)|kidney(1)	3			all cancers(3;4.15e-10)|GBM - Glioblastoma multiforme(3;6.34e-05)|Colorectal(7;0.00245)|OV - Ovarian serous cystadenocarcinoma(31;0.00301)|COAD - Colon adenocarcinoma(12;0.0264)|STAD - Stomach adenocarcinoma(119;0.206)			GGATGCCAGTTGGGCCGAAAG	0.483			T	IGL@	NHL,CLL								10	48	---	---	---	---	PASS
GSG1	83445	broad.mit.edu	37	12	13241724	13241724	+	Intron	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13241724G>A	uc001rbn.2	-						GSG1_uc001rbj.2_Intron|GSG1_uc001rbk.2_Missense_Mutation_p.R149W|GSG1_uc001rbl.2_Intron|GSG1_uc001rbm.2_Intron|GSG1_uc001rbo.2_Missense_Mutation_p.R185W|GSG1_uc001rbp.2_Intron|GSG1_uc001rbq.1_Missense_Mutation_p.R185W	NM_001080555	NP_001074024	Q2KHT4	GSG1_HUMAN	germ cell associated 1 isoform 4							endoplasmic reticulum membrane|integral to membrane					0		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		TCCATCAACCGCTTCCCTCCA	0.517													42	51	---	---	---	---	PASS
KIAA0528	9847	broad.mit.edu	37	12	22659657	22659657	+	Missense_Mutation	SNP	T	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22659657T>A	uc001rfq.2	-	10	1363	c.1135A>T	c.(1135-1137)ATC>TTC	p.I379F	KIAA0528_uc010sir.1_Missense_Mutation_p.I172F|KIAA0528_uc010sis.1_Missense_Mutation_p.I379F|KIAA0528_uc010sit.1_Missense_Mutation_p.I381F|KIAA0528_uc010siu.1_Missense_Mutation_p.I379F|KIAA0528_uc001rfr.2_Missense_Mutation_p.I370F|KIAA0528_uc009ziy.1_Missense_Mutation_p.I381F	NM_014802	NP_055617	Q86YS7	K0528_HUMAN	hypothetical protein LOC9847	379							protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						GGATTGTGGATACGATCCAAA	0.338													60	112	---	---	---	---	PASS
KIAA0528	9847	broad.mit.edu	37	12	22676435	22676435	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22676435G>A	uc001rfq.2	-	7	953	c.725C>T	c.(724-726)GCG>GTG	p.A242V	KIAA0528_uc010sir.1_Missense_Mutation_p.A44V|KIAA0528_uc010sis.1_Missense_Mutation_p.A242V|KIAA0528_uc010sit.1_Missense_Mutation_p.A242V|KIAA0528_uc010siu.1_Missense_Mutation_p.A242V|KIAA0528_uc001rfr.2_Missense_Mutation_p.A242V|KIAA0528_uc009ziy.1_Missense_Mutation_p.A242V	NM_014802	NP_055617	Q86YS7	K0528_HUMAN	hypothetical protein LOC9847	242							protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4						CAGAGTACACGCCGTTCCTAT	0.438													13	60	---	---	---	---	PASS
MYO1A	4640	broad.mit.edu	37	12	57437912	57437912	+	Missense_Mutation	SNP	G	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57437912G>C	uc001smw.3	-	9	965	c.722C>G	c.(721-723)GCC>GGC	p.A241G	MYO1A_uc010sqz.1_Missense_Mutation_p.A79G|MYO1A_uc009zpd.2_Missense_Mutation_p.A241G	NM_005379	NP_005370	Q9UBC5	MYO1A_HUMAN	myosin IA	241	Myosin head-like.				sensory perception of sound|vesicle localization	brush border|cortical actin cytoskeleton|filamentous actin|lateral plasma membrane|microvillus|myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|urinary_tract(1)	7						GAAGCTGGAGGCGTCGTCCAT	0.572													41	42	---	---	---	---	PASS
NAV3	89795	broad.mit.edu	37	12	78510561	78510561	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78510561C>T	uc001syp.2	+	13	2819	c.2646C>T	c.(2644-2646)GAC>GAT	p.D882D	NAV3_uc001syo.2_Silent_p.D882D|NAV3_uc010sub.1_Silent_p.D382D|NAV3_uc009zsf.2_5'Flank	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	882						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						GCTGGGATGACAGCAGTTCAG	0.453										HNSCC(70;0.22)			42	51	---	---	---	---	PASS
RASSF9	9182	broad.mit.edu	37	12	86198647	86198647	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86198647T>C	uc001taf.1	-	2	1480	c.1141A>G	c.(1141-1143)AGA>GGA	p.R381G		NM_005447	NP_005438	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family	381					endosome transport|protein targeting|signal transduction	cytosol|endosome|trans-Golgi network transport vesicle membrane	protein binding|transporter activity			ovary(1)	1						TCCTTCGCTCTGTTTTCCTTT	0.423													120	127	---	---	---	---	PASS
KCTD10	83892	broad.mit.edu	37	12	109894110	109894110	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109894110T>C	uc001toi.1	-	6	624	c.536A>G	c.(535-537)GAC>GGC	p.D179G	KCTD10_uc001toh.1_RNA|KCTD10_uc009zvi.1_Intron|KCTD10_uc001toj.1_Missense_Mutation_p.D188G|KCTD10_uc001tok.1_5'UTR	NM_031954	NP_114160	Q9H3F6	BACD3_HUMAN	potassium channel tetramerisation domain	179					proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination	Cul3-RING ubiquitin ligase complex|cytoplasm|nucleus|voltage-gated potassium channel complex	voltage-gated potassium channel activity				0						CATATTGTCGTCAGAATTGCT	0.313													20	74	---	---	---	---	PASS
FRY	10129	broad.mit.edu	37	13	32841387	32841387	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32841387C>A	uc001utx.2	+	55	8523	c.8027C>A	c.(8026-8028)GCC>GAC	p.A2676D	FRY_uc010tdw.1_RNA|FRY_uc001uty.2_Missense_Mutation_p.A231D|FRY_uc001utz.2_Missense_Mutation_p.A201D|FRY_uc010tdx.1_Missense_Mutation_p.A46D	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	2676					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CAGCCCGCAGCCTGTGACGAT	0.557													34	134	---	---	---	---	PASS
ATP7B	540	broad.mit.edu	37	13	52535998	52535998	+	Silent	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52535998A>G	uc001vfw.2	-	6	2078	c.1921T>C	c.(1921-1923)TTG>CTG	p.L641L	ATP7B_uc010adv.2_Intron|ATP7B_uc001vfx.2_Intron|ATP7B_uc001vfy.2_Silent_p.L530L|ATP7B_uc010tgt.1_Silent_p.L641L|ATP7B_uc010tgu.1_Silent_p.L641L|ATP7B_uc010tgv.1_Silent_p.L641L|ATP7B_uc001vfv.2_5'Flank|ATP7B_uc010tgs.1_5'UTR|ATP7B_uc010tgw.1_Intron	NM_000053	NP_000044	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	641	Cytoplasmic (Potential).		L -> S (in WD).		ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)		TTGTGGTCCAAGTGATGAGCG	0.478									Wilson_disease				101	68	---	---	---	---	PASS
MYCBP2	23077	broad.mit.edu	37	13	77786084	77786084	+	Intron	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77786084G>T	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TTTATTTCTGGTATTACCTAT	0.318													55	31	---	---	---	---	PASS
ATP11A	23250	broad.mit.edu	37	13	113526056	113526056	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113526056G>A	uc001vsi.3	+	26	3087	c.2999G>A	c.(2998-3000)GGA>GAA	p.G1000E	ATP11A_uc001vsj.3_Missense_Mutation_p.G1000E|ATP11A_uc010ago.2_RNA	NM_015205	NP_056020	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform a	1000	Extracellular (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				CAGATATTTGGAAACTGGACG	0.408													55	847	---	---	---	---	PASS
POLE2	5427	broad.mit.edu	37	14	50117145	50117145	+	Missense_Mutation	SNP	G	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50117145G>C	uc001wwu.2	-	17	1349	c.1335C>G	c.(1333-1335)ATC>ATG	p.I445M	SDCCAG1_uc010anj.1_Intron|POLE2_uc010ann.2_Missense_Mutation_p.I159M|POLE2_uc001wwv.2_RNA|POLE2_uc010ano.2_Missense_Mutation_p.I160M	NM_002692	NP_002683	P56282	DPOE2_HUMAN	DNA-directed DNA polymerase epsilon 2	445					DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	DNA binding|DNA-directed DNA polymerase activity			ovary(1)|skin(1)	2	all_epithelial(31;0.0021)|Breast(41;0.0124)					CTTGGGATAAGATAGTCTTTA	0.358													24	61	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64465690	64465690	+	Missense_Mutation	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64465690A>G	uc001xgm.2	+	27	3642	c.3412A>G	c.(3412-3414)ACT>GCT	p.T1138A	SYNE2_uc001xgl.2_Missense_Mutation_p.T1138A	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	1138	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		ATTCAGGATTACTTCTGATTT	0.338													63	64	---	---	---	---	PASS
TECPR2	9895	broad.mit.edu	37	14	102910044	102910044	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102910044C>T	uc001ylw.1	+	12	2961	c.2813C>T	c.(2812-2814)TCC>TTC	p.S938F	TECPR2_uc010awl.2_Missense_Mutation_p.S938F|TECPR2_uc010txx.1_Missense_Mutation_p.S101F	NM_014844	NP_055659	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	938							protein binding			lung(1)|central_nervous_system(1)|skin(1)	3						TACCCGCTGTCCCAGATCACA	0.622													47	71	---	---	---	---	PASS
SLC12A1	6557	broad.mit.edu	37	15	48527109	48527109	+	Missense_Mutation	SNP	A	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48527109A>T	uc001zwn.3	+	9	1339	c.1123A>T	c.(1123-1125)ACA>TCA	p.T375S	SLC12A1_uc010uew.1_Missense_Mutation_p.T181S|SLC12A1_uc010bem.2_Missense_Mutation_p.T375S|SLC12A1_uc010uex.1_Missense_Mutation_p.T375S|SLC12A1_uc001zwq.3_Missense_Mutation_p.T146S|SLC12A1_uc001zwr.3_Missense_Mutation_p.T102S	NM_000338	NP_000329	Q13621	S12A1_HUMAN	sodium potassium chloride cotransporter 2	375					potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	GCCACGCTTCACAAAGGGTGA	0.398													64	57	---	---	---	---	PASS
WDR72	256764	broad.mit.edu	37	15	53905856	53905856	+	Intron	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53905856C>A	uc002acj.2	-							NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)		GCCAGTAACTCTCTTACCATT	0.318													53	63	---	---	---	---	PASS
TCF12	6938	broad.mit.edu	37	15	57355944	57355944	+	Intron	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57355944T>G	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		TCTTCTCTTTTTAGGTATTGA	0.368			T	TEC	extraskeletal myxoid chondrosarcoma								39	109	---	---	---	---	PASS
TLE3	7090	broad.mit.edu	37	15	70344823	70344823	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70344823G>T	uc002asm.2	-	18	3143	c.2024C>A	c.(2023-2025)GCT>GAT	p.A675D	TLE3_uc002ask.2_Missense_Mutation_p.A602D|TLE3_uc002asl.2_Missense_Mutation_p.A675D|TLE3_uc010ukd.1_Missense_Mutation_p.A665D|TLE3_uc010bik.1_Missense_Mutation_p.A256D|TLE3_uc010bil.1_Missense_Mutation_p.A672D|TLE3_uc002asn.2_Missense_Mutation_p.A663D|TLE3_uc002asp.2_Missense_Mutation_p.A667D|TLE3_uc002aso.2_Missense_Mutation_p.A670D	NM_005078	NP_005069	Q04726	TLE3_HUMAN	transducin-like enhancer protein 3 isoform a	675	WD 5.				organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|protein binding			lung(2)	2						CATGCCCACAGCCAGCCACTC	0.617													17	9	---	---	---	---	PASS
RASGRF1	5923	broad.mit.edu	37	15	79339153	79339153	+	Silent	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79339153C>G	uc002beq.2	-	5	1188	c.813G>C	c.(811-813)CGG>CGC	p.R271R	RASGRF1_uc002bep.2_Silent_p.R271R|RASGRF1_uc010blm.1_Silent_p.R193R|RASGRF1_uc002ber.3_Silent_p.R271R	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine	271	DH.				activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6						TGGCGGCCATCCGCAGCGGGC	0.592													81	65	---	---	---	---	PASS
LYSMD4	145748	broad.mit.edu	37	15	100271607	100271607	+	Intron	SNP	T	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100271607T>A	uc002bvk.2	-						LYSMD4_uc002bvj.1_Intron|LYSMD4_uc010bou.1_Intron|LYSMD4_uc002bvl.2_Missense_Mutation_p.N72I|LYSMD4_uc002bvm.2_Intron|LYSMD4_uc010bov.2_Intron			Q5XG99	LYSM4_HUMAN	SubName: Full=cDNA FLJ77040, highly similar to Homo sapiens LysM, putative peptidoglycan-binding, domain containing 4, mRNA; SubName: Full=LysM, putative peptidoglycan-binding, domain containing 4, isoform CRA_c;						cell wall macromolecule catabolic process	integral to membrane					0	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208)			TCCAGCCCCATTAGGTCTAAA	0.393													72	70	---	---	---	---	PASS
RPS2	6187	broad.mit.edu	37	16	2012182	2012182	+	Nonsense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2012182G>A	uc002cnn.2	-	6	987	c.799C>T	c.(799-801)CAG>TAG	p.Q267*	RPS2_uc010bsa.1_RNA|RPS2_uc002cnl.2_Nonsense_Mutation_p.Q209*|RPS2_uc002cnm.2_RNA|RPS2_uc002cno.2_Nonsense_Mutation_p.Q267*|SNHG9_uc002cnr.2_5'Flank	NM_002952	NP_002943	P15880	RS2_HUMAN	ribosomal protein S2	267					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleoplasm	fibroblast growth factor 1 binding|fibroblast growth factor 3 binding|RNA binding|structural constituent of ribosome				0						GTGAACTCCTGATAGGGAGAC	0.512													39	75	---	---	---	---	PASS
PKD1	5310	broad.mit.edu	37	16	2142539	2142539	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2142539C>T	uc002cos.1	-	39	11420	c.11211G>A	c.(11209-11211)GGG>GGA	p.G3737G	PKD1_uc002cot.1_Silent_p.G3736G|MIR1225_hsa-mir-1225|MI0006311_5'Flank|PKD1_uc010bse.1_RNA	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	3737	Extracellular (Potential).				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(2)|skin(1)	3						TGGACTGGTTCCCGTGGACGT	0.662													14	20	---	---	---	---	PASS
PRSS22	64063	broad.mit.edu	37	16	2903228	2903228	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2903228C>A	uc002cry.1	-	6	886	c.820G>T	c.(820-822)GTC>TTC	p.V274F	PRSS22_uc002crz.1_Missense_Mutation_p.V164F	NM_022119	NP_071402	Q9GZN4	BSSP4_HUMAN	protease, serine, 22 precursor	274	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			central_nervous_system(1)	1						CTGATGTAGACCCCGGGCCTG	0.726													19	65	---	---	---	---	PASS
BTBD12	84464	broad.mit.edu	37	16	3641121	3641121	+	Missense_Mutation	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3641121C>G	uc002cvp.2	-	12	3145	c.2518G>C	c.(2518-2520)GAA>CAA	p.E840Q		NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	840	Potential.|Interaction with PLK1 and TERF2-TERF2IP.|Glu-rich.				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0						TGATCTTCTTCGTGGTCCTTG	0.468								Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				81	177	---	---	---	---	PASS
CREBBP	1387	broad.mit.edu	37	16	3795299	3795299	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3795299T>C	uc002cvv.2	-	22	4097	c.3893A>G	c.(3892-3894)TAT>TGT	p.Y1298C	CREBBP_uc002cvw.2_Missense_Mutation_p.Y1260C	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	1298	Cys/His-rich.				cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		AATGATGTCATAGTGCAGAAC	0.537			T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				15	56	---	---	---	---	PASS
CREBBP	1387	broad.mit.edu	37	16	3820624	3820624	+	Nonsense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3820624G>A	uc002cvv.2	-	14	3031	c.2827C>T	c.(2827-2829)CAG>TAG	p.Q943*	CREBBP_uc002cvw.2_Nonsense_Mutation_p.Q905*	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	943					cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TGCGATGACTGAGGGGTAGCC	0.622			T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				96	129	---	---	---	---	PASS
ABCC1	4363	broad.mit.edu	37	16	16146661	16146661	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16146661C>T	uc010bvi.2	+	11	1636	c.1461C>T	c.(1459-1461)ACC>ACT	p.T487T	ABCC1_uc010bvj.2_Silent_p.T487T|ABCC1_uc010bvk.2_Silent_p.T487T|ABCC1_uc010bvl.2_Silent_p.T487T|ABCC1_uc010bvm.2_Silent_p.T487T|ABCC1_uc002del.3_Silent_p.T371T|ABCC1_uc010bvn.2_Silent_p.T350T	NM_004996	NP_004987	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C, member 1	487	Cytoplasmic.|ABC transmembrane type-1 1.				hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	CGATGAAGACCAAGACGTATC	0.572													21	65	---	---	---	---	PASS
CRYM	1428	broad.mit.edu	37	16	21279036	21279036	+	Missense_Mutation	SNP	T	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21279036T>A	uc002dik.2	-	5	597	c.512A>T	c.(511-513)AAA>ATA	p.K171I	CRYM_uc010bwq.1_RNA|CRYM_uc002dil.2_Missense_Mutation_p.K129I|CRYM_uc002dim.2_Missense_Mutation_p.K171I	NM_001888	NP_001879	Q14894	CRYM_HUMAN	crystallin, mu isoform 1	171					negative regulation of transcription from RNA polymerase II promoter|sensory perception of sound|thyroid hormone transport	cytoplasm|nucleus|plasma membrane	NADP binding|protein homodimerization activity|thyroid hormone binding|transcription corepressor activity				0				GBM - Glioblastoma multiforme(48;0.0573)	Levothyroxine(DB00451)	TGCATTTTCTTTGGTGCGGTT	0.507													52	92	---	---	---	---	PASS
LDHD	197257	broad.mit.edu	37	16	75146775	75146775	+	Silent	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75146775G>T	uc002fdm.2	-	9	1250	c.1203C>A	c.(1201-1203)ATC>ATA	p.I401I	LDHD_uc002fdn.2_Silent_p.I378I	NM_153486	NP_705690	Q86WU2	LDHD_HUMAN	D-lactate dehydrogenase isoform 1 precursor	401							D-lactate dehydrogenase (cytochrome) activity|flavin adenine dinucleotide binding|protein binding				0						TCTGCACCACGATCTCCGGCA	0.617													20	24	---	---	---	---	PASS
CNTNAP4	85445	broad.mit.edu	37	16	76587808	76587808	+	Intron	SNP	A	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76587808A>C	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron|CNTNAP4_uc010chb.1_Intron|CNTNAP4_uc002fex.1_Intron	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						ATTGGAGGTAATAAGAAGCAT	0.373													4	33	---	---	---	---	PASS
C17orf81	23587	broad.mit.edu	37	17	7160277	7160277	+	Missense_Mutation	SNP	G	A	A	rs3190365		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7160277G>A	uc002gfg.1	+	6	666	c.559G>A	c.(559-561)GAG>AAG	p.E187K	C17orf81_uc002gfj.2_Missense_Mutation_p.E187K|C17orf81_uc010cmb.2_Missense_Mutation_p.E187K|C17orf81_uc002gfh.1_Missense_Mutation_p.E187K|C17orf81_uc002gfi.1_Missense_Mutation_p.E187K|C17orf81_uc002gfl.1_Missense_Mutation_p.E187K	NM_203415	NP_981960	Q8TE02	DERP6_HUMAN	S-phase 2 protein isoform 4	187					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding				0						TGCTCAGACTGAGGTGACCCT	0.612													30	17	---	---	---	---	PASS
MYH1	4619	broad.mit.edu	37	17	10401181	10401181	+	Missense_Mutation	SNP	T	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10401181T>A	uc002gmo.2	-	31	4329	c.4235A>T	c.(4234-4236)AAT>ATT	p.N1412I	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1412	Potential.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21						ACATTTGGCATTCACAGCTTC	0.483													54	46	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10427843	10427843	+	Silent	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10427843T>C	uc010coi.2	-	35	5243	c.5115A>G	c.(5113-5115)AGA>AGG	p.R1705R	uc002gml.1_Intron|MYH2_uc002gmp.3_Silent_p.R1705R|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1705	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						CTGCGATTTTTCTGCTCCTCT	0.542													72	82	---	---	---	---	PASS
FLII	2314	broad.mit.edu	37	17	18149623	18149623	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18149623G>A	uc002gsr.1	-	24	3256	c.3205C>T	c.(3205-3207)CGG>TGG	p.R1069W	FLII_uc002gsq.1_Missense_Mutation_p.R940W|FLII_uc010cpy.1_Missense_Mutation_p.R1058W|FLII_uc010vxn.1_Missense_Mutation_p.R1038W|FLII_uc010vxo.1_Missense_Mutation_p.R1014W	NM_002018	NP_002009	Q13045	FLII_HUMAN	flightless I homolog	1069	Gelsolin-like 4.				multicellular organismal development|muscle contraction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleus	actin binding			central_nervous_system(1)|skin(1)	2	all_neural(463;0.228)					GCCAGGCACCGGGTGCAGAGG	0.652													5	89	---	---	---	---	PASS
ABCA9	10350	broad.mit.edu	37	17	66981184	66981184	+	Intron	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66981184C>A	uc002jhu.2	-						ABCA9_uc010dez.2_Intron	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9						transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)					ACAACAAGCCCTGCCCGTACC	0.562													85	63	---	---	---	---	PASS
ITGB4	3691	broad.mit.edu	37	17	73732371	73732371	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73732371C>T	uc002jpg.2	+	15	1951	c.1764C>T	c.(1762-1764)GGC>GGT	p.G588G	ITGB4_uc002jph.2_Silent_p.G588G|ITGB4_uc010dgo.2_Silent_p.G588G|ITGB4_uc002jpi.3_Silent_p.G588G|ITGB4_uc010dgp.1_Silent_p.G588G|ITGB4_uc002jpj.2_Silent_p.G588G|ITGB4_uc010wsh.1_Silent_p.G143G	NM_000213	NP_000204	P16144	ITB4_HUMAN	integrin beta 4 isoform 1 precursor	588	Cysteine-rich tandem repeats.|Extracellular (Potential).|IV.				cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			TACCCCAGGGCATCTGTAATG	0.627													68	47	---	---	---	---	PASS
LAMA1	284217	broad.mit.edu	37	18	6980547	6980547	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6980547G>A	uc002knm.2	-	42	6074	c.5980C>T	c.(5980-5982)CTC>TTC	p.L1994F	LAMA1_uc010wzj.1_Missense_Mutation_p.L1470F	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1994	Domain II and I.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	AGTATCAAGAGTGATTCATTG	0.353													15	68	---	---	---	---	PASS
DSC2	1824	broad.mit.edu	37	18	28666711	28666711	+	Intron	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28666711G>A	uc002kwl.3	-						DSC2_uc002kwk.3_Intron	NM_024422	NP_077740	Q02487	DSC2_HUMAN	desmocollin 2 isoform Dsc2a preproprotein						homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			AGTGCCTAGAGAAGAAAAGTC	0.433													27	24	---	---	---	---	PASS
PLIN4	729359	broad.mit.edu	37	19	4511803	4511803	+	Missense_Mutation	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4511803C>G	uc002mar.1	-	3	2127	c.2127G>C	c.(2125-2127)AAG>AAC	p.K709N	PLIN4_uc010dub.1_5'Flank	NM_001080400	NP_001073869	Q96Q06	PLIN4_HUMAN	plasma membrane associated protein, S3-12	709	19.|27 X 33 AA approximate tandem repeat.					lipid particle|plasma membrane					0						TTAGGACAGTCTTGGTGGTGT	0.592													71	444	---	---	---	---	PASS
ZNF560	147741	broad.mit.edu	37	19	9577783	9577783	+	Missense_Mutation	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9577783C>G	uc002mlp.1	-	10	2050	c.1840G>C	c.(1840-1842)GAT>CAT	p.D614H	ZNF560_uc010dwr.1_Missense_Mutation_p.D508H	NM_152476	NP_689689	Q96MR9	ZN560_HUMAN	zinc finger protein 560	614	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|pancreas(1)|liver(1)	6						TTAGTAAGATCTGAGCGTTCT	0.408													53	160	---	---	---	---	PASS
ZSWIM4	65249	broad.mit.edu	37	19	13928130	13928130	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13928130C>T	uc002mxh.1	+	7	1470	c.1281C>T	c.(1279-1281)GCC>GCT	p.A427A	ZSWIM4_uc010xng.1_Silent_p.A350A	NM_023072	NP_075560	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	427							zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			TCCTGGAGGCCTGTCGTCTGG	0.642													49	64	---	---	---	---	PASS
PGLYRP2	114770	broad.mit.edu	37	19	15587093	15587093	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15587093C>T	uc002nbf.3	-	2	521	c.388G>A	c.(388-390)GCA>ACA	p.A130T	PGLYRP2_uc002nbg.3_Missense_Mutation_p.A130T	NM_052890	NP_443122	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2 precursor	130					defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptide amidation|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(3)	3						TGCAGCCCTGCCTCCAGCCCC	0.612													32	84	---	---	---	---	PASS
ZNF430	80264	broad.mit.edu	37	19	21216941	21216941	+	Silent	SNP	A	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21216941A>T	uc002npj.2	+	4	383	c.273A>T	c.(271-273)GGA>GGT	p.G91G	ZNF430_uc002npk.2_Silent_p.G90G	NM_025189	NP_079465	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	91	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2						TAGAGCAAGGAAAAGAGCCCT	0.408													56	61	---	---	---	---	PASS
ANKRD27	84079	broad.mit.edu	37	19	33113388	33113388	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33113388C>T	uc002ntn.1	-	18	1923	c.1767G>A	c.(1765-1767)GCG>GCA	p.A589A		NM_032139	NP_115515	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	589	ANK 5.				early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)	5	Esophageal squamous(110;0.137)					TCTCGGTGGACGCTCCGTTCT	0.527													237	359	---	---	---	---	PASS
SLC7A10	56301	broad.mit.edu	37	19	33703303	33703303	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33703303G>A	uc002num.2	-	5	830	c.683C>T	c.(682-684)ACG>ATG	p.T228M	SLC7A10_uc002nul.2_5'Flank|SLC7A10_uc010xrq.1_Missense_Mutation_p.T201M	NM_019849	NP_062823	Q9NS82	AAA1_HUMAN	solute carrier family 7, member 10	228					blood coagulation|cellular nitrogen compound metabolic process|ion transport|leukocyte migration	integral to plasma membrane	L-serine transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(110;0.137)					CACGGAGGGCGTCATCCAGAA	0.627													38	68	---	---	---	---	PASS
WDR62	284403	broad.mit.edu	37	19	36557157	36557157	+	Splice_Site	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36557157A>G	uc002odc.2	+	5	482	c.391_splice	c.e5-2	p.N131_splice	WDR62_uc002odd.2_Splice_Site_p.N131_splice|WDR62_uc002odb.2_Splice_Site_p.N131_splice	NM_173636	NP_775907	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 2						cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CACCTTCCCTAGAATGGGCAT	0.582													34	98	---	---	---	---	PASS
ZNF570	148268	broad.mit.edu	37	19	37975983	37975983	+	Missense_Mutation	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37975983C>G	uc002ogk.1	+	5	1988	c.1459C>G	c.(1459-1461)CAA>GAA	p.Q487E	ZNF570_uc010efl.1_Missense_Mutation_p.Q543E|ZNF570_uc010xtr.1_Missense_Mutation_p.Q284E	NM_144694	NP_653295	Q96NI8	ZN570_HUMAN	zinc finger protein 570	487	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATCCCTTGCCCAACATCAGAG	0.433													33	163	---	---	---	---	PASS
PSG8	440533	broad.mit.edu	37	19	43262355	43262355	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43262355C>T	uc002ouo.2	-	3	606	c.508G>A	c.(508-510)GAT>AAT	p.D170N	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG8_uc010eim.2_RNA|PSG8_uc002oui.2_Missense_Mutation_p.D9N|PSG8_uc002ouh.2_Missense_Mutation_p.D170N|PSG8_uc010ein.2_Missense_Mutation_p.D48N|PSG8_uc002ouj.3_Intron|PSG8_uc002ouk.3_Missense_Mutation_p.D9N|PSG8_uc002oul.3_Missense_Mutation_p.D170N|PSG8_uc002oum.3_Intron|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Intron	NM_182707	NP_874366	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8 isoform	170	Ig-like C2-type 1.					extracellular region					0		Prostate(69;0.00899)				GTCTCAGGATCACAGGTTAAG	0.532													90	526	---	---	---	---	PASS
KCNN4	3783	broad.mit.edu	37	19	44273660	44273660	+	Missense_Mutation	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44273660T>G	uc002oxl.2	-	6	1379	c.983A>C	c.(982-984)CAT>CCT	p.H328P	KCNN4_uc010eiz.2_Intron	NM_002250	NP_002241	O15554	KCNN4_HUMAN	intermediate conductance calcium-activated	328	Calmodulin-binding.				defense response	voltage-gated potassium channel complex	calcium-activated potassium channel activity|calmodulin binding			ovary(2)	2		Prostate(69;0.0352)			Clotrimazole(DB00257)|Halothane(DB01159)|Quinine(DB00468)	CCTGCGAGTATGTTTGTAGAA	0.582													33	204	---	---	---	---	PASS
ZNF765	91661	broad.mit.edu	37	19	53912214	53912214	+	Missense_Mutation	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53912214A>G	uc010ydx.1	+	6	1733	c.1406A>G	c.(1405-1407)AAT>AGT	p.N469S	ZNF765_uc002qbm.2_Missense_Mutation_p.N469S|ZNF765_uc002qbn.2_Intron	NM_001040185	NP_001035275	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	469	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00379)		TACAAGTGTAATGAGTGTGGC	0.378													53	159	---	---	---	---	PASS
KIR2DL1	3802	broad.mit.edu	37	19	55290069	55290069	+	Missense_Mutation	SNP	C	A	A	rs113506642		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55290069C>A	uc002qhb.1	+	5	708	c.670C>A	c.(670-672)CCT>ACT	p.P224T	KIR2DS4_uc010yfj.1_Intron|KIR2DS4_uc010yfk.1_Intron|KIR2DL3_uc010erw.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR3DP1_uc010yfi.1_Intron|KIR2DL1_uc010erz.1_Missense_Mutation_p.P224T	NM_014218	NP_055033	P43626	KI2L1_HUMAN	killer cell immunoglobulin-like receptor, two	224	Extracellular (Potential).				immune response|natural killer cell inhibitory signaling pathway	integral to plasma membrane	protein binding|receptor activity				0				GBM - Glioblastoma multiforme(193;0.0192)		TCTAGGAAACCCTTCAAATAG	0.498													42	138	---	---	---	---	PASS
NLRP11	204801	broad.mit.edu	37	19	56320484	56320484	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56320484G>T	uc010ygf.1	-	5	2203	c.1492C>A	c.(1492-1494)CTT>ATT	p.L498I	NLRP11_uc002qlz.2_Missense_Mutation_p.L399I|NLRP11_uc002qmb.2_Missense_Mutation_p.L399I|NLRP11_uc002qmc.2_RNA|NLRP11_uc010ete.1_RNA	NM_145007	NP_659444	P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	498							ATP binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		GCATTTAGAAGACCAAAAATG	0.418													74	222	---	---	---	---	PASS
NLRP13	126204	broad.mit.edu	37	19	56443411	56443411	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56443411G>T	uc010ygg.1	-	1	292	c.267C>A	c.(265-267)TTC>TTA	p.F89L		NM_176810	NP_789780	Q86W25	NAL13_HUMAN	NACHT, leucine rich repeat and PYD containing	89	DAPIN.						ATP binding			skin(4)|ovary(3)|pancreas(1)|lung(1)	9		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		TCATTGTCTGGAAGATGCCGA	0.507													72	120	---	---	---	---	PASS
DEFB125	245938	broad.mit.edu	37	20	77049	77049	+	Silent	SNP	T	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:77049T>A	uc002wcw.2	+	2	462	c.462T>A	c.(460-462)ACT>ACA	p.T154T		NM_153325	NP_697020	Q8N687	DB125_HUMAN	defensin, beta 125 preproprotein	154					defense response to bacterium	extracellular region				ovary(1)|central_nervous_system(1)|skin(1)	3		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.156)			CAGCTCTTACTCATAATTAAT	0.423													75	411	---	---	---	---	PASS
DEFB129	140881	broad.mit.edu	37	20	209915	209915	+	Intron	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:209915A>G	uc002wda.2	+							NM_080831	NP_543021	Q9H1M3	DB129_HUMAN	beta defensin 129 precursor						defense response to bacterium	extracellular region				ovary(1)	1		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			CTTTTTTTATACAGAATTTAT	0.373													47	69	---	---	---	---	PASS
MAVS	57506	broad.mit.edu	37	20	3842088	3842088	+	Missense_Mutation	SNP	A	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3842088A>T	uc002wjw.3	+	4	571	c.402A>T	c.(400-402)AGA>AGT	p.R134S	MAVS_uc010zqn.1_Intron|MAVS_uc002wjx.3_5'UTR|MAVS_uc002wjy.3_Intron	NM_020746	NP_065797	Q7Z434	MAVS_HUMAN	virus-induced signaling adapter	134	Pro-rich.|Cytoplasmic (Probable).				activation of innate immune response|cellular response to exogenous dsRNA|defense response to bacterium|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of chemokine (C-C motif) ligand 5 production|positive regulation of defense response to virus by host|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interleukin-8 production|positive regulation of IP-10 production|positive regulation of protein import into nucleus, translocation|positive regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|response to virus	integral to membrane|mitochondrial outer membrane	CARD domain binding|protein kinase binding|signal transducer activity				0						ACAGCTGCAGAGAGAAGGAGC	0.627													10	188	---	---	---	---	PASS
WFDC9	259240	broad.mit.edu	37	20	44236738	44236738	+	3'UTR	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44236738G>T	uc002xoy.2	-	5						NM_147198	NP_671731	Q8NEX5	WFDC9_HUMAN	protease inhibitor WAP9 precursor							extracellular region					0		Myeloproliferative disorder(115;0.0122)				GTAGTGATCGGCCAATAGAAT	0.438													148	100	---	---	---	---	PASS
CDH22	64405	broad.mit.edu	37	20	44806640	44806640	+	Silent	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44806640G>A	uc002xrm.2	-	10	2261	c.1860C>T	c.(1858-1860)GCC>GCT	p.A620A	CDH22_uc010ghk.1_Silent_p.A620A	NM_021248	NP_067071	Q9UJ99	CAD22_HUMAN	cadherin 22 precursor	620	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)				GGCTGAGGGAGGCGGCCATGA	0.647													32	13	---	---	---	---	PASS
CYP24A1	1591	broad.mit.edu	37	20	52779309	52779309	+	Missense_Mutation	SNP	T	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52779309T>G	uc002xwv.2	-	7	1335	c.937A>C	c.(937-939)AAG>CAG	p.K313Q	CYP24A1_uc002xwu.1_Missense_Mutation_p.K171Q|CYP24A1_uc002xww.2_Missense_Mutation_p.K313Q	NM_000782	NP_000773	Q07973	CP24A_HUMAN	cytochrome P450 family 24 subfamily A	313					hormone biosynthetic process|osteoblast differentiation|vitamin D catabolic process|vitamin D receptor signaling pathway|xenobiotic metabolic process	mitochondrial inner membrane	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity|electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		STAD - Stomach adenocarcinoma(23;0.206)		Calcidiol(DB00146)|Calcitriol(DB00136)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	AATTCTTTCTTTGAAAGCCGA	0.453													58	41	---	---	---	---	PASS
SLC2A4RG	56731	broad.mit.edu	37	20	62373567	62373567	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62373567C>T	uc002ygq.2	+	5	719	c.664C>T	c.(664-666)CGC>TGC	p.R222C	SLC2A4RG_uc002ygr.2_Missense_Mutation_p.R117C|SLC2A4RG_uc011abj.1_Missense_Mutation_p.R117C|SLC2A4RG_uc002ygs.2_Missense_Mutation_p.R24C|SLC2A4RG_uc002ygt.2_Missense_Mutation_p.R24C	NM_020062	NP_064446	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	222	C2H2-type.					cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					GAGACACATCCGCCTGGTGCA	0.706													12	6	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	21	10862857	10862857	+	IGR	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10862857C>A								None (None upstream) : TPTE (43886 downstream)																							TCACCAGCTACTGTATGCACT	0.567													11	148	---	---	---	---	PASS
ITSN1	6453	broad.mit.edu	37	21	35183447	35183447	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35183447C>T	uc002yta.1	+	21	2756	c.2488C>T	c.(2488-2490)CGT>TGT	p.R830C	DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_RNA|ITSN1_uc002ysz.2_Missense_Mutation_p.R825C|ITSN1_uc010gmg.2_Missense_Mutation_p.R788C|ITSN1_uc010gmh.2_RNA|ITSN1_uc002ysw.2_Missense_Mutation_p.R830C|ITSN1_uc010gmi.2_Missense_Mutation_p.R793C|ITSN1_uc010gmj.2_Missense_Mutation_p.R709C|ITSN1_uc002ysy.2_Missense_Mutation_p.R825C|ITSN1_uc002ysx.2_Missense_Mutation_p.R788C|ITSN1_uc002ytb.1_Missense_Mutation_p.R825C|ITSN1_uc002ytc.1_Missense_Mutation_p.R825C|ITSN1_uc002ytd.2_RNA|ITSN1_uc010gmk.2_Missense_Mutation_p.R793C|ITSN1_uc010gml.2_RNA|ITSN1_uc002ytj.2_Missense_Mutation_p.R825C|ITSN1_uc010gmm.1_RNA|ITSN1_uc002yte.2_Missense_Mutation_p.R764C|ITSN1_uc002ytf.1_RNA	NM_003024	NP_003015	Q15811	ITSN1_HUMAN	intersectin 1 isoform ITSN-l	830					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4						ACTGGCCTTGCGTGAGACCCC	0.557													55	105	---	---	---	---	PASS
KRTAP12-4	386684	broad.mit.edu	37	21	46074476	46074476	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46074476C>T	uc002zfs.1	-	1	101	c.56G>A	c.(55-57)TGC>TAC	p.C19Y	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198698	NP_941971	P60329	KR124_HUMAN	keratin associated protein 12-4	19	15 X 5 AA approximate repeats.					keratin filament				ovary(1)	1						GGGGACACAGCACGGGGAGCC	0.677													10	12	---	---	---	---	PASS
COL18A1	80781	broad.mit.edu	37	21	46896339	46896339	+	Silent	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46896339G>T	uc011afs.1	+	5	2139	c.2118G>T	c.(2116-2118)ACG>ACT	p.T706T	COL18A1_uc002zhg.2_Silent_p.T291T|COL18A1_uc002zhi.2_Silent_p.T471T	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	706	Nonhelical region 1 (NC1).				cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GCAGCAGCACGGAAGATTCCA	0.547													23	47	---	---	---	---	PASS
CCDC116	164592	broad.mit.edu	37	22	21988525	21988525	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21988525G>T	uc002zve.2	+	3	380	c.287G>T	c.(286-288)CGC>CTC	p.R96L	CCDC116_uc011aih.1_Missense_Mutation_p.R96L	NM_152612	NP_689825	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	96	Potential.									ovary(1)|skin(1)	2	Colorectal(54;0.105)					GCGACTGAGCGCATGGCTGCC	0.632													41	85	---	---	---	---	PASS
APOBEC3D	140564	broad.mit.edu	37	22	39421546	39421546	+	Intron	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39421546C>T	uc011aoe.1	+						APOBEC3D_uc011aod.1_Missense_Mutation_p.H228Y|APOBEC3D_uc011aof.1_Intron|APOBEC3D_uc003awu.3_Intron|APOBEC3D_uc003awt.3_Intron|APOBEC3D_uc010gxu.2_Intron	NM_152426	NP_689639	Q96AK3	ABC3D_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic						negative regulation of transposition		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding				0	Melanoma(58;0.04)					GAGTGCTTCCCACCTCTTCAT	0.552													54	155	---	---	---	---	PASS
SBF1	6305	broad.mit.edu	37	22	50897990	50897990	+	Silent	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50897990G>A	uc003blh.2	-	27	3792	c.3597C>T	c.(3595-3597)AGC>AGT	p.S1199S	SBF1_uc011arx.1_Silent_p.S863S	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1	1199	Myotubularin phosphatase.				protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		TGGACCGCCCGCTGCGCCAGC	0.672													34	19	---	---	---	---	PASS
DHRSX	207063	broad.mit.edu	37	X	2161101	2161101	+	Missense_Mutation	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2161101C>T	uc004cqf.3	-	6	816	c.767G>A	c.(766-768)CGT>CAT	p.R256H		NM_145177	NP_660160	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked	256							binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				CTTCGCCAGACGGGTGGCCCA	0.552													40	164	---	---	---	---	PASS
HCCS	3052	broad.mit.edu	37	X	11133044	11133044	+	Missense_Mutation	SNP	G	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11133044G>T	uc004cuk.2	+	3	456	c.190G>T	c.(190-192)GTG>TTG	p.V64L	HCCS_uc004cuj.2_Missense_Mutation_p.V64L|HCCS_uc004cul.1_Missense_Mutation_p.V64L	NM_005333	NP_005324	P53701	CCHL_HUMAN	holocytochrome c synthase	64					organ morphogenesis|oxidation-reduction process	mitochondrial inner membrane	holocytochrome-c synthase activity|metal ion binding				0						CTATGAGTACGTGGAGTGTCC	0.478													48	47	---	---	---	---	PASS
DMD	1756	broad.mit.edu	37	X	32486704	32486704	+	Missense_Mutation	SNP	T	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32486704T>A	uc004dda.1	-	23	3317	c.3073A>T	c.(3073-3075)ATT>TTT	p.I1025F	DMD_uc004dcz.2_Missense_Mutation_p.I902F|DMD_uc004dcy.1_Missense_Mutation_p.I1021F|DMD_uc004ddb.1_Missense_Mutation_p.I1017F|DMD_uc010ngo.1_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	1025	Spectrin 6.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				CGTCCCTCAATTTCTTCAAAT	0.428													3	36	---	---	---	---	PASS
SLC9A7	84679	broad.mit.edu	37	X	46502717	46502717	+	Missense_Mutation	SNP	T	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46502717T>C	uc004dgu.1	-	12	1575	c.1567A>G	c.(1567-1569)ATC>GTC	p.I523V		NM_032591	NP_115980	Q96T83	SL9A7_HUMAN	solute carrier family 9, member 7	523	Helical; (Potential).				regulation of pH	Golgi membrane|integral to membrane|recycling endosome membrane|trans-Golgi network	potassium:hydrogen antiporter activity|protein homodimerization activity|sodium:hydrogen antiporter activity			ovary(2)	2						CCTCCAATGATCCAGACAGTG	0.502													15	15	---	---	---	---	PASS
CXorf26	51260	broad.mit.edu	37	X	75394775	75394775	+	Silent	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75394775C>G	uc004ecl.1	+	3	350	c.147C>G	c.(145-147)GTC>GTG	p.V49V		NM_016500	NP_057584	Q9BVG4	CX026_HUMAN	hypothetical protein LOC51260	49											0						ATGCTGAAGTCTATTACAAGG	0.403													8	43	---	---	---	---	PASS
RPS6KA6	27330	broad.mit.edu	37	X	83362035	83362035	+	Silent	SNP	C	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83362035C>T	uc004eej.1	-	14	1202	c.1125G>A	c.(1123-1125)TTG>TTA	p.L375L	RPS6KA6_uc011mqt.1_Silent_p.L375L|RPS6KA6_uc011mqu.1_Silent_p.L272L	NM_014496	NP_055311	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase polypeptide 6	375	AGC-kinase C-terminal.				axon guidance|central nervous system development|intracellular protein kinase cascade|synaptic transmission	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|central_nervous_system(1)|skin(1)	8						CACTGGCTGGCAAACCGGGAG	0.333													22	19	---	---	---	---	PASS
DACH2	117154	broad.mit.edu	37	X	86068160	86068160	+	Missense_Mutation	SNP	G	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86068160G>A	uc004eew.2	+	9	1587	c.1417G>A	c.(1417-1419)GCT>ACT	p.A473T	DACH2_uc004eex.2_Missense_Mutation_p.A460T|DACH2_uc010nmq.2_Missense_Mutation_p.A339T|DACH2_uc011mra.1_Missense_Mutation_p.A306T|DACH2_uc010nmr.2_Missense_Mutation_p.A254T|DACH2_uc004eey.2_Missense_Mutation_p.A166T|DACH2_uc004eez.2_Missense_Mutation_p.A156T	NM_053281	NP_444511	Q96NX9	DACH2_HUMAN	dachshund 2 isoform a	473	Potential.|DACHbox-C.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5						TTTGGATAATGCTCGCATCCA	0.368													9	7	---	---	---	---	PASS
MIR18B	574033	broad.mit.edu	37	X	133304114	133304114	+	RNA	SNP	C	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133304114C>G	hsa-mir-18b|MI0001518	-			c.28C>G			MIR363_hsa-mir-363|MI0000764_5'Flank|MIR92A2_hsa-mir-92a-2|MI0000094_5'Flank|uc004exf.2_5'Flank|uc011mvi.1_5'Flank|MIR19B2_hsa-mir-19b-2|MI0000075_5'Flank|MIR20B_hsa-mir-20b|MI0001519_5'Flank																	0						AGCTGCTTCACTAACTGCACT	0.398													21	18	---	---	---	---	PASS
MCF2	4168	broad.mit.edu	37	X	138714595	138714595	+	Silent	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138714595A>G	uc004fau.2	-	2	364	c.70T>C	c.(70-72)TTG>CTG	p.L24L	MCF2_uc004fav.2_Silent_p.L24L|MCF2_uc011mwl.1_Silent_p.L24L|MCF2_uc010nsh.1_Silent_p.L24L|MCF2_uc011mwm.1_Silent_p.L24L|MCF2_uc011mwn.1_Silent_p.L169L|MCF2_uc004faw.2_Silent_p.L84L|MCF2_uc011mwo.1_Silent_p.L84L	NM_005369	NP_005360	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	24	CRAL-TRIO.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|membrane|membrane fraction	protein binding|Rho guanyl-nucleotide exchange factor activity			lung(1)|pleura(1)	2	Acute lymphoblastic leukemia(192;0.000127)					ACCAAGTGCAAGTTCCCAGGG	0.373													26	21	---	---	---	---	PASS
ATP11C	286410	broad.mit.edu	37	X	138867415	138867415	+	Missense_Mutation	SNP	G	C	C			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138867415G>C	uc004faz.2	-	16	1744	c.1645C>G	c.(1645-1647)CGT>GGT	p.R549G	ATP11C_uc004fay.2_RNA|ATP11C_uc004fba.2_Missense_Mutation_p.R549G	NM_173694	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C isoform a	549	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(5)|large_intestine(3)	8	Acute lymphoblastic leukemia(192;0.000127)					ACACTCATACGTCGCCGGACA	0.343													24	28	---	---	---	---	PASS
FMR1	2332	broad.mit.edu	37	X	147024824	147024824	+	Silent	SNP	A	G	G			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147024824A>G	uc010nst.2	+	14	1638	c.1449A>G	c.(1447-1449)AGA>AGG	p.R483R	FMR1_uc004fcj.2_Silent_p.R460R|FMR1_uc004fck.3_Silent_p.R462R|FMR1_uc004fcl.3_Silent_p.R323R|FMR1_uc011mxa.1_Silent_p.R130R	NM_002024	NP_002015	Q06787	FMR1_HUMAN	fragile X mental retardation 1	483	Interaction with RANBP9.				mRNA transport|negative regulation of translational initiation	cytoplasm|mRNA cap binding complex|nucleolus|nucleoplasm|soluble fraction	mRNA binding|protein binding			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					GGCACGGCAGACGCGGTCCTG	0.413									Fragile_X_syndrome				50	28	---	---	---	---	PASS
UTY	7404	broad.mit.edu	37	Y	15372158	15372158	+	Missense_Mutation	SNP	C	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:15372158C>A	uc004fsx.1	-	26	4851	c.3846G>T	c.(3844-3846)GAG>GAT	p.E1282D	UTY_uc004fsw.1_Missense_Mutation_p.E945D|UTY_uc010nwx.1_Missense_Mutation_p.E339D	NM_007125	NP_009056	O14607	UTY_HUMAN	tetratricopeptide repeat protein isoform 3	1282					chromatin modification	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						AGTTACTCACCTCACAAATGC	0.353													55	27	---	---	---	---	PASS
PAX7	5081	broad.mit.edu	37	1	18962314	18962315	+	Intron	INS	-	TG	TG	rs144259565	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18962314_18962315insTG	uc001bay.2	+						PAX7_uc001baz.2_Intron|PAX7_uc010oct.1_Intron	NM_002584	NP_002575	P23759	PAX7_HUMAN	paired box 7 isoform 1						anti-apoptosis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX7/FOXO1(197)	soft_tissue(197)|lung(3)|prostate(1)|ovary(1)|breast(1)	203		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		gtgtgtgtgtatgtgtgtgtgt	0.450			T	FOXO1A	alveolar rhabdomyosarcoma								4	3	---	---	---	---	
EIF3I	8668	broad.mit.edu	37	1	32690259	32690260	+	Intron	INS	-	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32690259_32690260insT	uc001bur.3	+						C1orf91_uc001buo.3_5'Flank|C1orf91_uc001bup.3_5'Flank|C1orf91_uc009vub.1_5'Flank|C1orf91_uc010oha.1_5'Flank|C1orf91_uc001buq.3_5'Flank|EIF3I_uc009vuc.2_Intron|EIF3I_uc001bus.2_Intron	NM_003757	NP_003748	Q13347	EIF3I_HUMAN	eukaryotic translation initiation factor 3,							cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)				ATTAAGTTTTCTTttttttttt	0.183													5	3	---	---	---	---	
HIVEP3	59269	broad.mit.edu	37	1	42010583	42010584	+	Intron	INS	-	CAT	CAT			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42010583_42010584insCAT	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron|HIVEP3_uc001cgy.2_Intron	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				accaccactaccacctctacca	0.000													4	2	---	---	---	---	
TCTEX1D1	200132	broad.mit.edu	37	1	67242261	67242262	+	Intron	DEL	TA	-	-	rs60960124		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67242261_67242262delTA	uc001dcv.2	+						TCTEX1D1_uc009wau.2_Intron|TCTEX1D1_uc009wav.2_Intron	NM_152665	NP_689878	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1												0						tgtgtgtgtgtATATACATAAA	0.233													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142538851	142538870	+	IGR	DEL	GAGTGGAGTGGAGTGGAGTG	-	-	rs150224251		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142538851_142538870delGAGTGGAGTGGAGTGGAGTG								None (None upstream) : None (None downstream)																							gaatggaatagagtggagtggagtggagtggagtggagtg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	243251423	243251423	+	RNA	DEL	A	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243251423delA	uc001hzq.1	-	8		c.1209delT								Homo sapiens cDNA FLJ52610 complete cds.																		actccatctcaaaaaaaaaaa	0.179													6	3	---	---	---	---	
COLEC11	78989	broad.mit.edu	37	2	3691412	3691412	+	Frame_Shift_Del	DEL	G	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3691412delG	uc002qya.2	+	7	668	c.520delG	c.(520-522)GGGfs	p.G174fs	COLEC11_uc002qxz.2_Frame_Shift_Del_p.G171fs|COLEC11_uc002qyb.2_Frame_Shift_Del_p.G150fs|COLEC11_uc002qyc.2_Frame_Shift_Del_p.G150fs|COLEC11_uc010ewo.2_Frame_Shift_Del_p.G126fs|COLEC11_uc010ewp.2_Frame_Shift_Del_p.G148fs|COLEC11_uc010ewq.2_Frame_Shift_Del_p.G124fs|COLEC11_uc010ewr.2_Frame_Shift_Del_p.G124fs|COLEC11_uc010ews.2_Frame_Shift_Del_p.G100fs	NM_024027	NP_076932	Q9BWP8	COL11_HUMAN	collectin sub-family member 11 isoform a	174	C-type lectin.					collagen	mannose binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		CCAGGGCCGCGGGGGCACGCT	0.667													51	24	---	---	---	---	
KIF3C	3797	broad.mit.edu	37	2	26152660	26152661	+	Intron	INS	-	A	A	rs138648504	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26152660_26152661insA	uc002rgu.2	-						KIF3C_uc010eyj.1_Intron|KIF3C_uc010ykr.1_Intron	NM_002254	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C						blood coagulation|microtubule-based movement	cytosol|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					aatttttgtatttttagtagag	0.000													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	121173004	121173005	+	IGR	DEL	GT	-	-	rs71652209		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121173004_121173005delGT								INHBB (63621 upstream) : LOC84931 (48906 downstream)																							TTGAGGTTCAgtgtgtgtgtgt	0.233													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	128825103	128825103	+	IGR	DEL	A	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128825103delA								SAP130 (39470 upstream) : UGGT1 (23651 downstream)																							tgtctctatgaaaaaaaaaaa	0.000													6	3	---	---	---	---	
DYTN	391475	broad.mit.edu	37	2	207574185	207574186	+	Intron	DEL	AC	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207574185_207574186delAC	uc002vbr.1	-							NM_001093730	NP_001087199	A2CJ06	DYTN_HUMAN	dystrotelin							plasma membrane	zinc ion binding			ovary(1)|central_nervous_system(1)	2				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		acacacacagacacacacacac	0.188													4	2	---	---	---	---	
SATB1	6304	broad.mit.edu	37	3	18457303	18457304	+	Intron	INS	-	T	T	rs112868614	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18457303_18457304insT	uc003cbh.2	-						SATB1_uc003cbi.2_Intron|SATB1_uc003cbj.2_Intron	NM_002971	NP_002962	Q01826	SATB1_HUMAN	special AT-rich sequence binding protein 1						cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter	nuclear matrix|PML body	double-stranded DNA binding|sequence-specific DNA binding			skin(2)|ovary(1)|lung(1)	4						TTGTGTGTGTGGGGGGGGGGAT	0.347													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	81190021	81190022	+	IGR	INS	-	GAGAAT	GAGAAT			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81190021_81190022insGAGAAT								None (None upstream) : GBE1 (348828 downstream)																							agggagggagggaggaaggaag	0.069													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	97926080	97926080	+	IGR	DEL	T	-	-	rs5851109		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97926080delT								OR5H15 (37597 upstream) : OR5H6 (57049 downstream)																							AAATATATGATTTTTTTCCAT	0.308													3	4	---	---	---	---	
WWTR1	25937	broad.mit.edu	37	3	149374544	149374551	+	Intron	DEL	TCTCTCTT	-	-	rs10665547		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149374544_149374551delTCTCTCTT	uc003exe.2	-						WWTR1_uc003exf.2_Intron|WWTR1_uc011bns.1_Intron|WWTR1_uc003exh.2_Intron|uc010hvg.1_5'Flank|uc003exi.1_5'Flank	NM_015472	NP_056287	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1						hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent	cytoplasm	transcription coactivator activity			breast(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			ACGCACCAtctctctctttctctctctc	0.365													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25624471	25624483	+	IGR	DEL	GTGACTCTCAAAA	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25624471_25624483delGTGACTCTCAAAA								ANAPC4 (204352 upstream) : SLC34A2 (32952 downstream)																							CAAACAATCTGTGACTCTCAAAATCATGTTGGA	0.366													21	14	---	---	---	---	
UGDH	7358	broad.mit.edu	37	4	39505927	39505928	+	Intron	INS	-	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39505927_39505928insA	uc003guk.1	-						UGDH_uc011byp.1_Intron|UGDH_uc003gul.1_Intron	NM_003359	NP_003350	O60701	UGDH_HUMAN	UDP-glucose dehydrogenase						glycosaminoglycan biosynthetic process|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	electron carrier activity|NAD binding|UDP-glucose 6-dehydrogenase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4					NADH(DB00157)	gactccatctcaaaaaaaaaaa	0.139													5	3	---	---	---	---	
SRP72	6731	broad.mit.edu	37	4	57340708	57340708	+	Intron	DEL	C	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57340708delC	uc003hbv.2	+						SRP72_uc010ihe.2_Intron|SRP72_uc003hbw.1_Intron	NM_006947	NP_008878	O76094	SRP72_HUMAN	signal recognition particle 72kDa						response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|nucleolus|plasma membrane|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding			ovary(1)	1	Glioma(25;0.08)|all_neural(26;0.101)					Ctttctctctctttttttttt	0.149													4	2	---	---	---	---	
PLA2G12A	81579	broad.mit.edu	37	4	110635888	110635889	+	Intron	DEL	TT	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110635888_110635889delTT	uc003hzp.2	-						PLA2G12A_uc010img.2_Intron	NM_030821	NP_110448	Q9BZM1	PG12A_HUMAN	phospholipase A2, group XIIA precursor						lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|calcium-dependent phospholipase A2 activity				0				OV - Ovarian serous cystadenocarcinoma(123;0.000268)		TTTAACCCAAtttttttttttt	0.153													4	2	---	---	---	---	
INTU	27152	broad.mit.edu	37	4	128564925	128564925	+	Frame_Shift_Del	DEL	T	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128564925delT	uc003ifk.1	+	2	466	c.396delT	c.(394-396)AATfs	p.N132fs	INTU_uc011cgq.1_RNA	NM_015693	NP_056508	Q9ULD6	PDZD6_HUMAN	PDZ domain containing 6	132										ovary(1)	1						ATAAAAAAAATAGCAATGACA	0.348													49	58	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	191044049	191044049	+	IGR	DEL	A	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:191044049delA								LOC653545 (33873 upstream) : None (None downstream)																							ggttagggttaagggttaggg	0.000													6	3	---	---	---	---	
ADAMTS16	170690	broad.mit.edu	37	5	5232302	5232302	+	Intron	DEL	A	-	-	rs10713189		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5232302delA	uc003jdl.2	+						ADAMTS16_uc003jdk.1_Intron|ADAMTS16_uc010itk.1_5'Flank	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8						TTGGGTAAGGAAAAAAAAAAC	0.363													1	7	---	---	---	---	
MARCH6	10299	broad.mit.edu	37	5	10350977	10350978	+	5'Flank	INS	-	AC	AC	rs67695728		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10350977_10350978insAC	uc003jet.1	+						MARCH6_uc011cmu.1_5'Flank|MARCH6_uc003jeu.1_5'Flank|MARCH6_uc011cmv.1_5'Flank	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						CGCAGCACAGTacacacacaca	0.317													2	7	---	---	---	---	
C5orf42	65250	broad.mit.edu	37	5	37120152	37120153	+	Intron	INS	-	A	A	rs75040582	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37120152_37120153insA	uc011cpa.1	-						C5orf42_uc003jko.1_Intron|C5orf42_uc003jkp.1_Intron|C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			CTTCAAAGCAGAAAAAAAAAAA	0.243													7	4	---	---	---	---	
TTC37	9652	broad.mit.edu	37	5	94877400	94877400	+	Intron	DEL	A	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94877400delA	uc003klb.2	-						TTC37_uc010jbf.1_Intron	NM_014639	NP_055454	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37								binding			ovary(3)|pancreas(1)	4						CAAATGTTTGAAAAAAAAAAA	0.279													6	3	---	---	---	---	
PANK3	79646	broad.mit.edu	37	5	167988138	167988138	+	Intron	DEL	A	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167988138delA	uc003lzz.1	-						uc003maa.1_5'Flank|MIR103-1_hsa-mir-103-1|MI0000109_5'Flank	NM_024594	NP_078870	Q9H999	PANK3_HUMAN	pantothenate kinase 3						coenzyme A biosynthetic process	cytoplasm|nucleus	ATP binding|pantothenate kinase activity			ovary(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0441)|all_lung(126;0.0909)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0989)|OV - Ovarian serous cystadenocarcinoma(192;0.147)|Epithelial(171;0.188)		TTACATCCTCAAGGGATTTAG	0.234													4	2	---	---	---	---	
USP42	84132	broad.mit.edu	37	7	6155229	6155231	+	Intron	DEL	GAA	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6155229_6155231delGAA	uc011jwo.1	+						USP42_uc011jwn.1_Intron|USP42_uc010kth.1_Intron|USP42_uc011jwp.1_Intron|USP42_uc011jwq.1_Intron|USP42_uc011jwr.1_5'Flank	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42						cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		AAATGAAAGTGAAGAATTAATCC	0.360													16	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	61822153	61822153	+	IGR	DEL	T	-	-	rs111806210		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61822153delT								None (None upstream) : LOC643955 (929519 downstream)																							GACATCTCCCTCGGGGCCCCA	0.627													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67206114	67206117	+	IGR	DEL	TTCT	-	-	rs56895053		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67206114_67206117delTTCT								STAG3L4 (419602 upstream) : None (None downstream)																							ccttccttccttctttccttcctt	0.113													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	68424782	68424782	+	IGR	DEL	A	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68424782delA								None (None upstream) : AUTS2 (639123 downstream)																							ggaaggaaggaaaggaaggaa	0.085													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98409055	98409057	+	IGR	DEL	TAG	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98409055_98409057delTAG								NPTX2 (149874 upstream) : TMEM130 (35055 downstream)																							gtagtggtgatagtggtgatggt	0.000													4	2	---	---	---	---	
TNPO3	23534	broad.mit.edu	37	7	128645359	128645359	+	Intron	DEL	T	-	-	rs142831893		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128645359delT	uc003vol.1	-						TNPO3_uc003vom.1_Intron|TNPO3_uc010lly.1_Intron|TNPO3_uc010llz.1_Intron	NM_012470	NP_036602	Q9Y5L0	TNPO3_HUMAN	transportin 3						splicing factor protein import into nucleus	cytoplasm|nucleus	protein binding|receptor activity			ovary(2)|skin(2)|lung(1)	5						AGTGTCACTGttttttttttt	0.204													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	50758484	50758487	+	IGR	DEL	GTGT	-	-	rs144266051		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50758484_50758487delGTGT								C8orf22 (769843 upstream) : SNTG1 (63862 downstream)																							gtgtgtgggagtgtgtgtgtgtgt	0.284													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	61226634	61226635	+	IGR	INS	-	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61226634_61226635insA								CA8 (32680 upstream) : RAB2A (202924 downstream)																							acaacaacaacacacacacaca	0.035													4	3	---	---	---	---	
C8orf34	116328	broad.mit.edu	37	8	69699867	69699867	+	Intron	DEL	A	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69699867delA	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			CAACTTCTGTAAAAAAAAAAA	0.318													4	2	---	---	---	---	
GDAP1	54332	broad.mit.edu	37	8	75275019	75275020	+	Intron	INS	-	TTTTTTT	TTTTTTT	rs6150661		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75275019_75275020insTTTTTTT	uc003yah.2	+						GDAP1_uc011lfj.1_Intron|GDAP1_uc003yai.2_Intron	NM_018972	NP_061845	Q8TB36	GDAP1_HUMAN	ganglioside-induced differentiation-associated							cytoplasm					0	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			CTCTCTCTCTCttttttttttt	0.396													4	2	---	---	---	---	
MATN2	4147	broad.mit.edu	37	8	99006489	99006490	+	Intron	INS	-	GAAGAAGGAGAA	GAAGAAGGAGAA	rs146393102	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99006489_99006490insGAAGAAGGAGAA	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron|MATN2_uc010mbi.1_Intron	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			ggaggaggagggaagaaggaga	0.149													6	3	---	---	---	---	
TG	7038	broad.mit.edu	37	8	134129130	134129131	+	Intron	INS	-	A	A	rs35664939		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134129130_134129131insA	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		cggggaaagttaaaaaaaaaaa	0.054													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	130209778	130209778	+	IGR	DEL	A	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130209778delA								ZNF79 (2128 upstream) : RPL12 (177 downstream)																							actctgtctcaaaaaaaaaaa	0.209													4	2	---	---	---	---	
MAMDC4	158056	broad.mit.edu	37	9	139753544	139753545	+	Frame_Shift_Ins	INS	-	G	G	rs142983311	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139753544_139753545insG	uc004cjs.2	+	24	3094_3095	c.3044_3045insG	c.(3043-3045)CTGfs	p.L1015fs	MAMDC4_uc011mej.1_Frame_Shift_Ins_p.L352fs	NM_206920	NP_996803	Q6UXC1	AEGP_HUMAN	apical early endosomal glycoprotein precursor	1094	Extracellular (Potential).|MAM 6.				protein transport	integral to membrane				breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1)	7	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		CACCAGTGGCTGGAGGCCCAGG	0.668													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	38368812	38368813	+	IGR	INS	-	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38368812_38368813insT								ZNF33A (14786 upstream) : ZNF37A (14462 downstream)																							tcttttttttcttttttttttt	0.223													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42374677	42374686	+	IGR	DEL	TTCATTCCTG	-	-	rs147699335	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42374677_42374686delTTCATTCCTG								None (None upstream) : LOC441666 (452629 downstream)																							tccattccatttcattcctgtccattccat	0.000													6	5	---	---	---	---	
KRTAP5-5	439915	broad.mit.edu	37	11	1651191	1651199	+	In_Frame_Del	DEL	GGCTGTGGA	-	-	rs144216147		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1651191_1651199delGGCTGTGGA	uc001lty.2	+	1	159_167	c.121_129delGGCTGTGGA	c.(121-129)GGCTGTGGAdel	p.GCG47del		NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	47_49						keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ctgtggctccggctgtggaggctgtgggg	0.129													15	14	---	---	---	---	
BBS1	582	broad.mit.edu	37	11	66283594	66283597	+	Intron	DEL	TTTT	-	-	rs35933115		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66283594_66283597delTTTT	uc001oij.1	+						BBS1_uc001oii.1_Intron|BBS1_uc010rpf.1_Intron|BBS1_uc010rpg.1_Intron|BBS1_uc001oik.1_Intron|BBS1_uc001oil.1_Intron	NM_024649	NP_078925	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1						nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1						TAGTGACAGCtttttttttttttt	0.225									Bardet-Biedl_syndrome				4	2	---	---	---	---	
MED17	9440	broad.mit.edu	37	11	93535276	93535276	+	Intron	DEL	T	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93535276delT	uc001pem.3	+							NM_004268	NP_004259	Q9NVC6	MED17_HUMAN	mediator complex subunit 17						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CTGTAGAGTGttttttttttt	0.139													5	3	---	---	---	---	
SLC35F2	54733	broad.mit.edu	37	11	107686319	107686320	+	Intron	INS	-	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107686319_107686320insA	uc001pjq.2	-						SLC35F2_uc010rvu.1_Intron|SLC35F2_uc001pjs.2_Intron	NM_017515	NP_059985	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2						transport	integral to membrane				central_nervous_system(1)	1		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		aacacacacacaaaaaaaaaaa	0.149													4	2	---	---	---	---	
POU2F3	25833	broad.mit.edu	37	11	120110998	120110998	+	5'UTR	DEL	G	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120110998delG	uc001pxc.2	+	1					POU2F3_uc010rzk.1_5'UTR|POU2F3_uc010rzl.1_5'UTR	NM_014352	NP_055167	Q9UKI9	PO2F3_HUMAN	POU transcription factor						negative regulation by host of viral transcription	cytoplasm	sequence-specific DNA binding			ovary(1)|skin(1)	2		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)		GGCCCCGGCTGGGGCAGAGGC	0.532													5	3	---	---	---	---	
LRRK2	120892	broad.mit.edu	37	12	40758608	40758609	+	Intron	INS	-	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40758608_40758609insT	uc001rmg.3	+						LRRK2_uc009zjw.2_Intron|LRRK2_uc001rmi.2_Intron	NM_198578	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2						activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CTCTTAATTGGTGGTAAAATTA	0.272											OREG0003828	type=REGULATORY REGION|Gene=LRRK2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	12	8	---	---	---	---	
ATXN2	6311	broad.mit.edu	37	12	111894232	111894232	+	Intron	DEL	A	-	-	rs10708872		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111894232delA	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron|ATXN2_uc001tsg.2_Intron|ATXN2_uc001tsl.1_Intron	NM_002973	NP_002964	Q99700	ATX2_HUMAN	ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2						CCATCTGGACAACTCCTTTCT	0.483													3	6	---	---	---	---	
LRCH1	23143	broad.mit.edu	37	13	47141627	47141628	+	Intron	INS	-	TG	TG	rs138817448	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47141627_47141628insTG	uc001vbj.2	+						LRCH1_uc010acp.2_Intron|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		TAAGGCAATTTtgtgtgtgtgt	0.307													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	75588839	75588840	+	IGR	INS	-	CTTCCTTC	CTTCCTTC	rs9543833		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75588839_75588840insCTTCCTTC								KLF12 (880445 upstream) : LOC647288 (223050 downstream)																							tttctttctttcttccttcctt	0.139													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	83420545	83420545	+	IGR	DEL	A	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83420545delA								None (None upstream) : None (None downstream)																							ggaaggaaggaaaagaaggga	0.025													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	20252508	20252509	+	IGR	DEL	AC	-	-	rs143646132		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20252508_20252509delAC								OR4M1 (3086 upstream) : OR4N2 (43099 downstream)																							aaggctggGTacacacacacac	0.010													4	2	---	---	---	---	
OR4K2	390431	broad.mit.edu	37	14	20341781	20341786	+	5'Flank	DEL	GCGCGC	-	-	rs10533709		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20341781_20341786delGCGCGC	uc001vwh.1	+							NM_001005501	NP_001005501	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(2)	4	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		gtgtgtgtgtgCGCGCGCGCGCGCGC	0.330													4	3	---	---	---	---	
SYNE2	23224	broad.mit.edu	37	14	64685822	64685823	+	Intron	INS	-	TT	TT	rs59649607		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64685822_64685823insTT	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron|SYNE2_uc010apy.2_Intron|SYNE2_uc001xgn.2_Intron|SYNE2_uc001xgo.2_Intron|SYNE2_uc010aqa.2_Intron|SYNE2_uc001xgq.2_Intron|SYNE2_uc001xgr.2_Intron|SYNE2_uc010tsi.1_Intron|SYNE2_uc001xgs.2_Intron|SYNE2_uc001xgt.2_Intron	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2						centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		CAGtttttttgttttttttttt	0.391													5	3	---	---	---	---	
ADAM6	8755	broad.mit.edu	37	14	106622575	106622576	+	Intron	INS	-	A	A	rs139778247	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106622575_106622576insA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0						ACAAATAAAAGAAAAAAAAAAC	0.391													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	40604470	40604470	+	IGR	DEL	T	-	-	rs35116724		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40604470delT								PLCB2 (4296 upstream) : C15orf52 (19184 downstream)																							TGGTCCAACCTTTTTTTTTTT	0.378													2	5	---	---	---	---	
THAP10	56906	broad.mit.edu	37	15	71184606	71184613	+	Translation_Start_Site	DEL	CGGCATGG	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71184606_71184613delCGGCATGG	uc002asv.2	-	1					LRRC49_uc002asu.2_Intron|LRRC49_uc002asw.2_5'Flank|LRRC49_uc002asx.2_5'Flank|LRRC49_uc010ukf.1_5'Flank	NM_020147	NP_064532	Q9P2Z0	THA10_HUMAN	THAP domain containing 10								DNA binding|metal ion binding			ovary(1)|skin(1)	2						CACAACGGGCCGGCATGGCGGCCGTCTT	0.707													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32416468	32416468	+	IGR	DEL	C	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32416468delC								HERC2P4 (252594 upstream) : TP53TG3B (268373 downstream)																							ATAGTCTTCTCCTCGGGTAAA	0.388													34	34	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	21228967	21228972	+	IGR	DEL	TCCTCT	-	-	rs3063482		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21228967_21228972delTCCTCT								MAP2K3 (10418 upstream) : KCNJ12 (50727 downstream)																							TTCCTCCTCCTCCtcttcctcttcct	0.184													4	2	---	---	---	---	
TBC1D16	125058	broad.mit.edu	37	17	77998378	77998384	+	Intron	DEL	CACACAC	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77998378_77998384delCACACAC	uc002jxj.2	-							NM_019020	NP_061893	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16							intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			accataggcacacacaccacacaccac	0.000													4	2	---	---	---	---	
LOC647946	647946	broad.mit.edu	37	18	37248431	37248454	+	Intron	DEL	AGGGAGGAAGGAAGGAAGGAAGGA	-	-	rs11270312	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37248431_37248454delAGGGAGGAAGGAAGGAAGGAAGGA	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0						ggagggagggagggaggaaggaaggaaggaaggaaggaaggaag	0.098													4	2	---	---	---	---	
KATNAL2	83473	broad.mit.edu	37	18	44547442	44547443	+	Intron	DEL	GT	-	-	rs72266255		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44547442_44547443delGT	uc002lco.2	+						KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lcp.3_Intron	NM_031303	NP_112593	Q8IYT4	KATL2_HUMAN	katanin p60 subunit A-like 2							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4						TTACTTAATGgtgtgtgtgtgt	0.233													3	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	60771216	60771217	+	IGR	DEL	TG	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60771216_60771217delTG								PHLPP1 (123551 upstream) : BCL2 (19362 downstream)																							tggggatgtatgtgtgtgtgtg	0.178													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	75998635	75998635	+	IGR	DEL	T	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75998635delT								None (None upstream) : SALL3 (741640 downstream)																							acgtggtgtgtgtgtgtgtcg	0.234													4	2	---	---	---	---	
MUC16	94025	broad.mit.edu	37	19	9006225	9006226	+	Intron	INS	-	CT	CT	rs142182629	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9006225_9006226insCT	uc002mkp.2	-						MUC16_uc010dwi.2_Intron|MUC16_uc010dwj.2_Intron|MUC16_uc010xki.1_Intron	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TCCTGGAGCCAGTTTCCTGGAT	0.480													3	3	---	---	---	---	
CACNA1A	773	broad.mit.edu	37	19	13445408	13445411	+	Intron	DEL	TGTG	-	-	rs138143360		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13445408_13445411delTGTG	uc010dze.2	-						CACNA1A_uc002mwy.3_Intron	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)	tgtgtgtgtttgtgtgtgtgtgtg	0.309													3	7	---	---	---	---	
EMR3	84658	broad.mit.edu	37	19	14732268	14732269	+	Intron	INS	-	A	A	rs75726167		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14732268_14732269insA	uc002mzi.3	-						EMR3_uc010dzp.2_Intron|EMR3_uc010xnv.1_Intron	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor						neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						ctctgtctcagaaaaaaaaaaa	0.059													6	3	---	---	---	---	
SLC5A5	6528	broad.mit.edu	37	19	17991503	17991504	+	Intron	INS	-	CAAAA	CAAAA	rs144134876	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17991503_17991504insCAAAA	uc002nhr.3	+							NM_000453	NP_000444	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium iodide						cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4						agatcttttctcaaaacaaaac	0.005													10	5	---	---	---	---	
MAST3	23031	broad.mit.edu	37	19	18235741	18235742	+	Intron	INS	-	CCC	CCC	rs150126286	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18235741_18235742insCCC	uc002nhz.3	+							NM_015016	NP_055831	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase								ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			large_intestine(2)|ovary(2)|stomach(1)	5						catggtggaaacccccccccta	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31384456	31384457	+	IGR	INS	-	TG	TG	rs143492161	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31384456_31384457insTG								ZNF536 (335491 upstream) : DKFZp566F0947 (256326 downstream)																							CCCACATCCATtgtgtgtgtgt	0.327													4	2	---	---	---	---	
HAUS5	23354	broad.mit.edu	37	19	36104473	36104474	+	Intron	DEL	AA	-	-	rs74172753		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36104473_36104474delAA	uc002oam.1	+							NM_015302	NP_056117	O94927	HAUS5_HUMAN	HAUS augmin-like complex, subunit 5						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle					0						actgtctcttaaaaaaaaaaaa	0.173													4	2	---	---	---	---	
ETV2	2116	broad.mit.edu	37	19	36135279	36135280	+	Intron	INS	-	T	T	rs147503261	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36135279_36135280insT	uc002oas.2	+						ETV2_uc002oar.2_Intron|ETV2_uc002oat.2_Intron|ETV2_uc002oau.2_Intron	NM_014209	NP_055024	O00321	ETV2_HUMAN	ets variant gene 2								sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CAGCCAAATCCGCCCCGTCTCT	0.673													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	36438500	36438501	+	IGR	DEL	GT	-	-	rs72461050		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36438500_36438501delGT								LRFN3 (2405 upstream) : SDHAF1 (47600 downstream)																							GGCACTGTTCgtgtgtgtgtgt	0.257													4	3	---	---	---	---	
MAP4K1	11184	broad.mit.edu	37	19	39086037	39086038	+	Intron	INS	-	T	T			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39086037_39086038insT	uc002oix.1	-						MAP4K1_uc002oiw.1_Intron|MAP4K1_uc002oiy.1_Intron	NM_007181	NP_009112	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|peptidyl-serine phosphorylation		ATP binding|MAP kinase kinase kinase kinase activity|protein binding|small GTPase regulator activity			skin(4)|lung(3)|ovary(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			ACTTCACACTCTGACTCAGGAG	0.446													34	23	---	---	---	---	
PVRL2	5819	broad.mit.edu	37	19	45376894	45376895	+	Intron	DEL	AC	-	-	rs34606745		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45376894_45376895delAC	uc002ozw.1	+						PVRL2_uc002ozv.2_Intron	NM_001042724	NP_001036189	Q92692	PVRL2_HUMAN	poliovirus receptor related 2 isoform delta						adherens junction organization|adhesion to symbiont|cell junction assembly|homophilic cell adhesion|positive regulation of immunoglobulin mediated immune response|positive regulation of mast cell activation|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target|susceptibility to natural killer cell mediated cytotoxicity|susceptibility to T cell mediated cytotoxicity|viral envelope fusion with host membrane|virion attachment, binding of host cell surface coreceptor	cell surface|integral to membrane|zonula adherens	cell adhesion molecule binding|coreceptor activity|protein homodimerization activity				0	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		tgtctcaaaaacacacacacac	0.173													4	2	---	---	---	---	
TNNT1	7138	broad.mit.edu	37	19	55645048	55645049	+	Intron	INS	-	A	A			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55645048_55645049insA	uc002qjb.3	-						TNNT1_uc002qiz.3_Intron|TNNT1_uc002qja.3_Intron|TNNT1_uc002qjc.3_Intron|TNNT1_uc002qje.3_Intron|TNNT1_uc002qjd.3_Intron	NM_003283	NP_003274	P13805	TNNT1_HUMAN	troponin T1, skeletal, slow isoform a						muscle filament sliding|negative regulation of muscle contraction	cytosol|troponin complex	tropomyosin binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		gcagtctcaataaaaaaaaaaa	0.188													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	1933874	1933875	+	Intron	DEL	AG	-	-	rs71193943		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1933874_1933875delAG	uc002wfu.1	+											Homo sapiens cDNA FLJ33362 fis, clone BRACE2005337.																		ggaaggaataagaggggaagga	0.010													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	56771864	56771867	+	IGR	DEL	ACAC	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56771864_56771867delACAC								C20orf85 (35683 upstream) : PPP4R1L (34322 downstream)																							acacacacagacacacacacacag	0.078													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	40497883	40497890	+	IGR	DEL	ACACACAT	-	-	rs148116414	by1000genomes	TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40497883_40497890delACACACAT								ETS2 (301007 upstream) : PSMG1 (49500 downstream)																							acacacacacacacacaTGCATTTGTCA	0.303											OREG0026218	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	40497885	40497890	+	IGR	DEL	ACACAT	-	-	rs59776542		TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40497885_40497890delACACAT								ETS2 (301009 upstream) : PSMG1 (49500 downstream)																							acacacacacacacaTGCATTTGTCA	0.306											OREG0026218	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	448557	448568	+	IGR	DEL	GGAAGGAAGGAA	-	-			TCGA-21-1081-01	TCGA-21-1081-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:448557_448568delGGAAGGAAGGAA								PPP2R3B (100930 upstream) : SHOX (136511 downstream)																							GAGACaggatggaaggaaggaaggaaggaagg	0.024													4	4	---	---	---	---	
