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
SPATA21	374955	broad.mit.edu	37	1	16736256	16736256	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16736256G>A	uc001ayn.2	-	6	910	c.427C>T	c.(427-429)CGG>TGG	p.R143W	SPATA21_uc001ayl.1_RNA|SPATA21_uc010occ.1_Missense_Mutation_p.R120W	NM_198546	NP_940948	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	143	Pro-rich.						calcium ion binding			ovary(2)|breast(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		GCTGGCAGCCGGGCCCACGAT	0.726													5	12	---	---	---	---	PASS
MYOM3	127294	broad.mit.edu	37	1	24416550	24416550	+	Intron	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24416550C>A	uc001bin.3	-						MYOM3_uc001bim.3_Intron|MYOM3_uc001bio.2_Intron|MYOM3_uc001bip.1_Intron	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3											skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		GAGGATCCCGCGTACCTTCAA	0.562													8	92	---	---	---	---	PASS
CNKSR1	10256	broad.mit.edu	37	1	26507113	26507113	+	Intron	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26507113C>T	uc001bln.3	+						CNKSR1_uc010oex.1_Intron|CNKSR1_uc001blm.3_Intron|CNKSR1_uc009vsd.2_Intron|CNKSR1_uc009vse.2_Intron|CNKSR1_uc001blo.2_Intron	NM_006314	NP_006305	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras						Rho protein signal transduction|transmembrane receptor protein tyrosine kinase signaling pathway	cell cortex|cell-cell junction	protein binding, bridging			lung(1)|kidney(1)	2		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		TGAGTGAATGCTGGTCACACT	0.647													3	85	---	---	---	---	PASS
YTHDF2	51441	broad.mit.edu	37	1	29095445	29095445	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29095445G>C	uc001brc.2	+	5	2218	c.1721G>C	c.(1720-1722)CGT>CCT	p.R574P	YTHDF2_uc001brd.2_Missense_Mutation_p.R571P|YTHDF2_uc010ofx.1_Missense_Mutation_p.R524P|YTHDF2_uc001bre.2_Missense_Mutation_p.R524P	NM_016258	NP_057342	Q9Y5A9	YTHD2_HUMAN	high glucose-regulated protein 8	574					humoral immune response					ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		CTGTAGGAACGTCAAGGTCGT	0.343													15	75	---	---	---	---	PASS
ADC	113451	broad.mit.edu	37	1	33585663	33585663	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33585663G>T	uc001bwr.2	+	12	1850	c.1263G>T	c.(1261-1263)CAG>CAT	p.Q421H	ADC_uc001bws.2_Missense_Mutation_p.Q421H|ADC_uc009vue.2_Missense_Mutation_p.Q421H|ADC_uc001bwt.1_3'UTR|ADC_uc001bwu.2_Missense_Mutation_p.Q326H|ADC_uc001bwv.2_Missense_Mutation_p.Q326H|ADC_uc001bww.2_Missense_Mutation_p.Q326H|ADC_uc001bwx.1_3'UTR|ADC_uc009vug.2_Missense_Mutation_p.Q441H	NM_052998	NP_443724	Q96A70	ADC_HUMAN	ODC antizyme inhibitor-2	421					polyamine biosynthetic process|spermatogenesis	cytosol	arginine decarboxylase activity			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)			L-Arginine(DB00125)|Pyridoxal Phosphate(DB00114)	TGCGAAGGCAGCTGATGGCTG	0.632													4	51	---	---	---	---	PASS
DPH2	1802	broad.mit.edu	37	1	44437508	44437508	+	Missense_Mutation	SNP	A	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44437508A>C	uc001ckz.2	+	4	1129	c.934A>C	c.(934-936)AAG>CAG	p.K312Q	DPH2_uc001cla.2_Intron|DPH2_uc010okk.1_Missense_Mutation_p.K177Q|DPH2_uc001clb.2_Missense_Mutation_p.K236Q	NM_001384	NP_001375	Q9BQC3	DPH2_HUMAN	diphthamide biosynthesis protein 2 isoform a	312					peptidyl-diphthamide biosynthetic process from peptidyl-histidine	cytoplasm				ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)				GGCTGCTGGCAAGCGTAGCTA	0.627													8	73	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70489063	70489063	+	Intron	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70489063C>G	uc001dep.2	+						LRRC7_uc009wbg.2_Intron	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						GACAGGTAGGCCTAGGTGTCT	0.493													22	130	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94526284	94526284	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94526284T>C	uc001dqh.2	-	14	2073	c.1969A>G	c.(1969-1971)ATC>GTC	p.I657V	ABCA4_uc010otn.1_Missense_Mutation_p.I657V	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	657	Helical; (Potential).				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		ACCATGAAGATAGGGAAACAG	0.363													9	43	---	---	---	---	PASS
DPYD	1806	broad.mit.edu	37	1	98058805	98058805	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98058805C>A	uc001drv.2	-	10	1234	c.1097G>T	c.(1096-1098)GGC>GTC	p.G366V		NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	366					'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	ATTAACAAAGCCTTTTCTGAA	0.438													45	261	---	---	---	---	PASS
DPYD	1806	broad.mit.edu	37	1	98058806	98058806	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98058806C>T	uc001drv.2	-	10	1233	c.1096G>A	c.(1096-1098)GGC>AGC	p.G366S		NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	366					'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	TTAACAAAGCCTTTTCTGAAG	0.443													42	263	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103491775	103491775	+	Silent	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103491775C>T	uc001dul.2	-	6	1212	c.894G>A	c.(892-894)ACG>ACA	p.T298T	COL11A1_uc001duk.2_5'UTR|COL11A1_uc001dum.2_Intron|COL11A1_uc001dun.2_Intron|COL11A1_uc009weh.2_Silent_p.T298T	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	298	Nonhelical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TTTTTACCTCCGTCTGTGCTA	0.433													5	96	---	---	---	---	PASS
SLC16A1	6566	broad.mit.edu	37	1	113460645	113460645	+	Missense_Mutation	SNP	A	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113460645A>C	uc001ecx.2	-	4	1215	c.383T>G	c.(382-384)TTG>TGG	p.L128W	SLC16A1_uc001ecy.2_Missense_Mutation_p.L128W|SLC16A1_uc001ecz.2_Missense_Mutation_p.L128W	NM_003051	NP_003042	P53985	MOT1_HUMAN	solute carrier family 16, member 1	128	Helical; (Potential).				blood coagulation|leukocyte migration|organic anion transport|pyruvate metabolic process	integral to membrane|membrane fraction|plasma membrane	mevalonate transmembrane transporter activity|protein binding|secondary active monocarboxylate transmembrane transporter activity|symporter activity			central_nervous_system(1)	1	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Pyruvic acid(DB00119)	AGCTGGATTCAAGTTGAAGGC	0.373													15	51	---	---	---	---	PASS
PHTF1	10745	broad.mit.edu	37	1	114253056	114253056	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114253056G>T	uc009wgp.1	-	10	1541	c.1089C>A	c.(1087-1089)AAC>AAA	p.N363K	PHTF1_uc001edn.2_Missense_Mutation_p.N363K|PHTF1_uc001edm.2_Missense_Mutation_p.N120K|PHTF1_uc001edo.1_Missense_Mutation_p.N120K	NM_006608	NP_006599	Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	363						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTCTTGACATGTTGAGGCTTC	0.453													5	44	---	---	---	---	PASS
CHD1L	9557	broad.mit.edu	37	1	146739123	146739123	+	Nonsense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146739123C>T	uc001epm.3	+	9	997	c.934C>T	c.(934-936)CAG>TAG	p.Q312*	uc001epp.2_Intron|CHD1L_uc001epn.3_Nonsense_Mutation_p.Q199*|CHD1L_uc010ozo.1_RNA|CHD1L_uc009wjg.2_RNA|CHD1L_uc009wjh.2_Nonsense_Mutation_p.Q312*|CHD1L_uc010ozp.1_Nonsense_Mutation_p.Q31*|CHD1L_uc001epo.3_Nonsense_Mutation_p.Q108*|CHD1L_uc010ozq.1_5'UTR|CHD1L_uc009wji.2_Nonsense_Mutation_p.Q31*	NM_004284	NP_004275	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein	312					chromatin remodeling|DNA repair	cytoplasm|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(3)|lung(2)|upper_aerodigestive_tract(1)	6	all_hematologic(923;0.0487)					AGTTAAACTACAGAACATTTT	0.378													18	77	---	---	---	---	PASS
SETDB1	9869	broad.mit.edu	37	1	150916462	150916462	+	Silent	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150916462C>T	uc001evu.2	+	8	1132	c.942C>T	c.(940-942)TGC>TGT	p.C314C	SETDB1_uc009wmf.2_Silent_p.C314C|SETDB1_uc001evv.2_Silent_p.C314C|SETDB1_uc001evw.3_Silent_p.C314C|SETDB1_uc009wmg.1_Silent_p.C314C	NM_001145415	NP_001138887	Q15047	SETB1_HUMAN	SET domain, bifurcated 1 isoform 1	314	Tudor 1.				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)			ATCCCATTTGCCGGCCACGTG	0.428													4	293	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152275778	152275778	+	Missense_Mutation	SNP	T	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152275778T>G	uc001ezu.1	-	3	11620	c.11584A>C	c.(11584-11586)AGT>CGT	p.S3862R		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	3862	Filaggrin 23.|Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGCTAACACTGGATCCCTGG	0.577									Ichthyosis				10	409	---	---	---	---	PASS
UBE2Q1	55585	broad.mit.edu	37	1	154523919	154523919	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154523919G>C	uc001fff.1	-	11	1215	c.1124C>G	c.(1123-1125)GCC>GGC	p.A375G		NM_017582	NP_060052	Q7Z7E8	UB2Q1_HUMAN	ubiquitin-conjugating enzyme E2Q	375							ATP binding|protein binding|ubiquitin-protein ligase activity				0	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			CACCAGTGTGGCACTGATCTG	0.567													44	220	---	---	---	---	PASS
UBE2Q1	55585	broad.mit.edu	37	1	154523920	154523920	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154523920C>A	uc001fff.1	-	11	1214	c.1123G>T	c.(1123-1125)GCC>TCC	p.A375S		NM_017582	NP_060052	Q7Z7E8	UB2Q1_HUMAN	ubiquitin-conjugating enzyme E2Q	375							ATP binding|protein binding|ubiquitin-protein ligase activity				0	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			ACCAGTGTGGCACTGATCTGC	0.562													47	222	---	---	---	---	PASS
FAM189B	10712	broad.mit.edu	37	1	155223486	155223486	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155223486G>A	uc001fjm.2	-	5	1157	c.551C>T	c.(550-552)GCC>GTC	p.A184V	RAG1AP1_uc010pey.1_Intron|FAM189B_uc009wql.2_5'Flank|FAM189B_uc001fjn.2_Missense_Mutation_p.A88V|FAM189B_uc001fjo.2_Missense_Mutation_p.A165V|FAM189B_uc001fjp.2_RNA|FAM189B_uc001fjq.1_Missense_Mutation_p.A184V	NM_006589	NP_006580	P81408	F189B_HUMAN	hypothetical protein LOC10712 isoform a	184	Helical; (Potential).					integral to membrane	WW domain binding			ovary(1)|breast(1)	2						GATTATAGCGGCACAAATGGT	0.552													4	163	---	---	---	---	PASS
SLAMF1	6504	broad.mit.edu	37	1	160593937	160593937	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160593937C>T	uc001fwl.3	-	4	1085	c.739G>A	c.(739-741)GGT>AGT	p.G247S	SLAMF1_uc010pjk.1_RNA|SLAMF1_uc010pjl.1_RNA|SLAMF1_uc010pjm.1_Intron	NM_003037	NP_003028	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family	247	Helical; (Potential).|Ig-like V-type.				interspecies interaction between organisms|lymphocyte activation|positive regulation of cell proliferation	integral to membrane	antigen binding|transmembrane receptor activity			ovary(1)|breast(1)	2	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			ATGATGACACCCCCTAACAGC	0.393													56	316	---	---	---	---	PASS
C1orf112	55732	broad.mit.edu	37	1	169801603	169801603	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169801603A>G	uc001ggp.2	+	17	1805	c.1495A>G	c.(1495-1497)ATA>GTA	p.I499V	C1orf112_uc001ggj.2_RNA|C1orf112_uc001ggq.2_Missense_Mutation_p.I499V|C1orf112_uc009wvt.2_Missense_Mutation_p.I176V|C1orf112_uc009wvu.1_Missense_Mutation_p.I375V|C1orf112_uc001ggr.2_Missense_Mutation_p.I364V|C1orf112_uc010plv.1_Missense_Mutation_p.I441V	NM_018186	NP_060656	Q9NSG2	CA112_HUMAN	hypothetical protein LOC55732	499											0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CAACCTATCAATACTGTTGAA	0.413													13	249	---	---	---	---	PASS
ABL2	27	broad.mit.edu	37	1	179077770	179077770	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179077770C>A	uc001gmj.3	-	12	2919	c.2632G>T	c.(2632-2634)GGG>TGG	p.G878W	ABL2_uc010pnf.1_Missense_Mutation_p.G775W|ABL2_uc010png.1_Missense_Mutation_p.G754W|ABL2_uc010pnh.1_Missense_Mutation_p.G857W|ABL2_uc001gmg.3_Missense_Mutation_p.G760W|ABL2_uc001gmi.3_Missense_Mutation_p.G863W|ABL2_uc001gmh.3_Missense_Mutation_p.G842W|ABL2_uc010pne.1_Missense_Mutation_p.G739W	NM_007314	NP_009298	P42684	ABL2_HUMAN	arg tyrosine kinase isoform b	878	F-actin-binding (By similarity).|Pro-rich.				axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(8)|breast(3)|ovary(2)|central_nervous_system(1)	14					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	ACTCCCACCCCTGGAGGGTCC	0.582			T	ETV6	AML								27	110	---	---	---	---	PASS
ZNF648	127665	broad.mit.edu	37	1	182026247	182026247	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182026247A>G	uc001goz.2	-	2	1107	c.899T>C	c.(898-900)CTG>CCG	p.L300P		NM_001009992	NP_001009992	Q5T619	ZN648_HUMAN	zinc finger protein 648	300	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GCCCGTGTGCAGGCGCCTGTG	0.697													3	49	---	---	---	---	PASS
CDC73	79577	broad.mit.edu	37	1	193099385	193099385	+	Intron	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193099385T>C	uc001gtb.2	+							NM_024529	NP_078805	Q6P1J9	CDC73_HUMAN	parafibromin						cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49						TGAGTACTTTTTAAATTGTTC	0.204									Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				19	70	---	---	---	---	PASS
DSTYK	25778	broad.mit.edu	37	1	205117394	205117394	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205117394C>A	uc001hbw.2	-	12	2605	c.2541G>T	c.(2539-2541)AAG>AAT	p.K847N	DSTYK_uc001hbx.2_Intron	NM_015375	NP_056190	Q6XUX3	DUSTY_HUMAN	receptor interacting protein kinase 5 isoform 1	847	Protein kinase.					cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(1)	1						CCTCAGGGAGCTTGACAGAGC	0.478													22	151	---	---	---	---	PASS
C1orf74	148304	broad.mit.edu	37	1	209956791	209956791	+	Silent	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209956791T>C	uc001hhp.1	-	2	432	c.189A>G	c.(187-189)GCA>GCG	p.A63A		NM_152485	NP_689698	Q96LT6	CA074_HUMAN	hypothetical protein LOC148304	63										skin(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0328)		GGAGCTCTGATGCCCCTGCAC	0.552													25	95	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	215972468	215972468	+	Splice_Site	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215972468C>A	uc001hku.1	-	50	10127	c.9740_splice	c.e50-1	p.G3247_splice		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B						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)		CATACTTCACCTGTCAATTTA	0.388										HNSCC(13;0.011)			8	34	---	---	---	---	PASS
NVL	4931	broad.mit.edu	37	1	224488255	224488255	+	Intron	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224488255C>A	uc001hok.2	-						NVL_uc001hol.2_Intron|NVL_uc010pvd.1_Intron|NVL_uc010pve.1_Intron|NVL_uc010pvf.1_Intron	NM_002533	NP_002524	O15381	NVL_HUMAN	nuclear VCP-like isoform 1							aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)		TAGTCATTAACTGACTCACCA	0.443													3	59	---	---	---	---	PASS
NUP133	55746	broad.mit.edu	37	1	229600521	229600521	+	Missense_Mutation	SNP	C	A	A	rs139160684		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229600521C>A	uc001htn.2	-	18	2493	c.2401G>T	c.(2401-2403)GTG>TTG	p.V801L		NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	801					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				TGCTCGGTCACGATGTTTCGG	0.483													17	92	---	---	---	---	PASS
WDR64	128025	broad.mit.edu	37	1	241912838	241912838	+	Intron	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241912838T>A	uc001hzf.1	+						WDR64_uc001hzg.1_5'Flank	NM_144625	NP_653226	B1ANS9	WDR64_HUMAN	WD repeat domain 64											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			TCTTTTTCTCTGTATGCTCAG	0.468													23	177	---	---	---	---	PASS
OR1C1	26188	broad.mit.edu	37	1	247921246	247921246	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247921246G>T	uc010pza.1	-	1	463	c.463C>A	c.(463-465)CAC>AAC	p.H155N		NM_012353	NP_036485	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C,	155	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)	all_cancers(173;0.0247)	OV - Ovarian serous cystadenocarcinoma(106;0.0168)			AGGAGGGCGTGGAGGTAAGTA	0.498													4	41	---	---	---	---	PASS
APOB	338	broad.mit.edu	37	2	21245917	21245917	+	Intron	SNP	A	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21245917A>G	uc002red.2	-							NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor						cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	GCCTGCATCTATAAGTCAGAA	0.468													12	114	---	---	---	---	PASS
NCOA1	8648	broad.mit.edu	37	2	24985567	24985567	+	Silent	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24985567C>G	uc002rfk.2	+	20	4335	c.4077C>G	c.(4075-4077)CCC>CCG	p.P1359P	NCOA1_uc010eye.2_Silent_p.P1359P|NCOA1_uc002rfi.2_Silent_p.P1208P|NCOA1_uc002rfj.2_Silent_p.P1359P|NCOA1_uc002rfl.2_Silent_p.P1359P|NCOA1_uc010eyf.2_Intron	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1	1359									PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAAATGATCCCGCACTGAGAC	0.393			T	PAX3	alveolar rhadomyosarcoma								18	530	---	---	---	---	PASS
OTOF	9381	broad.mit.edu	37	2	26689649	26689649	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26689649T>C	uc002rhk.2	-	36	4560	c.4433A>G	c.(4432-4434)TAC>TGC	p.Y1478C	OTOF_uc010yla.1_Missense_Mutation_p.Y208C|OTOF_uc002rhh.2_Missense_Mutation_p.Y711C|OTOF_uc002rhi.2_Missense_Mutation_p.Y788C|OTOF_uc002rhj.2_Missense_Mutation_p.Y711C	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	1478	Cytoplasmic (Potential).				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAACATGCCGTAGGTGGAGTC	0.597													17	142	---	---	---	---	PASS
PREB	10113	broad.mit.edu	37	2	27356432	27356432	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27356432T>C	uc002rix.1	-	2	546	c.293A>G	c.(292-294)CAT>CGT	p.H98R	PREB_uc002riy.1_Missense_Mutation_p.H26R|PREB_uc002riz.1_RNA|PREB_uc002rja.1_Missense_Mutation_p.H98R	NM_013388	NP_037520	Q9HCU5	PREB_HUMAN	prolactin regulatory element binding protein	98	Cytoplasmic (Potential).				COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|nucleus	DNA binding|guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGCTGTTGATGTGCCTGGAA	0.582													10	58	---	---	---	---	PASS
C2orf71	388939	broad.mit.edu	37	2	29287800	29287800	+	Silent	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29287800G>T	uc002rmt.1	-	2	3802	c.3802C>A	c.(3802-3804)CGG>AGG	p.R1268R		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	1268					response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1						TGGCCGGTCCGAGGCTCCGGT	0.682													8	28	---	---	---	---	PASS
QPCT	25797	broad.mit.edu	37	2	37586830	37586830	+	Silent	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37586830C>T	uc002rqg.2	+	3	497	c.375C>T	c.(373-375)AGC>AGT	p.S125S	QPCT_uc002rqh.2_Silent_p.S76S	NM_012413	NP_036545	Q16769	QPCT_HUMAN	glutaminyl-peptide cyclotransferase precursor	125					peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase|proteolysis	extracellular region	acyltransferase activity|glutaminyl-peptide cyclotransferase activity|peptidase activity|zinc ion binding			central_nervous_system(1)	1		Ovarian(717;0.051)|all_hematologic(82;0.21)				ATATCATCAGCACCCTCAATC	0.488													23	95	---	---	---	---	PASS
ABCG8	64241	broad.mit.edu	37	2	44071641	44071641	+	Intron	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44071641C>T	uc002rtq.2	+						ABCG8_uc010yoa.1_Intron	NM_022437	NP_071882	Q9H221	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				TCCTGTCTCCCACAGGGCCTC	0.522													15	46	---	---	---	---	PASS
ABCG8	64241	broad.mit.edu	37	2	44078862	44078862	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44078862C>A	uc002rtq.2	+	4	552	c.462C>A	c.(460-462)CAC>CAA	p.H154Q	ABCG8_uc010yoa.1_Missense_Mutation_p.H154Q	NM_022437	NP_071882	Q9H221	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8	154	ABC transporter.|Cytoplasmic (Potential).				cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				TGCGCCAGCACAACCAGCTGC	0.617													25	162	---	---	---	---	PASS
C2orf78	388960	broad.mit.edu	37	2	74041313	74041313	+	Nonsense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74041313C>A	uc002sjr.1	+	2	928	c.807C>A	c.(805-807)TAC>TAA	p.Y269*		NM_001080474	NP_001073943	A6NCI8	CB078_HUMAN	hypothetical protein LOC388960	269										ovary(2)	2						GGATGTATTACTCTGTGTCTT	0.453													32	210	---	---	---	---	PASS
C2orf89	129293	broad.mit.edu	37	2	85097839	85097839	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85097839T>C	uc010ysl.1	-	2	268	c.179A>G	c.(178-180)CAT>CGT	p.H60R	C2orf89_uc002sou.3_Missense_Mutation_p.H60R|C2orf89_uc010fgc.1_Missense_Mutation_p.H60R	NM_001080824	NP_001074293	Q86V40	CB089_HUMAN	hypothetical protein LOC129293 precursor	60	Extracellular (Potential).					integral to membrane				ovary(1)	1						GTACGGGACATGGATTGTGCC	0.478													4	22	---	---	---	---	PASS
IL1RL1	9173	broad.mit.edu	37	2	102968090	102968090	+	Silent	SNP	C	T	T	rs112596146		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102968090C>T	uc002tbu.1	+	11	1651	c.1380C>T	c.(1378-1380)TAC>TAT	p.Y460Y	IL18R1_uc002tbw.3_Intron	NM_016232	NP_057316	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1 isoform 1	460	TIR.|Cytoplasmic (Potential).				innate immune response	integral to membrane	interleukin-1 receptor activity|receptor signaling protein activity			skin(2)|ovary(1)|central_nervous_system(1)	4						AGTTTGCCTACGAGCAGGAGG	0.527													13	120	---	---	---	---	PASS
ANAPC1	64682	broad.mit.edu	37	2	112608394	112608394	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112608394T>C	uc002thi.2	-	14	1856	c.1609A>G	c.(1609-1611)ACT>GCT	p.T537A		NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	537					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2						GGCTTTGGAGTACTAACGCCA	0.433													5	282	---	---	---	---	PASS
MARCO	8685	broad.mit.edu	37	2	119752052	119752052	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119752052G>T	uc002tln.1	+	17	1651	c.1519G>T	c.(1519-1521)GAC>TAC	p.D507Y	MARCO_uc010yyf.1_Missense_Mutation_p.D429Y	NM_006770	NP_006761	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	507	SRCR.|Extracellular (Potential).				cell surface receptor linked signaling pathway|innate immune response	collagen|integral to plasma membrane	pattern recognition receptor activity|scavenger receptor activity			ovary(3)|skin(2)|central_nervous_system(1)	6						GGGCCATCATGACTGCAGCCA	0.587													13	64	---	---	---	---	PASS
LCT	3938	broad.mit.edu	37	2	136548329	136548329	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136548329A>T	uc002tuu.1	-	15	5245	c.5234T>A	c.(5233-5235)ATT>AAT	p.I1745N		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	1745	Extracellular (Potential).|4.|4 X approximate repeats.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|skin(2)|pancreas(1)|lung(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.169)		TGTGACATAAATTGGAGGGTC	0.498													18	119	---	---	---	---	PASS
LCT	3938	broad.mit.edu	37	2	136594716	136594716	+	Silent	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136594716G>C	uc002tuu.1	-	1	35	c.24C>G	c.(22-24)GTC>GTG	p.V8V		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	8					carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|skin(2)|pancreas(1)|lung(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.169)		GGGCAATAAAGACTACATGCC	0.423													4	137	---	---	---	---	PASS
ACVR1	90	broad.mit.edu	37	2	158595089	158595089	+	Intron	SNP	A	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158595089A>C	uc002tzm.3	-						ACVR1_uc002tzn.3_Intron|ACVR1_uc010fog.2_Intron	NM_001111067	NP_001104537	Q04771	ACVR1_HUMAN	activin A receptor, type I precursor						BMP signaling pathway|G1/S transition of mitotic cell cycle|negative regulation of activin receptor signaling pathway|negative regulation of apoptosis|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	activin receptor complex	activin binding|ATP binding|follistatin binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta binding			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	ATACCTGCACACAAGGACAAG	0.433													28	171	---	---	---	---	PASS
BAZ2B	29994	broad.mit.edu	37	2	160261636	160261636	+	Intron	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160261636C>A	uc002uao.2	-						BAZ2B_uc002uap.2_Intron|BAZ2B_uc002uaq.1_Intron|BAZ2B_uc002uar.1_Intron	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						CTGAAAAACACAAAATTTCAA	0.313													12	96	---	---	---	---	PASS
GALNT3	2591	broad.mit.edu	37	2	166616044	166616044	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166616044G>A	uc010fph.1	-	5	1262	c.875C>T	c.(874-876)GCC>GTC	p.A292V	GALNT3_uc010fpi.1_Missense_Mutation_p.A292V	NM_004482	NP_004473	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	292	Catalytic subdomain A.|Lumenal (Potential).				protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	Golgi cisterna membrane|integral to membrane|membrane fraction|nucleus|perinuclear region of cytoplasm	calcium ion binding|manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(2)|ovary(1)	3						AGCTATTCTGGCCAACAGAGG	0.363													3	30	---	---	---	---	PASS
GALNT3	2591	broad.mit.edu	37	2	166626805	166626805	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166626805C>G	uc010fph.1	-	2	793	c.406G>C	c.(406-408)GAA>CAA	p.E136Q	GALNT3_uc010fpi.1_Missense_Mutation_p.E136Q|GALNT3_uc002udi.2_Missense_Mutation_p.E136Q	NM_004482	NP_004473	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	136	Lumenal (Potential).				protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	Golgi cisterna membrane|integral to membrane|membrane fraction|nucleus|perinuclear region of cytoplasm	calcium ion binding|manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(2)|ovary(1)	3						TTTTGCTCTTCAACACTTAAA	0.458													25	155	---	---	---	---	PASS
WDR75	84128	broad.mit.edu	37	2	190331263	190331263	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190331263G>A	uc002uql.1	+	13	1462	c.1402G>A	c.(1402-1404)GGT>AGT	p.G468S	WDR75_uc002uqm.1_Missense_Mutation_p.G404S|WDR75_uc002uqn.1_Missense_Mutation_p.G246S|WDR75_uc002uqo.1_Missense_Mutation_p.G246S	NM_032168	NP_115544	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	468	WD 7.					nucleolus				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)			TAGCAAAGATGGTTACTTCAA	0.338													12	91	---	---	---	---	PASS
STAT4	6775	broad.mit.edu	37	2	191934419	191934419	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191934419C>T	uc002usm.1	-	6	798	c.544G>A	c.(544-546)GAT>AAT	p.D182N	STAT4_uc002usn.1_Missense_Mutation_p.D182N|STAT4_uc010zgk.1_Missense_Mutation_p.D27N|STAT4_uc002uso.2_Missense_Mutation_p.D182N	NM_003151	NP_003142	Q14765	STAT4_HUMAN	signal transducer and activator of transcription	182					JAK-STAT cascade	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(3)|skin(2)|lung(1)|ovary(1)|prostate(1)|pancreas(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			AAAAACTTACCCATTGTCTGA	0.318													7	68	---	---	---	---	PASS
CCDC150	284992	broad.mit.edu	37	2	197541455	197541455	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197541455G>C	uc002utp.1	+	12	1575	c.1440G>C	c.(1438-1440)GAG>GAC	p.E480D	CCDC150_uc010zgq.1_RNA|CCDC150_uc010zgr.1_RNA|CCDC150_uc010zgs.1_Missense_Mutation_p.E148D	NM_001080539	NP_001074008	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	480	Potential.										0						TTCAGAGGGAGGTAGGTAGAA	0.363													8	74	---	---	---	---	PASS
ALS2CR11	151254	broad.mit.edu	37	2	202430541	202430541	+	Silent	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202430541C>G	uc002uye.2	-	9	936	c.888G>C	c.(886-888)CTG>CTC	p.L296L	ALS2CR11_uc002uyf.2_Silent_p.L296L|ALS2CR11_uc010fti.2_Silent_p.L296L	NM_152525	NP_689738	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	296										large_intestine(1)|ovary(1)|skin(1)	3						CAGTAACATTCAGGTCTGGGG	0.383													13	76	---	---	---	---	PASS
PIKFYVE	200576	broad.mit.edu	37	2	209190987	209190987	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209190987T>A	uc002vcz.2	+	20	3610	c.3452T>A	c.(3451-3453)ATG>AAG	p.M1151K	PIKFYVE_uc010fun.1_Missense_Mutation_p.M832K|PIKFYVE_uc002vcy.1_Missense_Mutation_p.M1095K	NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type	1151					cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding			ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1)	10						TTGGGTAGAATGCTGGCCGAT	0.468													8	76	---	---	---	---	PASS
FN1	2335	broad.mit.edu	37	2	216298158	216298158	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216298158T>A	uc002vfa.2	-	3	570	c.304A>T	c.(304-306)ACT>TCT	p.T102S	FN1_uc002vfb.2_Missense_Mutation_p.T102S|FN1_uc002vfc.2_Missense_Mutation_p.T102S|FN1_uc002vfd.2_Missense_Mutation_p.T102S|FN1_uc002vfe.2_Missense_Mutation_p.T102S|FN1_uc002vff.2_Missense_Mutation_p.T102S|FN1_uc002vfg.2_Missense_Mutation_p.T102S|FN1_uc002vfh.2_Missense_Mutation_p.T102S|FN1_uc002vfi.2_Missense_Mutation_p.T102S|FN1_uc002vfj.2_Missense_Mutation_p.T102S|FN1_uc002vfl.2_Missense_Mutation_p.T102S	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	102	Fibronectin type-I 2.|Fibrin- and heparin-binding 1.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GTGTTCCCAGTGTACTTGTCA	0.493													15	103	---	---	---	---	PASS
SLC4A3	6508	broad.mit.edu	37	2	220504424	220504424	+	Silent	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220504424C>A	uc002vmp.3	+	20	3513	c.3244C>A	c.(3244-3246)CGG>AGG	p.R1082R	SLC4A3_uc002vmo.3_Silent_p.R1109R|SLC4A3_uc010fwm.2_Silent_p.R632R	NM_005070	NP_005061	P48751	B3A3_HUMAN	solute carrier family 4, anion exchanger, member	1082	Membrane (anion exchange).				bicarbonate transport	integral to plasma membrane|membrane fraction	inorganic anion exchanger activity			ovary(2)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	5		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCGGGAGCAGCGGGTCACTGG	0.637													6	45	---	---	---	---	PASS
PAX3	5077	broad.mit.edu	37	2	223084939	223084939	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223084939T>A	uc010fwo.2	-	7	1459	c.1093A>T	c.(1093-1095)AGC>TGC	p.S365C	PAX3_uc002vmt.1_Missense_Mutation_p.S365C|PAX3_uc002vmy.1_Missense_Mutation_p.S364C|PAX3_uc002vmv.1_Missense_Mutation_p.S365C|PAX3_uc002vmw.1_Missense_Mutation_p.S365C|PAX3_uc002vmx.1_Missense_Mutation_p.S365C	NM_181457	NP_852122	P23760	PAX3_HUMAN	paired box 3 isoform PAX3	365					apoptosis|organ morphogenesis|positive regulation of transcription from RNA polymerase II promoter|sensory perception of sound|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX3/FOXO1(749)|PAX3/NCOA1(8)|PAX3/NCOA2(4)	soft_tissue(761)|ovary(4)|skin(1)	766		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCTGTATAGCTGGAAAATCCA	0.567			T	FOXO1A|NCOA1	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome						10	63	---	---	---	---	PASS
SPHKAP	80309	broad.mit.edu	37	2	228892257	228892257	+	Silent	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228892257G>T	uc002vpq.2	-	4	296	c.249C>A	c.(247-249)GTC>GTA	p.V83V	SPHKAP_uc002vpp.2_Silent_p.V83V|SPHKAP_uc010zlx.1_Silent_p.V83V	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	83						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TCACAAAGCAGACCTGGGAAA	0.428													27	145	---	---	---	---	PASS
THUMPD3	25917	broad.mit.edu	37	3	9424981	9424981	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9424981C>T	uc003bro.3	+	8	1371	c.1223C>T	c.(1222-1224)CCA>CTA	p.P408L	LOC440944_uc003brm.2_Intron|THUMPD3_uc003brn.3_Missense_Mutation_p.P408L	NM_001114092	NP_001107564	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	408							methyltransferase activity|protein binding|RNA binding			ovary(1)	1	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		ACAGATTTGCCATTTGGAAAA	0.383													24	73	---	---	---	---	PASS
USP19	10869	broad.mit.edu	37	3	49153267	49153267	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49153267C>A	uc003cwd.1	-	10	1434	c.1273G>T	c.(1273-1275)GTG>TTG	p.V425L	USP19_uc003cwa.2_Missense_Mutation_p.V233L|USP19_uc003cvz.3_Missense_Mutation_p.V528L|USP19_uc011bcg.1_Missense_Mutation_p.V516L|USP19_uc003cwb.2_Missense_Mutation_p.V511L|USP19_uc003cwc.1_Missense_Mutation_p.V183L|USP19_uc011bch.1_Missense_Mutation_p.V526L|USP19_uc011bci.1_Missense_Mutation_p.V513L	NM_006677	NP_006668	O94966	UBP19_HUMAN	ubiquitin thioesterase 19	425	Cytoplasmic (Potential).				ER-associated protein catabolic process|positive regulation of cell cycle process|protein deubiquitination|regulation of protein stability|response to endoplasmic reticulum stress|skeletal muscle atrophy	endoplasmic reticulum membrane|integral to membrane	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(4)|breast(2)|lung(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TCCTTCTCCACAGCCCGGGCC	0.607													5	130	---	---	---	---	PASS
BSN	8927	broad.mit.edu	37	3	49698245	49698245	+	Silent	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49698245T>C	uc003cxe.3	+	6	9081	c.8967T>C	c.(8965-8967)TCT>TCC	p.S2989S		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	2989					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GCAAAGAGTCTTTGGCCAAAG	0.572													23	62	---	---	---	---	PASS
IFT57	55081	broad.mit.edu	37	3	107925521	107925521	+	Missense_Mutation	SNP	T	A	A	rs10704311		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107925521T>A	uc003dwx.3	-	5	856	c.608A>T	c.(607-609)GAA>GTA	p.E203V		NM_018010	NP_060480	Q9NWB7	IFT57_HUMAN	estrogen-related receptor beta like 1	203					activation of caspase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cilium|microtubule basal body	DNA binding|protein binding			ovary(1)|skin(1)|pancreas(1)	3			OV - Ovarian serous cystadenocarcinoma(3;0.0428)|Epithelial(53;0.246)			AATAAAGTTTTCTTCATTATC	0.279													19	130	---	---	---	---	PASS
PHLDB2	90102	broad.mit.edu	37	3	111637980	111637980	+	Missense_Mutation	SNP	G	A	A	rs148898642	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111637980G>A	uc010hqa.2	+	4	2192	c.1781G>A	c.(1780-1782)CGG>CAG	p.R594Q	PHLDB2_uc003dyc.2_Missense_Mutation_p.R621Q|PHLDB2_uc003dyd.2_Missense_Mutation_p.R594Q|PHLDB2_uc003dyg.2_Missense_Mutation_p.R594Q|PHLDB2_uc003dyh.2_Missense_Mutation_p.R594Q|PHLDB2_uc003dyi.2_Missense_Mutation_p.R180Q	NM_001134438	NP_001127910	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B,	594	Potential.					cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6						GAAGAAACCCGGATAGTCATT	0.408													4	360	---	---	---	---	PASS
GAP43	2596	broad.mit.edu	37	3	115395053	115395053	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115395053C>A	uc003ebq.2	+	2	610	c.224C>A	c.(223-225)GCC>GAC	p.A75D	GAP43_uc003ebr.2_Missense_Mutation_p.A111D	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2	75					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)		GCCCCTGTTGCCGATGGGGTG	0.537													14	115	---	---	---	---	PASS
GAP43	2596	broad.mit.edu	37	3	115395054	115395054	+	Silent	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115395054C>G	uc003ebq.2	+	2	611	c.225C>G	c.(223-225)GCC>GCG	p.A75A	GAP43_uc003ebr.2_Silent_p.A111A	NM_002045	NP_002036	P17677	NEUM_HUMAN	growth associated protein 43 isoform 2	75					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)		CCCCTGTTGCCGATGGGGTGG	0.537													15	114	---	---	---	---	PASS
ADPRH	141	broad.mit.edu	37	3	119306408	119306408	+	Nonsense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119306408G>T	uc003ecs.2	+	5	1055	c.757G>T	c.(757-759)GAG>TAG	p.E253*	ADPRH_uc010hqv.2_Nonsense_Mutation_p.E253*|ADPRH_uc011bjb.1_Nonsense_Mutation_p.E146*|ADPRH_uc003ect.2_Nonsense_Mutation_p.E253*	NM_001125	NP_001116	P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	253					protein de-ADP-ribosylation		ADP-ribosylarginine hydrolase activity|magnesium ion binding			ovary(1)	1		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		CGGTGTGAAGGAGAGGGATCA	0.522													8	186	---	---	---	---	PASS
CD86	942	broad.mit.edu	37	3	121825253	121825253	+	Silent	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121825253G>A	uc003eet.2	+	4	725	c.609G>A	c.(607-609)TTG>TTA	p.L203L	CD86_uc011bjo.1_Silent_p.L121L|CD86_uc011bjp.1_Silent_p.L91L|CD86_uc003eeu.2_Silent_p.L197L	NM_175862	NP_787058	P42081	CD86_HUMAN	CD86 antigen isoform 1	203	Ig-like C2-type.|Extracellular (Potential).				interspecies interaction between organisms|positive regulation of cell proliferation|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|positive regulation of lymphotoxin A biosynthetic process|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription, DNA-dependent|T cell costimulation		coreceptor activity|protein binding			pancreas(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)	CCATCAGCTTGTCTGTTTCAT	0.393													70	351	---	---	---	---	PASS
PARP14	54625	broad.mit.edu	37	3	122436926	122436926	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122436926A>G	uc003efq.3	+	13	4068	c.4009A>G	c.(4009-4011)AAA>GAA	p.K1337E	PARP14_uc010hrk.2_RNA|PARP14_uc003efr.2_Missense_Mutation_p.K1054E|PARP14_uc003efs.1_Missense_Mutation_p.K1054E	NM_017554	NP_060024	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1337	Macro 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)		AGGAAATGCCAAACAACACCC	0.388													6	66	---	---	---	---	PASS
MCM2	4171	broad.mit.edu	37	3	127335787	127335787	+	Silent	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127335787C>G	uc003ejp.2	+	10	1656	c.1599C>G	c.(1597-1599)CTC>CTG	p.L533L	MCM2_uc011bkm.1_Silent_p.L403L|MCM2_uc010hsl.2_RNA|MCM2_uc011bkn.1_Silent_p.L486L	NM_004526	NP_004517	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	533	MCM.				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|helicase activity|metal ion binding			ovary(3)|skin(1)	4						CGCAGTTTCTCAAGTATATTG	0.592													4	273	---	---	---	---	PASS
PCCB	5096	broad.mit.edu	37	3	136002707	136002707	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136002707C>G	uc003eqy.1	+	6	623	c.572C>G	c.(571-573)CCT>CGT	p.P191R	PCCB_uc003eqz.1_Missense_Mutation_p.P191R|PCCB_uc011bmc.1_Missense_Mutation_p.P211R|PCCB_uc011bmd.1_Missense_Mutation_p.P108R	NM_000532	NP_000523	P05166	PCCB_HUMAN	propionyl Coenzyme A carboxylase, beta	191	Carboxyltransferase.				fatty acid beta-oxidation	mitochondrial matrix	ATP binding|propionyl-CoA carboxylase activity				0					Biotin(DB00121)|L-Valine(DB00161)	GGAGTCATCCCTCAGATTTCT	0.483													20	115	---	---	---	---	PASS
RNF13	11342	broad.mit.edu	37	3	149677870	149677870	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149677870G>A	uc003exn.3	+	10	1512	c.728G>A	c.(727-729)TGT>TAT	p.C243Y	RNF13_uc003exp.3_Missense_Mutation_p.C243Y|RNF13_uc010hvh.2_Missense_Mutation_p.C124Y	NM_007282	NP_009213	O43567	RNF13_HUMAN	ring finger protein 13	243	Cytoplasmic (Potential).|RING-type; atypical.				protein autoubiquitination	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane|nuclear inner membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TGTGCCATTTGTTTGGATGAG	0.343													20	493	---	---	---	---	PASS
MED12L	116931	broad.mit.edu	37	3	150876521	150876521	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150876521G>A	uc003eyp.2	+	6	810	c.772G>A	c.(772-774)GTT>ATT	p.V258I	MED12L_uc011bnz.1_Missense_Mutation_p.V258I|MED12L_uc003eym.1_Missense_Mutation_p.V258I|MED12L_uc003eyn.2_Missense_Mutation_p.V258I|MED12L_uc003eyo.2_Missense_Mutation_p.V258I	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	258					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GATCCTGGATGTTTTAGAAAA	0.318													6	142	---	---	---	---	PASS
PLCH1	23007	broad.mit.edu	37	3	155241682	155241682	+	Intron	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155241682T>A	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TGCCTGCAACTTACATAATGG	0.433													6	642	---	---	---	---	PASS
SLITRK3	22865	broad.mit.edu	37	3	164907600	164907600	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164907600C>A	uc003fej.3	-	2	1463	c.1019G>T	c.(1018-1020)CGA>CTA	p.R340L	SLITRK3_uc003fek.2_Missense_Mutation_p.R340L	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	340	Extracellular (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10						CCTTGGTGTTCGAGGCTGTTT	0.483										HNSCC(40;0.11)			165	518	---	---	---	---	PASS
ALG3	10195	broad.mit.edu	37	3	183963051	183963051	+	Silent	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183963051C>T	uc003fne.2	-	4	571	c.540G>A	c.(538-540)GTG>GTA	p.V180V	ALG3_uc011brc.1_Silent_p.V145V|ALG3_uc011brd.1_Silent_p.V124V|ALG3_uc011bre.1_Silent_p.V132V|ALG3_uc003fnf.1_Silent_p.V140V|ALG3_uc011brf.1_Silent_p.V72V	NM_005787	NP_005778	Q92685	ALG3_HUMAN	alpha-1,3-mannosyltransferase ALG3 isoform a	180	Helical; (Potential).				dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity				0	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGAAGAGCAGCACCATGGCCA	0.547													13	31	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505712	195505712	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505712T>C	uc011bto.1	-	3	12815	c.12355A>G	c.(12355-12357)ACC>GCC	p.T4119A	MUC4_uc003fva.2_5'UTR|MUC4_uc003fvb.2_5'UTR|MUC4_uc003fvc.2_RNA|MUC4_uc003fvd.2_RNA|MUC4_uc003fve.2_5'UTR|MUC4_uc010hzr.2_RNA|MUC4_uc011btf.1_5'UTR|MUC4_uc011btg.1_RNA|MUC4_uc011bth.1_5'UTR|MUC4_uc011bti.1_5'UTR|MUC4_uc011btj.1_5'UTR|MUC4_uc011btk.1_5'UTR|MUC4_uc011btl.1_5'UTR|MUC4_uc011btm.1_5'UTR|MUC4_uc011btn.1_5'UTR|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Missense_Mutation_p.T859A	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	1004	Ser-rich.|Repeat.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAAGCTGAGGTAGCACTGCTG	0.587													9	54	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195517433	195517433	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195517433T>A	uc011bto.1	-	2	1478	c.1018A>T	c.(1018-1020)ACC>TCC	p.T340S	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Missense_Mutation_p.T222S	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	345					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTGTTGAGGGTGTTGATTTGA	0.468													14	722	---	---	---	---	PASS
C4orf44	345222	broad.mit.edu	37	4	3251171	3251171	+	Silent	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3251171G>T	uc003ggs.2	+	1	405	c.222G>T	c.(220-222)GTG>GTT	p.V74V	C4orf44_uc003ggt.2_Silent_p.V74V	NM_001042690	NP_001036155	Q6ZTZ1	CD044_HUMAN	hypothetical protein LOC345222 isoform a	74											0						ACGCCAAGGTGTACGAGAAGA	0.607													7	25	---	---	---	---	PASS
CRMP1	1400	broad.mit.edu	37	4	5868448	5868448	+	Silent	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5868448G>T	uc003gip.2	-	3	176	c.75C>A	c.(73-75)ATC>ATA	p.I25I	CRMP1_uc003gin.1_5'UTR|CRMP1_uc003giq.2_Silent_p.I25I|CRMP1_uc003gir.2_Silent_p.I20I|CRMP1_uc003gis.2_Silent_p.I139I	NM_001313	NP_001304	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1 isoform 2	25					axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding			ovary(2)	2				Colorectal(103;0.0721)		GGTCATCGTTGATGATCCGTC	0.443													10	156	---	---	---	---	PASS
KIAA1211	57482	broad.mit.edu	37	4	57180943	57180943	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57180943C>A	uc003hbk.2	+	8	1666	c.1275C>A	c.(1273-1275)GAC>GAA	p.D425E	KIAA1211_uc010iha.2_Missense_Mutation_p.D418E|KIAA1211_uc011bzz.1_Missense_Mutation_p.D335E|KIAA1211_uc003hbm.1_Missense_Mutation_p.D311E	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	425	Glu-rich.									ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)					TTCTGAACGACTTTGAGGAGA	0.458													3	8	---	---	---	---	PASS
AFF1	4299	broad.mit.edu	37	4	88005268	88005268	+	Intron	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88005268T>A	uc003hqj.3	+						AFF1_uc003hqh.1_Intron|AFF1_uc011ccy.1_Intron|AFF1_uc011ccz.1_Intron|AFF1_uc003hqk.3_Intron|AFF1_uc011cda.1_Intron	NM_005935	NP_005926	P51825	AFF1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		CTTTTCACTTTCAGCAGACCT	0.378													30	286	---	---	---	---	PASS
AFF1	4299	broad.mit.edu	37	4	88005269	88005269	+	Intron	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88005269C>A	uc003hqj.3	+						AFF1_uc003hqh.1_Intron|AFF1_uc011ccy.1_Intron|AFF1_uc011ccz.1_Intron|AFF1_uc003hqk.3_Intron|AFF1_uc011cda.1_Intron	NM_005935	NP_005926	P51825	AFF1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TTTTCACTTTCAGCAGACCTA	0.378													30	287	---	---	---	---	PASS
LEF1	51176	broad.mit.edu	37	4	109002828	109002828	+	Intron	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109002828G>T	uc003hyt.1	-						LEF1_uc011cfj.1_Intron|LEF1_uc011cfk.1_Intron|LEF1_uc003hyu.1_Intron|LEF1_uc003hyv.1_Intron|LEF1_uc010imb.1_Intron|LEF1_uc003hyw.1_5'Flank	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1						canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)		GACCTTGCCTGAGGTCACAGA	0.498													9	54	---	---	---	---	PASS
SEC24B	10427	broad.mit.edu	37	4	110415820	110415820	+	Silent	SNP	A	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110415820A>G	uc003hzk.2	+	6	1351	c.1296A>G	c.(1294-1296)GAA>GAG	p.E432E	SEC24B_uc003hzl.2_Silent_p.E397E|SEC24B_uc011cfp.1_Silent_p.E463E|SEC24B_uc011cfq.1_Silent_p.E432E|SEC24B_uc011cfr.1_Silent_p.E397E	NM_006323	NP_006314	O95487	SC24B_HUMAN	SEC24 (S. cerevisiae) homolog B isoform a	432					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)		CCGCCCCTGAACCTGATCCTG	0.483													44	139	---	---	---	---	PASS
ALPK1	80216	broad.mit.edu	37	4	113350351	113350351	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113350351C>G	uc003iap.3	+	10	1121	c.842C>G	c.(841-843)GCC>GGC	p.A281G	ALPK1_uc003ian.3_Missense_Mutation_p.A281G|ALPK1_uc011cfx.1_Missense_Mutation_p.A203G|ALPK1_uc003iao.3_RNA|ALPK1_uc010imo.2_Missense_Mutation_p.A109G	NM_025144	NP_079420	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	281							ATP binding|protein serine/threonine kinase activity			ovary(5)	5		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		GCTGCAGAAGCCTGCAAGCTG	0.527													60	180	---	---	---	---	PASS
MAD2L1	4085	broad.mit.edu	37	4	120981308	120981308	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120981308T>C	uc003idl.2	-	5	707	c.583A>G	c.(583-585)AGC>GGC	p.S195G	MAD2L1_uc003idm.2_3'UTR	NM_002358	NP_002349	Q13257	MD2L1_HUMAN	MAD2-like 1	195	HORMA.|Required for assuming the closed conformation and for interaction with CDC20.			S->D: Abolishes interaction with MAD1L1 and reduces interaction with CDC20; when associated with D-170 and D-178.|S->A: Abolishes phosphorylation on serine residues; when associated with A-170 and A-178.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of apoptosis|negative regulation of mitotic anaphase-promoting complex activity|positive regulation of mitotic cell cycle spindle assembly checkpoint	condensed chromosome kinetochore|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity				0						GCCACCATGCTATTTACTTTG	0.383													8	186	---	---	---	---	PASS
SPATA5	166378	broad.mit.edu	37	4	124177257	124177257	+	Silent	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124177257G>A	uc003iez.3	+	15	2500	c.2427G>A	c.(2425-2427)CAG>CAA	p.Q809Q		NM_145207	NP_660208	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	809					cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0						TTAAGCTGCAGTTTCACTCCA	0.423													39	149	---	---	---	---	PASS
LRBA	987	broad.mit.edu	37	4	151770705	151770705	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151770705C>A	uc010ipj.2	-	25	4501	c.4027G>T	c.(4027-4029)GAC>TAC	p.D1343Y	LRBA_uc003ilt.3_Missense_Mutation_p.D2Y|LRBA_uc003ilu.3_Missense_Mutation_p.D1343Y	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	1343	WD 1.					endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					TTCACGAAGTCCATAACTGTC	0.383													16	113	---	---	---	---	PASS
DCHS2	54798	broad.mit.edu	37	4	155256175	155256175	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155256175C>A	uc003inw.2	-	8	1061	c.1061G>T	c.(1060-1062)GGG>GTG	p.G354V	DCHS2_uc003inx.2_Missense_Mutation_p.G853V	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	354	Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AGCTGTGAGCCCACCACCGTC	0.418													11	139	---	---	---	---	PASS
TLL1	7092	broad.mit.edu	37	4	167020662	167020662	+	Silent	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167020662C>A	uc003irh.1	+	20	3537	c.2890C>A	c.(2890-2892)CGA>AGA	p.R964R	TLL1_uc011cjn.1_Silent_p.R987R|TLL1_uc011cjo.1_Silent_p.R788R	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor	964	CUB 5.				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		GGGGCTTGGTCGATTCTGTGG	0.423													5	292	---	---	---	---	PASS
AGA	175	broad.mit.edu	37	4	178360790	178360790	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178360790T>C	uc003iuu.1	-	3	396	c.334A>G	c.(334-336)ATT>GTT	p.I112V	AGA_uc003iuv.1_Missense_Mutation_p.I16V|AGA_uc003iuw.2_Missense_Mutation_p.I16V	NM_000027	NP_000018	P20933	ASPG_HUMAN	aspartylglucosaminidase precursor	112					asparagine catabolic process via L-aspartate|protein deglycosylation|protein maturation	endoplasmic reticulum|intermediate filament cytoskeleton|lysosome|microtubule cytoskeleton	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)		GCCACACCAATAGCATTTTTA	0.368													83	546	---	---	---	---	PASS
FAM173B	134145	broad.mit.edu	37	5	10239279	10239279	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10239279G>A	uc003jeo.2	-	2	235	c.206C>T	c.(205-207)CCG>CTG	p.P69L	FAM173B_uc003jep.2_RNA|FAM173B_uc010itr.2_Missense_Mutation_p.P69L	NM_199133	NP_954584	Q6P4H8	F173B_HUMAN	hypothetical protein LOC134145	69						integral to membrane				kidney(1)|central_nervous_system(1)	2						AGGTACAAACGGCAAACAGAC	0.527													71	189	---	---	---	---	PASS
MARCH6	10299	broad.mit.edu	37	5	10402650	10402650	+	Silent	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10402650T>C	uc003jet.1	+	14	1311	c.1128T>C	c.(1126-1128)TCT>TCC	p.S376S	MARCH6_uc011cmu.1_Silent_p.S328S|MARCH6_uc003jeu.1_Silent_p.S74S|MARCH6_uc011cmv.1_Silent_p.S271S	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6	376	Cytoplasmic (Potential).				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						TTAAGGTCTCTTTGTTAGTGG	0.338													18	524	---	---	---	---	PASS
SPEF2	79925	broad.mit.edu	37	5	35700863	35700863	+	Intron	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35700863G>A	uc003jjo.2	+						SPEF2_uc003jjq.3_Intron|SPEF2_uc003jjp.1_Intron	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AGGTAAGCTGGACACCTTTTT	0.318													12	94	---	---	---	---	PASS
H2AFY	9555	broad.mit.edu	37	5	134724756	134724756	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134724756A>G	uc003lam.1	-	2	238	c.28T>C	c.(28-30)TCC>CCC	p.S10P	H2AFY_uc003lao.1_Missense_Mutation_p.S10P|H2AFY_uc003lan.1_Missense_Mutation_p.S10P|H2AFY_uc003lap.1_RNA|H2AFY_uc003laq.1_RNA|H2AFY_uc003lar.1_RNA|H2AFY_uc011cxz.1_Missense_Mutation_p.S10P|H2AFY_uc003las.1_Missense_Mutation_p.S10P|H2AFY_uc003lat.1_Missense_Mutation_p.S10P	NM_138610	NP_613258	O75367	H2AY_HUMAN	H2A histone family, member Y isoform 3	10	Histone H2A.				chromatin modification|dosage compensation|nucleosome assembly	Barr body|nucleosome	DNA binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GTCTTGGTGGACTTCTTCTTC	0.612													7	59	---	---	---	---	PASS
PSD2	84249	broad.mit.edu	37	5	139216470	139216470	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139216470C>T	uc003leu.1	+	10	1683	c.1478C>T	c.(1477-1479)ACG>ATG	p.T493M		NM_032289	NP_115665	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	493					regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGAAGGTGACGCGAATCCTG	0.587													9	291	---	---	---	---	PASS
PCDHB1	29930	broad.mit.edu	37	5	140433228	140433228	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140433228A>G	uc003lik.1	+	1	2250	c.2173A>G	c.(2173-2175)ACA>GCA	p.T725A		NM_013340	NP_037472	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1 precursor	725	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGAAAAGTTCACAATTCAAGA	0.373													40	148	---	---	---	---	PASS
SLC36A2	153201	broad.mit.edu	37	5	150715081	150715081	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150715081T>A	uc003lty.2	-	6	683	c.553A>T	c.(553-555)AAC>TAC	p.N185Y	GM2A_uc011dcs.1_Intron|SLC36A2_uc003ltz.2_RNA|SLC36A2_uc003lua.2_5'UTR|SLC36A2_uc010jhv.2_Missense_Mutation_p.N185Y	NM_181776	NP_861441	Q495M3	S36A2_HUMAN	solute carrier family 36, member 2	185	Extracellular (Potential).				cellular nitrogen compound metabolic process	cytoplasm|integral to membrane|plasma membrane	glycine transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TAGCAGTTGTTGGTTGTGCTA	0.517													33	141	---	---	---	---	PASS
RNF130	55819	broad.mit.edu	37	5	179440314	179440314	+	Intron	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179440314G>A	uc003mll.1	-						RNF130_uc003mlm.1_Intron	NM_018434	NP_060904	Q86XS8	GOLI_HUMAN	ring finger protein 130 precursor						apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding			lung(2)|ovary(1)	3	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCCAGTGCCTGCAATATAAAA	0.313													11	62	---	---	---	---	PASS
KIAA0319	9856	broad.mit.edu	37	6	24569156	24569156	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24569156C>A	uc011djo.1	-	13	2230	c.1993G>T	c.(1993-1995)GGC>TGC	p.G665C	KIAA0319_uc011djp.1_Missense_Mutation_p.G620C|KIAA0319_uc003neh.1_Missense_Mutation_p.G665C|KIAA0319_uc011djq.1_Missense_Mutation_p.G656C|KIAA0319_uc011djr.1_Missense_Mutation_p.G665C|KIAA0319_uc010jpt.1_Missense_Mutation_p.G76C	NM_014809	NP_055624	Q5VV43	K0319_HUMAN	KIAA0319 precursor	665	PKD 4.|Extracellular (Potential).				negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2						GCACTGGGGCCTCTATAAAAC	0.453													18	64	---	---	---	---	PASS
SCUBE3	222663	broad.mit.edu	37	6	35209433	35209433	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35209433C>T	uc003okf.1	+	11	1315	c.1309C>T	c.(1309-1311)CCA>TCA	p.P437S	SCUBE3_uc003okg.1_Missense_Mutation_p.P436S|SCUBE3_uc003okh.1_Missense_Mutation_p.P324S	NM_152753	NP_689966	Q8IX30	SCUB3_HUMAN	signal peptide, CUB domain, EGF-like 3	437					protein heterooligomerization|protein homooligomerization	cell surface|extracellular region	calcium ion binding|protein binding			skin(1)	1						CCGATTTTTGCCAGGTACATG	0.602											OREG0017372	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	185	---	---	---	---	PASS
PI16	221476	broad.mit.edu	37	6	36930839	36930839	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36930839C>T	uc003ona.2	+	5	1049	c.721C>T	c.(721-723)CCG>TCG	p.P241S	PI16_uc003omz.1_Intron|PI16_uc003onb.2_Intron|PI16_uc011dts.1_Missense_Mutation_p.P12S	NM_153370	NP_699201	Q6UXB8	PI16_HUMAN	protease inhibitor 16 precursor	241	Extracellular (Potential).					extracellular region|integral to membrane	peptidase inhibitor activity				0						AACGGGGATTCCGGCTTTCTT	0.562													8	297	---	---	---	---	PASS
PPP2R5D	5528	broad.mit.edu	37	6	42976217	42976217	+	Intron	SNP	A	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42976217A>G	uc003oth.2	+						MEA1_uc010jyc.1_Intron|PPP2R5D_uc003otg.2_Intron|PPP2R5D_uc010jyd.2_Intron|PPP2R5D_uc011dva.1_Intron|PPP2R5D_uc003oti.2_Intron|PPP2R5D_uc003otj.2_Intron	NM_006245	NP_006236	Q14738	2A5D_HUMAN	delta isoform of regulatory subunit B56, protein						nervous system development|signal transduction	cytoplasm|nucleus|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			breast(1)|central_nervous_system(1)	2			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CCCTCAGGTGAGCTGCCTTCC	0.537													10	171	---	---	---	---	PASS
MCHR2	84539	broad.mit.edu	37	6	100369022	100369022	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100369022C>A	uc003pqh.1	-	6	1132	c.817G>T	c.(817-819)GTG>TTG	p.V273L	MCHR2_uc003pqi.1_Missense_Mutation_p.V273L	NM_001040179	NP_001035269	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	273	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	8		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		TGTAAGTTCACCAGTTGTATC	0.468													36	151	---	---	---	---	PASS
ASCC3	10973	broad.mit.edu	37	6	100957342	100957342	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100957342G>C	uc003pqk.2	-	42	6858	c.6529C>G	c.(6529-6531)CTC>GTC	p.L2177V		NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	2177	SEC63 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GTAACGTTGAGATAGATGTCA	0.388													5	304	---	---	---	---	PASS
HACE1	57531	broad.mit.edu	37	6	105177550	105177550	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105177550T>C	uc003pqu.1	-	24	2994	c.2717A>G	c.(2716-2718)TAC>TGC	p.Y906C	HACE1_uc010kcy.1_Missense_Mutation_p.Y388C|HACE1_uc010kcz.1_Missense_Mutation_p.Y691C|HACE1_uc010kcx.1_Missense_Mutation_p.Y315C|HACE1_uc003pqt.1_Missense_Mutation_p.Y559C	NM_020771	NP_065822	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing, E3	906	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	endoplasmic reticulum	ubiquitin-protein ligase activity			ovary(5)|lung(2)	7		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		TGCCATTGTGTAACCATAGCT	0.388													10	66	---	---	---	---	PASS
SAMD3	154075	broad.mit.edu	37	6	130475977	130475977	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130475977G>A	uc003qbv.2	-	10	1342	c.1016C>T	c.(1015-1017)CCT>CTT	p.P339L	SAMD3_uc003qbx.2_Missense_Mutation_p.P339L|SAMD3_uc003qbw.2_Missense_Mutation_p.P339L	NM_001017373	NP_001017373	Q8N6K7	SAMD3_HUMAN	sterile alpha motif domain containing 3 isoform	339										ovary(1)	1				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)		TACCTGATAAGGGCACTTCAA	0.234													13	76	---	---	---	---	PASS
VNN2	8875	broad.mit.edu	37	6	133077133	133077133	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133077133G>T	uc003qdt.2	-	3	397	c.386C>A	c.(385-387)GCC>GAC	p.A129D	VNN2_uc003qds.2_5'UTR|VNN2_uc010kgb.2_Missense_Mutation_p.A129D|VNN2_uc003qdv.2_Missense_Mutation_p.A76D	NM_004665	NP_004656	O95498	VNN2_HUMAN	vanin 2 isoform 1 precursor	129	CN hydrolase.				cellular component movement|pantothenate metabolic process	anchored to membrane|plasma membrane	pantetheine hydrolase activity				0				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		GTTGTCCTTGGCCAGGCAGCT	0.348													17	48	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152738071	152738071	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152738071C>A	uc010kiw.2	-	41	6103	c.5501G>T	c.(5500-5502)GGC>GTC	p.G1834V	SYNE1_uc003qot.3_Missense_Mutation_p.G1841V|SYNE1_uc003qou.3_Missense_Mutation_p.G1834V|SYNE1_uc010kjb.1_Missense_Mutation_p.G1817V	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1834	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)		CTCAGCACGGCCCAGAGAACC	0.577										HNSCC(10;0.0054)			9	281	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152841636	152841636	+	Silent	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152841636C>A	uc010kiw.2	-	6	869	c.267G>T	c.(265-267)GTG>GTT	p.V89V	SYNE1_uc003qot.3_Silent_p.V89V|SYNE1_uc003qou.3_Silent_p.V89V|SYNE1_uc010kjb.1_Silent_p.V89V|SYNE1_uc003qpa.1_Silent_p.V89V	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	89	Actin-binding.|Cytoplasmic (Potential).|CH 1.				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)		CAATGTTAGCCACAGCATGGA	0.418										HNSCC(10;0.0054)			51	254	---	---	---	---	PASS
PRKAR1B	5575	broad.mit.edu	37	7	720268	720268	+	Silent	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:720268C>A	uc003siu.1	-	4	379	c.273G>T	c.(271-273)GTG>GTT	p.V91V	PRKAR1B_uc003siv.2_Silent_p.V91V|PRKAR1B_uc003siw.1_Silent_p.V91V	NM_002735	NP_002726	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type	91	Dimerization and phosphorylation.				activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		GGCGGGCCTTCACCACAGGGT	0.632													16	51	---	---	---	---	PASS
MRPL32	64983	broad.mit.edu	37	7	42972022	42972022	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42972022T>A	uc003tia.2	+	1	84	c.37T>A	c.(37-39)TGG>AGG	p.W13R	C7orf25_uc010kxr.2_5'Flank|PSMA2_uc003thy.2_5'Flank|PSMA2_uc010kxt.2_5'Flank|PSMA2_uc003thz.1_5'Flank|MRPL32_uc003tib.2_RNA|MRPL32_uc003tic.2_5'UTR	NM_031903	NP_114109	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32 precursor	13				SPWSAARGVLRNYWERLLRKLPQSRPGFPSPPW -> RRGL RPGECFETTGSDCYGSFRRAGRAFPVLRGV (in Ref. 3).	translation	large ribosomal subunit|mitochondrial ribosome	structural constituent of ribosome				0						GGTTTCGCCGTGGTCTGCGGC	0.647													4	108	---	---	---	---	PASS
ZNF107	51427	broad.mit.edu	37	7	64167834	64167834	+	Nonsense_Mutation	SNP	T	G	G	rs142998629		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64167834T>G	uc003ttd.2	+	7	1938	c.1152T>G	c.(1150-1152)TAT>TAG	p.Y384*	ZNF107_uc003tte.2_Nonsense_Mutation_p.Y384*	NM_016220	NP_057304	Q9UII5	ZN107_HUMAN	zinc finger protein 107	384	C2H2-type 12; atypical.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.00948)|all_lung(88;0.0249)				AGAAATCCTATAAATGTGAAG	0.338													11	75	---	---	---	---	PASS
CTTNBP2	83992	broad.mit.edu	37	7	117417585	117417585	+	Missense_Mutation	SNP	C	A	A	rs147958874	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117417585C>A	uc003vjf.2	-	8	2850	c.2758G>T	c.(2758-2760)GCT>TCT	p.A920S		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	920	ANK 6.									ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TTGGAAGCAGCAATGTGGGCA	0.493													17	107	---	---	---	---	PASS
TBXAS1	6916	broad.mit.edu	37	7	139661861	139661861	+	Silent	SNP	T	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139661861T>G	uc011kqv.1	+	10	1268	c.1104T>G	c.(1102-1104)CCT>CCG	p.P368P	TBXAS1_uc003vvh.2_Silent_p.P322P|TBXAS1_uc010lne.2_Silent_p.P254P|TBXAS1_uc011kqu.1_Silent_p.P273P|TBXAS1_uc003vvi.2_Silent_p.P322P|TBXAS1_uc003vvj.2_Silent_p.P322P|TBXAS1_uc011kqw.1_Silent_p.P302P	NM_001130966	NP_001124438	P24557	THAS_HUMAN	thromboxane A synthase 1, platelet isoform	321	Lumenal (Potential).				hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)					AGCCCAGCCCTATGGCCAGGC	0.542													13	56	---	---	---	---	PASS
NOBOX	135935	broad.mit.edu	37	7	144098541	144098541	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144098541C>T	uc011kue.1	-	4	442	c.442G>A	c.(442-444)GGA>AGA	p.G148R		NM_001080413	NP_001073882	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	148					cell differentiation|oogenesis	nucleus	sequence-specific DNA binding			ovary(1)	1	Melanoma(164;0.14)					GTGGCTTCTCCAGAGACTGCT	0.647													4	23	---	---	---	---	PASS
CNTNAP2	26047	broad.mit.edu	37	7	147183133	147183133	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147183133T>A	uc003weu.1	+	11	2293	c.1777T>A	c.(1777-1779)TCT>ACT	p.S593T		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	593	Extracellular (Potential).|Fibrinogen C-terminal.				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CTGCCACAACTGTGAGTGCCA	0.448										HNSCC(39;0.1)			5	59	---	---	---	---	PASS
EZH2	2146	broad.mit.edu	37	7	148512021	148512021	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148512021G>C	uc003wfd.1	-	14	1808	c.1642C>G	c.(1642-1644)CAA>GAA	p.Q548E	EZH2_uc011kug.1_Intron|EZH2_uc003wfb.1_Missense_Mutation_p.Q553E|EZH2_uc003wfc.1_Missense_Mutation_p.Q509E|EZH2_uc011kuh.1_Missense_Mutation_p.Q539E	NM_004456	NP_004447	Q15910	EZH2_HUMAN	enhancer of zeste 2 isoform a	548	Cys-rich.				negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|histone-lysine N-methyltransferase activity|protein binding			haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1)	183	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			GAACTACATTGACAAAACTTT	0.353			Mis		DLBCL								6	75	---	---	---	---	PASS
GALNTL5	168391	broad.mit.edu	37	7	151704912	151704912	+	Silent	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151704912G>C	uc003wkp.2	+	7	1132	c.909G>C	c.(907-909)CGG>CGC	p.R303R	GALNTL5_uc003wkq.2_Silent_p.R54R|GALNTL5_uc003wkr.2_RNA|GALNTL5_uc003wks.2_RNA|GALNTL5_uc010lqf.2_Silent_p.R192R	NM_145292	NP_660335	Q7Z4T8	GLTL5_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	303	Catalytic subdomain B.|Lumenal (Potential).					Golgi membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		CCCTTTCTAGGTCACCTGCAA	0.299													37	265	---	---	---	---	PASS
DOCK5	80005	broad.mit.edu	37	8	25250371	25250371	+	Silent	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25250371G>A	uc003xeg.2	+	44	4637	c.4500G>A	c.(4498-4500)AAG>AAA	p.K1500K	PPP2R2A_uc003xek.2_Intron|DOCK5_uc003xei.2_Silent_p.K1070K|DOCK5_uc003xej.2_RNA	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1500	DHR-2.					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		GGATTCTCAAGTGGTTTGAAG	0.378													4	34	---	---	---	---	PASS
SFRP1	6422	broad.mit.edu	37	8	41166547	41166547	+	Silent	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41166547G>T	uc003xnt.2	-	1	434	c.132C>A	c.(130-132)GGC>GGA	p.G44G		NM_003012	NP_003003	Q8N474	SFRP1_HUMAN	secreted frizzled-related protein 1 precursor	44					brain development|canonical Wnt receptor signaling pathway|cellular response to BMP stimulus|cellular response to estradiol stimulus|cellular response to fibroblast growth factor stimulus|cellular response to heparin|cellular response to hypoxia|cellular response to interleukin-1|cellular response to prostaglandin E stimulus|cellular response to starvation|cellular response to transforming growth factor beta stimulus|cellular response to tumor necrosis factor|cellular response to vitamin D|DNA fragmentation involved in apoptotic nuclear change|dorsal/ventral axis specification|hemopoietic progenitor cell differentiation|hemopoietic stem cell differentiation|menstrual cycle phase|negative regulation of androgen receptor signaling pathway|negative regulation of B cell differentiation|negative regulation of bone remodeling|negative regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cysteine-type endopeptidase activity|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast apoptosis|negative regulation of fibroblast proliferation|negative regulation of insulin secretion|negative regulation of ossification|negative regulation of osteoblast proliferation|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|osteoblast differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell growth|positive regulation of epithelial cell proliferation|positive regulation of fat cell differentiation|positive regulation of fibroblast apoptosis|positive regulation of focal adhesion assembly|positive regulation of non-canonical Wnt receptor signaling pathway|positive regulation of Rac GTPase activity|positive regulation of smoothened signaling pathway|positive regulation of stress fiber assembly|positive regulation of transcription, DNA-dependent|regulation of angiogenesis|regulation of cell cycle process|response to drug|response to organic cyclic compound|vasculature development	cell surface|cytosol|extracellular space|plasma membrane|proteinaceous extracellular matrix	cysteine-type endopeptidase activity|drug binding|frizzled binding|heparin binding|identical protein binding|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)	1	Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211)	all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559)	BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174)			TCTGGTACGGGCCGATGTCCG	0.687													6	37	---	---	---	---	PASS
SNAI2	6591	broad.mit.edu	37	8	49832867	49832867	+	Silent	SNP	A	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49832867A>G	uc003xqp.2	-	2	377	c.213T>C	c.(211-213)AAT>AAC	p.N71N		NM_003068	NP_003059	O43623	SNAI2_HUMAN	snail 2	71					canonical Wnt receptor signaling pathway|ectoderm and mesoderm interaction|multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		all_cancers(86;0.0368)|all_epithelial(80;0.000624)|Lung NSC(129;0.0019)|all_lung(136;0.00502)				GAGAGAGGCCATTGGGTAGCT	0.577													57	230	---	---	---	---	PASS
CA8	767	broad.mit.edu	37	8	61135250	61135250	+	Silent	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61135250G>T	uc003xtz.1	-	7	944	c.696C>A	c.(694-696)ACC>ACA	p.T232T	CA8_uc003xua.1_Silent_p.T232T	NM_004056	NP_004047	P35219	CAH8_HUMAN	carbonic anhydrase VIII	232					one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)				ATAATATCCAGGTGACACCTT	0.458													5	86	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77767540	77767540	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77767540C>A	uc003yav.2	+	10	8635	c.8248C>A	c.(8248-8250)CAA>AAA	p.Q2750K	ZFHX4_uc003yau.1_Missense_Mutation_p.Q2795K|ZFHX4_uc003yaw.1_Missense_Mutation_p.Q2750K	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2750						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)			TGGGTATGATCAAAATAAAAC	0.448										HNSCC(33;0.089)			16	67	---	---	---	---	PASS
LYPD2	137797	broad.mit.edu	37	8	143831824	143831824	+	Silent	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143831824G>T	uc003ywz.2	-	3	338	c.255C>A	c.(253-255)ATC>ATA	p.I85I		NM_205545	NP_991108	Q6UXB3	LYPD2_HUMAN	LY6/PLAUR domain containing 2 precursor	85	UPAR/Ly6.					anchored to membrane|plasma membrane					0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GGGTCTGGCCGATGCCATCCA	0.637													3	9	---	---	---	---	PASS
CDKN2A	1029	broad.mit.edu	37	9	21970901	21970901	+	Missense_Mutation	SNP	C	T	T	rs45476696		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21970901C>T	uc003zpk.2	-	2	669	c.457G>A	c.(457-459)GAC>AAC	p.D153N	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_3'UTR	NM_000077	NP_000068	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 1	153					cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(1112)|p.?(16)|p.D153Y(1)		haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3678		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CAGTCCTCACCTGAGGGACCT	0.597		17							Uveal_Melanoma_Familial|Familial_Malignant_Melanoma_and_Tumors_of_the_Nervous_System|Hereditary_Melanoma	HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)			14	56	---	---	---	---	PASS
DMRTA1	63951	broad.mit.edu	37	9	22451294	22451294	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22451294T>C	uc003zpp.1	+	2	1124	c.899T>C	c.(898-900)CTG>CCG	p.L300P		NM_022160	NP_071443	Q5VZB9	DMRTA_HUMAN	DMRT-like family A1	300					cell differentiation|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|skin(1)	2		all_cancers(5;4.09e-243)|Acute lymphoblastic leukemia(3;8.25e-150)|all_hematologic(3;4.25e-147)|Esophageal squamous(3;2.32e-09)|Renal(3;1.71e-07)|Breast(3;2.07e-06)|Hepatocellular(5;0.00563)		GBM - Glioblastoma multiforme(1;5.12e-278)|Lung(24;8.2e-52)|LUSC - Lung squamous cell carcinoma(38;1.46e-37)|OV - Ovarian serous cystadenocarcinoma(39;0.0517)		TCCTCTGATCTGGAATCAGGA	0.468													11	50	---	---	---	---	PASS
DDX58	23586	broad.mit.edu	37	9	32488093	32488093	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32488093G>T	uc003zra.2	-	8	1220	c.1062C>A	c.(1060-1062)AAC>AAA	p.N354K	DDX58_uc010mjj.2_RNA|DDX58_uc010mjk.1_Missense_Mutation_p.N309K|DDX58_uc011lnr.1_Missense_Mutation_p.N151K|DDX58_uc010mji.2_Missense_Mutation_p.N283K	NM_014314	NP_055129	O95786	DDX58_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide	354	Helicase ATP-binding.				detection of virus|innate immune response|negative regulation of type I interferon production|positive regulation of defense response to virus by host|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	cytosol	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|protein binding|zinc ion binding			ovary(2)|liver(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		CCTTTTTAAGGTTGTTCACAA	0.378													48	149	---	---	---	---	PASS
OR1L4	254973	broad.mit.edu	37	9	125487119	125487119	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125487119C>A	uc004bmu.1	+	1	851	c.851C>A	c.(850-852)CCC>CAC	p.P284H		NM_001005235	NP_001005235	Q8NGR5	OR1L4_HUMAN	olfactory receptor, family 1, subfamily L,	284	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						GTAGTGACACCCATGCTGAAC	0.413													17	67	---	---	---	---	PASS
OR1L4	254973	broad.mit.edu	37	9	125487120	125487120	+	Silent	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125487120C>A	uc004bmu.1	+	1	852	c.852C>A	c.(850-852)CCC>CCA	p.P284P		NM_001005235	NP_001005235	Q8NGR5	OR1L4_HUMAN	olfactory receptor, family 1, subfamily L,	284	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						TAGTGACACCCATGCTGAACC	0.413													16	68	---	---	---	---	PASS
DENND1A	57706	broad.mit.edu	37	9	126144596	126144596	+	Silent	SNP	T	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126144596T>G	uc004bnz.1	-	22	2378	c.2145A>C	c.(2143-2145)CCA>CCC	p.P715P	DENND1A_uc011lzl.1_Silent_p.P533P|DENND1A_uc004bny.1_Silent_p.P497P|DENND1A_uc011lzm.1_Silent_p.P726P|DENND1A_uc010mwh.1_Silent_p.P136P	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1	715	Pro-rich.					cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						GAATGGGCGGTGGAGGCACGA	0.692													4	25	---	---	---	---	PASS
SOHLH1	402381	broad.mit.edu	37	9	138586250	138586250	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138586250C>G	uc004cgl.2	-	7	990	c.929G>C	c.(928-930)GGT>GCT	p.G310A	SOHLH1_uc010nbe.2_Missense_Mutation_p.G310A	NM_001012415	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic	310					cell differentiation|multicellular organismal development|oogenesis|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			breast(1)|central_nervous_system(1)	2		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		CGAGCTGGGACCAGCAGTCAG	0.637													14	54	---	---	---	---	PASS
ENTPD2	954	broad.mit.edu	37	9	139945972	139945972	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139945972G>A	uc004ckw.1	-	3	432	c.376C>T	c.(376-378)CGC>TGC	p.R126C	ENTPD2_uc004ckv.1_5'Flank|ENTPD2_uc004ckx.1_Missense_Mutation_p.R126C	NM_203468	NP_982293	Q9Y5L3	ENTP2_HUMAN	ectonucleoside triphosphate diphosphohydrolase 2	126	Extracellular (Potential).					integral to membrane	ATP binding				0	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		TTGAGCAGGCGCATACCCGCT	0.637													5	95	---	---	---	---	PASS
DCLRE1C	64421	broad.mit.edu	37	10	14974877	14974877	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14974877C>G	uc001inn.2	-	9	841	c.756G>C	c.(754-756)CAG>CAC	p.Q252H	DCLRE1C_uc010qbx.1_Missense_Mutation_p.Q252H|DCLRE1C_uc001inl.2_Missense_Mutation_p.Q132H|DCLRE1C_uc009xji.2_Missense_Mutation_p.Q137H|DCLRE1C_uc001inm.2_Missense_Mutation_p.Q132H|DCLRE1C_uc001ino.2_Missense_Mutation_p.Q137H|DCLRE1C_uc009xjh.2_RNA|DCLRE1C_uc001inp.2_Missense_Mutation_p.Q132H|DCLRE1C_uc001inq.2_Missense_Mutation_p.Q132H|DCLRE1C_uc001inr.2_Missense_Mutation_p.Q137H|DCLRE1C_uc009xjj.1_RNA	NM_001033855	NP_001029027	Q96SD1	DCR1C_HUMAN	artemis protein isoform a	252					DNA recombination	nucleus	5'-3' exonuclease activity|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)	1						ATGCATGGATCTGAGTGTTGC	0.418								Involved_in_tolerance_or_repair_of_DNA_crosslinks|NHEJ					55	220	---	---	---	---	PASS
ANKRD30A	91074	broad.mit.edu	37	10	37425591	37425591	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37425591C>A	uc001iza.1	+	6	743	c.644C>A	c.(643-645)ACC>AAC	p.T215N		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	271	ANK 6.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						CATCAAAATACCAATCCAGGT	0.284													3	5	---	---	---	---	PASS
ANKRD30A	91074	broad.mit.edu	37	10	37440998	37440998	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37440998C>G	uc001iza.1	+	12	1587	c.1488C>G	c.(1486-1488)TTC>TTG	p.F496L		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	552						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						ATCCGATGTTCCCACCAGAAT	0.284													6	31	---	---	---	---	PASS
CRTAC1	55118	broad.mit.edu	37	10	99661269	99661269	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99661269C>A	uc001kou.1	-	8	1480	c.1124G>T	c.(1123-1125)CGC>CTC	p.R375L	CRTAC1_uc001kov.2_Missense_Mutation_p.R364L|CRTAC1_uc001kot.1_Missense_Mutation_p.R165L	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor	375						proteinaceous extracellular matrix	calcium ion binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		CCGGAAGAGGCGGTTGGCTGA	0.572													14	36	---	---	---	---	PASS
EIF3A	8661	broad.mit.edu	37	10	120795713	120795713	+	Silent	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120795713T>A	uc001ldu.2	-	22	4133	c.3987A>T	c.(3985-3987)CGA>CGT	p.R1329R	EIF3A_uc010qsu.1_Silent_p.R1295R	NM_003750	NP_003741	Q14152	EIF3A_HUMAN	eukaryotic translation initiation factor 3,	1329					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)		GGGGAGGAACTCGACGAGGAG	0.458													31	115	---	---	---	---	PASS
KCNQ1	3784	broad.mit.edu	37	11	2604765	2604765	+	Missense_Mutation	SNP	C	T	T	rs12720459		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2604765C>T	uc001lwn.2	+	7	1130	c.1022C>T	c.(1021-1023)GCG>GTG	p.A341V	KCNQ1_uc009ydp.1_Missense_Mutation_p.A125V|KCNQ1_uc001lwo.2_Missense_Mutation_p.A214V	NM_000218	NP_000209	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like	341	Helical; Name=Segment S6; (Potential).		A -> V (in LQT1).		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)	TCCTTCTTTGCGCTCCCAGCG	0.637													5	233	---	---	---	---	PASS
OR52H1	390067	broad.mit.edu	37	11	5566079	5566079	+	Silent	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5566079G>C	uc010qzh.1	-	1	675	c.675C>G	c.(673-675)TCC>TCG	p.S225S	HBG2_uc001mak.1_Intron	NM_001005289	NP_001005289	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H,	225	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTGTGCGTAGGAAACAGCAA	0.507													18	81	---	---	---	---	PASS
OR56A3	390083	broad.mit.edu	37	11	5969275	5969275	+	Silent	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5969275G>A	uc010qzt.1	+	1	699	c.699G>A	c.(697-699)AAG>AAA	p.K233K		NM_001003443	NP_001003443	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A,	233	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGAGACTCAAGGCAGAGGGTG	0.517													37	331	---	---	---	---	PASS
ABCC8	6833	broad.mit.edu	37	11	17435029	17435029	+	Intron	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17435029G>T	uc001mnc.2	-							NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8						carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)	CTTGTACCTGGCGTGGGTAGA	0.587													39	260	---	---	---	---	PASS
USH1C	10083	broad.mit.edu	37	11	17517143	17517143	+	Intron	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17517143G>T	uc001mnf.2	-						USH1C_uc001mne.2_Missense_Mutation_p.H876Q|USH1C_uc009yhb.2_Intron|USH1C_uc001mng.2_Intron|USH1C_uc001mnd.2_Intron	NM_005709	NP_005700	Q9Y6N9	USH1C_HUMAN	harmonin isoform a						equilibrioception|G2/M transition of mitotic cell cycle|photoreceptor cell maintenance|sensory perception of sound	apical part of cell|cytoplasm|stereocilium	protein binding			ovary(1)	1						GGAGGAACCCGTGTCTGTGCA	0.612													40	288	---	---	---	---	PASS
KCNA4	3739	broad.mit.edu	37	11	30033616	30033616	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30033616C>G	uc001msk.2	-	2	1762	c.610G>C	c.(610-612)GAC>CAC	p.D204H		NM_002233	NP_002224	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related	204						voltage-gated potassium channel complex	potassium ion binding|protein binding|voltage-gated potassium channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						TTTTCAGGGTCTCCCAACAAA	0.448													20	135	---	---	---	---	PASS
OR5D18	219438	broad.mit.edu	37	11	55587239	55587239	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55587239G>T	uc010rin.1	+	1	134	c.134G>T	c.(133-135)GGG>GTG	p.G45V		NM_001001952	NP_001001952	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D,	45	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.208)				GGGAATATTGGGTTGATTGTG	0.453													64	283	---	---	---	---	PASS
OR5I1	10798	broad.mit.edu	37	11	55703110	55703110	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55703110G>C	uc010ris.1	-	1	767	c.767C>G	c.(766-768)ACT>AGT	p.T256S		NM_006637	NP_006628	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I,	256	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						AAAGAGGAGAGTCCCTTGGTA	0.443													5	20	---	---	---	---	PASS
SF3B2	10992	broad.mit.edu	37	11	65835483	65835483	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65835483G>T	uc001ogy.1	+	20	2437	c.2397G>T	c.(2395-2397)ATG>ATT	p.M799I	PACS1_uc001ogz.1_5'Flank|PACS1_uc001oha.1_5'Flank	NM_006842	NP_006833	Q13435	SF3B2_HUMAN	splicing factor 3B subunit 2	799					interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(2)|breast(1)	3						GAGGGGCCATGATGGGATCAA	0.512											OREG0021094	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	38	188	---	---	---	---	PASS
MYEOV	26579	broad.mit.edu	37	11	69062870	69062870	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69062870C>G	uc001oov.2	+	2	499	c.49C>G	c.(49-51)CTC>GTC	p.L17V	MYEOV_uc001oox.2_Intron|MYEOV_uc009ysl.2_Missense_Mutation_p.L17V|MYEOV_uc001oow.2_5'UTR	NM_138768	NP_620123	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	17											0	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)		cccgataggtctctgcactcg	0.154													199	109	---	---	---	---	PASS
PATE1	160065	broad.mit.edu	37	11	125618609	125618609	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125618609T>A	uc001qct.2	+	5	374	c.362T>A	c.(361-363)CTG>CAG	p.L121Q	PATE1_uc009zbr.2_Missense_Mutation_p.L109Q	NM_138294	NP_612151	Q8WXA2	PATE1_HUMAN	expressed in prostate and testis precursor	121						extracellular region					0						AGCCATGACCTGTGCAATGAA	0.438													39	141	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2774140	2774140	+	Missense_Mutation	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2774140T>A	uc009zdu.1	+	37	4839	c.4526T>A	c.(4525-4527)ATG>AAG	p.M1509K	CACNA1C_uc009zdv.1_Missense_Mutation_p.M1458K|CACNA1C_uc001qkb.2_Missense_Mutation_p.M1461K|CACNA1C_uc001qkc.2_Missense_Mutation_p.M1461K|CACNA1C_uc001qke.2_Missense_Mutation_p.M1450K|CACNA1C_uc001qkf.2_Missense_Mutation_p.M1450K|CACNA1C_uc001qjz.2_Missense_Mutation_p.M1461K|CACNA1C_uc001qkd.2_Missense_Mutation_p.M1461K|CACNA1C_uc001qkg.2_Missense_Mutation_p.M1448K|CACNA1C_uc009zdw.1_Missense_Mutation_p.M1483K|CACNA1C_uc001qkh.2_Missense_Mutation_p.M1450K|CACNA1C_uc001qkl.2_Missense_Mutation_p.M1509K|CACNA1C_uc001qkn.2_Missense_Mutation_p.M1461K|CACNA1C_uc001qko.2_Missense_Mutation_p.M1481K|CACNA1C_uc001qkp.2_Missense_Mutation_p.M1461K|CACNA1C_uc001qkr.2_Missense_Mutation_p.M1478K|CACNA1C_uc001qku.2_Missense_Mutation_p.M1461K|CACNA1C_uc001qkq.2_Missense_Mutation_p.M1489K|CACNA1C_uc001qks.2_Missense_Mutation_p.M1461K|CACNA1C_uc001qkt.2_Missense_Mutation_p.M1461K|CACNA1C_uc001qki.1_Missense_Mutation_p.M1197K|CACNA1C_uc001qkj.1_Missense_Mutation_p.M1197K|CACNA1C_uc001qkk.1_Missense_Mutation_p.M1197K|CACNA1C_uc001qkm.1_Missense_Mutation_p.M1186K|CACNA1C_uc010sea.1_Missense_Mutation_p.M152K	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	1509	Phenylalkylamine binding (By similarity).|Dihydropyridine binding (By similarity).|Helical; Name=S6 of repeat IV; (Potential).|IV.				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	AGCTTCTACATGCTCTGTGCC	0.567													5	60	---	---	---	---	PASS
PHB2	11331	broad.mit.edu	37	12	7074847	7074847	+	3'UTR	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7074847C>T	uc001qsd.2	-	10					PHB2_uc001qse.1_RNA|PHB2_uc001qsf.1_RNA|PHB2_uc009zfn.1_RNA	NM_001144831	NP_001138303	Q99623	PHB2_HUMAN	prohibitin 2 isoform 1						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial inner membrane|nucleus	estrogen receptor binding|receptor activity			ovary(2)|pancreas(1)	3						GGTGACTAGGCTCATTTCTTA	0.502											OREG0021644	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	58	---	---	---	---	PASS
CLEC6A	93978	broad.mit.edu	37	12	8610514	8610514	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8610514C>A	uc001qum.1	+	2	169	c.52C>A	c.(52-54)CTG>ATG	p.L18M		NM_001007033	NP_001007034	Q6EIG7	CLC6A_HUMAN	dectin-2	18	Cytoplasmic (Potential).				defense response to fungus|innate immune response|positive regulation of cytokine secretion|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	sugar binding			breast(1)	1	Lung SC(5;0.184)					CTGGTTGTCCCTGAGACTCTG	0.493													8	57	---	---	---	---	PASS
RIMKLB	57494	broad.mit.edu	37	12	8926333	8926333	+	Missense_Mutation	SNP	A	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8926333A>C	uc001quu.2	+	6	1365	c.1114A>C	c.(1114-1116)AAC>CAC	p.N372H	RIMKLB_uc009zgf.1_Intron|RIMKLB_uc001qux.2_Missense_Mutation_p.N372H|RIMKLB_uc010sgl.1_Missense_Mutation_p.N372H|RIMKLB_uc001quw.2_Intron	NM_020734	NP_065785	Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family	372					protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0						GGGCCTGTTCAACATGAACCA	0.483													25	104	---	---	---	---	PASS
SOX5	6660	broad.mit.edu	37	12	23696294	23696294	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23696294C>G	uc001rfw.2	-	13	1724	c.1622G>C	c.(1621-1623)AGA>ACA	p.R541T	SOX5_uc001rfx.2_Missense_Mutation_p.R528T|SOX5_uc001rfy.2_Missense_Mutation_p.R420T|SOX5_uc001rfv.2_Missense_Mutation_p.R155T|SOX5_uc010siv.1_Missense_Mutation_p.R528T|SOX5_uc010siw.1_RNA|SOX5_uc001rfz.1_Missense_Mutation_p.R493T	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a	541					transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						CCTATAAATTCTTGACTCTGA	0.438													8	232	---	---	---	---	PASS
BCDIN3D	144233	broad.mit.edu	37	12	50236666	50236666	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50236666G>C	uc001rvh.2	-	1	247	c.205C>G	c.(205-207)CTG>GTG	p.L69V		NM_181708	NP_859059	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	69	Bin3-type SAM.						methyltransferase activity			ovary(1)	1						TCGAGCCCCAGAATCGGCCCG	0.617													12	239	---	---	---	---	PASS
OS9	10956	broad.mit.edu	37	12	58114586	58114586	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58114586C>T	uc001spj.2	+	15	1957	c.1898C>T	c.(1897-1899)GCC>GTC	p.A633V	OS9_uc010srx.1_Missense_Mutation_p.A372V|OS9_uc001spk.2_Missense_Mutation_p.A618V|OS9_uc001spl.2_Missense_Mutation_p.A578V|OS9_uc001spm.2_Missense_Mutation_p.A563V|OS9_uc001spn.2_Missense_Mutation_p.A579V|OS9_uc010sry.1_Missense_Mutation_p.A546V|OS9_uc010srz.1_Missense_Mutation_p.A504V	NM_006812	NP_006803	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum	633					ER-associated protein catabolic process|protein retention in ER lumen|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to endoplasmic reticulum stress	endoplasmic reticulum lumen|Hrd1p ubiquitin ligase complex	glycoprotein binding|protein binding|sugar binding			ovary(1)	1	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			GCTGAAGAGGCCCAGAAGGAA	0.657													21	70	---	---	---	---	PASS
TMTC3	160418	broad.mit.edu	37	12	88586608	88586608	+	Splice_Site	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88586608G>T	uc001tau.2	+	13	2153	c.1933_splice	c.e13+1	p.G645_splice		NM_181783	NP_861448	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat							integral to membrane	binding			skin(1)	1						CAAGAATCAGGTATGTTTTCT	0.279													7	43	---	---	---	---	PASS
NEDD1	121441	broad.mit.edu	37	12	97328810	97328810	+	Silent	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97328810G>T	uc001teu.3	+	7	885	c.546G>T	c.(544-546)TCG>TCT	p.S182S	NEDD1_uc001tev.3_Silent_p.S182S|NEDD1_uc010svc.1_Silent_p.S93S|NEDD1_uc001tew.2_Silent_p.S189S|NEDD1_uc001tex.2_Silent_p.S93S	NM_152905	NP_690869	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally	182	WD 5.				cell division|G2/M transition of mitotic cell cycle|mitosis	cytosol					0						GCAGTGTTTCGGATAATGGAA	0.363													4	319	---	---	---	---	PASS
KIAA0564	23078	broad.mit.edu	37	13	42245198	42245198	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42245198C>T	uc001uyj.2	-	37	4565	c.4495G>A	c.(4495-4497)GTT>ATT	p.V1499I		NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a	1499						extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)		ACAGTAACAACACCGCTTTTG	0.478													55	255	---	---	---	---	PASS
ERCC5	2073	broad.mit.edu	37	13	103513987	103513987	+	Missense_Mutation	SNP	A	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103513987A>G	uc001vpw.2	+	7	1246	c.803A>G	c.(802-804)GAT>GGT	p.D268G	ERCC5_uc001vpu.1_Missense_Mutation_p.D722G|ERCC5_uc010tjb.1_Missense_Mutation_p.D268G|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_Missense_Mutation_p.D100G	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	268					negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CAGTATGAAGATGAAGGGGGC	0.403			Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				43	157	---	---	---	---	PASS
RALGAPA1	253959	broad.mit.edu	37	14	36133969	36133969	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36133969G>A	uc001wti.2	-	26	4080	c.3689C>T	c.(3688-3690)CCA>CTA	p.P1230L	RALGAPA1_uc010amp.2_RNA|RALGAPA1_uc001wtj.2_Missense_Mutation_p.P1230L|RALGAPA1_uc010tpv.1_Missense_Mutation_p.P1243L|RALGAPA1_uc010tpw.1_Missense_Mutation_p.P1277L	NM_014990	NP_055805	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1	1230					activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4						TTCTACTCTTGGTGCCTATGT	0.353													8	73	---	---	---	---	PASS
MDGA2	161357	broad.mit.edu	37	14	47389251	47389251	+	Silent	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47389251C>T	uc001wwj.3	-	10	2191	c.1995G>A	c.(1993-1995)GTG>GTA	p.V665V	MDGA2_uc001wwi.3_Silent_p.V436V|MDGA2_uc010ani.2_Silent_p.V225V	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1	665					spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						CAATCCGATCCACTGCATCAG	0.428													12	73	---	---	---	---	PASS
DCAF5	8816	broad.mit.edu	37	14	69521877	69521877	+	Missense_Mutation	SNP	C	A	A	rs150859516		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69521877C>A	uc001xkp.2	-	9	1745	c.1526G>T	c.(1525-1527)CGC>CTC	p.R509L	DCAF5_uc001xkq.2_Missense_Mutation_p.R508L	NM_003861	NP_003852	Q96JK2	DCAF5_HUMAN	WD repeat domain 22	509						CUL4 RING ubiquitin ligase complex				ovary(1)|central_nervous_system(1)	2						ACGCTGCTGGCGAGAGGCTGC	0.592													15	27	---	---	---	---	PASS
C14orf48	256369	broad.mit.edu	37	14	94467537	94467537	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94467537G>C	uc001ycg.1	+	4	643	c.37G>C	c.(37-39)GGT>CGT	p.G13R	C14orf48_uc001ycf.2_RNA|C14orf48_uc010twp.1_RNA	NR_024184				Homo sapiens cDNA FLJ40422 fis, clone TESTI2038858.												0				Epithelial(152;0.114)|all cancers(159;0.191)|COAD - Colon adenocarcinoma(157;0.208)		TGGAGGCCACGGTGAAGCACT	0.667													12	35	---	---	---	---	PASS
C14orf68	283600	broad.mit.edu	37	14	100795213	100795213	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100795213C>T	uc001yhc.2	+	5	551	c.478C>T	c.(478-480)CGC>TGC	p.R160C	C14orf68_uc001yhd.2_Missense_Mutation_p.R14C	NM_207117	NP_997000	Q6Q0C1	S2547_HUMAN	chromosome 14 open reading frame 68	160	Solcar 2.				transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0		Melanoma(154;0.152)				GCCCAAGTACCGCGGGCCACT	0.701													4	31	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106845549	106845549	+	RNA	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106845549G>T	uc010tyt.1	-	304		c.12168C>A								Parts of antibodies, mostly variable regions.												0						TCCAGAGGCTGCACAGGAGAG	0.572													14	215	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	25429530	25429530	+	Intron	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25429530G>A	uc001yyy.1	+						uc001yza.1_Intron|SNORD115-8_uc001yzb.1_RNA|SNORD115-9_uc001yzc.1_5'Flank					Homo sapiens clone Rt-7 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.																		ATTACGCTGAGGCCCAGCCTA	0.517													127	569	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34105732	34105732	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34105732G>T	uc001zhi.2	+	74	10524	c.10454G>T	c.(10453-10455)CGG>CTG	p.R3485L	RYR3_uc010bar.2_Missense_Mutation_p.R3480L	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3485					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CAACGGAAACGGGCAGTGGTG	0.522													25	190	---	---	---	---	PASS
SHC4	399694	broad.mit.edu	37	15	49255141	49255141	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49255141C>A	uc001zxb.1	-	1	501	c.72G>T	c.(70-72)ATG>ATT	p.M24I		NM_203349	NP_976224	Q6S5L8	SHC4_HUMAN	rai-like protein	24	CH2.				intracellular signal transduction	cell junction|postsynaptic membrane				ovary(3)|pancreas(2)	5		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		CCCTGTGCAGCATCCCGGGGT	0.622													26	154	---	---	---	---	PASS
LINGO1	84894	broad.mit.edu	37	15	77907356	77907356	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77907356G>A	uc002bct.1	-	2	945	c.893C>T	c.(892-894)CCC>CTC	p.P298L	LINGO1_uc002bcu.1_Missense_Mutation_p.P292L	NM_032808	NP_116197	Q96FE5	LIGO1_HUMAN	leucine-rich repeat neuronal 6A	298	Extracellular (Potential).|LRR 9.			P -> R (in Ref. 5; AAH68558).	negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane				ovary(1)|lung(1)	2						GGTGCTGATGGGGTTGTAGGA	0.617													11	82	---	---	---	---	PASS
ACSBG1	23205	broad.mit.edu	37	15	78473261	78473261	+	Silent	SNP	C	A	A	rs147846122		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78473261C>A	uc002bdh.2	-	9	1145	c.1089G>T	c.(1087-1089)ACG>ACT	p.T363T	ACSBG1_uc010umw.1_Silent_p.T359T|ACSBG1_uc010umx.1_Silent_p.T121T|ACSBG1_uc010umy.1_Silent_p.T256T	NM_015162	NP_055977	Q96GR2	ACBG1_HUMAN	lipidosin	363					long-chain fatty acid metabolic process|myelination|very long-chain fatty acid metabolic process	cytoplasmic membrane-bounded vesicle|endoplasmic reticulum|microsome	ATP binding|long-chain fatty acid-CoA ligase activity|very long-chain fatty acid-CoA ligase activity			ovary(1)	1						CCTCCCGCAGCGTGTTCACCA	0.652													3	107	---	---	---	---	PASS
ACSBG1	23205	broad.mit.edu	37	15	78526837	78526837	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78526837G>T	uc002bdh.2	-	1	63	c.7C>A	c.(7-9)CGC>AGC	p.R3S	ACSBG1_uc010umw.1_Missense_Mutation_p.R3S|ACSBG1_uc010umx.1_5'UTR|ACSBG1_uc010umy.1_5'UTR	NM_015162	NP_055977	Q96GR2	ACBG1_HUMAN	lipidosin	3					long-chain fatty acid metabolic process|myelination|very long-chain fatty acid metabolic process	cytoplasmic membrane-bounded vesicle|endoplasmic reticulum|microsome	ATP binding|long-chain fatty acid-CoA ligase activity|very long-chain fatty acid-CoA ligase activity			ovary(1)	1						CCAGAATTGCGTGGCATCTGC	0.632													15	99	---	---	---	---	PASS
OR4F6	390648	broad.mit.edu	37	15	102346435	102346435	+	Silent	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102346435T>C	uc010utr.1	+	1	513	c.513T>C	c.(511-513)CCT>CCC	p.P171P		NM_001005326	NP_001005326	Q8NGB9	OR4F6_HUMAN	olfactory receptor, family 4, subfamily F,	171	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			TCTGTGGCCCTAATGAATTAG	0.383													4	520	---	---	---	---	PASS
TSC2	7249	broad.mit.edu	37	16	2138231	2138231	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2138231G>C	uc002con.2	+	41	5270	c.5164G>C	c.(5164-5166)GCC>CCC	p.A1722P	TSC2_uc010bsd.2_Missense_Mutation_p.A1699P|TSC2_uc002coo.2_Missense_Mutation_p.A1655P|TSC2_uc010uvv.1_Missense_Mutation_p.A1619P|TSC2_uc010uvw.1_Missense_Mutation_p.A1607P|TSC2_uc002cop.2_Missense_Mutation_p.A1478P|TSC2_uc002coq.2_Missense_Mutation_p.A497P|TSC2_uc002cor.2_Missense_Mutation_p.A423P	NM_000548	NP_000539	P49815	TSC2_HUMAN	tuberous sclerosis 2 isoform 1	1722	Rap-GAP.				cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)				TCCCCAGATGGCCTCACAGGT	0.647			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				8	135	---	---	---	---	PASS
ABCC12	94160	broad.mit.edu	37	16	48158195	48158195	+	Missense_Mutation	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48158195C>A	uc002efc.1	-	10	1862	c.1516G>T	c.(1516-1518)GGG>TGG	p.G506W	ABCC12_uc002eey.1_RNA|ABCC12_uc002eez.1_RNA|ABCC12_uc002efa.1_RNA|ABCC12_uc002efb.1_RNA|ABCC12_uc002efd.1_RNA|ABCC12_uc002efe.1_Missense_Mutation_p.G506W	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	506	ABC transporter 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)				AAGATCTTCCCCTGCCAGAGA	0.537													66	256	---	---	---	---	PASS
CYLD	1540	broad.mit.edu	37	16	50825602	50825602	+	Splice_Site	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50825602G>T	uc002egp.1	+	15	2656	c.2241_splice	c.e15+1	p.E747_splice	CYLD_uc010cbs.1_Splice_Site_p.E744_splice|CYLD_uc002egq.1_Splice_Site_p.E744_splice|CYLD_uc002egr.1_Splice_Site_p.E744_splice	NM_015247	NP_056062	Q9NQC7	CYLD_HUMAN	ubiquitin carboxyl-terminal hydrolase CYLD						cell cycle|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K63-linked deubiquitination|regulation of microtubule cytoskeleton organization|regulation of mitotic cell cycle|translation|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	cytosol|extrinsic to internal side of plasma membrane|microtubule|perinuclear region of cytoplasm|ribosome	proline-rich region binding|protein kinase binding|structural constituent of ribosome|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			skin(19)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|central_nervous_system(3)	28		all_cancers(37;0.0156)				ATTTGCAGAGGTTAGTGATAC	0.343			Mis|N|F|S		cylindroma	cylindroma			Familial_Cylindromatosis|Multiple_Trichoepithelioma_Familial				20	103	---	---	---	---	PASS
SALL1	6299	broad.mit.edu	37	16	51175941	51175941	+	Silent	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51175941G>A	uc010vgs.1	-	2	223	c.192C>T	c.(190-192)AAC>AAT	p.N64N	SALL1_uc010vgr.1_5'UTR|SALL1_uc010cbv.2_Intron	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a	64					adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(5)|ovary(3)	8		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			TTTTAGTACAGTTCTTCTTGT	0.478													70	304	---	---	---	---	PASS
CCDC135	84229	broad.mit.edu	37	16	57760200	57760200	+	Intron	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57760200G>T	uc002emi.2	+						CCDC135_uc002emj.2_Intron|CCDC135_uc002emk.2_Intron	NM_032269	NP_115645	Q8IY82	CC135_HUMAN	coiled-coil domain containing 135							cytoplasm				central_nervous_system(1)	1						TTCGAGGTGGGCCTGGGGGCC	0.637													7	47	---	---	---	---	PASS
OR3A2	4995	broad.mit.edu	37	17	3181486	3181486	+	Silent	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3181486G>T	uc002fvg.2	-	1	783	c.744C>A	c.(742-744)TCC>TCA	p.S248S		NM_002551	NP_002542	P47893	OR3A2_HUMAN	olfactory receptor, family 3, subfamily A,	248	Helical; Name=6; (Potential).				sensory perception of smell	integral to plasma membrane	olfactory receptor activity			ovary(1)	1						AGCCACACGTGGAGAAGGCCT	0.522													17	69	---	---	---	---	PASS
UBB	7314	broad.mit.edu	37	17	16285542	16285542	+	Silent	SNP	G	A	A	rs17052364		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16285542G>A	uc002gpx.2	+	2	459	c.321G>A	c.(319-321)CAG>CAA	p.Q107Q	UBB_uc010vwe.1_Intron	NM_018955	NP_061828	P0CG47	UBB_HUMAN	ubiquitin B precursor	107	Ubiquitin-like 2.				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding			skin(3)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		CCAAGATCCAGGATAAAGAAG	0.537													4	174	---	---	---	---	PASS
PPP1R1B	84152	broad.mit.edu	37	17	37790145	37790145	+	Missense_Mutation	SNP	G	A	A	rs139360619		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37790145G>A	uc002hrz.2	+	5	718	c.251G>A	c.(250-252)CGC>CAC	p.R84H	PPP1R1B_uc002hsa.2_Missense_Mutation_p.R95H|PPP1R1B_uc010cvx.2_Missense_Mutation_p.R51H|PPP1R1B_uc002hsb.2_Missense_Mutation_p.R48H|PPP1R1B_uc002hsc.2_Missense_Mutation_p.R48H	NM_032192	NP_115568	Q9UD71	PPR1B_HUMAN	protein phosphatase 1, regulatory (inhibitor)	84					signal transduction	cytosol	protein kinase inhibitor activity|protein phosphatase inhibitor activity				0	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			GCTGTGCAGCGCATTGCTGAG	0.577													14	377	---	---	---	---	PASS
CCR10	2826	broad.mit.edu	37	17	40832121	40832121	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40832121C>G	uc002iax.3	-	2	543	c.539G>C	c.(538-540)AGC>ACC	p.S180T	CNTNAP1_uc002iay.2_5'Flank|CNTNAP1_uc010wgs.1_5'Flank	NM_016602	NP_057686	P46092	CCR10_HUMAN	CC chemokine receptor 10	180	Extracellular (Potential).					integral to plasma membrane					0		Breast(137;0.000153)		BRCA - Breast invasive adenocarcinoma(366;0.14)		CCCATCCTGGCTGAAGAGCAG	0.716													3	19	---	---	---	---	PASS
MYST2	11143	broad.mit.edu	37	17	47904775	47904775	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47904775G>A	uc002ipm.2	+	15	1873	c.1747G>A	c.(1747-1749)GAG>AAG	p.E583K	MYST2_uc010wma.1_Missense_Mutation_p.E444K|MYST2_uc010wmb.1_Missense_Mutation_p.E473K|MYST2_uc010wmc.1_Missense_Mutation_p.E414K|MYST2_uc010wmd.1_Missense_Mutation_p.E427K|MYST2_uc010wme.1_Missense_Mutation_p.E397K|MYST2_uc010wmf.1_Missense_Mutation_p.E248K|MYST2_uc010wmg.1_Missense_Mutation_p.E138K	NM_007067	NP_008998	O95251	MYST2_HUMAN	MYST histone acetyltransferase 2	583					DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	histone acetyltransferase activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3						CCTGATTGATGAGTGGATAGC	0.443													7	61	---	---	---	---	PASS
LUC7L3	51747	broad.mit.edu	37	17	48824020	48824020	+	Silent	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48824020C>T	uc002isr.2	+	9	1212	c.1095C>T	c.(1093-1095)AGC>AGT	p.S365S	LUC7L3_uc010wmw.1_Silent_p.S289S|LUC7L3_uc002isq.2_Silent_p.S365S|LUC7L3_uc002iss.2_Silent_p.S365S	NM_006107	NP_006098	O95232	LC7L3_HUMAN	LUC7-like 3	365	Arg/Ser-rich.				apoptosis|mRNA processing|response to stress|RNA splicing	focal adhesion|nuclear speck	DNA binding|mRNA binding|protein binding				0						AGCACAGGAGCAAAAGTCGGG	0.413													6	120	---	---	---	---	PASS
KIAA0195	9772	broad.mit.edu	37	17	73494306	73494306	+	Silent	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73494306C>A	uc002jnz.3	+	28	3815	c.3540C>A	c.(3538-3540)ATC>ATA	p.I1180I	KIAA0195_uc010wsa.1_Silent_p.I1190I|KIAA0195_uc010wsb.1_Silent_p.I820I|KIAA0195_uc002job.3_Silent_p.I188I	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772	1180	Helical; (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCCTCACCATCAGCTCCTGCC	0.617													8	169	---	---	---	---	PASS
EPB41L3	23136	broad.mit.edu	37	18	5397278	5397278	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5397278C>T	uc002kmt.1	-	18	2706	c.2620G>A	c.(2620-2622)GCG>ACG	p.A874T	EPB41L3_uc010wzh.1_Missense_Mutation_p.A705T|EPB41L3_uc002kmu.1_Missense_Mutation_p.A652T|EPB41L3_uc010dkq.1_Missense_Mutation_p.A543T|EPB41L3_uc002kms.1_Missense_Mutation_p.A109T|EPB41L3_uc010wze.1_Missense_Mutation_p.A179T|EPB41L3_uc010wzf.1_Missense_Mutation_p.A171T|EPB41L3_uc010wzg.1_Missense_Mutation_p.A146T|EPB41L3_uc010dkr.2_Missense_Mutation_p.A266T	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	874	Carboxyl-terminal (CTD).				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5						CTGTCTCCCGCCGAGTAAGAA	0.622													32	121	---	---	---	---	PASS
RIT2	6014	broad.mit.edu	37	18	40500726	40500726	+	Intron	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40500726C>A	uc002lav.2	-						RIT2_uc010dnf.2_Splice_Site_p.P143_splice	NM_002930	NP_002921	Q99578	RIT2_HUMAN	Ras-like without CAAX 2						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1						TCAGTGTAGGCTGATAAGGAA	0.378													8	39	---	---	---	---	PASS
SETBP1	26040	broad.mit.edu	37	18	42532153	42532153	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42532153G>A	uc010dni.2	+	4	3144	c.2848G>A	c.(2848-2850)GAC>AAC	p.D950N		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	950						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		AAACCGCGATGACCTCCAGTT	0.507									Schinzel-Giedion_syndrome				36	154	---	---	---	---	PASS
WDR7	23335	broad.mit.edu	37	18	54398770	54398770	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54398770C>G	uc002lgk.1	+	14	2142	c.1931C>G	c.(1930-1932)GCC>GGC	p.A644G	WDR7_uc010dpk.1_RNA|WDR7_uc002lgl.1_Missense_Mutation_p.A644G	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	644										ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)		AAAAATATGGCCCATCATAAG	0.443													28	168	---	---	---	---	PASS
ALPK2	115701	broad.mit.edu	37	18	56191230	56191230	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56191230A>T	uc002lhj.3	-	7	5780	c.5566T>A	c.(5566-5568)TAT>AAT	p.Y1856N		NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	1856	Ig-like 2.						ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						CAGCAGTAATAGAGTCCCTGG	0.468													11	58	---	---	---	---	PASS
THEG	51298	broad.mit.edu	37	19	371313	371313	+	Silent	SNP	A	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:371313A>T	uc002lol.2	-	6	684	c.645T>A	c.(643-645)CCT>CCA	p.P215P	THEG_uc002lom.2_Silent_p.P191P	NM_016585	NP_057669	Q9P2T0	THEG_HUMAN	Theg homolog isoform 1	215					cell differentiation|chaperone-mediated protein complex assembly|multicellular organismal development|spermatogenesis	nucleus	protein binding			ovary(1)	1		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGGCCAGACAGGAGTCGTCC	0.488													50	235	---	---	---	---	PASS
OR2Z1	284383	broad.mit.edu	37	19	8842130	8842130	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8842130T>C	uc010xkg.1	+	1	740	c.740T>C	c.(739-741)GTA>GCA	p.V247A		NM_001004699	NP_001004699	Q8NG97	OR2Z1_HUMAN	olfactory receptor, family 2, subfamily Z,	247	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|skin(1)	2						CACATCACGGTAGTGGGGCTC	0.567													24	128	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9046738	9046738	+	Silent	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9046738C>A	uc002mkp.2	-	5	35097	c.34893G>T	c.(34891-34893)GTG>GTT	p.V11631V		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	11633	Thr-rich.|Extracellular (Potential).				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						CCTGTGAGGTCACTACCCCTG	0.527													31	208	---	---	---	---	PASS
OR7E24	26648	broad.mit.edu	37	19	9362030	9362030	+	Missense_Mutation	SNP	A	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9362030A>C	uc002mlb.1	+	1	311	c.311A>C	c.(310-312)CAA>CCA	p.Q104P		NM_001079935	NP_001073404	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E,	104	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						GTGGACATGCAAACTCACAGC	0.507													4	129	---	---	---	---	PASS
KRI1	65095	broad.mit.edu	37	19	10671094	10671094	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10671094C>G	uc002moy.1	-	9	721	c.712G>C	c.(712-714)GAG>CAG	p.E238Q	KRI1_uc002mow.1_5'UTR|KRI1_uc002mox.1_Missense_Mutation_p.E234Q	NM_023008	NP_075384	Q8N9T8	KRI1_HUMAN	KRI1 homolog	238	Glu-rich.									ovary(1)	1			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			TCATCCAACTCAGGGTCGTTC	0.423													6	151	---	---	---	---	PASS
GCDH	2639	broad.mit.edu	37	19	13006857	13006857	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13006857G>C	uc002mvq.2	+	7	634	c.557G>C	c.(556-558)AGT>ACT	p.S186T	GCDH_uc010xms.1_Missense_Mutation_p.S153T|GCDH_uc002mvp.2_Missense_Mutation_p.S186T|GCDH_uc010xmt.1_Missense_Mutation_p.V32L|GCDH_uc010xmu.1_Missense_Mutation_p.S142T	NM_000159	NP_000150	Q92947	GCDH_HUMAN	glutaryl-Coenzyme A dehydrogenase isoform a	186	FAD.	Substrate; via carbonyl oxygen.			lysine catabolic process	mitochondrial matrix	flavin adenine dinucleotide binding|glutaryl-CoA dehydrogenase activity|protein binding				0						AACAGCGGAAGTGACCCCAGC	0.592													20	226	---	---	---	---	PASS
ZNF100	163227	broad.mit.edu	37	19	21910571	21910571	+	Silent	SNP	T	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21910571T>A	uc002nqi.2	-	5	742	c.543A>T	c.(541-543)CCA>CCT	p.P181P	ZNF100_uc002nqh.2_Silent_p.P117P	NM_173531	NP_775802	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	181	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CTTTTGCAGATGGATCACATT	0.303													38	179	---	---	---	---	PASS
WDR62	284403	broad.mit.edu	37	19	36549714	36549714	+	Silent	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36549714C>A	uc002odc.2	+	2	301	c.210C>A	c.(208-210)GCC>GCA	p.A70A	WDR62_uc002odd.2_Silent_p.A70A|WDR62_uc010eer.2_Silent_p.A70A|WDR62_uc002odb.2_Silent_p.A70A	NM_173636	NP_775907	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 2	70					cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GCATCACAGCCCAGAACAGCA	0.587													4	70	---	---	---	---	PASS
TIMM50	92609	broad.mit.edu	37	19	39976247	39976247	+	Intron	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39976247G>T	uc002olu.1	+						TIMM50_uc002olt.1_Intron|TIMM50_uc002olv.1_5'UTR	NM_001001563	NP_001001563	Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50						mitochondrial membrane organization|protein transport|release of cytochrome c from mitochondria|transmembrane transport	integral to membrane|mitochondrial inner membrane presequence translocase complex|nuclear speck	interleukin-2 receptor binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|ribonucleoprotein binding|RNA binding			ovary(1)	1	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGACAGGTGAGCAGAAGCCCT	0.527													33	187	---	---	---	---	PASS
SIGLEC9	27180	broad.mit.edu	37	19	51628484	51628484	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51628484G>C	uc002pvu.2	+	1	320	c.253G>C	c.(253-255)GAG>CAG	p.E85Q	SIGLEC9_uc010yct.1_Missense_Mutation_p.E85Q	NM_014441	NP_055256	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9 precursor	85	Extracellular (Potential).|Ig-like V-type.				cell adhesion|cell surface receptor linked signaling pathway	integral to plasma membrane	sugar binding			skin(1)	1		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		GGCAGTGTGGGAGGAGACTCG	0.567													20	189	---	---	---	---	PASS
SIGLEC14	100049587	broad.mit.edu	37	19	52148782	52148782	+	Silent	SNP	A	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52148782A>G	uc002pxf.3	-	4	822	c.702T>C	c.(700-702)TAT>TAC	p.Y234Y		NM_001098612	NP_001092082	Q08ET2	SIG14_HUMAN	sialic acid binding Ig-like lectin 14 precursor	234	Extracellular (Potential).				cell adhesion	integral to membrane|plasma membrane	protein binding|sugar binding			ovary(1)	1		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000965)|OV - Ovarian serous cystadenocarcinoma(262;0.0195)		TCTGTGGAGCATCTGGGATAG	0.567													10	180	---	---	---	---	PASS
ZNF649	65251	broad.mit.edu	37	19	52394814	52394814	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52394814T>C	uc002pxy.2	-	5	843	c.575A>G	c.(574-576)CAG>CGG	p.Q192R	ZNF577_uc010ydf.1_5'Flank	NM_023074	NP_075562	Q9BS31	ZN649_HUMAN	zinc finger protein 649	192	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00152)|OV - Ovarian serous cystadenocarcinoma(262;0.0185)		CTCAGTGAGCTGAGACTTCTT	0.448													4	510	---	---	---	---	PASS
USP29	57663	broad.mit.edu	37	19	57640252	57640252	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57640252G>T	uc002qny.2	+	4	565	c.209G>T	c.(208-210)AGT>ATT	p.S70I		NM_020903	NP_065954	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	70					protein modification process|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity			lung(6)|ovary(2)|breast(2)|pancreas(1)	11		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AAAAGACAAAGTCACCTGCGT	0.338													4	97	---	---	---	---	PASS
SLC13A3	64849	broad.mit.edu	37	20	45192146	45192146	+	Silent	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45192146G>C	uc002xsf.1	-	12	1577	c.1539C>G	c.(1537-1539)GGC>GGG	p.G513G	SLC13A3_uc010ghn.1_Silent_p.G482G|SLC13A3_uc010zxw.1_Silent_p.G463G|SLC13A3_uc002xsg.1_Silent_p.G466G|SLC13A3_uc010gho.1_Silent_p.G431G|SLC13A3_uc010zxx.1_Silent_p.G415G|SLC13A3_uc002xse.1_Silent_p.G4G|SLC13A3_uc010ghm.1_Silent_p.G100G|SLC13A3_uc010zxv.1_Silent_p.G98G	NM_022829	NP_073740	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform a	513	Helical; (Potential).					integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	AGCCGACTGTGCCCGGAATCA	0.607													3	45	---	---	---	---	PASS
ZBP1	81030	broad.mit.edu	37	20	56190586	56190586	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56190586G>C	uc002xyo.2	-	3	591	c.310C>G	c.(310-312)CAG>GAG	p.Q104E	ZBP1_uc010gjm.2_Missense_Mutation_p.Q104E|ZBP1_uc002xyp.2_Missense_Mutation_p.Q29E|ZBP1_uc010zzn.1_Missense_Mutation_p.Q104E	NM_030776	NP_110403	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1 isoform a	104	DRADA 2.					cytoplasm|nucleus	double-stranded RNA adenosine deaminase activity|left-handed Z-DNA binding|RNA binding			ovary(2)	2	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			TGGCTGAACTGAGGGCCAGGG	0.582													31	135	---	---	---	---	PASS
CDH4	1002	broad.mit.edu	37	20	60419830	60419830	+	Missense_Mutation	SNP	G	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60419830G>T	uc002ybn.1	+	5	697	c.683G>T	c.(682-684)CGG>CTG	p.R228L	CDH4_uc002ybp.1_Missense_Mutation_p.R154L	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein	228	Cadherin 1.|Extracellular (Potential).				adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			ATGTCCGGCCGGATGTACGTC	0.632													18	60	---	---	---	---	PASS
NTSR1	4923	broad.mit.edu	37	20	61386218	61386218	+	Missense_Mutation	SNP	G	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61386218G>A	uc002ydf.2	+	2	1267	c.896G>A	c.(895-897)CGG>CAG	p.R299Q		NM_002531	NP_002522	P30989	NTR1_HUMAN	neurotensin receptor 1	299	Cytoplasmic (Potential).					endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	neurotensin receptor activity, G-protein coupled			skin(2)|lung(1)|central_nervous_system(1)	4	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)			CAGGCCCTGCGGCACGGCGTG	0.697													7	25	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11097586	11097586	+	Missense_Mutation	SNP	C	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11097586C>G	uc002yit.1	-	2	284	c.76G>C	c.(76-78)GTG>CTG	p.V26L	BAGE_uc002yix.2_RNA	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		cagctcaccacaggggactcc	0.124													6	106	---	---	---	---	PASS
TRPM2	7226	broad.mit.edu	37	21	45821654	45821654	+	Silent	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45821654C>A	uc002zet.1	+	17	2625	c.2412C>A	c.(2410-2412)CTC>CTA	p.L804L	TRPM2_uc002zeu.1_Silent_p.L804L|TRPM2_uc002zew.1_Silent_p.L804L|TRPM2_uc010gpt.1_Silent_p.L804L|TRPM2_uc002zex.1_Silent_p.L590L|TRPM2_uc002zey.1_Silent_p.L317L	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	804	Helical; (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						TGAACATCCTCTCCTACTTCG	0.642													52	737	---	---	---	---	PASS
CECR1	51816	broad.mit.edu	37	22	17690370	17690370	+	Silent	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17690370G>C	uc002zmk.1	-	1	410	c.198C>G	c.(196-198)CTC>CTG	p.L66L	CECR1_uc010gqu.1_Silent_p.L66L|CECR1_uc011agi.1_Silent_p.L24L|CECR1_uc011agj.1_Silent_p.L24L	NM_017424	NP_059120	Q9NZK5	CECR1_HUMAN	cat eye syndrome critical region protein 1	66	Dimerization.				adenosine catabolic process|hypoxanthine salvage|inosine biosynthetic process|multicellular organismal development|purine ribonucleoside monophosphate biosynthetic process	extracellular space|Golgi apparatus	adenosine deaminase activity|adenosine receptor binding|growth factor activity|heparin binding|protein homodimerization activity|proteoglycan binding|zinc ion binding			ovary(1)	1		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				CAGCGATTTTGAGCGTCATGA	0.532													18	108	---	---	---	---	PASS
SMCR7L	54471	broad.mit.edu	37	22	39908337	39908337	+	Silent	SNP	T	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39908337T>G	uc003axx.2	+	5	921	c.423T>G	c.(421-423)ACT>ACG	p.T141T	SMCR7L_uc003axw.2_Silent_p.T141T|SMCR7L_uc010gxz.1_5'UTR|SMCR7L_uc003axy.2_5'UTR	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	141						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)					AACTTCTTACTTACTACCGGA	0.612													43	78	---	---	---	---	PASS
ST13	6767	broad.mit.edu	37	22	41222545	41222545	+	Silent	SNP	C	A	A	rs12373984		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41222545C>A	uc003aze.2	-	12	1250	c.1107G>T	c.(1105-1107)GCG>GCT	p.A369A	ST13_uc011aow.1_Silent_p.A359A	NM_003932	NP_003923	P50502	F10A1_HUMAN	heat shock 70kD protein binding protein	369							protein binding, bridging				0						AAGGACATTACGCTTGACCTC	0.413													156	469	---	---	---	---	PASS
PRR5-ARHGAP8	553158	broad.mit.edu	37	22	45258351	45258351	+	Missense_Mutation	SNP	C	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45258351C>T	uc003bfd.2	+	17	2080	c.1808C>T	c.(1807-1809)GCA>GTA	p.A603V	PRR5-ARHGAP8_uc003bfc.2_Missense_Mutation_p.A524V|PRR5-ARHGAP8_uc011aqi.1_Missense_Mutation_p.A515V|PRR5-ARHGAP8_uc011aqj.1_Missense_Mutation_p.A446V|ARHGAP8_uc010gzv.2_3'UTR|ARHGAP8_uc003bfj.2_Missense_Mutation_p.A424V|ARHGAP8_uc003bfk.2_Missense_Mutation_p.A393V|ARHGAP8_uc003bfl.2_RNA	NM_181335	NP_851852			Rho GTPase activating protein 8 isoform 2											skin(2)	2						CACGGCCTGGCACCATGGGAA	0.617													8	135	---	---	---	---	PASS
ARHGAP6	395	broad.mit.edu	37	X	11204358	11204358	+	Missense_Mutation	SNP	T	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11204358T>C	uc004cup.1	-	5	2144	c.1271A>G	c.(1270-1272)CAT>CGT	p.H424R	ARHGAP6_uc004cuo.1_RNA|ARHGAP6_uc004cur.1_Missense_Mutation_p.H424R|ARHGAP6_uc004cum.1_Missense_Mutation_p.H221R|ARHGAP6_uc004cun.1_Missense_Mutation_p.H244R|ARHGAP6_uc010neb.1_Missense_Mutation_p.H246R|ARHGAP6_uc011mif.1_Missense_Mutation_p.H221R	NM_013427	NP_038286	O43182	RHG06_HUMAN	Rho GTPase activating protein 6 isoform 1	424	Rho-GAP.				actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity			urinary_tract(1)|lung(1)	2						CTACTTACCATGTTTTTCTAG	0.393													61	79	---	---	---	---	PASS
KIAA2022	340533	broad.mit.edu	37	X	73959296	73959296	+	Missense_Mutation	SNP	A	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73959296A>T	uc004eby.2	-	4	5112	c.4495T>A	c.(4495-4497)TTT>ATT	p.F1499I		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	1499					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15						AAAACCCAAAAGGTTGTTTCT	0.358													18	27	---	---	---	---	PASS
MAGEE2	139599	broad.mit.edu	37	X	75004435	75004435	+	Missense_Mutation	SNP	G	T	T	rs143829521	byFrequency	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75004435G>T	uc004ecj.1	-	1	637	c.452C>A	c.(451-453)GCT>GAT	p.A151D		NM_138703	NP_619648	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	151	MAGE 1.									ovary(1)|skin(1)	2						GTAGGTGTCAGCCTGAGGATC	0.517													9	34	---	---	---	---	PASS
TBX22	50945	broad.mit.edu	37	X	79278709	79278709	+	Missense_Mutation	SNP	G	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79278709G>C	uc010nmg.1	+	3	460	c.326G>C	c.(325-327)GGG>GCG	p.G109A	TBX22_uc004edi.1_5'UTR|TBX22_uc004edj.1_Missense_Mutation_p.G109A	NM_001109878	NP_001103348	Q9Y458	TBX22_HUMAN	T-box 22 isoform 1	109	T-box.				multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(7)|large_intestine(3)|central_nervous_system(2)|breast(1)|skin(1)|ovary(1)	15						CATGACATCGGGACTGAGATG	0.468													22	54	---	---	---	---	PASS
F9	2158	broad.mit.edu	37	X	138643921	138643921	+	Silent	SNP	C	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138643921C>A	uc004fas.1	+	8	1106	c.1077C>A	c.(1075-1077)GTC>GTA	p.V359V	F9_uc004fat.1_Silent_p.V321V	NM_000133	NP_000124	P00740	FA9_HUMAN	coagulation factor IX preproprotein	359	Peptidase S1.				blood coagulation, extrinsic pathway|blood coagulation, intrinsic pathway|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen|plasma membrane	calcium ion binding|serine-type endopeptidase activity			lung(2)|ovary(1)	3	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Heparin(DB01109)|Menadione(DB00170)	GGGGAAGAGTCTTCCACAAAG	0.428													44	67	---	---	---	---	PASS
CROCC	9696	broad.mit.edu	37	1	17297706	17297713	+	Intron	DEL	GTGTGTGT	-	-	rs112384534		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17297706_17297713delGTGTGTGT	uc001azt.2	+						CROCC_uc001azu.2_Intron|CROCC_uc001azv.2_Intron	NM_014675	NP_055490	Q5TZA2	CROCC_HUMAN	ciliary rootlet coiled-coil						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		tgatgtctgagtgtgtgtgtgtgtgtgt	0.399													4	2	---	---	---	---	
PGLYRP4	57115	broad.mit.edu	37	1	153302926	153302927	+	3'UTR	DEL	GA	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153302926_153302927delGA	uc001fbo.2	-	9					PGLYRP4_uc001fbp.2_3'UTR	NM_020393	NP_065126	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein-I-beta						defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(3)|skin(1)	4	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			GAGGGGAATGGAGAGAGAGAGA	0.550													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	57775131	57775162	+	IGR	DEL	AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG	-	-	rs58710429		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57775131_57775162delAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG								None (None upstream) : VRK2 (359624 downstream)																							gaaagaaagaaaggaaggaaggaaggaaggaaggaaggaaggaaggaaaaga	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	114627719	114627720	+	IGR	DEL	TG	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114627719_114627720delTG								SLC35F5 (113319 upstream) : ACTR3 (19817 downstream)																							tgtgtatatttgtgtgtgtgtg	0.109													3	3	---	---	---	---	
DNAJC10	54431	broad.mit.edu	37	2	183597068	183597069	+	Intron	DEL	TG	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183597068_183597069delTG	uc002uow.1	+						DNAJC10_uc002uox.1_Intron|DNAJC10_uc002uoy.1_Intron|DNAJC10_uc002uoz.1_Intron|DNAJC10_uc010fro.1_Intron	NM_018981	NP_061854	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10						apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|ER-associated protein catabolic process|glycerol ether metabolic process|negative regulation of protein phosphorylation|protein folding|response to endoplasmic reticulum stress	endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|extracellular region	ATPase activator activity|ATPase binding|chaperone binding|electron carrier activity|heat shock protein binding|misfolded protein binding|protein disulfide oxidoreductase activity|unfolded protein binding			ovary(1)|large_intestine(1)|breast(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			tgtgtttgtatgtgtgtgtgtg	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	202876856	202876867	+	IGR	DEL	GAAAGAAAGAAT	-	-	rs72289966		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202876856_202876867delGAAAGAAAGAAT								CDK15 (118593 upstream) : FZD7 (22443 downstream)																							gagagagaaagaaagaaagaatgaaagaaaga	0.085													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	218879590	218879593	+	IGR	DEL	GGAC	-	-	rs61462261		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218879590_218879593delGGAC								TNS1 (11872 upstream) : RUFY4 (20118 downstream)																							agggaaggaaggacggaaggaagg	0.064													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	234699094	234699094	+	IGR	DEL	C	-	-	rs67025076		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234699094delC								UGT1A10 (17145 upstream) : HJURP (46393 downstream)																							cttcctccctcccccccttcc	0.045													3	3	---	---	---	---	
RBMS3	27303	broad.mit.edu	37	3	29492421	29492424	+	Intron	DEL	CACC	-	-	rs71628523		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29492421_29492424delCACC	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793	Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)				cacacacacacaccccccacacac	0.152													3	4	---	---	---	---	
RBM6	10180	broad.mit.edu	37	3	50114316	50114316	+	Intron	DEL	A	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50114316delA	uc003cyc.2	+						RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768	P78332	RBM6_HUMAN	RNA binding motif protein 6						RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		gactccatctaaaaaaaaaaa	0.184													4	2	---	---	---	---	
SEMA5B	54437	broad.mit.edu	37	3	122631464	122631464	+	Intron	DEL	A	-	-	rs150722244		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122631464delA	uc003efz.1	-						SEMA5B_uc011bju.1_Intron|SEMA5B_uc003ega.1_Intron|SEMA5B_uc003egb.1_Intron|SEMA5B_uc003efy.1_5'Flank	NM_001031702	NP_001026872	Q9P283	SEM5B_HUMAN	semaphorin 5B isoform 1						cell differentiation|nervous system development	integral to membrane	receptor activity			ovary(2)|breast(2)|pancreas(2)|central_nervous_system(1)	7				GBM - Glioblastoma multiforme(114;0.0367)		AAGAAAGGTGAAAAAAAAAAA	0.537													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	122779228	122779231	+	IGR	DEL	CTTC	-	-	rs12632332		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122779228_122779231delCTTC								SEMA5B (31776 upstream) : PDIA5 (6734 downstream)																							tccttcctttcttccttccttctt	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180271430	180271431	+	IGR	DEL	AC	-	-	rs146505715		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180271430_180271431delAC								PEX5L (516913 upstream) : TTC14 (48487 downstream)																							tcacacacaaacacacacacac	0.000													3	3	---	---	---	---	
ST6GAL1	6480	broad.mit.edu	37	3	186704984	186704985	+	Intron	INS	-	A	A	rs59834484		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186704984_186704985insA	uc003frb.2	+						ST6GAL1_uc003frc.2_Intron	NM_173216	NP_775323	P15907	SIAT1_HUMAN	ST6 beta-galactosamide						humoral immune response|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			central_nervous_system(1)	1	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		gggagggagggagggaaggaaa	0.099													11	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	193504631	193504631	+	IGR	DEL	G	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193504631delG								OPA1 (89032 upstream) : LOC100128023 (206253 downstream)																							aaggaaggaaggaaggaaAAG	0.154													4	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	6776561	6776561	+	IGR	DEL	A	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6776561delA								CNO (57174 upstream) : KIAA0232 (7898 downstream)																							agaaagaaagaaagaaagaaa	0.030													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	190514054	190514055	+	IGR	DEL	GT	-	-	rs79143395		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190514054_190514055delGT								None (None upstream) : FRG1 (347919 downstream)																							GTtgtgtgtggtgtgtgtgtgt	0.193													4	3	---	---	---	---	
MGC42105	167359	broad.mit.edu	37	5	43198441	43198444	+	Intron	DEL	TCTT	-	-	rs111242417		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43198441_43198444delTCTT	uc003jno.2	+							NM_153361	NP_699192	Q8IY84	NIM1_HUMAN	serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9						tgtctttctgtctttctttctttc	0.000													4	3	---	---	---	---	
CKMT2	1160	broad.mit.edu	37	5	80546759	80546760	+	Intron	INS	-	AC	AC	rs142418532	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80546759_80546760insAC	uc003khc.3	+						RNU5E_uc011cto.1_Intron|CKMT2_uc010jaq.2_Intron|CKMT2_uc003khd.3_Intron|uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NM_001825	NP_001816	P17540	KCRS_HUMAN	sarcomeric mitochondrial creatine kinase						creatine metabolic process|muscle contraction	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	agaaatagaaaacacacacaca	0.233													14	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	85255606	85255606	+	IGR	DEL	T	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85255606delT								None (None upstream) : NBPF22P (322656 downstream)																							ccttccttccttttctttctt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	103837910	103837911	+	IGR	INS	-	T	T			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103837910_103837911insT								NUDT12 (939420 upstream) : RAB9BP1 (597264 downstream)																							ttctttctttctttctttcttt	0.000													4	2	---	---	---	---	
FAM13B	51306	broad.mit.edu	37	5	137289730	137289731	+	Intron	INS	-	T	T	rs147698927		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137289730_137289731insT	uc003lbz.2	-						FAM13B_uc003lcb.2_Intron|FAM13B_uc003lca.2_Intron	NM_016603	NP_057687	Q9NYF5	FA13B_HUMAN	hypothetical protein LOC51306 isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0						CAATCTCTCTCttttttttttt	0.262													4	2	---	---	---	---	
CYFIP2	26999	broad.mit.edu	37	5	156750834	156750835	+	Intron	INS	-	A	A	rs111716109		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156750834_156750835insA	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GACATCTGCAGAAAAAAAAAAA	0.416													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	13840911	13840912	+	IGR	INS	-	AC	AC	rs145411314	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13840911_13840912insAC								CCDC90A (26122 upstream) : RNF182 (84291 downstream)																							CAGAAAAAGAAacacacacaca	0.262													5	3	---	---	---	---	
STX11	8676	broad.mit.edu	37	6	144490800	144490800	+	Intron	DEL	C	-	-	rs144586806	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144490800delC	uc003qks.3	+							NM_003764	NP_003755	O75558	STX11_HUMAN	syntaxin 11						cellular membrane fusion|intracellular protein transport|vesicle-mediated transport	Golgi apparatus|membrane	SNAP receptor activity			ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(155;2.17e-06)|GBM - Glioblastoma multiforme(68;0.0492)		ctccctccctcccttccttcc	0.000									Familial_Hemophagocytic_Lymphohistiocytosis				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	151546282	151546289	+	Intron	DEL	CTTCCTTT	-	-	rs72359904	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151546282_151546289delCTTCCTTT	uc003qod.2	-											Homo sapiens cDNA clone IMAGE:4838370.																		tccttccttccttcctttctttctttcc	0.000													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	166319534	166319534	+	Intron	DEL	T	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166319534delT	uc003qup.1	-											Homo sapiens cDNA FLJ33369 fis, clone BRACE2005904.																		ccttccttccttccctccctc	0.065													5	4	---	---	---	---	
ADAP1	11033	broad.mit.edu	37	7	944936	944936	+	Intron	DEL	A	-	-	rs56919223	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:944936delA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860	O75689	ADAP1_HUMAN	centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1						GGACACGGACAGGGGGAGACG	0.493													6	3	---	---	---	---	
TTYH3	80727	broad.mit.edu	37	7	2690212	2690213	+	Intron	INS	-	A	A			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2690212_2690213insA	uc003smp.2	+						TTYH3_uc010ksn.2_Intron|TTYH3_uc003smq.2_Intron	NM_025250	NP_079526	Q9C0H2	TTYH3_HUMAN	tweety 3							chloride channel complex|plasma membrane	chloride channel activity				0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)		aactccatctcaaaaaaaaaaa	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	6714962	6714962	+	IGR	DEL	T	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6714962delT								ZNF853 (51043 upstream) : ZNF12 (13102 downstream)																							AAGTCACAtcttttttttttt	0.189													4	2	---	---	---	---	
MACC1	346389	broad.mit.edu	37	7	20229372	20229373	+	Intron	DEL	AA	-	-	rs72309121		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20229372_20229373delAA	uc003sus.3	-						MACC1_uc010kug.2_Intron	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3						acaaacacataaacacacacac	0.163													1	5	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23940354	23940355	+	Intron	INS	-	CCTT	CCTT	rs72083241		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23940354_23940355insCCTT	uc003swv.1	+									Q9BXU1	STK31_HUMAN	SubName: Full=Putative uncharacterized protein STK31;								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						TTCAGTAATTCccttccttcct	0.158													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	24182451	24182452	+	IGR	INS	-	TGTC	TGTC	rs149454885	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24182451_24182452insTGTC								STK31 (238086 upstream) : NPY (141357 downstream)																							AGGGgtgtgtgtgtgtgtgtgt	0.272													4	2	---	---	---	---	
WBSCR27	155368	broad.mit.edu	37	7	73249451	73249456	+	Intron	DEL	CTCTCC	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73249451_73249456delCTCTCC	uc003tzj.2	-						RFC2_uc011kfa.1_Intron	NM_152559	NP_689772	Q8N6F8	WBS27_HUMAN	Williams-Beuren syndrome chromosome region 27											central_nervous_system(1)	1		Lung NSC(55;0.159)				TGGGGACGCTctctccctctccctct	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	125588469	125588472	+	IGR	DEL	AAGA	-	-	rs143156574		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125588469_125588472delAAGA								None (None upstream) : GRM8 (490180 downstream)																							gaaagaaagcaagaaagaaagcaa	0.000													4	2	---	---	---	---	
HIPK2	28996	broad.mit.edu	37	7	139328128	139328129	+	Intron	DEL	AC	-	-	rs36032133		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139328128_139328129delAC	uc003vvf.3	-						HIPK2_uc003vvd.3_Intron	NM_022740	NP_073577	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2 isoform						apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)					TGTACTAAATacacacacacac	0.337													4	2	---	---	---	---	
DNAJB6	10049	broad.mit.edu	37	7	157149831	157149831	+	Intron	DEL	A	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157149831delA	uc003wnk.2	+						DNAJB6_uc003wnj.2_Intron|DNAJB6_uc003wnl.2_Intron|DNAJB6_uc011kvy.1_Intron|DNAJB6_uc011kvz.1_Intron|DNAJB6_uc010lqt.2_Intron	NM_058246	NP_490647	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6						intermediate filament organization|negative regulation of caspase activity|protein folding|response to unfolded protein	nucleus|perinuclear region of cytoplasm	ATPase activator activity|chaperone binding|heat shock protein binding|unfolded protein binding			ovary(2)	2	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		tgtctcaattaaaaaaaaaaa	0.114													6	3	---	---	---	---	
MYOM2	9172	broad.mit.edu	37	8	2024249	2024250	+	Frame_Shift_Del	DEL	CG	-	-	rs145411559		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2024249_2024250delCG	uc003wpx.3	+	11	1287_1288	c.1149_1150delCG	c.(1147-1152)CCCGGTfs	p.P383fs	MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2	383_384	Fibronectin type-III 1.				muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		CAGGGGCCCCCGGTGCACCCAT	0.609													34	16	---	---	---	---	
MSR1	4481	broad.mit.edu	37	8	16012445	16012446	+	Intron	DEL	AC	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16012445_16012446delAC	uc003wwz.2	-						MSR1_uc010lsu.2_Intron|MSR1_uc003wxa.2_Intron|MSR1_uc003wxb.2_Intron|MSR1_uc011kxz.1_Intron	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1						cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		gtgcgtgcatacacacacacac	0.257													4	2	---	---	---	---	
PPP2R2A	5520	broad.mit.edu	37	8	25985808	25985809	+	Intron	INS	-	GGAGGGAA	GGAGGGAA	rs149982442	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25985808_25985809insGGAGGGAA	uc003xek.2	+							NM_002717	NP_002708	P63151	2ABA_HUMAN	alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		gaaggagggagggaaggaagga	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	65747143	65747143	+	IGR	DEL	T	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65747143delT								CYP7B1 (35795 upstream) : ARMC1 (767929 downstream)																							cttcctttccttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	127426687	127426690	+	IGR	DEL	CTTT	-	-	rs150461508	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127426687_127426690delCTTT								TRIB1 (976045 upstream) : FAM84B (137997 downstream)																							ttctttcttcctttcttcctttct	0.000													9	5	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141255564	141255565	+	Intron	DEL	GT	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141255564_141255565delGT	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						ttgttttgtggtgtgtgtgtgt	0.000													4	2	---	---	---	---	
ZCCHC7	84186	broad.mit.edu	37	9	37126116	37126117	+	Intron	DEL	GG	-	-	rs73646324	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37126116_37126117delGG	uc003zzq.2	+						ZCCHC7_uc011lqh.1_Intron|ZCCHC7_uc011lqi.1_Intron|ZCCHC7_uc010mlt.2_Intron|ZCCHC7_uc003zzs.1_Intron	NM_032226	NP_115602	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7								nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(29;0.0137)		AATTCTCGTTGGGGAGTGGTGG	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	107008316	107008317	+	IGR	INS	-	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107008316_107008317insG								SMC2 (104623 upstream) : OR13F1 (258227 downstream)																							gaaggaaggaagaaggaaggga	0.064													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	8848562	8848562	+	IGR	DEL	A	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8848562delA								GATA3 (731400 upstream) : None (None downstream)																							CTCCCCTAGGAAAAAAAAAAA	0.299													2	4	---	---	---	---	
DHTKD1	55526	broad.mit.edu	37	10	12132423	12132423	+	Intron	DEL	C	-	-	rs57211373		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12132423delC	uc001ild.3	+							NM_018706	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain						glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			ttccttccttcctttttcctt	0.095													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	33895760	33895763	+	IGR	DEL	CTTC	-	-	rs148966189		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33895760_33895763delCTTC								NRP1 (271754 upstream) : PARD3 (504335 downstream)																							tccctcccttcttccttccttcct	0.044													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	72800810	72800811	+	IGR	DEL	GT	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72800810_72800811delGT								PCBD1 (152269 upstream) : UNC5B (171487 downstream)																							ACGCATGACCgtgtgtgtgtgt	0.416													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	1753569	1753569	+	IGR	DEL	G	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1753569delG								KRTAP5-6 (34585 upstream) : CTSD (20416 downstream)																							AAAGTCACCTGACTCCCCAAA	0.483													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	45764950	45764965	+	IGR	DEL	AAGGAAGGAAGGAAGA	-	-	rs56170165	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45764950_45764965delAAGGAAGGAAGGAAGA								CHST1 (77778 upstream) : DKFZp779M0652 (28018 downstream)																							ggaaggaaggaaggaaggaaggaagagagagagaga	0.000													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	69503767	69503768	+	IGR	INS	-	AC	AC	rs138348487	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69503767_69503768insAC								ORAOV1 (13602 upstream) : FGF19 (9239 downstream)																							cGTGTGTGTATacacacacaca	0.153													15	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	76047379	76047380	+	IGR	DEL	AC	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76047379_76047380delAC								WNT11 (125576 upstream) : PRKRIR (13624 downstream)																							ACCTTCCTGTacacacacacac	0.356													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	130415428	130415428	+	IGR	DEL	T	-	-	rs34086439		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130415428delT								ADAMTS15 (71713 upstream) : SNX19 (330339 downstream)																							TTTTTTCTCCTTTTTTTTTTT	0.299													3	3	---	---	---	---	
VWF	7450	broad.mit.edu	37	12	6089258	6089273	+	Intron	DEL	AAGGAAGGAAGGAAGG	-	-	rs150776345	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6089258_6089273delAAGGAAGGAAGGAAGG	uc001qnn.1	-						VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	aaaagaaagaaaggaaggaaggaaggaaggaaggaa	0.014													10	9	---	---	---	---	
KRT72	140807	broad.mit.edu	37	12	52983786	52983787	+	Intron	DEL	TG	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52983786_52983787delTG	uc001sar.2	-						KRT72_uc001saq.2_Intron|KRT72_uc010sns.1_Intron|KRT72_uc010snt.1_Intron	NM_001146225	NP_001139697	Q14CN4	K2C72_HUMAN	keratin 72 isoform 1							keratin filament	structural molecule activity			ovary(5)|pancreas(1)	6				BRCA - Breast invasive adenocarcinoma(357;0.195)		tgtgtgtgtctgtgtgtgtgtg	0.371													4	2	---	---	---	---	
DPY19L2	283417	broad.mit.edu	37	12	64038437	64038438	+	Intron	DEL	TG	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64038437_64038438delTG	uc001srp.1	-						DPY19L2_uc009zqk.1_Intron	NM_173812	NP_776173	Q6NUT2	D19L2_HUMAN	dpy-19-like 2						multicellular organismal development|spermatid development	integral to membrane				central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		TATAAGAGTTTGTGTGTGTGTG	0.282													4	2	---	---	---	---	
IL22	50616	broad.mit.edu	37	12	68646870	68646871	+	Intron	INS	-	A	A	rs34979529		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68646870_68646871insA	uc001sty.1	-						IL22_uc010stb.1_Intron	NM_020525	NP_065386	Q9GZX6	IL22_HUMAN	interleukin 22 precursor						acute-phase response	extracellular space	cytokine activity|interleukin-22 receptor binding				0		Myeloproliferative disorder(1001;0.0255)	Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;5.06e-05)|BRCA - Breast invasive adenocarcinoma(357;0.00104)		AGAAGTTCAAGAAAAAAAAAAA	0.356													4	3	---	---	---	---	
ELK3	2004	broad.mit.edu	37	12	96635204	96635205	+	Intron	INS	-	TG	TG	rs138999912	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96635204_96635205insTG	uc001teo.1	+							NM_005230	NP_005221	P41970	ELK3_HUMAN	ELK3 protein						negative regulation of transcription, DNA-dependent|signal transduction	mitochondrion	protein binding|purine-rich negative regulatory element binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	all_cancers(2;0.00173)					AGTGGAGCGTTtgtgtgtgtgt	0.302													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	121483372	121483373	+	IGR	INS	-	CTTC	CTTC	rs12821785		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121483372_121483373insCTTC								OASL (6592 upstream) : P2RX7 (87305 downstream)																							ttccttccttcctttctttctc	0.010													4	2	---	---	---	---	
TMEM132B	114795	broad.mit.edu	37	12	126141882	126141883	+	3'UTR	INS	-	GT	GT	rs147608126		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126141882_126141883insGT	uc001uhe.1	+	9					TMEM132B_uc001uhf.1_3'UTR	NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B							integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		TACATATACCCgtgtgtgtgtg	0.317													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	64527945	64527951	+	IGR	DEL	CTCTCTC	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64527945_64527951delCTCTCTC								OR7E156P (211244 upstream) : None (None downstream)																							ctttctttctctctctcccttccttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	29231228	29231229	+	IGR	DEL	TG	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29231228_29231229delTG								None (None upstream) : FOXG1 (5058 downstream)																							GTTTTAGTGCtgtgtgtgtgtg	0.446													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	50519464	50519465	+	IGR	DEL	AC	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50519464_50519465delAC								C14orf182 (45226 upstream) : C14orf183 (30905 downstream)																							gcacacacagacacacacacac	0.361													5	3	---	---	---	---	
NF1P1	440225	broad.mit.edu	37	15	21135196	21135197	+	5'Flank	DEL	GT	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21135196_21135197delGT	uc001ytv.1	-											Human NF1-related locus DNA in A9 mouse DNA background.												0						gtcttTGAGAgtgtgtgtgtgt	0.233													6	3	---	---	---	---	
LMAN1L	79748	broad.mit.edu	37	15	75109145	75109146	+	Intron	INS	-	C	C			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75109145_75109146insC	uc002ayt.1	+						LMAN1L_uc010bkd.2_Intron|LMAN1L_uc010ulo.1_Intron|LMAN1L_uc010bke.1_Intron	NM_021819	NP_068591	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like precursor							ER-Golgi intermediate compartment membrane|integral to membrane	sugar binding				0						ACCCTGCCGGGCCGCCATACTT	0.634													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	8172840	8172845	+	IGR	DEL	ACACAT	-	-	rs71150366		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8172840_8172845delACACAT								A2BP1 (409500 upstream) : TMEM114 (446658 downstream)																							acacacacacacacatacacacaTTA	0.146													4	2	---	---	---	---	
SRCAP	10847	broad.mit.edu	37	16	30725221	30725222	+	Intron	INS	-	T	T	rs71374028		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30725221_30725222insT	uc002dze.1	+						SRCAP_uc002dzf.2_Intron|SRCAP_uc002dzg.1_Intron|SRCAP_uc010bzz.1_Intron	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein						interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)			CATCAAttctgttttttttttt	0.223													7	4	---	---	---	---	
ABR	29	broad.mit.edu	37	17	960546	960553	+	Intron	DEL	GTTTGTGT	-	-	rs149516150	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:960546_960553delGTTTGTGT	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc010vqg.1_Intron|ABR_uc002fsg.2_Intron|ABR_uc002fsh.1_Intron	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		AACTGAAGAGGTTtgtgtgtgtgtgtgt	0.264													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	13709036	13709039	+	IGR	DEL	AGGT	-	-	rs12938908		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13709036_13709039delAGGT								HS3ST3A1 (203792 upstream) : CDRT15P (218776 downstream)																							gaaggaaggaaggtaggaaggaag	0.103													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53285935	53285938	+	IGR	DEL	GGAA	-	-	rs56317828	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53285935_53285938delGGAA								STXBP4 (44486 upstream) : HLF (56383 downstream)																							agggagggagggaagaaggaagga	0.162													6	3	---	---	---	---	
C17orf56	146705	broad.mit.edu	37	17	79204736	79204736	+	Intron	DEL	C	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79204736delC	uc002jzu.1	-						C17orf56_uc002jzr.1_Intron|C17orf56_uc002jzs.1_Intron|C17orf56_uc002jzt.1_Intron|C17orf56_uc002jzv.1_Intron|uc002jzw.1_RNA	NM_144679	NP_653280	Q96N21	CQ056_HUMAN	hypothetical protein LOC146705							integral to membrane					0	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CACCCCAGCTCCCGGACACCA	0.642													4	2	---	---	---	---	
FOXK2	3607	broad.mit.edu	37	17	80544327	80544328	+	Intron	INS	-	T	T	rs57717357		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80544327_80544328insT	uc002kfn.2	+						FOXK2_uc002kfm.1_Intron|FOXK2_uc010diu.2_Intron	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter 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				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			aaggtgggccggggggggaaag	0.000													8	5	---	---	---	---	
RPRD1A	55197	broad.mit.edu	37	18	33607447	33607448	+	Intron	INS	-	TA	TA	rs142934701	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33607447_33607448insTA	uc002kzf.1	-						RPRD1A_uc002kze.1_Intron|RPRD1A_uc002kzg.2_Intron|RPRD1A_uc010dmw.2_Intron|RPRD1A_uc010dmx.2_Intron	NM_018170	NP_060640	Q96P16	RPR1A_HUMAN	regulation of nuclear pre-mRNA domain containing											ovary(1)|breast(1)	2						GGAGGCTAtactatgttaggtg	0.168													4	2	---	---	---	---	
KIAA1468	57614	broad.mit.edu	37	18	59888803	59888803	+	Intron	DEL	T	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59888803delT	uc002lil.2	+						KIAA1468_uc002lik.1_Intron|KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_Intron	NM_020854	NP_065905	Q9P260	K1468_HUMAN	hypothetical protein LOC57614								binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)				ACGTAGTTTCttttttttttt	0.264													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	62086991	62086992	+	Intron	DEL	TG	-	-	rs111335881		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62086991_62086992delTG	uc002ljx.2	+											Homo sapiens hypothetical protein LOC284294, mRNA (cDNA clone IMAGE:4823205).																		AGATTTGgtatgtgtgtgtgtg	0.178													4	2	---	---	---	---	
CDH7	1005	broad.mit.edu	37	18	63482006	63482006	+	Intron	DEL	A	-	-	rs146003873		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63482006delA	uc002ljz.2	+						CDH7_uc002lka.2_Intron|CDH7_uc002lkb.2_Intron	NM_033646	NP_387450	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4		Esophageal squamous(42;0.129)				ATCACCttttaaaaatatttt	0.239													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	30149471	30149472	+	IGR	DEL	AC	-	-	rs35098556		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30149471_30149472delAC								POP4 (41309 upstream) : PLEKHF1 (6855 downstream)																							TGCCAGCAATacacacacacac	0.248													4	3	---	---	---	---	
ZNF792	126375	broad.mit.edu	37	19	35451487	35451488	+	Intron	DEL	CC	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35451487_35451488delCC	uc002nxh.1	-							NM_175872	NP_787068	Q3KQV3	ZN792_HUMAN	zinc finger protein 792						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TGGATAATCACCCAGGAGGGAA	0.525													3	3	---	---	---	---	
LTBP4	8425	broad.mit.edu	37	19	41128711	41128711	+	Intron	DEL	A	-	-	rs112865912		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41128711delA	uc002ooh.1	+						LTBP4_uc002oog.1_Intron|LTBP4_uc002ooi.1_Intron|LTBP4_uc002ooj.1_Intron|LTBP4_uc002ook.1_Intron|LTBP4_uc002ool.1_Intron|LTBP4_uc010xvp.1_Intron	NM_001042544	NP_001036009	Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding						growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCTGCCAGGCAGGTGGGCATG	0.617													5	3	---	---	---	---	
RPS21	6227	broad.mit.edu	37	20	60963180	60963181	+	Intron	INS	-	C	C	rs140197118	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60963180_60963181insC	uc002ycr.2	+						RPS21_uc002ycs.2_Intron|RPS21_uc002yct.2_3'UTR|RPS21_uc002ycu.2_Intron	NM_001024	NP_001015	P63220	RS21_HUMAN	ribosomal protein S21						endocrine pancreas development|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein N-terminus binding|structural constituent of ribosome				0	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			ACTAGGAGGTGCCCCCCCGACC	0.668													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11144771	11144772	+	IGR	DEL	TC	-	-	rs55756166		TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11144771_11144772delTC								BAGE (45834 upstream) : None (None downstream)																							GGTGGAtgtgtctgtgtgtgtg	0.371													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	15449557	15449558	+	Intron	INS	-	AAGA	AAGA			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15449557_15449558insAAGA	uc002yjk.2	+						uc002yjl.2_Intron					Homo sapiens, clone IMAGE:4102980, mRNA.																		aaggaaggaagaagaaaggaag	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	42392892	42392903	+	IGR	DEL	AAGGAAGGAAGG	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42392892_42392903delAAGGAAGGAAGG								DSCAM (173853 upstream) : C21orf130 (120524 downstream)																							aaaagaaagaaaggaaggaaggaaggaaggaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	23909806	23909807	+	IGR	INS	-	AG	AG	rs150197100	by1000genomes	TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23909806_23909807insAG								ZDHHC8P1 (165007 upstream) : IGLL1 (5508 downstream)																							CTAAGAGGGCCagagagagaga	0.554													5	3	---	---	---	---	
CACNG2	10369	broad.mit.edu	37	22	37051859	37051859	+	Intron	DEL	T	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37051859delT	uc003aps.1	-							NM_006078	NP_006069	Q9Y698	CCG2_HUMAN	voltage-dependent calcium channel gamma-2						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0						tctttctttcttttttttttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	43267855	43267855	+	IGR	DEL	A	-	-			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43267855delA								PPP1R2P9 (630369 upstream) : MAOA (247554 downstream)																							GCTGGACTGTAAAAAAAAAAG	0.383													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	8125122	8125123	+	IGR	INS	-	G	G			TCGA-60-2725-01A-01D-1267-08	TCGA-60-2725-11A-01D-1267-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:8125122_8125123insG								TTTY12 (446401 upstream) : TTTY18 (426288 downstream)																							aagagaagagaagggagagagg	0.054													4	4	---	---	---	---	
