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
CHD5	26038	broad.mit.edu	37	1	6212526	6212526	+	Silent	SNP	G	A	A	rs140463225	byFrequency	TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6212526G>A	uc001amb.1	-	6	916	c.816C>T	c.(814-816)GCC>GCT	p.A272A		NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	272	Lys-rich.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		ACTTGAGCCCGGCCGTCTTTT	0.403													14	18	---	---	---	---	PASS
ZYG11B	79699	broad.mit.edu	37	1	53237222	53237222	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53237222G>C	uc001cuj.2	+	3	922	c.727G>C	c.(727-729)GAT>CAT	p.D243H	ZYG11B_uc009vzg.2_RNA|ZYG11B_uc010onj.1_Missense_Mutation_p.D234H	NM_024646	NP_078922	Q9C0D3	ZY11B_HUMAN	zyg-11 homolog B	243	LRR 3.						protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						GAATCATCTTGATATCTCAGA	0.393													12	39	---	---	---	---	PASS
YIPF1	54432	broad.mit.edu	37	1	54332003	54332003	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54332003G>A	uc001cvu.2	-	9	1038	c.701C>T	c.(700-702)GCC>GTC	p.A234V	YIPF1_uc001cvv.2_RNA|YIPF1_uc001cvw.2_RNA|YIPF1_uc001cvx.2_RNA|YIPF1_uc001cvy.2_RNA	NM_018982	NP_061855	Q9Y548	YIPF1_HUMAN	Yip1 domain family, member 1	234	Helical; (Potential).					integral to membrane|transport vesicle				large_intestine(1)|ovary(1)	2						GATGCCCAGGGCAATCATGAC	0.483													3	55	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94476403	94476403	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94476403G>T	uc001dqh.2	-	40	5771	c.5667C>A	c.(5665-5667)TAC>TAA	p.Y1889*	ABCA4_uc001dqi.1_Nonsense_Mutation_p.Y8*|ABCA4_uc009wdp.1_Nonsense_Mutation_p.Y157*	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	1889	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)		TCAGGAGGAAGTACACCACCC	0.582													10	35	---	---	---	---	PASS
ABCA4	24	broad.mit.edu	37	1	94564377	94564377	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94564377G>T	uc001dqh.2	-	6	845	c.741C>A	c.(739-741)AAC>AAA	p.N247K	ABCA4_uc010otn.1_Missense_Mutation_p.N247K	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	247	Extracellular.		N -> S (in STGD1).		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)		AGAAGTCCACGTTGGCATACA	0.562													15	54	---	---	---	---	PASS
COL11A1	1301	broad.mit.edu	37	1	103405991	103405991	+	Splice_Site	SNP	C	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103405991C>A	uc001dul.2	-	43	3595	c.3277_splice	c.e43-1	p.G1093_splice	COL11A1_uc001duk.2_Splice_Site_p.G289_splice|COL11A1_uc001dum.2_Splice_Site_p.G1105_splice|COL11A1_uc001dun.2_Splice_Site_p.G1054_splice|COL11A1_uc009weh.2_Splice_Site_p.G977_splice	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A						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)		CTTTTTCTCCCTGTATTGAAT	0.458													10	24	---	---	---	---	PASS
CD53	963	broad.mit.edu	37	1	111437650	111437650	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111437650G>C	uc001dzw.2	+	6	567	c.396G>C	c.(394-396)AAG>AAC	p.K132N	CD53_uc001dzx.2_Missense_Mutation_p.K132N|CD53_uc010owa.1_Intron|CD53_uc001dzy.2_Missense_Mutation_p.K132N	NM_001040033	NP_001035122	P19397	CD53_HUMAN	CD53 antigen	132	Extracellular (Potential).				signal transduction	integral to membrane|plasma membrane					0		all_cancers(81;1.06e-05)|all_epithelial(167;1.95e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0264)|Colorectal(144;0.0375)|all cancers(265;0.11)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.141)|LUSC - Lung squamous cell carcinoma(189;0.144)		ATAGCACCAAGGCAGCGTGGG	0.517													20	72	---	---	---	---	PASS
C1orf103	55791	broad.mit.edu	37	1	111494385	111494385	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111494385A>G	uc001eaa.2	-	2	1377	c.1121T>C	c.(1120-1122)GTT>GCT	p.V374A	C1orf103_uc001dzz.2_Intron|C1orf103_uc001eab.2_Intron|C1orf103_uc001eac.1_Intron	NM_018372	NP_060842	Q5T3J3	LRIF1_HUMAN	receptor-interacting factor 1 isoform 1	374					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear matrix	protein binding				0		all_cancers(81;1.02e-05)|all_epithelial(167;1.87e-05)|all_lung(203;0.000234)|Lung NSC(277;0.000451)		Lung(183;0.0155)|Colorectal(144;0.0314)|all cancers(265;0.082)|LUSC - Lung squamous cell carcinoma(189;0.0826)|Epithelial(280;0.0891)|COAD - Colon adenocarcinoma(174;0.134)		TGATGGCAGAACATCTGTCCC	0.393													72	186	---	---	---	---	PASS
JTB	10899	broad.mit.edu	37	1	153949705	153949705	+	Silent	SNP	A	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153949705A>T	uc001fds.2	-	1	747	c.24T>A	c.(22-24)CCT>CCA	p.P8P		NM_006694	NP_006685	O76095	JTB_HUMAN	jumping translocation breakpoint precursor	8					apoptosis|cell cycle cytokinesis|mitosis|positive regulation of protein kinase activity	integral to plasma membrane|membrane fraction|microtubule organizing center|midbody|mitochondrion|spindle	protein kinase binding				0	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GGGGGAGGCCAGGCCTCCCGG	0.642													22	65	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158582749	158582749	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158582749T>C	uc001fst.1	-	51	7191	c.6992A>G	c.(6991-6993)AAG>AGG	p.K2331R		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2331	EF-hand 2.|2 (Potential).				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					GACATAGCCCTTCCTGTGGGA	0.473													8	31	---	---	---	---	PASS
BRP44	25874	broad.mit.edu	37	1	167893736	167893736	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167893736C>T	uc001ges.2	-	2	450	c.149G>A	c.(148-150)TGG>TAG	p.W50*	BRP44_uc001get.2_Nonsense_Mutation_p.W50*|BRP44_uc001geu.2_Nonsense_Mutation_p.W50*|BRP44_uc009wvn.2_Nonsense_Mutation_p.W50*	NM_015415	NP_056230	O95563	BR44_HUMAN	brain protein 44	50						mitochondrion					0	all_hematologic(923;0.215)			KIRC - Kidney renal clear cell carcinoma(1967;0.247)		AAGACTTACCCATTTCATAAT	0.294													4	17	---	---	---	---	PASS
TIPRL	261726	broad.mit.edu	37	1	168153162	168153162	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168153162C>T	uc001gfg.2	+	2	272	c.127C>T	c.(127-129)CCA>TCA	p.P43S	TIPRL_uc001gfh.2_Missense_Mutation_p.P43S|TIPRL_uc001gff.2_Missense_Mutation_p.P43S	NM_152902	NP_690866	O75663	TIPRL_HUMAN	TIP41, TOR signalling pathway regulator-like	43					DNA damage checkpoint|negative regulation of protein phosphatase type 2A activity	cytoplasm	protein binding			ovary(1)	1	all_hematologic(923;0.215)					ATTACATATGCCATCTCTCCC	0.388													27	121	---	---	---	---	PASS
SEC16B	89866	broad.mit.edu	37	1	177906454	177906454	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177906454A>G	uc001gli.1	-	19	2488	c.2398T>C	c.(2398-2400)TCA>CCA	p.S800P	SEC16B_uc001glk.1_Missense_Mutation_p.S477P|SEC16B_uc009wwy.1_Missense_Mutation_p.S355P|SEC16B_uc001glh.1_Missense_Mutation_p.S459P|SEC16B_uc009wwz.1_Missense_Mutation_p.S459P|SEC16B_uc001glj.1_Missense_Mutation_p.S801P	NM_033127	NP_149118	Q96JE7	SC16B_HUMAN	leucine zipper transcription regulator 2	800					protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane				ovary(3)|central_nervous_system(1)	4						TCAGGAACTGAGTAAAAAGGC	0.637													10	21	---	---	---	---	PASS
PPFIA4	8497	broad.mit.edu	37	1	203013203	203013203	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203013203C>A	uc009xaj.2	+	8	922	c.922C>A	c.(922-924)CAC>AAC	p.H308N	PPFIA4_uc010pqf.1_5'Flank			O75335	LIPA4_HUMAN	SubName: Full=Liprin alpha4;	Error:Variant_position_missing_in_O75335_after_alignment					cell communication	cell surface|cytoplasm	protein binding			ovary(4)|skin(1)	5						GTTTGAGCACCACAAGGCCCT	0.622													7	21	---	---	---	---	PASS
TRAF5	7188	broad.mit.edu	37	1	211542827	211542827	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211542827G>A	uc001hih.2	+	9	883	c.823G>A	c.(823-825)GAA>AAA	p.E275K	TRAF5_uc001hii.2_Missense_Mutation_p.E275K|TRAF5_uc010psx.1_Missense_Mutation_p.E286K|TRAF5_uc010psy.1_Missense_Mutation_p.E169K|TRAF5_uc001hij.2_Missense_Mutation_p.E275K	NM_004619	NP_004610	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	275	Potential.				apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis	CD40 receptor complex|centrosome|internal side of plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(2)|ovary(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		AGAACAGAAAGAAAGTAAAAT	0.353													27	122	---	---	---	---	PASS
RAB3GAP2	25782	broad.mit.edu	37	1	220445640	220445640	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220445640G>T	uc010puk.1	-	1	204	c.40C>A	c.(40-42)CTC>ATC	p.L14I	RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_5'UTR|RAB3GAP2_uc010pum.1_Missense_Mutation_p.L14I	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	14					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)		GCGGCCTGGAGGTCCTGGAAG	0.657													9	11	---	---	---	---	PASS
CHML	1122	broad.mit.edu	37	1	241797696	241797696	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241797696A>T	uc001hzd.2	-	1	1537	c.1373T>A	c.(1372-1374)GTA>GAA	p.V458E	OPN3_uc001hza.2_Intron|OPN3_uc001hzb.2_Intron|OPN3_uc001hzc.2_Intron	NM_001821	NP_001812	P26374	RAE2_HUMAN	choroideremia-like Rab escort protein 2	458					intracellular protein transport|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(4)|skin(2)	6	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			TGTAATGAGTACTGCCCTAGA	0.403													49	136	---	---	---	---	PASS
OR1C1	26188	broad.mit.edu	37	1	247921449	247921449	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247921449G>C	uc010pza.1	-	1	260	c.260C>G	c.(259-261)ACT>AGT	p.T87S		NM_012353	NP_036485	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C,	87	Extracellular (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)			CTTGGTGCCAGTCAAGATATT	0.463													8	27	---	---	---	---	PASS
UGGT1	56886	broad.mit.edu	37	2	128867214	128867214	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128867214G>A	uc002tps.2	+	5	593	c.415G>A	c.(415-417)GCT>ACT	p.A139T	UGGT1_uc010fme.1_Missense_Mutation_p.A14T|UGGT1_uc002tpr.2_Missense_Mutation_p.A115T	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1	139					'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1						ACAGATAGCAGCTGATGAACC	0.363													18	67	---	---	---	---	PASS
UGGT1	56886	broad.mit.edu	37	2	128867224	128867224	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128867224C>A	uc002tps.2	+	5	603	c.425C>A	c.(424-426)CCT>CAT	p.P142H	UGGT1_uc010fme.1_Missense_Mutation_p.P17H|UGGT1_uc002tpr.2_Missense_Mutation_p.P118H	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1	142					'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1						GCTGATGAACCTCCACCAGAA	0.373													20	74	---	---	---	---	PASS
GALNT13	114805	broad.mit.edu	37	2	155099221	155099221	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155099221G>T	uc002tyr.3	+	6	1056	c.489G>T	c.(487-489)AAG>AAT	p.K163N	GALNT13_uc002tyt.3_Missense_Mutation_p.K163N|GALNT13_uc010foc.1_5'UTR	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	163	Lumenal (Potential).|Catalytic subdomain A.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						ATTTTCTCAAGTTGACATTAG	0.333													7	39	---	---	---	---	PASS
COBLL1	22837	broad.mit.edu	37	2	165557144	165557144	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165557144C>T	uc010zcw.1	-	13	1787	c.1663G>A	c.(1663-1665)GAT>AAT	p.D555N	COBLL1_uc002ucp.2_Missense_Mutation_p.D489N|COBLL1_uc002ucq.2_Missense_Mutation_p.D450N|COBLL1_uc010zcx.1_Missense_Mutation_p.D496N|COBLL1_uc002ucs.1_RNA|COBLL1_uc002ucn.2_5'Flank|COBLL1_uc002uco.2_Missense_Mutation_p.D219N	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	527										ovary(2)|pancreas(1)	3						TTTATTATATCAGTAGATACA	0.363													35	145	---	---	---	---	PASS
HNRNPA3	220988	broad.mit.edu	37	2	178084035	178084035	+	3'UTR	SNP	A	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178084035A>C	uc002ulb.1	+	10					HNRNPA3_uc002ulc.1_3'UTR|HNRNPA3_uc002uld.2_3'UTR|HNRNPA3_uc002ule.2_3'UTR	NM_194247	NP_919223	P51991	ROA3_HUMAN	heterogeneous nuclear ribonucleoprotein A3							catalytic step 2 spliceosome|nucleolus|nucleoplasm	nucleotide binding|protein binding|RNA binding			ovary(2)	2						TAAAAACAGCAGAAAAGGGTA	0.313													17	45	---	---	---	---	PASS
ORC2L	4999	broad.mit.edu	37	2	201776015	201776015	+	3'UTR	SNP	A	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201776015A>T	uc002uwr.2	-	18						NM_006190	NP_006181	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2						cell cycle checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0						TCAAGAATAAAGGAAAGCTTC	0.383													10	36	---	---	---	---	PASS
STK11IP	114790	broad.mit.edu	37	2	220465991	220465991	+	Silent	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220465991C>T	uc002vml.2	+	3	172	c.129C>T	c.(127-129)AGC>AGT	p.S43S	STK11IP_uc010zlj.1_Silent_p.S32S|STK11IP_uc010zlk.1_Silent_p.S32S|STK11IP_uc010zll.1_Silent_p.S32S|STK11IP_uc002vmm.1_Silent_p.S32S	NM_052902	NP_443134	Q8N1F8	S11IP_HUMAN	LKB1 interacting protein	43					protein localization	cytoplasm	protein kinase binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCACCCTGAGCCTGCTGACTC	0.552													17	46	---	---	---	---	PASS
TRIP12	9320	broad.mit.edu	37	2	230642131	230642131	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230642131G>T	uc002vpw.1	-	36	5313	c.5204C>A	c.(5203-5205)TCA>TAA	p.S1735*	TRIP12_uc002vpx.1_Nonsense_Mutation_p.S1783*|TRIP12_uc002vpy.1_Nonsense_Mutation_p.S1465*	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1735					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		CAAATCGTGTGATGTCAGTGA	0.403													53	185	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10188215	10188215	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10188215A>G	uc003bvc.2	+	2	571	c.358A>G	c.(358-360)AGA>GGA	p.R120G	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	120	Involved in binding to CCT complex.				anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.R120fs*38(1)|p.R120fs*39(1)|p.?(1)|p.R120*(1)|p.R120fs*34(1)|p.F119fs*11(1)|p.D121fs*10(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTGGCTCTTCAGAGATGCAGG	0.363		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				40	92	---	---	---	---	PASS
XCR1	2829	broad.mit.edu	37	3	46063001	46063001	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46063001C>T	uc003cpe.2	-	3	663	c.439G>A	c.(439-441)GTG>ATG	p.V147M	uc003cpd.1_5'Flank|XCR1_uc003cpf.2_Missense_Mutation_p.V147M	NM_005283	NP_005274	P46094	XCR1_HUMAN	XC chemokine receptor 1	147	Helical; Name=4; (Potential).				chemotaxis|G-protein signaling, coupled to cyclic nucleotide second messenger|inflammatory response	integral to plasma membrane	chemokine receptor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		GTCACCAGCACCCGGCAGCGG	0.592													6	8	---	---	---	---	PASS
C3orf45	132228	broad.mit.edu	37	3	50324295	50324295	+	Splice_Site	SNP	T	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50324295T>A	uc003cyz.2	+	3	388	c.361_splice	c.e3+2	p.V121_splice		NM_153215	NP_694947	Q8N112	CC045_HUMAN	hypothetical protein LOC132228							integral to membrane				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		ACCTGAGCGGTATGGACGCAT	0.597													10	19	---	---	---	---	PASS
C3orf37	56941	broad.mit.edu	37	3	128998744	128998744	+	Silent	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128998744C>T	uc003elt.2	+	2	257	c.169C>T	c.(169-171)CTG>TTG	p.L57L	C3orf37_uc003elu.2_Silent_p.L57L|C3orf37_uc003elv.2_Silent_p.L57L|C3orf37_uc003elw.2_Silent_p.L57L	NM_020187	NP_064572	Q96FZ2	CC037_HUMAN	hypothetical protein LOC56941	57										ovary(1)	1						TCTGTCTCGACTGCACTTTGA	0.567													14	50	---	---	---	---	PASS
COL6A6	131873	broad.mit.edu	37	3	130285927	130285927	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130285927A>G	uc010htl.2	+	4	1695	c.1664A>G	c.(1663-1665)GAG>GGG	p.E555G		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	555	VWFA 3.|Nonhelical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8						AGCATCTTGGAGCCTGCAAAC	0.473													36	119	---	---	---	---	PASS
DNAJC13	23317	broad.mit.edu	37	3	132193851	132193851	+	Silent	SNP	A	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132193851A>G	uc003eor.2	+	22	2432	c.2367A>G	c.(2365-2367)GAA>GAG	p.E789E		NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	789							heat shock protein binding			ovary(1)|breast(1)	2						ATACTCTTGAATCTGAAATGA	0.363													31	132	---	---	---	---	PASS
FOXL2	668	broad.mit.edu	37	3	138664421	138664421	+	3'UTR	SNP	A	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138664421A>T	uc003esw.2	-	1					uc003esv.1_5'Flank|C3orf72_uc003esx.1_5'Flank|C3orf72_uc011bmr.1_5'Flank	NM_023067	NP_075555	P58012	FOXL2_HUMAN	forkhead box L2						convergent extension|DNA fragmentation involved in apoptotic nuclear change|embryonic eye morphogenesis|extraocular skeletal muscle development|female somatic sex determination|induction of apoptosis|menstruation|negative regulation of transcription, DNA-dependent|ovarian follicle development|pattern specification process|positive regulation of caspase activity|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	caspase regulator activity|DNA bending activity|double-stranded DNA binding|estrogen receptor 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|ubiquitin conjugating enzyme binding			ovary(266)|large_intestine(1)|skin(1)	268						CTGCACCGGCATGCGGTGGGC	0.706			Mis		granulosa-cell tumour of the ovary		Blepharophimosis|ptosis and epicanthus inversus Types I|II; Premature ovarian failure type III						5	37	---	---	---	---	PASS
EIF2A	83939	broad.mit.edu	37	3	150301775	150301775	+	3'UTR	SNP	A	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150301775A>T	uc003eya.2	+	14					SERP1_uc003exz.2_Intron|EIF2A_uc003eyb.2_3'UTR|EIF2A_uc003eyc.2_3'UTR|EIF2A_uc011bnv.1_3'UTR|EIF2A_uc011bnw.1_3'UTR|EIF2A_uc003eyd.2_3'UTR|uc003eye.1_Intron	NM_032025	NP_114414	Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A						regulation of translation|ribosome assembly	eukaryotic translation initiation factor 2 complex	ribosome binding|translation initiation factor activity|tRNA binding				0		Melanoma(1037;0.0575)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TATACACAGAATATTCCTGTG	0.303													4	6	---	---	---	---	PASS
USP13	8975	broad.mit.edu	37	3	179501956	179501956	+	3'UTR	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179501956G>A	uc003fkh.2	+	21						NM_003940	NP_003931	Q92995	UBP13_HUMAN	ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			TTGGCGAAAAGAAGCCATACG	0.358													10	98	---	---	---	---	PASS
TM4SF19	116211	broad.mit.edu	37	3	196051159	196051159	+	Silent	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196051159G>A	uc003fwl.1	-	4	557	c.432C>T	c.(430-432)TTC>TTT	p.F144F	TM4SF19_uc003fwj.2_RNA|uc003fwk.1_3'UTR|TM4SF19_uc010iad.1_Silent_p.F144F|TM4SF19_uc011btv.1_Silent_p.F118F	NM_138461	NP_612470	Q96DZ7	T4S19_HUMAN	transmembrane 4 L six family member 19	144	Extracellular (Potential).					integral to membrane					0	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;4.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		GCAGGTCTTTGAATGGGTAAC	0.433													15	65	---	---	---	---	PASS
PDCL2	132954	broad.mit.edu	37	4	56435977	56435977	+	Silent	SNP	T	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56435977T>C	uc003hbb.2	-	4	373	c.270A>G	c.(268-270)GGA>GGG	p.G90G		NM_152401	NP_689614	Q8N4E4	PDCL2_HUMAN	phosducin-like 2	90											0	Lung NSC(11;0.00256)|Glioma(25;0.08)|all_epithelial(27;0.0863)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.69e-07)|Lung(4;1.03e-06)|Epithelial(7;0.00669)			CTCTTAATTCTCCAAATTTTT	0.289													4	14	---	---	---	---	PASS
TECRL	253017	broad.mit.edu	37	4	65274994	65274994	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65274994G>C	uc003hcv.2	-	1	185	c.76C>G	c.(76-78)CTG>GTG	p.L26V	TECRL_uc003hcw.2_Missense_Mutation_p.L26V	NM_001010874	NP_001010874	Q5HYJ1	TECRL_HUMAN	steroid 5 alpha-reductase 2-like 2	26					lipid metabolic process	cytoplasm|integral to membrane	oxidoreductase activity, acting on the CH-CH group of donors				0						TCATCCTTCAGTATGAACCGT	0.438													33	115	---	---	---	---	PASS
TECRL	253017	broad.mit.edu	37	4	65274995	65274995	+	Silent	SNP	T	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65274995T>A	uc003hcv.2	-	1	184	c.75A>T	c.(73-75)ATA>ATT	p.I25I	TECRL_uc003hcw.2_Silent_p.I25I	NM_001010874	NP_001010874	Q5HYJ1	TECRL_HUMAN	steroid 5 alpha-reductase 2-like 2	25					lipid metabolic process	cytoplasm|integral to membrane	oxidoreductase activity, acting on the CH-CH group of donors				0						CATCCTTCAGTATGAACCGTG	0.443													34	115	---	---	---	---	PASS
SULT1E1	6783	broad.mit.edu	37	4	70707775	70707775	+	Silent	SNP	T	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70707775T>C	uc003heo.2	-	8	935	c.822A>G	c.(820-822)AAA>AAG	p.K274K		NM_005420	NP_005411	P49888	ST1E1_HUMAN	estrogen sulfotransferase	274					3'-phosphoadenosine 5'-phosphosulfate metabolic process|sulfation|xenobiotic metabolic process	cytosol|nuclear membrane	estrone sulfotransferase activity|flavonol 3-sulfotransferase activity|steroid binding|steroid sulfotransferase activity			ovary(1)	1						GTTTATCAAATTTTTCATTCA	0.308													21	77	---	---	---	---	PASS
SHROOM3	57619	broad.mit.edu	37	4	77661527	77661527	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77661527C>G	uc011cbx.1	+	5	3154	c.2201C>G	c.(2200-2202)TCT>TGT	p.S734C	SHROOM3_uc011cbz.1_Missense_Mutation_p.S558C|SHROOM3_uc003hkf.1_Missense_Mutation_p.S609C|SHROOM3_uc003hkg.2_Missense_Mutation_p.S512C	NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein	734					apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)			GCCTCGGCTTCTTTCAACAGC	0.701													19	49	---	---	---	---	PASS
C4orf37	285555	broad.mit.edu	37	4	98761954	98761954	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98761954G>A	uc003htt.1	-	9	1264	c.1174C>T	c.(1174-1176)CGG>TGG	p.R392W		NM_174952	NP_777612	Q8N412	CD037_HUMAN	hypothetical protein LOC285555	392											0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)		TCTAGGCACCGAGGAGTTGCA	0.363													44	136	---	---	---	---	PASS
SKP2	6502	broad.mit.edu	37	5	36177323	36177323	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36177323A>T	uc003jkc.1	+	9	1172	c.990A>T	c.(988-990)GAA>GAT	p.E330D	SKP2_uc011cou.1_Missense_Mutation_p.E116D|SKP2_uc003jkd.2_Missense_Mutation_p.E330D	NM_005983	NP_005974	Q13309	SKP2_HUMAN	S-phase kinase-associated protein 2 isoform 1	330	LRR 8.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G1/S transition of mitotic cell cycle|S phase of mitotic cell cycle	nucleoplasm|SCF ubiquitin ligase complex	protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4	all_lung(31;5.63e-05)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GCTTTCAGGAATTTTTCCAGC	0.343													26	63	---	---	---	---	PASS
ISL1	3670	broad.mit.edu	37	5	50685530	50685530	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50685530C>T	uc003jor.2	+	4	1077	c.529C>T	c.(529-531)CAG>TAG	p.Q177*		NM_002202	NP_002193	P61371	ISL1_HUMAN	islet-1	177					generation of precursor metabolites and energy|multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3		Lung NSC(810;0.000845)|Breast(144;0.0411)				CGTCCACAAGCAGCCGGAGAA	0.652													13	34	---	---	---	---	PASS
BDP1	55814	broad.mit.edu	37	5	70785431	70785431	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70785431G>A	uc003kbp.1	+	10	1677	c.1414G>A	c.(1414-1416)GCT>ACT	p.A472T	BDP1_uc003kbn.1_Missense_Mutation_p.A472T|BDP1_uc003kbo.2_Missense_Mutation_p.A472T	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	472					regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		GCAAGATGGAGCTAATGAACT	0.388													20	67	---	---	---	---	PASS
ENC1	8507	broad.mit.edu	37	5	73930721	73930721	+	Silent	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73930721G>A	uc003kdc.3	-	2	2721	c.1590C>T	c.(1588-1590)AGC>AGT	p.S530S	ENC1_uc011css.1_Silent_p.S457S	NM_003633	NP_003624	O14682	ENC1_HUMAN	ectodermal-neural cortex (with BTB-like domain)	530	Kelch 5.			YTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQWTKVGDV TAKRMSCHAVASGNKLYVVGGYFGIQRCKTLDCYDPTLDVW NSITTVPYSLIPTAFVSTWKHLPS -> IHSQASCPGGTQD FLLWGVIQNFSACFCL (in Ref. 1; AAC39532).	nervous system development	cytoplasm|cytoskeleton|nuclear matrix	actin binding			ovary(1)|pancreas(1)|skin(1)	3		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		CAGCATGGCAGCTCATGCGCT	0.493													3	89	---	---	---	---	PASS
POLK	51426	broad.mit.edu	37	5	74865216	74865216	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74865216A>G	uc003kdw.2	+	4	403	c.307A>G	c.(307-309)ATA>GTA	p.I103V	POLK_uc003kdx.2_RNA|POLK_uc003kdy.2_RNA|POLK_uc003kdz.2_Missense_Mutation_p.I103V|POLK_uc003kea.2_Missense_Mutation_p.I103V|POLK_uc003keb.2_Missense_Mutation_p.I103V|POLK_uc010izq.2_Missense_Mutation_p.I103V|POLK_uc003kec.2_Missense_Mutation_p.I13V|POLK_uc010izr.2_RNA|POLK_uc010izs.2_RNA|POLK_uc003ked.2_Missense_Mutation_p.I13V|POLK_uc003kee.2_Missense_Mutation_p.I103V|POLK_uc003kef.2_Missense_Mutation_p.I13V	NM_016218	NP_057302	Q9UBT6	POLK_HUMAN	DNA-directed DNA polymerase kappa	103	UmuC.				DNA replication|nucleotide-excision repair, DNA gap filling	nucleus	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			ovary(2)|kidney(2)	4		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		GAGCAATACCATAGTGCACAT	0.338								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					12	48	---	---	---	---	PASS
PPIP5K2	23262	broad.mit.edu	37	5	102513641	102513641	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102513641A>C	uc003kod.3	+	23	3233	c.2714A>C	c.(2713-2715)AAT>ACT	p.N905T	PPIP5K2_uc011cva.1_RNA|PPIP5K2_uc003koe.2_Missense_Mutation_p.N905T|PPIP5K2_uc003kof.2_Missense_Mutation_p.N206T	NM_015216	NP_056031	O43314	VIP2_HUMAN	Histidine acid phosphatase domain containing 1	905					inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity			ovary(1)|skin(1)	2						GAAGACAAAAATTTGCCATCT	0.393													31	103	---	---	---	---	PASS
LMNB1	4001	broad.mit.edu	37	5	126158526	126158526	+	Silent	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126158526C>T	uc003kud.1	+	8	1808	c.1440C>T	c.(1438-1440)GTC>GTT	p.V480V	LMNB1_uc010jdb.1_RNA|LMNB1_uc011cxb.1_Silent_p.V270V	NM_005573	NP_005564	P20700	LMNB1_HUMAN	lamin B1	480	Tail.				cellular component disassembly involved in apoptosis	lamin filament|nuclear inner membrane	protein binding|structural molecule activity			kidney(1)|central_nervous_system(1)	2		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)		ACACATCAGTCAGTTATAAAT	0.388													9	54	---	---	---	---	PASS
NSD1	64324	broad.mit.edu	37	5	176720945	176720945	+	Silent	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176720945C>T	uc003mfr.3	+	23	6714	c.6576C>T	c.(6574-6576)TTC>TTT	p.F2192F	NSD1_uc003mft.3_Silent_p.F1923F|NSD1_uc011dfx.1_Silent_p.F1840F	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2192					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		GGATGCTTTTCATTTCCAAAC	0.557			T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			26	74	---	---	---	---	PASS
RREB1	6239	broad.mit.edu	37	6	7248780	7248780	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7248780C>G	uc003mxc.2	+	12	5033	c.4643C>G	c.(4642-4644)ACC>AGC	p.T1548S	RREB1_uc003mxb.2_Missense_Mutation_p.T1603S|RREB1_uc010jnx.2_Missense_Mutation_p.T1337S	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform	1548	C2H2-type 15.				multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				TGCGAGCGAACCTTCACCTTG	0.547													9	47	---	---	---	---	PASS
TUBB	203068	broad.mit.edu	37	6	30688293	30688293	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30688293A>C	uc003nrl.2	+	1	137	c.10A>C	c.(10-12)ATC>CTC	p.I4L	MDC1_uc003nrg.3_5'Flank|TUBB_uc003nrk.1_Missense_Mutation_p.I4L|TUBB_uc011dmq.1_5'Flank	NM_178014	NP_821133	P07437	TBB5_HUMAN	tubulin, beta	4					cellular component movement|G2/M transition of mitotic cell cycle|microtubule-based movement|natural killer cell mediated cytotoxicity|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|MHC class I protein binding			ovary(1)	1					Colchicine(DB01394)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)	CATGAGGGAAATCGTGCACAT	0.413													26	84	---	---	---	---	PASS
BAT2	7916	broad.mit.edu	37	6	31594808	31594808	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31594808G>A	uc003nvb.3	+	11	1372	c.1123G>A	c.(1123-1125)GGC>AGC	p.G375S	BAT2_uc011dnv.1_RNA|BAT2_uc003nvc.3_Missense_Mutation_p.G375S	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	375	4 X 57 AA type A repeats.|2 X type B repeats.|2-1.					cytoplasm|nucleus	protein binding				0						TGAAGCAGATGGCAAAAAGGG	0.562													13	87	---	---	---	---	PASS
C6orf47	57827	broad.mit.edu	37	6	31627604	31627604	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31627604T>A	uc003nvm.1	-	1	946	c.121A>T	c.(121-123)AGT>TGT	p.S41C		NM_021184	NP_067007	O95873	CF047_HUMAN	G4 protein	41										ovary(1)	1						TCCCAGTCACTTCCTGAATTC	0.602													9	27	---	---	---	---	PASS
PSMB8	5696	broad.mit.edu	37	6	32808790	32808790	+	Silent	SNP	T	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32808790T>A	uc003oce.2	-	6	820	c.777A>T	c.(775-777)GTA>GTT	p.V259V	TAP2_uc011dqf.1_5'Flank|TAP2_uc003ocb.1_5'Flank|TAP2_uc003occ.2_5'Flank|TAP2_uc003ocd.2_5'Flank|PSMB8_uc003ocf.2_Silent_p.V255V	NM_148919	NP_683720	P28062	PSB8_HUMAN	proteasome beta 8 subunit isoform E2 proprotein	259					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|type I interferon-mediated signaling pathway|viral reproduction	cytoplasm|nucleus|proteasome core complex	protein binding|threonine-type endopeptidase activity			skin(1)	1						CTGTACTTTCTACTTTCACCC	0.502													22	69	---	---	---	---	PASS
RXRB	6257	broad.mit.edu	37	6	33163416	33163416	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33163416A>G	uc003odb.2	-	7	1366	c.1187T>C	c.(1186-1188)CTC>CCC	p.L396P	RXRB_uc003odc.2_Missense_Mutation_p.L396P|RXRB_uc003odd.2_Missense_Mutation_p.L300P|RXRB_uc011dqr.1_Missense_Mutation_p.L206P|RXRB_uc011dqs.1_3'UTR	NM_021976	NP_068811	P28702	RXRB_HUMAN	retinoid X receptor, beta	396	Ligand-binding (By similarity).				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	ligand-regulated transcription factor activity|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			ovary(3)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etretinate(DB00926)|Tazarotene(DB00799)|Tretinoin(DB00755)	TGTGGCAAGGAGGATGCCATC	0.567													18	38	---	---	---	---	PASS
STK38	11329	broad.mit.edu	37	6	36508022	36508022	+	5'UTR	SNP	T	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36508022T>A	uc003omg.2	-	1					STK38_uc003omh.2_Intron|STK38_uc003omi.2_Intron	NM_007271	NP_009202	Q15208	STK38_HUMAN	serine/threonine kinase 38						intracellular protein kinase cascade|negative regulation of MAP kinase activity	cytoplasm|MLL5-L complex	ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6						agatttggagttagaatccac	0.139													21	91	---	---	---	---	PASS
KIAA0240	23506	broad.mit.edu	37	6	42796273	42796273	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42796273C>T	uc003osn.1	+	6	353	c.202C>T	c.(202-204)CTT>TTT	p.L68F	KIAA0240_uc003osm.1_Missense_Mutation_p.L68F|KIAA0240_uc011duw.1_Missense_Mutation_p.L68F|KIAA0240_uc003oso.1_Missense_Mutation_p.L68F|KIAA0240_uc003osp.1_Missense_Mutation_p.L68F	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506	68										ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)			AAGCAACCAGCTTGGAGAAGG	0.428													15	68	---	---	---	---	PASS
ELOVL5	60481	broad.mit.edu	37	6	53135376	53135376	+	Intron	SNP	A	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53135376A>C	uc003pbq.1	-						ELOVL5_uc003pbr.1_Intron|ELOVL5_uc011dwx.1_Intron|ELOVL5_uc003pbs.1_Intron|ELOVL5_uc003pbt.3_RNA	NM_021814	NP_068586	Q9NYP7	ELOV5_HUMAN	elongation of very long chain fatty acids-like						fatty acid elongation, monounsaturated fatty acid|fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Lung NSC(77;0.116)					AGTCCCAGAGAAGGGTGAGAT	0.328													14	33	---	---	---	---	PASS
TINAG	27283	broad.mit.edu	37	6	54214608	54214608	+	Missense_Mutation	SNP	C	T	T	rs35758529		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54214608C>T	uc003pcj.2	+	7	1140	c.994C>T	c.(994-996)CGG>TGG	p.R332W	TINAG_uc010jzt.2_RNA	NM_014464	NP_055279	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	332					cell adhesion|immune response|Malpighian tubule morphogenesis|proteolysis	basement membrane	cysteine-type endopeptidase activity|nucleotide binding|polysaccharide binding|scavenger receptor activity			ovary(3)|central_nervous_system(1)	4	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			GCGAGGAAAACGGCATGCCAC	0.458													28	106	---	---	---	---	PASS
EYS	346007	broad.mit.edu	37	6	66112428	66112428	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66112428G>A	uc011dxu.1	-	7	1665	c.1127C>T	c.(1126-1128)TCA>TTA	p.S376L	EYS_uc003peq.2_Missense_Mutation_p.S376L|EYS_uc003per.1_Missense_Mutation_p.S376L	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	376	EGF-like 5.				response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						CAAAGGAAATGACTCACATGA	0.284													7	66	---	---	---	---	PASS
HTR1E	3354	broad.mit.edu	37	6	87725418	87725418	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87725418G>T	uc003pli.2	+	2	1069	c.366G>T	c.(364-366)TGG>TGT	p.W122C		NM_000865	NP_000856	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E	122	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane	protein binding|serotonin binding|serotonin receptor activity			ovary(2)|skin(1)	3		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Eletriptan(DB00216)	ACAGGTACTGGGCCATCACCA	0.557													17	49	---	---	---	---	PASS
IFNGR1	3459	broad.mit.edu	37	6	137528120	137528120	+	Silent	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137528120G>A	uc003qho.2	-	2	283	c.180C>T	c.(178-180)ACC>ACT	p.T60T	IFNGR1_uc011edm.1_Silent_p.T32T|IFNGR1_uc011edn.1_Silent_p.T50T	NM_000416	NP_000407	P15260	INGR1_HUMAN	interferon gamma receptor 1 precursor	60	Extracellular (Potential).				regulation of interferon-gamma-mediated signaling pathway|response to virus	integral to plasma membrane	interferon-gamma receptor activity			upper_aerodigestive_tract(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	TTACCTCTACGGTAAAAACAG	0.373													19	76	---	---	---	---	PASS
C7orf42	55069	broad.mit.edu	37	7	66420696	66420696	+	3'UTR	SNP	A	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66420696A>C	uc003tvk.2	+	7					C7orf42_uc010lah.2_RNA|C7orf42_uc003tvl.2_3'UTR	NM_017994	NP_060464	Q9NWD8	CG042_HUMAN	hypothetical protein LOC55069							integral to membrane				ovary(1)	1						AAATTGGTCCAATAATGCACG	0.433													3	5	---	---	---	---	PASS
HIP1	3092	broad.mit.edu	37	7	75168737	75168737	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75168737C>A	uc003uds.1	-	30	3008	c.2967G>T	c.(2965-2967)GAG>GAT	p.E989D	HIP1_uc011kfz.1_Missense_Mutation_p.E815D	NM_005338	NP_005329	O00291	HIP1_HUMAN	huntingtin interacting protein 1	989	I/LWEQ.				activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8						CATTTTCTAGCTCTAGCACCC	0.378			T	PDGFRB	CMML								80	269	---	---	---	---	PASS
FZD1	8321	broad.mit.edu	37	7	90895797	90895797	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90895797G>T	uc003ula.2	+	1	2015	c.1602G>T	c.(1600-1602)ATG>ATT	p.M534I		NM_003505	NP_003496	Q9UP38	FZD1_HUMAN	frizzled 1 precursor	534	Cytoplasmic (Potential).				autocrine signaling|axonogenesis|brain development|canonical Wnt receptor signaling pathway involved in mesenchymal stem cell differentiation|canonical Wnt receptor signaling pathway involved in osteoblast differentiation|embryo development|epithelial cell differentiation|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|lung alveolus development|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to drug|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cell surface|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|receptor binding|Wnt receptor activity|Wnt-protein binding				0	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			AGAAGCTCATGGTGCGCATTG	0.597													33	89	---	---	---	---	PASS
FAM66D	100132923	broad.mit.edu	37	8	12216907	12216907	+	Intron	SNP	T	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12216907T>G	uc011kxp.1	+						uc003wvm.1_Intron|uc010lsh.1_3'UTR|FAM66A_uc010lsi.2_5'Flank					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0						TTAGATGACATGAGAGAACAC	0.408													10	90	---	---	---	---	PASS
PPP2R2A	5520	broad.mit.edu	37	8	26217736	26217736	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26217736G>T	uc003xeu.2	+	5	700	c.398G>T	c.(397-399)GGG>GTG	p.G133V	PPP2R2A_uc003xek.2_Intron|PPP2R2A_uc011laf.1_Missense_Mutation_p.G143V	NM_002717	NP_002708	P63151	2ABA_HUMAN	alpha isoform of regulatory subunit B55, protein	133					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)		AGACCAGAAGGGTATAACTTG	0.328													5	51	---	---	---	---	PASS
CALB1	793	broad.mit.edu	37	8	91090640	91090640	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91090640C>A	uc003yel.1	-	3	374	c.192G>T	c.(190-192)CAG>CAT	p.Q64H	CALB1_uc003yem.1_RNA|CALB1_uc011lge.1_Missense_Mutation_p.Q7H	NM_004929	NP_004920	P05937	CALB1_HUMAN	calbindin 1	64	EF-hand 2.					nucleus	calcium ion binding|vitamin D binding			pancreas(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.00953)			TTTGCCCATACTGATCCACAA	0.299													8	136	---	---	---	---	PASS
ELAVL2	1993	broad.mit.edu	37	9	23705049	23705049	+	Silent	SNP	A	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23705049A>G	uc003zpu.2	-	4	629	c.354T>C	c.(352-354)AGT>AGC	p.S118S	ELAVL2_uc003zps.2_Silent_p.S118S|ELAVL2_uc003zpt.2_Silent_p.S118S|ELAVL2_uc003zpv.2_Silent_p.S118S|ELAVL2_uc003zpw.2_Silent_p.S118S	NM_004432	NP_004423	Q12926	ELAV2_HUMAN	ELAV (embryonic lethal, abnormal vision,	118					regulation of transcription, DNA-dependent		mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		TAGAAGCTGAACTTGGGCGAG	0.403													20	47	---	---	---	---	PASS
ACO1	48	broad.mit.edu	37	9	32427337	32427337	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32427337G>A	uc003zqw.3	+	12	1542	c.1387G>A	c.(1387-1389)GTG>ATG	p.V463M	ACO1_uc010mjh.1_Missense_Mutation_p.V297M|ACO1_uc003zqx.3_Missense_Mutation_p.V463M|ACO1_uc003zqy.3_RNA	NM_002197	NP_002188	P21399	ACOC_HUMAN	aconitase 1	463					citrate metabolic process|response to iron(II) ion|tricarboxylic acid cycle	cytosol|endoplasmic reticulum|Golgi apparatus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron-responsive element binding|isocitrate hydro-lyase (cis-aconitate-forming) activity|metal ion binding|protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		TGGCCTGAACGTGATGCCTTA	0.517													19	49	---	---	---	---	PASS
RUSC2	9853	broad.mit.edu	37	9	35547730	35547730	+	Silent	SNP	A	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35547730A>T	uc003zww.2	+	2	1467	c.1212A>T	c.(1210-1212)CTA>CTT	p.L404L	RUSC2_uc010mkq.2_RNA|RUSC2_uc003zwx.3_Silent_p.L404L	NM_014806	NP_055621	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	404						cytosol				ovary(1)	1			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			CCTGTGACCTATCTTCCCAAT	0.562													46	80	---	---	---	---	PASS
C9orf84	158401	broad.mit.edu	37	9	114454520	114454520	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114454520A>T	uc004bfr.2	-	25	3680	c.3545T>A	c.(3544-3546)GTG>GAG	p.V1182E	C9orf84_uc011lwt.1_RNA|C9orf84_uc004bfq.2_Missense_Mutation_p.V1143E|C9orf84_uc010mug.2_Missense_Mutation_p.V1093E	NM_173521	NP_775792	Q5VXU9	CI084_HUMAN	hypothetical protein LOC158401 isoform 1	1182										ovary(2)	2						GTATGAAGTCACAGGTGGTAA	0.373													29	86	---	---	---	---	PASS
ASS1	445	broad.mit.edu	37	9	133333803	133333803	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133333803G>T	uc004bzm.2	+	5	546	c.190G>T	c.(190-192)GTC>TTC	p.V64F	ASS1_uc004bzn.2_Missense_Mutation_p.V64F|ASS1_uc010mza.2_Missense_Mutation_p.V140F|ASS1_uc004bzo.2_Missense_Mutation_p.V64F|ASS1_uc010mzb.2_Missense_Mutation_p.V102F|ASS1_uc004bzp.2_Missense_Mutation_p.V64F|ASS1_uc010mzc.2_Missense_Mutation_p.V64F	NM_000050	NP_000041	P00966	ASSY_HUMAN	argininosuccinate synthetase 1	64					arginine biosynthetic process|urea cycle	cytosol	argininosuccinate synthase activity|ATP binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	CATTGAGGATGTCAGCAGGGA	0.602													22	38	---	---	---	---	PASS
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	Missense_Mutation	SNP	A	G	G	rs2257765		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38654432A>G	uc010qex.1	+	5	599	c.524A>G	c.(523-525)AAT>AGT	p.N175S	HSD17B7P2_uc001izq.2_RNA|HSD17B7P2_uc001izo.1_RNA|HSD17B7P2_uc001izp.1_Missense_Mutation_p.N173S					SubName: Full=cDNA FLJ60462, highly similar to 3-keto-steroid reductase (EC 1.1.1.270);												0						TCATCTCGCAATGCAAGGAAA	0.453													3	66	---	---	---	---	PASS
ANK3	288	broad.mit.edu	37	10	61834076	61834076	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61834076G>T	uc001jky.2	-	37	6755	c.6563C>A	c.(6562-6564)CCA>CAA	p.P2188Q	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	2188					establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						AGGCTCCTCTGGTTGGGTCTG	0.448													5	128	---	---	---	---	PASS
DNA2	1763	broad.mit.edu	37	10	70227941	70227941	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70227941C>T	uc001jof.2	-	3	638	c.638G>A	c.(637-639)GGC>GAC	p.G213D	DNA2_uc001jog.1_Missense_Mutation_p.G127D|DNA2_uc001joh.1_RNA	NM_001080449	NP_001073918	P51530	DNA2L_HUMAN	DNA replication helicase 2 homolog	127					base-excision repair|DNA replication, removal of RNA primer|mitochondrial DNA repair|mitochondrial DNA replication|positive regulation of DNA replication|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	mitochondrial nucleoid|nucleoplasm	5'-flap endonuclease activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|site-specific endodeoxyribonuclease activity, specific for altered base				0						TATGCTGGTGCCAGAAATCAG	0.328													18	52	---	---	---	---	PASS
ENTPD1	953	broad.mit.edu	37	10	97607250	97607250	+	Silent	SNP	T	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97607250T>C	uc001klh.3	+	7	1185	c.861T>C	c.(859-861)TAT>TAC	p.Y287Y	ENTPD1_uc001kli.3_Silent_p.Y294Y|uc001klg.1_Intron|ENTPD1_uc010qoj.1_Silent_p.Y299Y|ENTPD1_uc010qok.1_Silent_p.Y179Y|ENTPD1_uc010qol.1_Silent_p.Y179Y|ENTPD1_uc010qom.1_Intron|ENTPD1_uc010qon.1_Silent_p.Y149Y|ENTPD1_uc009xva.2_Silent_p.Y149Y|ENTPD1_uc009xuz.2_Intron	NM_001776	NP_001767	P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	287	Extracellular (Potential).				cell adhesion	integral to plasma membrane	ATP binding			ovary(3)	3		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		ATCCTGGATATAAGAAGGTAG	0.413													30	127	---	---	---	---	PASS
UBTD1	80019	broad.mit.edu	37	10	99330453	99330453	+	3'UTR	SNP	C	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99330453C>A	uc001knv.1	+	3					ANKRD2_uc001knw.2_5'Flank|ANKRD2_uc009xvu.2_5'Flank	NM_024954	NP_079230	Q9HAC8	UBTD1_HUMAN	ubiquitin domain containing 1												0		Colorectal(252;0.162)		Epithelial(162;3.04e-10)|all cancers(201;2.86e-08)		TTCCCGGTACCCAGGGAGCAG	0.632													2	0	---	---	---	---	PASS
TACC2	10579	broad.mit.edu	37	10	123846868	123846868	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123846868T>C	uc001lfv.2	+	4	5213	c.4853T>C	c.(4852-4854)TTT>TCT	p.F1618S	TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Missense_Mutation_p.F1618S|TACC2_uc010qtv.1_Missense_Mutation_p.F1618S	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	1618						microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CCCGGGGACTTTGCTCACACA	0.582													19	73	---	---	---	---	PASS
FAM196A	642938	broad.mit.edu	37	10	128974169	128974169	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128974169G>A	uc001lju.1	-	1	532	c.491C>T	c.(490-492)GCG>GTG	p.A164V	DOCK1_uc001ljt.2_Intron|DOCK1_uc010qun.1_Intron|FAM196A_uc010quo.1_Missense_Mutation_p.A164V|FAM196A_uc001ljv.1_Missense_Mutation_p.A164V|FAM196A_uc009yap.1_Missense_Mutation_p.A164V	NM_001039762	NP_001034851	Q6ZSG2	F196A_HUMAN	hypothetical protein LOC642938	164										ovary(2)	2						CACCCGCCCCGCGCCACATGG	0.547													19	68	---	---	---	---	PASS
MKI67	4288	broad.mit.edu	37	10	129913433	129913433	+	Silent	SNP	A	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129913433A>C	uc001lke.2	-	7	1434	c.1239T>G	c.(1237-1239)ACT>ACG	p.T413T	MKI67_uc001lkf.2_Intron|MKI67_uc009yav.1_Intron|MKI67_uc009yaw.1_Intron	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	413					cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTTCTGGCTTAGTGGCAGAGT	0.428													21	122	---	---	---	---	PASS
JAKMIP3	282973	broad.mit.edu	37	10	133930691	133930691	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133930691G>C	uc001lkx.3	+	2	246	c.246G>C	c.(244-246)GAG>GAC	p.E82D		NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		TGCACGAGGAGAAGATGAAGG	0.592													18	58	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1267138	1267138	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1267138G>A	uc009ycr.1	+	49	10903	c.10777G>A	c.(10777-10779)GCC>ACC	p.A3593T	MUC5B_uc001ltb.2_Missense_Mutation_p.A3013T	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	3010	7 X Cys-rich subdomain repeats.|Thr-rich.|17 X approximate tandem repeats, Ser/Thr- rich.			Missing (in Ref. 6; AAB61398).	cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		TGGATCCACGGCCATCCCGTC	0.647													4	162	---	---	---	---	PASS
LOC650368	650368	broad.mit.edu	37	11	3427759	3427759	+	RNA	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3427759C>T	uc010qxs.1	+	9		c.752C>T			LOC650368_uc001lxx.2_RNA|LOC650368_uc001lxy.2_RNA	NR_024248				Homo sapiens cDNA FLJ41654 fis, clone FEBRA2025463, weakly  similar to Homo sapiens HMT-1 mRNA for beta-1,4 mannosyltransferase.												0						TGTCTGCACACGTCCTGCAGT	0.612													4	46	---	---	---	---	PASS
NUP160	23279	broad.mit.edu	37	11	47828687	47828687	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47828687G>A	uc001ngm.2	-	19	2466	c.2381C>T	c.(2380-2382)TCT>TTT	p.S794F	NUP160_uc009ylw.2_RNA	NM_015231	NP_056046	Q12769	NU160_HUMAN	nucleoporin 160kDa	794					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7						TTGGAGATTAGACTCCCTGTG	0.358													17	54	---	---	---	---	PASS
LOC440040	440040	broad.mit.edu	37	11	49831711	49831711	+	3'UTR	SNP	A	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49831711A>G	uc010rhy.1	+	7					LOC440040_uc009ymb.2_3'UTR	NR_027044				SubName: Full=cDNA FLJ60249, highly similar to Metabotropic glutamate receptor 5;												0						GTTGATGTTAATCAAAGCTCC	0.448													4	201	---	---	---	---	PASS
BBS1	582	broad.mit.edu	37	11	66287216	66287216	+	Silent	SNP	C	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66287216C>G	uc001oij.1	+	8	732	c.720C>G	c.(718-720)GCC>GCG	p.A240A	BBS1_uc001oii.1_Silent_p.A277A|BBS1_uc010rpf.1_RNA|BBS1_uc010rpg.1_Intron|BBS1_uc001oik.1_Silent_p.A164A|BBS1_uc001oil.1_Silent_p.A240A	NM_024649	NP_078925	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	240					nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1						CCATTTTAGCCAAGGTCAGCG	0.552									Bardet-Biedl_syndrome				6	31	---	---	---	---	PASS
PCF11	51585	broad.mit.edu	37	11	82868704	82868704	+	Intron	SNP	T	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82868704T>A	uc001ozx.3	+						PCF11_uc010rsu.1_Intron|PCF11_uc001ozy.2_Missense_Mutation_p.F75I	NM_015885	NP_056969	O94913	PCF11_HUMAN	pre-mRNA cleavage complex II protein Pcf11						mRNA 3'-end processing|mRNA cleavage|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage factor complex				ovary(1)	1						CTCCTATTACTTCTAATACTC	0.552													16	65	---	---	---	---	PASS
RIMKLB	57494	broad.mit.edu	37	12	8904578	8904578	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8904578G>A	uc001quu.2	+	4	683	c.432G>A	c.(430-432)ATG>ATA	p.M144I	RIMKLB_uc009zgf.1_RNA|RIMKLB_uc001qux.2_Missense_Mutation_p.M144I|RIMKLB_uc010sgl.1_Missense_Mutation_p.M144I|RIMKLB_uc001quw.2_Missense_Mutation_p.M144I	NM_020734	NP_065785	Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family	144	ATP-grasp.				protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0						TTGCTAAAATGATTGATGAGG	0.373													37	106	---	---	---	---	PASS
TSPAN11	441631	broad.mit.edu	37	12	31136075	31136075	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31136075C>A	uc010sju.1	+	7	1072	c.692C>A	c.(691-693)GCC>GAC	p.A231D	TSPAN11_uc001rjp.2_Missense_Mutation_p.A231D|TSPAN11_uc010sjv.1_Missense_Mutation_p.A221D	NM_001080509	NP_001073978	A1L157	TSN11_HUMAN	tetraspanin 11	231	Helical; (Potential).					integral to membrane					0	all_lung(12;3.11e-10)|Lung NSC(12;5.24e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					ATCGGGGTGGCCTGCCTGCAG	0.622													7	16	---	---	---	---	PASS
SRGAP1	57522	broad.mit.edu	37	12	64377845	64377845	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64377845A>C	uc010ssp.1	+	2	242	c.186A>C	c.(184-186)GAA>GAC	p.E62D	SRGAP1_uc001srt.2_Missense_Mutation_p.E62D|SRGAP1_uc001srv.2_Missense_Mutation_p.E22D	NM_020762	NP_065813	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	62	FCH.				axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		TTGAGACGGAATATTCCCGGA	0.393													43	157	---	---	---	---	PASS
XPOT	11260	broad.mit.edu	37	12	64828368	64828368	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64828368G>T	uc001ssb.2	+	20	2960	c.2534G>T	c.(2533-2535)TGT>TTT	p.C845F		NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	845	Necessary for tRNA-binding, cytoplasmic localization and nuclear export.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)		CAGAAAACATGTTTTATCATC	0.353													17	94	---	---	---	---	PASS
SAP18	10284	broad.mit.edu	37	13	21721465	21721465	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21721465G>A	uc001uns.2	+	4	542	c.503G>A	c.(502-504)CGC>CAC	p.R168H		NM_005870	NP_005861	O00422	SAP18_HUMAN	Sin3A-associated protein, 18kDa	149					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|plasma membrane	protein binding|transcription corepressor activity				0		all_cancers(29;2.16e-20)|all_epithelial(30;2.97e-18)|all_lung(29;4.58e-16)|Lung SC(185;0.0262)|Breast(139;0.147)		all cancers(112;9.79e-05)|Epithelial(112;0.000292)|OV - Ovarian serous cystadenocarcinoma(117;0.00276)|Lung(94;0.0941)		CCTTCAGGGCGCATGAGACCA	0.403													6	171	---	---	---	---	PASS
FAM123A	219287	broad.mit.edu	37	13	25743823	25743823	+	Silent	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25743823C>T	uc001uqb.2	-	1	2035	c.1935G>A	c.(1933-1935)CTG>CTA	p.L645L	FAM123A_uc001uqa.2_Silent_p.L526L|FAM123A_uc001uqc.2_Silent_p.L526L	NM_152704	NP_689917	Q8N7J2	F123A_HUMAN	hypothetical protein LOC219287 isoform 1	645										ovary(2)|large_intestine(1)|lung(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		CTCTGCGGACCAGCACTTTGG	0.577													25	91	---	---	---	---	PASS
KLHL1	57626	broad.mit.edu	37	13	70281831	70281831	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70281831C>T	uc001vip.2	-	10	2907	c.2113G>A	c.(2113-2115)GTT>ATT	p.V705I	KLHL1_uc010thm.1_Missense_Mutation_p.V644I	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein	705	Kelch 6.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		TAGCCACCAACAGCATATAAT	0.448													21	66	---	---	---	---	PASS
DIS3	22894	broad.mit.edu	37	13	73335571	73335571	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73335571T>C	uc001vix.3	-	19	2974	c.2600A>G	c.(2599-2601)TAT>TGT	p.Y867C	DIS3_uc001viy.3_Missense_Mutation_p.Y837C|DIS3_uc001viz.2_RNA	NM_014953	NP_055768	Q9Y2L1	RRP44_HUMAN	DIS3 mitotic control isoform a	867					CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding			central_nervous_system(1)	1		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		TTCTAAACCATACTTTGGAAT	0.313										Multiple Myeloma(4;0.011)			30	86	---	---	---	---	PASS
SLITRK6	84189	broad.mit.edu	37	13	86370298	86370298	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86370298G>T	uc001vll.1	-	2	805	c.346C>A	c.(346-348)CAA>AAA	p.Q116K	SLITRK6_uc010afe.1_5'Flank	NM_032229	NP_115605	Q9H5Y7	SLIK6_HUMAN	slit and trk like 6 precursor	116	Extracellular (Potential).|LRR 2.					integral to membrane				large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		ATATGAAGTTGTTTCAGGAGG	0.358													28	85	---	---	---	---	PASS
SMEK1	55671	broad.mit.edu	37	14	91924967	91924967	+	3'UTR	SNP	C	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91924967C>A	uc001xzn.2	-	15					SMEK1_uc001xzm.2_3'UTR|SMEK1_uc001xzo.2_3'UTR|SMEK1_uc010atz.2_3'UTR	NM_032560	NP_115949	Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1							microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		ACTTGATGAGCAGAAGTCAAG	0.473													4	35	---	---	---	---	PASS
SPTBN5	51332	broad.mit.edu	37	15	42175214	42175214	+	Silent	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42175214C>T	uc001zos.2	-	9	2100	c.1767G>A	c.(1765-1767)CTG>CTA	p.L589L		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	624	Spectrin 3.				actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CAAGAGCCACCAGGCTCTGTT	0.572													3	4	---	---	---	---	PASS
VPS39	23339	broad.mit.edu	37	15	42480038	42480038	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42480038T>A	uc001zpd.2	-	7	543	c.392A>T	c.(391-393)GAG>GTG	p.E131V	VPS39_uc001zpc.2_Missense_Mutation_p.E120V	NM_015289	NP_056104	Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39	131	CNH.				protein transport	HOPS complex|late endosome membrane|lysosomal membrane	small GTPase regulator activity			ovary(1)|pancreas(1)|skin(1)	3		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		TAACACCTCCTCACCGGTCTC	0.433													42	160	---	---	---	---	PASS
CAPN3	825	broad.mit.edu	37	15	42695072	42695072	+	Silent	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42695072C>T	uc001zpn.1	+	13	1923	c.1617C>T	c.(1615-1617)AAC>AAT	p.N539N	CAPN3_uc001zpk.1_Silent_p.N312N|CAPN3_uc001zpl.1_Silent_p.N452N|CAPN3_uc010udf.1_Silent_p.N452N|CAPN3_uc010udg.1_Silent_p.N404N|CAPN3_uc001zpo.1_Silent_p.N539N|CAPN3_uc001zpp.1_Silent_p.N491N|CAPN3_uc001zpq.1_Silent_p.N27N|CAPN3_uc010bcv.1_5'Flank|CAPN3_uc001zpr.1_5'Flank|CAPN3_uc001zps.1_5'Flank|CAPN3_uc001zpt.1_5'Flank	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a	539	Domain III.				muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		CCTACATCAACATGCGGGAGG	0.612													33	82	---	---	---	---	PASS
SECISBP2L	9728	broad.mit.edu	37	15	49301485	49301485	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49301485G>C	uc001zxe.1	-	14	2089	c.1955C>G	c.(1954-1956)CCT>CGT	p.P652R	SECISBP2L_uc001zxd.1_Missense_Mutation_p.P607R|SECISBP2L_uc010bep.1_Missense_Mutation_p.P414R	NM_014701	NP_055516	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	652										breast(1)|skin(1)	2						AGAACTAGCAGGAGAGCCTTG	0.423													37	111	---	---	---	---	PASS
C15orf33	196951	broad.mit.edu	37	15	49868999	49868999	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49868999A>T	uc001zxl.2	-	7	779	c.485T>A	c.(484-486)CTA>CAA	p.L162Q	C15orf33_uc001zxm.2_Missense_Mutation_p.L162Q	NM_152647	NP_689860	Q96M60	CO033_HUMAN	hypothetical protein LOC196951	162										ovary(1)	1		all_lung(180;0.00187)		all cancers(107;3.45e-08)|GBM - Glioblastoma multiforme(94;0.000124)		ATGTCTGGGTAGCTGAGTAAG	0.308													6	34	---	---	---	---	PASS
HEXA	3073	broad.mit.edu	37	15	72645420	72645420	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72645420G>T	uc002aun.3	-	5	766	c.559C>A	c.(559-561)CTG>ATG	p.L187M	CELF6_uc002auk.3_Intron|HEXA_uc010ukn.1_Missense_Mutation_p.L198M|HEXA_uc002auo.3_Missense_Mutation_p.L50M|HEXA_uc010bix.2_Missense_Mutation_p.L187M|HEXA_uc010biy.2_Missense_Mutation_p.L50M|HEXA_uc010uko.1_Intron|HEXA_uc010biz.1_RNA	NM_000520	NP_000511	P06865	HEXA_HUMAN	hexosaminidase A preproprotein	187					cell death	lysosome	beta-N-acetylhexosaminidase activity|cation binding|protein heterodimerization activity			ovary(3)|upper_aerodigestive_tract(1)	4						AGAGTGTCCAGGATGCTAGAG	0.478													8	39	---	---	---	---	PASS
SYNM	23336	broad.mit.edu	37	15	99672128	99672128	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99672128T>C	uc002bup.2	+	6	3683	c.3563T>C	c.(3562-3564)ATC>ACC	p.I1188T	SYNM_uc002buo.2_Intron|SYNM_uc002buq.2_Intron	NM_145728	NP_663780	O15061	SYNEM_HUMAN	desmuslin isoform A	1188	Tail.|Interaction with TLN1 and VCL.				intermediate filament cytoskeleton organization	adherens junction|costamere|intermediate filament|neurofilament cytoskeleton	intermediate filament binding|structural constituent of cytoskeleton|structural constituent of muscle|vinculin binding			ovary(3)|central_nervous_system(1)	4						AGAGAAGTCATCTTCCTAGGC	0.632													9	21	---	---	---	---	PASS
ZNF764	92595	broad.mit.edu	37	16	30569111	30569111	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30569111A>C	uc002dyq.2	-	2	334	c.253T>G	c.(253-255)TGG>GGG	p.W85G	ZNF764_uc002dyr.1_Missense_Mutation_p.W85G	NM_033410	NP_219363	Q96H86	ZN764_HUMAN	zinc finger protein 764	85	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GCCGGACCCCACAGTTCGGCC	0.617													3	11	---	---	---	---	PASS
SRCAP	10847	broad.mit.edu	37	16	30749422	30749422	+	Silent	SNP	A	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30749422A>T	uc002dze.1	+	34	8446	c.8061A>T	c.(8059-8061)CCA>CCT	p.P2687P	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Silent_p.P2482P	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	2687	Pro-rich.				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)			CCTCCAGCCCAGAGAAGCCAC	0.602													11	50	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	21730916	21730916	+	Missense_Mutation	SNP	G	T	T	rs111245273	by1000genomes	TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21730916G>T	uc002gyy.3	+	2	343	c.218G>T	c.(217-219)CGG>CTG	p.R73L						SubName: Full=cDNA FLJ51326, highly similar to Homo sapiens ubiquitin B (UBB), mRNA;																		GTCCTGCGTCGGAGAGGTGGT	0.552													4	63	---	---	---	---	PASS
SDF2	6388	broad.mit.edu	37	17	26975938	26975938	+	3'UTR	SNP	A	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26975938A>G	uc002hbw.2	-	3					SDF2_uc002hbx.2_RNA	NM_006923	NP_008854	Q99470	SDF2_HUMAN	stromal cell-derived factor 2 precursor						protein glycosylation	extracellular space|membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity				0	Lung NSC(42;0.00431)					TGTGGCAGGGATCCCAAGGTG	0.498													4	31	---	---	---	---	PASS
IKZF3	22806	broad.mit.edu	37	17	37922736	37922736	+	Silent	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37922736G>T	uc002hsu.2	-	8	899	c.837C>A	c.(835-837)CGC>CGA	p.R279R	IKZF3_uc002htd.2_Silent_p.R245R|IKZF3_uc010cwd.2_Silent_p.R136R|IKZF3_uc002hsv.2_Silent_p.R206R|IKZF3_uc010cwe.2_Silent_p.R145R|IKZF3_uc010cwf.2_Silent_p.R97R|IKZF3_uc010cwg.2_Silent_p.R58R|IKZF3_uc002hsw.2_Silent_p.R240R|IKZF3_uc002hsx.2_Silent_p.R223R|IKZF3_uc002hsy.2_Silent_p.R240R|IKZF3_uc002hsz.2_Silent_p.R184R|IKZF3_uc002hta.2_Silent_p.R201R|IKZF3_uc002htb.2_RNA|IKZF3_uc010cwh.2_Silent_p.R192R|IKZF3_uc002htc.2_Silent_p.R32R|IKZF3_uc010wel.1_Silent_p.R32R	NM_012481	NP_036613	Q9UKT9	IKZF3_HUMAN	aiolos isoform 1	279					B cell activation|mesoderm development|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)|kidney(2)|skin(2)	6	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CAAAGCAGTGGCGCTTCTCAC	0.438													18	69	---	---	---	---	PASS
IKZF3	22806	broad.mit.edu	37	17	37922737	37922737	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37922737C>G	uc002hsu.2	-	8	898	c.836G>C	c.(835-837)CGC>CCC	p.R279P	IKZF3_uc002htd.2_Missense_Mutation_p.R245P|IKZF3_uc010cwd.2_Missense_Mutation_p.R136P|IKZF3_uc002hsv.2_Missense_Mutation_p.R206P|IKZF3_uc010cwe.2_Missense_Mutation_p.R145P|IKZF3_uc010cwf.2_Missense_Mutation_p.R97P|IKZF3_uc010cwg.2_Missense_Mutation_p.R58P|IKZF3_uc002hsw.2_Missense_Mutation_p.R240P|IKZF3_uc002hsx.2_Missense_Mutation_p.R223P|IKZF3_uc002hsy.2_Missense_Mutation_p.R240P|IKZF3_uc002hsz.2_Missense_Mutation_p.R184P|IKZF3_uc002hta.2_Missense_Mutation_p.R201P|IKZF3_uc002htb.2_RNA|IKZF3_uc010cwh.2_Missense_Mutation_p.R192P|IKZF3_uc002htc.2_Missense_Mutation_p.R32P|IKZF3_uc010wel.1_Missense_Mutation_p.R32P	NM_012481	NP_036613	Q9UKT9	IKZF3_HUMAN	aiolos isoform 1	279					B cell activation|mesoderm development|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)|kidney(2)|skin(2)	6	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			AAAGCAGTGGCGCTTCTCACC	0.438													17	69	---	---	---	---	PASS
FZD2	2535	broad.mit.edu	37	17	42636336	42636336	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42636336G>A	uc002igx.1	+	1	1412	c.1280G>A	c.(1279-1281)GGC>GAC	p.G427D		NM_001466	NP_001457	Q14332	FZD2_HUMAN	frizzled 2 precursor	427	Helical; Name=5; (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|epithelial cell differentiation|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|positive regulation of cGMP metabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			ovary(2)|lung(1)	3		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		CTGTTCATCGGCACGTCCTTC	0.642													4	95	---	---	---	---	PASS
NFE2L1	4779	broad.mit.edu	37	17	46135813	46135813	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46135813C>G	uc002imz.3	+	6	1780	c.1129C>G	c.(1129-1131)CTC>GTC	p.L377V	NFE2L1_uc002ina.3_Missense_Mutation_p.L347V|NFE2L1_uc002inb.3_Missense_Mutation_p.L347V|NFE2L1_uc010wle.1_Missense_Mutation_p.L189V|NFE2L1_uc010wlf.1_Missense_Mutation_p.L221V	NM_003204	NP_003195	Q14494	NF2L1_HUMAN	nuclear factor erythroid 2-like 1	377					anatomical structure morphogenesis|heme biosynthetic process|inflammatory response|transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			skin(1)	1						GGACTTCTTACTCTTCAGCCC	0.612													31	104	---	---	---	---	PASS
NPTX1	4884	broad.mit.edu	37	17	78445540	78445540	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78445540G>T	uc002jyp.1	-	4	1227	c.1069C>A	c.(1069-1071)CAG>AAG	p.Q357K		NM_002522	NP_002513	Q15818	NPTX1_HUMAN	neuronal pentraxin I precursor	357	Pentaxin.				central nervous system development|synaptic transmission|transport	transport vesicle	metal ion binding				0	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			ACCTGCTCCTGGCCCAGCACC	0.657													14	36	---	---	---	---	PASS
NARF	26502	broad.mit.edu	37	17	80443460	80443460	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80443460G>T	uc002kfg.3	+	10	1199	c.1059G>T	c.(1057-1059)CAG>CAT	p.Q353H	NARF_uc002kff.3_Missense_Mutation_p.Q294H|NARF_uc010dit.2_Missense_Mutation_p.Q399H|NARF_uc002kfj.3_Missense_Mutation_p.Q305H|NARF_uc002kfi.3_RNA|NARF_uc002kfh.3_Missense_Mutation_p.Q399H|NARF_uc002kfk.2_RNA	NM_012336	NP_036468	Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor isoform a	353						lamin filament	lamin binding			skin(1)	1	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			GAAACATCCAGAACATGATCC	0.512													30	92	---	---	---	---	PASS
ABCA7	10347	broad.mit.edu	37	19	1056479	1056479	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1056479C>A	uc002lqw.3	+	33	4798	c.4567C>A	c.(4567-4569)CAG>AAG	p.Q1523K	ABCA7_uc002lqy.2_5'Flank|ABCA7_uc010dsc.2_5'Flank	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	1523	Extracellular (By similarity).				phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		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)		CACCAAGGAGCAGCTGTCTGA	0.632													4	28	---	---	---	---	PASS
CELF5	60680	broad.mit.edu	37	19	3281241	3281241	+	Silent	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3281241G>A	uc002lxm.2	+	6	685	c.648G>A	c.(646-648)AAG>AAA	p.K216K	CELF5_uc002lxl.1_Silent_p.K216K|CELF5_uc010dtj.1_Silent_p.K216K|CELF5_uc010xhg.1_Silent_p.K102K|CELF5_uc002lxn.2_RNA	NM_021938	NP_068757	Q8N6W0	CELF5_HUMAN	bruno-like 5, RNA binding protein	216					mRNA processing	cytoplasm|nucleus	nucleotide binding|RNA binding			ovary(2)	2						ACACGGACAAGGAGCGGACGC	0.677													22	103	---	---	---	---	PASS
FBN3	84467	broad.mit.edu	37	19	8194141	8194141	+	Nonsense_Mutation	SNP	G	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8194141G>C	uc002mjf.2	-	16	2174	c.2153C>G	c.(2152-2154)TCA>TGA	p.S718*		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	718	EGF-like 8; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						GTCCTTGCCTGAGGCACCTGC	0.637													12	40	---	---	---	---	PASS
DMKN	93099	broad.mit.edu	37	19	36003325	36003325	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36003325C>T	uc002nzm.3	-	3	865	c.682G>A	c.(682-684)GGG>AGG	p.G228R	DMKN_uc002nzj.2_5'Flank|DMKN_uc002nzk.3_5'Flank|DMKN_uc002nzl.3_5'Flank|DMKN_uc002nzo.3_Missense_Mutation_p.G228R|DMKN_uc002nzn.3_Missense_Mutation_p.G228R|DMKN_uc002nzw.2_5'Flank|DMKN_uc002nzr.2_5'Flank|DMKN_uc002nzp.2_5'Flank|DMKN_uc002nzq.2_5'Flank|DMKN_uc002nzt.2_5'Flank|DMKN_uc002nzs.2_5'Flank|DMKN_uc002nzu.2_5'Flank|DMKN_uc002nzv.2_5'Flank|DMKN_uc010xsv.1_5'Flank|DMKN_uc010xsw.1_5'Flank|DMKN_uc002nzx.3_5'Flank|DMKN_uc002nzy.3_5'Flank|DMKN_uc002nzz.2_5'Flank|DMKN_uc002oac.3_Missense_Mutation_p.G228R|DMKN_uc010eeb.2_Missense_Mutation_p.G228R|DMKN_uc002oaa.3_Missense_Mutation_p.G228R|DMKN_uc002oab.3_Missense_Mutation_p.G228R	NM_033317	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine isoform 2 precursor	228	Gly-rich.					extracellular region				large_intestine(1)|ovary(1)|skin(1)	3	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CCTCTTACCCCTTCATTCTGG	0.567													7	43	---	---	---	---	PASS
YIF1B	90522	broad.mit.edu	37	19	38798068	38798068	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38798068C>A	uc002ohz.2	-	7	838	c.789G>T	c.(787-789)ATG>ATT	p.M263I	YIF1B_uc002ohw.2_Missense_Mutation_p.M232I|YIF1B_uc002ohx.2_Missense_Mutation_p.M248I|YIF1B_uc010xtx.1_Missense_Mutation_p.M246I|YIF1B_uc010xty.1_Missense_Mutation_p.M232I|YIF1B_uc002oia.2_Missense_Mutation_p.M260I|YIF1B_uc002ohy.2_Missense_Mutation_p.M260I|YIF1B_uc002oib.2_Missense_Mutation_p.M260I	NM_001039672	NP_001034761	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B isoform 5	263	Cytoplasmic (Potential).					integral to membrane					0	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CCCAGCTCACCATGAACACAA	0.597													6	30	---	---	---	---	PASS
CYP2F1	1572	broad.mit.edu	37	19	41627951	41627951	+	Silent	SNP	C	T	T	rs139489388		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41627951C>T	uc002opu.1	+	6	791	c.735C>T	c.(733-735)ATC>ATT	p.I245I	CYP2F1_uc010xvw.1_Silent_p.I31I|CYP2F1_uc010xvv.1_Silent_p.I245I|CYP2F1_uc002opv.1_RNA	NM_000774	NP_000765	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F,	245					naphthalene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0						GAGACCTCATCGCCCACAGCG	0.602													21	31	---	---	---	---	PASS
LYPD3	27076	broad.mit.edu	37	19	43967403	43967403	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43967403C>T	uc002owl.1	-	4	527	c.419G>A	c.(418-420)TGC>TAC	p.C140Y	LYPD3_uc002owm.2_3'UTR	NM_014400	NP_055215	O95274	LYPD3_HUMAN	GPI-anchored metastasis-associated protein	140	UPAR/Ly6 2.					anchored to plasma membrane				pancreas(1)	1		Prostate(69;0.0153)				ACAGCTGTAGCACTCCACGCC	0.622													21	56	---	---	---	---	PASS
LAIR1	3903	broad.mit.edu	37	19	54876460	54876460	+	5'UTR	SNP	G	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54876460G>A	uc002qfk.1	-	1					LAIR1_uc002qfl.1_5'UTR|LAIR1_uc002qfm.1_5'UTR|LAIR1_uc002qfn.1_5'UTR|LAIR1_uc010yex.1_Intron|LAIR1_uc002qfo.2_Intron	NM_002287	NP_002278	Q6GTX8	LAIR1_HUMAN	leukocyte-associated immunoglobulin-like							integral to membrane|plasma membrane	protein binding|receptor activity			ovary(4)	4	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0573)		CCAATGCAAGGACAGAACTCT	0.642											OREG0003657	type=REGULATORY REGION|Gene=LAIR1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	5	40	---	---	---	---	PASS
PANK2	80025	broad.mit.edu	37	20	3897581	3897581	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3897581A>C	uc002wkc.2	+	5	1426	c.1420A>C	c.(1420-1422)AAC>CAC	p.N474H	PANK2_uc002wkb.2_Missense_Mutation_p.N183H|PANK2_uc002wkd.2_RNA|PANK2_uc002wke.2_Missense_Mutation_p.N183H|PANK2_uc002wkf.2_Missense_Mutation_p.N38H|uc002wkg.2_5'Flank|MIR103-2_hsa-mir-103-2|MI0000108_5'Flank	NM_153638	NP_705902	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2 isoform 1 preproprotein	474					cell death|coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial intermembrane space|nucleus	ATP binding|pantothenate kinase activity|protein binding				0						CAGCTTTGGAAACATGATGAG	0.413													10	46	---	---	---	---	PASS
CTCFL	140690	broad.mit.edu	37	20	56090853	56090853	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56090853C>T	uc010gix.1	-	5	1759	c.1097G>A	c.(1096-1098)GGG>GAG	p.G366E	CTCFL_uc010giw.1_Missense_Mutation_p.G366E|CTCFL_uc002xym.2_Missense_Mutation_p.G366E|CTCFL_uc010giz.1_5'UTR|CTCFL_uc010giy.1_5'UTR|CTCFL_uc010gja.1_Missense_Mutation_p.G366E|CTCFL_uc010gjb.1_Missense_Mutation_p.G366E|CTCFL_uc010gjc.1_Missense_Mutation_p.G366E|CTCFL_uc010gjd.1_Missense_Mutation_p.G366E|CTCFL_uc010gje.2_Missense_Mutation_p.G366E|CTCFL_uc010gjf.2_Missense_Mutation_p.G161E|CTCFL_uc010gjg.2_Missense_Mutation_p.G98E|CTCFL_uc010gjh.1_Intron|CTCFL_uc010gji.1_Missense_Mutation_p.G161E|CTCFL_uc010gjj.1_Missense_Mutation_p.G366E	NM_080618	NP_542185	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor-like protein	366					cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|skin(1)	4	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			GGGGCGCTCCCCAGTGTGGGA	0.468													42	194	---	---	---	---	PASS
MORC3	23515	broad.mit.edu	37	21	37721695	37721695	+	Silent	SNP	T	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37721695T>C	uc002yvi.2	+	9	1168	c.1092T>C	c.(1090-1092)ACT>ACC	p.T364T		NM_015358	NP_056173	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	364					cell aging|maintenance of protein location in nucleus|negative regulation of fibroblast proliferation|peptidyl-serine phosphorylation|protein stabilization	aggresome|intermediate filament cytoskeleton|PML body	ATP binding|zinc ion binding			ovary(2)	2						TCGACTATACTAATGAGTACA	0.333													20	61	---	---	---	---	PASS
KRTAP10-11	386678	broad.mit.edu	37	21	46066342	46066342	+	5'UTR	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46066342C>T	uc002zfr.3	+	1					C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198692	NP_941965	P60412	KR10B_HUMAN	keratin associated protein 10-11							keratin filament				ovary(1)	1						cactcacttacacCTCCCCCA	0.502													13	49	---	---	---	---	PASS
SMARCB1	6598	broad.mit.edu	37	22	24143192	24143192	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24143192T>A	uc002zyb.2	+	4	631	c.424T>A	c.(424-426)TTA>ATA	p.L142I	SMARCB1_uc002zyg.2_Missense_Mutation_p.L142I|SMARCB1_uc011ajb.1_Missense_Mutation_p.L133I|SMARCB1_uc002zya.2_Missense_Mutation_p.L142I|SMARCB1_uc002zyc.2_Missense_Mutation_p.L133I|SMARCB1_uc002zyd.2_Missense_Mutation_p.L133I|SMARCB1_uc002zye.1_Intron|SMARCB1_uc002zyf.1_Intron|SMARCB1_uc010gue.1_Intron	NM_003073	NP_003064	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin	142	DNA-binding (Potential).				cell cycle|chromatin remodeling|DNA integration|interspecies interaction between organisms|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|retroviral genome replication|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleolus|nucleoplasm|SWI/SNF complex	p53 binding	p.?(5)|p.L142*(1)		soft_tissue(193)|central_nervous_system(172)|haematopoietic_and_lymphoid_tissue(23)|meninges(5)|skin(5)|bone(4)|ovary(2)|endometrium(1)|lung(1)|pancreas(1)	407		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				CTCCCACCACTTAGATGCCGT	0.557			D|N|F|S		malignant rhabdoid 	malignant rhabdoid			Rhabdoid_Predisposition_syndrome|Schwannomatosis				15	64	---	---	---	---	PASS
SEC14L3	266629	broad.mit.edu	37	22	30856107	30856107	+	Silent	SNP	G	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30856107G>T	uc003ahy.2	-	12	1193	c.1104C>A	c.(1102-1104)ACC>ACA	p.T368T	SEC14L3_uc003ahz.2_Silent_p.T291T|SEC14L3_uc003aia.2_Silent_p.T309T|SEC14L3_uc003aib.2_Silent_p.T309T	NM_174975	NP_777635	Q9UDX4	S14L3_HUMAN	SEC14-like 3	368	GOLD.					integral to membrane|intracellular	lipid binding|transporter activity			ovary(3)|pancreas(1)|skin(1)	5					Vitamin E(DB00163)	CAAAGCTATAGGTGTTGTCGA	0.542													18	76	---	---	---	---	PASS
MCM5	4174	broad.mit.edu	37	22	35815920	35815920	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35815920A>C	uc003anu.3	+	14	1841	c.1747A>C	c.(1747-1749)AAG>CAG	p.K583Q	MCM5_uc010gwr.2_Missense_Mutation_p.K392Q|MCM5_uc003anv.3_Missense_Mutation_p.K540Q|MCM5_uc003anw.1_Missense_Mutation_p.K367Q	NM_006739	NP_006730	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	583					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	MCM complex	ATP binding|DNA binding|helicase activity|protein binding			ovary(1)	1						AGAGAAACTGAAGAACCGCTA	0.642													20	70	---	---	---	---	PASS
TRIOBP	11078	broad.mit.edu	37	22	38119859	38119859	+	Silent	SNP	C	T	T	rs66505048		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38119859C>T	uc003atr.2	+	7	1567	c.1296C>T	c.(1294-1296)TGC>TGT	p.C432C	TRIOBP_uc003atu.2_Silent_p.C260C|TRIOBP_uc003atq.1_Silent_p.C432C|TRIOBP_uc003ats.1_Silent_p.C260C	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	432					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					GAACATCCTGCGCCCAGCGGG	0.582													4	88	---	---	---	---	PASS
TNRC6B	23112	broad.mit.edu	37	22	40719353	40719353	+	3'UTR	SNP	G	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40719353G>C	uc011aor.1	+	23					TNRC6B_uc003aym.2_3'UTR|TNRC6B_uc003ayn.3_3'UTR	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0						TTTTTAAAAGGAAAAAAGAAA	0.358													7	12	---	---	---	---	PASS
EP300	2033	broad.mit.edu	37	22	41572994	41572994	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41572994A>G	uc003azl.3	+	31	5674	c.5279A>G	c.(5278-5280)AAG>AGG	p.K1760R		NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300	1760	Binding region for E1A adenovirus.|TAZ-type 2.				apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64						TCCTGCCAGAAGATGAAGCGG	0.577			T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				17	55	---	---	---	---	PASS
PRR5	55615	broad.mit.edu	37	22	45075628	45075628	+	5'UTR	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45075628C>T	uc010gzt.1	+	2					PRR5_uc003bew.1_Intron|PRR5_uc003bex.1_Intron|PRR5_uc010gzu.1_Intron|PRR5_uc003bey.1_Intron|PRR5_uc003bez.1_Intron	NM_001017530	NP_001017530	P85299	PRR5_HUMAN	proline rich 5 (renal) isoform 3						cell cycle					skin(1)	1		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)		TCAGCCTCCCCGCTCTGGGAC	0.338													2	3	---	---	---	---	PASS
XPNPEP2	7512	broad.mit.edu	37	X	128878023	128878023	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128878023C>G	uc004eut.1	+	3	454	c.210C>G	c.(208-210)ATC>ATG	p.I70M	XPNPEP2_uc011mum.1_Missense_Mutation_p.I70M	NM_003399	NP_003390	O43895	XPP2_HUMAN	X-prolyl aminopeptidase 2, membrane-bound	70					cellular process|proteolysis	anchored to membrane|plasma membrane	aminopeptidase activity|metal ion binding|metalloexopeptidase activity				0						CAGCCTACATCATCCCAGGCA	0.517													3	122	---	---	---	---	PASS
NAA10	8260	broad.mit.edu	37	X	153196257	153196257	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153196257C>T	uc004fjm.1	-	7	541	c.430G>A	c.(430-432)GCC>ACC	p.A144T	NAA10_uc004fjn.1_Missense_Mutation_p.A129T	NM_003491	NP_003482	P41227	NAA10_HUMAN	alpha-N-acetyltransferase 1A	144	N-acetyltransferase.				DNA packaging|internal protein amino acid acetylation|N-terminal protein amino acid acetylation	cytoplasm|nucleus	peptide alpha-N-acetyltransferase activity|protein binding			ovary(1)	1						ATGGCATAGGCGTCCTCCCCA	0.612													25	50	---	---	---	---	PASS
KDM5D	8284	broad.mit.edu	37	Y	21903350	21903350	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:21903350C>T	uc004fug.2	-	5	664	c.376G>A	c.(376-378)GAA>AAA	p.E126K	KDM5D_uc011naz.1_Missense_Mutation_p.E126K|KDM5D_uc010nwy.2_Intron|KDM5D_uc011nba.1_Missense_Mutation_p.E126K|KDM5D_uc004fuh.2_Missense_Mutation_p.E126K	NM_004653	NP_004644	Q9BY66	KDM5D_HUMAN	jumonji, AT rich interactive domain 1D isoform	126	ARID.				chromatin modification|spermatogenesis	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1					Vitamin C(DB00126)	CAGATGGCTTCATAGCCACCT	0.478													3	10	---	---	---	---	PASS
C1orf159	54991	broad.mit.edu	37	1	1019876	1019876	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1019876delC	uc001act.2	-	10	1050	c.564delG	c.(562-564)CTGfs	p.L188fs	C1orf159_uc001acu.2_Frame_Shift_Del_p.L152fs|C1orf159_uc001acr.2_RNA|C1orf159_uc001acs.2_RNA|C1orf159_uc010nyd.1_RNA|C1orf159_uc001acm.2_Intron|C1orf159_uc009vju.1_Frame_Shift_Del_p.L130fs|C1orf159_uc001acn.2_Frame_Shift_Del_p.L152fs|C1orf159_uc001acp.2_Frame_Shift_Del_p.L152fs	NM_017891	NP_060361	Q96HA4	CA159_HUMAN	hypothetical protein LOC54991	188						integral to membrane					0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.96e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.77e-22)|Colorectal(212;6.51e-05)|COAD - Colon adenocarcinoma(227;0.000214)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		CGCCAGGCTGCAGGGCCGGAG	0.662													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	100288423	100288431	+	IGR	DEL	CCTCTACCT	-	-	rs71075457		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100288423_100288431delCCTCTACCT								FRRS1 (57074 upstream) : AGL (27209 downstream)																							tctacctctacctctacctcctctacctc	0.105													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	153198375	153198376	+	IGR	INS	-	G	G			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153198375_153198376insG								LELP1 (20781 upstream) : LOR (33803 downstream)																							ctgctgcccctggggccactgc	0.347													5	3	---	---	---	---	
EXOC6B	23233	broad.mit.edu	37	2	72958237	72958237	+	Intron	DEL	A	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72958237delA	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004	Q9Y2D4	EXC6B_HUMAN	SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2						TAATTAAAGCAAAAAAAAAAT	0.338													8	4	---	---	---	---	
CYP20A1	57404	broad.mit.edu	37	2	204154664	204154665	+	Intron	DEL	TA	-	-	rs71425992		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204154664_204154665delTA	uc002uzv.3	+						CYP20A1_uc002uzx.3_Intron|CYP20A1_uc010zif.1_Intron|CYP20A1_uc002uzy.3_Intron|CYP20A1_uc002uzw.3_Intron|CYP20A1_uc010ftw.2_Intron	NM_177538	NP_803882	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A,							integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0						TGTGTGTGTGTATATATATATA	0.163													4	2	---	---	---	---	
SLC16A14	151473	broad.mit.edu	37	2	230910277	230910277	+	Intron	DEL	A	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230910277delA	uc002vqd.1	-						FBXO36_uc010fxi.1_Intron	NM_152527	NP_689740	Q7RTX9	MOT14_HUMAN	solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			ovary(4)|skin(2)	6		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		ctccgtcttgaaaaaaaaaaa	0.134													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	175832199	175832199	+	IGR	DEL	C	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175832199delC								NAALADL2 (308773 upstream) : TBL1XR1 (906344 downstream)																							CATGCCACTGCCCCTGCTGCT	0.458													4	2	---	---	---	---	
ADH5	128	broad.mit.edu	37	4	99998098	99998099	+	Intron	INS	-	C	C			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99998098_99998099insC	uc003hui.2	-						ADH5_uc003huk.1_Intron|ADH5_uc003huj.2_Intron	NM_000671	NP_000662	P11766	ADHX_HUMAN	class III alcohol dehydrogenase, chi subunit						ethanol oxidation|response to redox state		alcohol dehydrogenase (NAD) activity|electron carrier activity|fatty acid binding|formaldehyde dehydrogenase activity|S-(hydroxymethyl)glutathione dehydrogenase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;2.5e-07)	NADH(DB00157)	AAGGAAAAAGGCAAGTTGGAAT	0.307													14	7	---	---	---	---	
SLC17A2	10246	broad.mit.edu	37	6	25925757	25925757	+	Intron	DEL	G	-	-	rs112138836		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25925757delG	uc011dkb.1	-						SLC17A2_uc011dkc.1_Intron|SLC17A2_uc003nfl.2_Intron			O00624	NPT3_HUMAN	SubName: Full=Solute carrier family 17 (Sodium phosphate), member 2, isoform CRA_b; SubName: Full=Putative uncharacterized protein SLC17A2;						phosphate metabolic process	integral to plasma membrane|membrane fraction	sodium:phosphate symporter activity			ovary(1)	1						aaaaaaaaaaGACTTTCCCAA	0.194													4	2	---	---	---	---	
MAP7	9053	broad.mit.edu	37	6	136732877	136732878	+	Intron	INS	-	A	A			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136732877_136732878insA	uc003qgz.2	-						MAP7_uc011edf.1_Intron|MAP7_uc011edg.1_Intron|MAP7_uc010kgu.2_Intron|MAP7_uc011edh.1_Intron|MAP7_uc010kgv.2_Intron|MAP7_uc010kgs.2_Intron|MAP7_uc011edi.1_Intron|MAP7_uc010kgq.1_Intron|MAP7_uc003qha.1_Intron|MAP7_uc010kgr.2_Intron|MAP7_uc010kgt.2_Intron	NM_003980	NP_003971	Q14244	MAP7_HUMAN	microtubule-associated protein 7						establishment or maintenance of cell polarity|microtubule cytoskeleton organization|protein localization in plasma membrane|response to osmotic stress	basolateral plasma membrane|microtubule|microtubule associated complex|nucleus|perinuclear region of cytoplasm	receptor binding|structural molecule activity				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		AAGAGTGGATTAAAAAAAAAAA	0.391													4	2	---	---	---	---	
ACAT2	39	broad.mit.edu	37	6	160199454	160199455	+	Intron	DEL	TT	-	-	rs71808548		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160199454_160199455delTT	uc010kjy.2	+						ACAT2_uc011efw.1_Intron	NM_005891	NP_005882	Q9BWD1	THIC_HUMAN	acetyl-Coenzyme A acetyltransferase 2							mitochondrion|nucleolus	acetyl-CoA C-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CTTCCCAAGGTTTaaaaaaaaa	0.317													3	3	---	---	---	---	
QKI	9444	broad.mit.edu	37	6	163836175	163836176	+	5'UTR	INS	-	CGG	CGG			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163836175_163836176insCGG	uc003qui.2	+	1					QKI_uc003que.2_5'UTR|QKI_uc003quf.2_5'UTR|QKI_uc003qug.2_5'UTR|QKI_uc003quh.2_5'UTR|QKI_uc003quj.2_5'UTR	NM_006775	NP_006766	Q96PU8	QKI_HUMAN	quaking homolog, KH domain RNA binding isoform						mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding			large_intestine(1)|ovary(1)	2		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)		TCCCTCCTCTCcggcggcggcg	0.257													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	31404676	31404676	+	IGR	DEL	A	-	-	rs35317967		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31404676delA								NEUROD6 (24138 upstream) : CCDC129 (149009 downstream)																							actctgtctcaaaaaaaaaaa	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64039218	64039219	+	Intron	INS	-	T	T	rs35346430		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64039218_64039219insT	uc003ttc.1	+											Homo sapiens cDNA FLJ43440 fis, clone OCBBF2030517.																		ACCTTTTTAGAttttttttttt	0.267													4	2	---	---	---	---	
AKAP9	10142	broad.mit.edu	37	7	91706403	91706403	+	Intron	DEL	T	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91706403delT	uc003ulg.2	+						AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron|AKAP9_uc003ulj.2_Intron	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			attattattattTCtttcttt	0.100			T	BRAF	papillary thyroid								4	2	---	---	---	---	
BAIAP2L1	55971	broad.mit.edu	37	7	97933774	97933775	+	Intron	DEL	AC	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97933774_97933775delAC	uc003upj.2	-							NM_018842	NP_061330	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1						filopodium assembly|positive regulation of actin cytoskeleton reorganization|positive regulation of actin filament polymerization|response to bacterium|signal transduction	cell junction|cytoskeleton|cytosol|nucleus	actin binding|cytoskeletal adaptor activity|proline-rich region binding|SH3 domain binding			ovary(1)	1	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			ACCAAGGACAACAGTAATAGTA	0.406													4	5	---	---	---	---	
SPDYE6	729597	broad.mit.edu	37	7	101987478	101987478	+	3'UTR	DEL	C	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101987478delC	uc011kkp.1	-	8					SPDYE6_uc003uzb.2_3'UTR	NM_001146210	NP_001139682	P0CI01	SPDE6_HUMAN	speedy homolog E6												0						AAGGACCCCACCCCCCTCCCC	0.512													7	5	---	---	---	---	
MNX1	3110	broad.mit.edu	37	7	156798268	156798268	+	Frame_Shift_Del	DEL	G	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156798268delG	uc003wnd.1	-	3	1455	c.1152delC	c.(1150-1152)TCCfs	p.S384fs	MNX1_uc003wmz.2_Intron|MNX1_uc003wna.2_Intron|MNX1_uc010lqq.1_Frame_Shift_Del_p.S177fs|MNX1_uc003wnc.1_Frame_Shift_Del_p.S172fs|MNX1_uc010lqr.1_RNA	NM_005515	NP_005506	P50219	MNX1_HUMAN	motor neuron and pancreas homeobox 1 isoform 1	384					humoral immune response|regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CGTCCTCCGAGGAGCAGTCGG	0.751									Currarino_syndrome				6	3	---	---	---	---	
ERMP1	79956	broad.mit.edu	37	9	5824041	5824041	+	Intron	DEL	T	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5824041delT	uc003zjm.1	-						ERMP1_uc011lme.1_Intron|ERMP1_uc010mhs.1_Intron|ERMP1_uc003zjn.1_Intron	NM_024896	NP_079172	Q7Z2K6	ERMP1_HUMAN	aminopeptidase Fxna						proteolysis	endoplasmic reticulum membrane|integral to membrane	metal ion binding|metallopeptidase activity			ovary(1)	1		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		TGTTAAACAATCTTAAATTAT	0.358													12	9	---	---	---	---	
C5	727	broad.mit.edu	37	9	123770864	123770865	+	Intron	INS	-	TTTT	TTTT			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123770864_123770865insTTTT	uc004bkv.2	-						C5_uc010mvm.1_Intron	NM_001735	NP_001726	P01031	CO5_HUMAN	complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)	TAATCTGTAACTTAAGCATTTT	0.198													10	5	---	---	---	---	
GPSM1	26086	broad.mit.edu	37	9	139250012	139250013	+	Intron	DEL	AG	-	-	rs10647805		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139250012_139250013delAG	uc004chd.2	+						GPSM1_uc011mdu.1_Intron|GPSM1_uc004che.2_5'UTR	NM_001145638	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1 (AGS3-like, C.						cell differentiation|nervous system development|signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|plasma membrane	binding|GTPase activator activity				0		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		GGTAGCCGACAGGGGGCAGGTT	0.688													8	4	---	---	---	---	
MIR606	693191	broad.mit.edu	37	10	77312184	77312184	+	5'Flank	DEL	C	-	-	rs1367290		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77312184delC	hsa-mir-606|MI0003619	+																							0						ttttttttttcccccccctct	0.000													3	3	---	---	---	---	
HRAS	3265	broad.mit.edu	37	11	534404	534415	+	Intron	DEL	CCCAGGCCCAGC	-	-	rs45443193		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:534404_534415delCCCAGGCCCAGC	uc001lpv.2	-						HRAS_uc010qvw.1_Intron|HRAS_uc010qvx.1_Intron|HRAS_uc010qvy.1_Intron	NM_005343	NP_005334	P01112	RASH_HUMAN	v-Ha-ras Harvey rat sarcoma viral oncogene						activation of MAPKK activity|axon guidance|blood coagulation|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|Ras protein signal transduction|synaptic transmission	cytosol|Golgi membrane|plasma membrane	GTP binding|GTPase activity|protein C-terminus binding			urinary_tract(174)|thyroid(155)|skin(126)|upper_aerodigestive_tract(112)|soft_tissue(37)|prostate(29)|salivary_gland(24)|cervix(23)|stomach(14)|pituitary(10)|lung(9)|haematopoietic_and_lymphoid_tissue(9)|breast(6)|testis(5)|endometrium(4)|bone(3)|large_intestine(2)|oesophagus(2)|penis(2)|kidney(1)|adrenal_gland(1)|thymus(1)	749		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Sulindac(DB00605)	CTCAGCCAGGCCCAGGCCCAGCCCCAGGCCCC	0.698		6	Mis		infrequent sarcomas|rare other types	rhadomyosarcoma|ganglioneuroblastoma|bladder			Costello_syndrome	HNSCC(11;0.0054)			8	4	---	---	---	---	
KBTBD4	55709	broad.mit.edu	37	11	47597411	47597412	+	Intron	INS	-	T	T	rs35653820		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47597411_47597412insT	uc001nfx.2	-						NDUFS3_uc001nft.3_Intron|KBTBD4_uc001nfw.1_Intron|KBTBD4_uc001nfz.2_Intron|KBTBD4_uc001nfy.2_Intron	NM_016506	NP_057590	Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4											ovary(1)|central_nervous_system(1)	2						CCTAAAATTGCttttttttttt	0.173													4	3	---	---	---	---	
ANO1	55107	broad.mit.edu	37	11	69995756	69995756	+	Intron	DEL	A	-	-	rs72410022		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69995756delA	uc001opj.2	+						ANO1_uc001opk.1_Intron|ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_Intron	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						aactctgtctaaaaaaaaaaa	0.234													6	3	---	---	---	---	
LRRC23	10233	broad.mit.edu	37	12	6993420	6993420	+	Intron	DEL	C	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6993420delC	uc001qrn.1	+						RPL13P5_uc009zff.2_RNA	NM_006992	NP_008923	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23 isoform b											ovary(1)	1						AAGAAGGTGGCCCAGACCATT	0.582													4	2	---	---	---	---	
BHLHE41	79365	broad.mit.edu	37	12	26277186	26277187	+	Intron	INS	-	C	C	rs35292879		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26277186_26277187insC	uc001rhb.2	-							NM_030762	NP_110389	Q9C0J9	BHE41_HUMAN	basic helix-loop-helix domain containing, class						cell differentiation|cell proliferation|organ morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0						ACCCTCGTCTGCCCCCCCCGCC	0.406													4	2	---	---	---	---	
MSRB3	253827	broad.mit.edu	37	12	65672498	65672501	+	5'UTR	DEL	GGGA	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65672498_65672501delGGGA	uc001ssn.2	+	1					MSRB3_uc001ssm.2_5'UTR|MSRB3_uc009zqp.2_5'UTR	NM_198080	NP_932346	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3 isoform 1						protein repair	endoplasmic reticulum|mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		CCCGGAGCCGGGGAGGGAGGGAGC	0.632													4	2	---	---	---	---	
KIAA1033	23325	broad.mit.edu	37	12	105504842	105504843	+	Intron	DEL	GT	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105504842_105504843delGT	uc001tld.2	+						KIAA1033_uc010swr.1_Intron	NM_015275	NP_056090	Q2M389	WAHS7_HUMAN	hypothetical protein LOC23325						endosome transport	WASH complex				kidney(1)|central_nervous_system(1)	2						GTTATTTGAAGTAAATGTCCTG	0.317													15	7	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	117965106	117965107	+	Intron	DEL	AG	-	-	rs68177299		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117965106_117965107delAG	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					acacacacacagacacacacac	0.223													4	3	---	---	---	---	
GPR133	283383	broad.mit.edu	37	12	131488937	131488938	+	Intron	INS	-	CTGCGGTGCTCCCCCGGGCCGC	CTGCGGTGCTCCCCCGGGCCGC	rs67815261		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131488937_131488938insCTGCGGTGCTCCCCCGGGCCGC	uc001uit.3	+						GPR133_uc010tbm.1_Intron	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		GCGCCAGGGAGCTGCGGTGCTC	0.609													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	21835723	21835728	+	IGR	DEL	GGCGAG	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21835723_21835728delGGCGAG								MRP63 (82505 upstream) : ZDHHC20 (114782 downstream)																							GATGGACTGAGGCGAGGGGTGGGACT	0.646													4	2	---	---	---	---	
TRPC4	7223	broad.mit.edu	37	13	38213495	38213495	+	Intron	DEL	T	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38213495delT	uc001uws.2	-						TRPC4_uc010abv.2_Intron|TRPC4_uc001uwt.2_Intron|TRPC4_uc010tey.1_Intron|TRPC4_uc010abw.2_Intron|TRPC4_uc010abx.2_Intron|TRPC4_uc010aby.2_Intron	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,						axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TTCtaaaaaataatttatttt	0.318													29	15	---	---	---	---	
TJP1	7082	broad.mit.edu	37	15	30022801	30022801	+	Intron	DEL	A	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30022801delA	uc001zcr.2	-						TJP1_uc010azl.2_Intron|TJP1_uc001zcq.2_Intron|TJP1_uc001zcs.2_Intron	NM_003257	NP_003248	Q07157	ZO1_HUMAN	tight junction protein 1 isoform a						cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		tctgtctctgaaaaaaaaaaa	0.289													4	2	---	---	---	---	
SPN	6693	broad.mit.edu	37	16	29676379	29676379	+	3'UTR	DEL	T	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29676379delT	uc002dtm.2	+	2					uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SPN_uc002dtn.2_3'UTR|SPN_uc010bzd.2_RNA	NM_001030288	NP_001025459	P16150	LEUK_HUMAN	sialophorin precursor						blood coagulation|cellular defense response|chemotaxis|defense response to bacterium|establishment or maintenance of cell polarity|immune response|leukocyte migration|negative regulation of cell adhesion|positive regulation of tumor necrosis factor biosynthetic process	extracellular space|integral to plasma membrane	bacterial cell surface binding|transmembrane receptor activity			central_nervous_system(2)	2						CCGAATCTCCttttttttttt	0.318													4	2	---	---	---	---	
RPGRIP1L	23322	broad.mit.edu	37	16	53653134	53653134	+	Intron	DEL	A	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53653134delA	uc002ehp.2	-						RPGRIP1L_uc002eho.3_Intron|RPGRIP1L_uc010vgy.1_Intron|RPGRIP1L_uc010cbx.2_Intron|RPGRIP1L_uc010vgz.1_Intron	NM_015272	NP_056087	Q68CZ1	FTM_HUMAN	RPGRIP1-like isoform a						negative regulation of G-protein coupled receptor protein signaling pathway	cell-cell junction|centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)				TTTAAAGAGCAAAAACAAAAA	0.328													68	30	---	---	---	---	
ZZEF1	23140	broad.mit.edu	37	17	3967494	3967494	+	Intron	DEL	A	-	-	rs112787658		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3967494delA	uc002fxe.2	-						ZZEF1_uc002fxh.2_5'Flank|ZZEF1_uc002fxi.2_Intron|ZZEF1_uc002fxj.1_Intron	NM_015113	NP_055928	O43149	ZZEF1_HUMAN	zinc finger, ZZ type with EF hand domain 1								calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4						TTCTTTAAAGAAAAAAAAAAA	0.149													4	2	---	---	---	---	
EXOC7	23265	broad.mit.edu	37	17	74090830	74090830	+	Intron	DEL	T	-	-	rs35625794		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74090830delT	uc002jqs.2	-						EXOC7_uc010dgv.1_Intron|EXOC7_uc002jqq.2_Intron|EXOC7_uc010wsw.1_Intron|EXOC7_uc010wsx.1_Intron|EXOC7_uc002jqr.2_Intron|EXOC7_uc010wsv.1_Intron|EXOC7_uc002jqu.2_Intron	NM_001145297	NP_001138769	Q9UPT5	EXOC7_HUMAN	exocyst complex component 7 isoform 4						exocytosis|protein transport	centriolar satellite|cytosol|exocyst|plasma membrane	protein binding				0			LUSC - Lung squamous cell carcinoma(166;0.187)			TTTCAAAGtcttttttttttt	0.234													3	3	---	---	---	---	
ZNF404	342908	broad.mit.edu	37	19	44376785	44376785	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44376785delT	uc002oxs.3	-	2	1581	c.1572delA	c.(1570-1572)GAAfs	p.E524fs		NM_001033719	NP_001028891	Q494X3	ZN404_HUMAN	zinc finger protein 404	527	C2H2-type 15.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)				CCTTACCACATTCTTTGCATT	0.388													23	15	---	---	---	---	
ZNF578	147660	broad.mit.edu	37	19	53004973	53004974	+	Intron	INS	-	C	C	rs146856334	by1000genomes	TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53004973_53004974insC	uc002pzp.3	+							NM_001099694	NP_001093164	Q96N58	ZN578_HUMAN	zinc finger protein 578						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GTGGGCAGTGGGGGGGGCTTCT	0.490													5	7	---	---	---	---	
COL6A1	1291	broad.mit.edu	37	21	47407704	47407704	+	Intron	DEL	G	-	-	rs66929103		TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47407704delG	uc002zhu.1	+							NM_001848	NP_001839	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1 precursor						axon guidance|cell adhesion|protein heterotrimerization	collagen type VI|protein complex	platelet-derived growth factor binding			ovary(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)	Palifermin(DB00039)	AGGGGACGGCGGGGGTCCAGA	0.716													4	2	---	---	---	---	
ADRBK2	157	broad.mit.edu	37	22	26043916	26043916	+	Intron	DEL	A	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26043916delA	uc003abx.3	+						ADRBK2_uc010gux.2_Intron|ADRBK2_uc003abw.2_Intron|ADRBK2_uc003aby.3_Intron	NM_005160	NP_005151	P35626	ARBK2_HUMAN	beta-adrenergic receptor kinase 2								ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)	catctctactaaaaaaaaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	51109951	51109951	+	IGR	DEL	G	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51109951delG								ARSA (43344 upstream) : SHANK3 (3119 downstream)																							TGTGGGGGCAGGTGGGGAAGA	0.527													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	24334947	24334947	+	IGR	DEL	A	-	-			TCGA-CJ-6030-01A-11D-1669-08	TCGA-CJ-6030-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24334947delA								FAM48B2 (3515 upstream) : FAM48B1 (45931 downstream)																							CACAACCCATAAGTGCTGCAC	0.423													28	25	---	---	---	---	
