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
MFSD2A	84879	broad.mit.edu	37	1	40434358	40434358	+	Silent	SNP	A	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40434358A>G	uc001cev.2	+	13	1690	c.1509A>G	c.(1507-1509)AAA>AAG	p.K503K	MFSD2A_uc010ojb.1_Silent_p.K451K|MFSD2A_uc001ceu.2_Silent_p.K490K|MFSD2A_uc010ojc.1_Silent_p.K334K|MFSD2A_uc009vvy.2_RNA|MFSD2A_uc001cex.2_Silent_p.K154K	NM_001136493	NP_001129965	Q8NA29	MFS2A_HUMAN	major facilitator superfamily domain containing	503					transmembrane transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)|pancreas(1)	2						TGCTCTTCAAAATGTACCCCA	0.587													13	157	---	---	---	---	PASS
POMGNT1	55624	broad.mit.edu	37	1	46658993	46658993	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46658993T>G	uc001cpe.2	-	12	1258	c.1094A>C	c.(1093-1095)AAT>ACT	p.N365T	POMGNT1_uc010olx.1_Missense_Mutation_p.N343T|POMGNT1_uc010oly.1_RNA|POMGNT1_uc010olz.1_Missense_Mutation_p.N222T|POMGNT1_uc001cpg.2_Missense_Mutation_p.N365T|POMGNT1_uc001cpf.2_Missense_Mutation_p.N32T|POMGNT1_uc001cph.1_5'Flank|POMGNT1_uc001cpi.1_Missense_Mutation_p.N32T	NM_017739	NP_060209	Q8WZA1	PMGT1_HUMAN	O-linked mannose	365	Lumenal (Potential).				protein N-linked glycosylation|protein O-linked glycosylation	Golgi membrane|integral to membrane|microsome	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					CACGCGGGCATTCTTGATGCT	0.577													4	28	---	---	---	---	PASS
MIER1	57708	broad.mit.edu	37	1	67396021	67396021	+	Intron	SNP	G	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67396021G>C	uc001dde.2	+						MIER1_uc001dda.3_Intron|MIER1_uc010opf.1_Intron|MIER1_uc009way.2_Intron|MIER1_uc001ddc.2_Intron|MIER1_uc001ddh.2_Intron|MIER1_uc001ddf.2_Intron|MIER1_uc001ddg.2_Intron|MIER1_uc010opg.1_Intron|MIER1_uc001ddj.1_5'UTR|MIER1_uc001ddi.2_5'UTR	NM_001077700	NP_001071168	Q8N108	MIER1_HUMAN	mesoderm induction early response 1 isoform b						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)	1						TCCGGGTTCTGGCCGTGACCC	0.697													4	37	---	---	---	---	PASS
SYCP1	6847	broad.mit.edu	37	1	115489894	115489894	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115489894G>T	uc001efr.2	+	27	2484	c.2275G>T	c.(2275-2277)GAA>TAA	p.E759*	SYCP1_uc010owt.1_RNA|SYCP1_uc001efq.2_Nonsense_Mutation_p.E759*|SYCP1_uc009wgw.2_Intron	NM_003176	NP_003167	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	759	Potential.				cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCTCAAAGCTGAACTTTTGTC	0.318													22	144	---	---	---	---	PASS
NES	10763	broad.mit.edu	37	1	156646329	156646329	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156646329T>A	uc001fpq.2	-	1	861	c.728A>T	c.(727-729)GAA>GTA	p.E243V		NM_006617	NP_006608	P48681	NEST_HUMAN	nestin	243	Coil 2B.|Rod.				brain development|embryonic camera-type eye development|G2/M transition of mitotic cell cycle|negative regulation of apoptosis|positive regulation of intermediate filament depolymerization|positive regulation of neural precursor cell proliferation|stem cell proliferation	cytoplasm|intermediate filament	intermediate filament binding|structural molecule activity			ovary(6)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CAACCTCTGTTCCAACGCTGC	0.692													3	20	---	---	---	---	PASS
CD1B	910	broad.mit.edu	37	1	158297960	158297960	+	3'UTR	SNP	C	T	T	rs16840096	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158297960C>T	uc001frx.2	-	6					CD1B_uc001frw.2_3'UTR	NM_001764	NP_001755	P29016	CD1B_HUMAN	CD1B antigen precursor						antigen processing and presentation|immune response	endosome membrane|integral to membrane|lysosomal membrane|plasma membrane	protein binding			ovary(2)	2	all_hematologic(112;0.0378)					ATAAGATTGACTTTTGGGCTG	0.308													19	100	---	---	---	---	PASS
DCAF8	50717	broad.mit.edu	37	1	160209814	160209814	+	Silent	SNP	A	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160209814A>G	uc001fvo.2	-	4	708	c.396T>C	c.(394-396)GAT>GAC	p.D132D	DCAF8_uc001fvn.2_Silent_p.D132D|DCAF8_uc009wth.2_Silent_p.D132D|DCAF8_uc010pjb.1_Silent_p.D132D|DCAF8_uc010pjc.1_Silent_p.D286D|DCAF8_uc001fvq.3_Silent_p.D132D|DCAF8_uc001fvp.3_Silent_p.D132D|uc010pjd.1_3'UTR	NM_015726	NP_056541	Q5TAQ9	DCAF8_HUMAN	DDB1 and CUL4 associated factor 8	132						CUL4 RING ubiquitin ligase complex	protein binding			skin(2)	2						GGGCCCGCTCATCATCTGATG	0.512													16	68	---	---	---	---	PASS
DYRK3	8444	broad.mit.edu	37	1	206822277	206822277	+	Silent	SNP	C	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206822277C>T	uc001hej.2	+	3	1902	c.1734C>T	c.(1732-1734)CCC>CCT	p.P578P	DYRK3_uc001hek.2_Intron|DYRK3_uc001hei.2_Silent_p.P558P	NM_003582	NP_003573	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	578					erythrocyte differentiation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)|central_nervous_system(1)	3	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			GTAGTATACCCCTATGCAGTG	0.398													29	127	---	---	---	---	PASS
IL19	29949	broad.mit.edu	37	1	206972280	206972280	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206972280C>G	uc001heo.2	+	1	66	c.41C>G	c.(40-42)TCC>TGC	p.S14C		NM_153758	NP_715639	Q9UHD0	IL19_HUMAN	interleukin 19 isoform 1 precursor	Error:Variant_position_missing_in_Q9UHD0_after_alignment					apoptosis|immune response|signal transduction	extracellular space	cytokine activity			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(75;0.211)			TCTGCGTGTTCCTTACCACTC	0.507													14	82	---	---	---	---	PASS
PIGR	5284	broad.mit.edu	37	1	207108891	207108891	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207108891A>G	uc001hez.2	-	5	1502	c.1318T>C	c.(1318-1320)TGG>CGG	p.W440R	PIGR_uc009xbz.2_Missense_Mutation_p.W440R	NM_002644	NP_002635	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor precursor	440	Ig-like V-type 4.|Extracellular (Potential).					extracellular region|integral to plasma membrane	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3						GTCAGACACCAGTAGAAGCCG	0.592											OREG0014186	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	101	---	---	---	---	PASS
SLC35F3	148641	broad.mit.edu	37	1	234454501	234454501	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234454501T>A	uc001hwa.1	+	5	980	c.752T>A	c.(751-753)TTG>TAG	p.L251*	SLC35F3_uc001hvy.1_Nonsense_Mutation_p.L320*	NM_173508	NP_775779	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	251	Helical; (Potential).				transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			CTACAGGTTTTGTTCAAGCTC	0.488													38	249	---	---	---	---	PASS
OR2M4	26245	broad.mit.edu	37	1	248402458	248402458	+	Silent	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248402458C>A	uc010pzh.1	+	1	228	c.228C>A	c.(226-228)ACC>ACA	p.T76T		NM_017504	NP_059974	Q96R27	OR2M4_HUMAN	olfactory receptor, family 2, subfamily M,	76	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(2)	2	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TCATCTGCACCACTCTACCCA	0.473													8	187	---	---	---	---	PASS
APOB	338	broad.mit.edu	37	2	21247881	21247881	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21247881G>A	uc002red.2	-	16	2488	c.2360C>T	c.(2359-2361)GCC>GTC	p.A787V		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	787					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)	ATGGAGACTGGCAAAACCAAG	0.547													25	111	---	---	---	---	PASS
SLC5A6	8884	broad.mit.edu	37	2	27429797	27429797	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27429797C>A	uc002rjd.2	-	4	798	c.407G>T	c.(406-408)CGA>CTA	p.R136L	SLC5A6_uc010eyv.1_Missense_Mutation_p.R136L	NM_021095	NP_066918	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium-dependent	136					biotin metabolic process|pantothenate metabolic process	integral to plasma membrane|membrane fraction	sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|Lipoic Acid(DB00166)	TTTATTGAATCGAAGCTCCAG	0.463													49	328	---	---	---	---	PASS
IL1F5	26525	broad.mit.edu	37	2	113820292	113820292	+	3'UTR	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113820292C>A	uc002tis.2	+	5					IL1F5_uc002tit.2_3'UTR	NM_173170	NP_775262	Q9UBH0	I36RA_HUMAN	interleukin 1 family, member 5							extracellular space	cytokine activity|interleukin-1 receptor antagonist activity				0						GCAGAGCCAGCTCGGGTGAGG	0.597													3	10	---	---	---	---	PASS
PTPN4	5775	broad.mit.edu	37	2	120718482	120718482	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120718482G>A	uc002tmf.1	+	23	3004	c.2233G>A	c.(2233-2235)GGC>AGC	p.G745S	PTPN4_uc010flj.1_Missense_Mutation_p.G458S|PTPN4_uc010yyr.1_Missense_Mutation_p.G378S	NM_002830	NP_002821	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type	745	Tyrosine-protein phosphatase.					cytoplasm|cytoskeleton|internal side of plasma membrane	cytoskeletal protein binding|non-membrane spanning protein tyrosine phosphatase activity			ovary(2)	2					Alendronate(DB00630)	TTGGGAACAAGGCTCCTCTAT	0.393													43	220	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170136059	170136059	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170136059T>C	uc002ues.2	-	12	1601	c.1388A>G	c.(1387-1389)AAT>AGT	p.N463S	LRP2_uc010zdf.1_Missense_Mutation_p.N463S	NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	463	LDL-receptor class B 1.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	AACAGAAACATTGAGAACCTC	0.348													26	134	---	---	---	---	PASS
HAT1	8520	broad.mit.edu	37	2	172821890	172821890	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172821890T>G	uc002uhi.2	+	5	417	c.341T>G	c.(340-342)ATC>AGC	p.I114S	HAT1_uc010fqi.2_5'UTR|HAT1_uc002uhj.2_Missense_Mutation_p.I29S	NM_003642	NP_003633	O14929	HAT1_HUMAN	histone acetyltransferase 1	114					chromatin silencing at telomere|DNA packaging	cytoplasm|nuclear matrix|nucleoplasm	histone acetyltransferase activity|protein binding			large_intestine(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.216)			ATTAGACAAATCATTCCACCT	0.318													15	67	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179424711	179424711	+	Silent	SNP	T	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179424711T>A	uc010zfg.1	-	275	78668	c.78444A>T	c.(78442-78444)ACA>ACT	p.T26148T	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.T19843T|TTN_uc010zfi.1_Silent_p.T19776T|TTN_uc010zfj.1_Silent_p.T19651T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	27075							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAGCTCCTGTTGTTAGTCCGC	0.398													10	109	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179480458	179480458	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179480458C>G	uc010zfg.1	-	207	40890	c.40666G>C	c.(40666-40668)GAG>CAG	p.E13556Q	TTN_uc010zfh.1_Missense_Mutation_p.E7251Q|TTN_uc010zfi.1_Missense_Mutation_p.E7184Q|TTN_uc010zfj.1_Missense_Mutation_p.E7059Q	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	14483							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AATAAGTACTCTTTTCCTTGA	0.373													9	166	---	---	---	---	PASS
AOX1	316	broad.mit.edu	37	2	201485970	201485970	+	Splice_Site	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201485970G>A	uc002uvx.2	+	18	2102	c.2001_splice	c.e18+1	p.K667_splice	AOX1_uc010zhf.1_Splice_Site_p.K223_splice|AOX1_uc010fsu.2_Splice_Site_p.K33_splice	NM_001159	NP_001150	Q06278	ADO_HUMAN	aldehyde oxidase 1						inflammatory response|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)|skin(1)	6					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	GACAGATAAGGTACTGCATTT	0.393													11	164	---	---	---	---	PASS
SLC19A3	80704	broad.mit.edu	37	2	228560780	228560780	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228560780C>A	uc002vpi.2	-	4	1086	c.997G>T	c.(997-999)GCA>TCA	p.A333S	SLC19A3_uc002vpj.2_RNA|SLC19A3_uc010zlv.1_Missense_Mutation_p.A329S	NM_025243	NP_079519	Q9BZV2	S19A3_HUMAN	solute carrier family 19, member 3	333	Helical; (Potential).				thiamine-containing compound metabolic process	integral to membrane|plasma membrane	folic acid binding|reduced folate carrier activity|thiamine uptake transmembrane transporter activity			ovary(2)	2		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	TAACCCACTGCAAAGGCAGCC	0.448													13	66	---	---	---	---	PASS
ZNF860	344787	broad.mit.edu	37	3	32030516	32030516	+	5'UTR	SNP	G	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32030516G>C	uc011axg.1	+	2						NM_001137674	NP_001131146	A6NHJ4	ZN860_HUMAN	zinc finger protein 860						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						tacaGAGCAGGAAGCAGATCG	0.254													4	40	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52443600	52443600	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52443600T>G	uc003ddx.2	-	3	207	c.92A>C	c.(91-93)GAG>GCG	p.E31A	PHF7_uc003ddy.2_5'Flank|PHF7_uc003ddz.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	31					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GTCGTAGATCTCCTCCACTTG	0.617			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								49	285	---	---	---	---	PASS
A4GNT	51146	broad.mit.edu	37	3	137843364	137843364	+	Silent	SNP	T	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137843364T>C	uc003ers.2	-	3	967	c.765A>G	c.(763-765)TTA>TTG	p.L255L		NM_016161	NP_057245	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	255	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|Golgi stack|integral to membrane|membrane fraction	acetylglucosaminyltransferase activity|galactosyltransferase activity			central_nervous_system(1)	1						TTTGGGGGTGTAAGAAGGATA	0.483													15	89	---	---	---	---	PASS
SIAH2	6478	broad.mit.edu	37	3	150460186	150460186	+	Nonsense_Mutation	SNP	G	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150460186G>C	uc003eyi.2	-	2	1344	c.717C>G	c.(715-717)TAC>TAG	p.Y239*		NM_005067	NP_005058	O43255	SIAH2_HUMAN	seven in absentia homolog 2	239	SBD.				apoptosis|axon guidance|cell cycle|negative regulation of canonical Wnt receptor signaling pathway|small GTPase mediated signal transduction|ubiquitin-dependent protein catabolic process	cytosol|nucleus	transcription corepressor activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GGTGGCCTTCGTACTTCTCTT	0.522													11	97	---	---	---	---	PASS
LPP	4026	broad.mit.edu	37	3	188584127	188584127	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188584127A>C	uc003frs.1	+	9	1796	c.1550A>C	c.(1549-1551)GAT>GCT	p.D517A	LPP_uc011bsg.1_Missense_Mutation_p.D370A|LPP_uc011bsi.1_Missense_Mutation_p.D517A|LPP_uc011bsj.1_Missense_Mutation_p.D354A	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation	517	LIM zinc-binding 2.				cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TTCACTGTGGATGCTGGCGGG	0.557			T	HMGA2|MLL|C12orf9	lipoma|leukemia								3	62	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195515102	195515102	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195515102G>C	uc011bto.1	-	2	3809	c.3349C>G	c.(3349-3351)CAC>GAC	p.H1117D	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	994	Ser-rich.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGGTGGTGTGACCTGTGGAT	0.567													2	1	---	---	---	---	PASS
RGS12	6002	broad.mit.edu	37	4	3317854	3317854	+	5'UTR	SNP	A	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3317854A>C	uc003ggw.2	+	2					RGS12_uc003ggu.2_5'UTR|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_RNA|RGS12_uc003ggv.2_5'UTR|RGS12_uc003ggx.1_5'UTR	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1							condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ATATGGCTCCAAGGGAACAAT	0.488													14	91	---	---	---	---	PASS
ZNF518B	85460	broad.mit.edu	37	4	10447285	10447285	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10447285T>C	uc003gmn.2	-	3	1155	c.668A>G	c.(667-669)AAA>AGA	p.K223R		NM_053042	NP_444270	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	223					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)	4						GGCAACAGCTTTGACTGGCCG	0.418													46	389	---	---	---	---	PASS
PCDH7	5099	broad.mit.edu	37	4	31144244	31144244	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31144244G>T	uc011bxx.1	+	3	4525	c.3517G>T	c.(3517-3519)GAT>TAT	p.D1173Y	PCDH7_uc011bxw.1_Missense_Mutation_p.D1126Y	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	Error:Variant_position_missing_in_O60245_after_alignment					homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						CATGCCTGTTGATGAACGAGG	0.537													28	142	---	---	---	---	PASS
PAPSS1	9061	broad.mit.edu	37	4	108615140	108615140	+	Silent	SNP	A	G	G	rs113388762		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108615140A>G	uc003hyk.2	-	3	282	c.198T>C	c.(196-198)ACT>ACC	p.T66T	PAPSS1_uc011cfh.1_RNA	NM_005443	NP_005434	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase	66	Adenylyl-sulfate kinase.|ATP (Potential).				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|sulfate adenylyltransferase (ATP) activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		TGCTCACAGTAGTCTTTCCCG	0.378													5	58	---	---	---	---	PASS
HADH	3033	broad.mit.edu	37	4	108935617	108935617	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108935617A>G	uc003hyq.2	+	3	441	c.292A>G	c.(292-294)AGC>GGC	p.S98G	HADH_uc010ilx.2_Missense_Mutation_p.S98G|HADH_uc010ily.2_Intron|HADH_uc003hyr.2_Missense_Mutation_p.S102G	NM_005327	NP_005318	Q16836	HCDH_HUMAN	L-3-hydroxyacyl-Coenzyme A dehydrogenase	98					fatty acid beta-oxidation	mitochondrial matrix	3-hydroxyacyl-CoA dehydrogenase activity|NAD+ binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000168)	NADH(DB00157)	GAAGACCCTGAGCACCATAGC	0.512													17	144	---	---	---	---	PASS
TMEM154	201799	broad.mit.edu	37	4	153573992	153573992	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153573992G>A	uc003imw.1	-	2	258	c.152C>T	c.(151-153)GCA>GTA	p.A51V		NM_152680	NP_689893	Q6P9G4	TM154_HUMAN	transmembrane protein 154 precursor	51	Extracellular (Potential).					integral to membrane					0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				GATGGTCACTGCAGCAAATGT	0.353													7	112	---	---	---	---	PASS
RHOBTB3	22836	broad.mit.edu	37	5	95091182	95091182	+	Silent	SNP	C	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95091182C>T	uc003klm.2	+	6	1302	c.765C>T	c.(763-765)GAC>GAT	p.D255D	RHOBTB3_uc003klk.1_Silent_p.D49D	NM_014899	NP_055714	O94955	RHBT3_HUMAN	rho-related BTB domain containing 3	255	BTB 1.				retrograde transport, endosome to Golgi	Golgi apparatus	ATP binding|ATPase activity|Rab GTPase binding			lung(1)|skin(1)	2		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		AGTGTGTGGACGTGGTATTTT	0.393													12	320	---	---	---	---	PASS
NRG2	9542	broad.mit.edu	37	5	139244754	139244754	+	Intron	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139244754G>A	uc003lex.1	-						NRG2_uc003lev.1_Intron|NRG2_uc003lew.1_Missense_Mutation_p.P373S|NRG2_uc003ley.1_Missense_Mutation_p.P373S	NM_004883	NP_004874	O14511	NRG2_HUMAN	neuregulin 2 isoform 1						embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TATCCCACAGGACACCTACCA	0.517													6	58	---	---	---	---	PASS
C6orf218	221718	broad.mit.edu	37	6	10430189	10430189	+	RNA	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10430189G>A	uc003myz.2	-	3		c.847C>T				NR_027793				Homo sapiens chromosome 6 open reading frame 218, mRNA (cDNA clone IMAGE:3917693).												0	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.124)				ACAGGGCGGGGAAGCAGGGAG	0.468											OREG0017184	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	35	268	---	---	---	---	PASS
RFX6	222546	broad.mit.edu	37	6	117248535	117248535	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117248535G>T	uc003pxm.2	+	17	2294	c.2231G>T	c.(2230-2232)TGT>TTT	p.C744F		NM_173560	NP_775831	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	744					glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	protein binding|transcription regulatory region DNA binding			ovary(1)|pancreas(1)|skin(1)	3						AGTGGCAGCTGTGCGGGGTCT	0.522													8	39	---	---	---	---	PASS
INHBA	3624	broad.mit.edu	37	7	41729120	41729120	+	3'UTR	SNP	T	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41729120T>G	uc003thq.2	-	2					INHBA_uc003thr.2_3'UTR	NM_002192	NP_002183	P08476	INHBA_HUMAN	inhibin beta A precursor						cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity			lung(5)|ovary(1)	6						tgtttttttttgttttttttt	0.274										TSP Lung(11;0.080)			2	10	---	---	---	---	PASS
ZPBP	11055	broad.mit.edu	37	7	50070788	50070788	+	Silent	SNP	A	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50070788A>T	uc003tou.2	-	5	676	c.606T>A	c.(604-606)CTT>CTA	p.L202L	ZPBP_uc011kci.1_Silent_p.L128L|ZPBP_uc010kyw.2_Silent_p.L201L	NM_007009	NP_008940	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein isoform 1	202					binding of sperm to zona pellucida	extracellular region					0	Glioma(55;0.08)|all_neural(89;0.245)					AAAGGTCAAGAAGCAGTTTGC	0.343													29	150	---	---	---	---	PASS
TMEM130	222865	broad.mit.edu	37	7	98457932	98457932	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98457932G>A	uc003upo.2	-	3	610	c.421C>T	c.(421-423)CAG>TAG	p.Q141*	TMEM130_uc011kiq.1_Nonsense_Mutation_p.Q122*|TMEM130_uc011kir.1_Nonsense_Mutation_p.Q141*|TMEM130_uc003upn.2_Nonsense_Mutation_p.Q39*	NM_001134450	NP_001127922	Q8N3G9	TM130_HUMAN	transmembrane protein 130 isoform a	141	Extracellular (Potential).					Golgi membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			GAAGTGTTCTGGGTGACAACA	0.557													7	66	---	---	---	---	PASS
ZNF425	155054	broad.mit.edu	37	7	148802500	148802500	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148802500T>G	uc003wfj.2	-	4	536	c.463A>C	c.(463-465)AAT>CAT	p.N155H		NM_001001661	NP_001001661	Q6IV72	ZN425_HUMAN	zinc finger protein 425	155					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			ACTTTTTTATTTAGAATCTCT	0.478													37	214	---	---	---	---	PASS
CCDC25	55246	broad.mit.edu	37	8	27605739	27605739	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27605739T>G	uc003xgc.2	-	7	519	c.406A>C	c.(406-408)ACC>CCC	p.T136P	CCDC25_uc003xgd.2_Missense_Mutation_p.T68P|CCDC25_uc011lan.1_RNA|CCDC25_uc011lao.1_RNA|CCDC25_uc003xge.2_RNA|CCDC25_uc003xgf.1_RNA	NM_018246	NP_060716	Q86WR0	CCD25_HUMAN	coiled-coil domain containing 25	136	Potential.										0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0223)|KIRC - Kidney renal clear cell carcinoma(542;0.11)|Kidney(114;0.131)|Colorectal(74;0.154)		TCGACTTTGGTCTTTTCTAAT	0.388													16	113	---	---	---	---	PASS
ZFPM2	23414	broad.mit.edu	37	8	106815671	106815671	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106815671T>C	uc003ymd.2	+	8	3384	c.3361T>C	c.(3361-3363)TGC>CGC	p.C1121R	ZFPM2_uc011lhs.1_Missense_Mutation_p.C852R	NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2	1121	C2HC-type 5.				blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			TGGGAAATATTGCCGGCTATG	0.418													7	37	---	---	---	---	PASS
COL5A1	1289	broad.mit.edu	37	9	137591804	137591804	+	Silent	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137591804G>A	uc004cfe.2	+	3	709	c.327G>A	c.(325-327)AAG>AAA	p.K109K		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	109	TSP N-terminal.|Laminin G-like.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		TGAAAGCCAAGAAAGGCAGCC	0.587													8	113	---	---	---	---	PASS
NMT2	9397	broad.mit.edu	37	10	15161511	15161511	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15161511A>T	uc001inz.1	-	9	1085	c.1001T>A	c.(1000-1002)GTT>GAT	p.V334D	NMT2_uc001ioa.1_Missense_Mutation_p.V321D|NMT2_uc009xjo.1_Missense_Mutation_p.V334D|NMT2_uc010qbz.1_Missense_Mutation_p.V146D	NM_004808	NP_004799	O60551	NMT2_HUMAN	N-myristoyltransferase 2	334					N-terminal protein myristoylation|protein lipoylation	Golgi apparatus|plasma membrane	glycylpeptide N-tetradecanoyltransferase activity			ovary(1)	1						AGTCTTTGTAACCTTGTTGGA	0.323													8	79	---	---	---	---	PASS
ST8SIA6	338596	broad.mit.edu	37	10	17432566	17432566	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17432566T>A	uc001ipd.2	-	3	254	c.254A>T	c.(253-255)CAA>CTA	p.Q85L	ST8SIA6_uc010qce.1_RNA|uc001ipe.2_Intron|uc001ipf.1_Intron	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide	85	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						AATGCCATATTGCAGATTTTT	0.333													28	247	---	---	---	---	PASS
IFIT2	3433	broad.mit.edu	37	10	91065757	91065757	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91065757A>C	uc009xts.2	+	2	219	c.44A>C	c.(43-45)CAA>CCA	p.Q15P	LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron|uc001kgd.2_Intron	NM_001547	NP_001538	P09913	IFIT2_HUMAN	interferon-induced protein with	15					negative regulation of protein binding|response to virus|type I interferon-mediated signaling pathway		protein binding			ovary(1)|skin(1)	2		Colorectal(252;0.0161)				AGCCTACGGCAACTAAAATGC	0.403													22	112	---	---	---	---	PASS
WDR11	55717	broad.mit.edu	37	10	122661797	122661797	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122661797G>T	uc010qtf.1	+	22	2954	c.2716G>T	c.(2716-2718)GAA>TAA	p.E906*	WDR11_uc010qte.1_Nonsense_Mutation_p.E508*|WDR11_uc001lfd.1_Nonsense_Mutation_p.E424*|WDR11_uc009xzn.2_Nonsense_Mutation_p.E197*	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2	906	WD 9.					integral to membrane					0						GCTTGATCCAGAATTCACTCT	0.358													14	75	---	---	---	---	PASS
OR52A5	390054	broad.mit.edu	37	11	5153240	5153240	+	Silent	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5153240C>A	uc010qyx.1	-	1	633	c.633G>T	c.(631-633)GGG>GGT	p.G211G		NM_001005160	NP_001005160	Q9H2C5	O52A5_HUMAN	olfactory receptor, family 52, subfamily A,	211	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|lung(1)|central_nervous_system(1)	4		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		TTATGTCAAACCCTAGGATTG	0.423													5	117	---	---	---	---	PASS
KIAA0652	9776	broad.mit.edu	37	11	46691049	46691049	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46691049A>G	uc009yld.2	+	17	2127	c.1443A>G	c.(1441-1443)ATA>ATG	p.I481M	KIAA0652_uc001nda.2_Missense_Mutation_p.I514M|KIAA0652_uc001ndb.2_Missense_Mutation_p.I481M|KIAA0652_uc001ncz.2_Missense_Mutation_p.I444M|KIAA0652_uc001ndc.2_Missense_Mutation_p.I444M|KIAA0652_uc010rgv.1_Missense_Mutation_p.I365M	NM_001142673	NP_001136145	O75143	ATG13_HUMAN	autophagy-related protein 13 isoform 1	481					autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)		GCCTCTCCATAGATATTGGAG	0.473													19	88	---	---	---	---	PASS
LRP4	4038	broad.mit.edu	37	11	46880582	46880582	+	Silent	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46880582G>A	uc001ndn.3	-	38	5816	c.5670C>T	c.(5668-5670)GAC>GAT	p.D1890D	uc001ndl.2_Intron|LRP4_uc001ndm.3_Silent_p.D132D	NM_002334	NP_002325	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein	1890	Cytoplasmic (Potential).				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4				Lung(87;0.159)		TCCAGCCCGTGTCTGGCAGAG	0.542													10	96	---	---	---	---	PASS
OR4A16	81327	broad.mit.edu	37	11	55111083	55111083	+	Missense_Mutation	SNP	G	T	T	rs143065334	byFrequency	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55111083G>T	uc010rie.1	+	1	407	c.407G>T	c.(406-408)CGA>CTA	p.R136L		NM_001005274	NP_001005274	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A,	136	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(2)|pancreas(1)	3						ATCATGAATCGACTGGTTTGC	0.478													37	210	---	---	---	---	PASS
SLC22A6	9356	broad.mit.edu	37	11	62751897	62751897	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62751897G>T	uc001nwk.2	-	1	573	c.266C>A	c.(265-267)CCC>CAC	p.P89H	SLC22A6_uc001nwl.2_Missense_Mutation_p.P89H|SLC22A6_uc001nwj.2_Missense_Mutation_p.P89H|SLC22A6_uc001nwm.2_Missense_Mutation_p.P89H	NM_004790	NP_004781	Q4U2R8	S22A6_HUMAN	solute carrier family 22 member 6 isoform a	89	Extracellular (Potential).				alpha-ketoglutarate transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	inorganic anion exchanger activity|protein binding				0						ATTGAGAAAGGGCAGTCCCCA	0.627													12	124	---	---	---	---	PASS
OTUB1	55611	broad.mit.edu	37	11	63764641	63764641	+	Silent	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63764641C>A	uc001nyf.1	+	6	1147	c.543C>A	c.(541-543)GGC>GGA	p.G181G	OTUB1_uc001nyg.1_Silent_p.G224G|OTUB1_uc010rmz.1_Silent_p.G218G|OTUB1_uc010rna.1_Silent_p.G190G|OTUB1_uc009ypa.2_Silent_p.G80G|OTUB1_uc009ypb.1_Silent_p.G151G	NM_017670	NP_060140	Q96FW1	OTUB1_HUMAN	otubain 1	181	OTU.				protein K48-linked deubiquitination	cytoplasm	NEDD8-specific protease activity|omega peptidase activity|ubiquitin binding|ubiquitin-specific protease activity			breast(1)	1						TCACCTCGGGCTACCTGCAGC	0.607													23	134	---	---	---	---	PASS
KDM4DL	390245	broad.mit.edu	37	11	94759338	94759338	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94759338C>A	uc010ruf.1	+	1	917	c.617C>A	c.(616-618)CCC>CAC	p.P206H		NM_001161630	NP_001155102	B2RXH2	KD4DL_HUMAN	lysine (K)-specific demethylase 4D-like	206	JmjC.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						TTTGGGGAGCCCAAAACTTGG	0.562													10	89	---	---	---	---	PASS
MMP1	4312	broad.mit.edu	37	11	102668828	102668828	+	5'UTR	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102668828G>A	uc001phi.2	-	1					uc001phh.1_RNA|MMP1_uc010ruv.1_Intron	NM_002421	NP_002412	P03956	MMP1_HUMAN	matrix metalloproteinase 1 isoform 1						blood coagulation|collagen catabolic process|interspecies interaction between organisms|leukocyte migration|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(2)|ovary(1)|lung(1)	4	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)		GTGCATACTGGCCTTTGTCTT	0.512													8	39	---	---	---	---	PASS
BLID	414899	broad.mit.edu	37	11	121986299	121986299	+	3'UTR	SNP	T	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121986299T>C	uc001pyf.2	-	1					LOC399959_uc009zba.2_Intron	NM_001001786	NP_001001786	Q8IZY5	BLID_HUMAN	BRCC2 protein						apoptosis	mitochondrion					0		Breast(109;0.0164)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;2.08e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.101)		CCTAACTCACTCCTTTTACAG	0.423													16	90	---	---	---	---	PASS
TAS2R50	259296	broad.mit.edu	37	12	11139225	11139225	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11139225C>A	uc001qzl.2	-	1	287	c.235G>T	c.(235-237)GAA>TAA	p.E79*	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176890	NP_795371	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	79	Extracellular (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			ovary(2)	2						ATTCTTAATTCTACACTATAA	0.378													22	147	---	---	---	---	PASS
PPFIBP1	8496	broad.mit.edu	37	12	27799072	27799072	+	Silent	SNP	C	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27799072C>T	uc001ric.1	+	5	725	c.348C>T	c.(346-348)CTC>CTT	p.L116L	PPFIBP1_uc001rhz.1_Silent_p.L116L|PPFIBP1_uc010sjr.1_5'UTR|PPFIBP1_uc001rib.1_Silent_p.L116L|PPFIBP1_uc001ria.2_Silent_p.L116L|PPFIBP1_uc001rid.1_5'UTR	NM_003622	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein binding protein 1	116					cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)					AAGAATCCCTCGTTCTTCAGG	0.318													5	46	---	---	---	---	PASS
EIF4B	1975	broad.mit.edu	37	12	53433572	53433572	+	Intron	SNP	T	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53433572T>C	uc001sbh.3	+						EIF4B_uc010snu.1_Intron|EIF4B_uc010snv.1_Intron|EIF4B_uc001sbi.2_Intron|uc001sbj.1_RNA	NM_001417	NP_001408	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B						insulin receptor signaling pathway|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	nucleotide binding|translation initiation factor activity			breast(1)|kidney(1)	2						TAAAAATTCTTAGTATTCTAA	0.313													3	8	---	---	---	---	PASS
EP400	57634	broad.mit.edu	37	12	132497632	132497632	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132497632C>T	uc001ujn.2	+	16	3555	c.3520C>T	c.(3520-3522)CGA>TGA	p.R1174*	EP400_uc001ujl.2_Nonsense_Mutation_p.R1173*|EP400_uc001ujm.2_Nonsense_Mutation_p.R1174*	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	1210	Interactions with RUVBL1 and RUVBL2.|Helicase ATP-binding.				histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CGCCTTCACACGAGTGCGCTG	0.597													5	45	---	---	---	---	PASS
GPR180	160897	broad.mit.edu	37	13	95257668	95257668	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95257668A>G	uc001vly.2	+	2	247	c.169A>G	c.(169-171)AGA>GGA	p.R57G	GPR180_uc001vlz.2_Splice_Site|GPR180_uc010afi.2_5'UTR	NM_180989	NP_851320	Q86V85	GP180_HUMAN	G protein-coupled receptor 180 precursor	57						integral to membrane				breast(1)	1	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					TCTGTGTGTCAGAATCAACAA	0.408													24	128	---	---	---	---	PASS
RBM23	55147	broad.mit.edu	37	14	23378782	23378782	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23378782A>G	uc001whg.2	-	3	288	c.89T>C	c.(88-90)GTT>GCT	p.V30A	RBM23_uc001whh.2_Missense_Mutation_p.V30A|RBM23_uc001whi.2_Missense_Mutation_p.V30A|RBM23_uc010tne.1_Intron|RBM23_uc001whj.2_Intron|RBM23_uc001whk.1_Missense_Mutation_p.V30A	NM_001077351	NP_001070819	Q86U06	RBM23_HUMAN	RNA binding motif protein 23 isoform 1	30					mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)		ATCCTTTTTAACTTCTTTCCT	0.483													40	354	---	---	---	---	PASS
MYH6	4624	broad.mit.edu	37	14	23855795	23855795	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23855795G>A	uc001wjv.2	-	33	4755	c.4688C>T	c.(4687-4689)GCC>GTC	p.A1563V		NM_002471	NP_002462	P13533	MYH6_HUMAN	myosin heavy chain 6	1563	Potential.				adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development	cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle			pancreas(2)|ovary(1)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CTCTAGCTGGGCCCGGAGGAT	0.647													18	252	---	---	---	---	PASS
RIPK3	11035	broad.mit.edu	37	14	24808448	24808448	+	Missense_Mutation	SNP	C	T	T	rs148690006	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24808448C>T	uc001wpb.2	-	3	454	c.244G>A	c.(244-246)GTG>ATG	p.V82M	RIPK3_uc001wpa.2_5'Flank|RIPK3_uc010alq.2_RNA|RIPK3_uc010toi.1_Translation_Start_Site|RIPK3_uc010toj.1_Missense_Mutation_p.V82M	NM_006871	NP_006862	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	82	Protein kinase.				apoptosis|induction of apoptosis by extracellular signals	cytoplasm	ATP binding|protein binding|transcription coactivator activity			central_nervous_system(2)|ovary(1)|lung(1)	4				GBM - Glioblastoma multiforme(265;0.0181)		TCCCAGTTCACCTTCTCGATA	0.582													6	87	---	---	---	---	PASS
SDCCAG1	9147	broad.mit.edu	37	14	50295452	50295452	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50295452C>T	uc001wxc.2	-	14	1374	c.1306G>A	c.(1306-1308)GAA>AAA	p.E436K	SDCCAG1_uc010anj.1_Missense_Mutation_p.E436K|SDCCAG1_uc010tqi.1_Missense_Mutation_p.E436K|SDCCAG1_uc001wxe.2_Missense_Mutation_p.E394K|SDCCAG1_uc001wxd.1_5'UTR|SDCCAG1_uc010anq.1_Missense_Mutation_p.E207K	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1	436						cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)		TTTGGTGGTTCAGTTTCATTT	0.343													9	123	---	---	---	---	PASS
SERPINA5	5104	broad.mit.edu	37	14	95057024	95057024	+	Intron	SNP	G	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95057024G>T	uc001ydm.2	+						SERPINA5_uc010ave.2_3'UTR|SERPINA3_uc001ydo.3_5'Flank	NM_000624	NP_000615	P05154	IPSP_HUMAN	serine (or cysteine) proteinase inhibitor, clade						fusion of sperm to egg plasma membrane|regulation of proteolysis|spermatogenesis	extracellular region|membrane|protein complex	acrosin binding|heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(2)	2				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	TGAATCCAAGGGGTGAGGCTC	0.463													3	34	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106091290	106091290	+	RNA	SNP	T	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106091290T>A	uc010tyt.1	-	3647		c.62218A>T			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron					Parts of antibodies, mostly variable regions.												0						TTGGAGACCTTGCACTTGTAC	0.602													45	278	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34072416	34072416	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34072416C>T	uc001zhi.2	+	65	9212	c.9142C>T	c.(9142-9144)CGC>TGC	p.R3048C	RYR3_uc010bar.2_Missense_Mutation_p.R3048C	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3048					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TTCCAGGCAACGCCCTGCCCT	0.552													6	39	---	---	---	---	PASS
CGNL1	84952	broad.mit.edu	37	15	57732654	57732654	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57732654A>G	uc002aeg.2	+	3	1758	c.1682A>G	c.(1681-1683)AAT>AGT	p.N561S	CGNL1_uc010bfw.2_Missense_Mutation_p.N561S	NM_032866	NP_116255	Q0VF96	CGNL1_HUMAN	cingulin-like 1	561						myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		ATTCTCTACAATTACCTCAAA	0.443													3	16	---	---	---	---	PASS
WDR59	79726	broad.mit.edu	37	16	74945997	74945997	+	Intron	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74945997C>A	uc002fdh.1	-						WDR59_uc002fdi.2_Intron|WDR59_uc002fdj.2_3'UTR|WDR59_uc002fdg.1_Intron	NM_030581	NP_085058	Q6PJI9	WDR59_HUMAN	WD repeat domain 59											ovary(1)|breast(1)	2						AAACAGATGACTTCCGAATCT	0.373													3	24	---	---	---	---	PASS
ZZEF1	23140	broad.mit.edu	37	17	3988990	3988990	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3988990G>C	uc002fxe.2	-	16	2684	c.2620C>G	c.(2620-2622)CGA>GGA	p.R874G	ZZEF1_uc002fxk.1_Missense_Mutation_p.R874G	NM_015113	NP_055928	O43149	ZZEF1_HUMAN	zinc finger, ZZ type with EF hand domain 1	874							calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4						TGGTTCCGTCGGGTCTGTCGA	0.438													22	105	---	---	---	---	PASS
MYH13	8735	broad.mit.edu	37	17	10247205	10247205	+	Silent	SNP	G	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10247205G>T	uc002gmk.1	-	16	1896	c.1806C>A	c.(1804-1806)CCC>CCA	p.P602P	MYH13_uc010vvf.1_Silent_p.P277P	NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	602	Myosin head-like.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6						TCTCGTTCAGGGGGTCCTTGT	0.537													11	77	---	---	---	---	PASS
CDK5R1	8851	broad.mit.edu	37	17	30814589	30814589	+	5'UTR	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30814589C>A	uc002hhn.2	+	2					CDK5R1_uc010wca.1_5'Flank|CDK5R1_uc010ctc.2_5'Flank	NM_003885	NP_003876	Q15078	CD5R1_HUMAN	cyclin-dependent kinase 5, regulatory subunit 1						axon guidance|axonal fasciculation|brain development|cell proliferation|embryo development|ionotropic glutamate receptor signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of transcription, DNA-dependent|neuron cell-cell adhesion|neuron migration|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of neuron apoptosis|regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation	axon|contractile fiber|cyclin-dependent protein kinase 5 holoenzyme complex|cytosol|dendritic spine|growth cone|neuromuscular junction|neuronal cell body|perinuclear region of cytoplasm|plasma membrane	cadherin binding|calcium ion binding|protein kinase binding			ovary(1)	1		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.0938)			CTCCGGCCGGCAGGCTgggcg	0.577													2	0	---	---	---	---	PASS
PGAP3	93210	broad.mit.edu	37	17	37829071	37829071	+	Silent	SNP	C	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37829071C>T	uc002hsj.2	-	8	991	c.948G>A	c.(946-948)AAG>AAA	p.K316K	PGAP3_uc010cvy.2_RNA|PGAP3_uc010wej.1_Silent_p.K295K|PGAP3_uc002hsk.2_Silent_p.K265K|PGAP3_uc010cvz.2_3'UTR	NM_033419	NP_219487	Q96FM1	PGAP3_HUMAN	per1-like domain containing 1 precursor	316	Cytoplasmic (Potential).				GPI anchor biosynthetic process	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	hydrolase activity, acting on ester bonds			upper_aerodigestive_tract(1)	1						CCAGCTTGAACTTGTCCTCTG	0.567													11	51	---	---	---	---	PASS
WNK4	65266	broad.mit.edu	37	17	40947998	40947998	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40947998A>T	uc002ibj.2	+	16	3399	c.3378A>T	c.(3376-3378)GAA>GAT	p.E1126D	WNK4_uc010wgx.1_Missense_Mutation_p.E790D|CCDC56_uc010wgz.1_Missense_Mutation_p.F87Y|CNTD1_uc002ibm.3_5'Flank|CNTD1_uc010wha.1_5'Flank	NM_032387	NP_115763	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	1126					intracellular protein kinase cascade	tight junction	ATP binding|protein serine/threonine kinase activity			ovary(3)|skin(3)|stomach(1)	7		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		AGGAGTCAGAAAGCAGTGGGG	0.587													11	92	---	---	---	---	PASS
NFE2L1	4779	broad.mit.edu	37	17	46136474	46136474	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46136474A>G	uc002imz.3	+	6	2441	c.1790A>G	c.(1789-1791)AAA>AGA	p.K597R	NFE2L1_uc002ina.3_Missense_Mutation_p.K567R|NFE2L1_uc002inb.3_Missense_Mutation_p.K567R|NFE2L1_uc010wle.1_Missense_Mutation_p.K409R|NFE2L1_uc010wlf.1_Missense_Mutation_p.K441R	NM_003204	NP_003195	Q14494	NF2L1_HUMAN	nuclear factor erythroid 2-like 1	597					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						GCCCTCAAGAAAGGCAGCAAG	0.587													6	71	---	---	---	---	PASS
MYST2	11143	broad.mit.edu	37	17	47899078	47899078	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47899078G>C	uc002ipm.2	+	11	1438	c.1312G>C	c.(1312-1314)GTG>CTG	p.V438L	MYST2_uc002ipl.1_Missense_Mutation_p.V408L|MYST2_uc010wma.1_Missense_Mutation_p.V299L|MYST2_uc010wmb.1_Missense_Mutation_p.V328L|MYST2_uc010wmc.1_Missense_Mutation_p.V269L|MYST2_uc010wmd.1_Missense_Mutation_p.V282L|MYST2_uc010wme.1_Missense_Mutation_p.V252L|MYST2_uc010wmf.1_Missense_Mutation_p.V103L|MYST2_uc010wmg.1_5'UTR	NM_007067	NP_008998	O95251	MYST2_HUMAN	MYST histone acetyltransferase 2	438					DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	histone acetyltransferase activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3						ATATTATGATGTGGAGCCCTT	0.448													14	152	---	---	---	---	PASS
BRIP1	83990	broad.mit.edu	37	17	59853839	59853839	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59853839C>A	uc002izk.1	-	14	2161	c.2020G>T	c.(2020-2022)GAT>TAT	p.D674Y	BRIP1_uc002izl.1_Missense_Mutation_p.D55Y	NM_032043	NP_114432	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	674					DNA damage checkpoint|double-strand break repair|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(1)	1						CCCACTTCATCTTGGAACTCA	0.423			F|N|Mis			AML|leukemia|breast		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				21	163	---	---	---	---	PASS
DCAF7	10238	broad.mit.edu	37	17	61628100	61628100	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61628100C>T	uc002jbc.2	+	1	279	c.62C>T	c.(61-63)GCG>GTG	p.A21V	DCAF7_uc002jbb.2_RNA|DCAF7_uc010wpn.1_Missense_Mutation_p.A21V	NM_005828	NP_005819	P61962	DCAF7_HUMAN	WD-repeat protein	21					multicellular organismal development	CUL4 RING ubiquitin ligase complex|cytoplasm|nucleus	protein binding			ovary(1)	1						ACAGTCTACGCGATGAACTGG	0.627													6	52	---	---	---	---	PASS
SOCS3	9021	broad.mit.edu	37	17	76354730	76354730	+	Silent	SNP	C	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76354730C>T	uc002jvl.2	-	2	863	c.447G>A	c.(445-447)GAG>GAA	p.E149E		NM_003955	NP_003946	O14543	SOCS3_HUMAN	suppressor of cytokine signaling 3	149					anti-apoptosis|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|regulation of growth|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytosol	protein kinase inhibitor activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(99;0.000688)|OV - Ovarian serous cystadenocarcinoma(97;0.0554)			CAGACGGCTGCTCGGGCACCT	0.662													7	43	---	---	---	---	PASS
FOXK2	3607	broad.mit.edu	37	17	80477948	80477948	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80477948C>A	uc002kfn.2	+	1	355	c.184C>A	c.(184-186)CAG>AAG	p.Q62K	FOXK2_uc002kfm.1_Missense_Mutation_p.Q62K|FOXK2_uc010diu.2_Missense_Mutation_p.Q62K	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2	62	FHA.|Gly-rich.			AAAAALSGAGTPPAGGGAGGGGAGGGGSPPGGWAVARLEGR EFEYLMKKRSVTIGRNSSQGSVDVSMGHSSFISRRHLEIFT PPGGGGHGGAAPELPPAQPRPDAGGDFYLRCLGKNG -> Q (in Ref. 1; CAA43200).	embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			CAACTCGTCGCAGGGCTCGGT	0.557													5	38	---	---	---	---	PASS
PCSK4	54760	broad.mit.edu	37	19	1482902	1482902	+	Silent	SNP	G	A	A	rs143738061	byFrequency	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1482902G>A	uc002ltb.1	-	13	1751	c.1689C>T	c.(1687-1689)TTC>TTT	p.F563F	PCSK4_uc002lsz.2_Silent_p.F50F|PCSK4_uc002lta.2_Intron	NM_017573	NP_060043	Q6UW60	PCSK4_HUMAN	proprotein convertase subtilisin/kexin type 4	563					proteolysis	integral to membrane	serine-type endopeptidase activity				0		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|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)		CACCCGTGTTGAAATAGTAGC	0.617													6	33	---	---	---	---	PASS
OR7G2	390882	broad.mit.edu	37	19	9213720	9213720	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9213720G>C	uc010xkk.1	-	1	263	c.263C>G	c.(262-264)TCC>TGC	p.S88C		NM_001005193	NP_001005193	Q8NG99	OR7G2_HUMAN	olfactory receptor, family 7, subfamily G,	67	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1						GTCCAAAAAGGAGAGATTGGA	0.507													14	136	---	---	---	---	PASS
PDE4A	5141	broad.mit.edu	37	19	10574595	10574595	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10574595G>A	uc002moj.2	+	14	1978	c.1870G>A	c.(1870-1872)GGC>AGC	p.G624S	PDE4A_uc002mok.2_Missense_Mutation_p.G598S|PDE4A_uc002mol.2_Missense_Mutation_p.G563S|PDE4A_uc002mom.2_Missense_Mutation_p.G385S|PDE4A_uc002mon.2_Missense_Mutation_p.G79S|PDE4A_uc002moo.2_Missense_Mutation_p.G290S	NM_001111307	NP_001104777	P27815	PDE4A_HUMAN	phosphodiesterase 4A isoform 1	624	Catalytic.				signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)	GCGCGAGCGTGGCATGGAAAT	0.622													6	78	---	---	---	---	PASS
DAND5	199699	broad.mit.edu	37	19	13080675	13080675	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13080675G>C	uc002mwc.1	+	1	244	c.201G>C	c.(199-201)CAG>CAC	p.Q67H	DAND5_uc010dyz.1_Missense_Mutation_p.Q97H	NM_152654	NP_689867	Q8N907	DAND5_HUMAN	dante precursor	67						extracellular region				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(19;1.87e-18)			TGGGCCTGCAGAAAGCCAGGC	0.662													13	100	---	---	---	---	PASS
UPF1	5976	broad.mit.edu	37	19	18974988	18974988	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18974988T>C	uc002nkg.2	+	20	3093	c.2818T>C	c.(2818-2820)TTC>CTC	p.F940L	UPF1_uc002nkf.2_Missense_Mutation_p.F929L|UPF1_uc002nkh.2_Missense_Mutation_p.F184L	NM_002911	NP_002902	Q92900	RENT1_HUMAN	regulator of nonsense transcripts 1	940					cell cycle|DNA repair|DNA replication|histone mRNA catabolic process|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational termination	chromatin|cytoplasmic mRNA processing body|exon-exon junction complex	ATP binding|ATP-dependent RNA helicase activity|chromatin binding|DNA binding|protein binding|protein binding|RNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2						GGGAGCCCGCTTCATGACCAC	0.602													38	163	---	---	---	---	PASS
PEPD	5184	broad.mit.edu	37	19	33882246	33882246	+	Silent	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33882246G>A	uc002nur.3	-	13	1242	c.1107C>T	c.(1105-1107)GGC>GGT	p.G369G	PEPD_uc010xrr.1_Silent_p.G328G|PEPD_uc010xrs.1_Silent_p.G305G|PEPD_uc002nuq.3_5'Flank	NM_000285	NP_000276	P12955	PEPD_HUMAN	prolidase isoform 1	369					cellular amino acid metabolic process|collagen catabolic process|proteolysis		aminopeptidase activity|dipeptidase activity|manganese ion binding|metallocarboxypeptidase activity			ovary(2)	2	Esophageal squamous(110;0.137)					CCAGGAAGTGGCCAAGCCCGT	0.662													3	22	---	---	---	---	PASS
GRAMD1A	57655	broad.mit.edu	37	19	35500996	35500996	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35500996A>G	uc010xse.1	+	5	463	c.326A>G	c.(325-327)GAT>GGT	p.D109G	GRAMD1A_uc002nxi.1_Missense_Mutation_p.D196G|GRAMD1A_uc002nxk.2_Missense_Mutation_p.D102G|GRAMD1A_uc002nxl.2_5'UTR|GRAMD1A_uc010xsf.1_Missense_Mutation_p.D114G	NM_020895	NP_065946	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A isoform 1	109	GRAM.					integral to membrane					0	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CCCCTCTCAGATTACTCCTGC	0.647													12	172	---	---	---	---	PASS
FBXO17	115290	broad.mit.edu	37	19	39433181	39433181	+	3'UTR	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39433181G>A	uc002okg.1	-	6					SARS2_uc010xuq.1_Intron|FBXO17_uc002okf.1_3'UTR	NM_024907	NP_079183	Q96EF6	FBX17_HUMAN	F-box protein FBG4 isoform 2						protein catabolic process	SCF ubiquitin ligase complex	glycoprotein binding				0	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			ggattccacaggtgtgagcca	0.224													7	43	---	---	---	---	PASS
CYP2A7	1549	broad.mit.edu	37	19	41533038	41533038	+	Intron	SNP	C	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41533038C>T	uc002opo.2	-						uc002ops.1_RNA	NM_000764	NP_000755	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CGAAGGTGGCCTGCTCGCCTC	0.667													5	41	---	---	---	---	PASS
GEMIN7	79760	broad.mit.edu	37	19	45593483	45593483	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45593483G>T	uc002pap.1	+	3	262	c.111G>T	c.(109-111)GAG>GAT	p.E37D	uc002pas.2_5'Flank|GEMIN7_uc002paq.1_Missense_Mutation_p.E37D|GEMIN7_uc002par.1_Missense_Mutation_p.E37D	NM_001007270	NP_001007271	Q9H840	GEMI7_HUMAN	gemin 7	37					ncRNA metabolic process|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding			ovary(1)	1		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0131)		TGAGGCCAGAGGTTCCTGAAA	0.647													15	95	---	---	---	---	PASS
DGCR6L	85359	broad.mit.edu	37	22	20307319	20307319	+	Silent	SNP	A	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20307319A>G	uc002zrx.2	-	2	211	c.114T>C	c.(112-114)TCT>TCC	p.S38S	DGCR6L_uc010gsb.2_RNA|DGCR6L_uc010gsc.2_Silent_p.S38S	NM_033257	NP_150282	Q9BY27	DGC6L_HUMAN	DiGeorge syndrome critical region gene 6 like	38						nucleus					0	Colorectal(54;0.0993)					GCTGCTGGAAAGAGCTGCGGG	0.697													3	21	---	---	---	---	PASS
HPS4	89781	broad.mit.edu	37	22	26860453	26860453	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26860453T>G	uc003acl.2	-	11	1802	c.1143A>C	c.(1141-1143)GAA>GAC	p.E381D	HPS4_uc003aci.2_Missense_Mutation_p.E376D|HPS4_uc003acj.2_Missense_Mutation_p.E245D|HPS4_uc003ack.2_Missense_Mutation_p.E172D|HPS4_uc003acn.2_Missense_Mutation_p.E227D|HPS4_uc010gvd.1_Missense_Mutation_p.E399D|HPS4_uc003ach.2_Missense_Mutation_p.E116D	NM_022081	NP_071364	Q9NQG7	HPS4_HUMAN	light ear protein isoform a	381					lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0						CTGAGGCCATTTCCACTTCCT	0.537									Hermansky-Pudlak_syndrome				9	75	---	---	---	---	PASS
RFPL3	10738	broad.mit.edu	37	22	32756660	32756660	+	Silent	SNP	C	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32756660C>A	uc003amj.2	+	2	1000	c.795C>A	c.(793-795)TCC>TCA	p.S265S	RFPL3_uc010gwn.2_Silent_p.S236S|RFPL3S_uc003amk.2_RNA|RFPL3S_uc003aml.2_RNA	NM_001098535	NP_001092005	O75679	RFPL3_HUMAN	ret finger protein-like 3 isoform 1	265	B30.2/SPRY.						zinc ion binding			ovary(1)	1						AAAGTGGTTCCCATGTCTATA	0.478													9	114	---	---	---	---	PASS
APOL2	23780	broad.mit.edu	37	22	36634598	36634598	+	Intron	SNP	T	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36634598T>A	uc003aoz.2	-						APOL2_uc011amm.1_Intron|APOL2_uc003apa.2_Intron|uc003apb.1_RNA	NM_030882	NP_112092	Q9BQE5	APOL2_HUMAN	apolipoprotein L2						acute-phase response|cholesterol metabolic process|lipid transport|lipoprotein metabolic process|maternal process involved in female pregnancy|multicellular organismal development	endoplasmic reticulum membrane|extracellular region	high-density lipoprotein particle binding|lipid binding|receptor binding				0						AATGGGTGATTTTAATAATCC	0.239													11	43	---	---	---	---	PASS
SUN2	25777	broad.mit.edu	37	22	39146323	39146323	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39146323A>G	uc003awh.1	-	6	711	c.427T>C	c.(427-429)TAC>CAC	p.Y143H	SUN2_uc011anz.1_Missense_Mutation_p.Y178H|SUN2_uc011aoa.1_Missense_Mutation_p.Y132H|SUN2_uc003awi.1_Missense_Mutation_p.Y143H|SUN2_uc010gxq.1_Missense_Mutation_p.Y164H|SUN2_uc010gxr.1_Missense_Mutation_p.Y143H|SUN2_uc010gxs.1_Missense_Mutation_p.Y143H	NM_015374	NP_056189	Q9UH99	SUN2_HUMAN	unc-84 homolog B	143	Nuclear.|Ser-rich.				centrosome localization|cytoskeletal anchoring at nuclear membrane|mitotic spindle organization|nuclear envelope organization|nuclear matrix anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	endosome membrane|integral to membrane|nuclear inner membrane|SUN-KASH complex	lamin binding|microtubule binding			large_intestine(1)|skin(1)	2						ACATCCGAGTAGCCTGCGGGG	0.612													4	31	---	---	---	---	PASS
PAGE5	90737	broad.mit.edu	37	X	55247032	55247032	+	5'UTR	SNP	G	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55247032G>C	uc004duj.2	+	1					PAGE5_uc004duk.2_Intron	NM_130467	NP_569734	Q96GU1	GGEE1_HUMAN	P antigen family, member 5 isoform 1												0						CCCAGGTCCTGATGCAGGCGC	0.662													4	9	---	---	---	---	PASS
RAB9B	51209	broad.mit.edu	37	X	103080261	103080261	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103080261C>T	uc004ell.1	-	3	739	c.454G>A	c.(454-456)GAA>AAA	p.E152K	RAB9B_uc004eli.1_Intron	NM_016370	NP_057454	Q9NP90	RAB9B_HUMAN	RAB9B, member RAS oncogene family	152					Golgi to endosome transport|protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|protein binding			lung(3)	3						GCACTAGTTTCTAAATAAGGG	0.473													12	221	---	---	---	---	PASS
LHFPL1	340596	broad.mit.edu	37	X	111914248	111914248	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111914248T>A	uc004epq.2	-	2	704	c.371A>T	c.(370-372)CAG>CTG	p.Q124L	LHFPL1_uc004epp.2_Missense_Mutation_p.Q147L|LHFPL1_uc010nqa.2_Intron|LHFPL1_uc010nqb.2_Missense_Mutation_p.Q124L	NM_178175	NP_835469	Q86WI0	LHPL1_HUMAN	lipoma HMGIC fusion partner-like 1 precursor	124	Helical; (Potential).					integral to membrane					0						TCCAACAAACTGCGCTGCTCC	0.572													21	40	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	7858	7858	+	RNA	SNP	C	T	T			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:7858C>T	uc004cou.3	+	1		c.273C>T			uc011mfi.1_5'Flank|uc004cov.3_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP42.																		GACGAGGTCAACGATCCCTCC	0.502													5	21	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	11196	11196	+	RNA	SNP	G	A	A			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:11196G>A	uc004cov.3	+	1		c.619G>A			uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		CCTGAACGCAGGCACATACTT	0.458													16	16	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14094	14094	+	RNA	SNP	T	C	C			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14094T>C	uc004cox.3	+	1		c.1758T>C			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		ATAATTAAACTTTACTTCCTC	0.388													8	27	---	---	---	---	PASS
CD84	8832	broad.mit.edu	37	1	160534995	160534995	+	Intron	DEL	A	-	-	rs74589384		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160534995delA	uc001fwh.3	-						CD84_uc001fwf.3_Intron|CD84_uc001fwg.3_Intron|CD84_uc009wtn.2_Intron|CD84_uc001fwi.3_Intron|CD84_uc001fwj.2_Intron|CD84_uc001fwk.2_Intron	NM_003874	NP_003865	Q9UIB8	SLAF5_HUMAN	CD84 molecule						blood coagulation|defense response|homophilic cell adhesion|leukocyte migration	integral to plasma membrane	receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			ctgatggaagaattacatagc	0.070													0	6	---	---	---	---	
CENPL	91687	broad.mit.edu	37	1	173772816	173772816	+	Intron	DEL	T	-	-	rs141936109		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173772816delT	uc001gje.3	-						CENPL_uc009wwg.2_Intron|CENPL_uc001gjg.3_Intron|CENPL_uc001gjf.3_Intron	NM_033319	NP_201576	Q8N0S6	CENPL_HUMAN	centromere protein L isoform 2						mitotic prometaphase	chromosome, centromeric region|cytosol|nucleus					0						ATAATTGGCCttttttttttt	0.164													6	4	---	---	---	---	
TMEM63A	9725	broad.mit.edu	37	1	226061869	226061870	+	Intron	DEL	AC	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226061869_226061870delAC	uc001hpm.1	-						TMEM63A_uc010pvi.1_Intron	NM_014698	NP_055513	O94886	TM63A_HUMAN	transmembrane protein 63A							integral to membrane|lysosomal membrane	nucleotide binding			ovary(1)|breast(1)	2	Breast(184;0.197)					CATTCCAGGGacacacacacac	0.292													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	113103992	113103992	+	IGR	DEL	C	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113103992delC								ZC3H6 (6352 upstream) : RGPD8 (21974 downstream)																							tcaccaccatcaccactgcca	0.000													5	3	---	---	---	---	
SPOPL	339745	broad.mit.edu	37	2	139287069	139287070	+	Intron	DEL	TG	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139287069_139287070delTG	uc002tvh.2	+							NM_001001664	NP_001001664	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like							nucleus				skin(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0296)		tgcatgtgcctgtgtgtgtgtg	0.144													4	3	---	---	---	---	
PKP4	8502	broad.mit.edu	37	2	159488063	159488063	+	Intron	DEL	T	-	-	rs75092706		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159488063delT	uc002tzv.2	+						PKP4_uc002tzt.1_Intron|PKP4_uc002tzu.2_Intron|PKP4_uc002tzw.2_Intron|PKP4_uc002tzx.2_Intron|PKP4_uc002tzy.1_Intron|PKP4_uc002tzz.1_Intron|PKP4_uc002uaa.2_Intron	NM_003628	NP_003619	Q99569	PKP4_HUMAN	plakophilin 4 isoform a						cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7						acccaactaattttttttttt	0.000										HNSCC(62;0.18)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	206708888	206708895	+	IGR	DEL	AAGGAAGG	-	-	rs71882224		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206708888_206708895delAAGGAAGG								NRP2 (46032 upstream) : INO80D (149551 downstream)																							aagaaagagaaaggaaggaaggaaggaa	0.000													5	3	---	---	---	---	
AGAP1	116987	broad.mit.edu	37	2	236908245	236908247	+	Intron	DEL	GGT	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236908245_236908247delGGT	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3						gatggtgagaggtggtggtggtg	0.000													4	2	---	---	---	---	
OTOS	150677	broad.mit.edu	37	2	241078958	241078960	+	Intron	DEL	GAA	-	-	rs10526200		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241078958_241078960delGAA	uc002vyv.2	-							NM_148961	NP_683764	Q8NHW6	OTOSP_HUMAN	otospiralin precursor							extracellular region					0		all_epithelial(40;2.79e-15)|Breast(86;3.04e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|Hepatocellular(293;0.148)|all_hematologic(139;0.158)|Melanoma(123;0.16)		Epithelial(32;2.56e-30)|all cancers(36;7.18e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.37e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.07e-06)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)|Colorectal(34;0.019)|COAD - Colon adenocarcinoma(134;0.141)		GGAGACAGAGGAAGAAGAAGAAG	0.581													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	27997118	27997121	+	IGR	DEL	CCTT	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27997118_27997121delCCTT								EOMES (232912 upstream) : CMC1 (286003 downstream)																							ccttcctttcccttccttccttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	34320606	34320607	+	IGR	INS	-	TTCC	TTCC	rs145566763	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34320606_34320607insTTCC								PDCD6IP (409412 upstream) : None (None downstream)																							tccttccttctttccttccttc	0.134													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	115529092	115529093	+	IGR	INS	-	TCTC	TCTC	rs56145932		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115529092_115529093insTCTC								LSAMP (5074 upstream) : LOC285194 (899542 downstream)																							ctctctctctgtctctctctct	0.262													6	3	---	---	---	---	
TOPBP1	11073	broad.mit.edu	37	3	133361872	133361872	+	Intron	DEL	T	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133361872delT	uc003eps.2	-							NM_007027	NP_008958	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1						DNA repair|response to ionizing radiation	microtubule organizing center|PML body|spindle pole	DNA binding|protein C-terminus binding			ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1)	7						ACAGAGGCACTTTTTTTTTTT	0.100								Other_conserved_DNA_damage_response_genes					4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	153606753	153606754	+	IGR	INS	-	GTGT	GTGT	rs35813625		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153606753_153606754insGTGT								C3orf79 (386270 upstream) : SGEF (232395 downstream)																							AATTTTGCTCCgtgtgtgtgtg	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	189218951	189218955	+	IGR	DEL	CTTCA	-	-	rs56309775		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189218951_189218955delCTTCA								TPRG1 (177681 upstream) : TP63 (130261 downstream)																							tccttccttccttcacttccttcac	0.020													4	2	---	---	---	---	
GRK4	2868	broad.mit.edu	37	4	3038811	3038812	+	Intron	DEL	TG	-	-	rs34216391		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3038811_3038812delTG	uc003ggn.1	+						GRK4_uc003ggo.1_Intron|GRK4_uc003ggp.1_Intron|GRK4_uc003ggq.1_Intron	NM_182982	NP_892027	P32298	GRK4_HUMAN	G protein-coupled receptor kinase 4 isoform							cell cortex	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		tgtgtgtgtatgtgtgtgtgtg	0.371													4	2	---	---	---	---	
SLIT2	9353	broad.mit.edu	37	4	20308668	20308671	+	Intron	DEL	CCTT	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20308668_20308671delCCTT	uc003gpr.1	+						SLIT2_uc003gps.1_Intron	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11						tttttacctaccttccttccttcc	0.039													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	24697433	24697434	+	IGR	INS	-	TTCC	TTCC	rs142180318	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24697433_24697434insTTCC								DHX15 (111249 upstream) : SOD3 (99651 downstream)																							tccttccttctttccttccttc	0.168													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	110475293	110475294	+	IGR	INS	-	CTTCAGGAAG	CTTCAGGAAG	rs148787567	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110475293_110475294insCTTCAGGAAG								SEC24B (13679 upstream) : CCDC109B (6061 downstream)																							GTCTCCTTGCTCAGGCAGAAAA	0.460													2	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	111323462	111323462	+	IGR	DEL	T	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111323462delT								ELOVL6 (203642 upstream) : ENPEP (73767 downstream)																							ttcccttcccttcccttccct	0.055													6	3	---	---	---	---	
ANK2	287	broad.mit.edu	37	4	114257629	114257630	+	Intron	INS	-	A	A	rs139683953	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114257629_114257630insA	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc011cgb.1_Intron	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1						axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ATTTGTAAGATAAAAAATACTT	0.257													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	117536739	117536742	+	IGR	DEL	GGAA	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117536739_117536742delGGAA								MIR1973 (315815 upstream) : TRAM1L1 (467974 downstream)																							aaggaaggagggaaggaaggaagg	0.000													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	188980242	188980243	+	IGR	INS	-	TTCC	TTCC	rs147035050	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188980242_188980243insTTCC								ZFP42 (54043 upstream) : TRIML2 (32184 downstream)																							tcctttcttttttccttccttc	0.035													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	7939973	7939974	+	IGR	DEL	TA	-	-	rs62358782		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7939973_7939974delTA								MTRR (38740 upstream) : None (None downstream)																							AGGAGTGTTTTATATATATATA	0.312													4	3	---	---	---	---	
RNASEN	29102	broad.mit.edu	37	5	31405874	31405874	+	Intron	DEL	C	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31405874delC	uc003jhg.2	-						RNASEN_uc003jhh.2_Intron	NM_013235	NP_037367	Q9NRR4	RNC_HUMAN	ribonuclease III, nuclear isoform 1						gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0						TTTCAAGAttctttttttttt	0.303													4	3	---	---	---	---	
NPR3	4883	broad.mit.edu	37	5	32786466	32786466	+	3'UTR	DEL	T	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32786466delT	uc003jhv.2	+	8					NPR3_uc011cnz.1_3'UTR|NPR3_uc003jhu.2_3'UTR|C5orf23_uc003jhw.1_5'Flank	NM_000908	NP_000899	P17342	ANPRC_HUMAN	natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)	AGCCCCCCACTTTTTTTTTTT	0.408													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	90475747	90475747	+	IGR	DEL	A	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90475747delA								GPR98 (15715 upstream) : ARRDC3 (188794 downstream)																							ggaaggaaggaaggaaggaag	0.030													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	138926406	138926406	+	IGR	DEL	C	-	-	rs142505515	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138926406delC								TMEM173 (64114 upstream) : UBE2D2 (14345 downstream)																							tttctttcttccttccttcct	0.000													8	5	---	---	---	---	
DSP	1832	broad.mit.edu	37	6	7565382	7565382	+	Intron	DEL	A	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7565382delA	uc003mxp.1	+						DSP_uc003mxq.1_Intron	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I						cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		agtccgtctcaaaaaaaaaaa	0.189													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	16066833	16066844	+	IGR	DEL	ACACACACACAT	-	-	rs72359178		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16066833_16066844delACACACACACAT								DTNBP1 (403562 upstream) : MYLIP (62473 downstream)																							acacacacacacacacacacatacacacacaA	0.156													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	82972688	82972688	+	IGR	DEL	A	-	-	rs147865560		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82972688delA								IBTK (15240 upstream) : TPBG (100235 downstream)																							gactctgtcgaaaaaaaaaaa	0.000													4	3	---	---	---	---	
NKAIN2	154215	broad.mit.edu	37	6	124676217	124676217	+	Intron	DEL	A	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124676217delA	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		ctttgtcattaaaaaaaaaaa	0.124													3	3	---	---	---	---	
AIG1	51390	broad.mit.edu	37	6	143648833	143648834	+	Intron	INS	-	A	A	rs143844999		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143648833_143648834insA	uc003qjh.2	+						AIG1_uc003qjf.2_Intron|AIG1_uc003qji.2_Intron	NM_016108	NP_057192	Q9NVV5	AIG1_HUMAN	androgen-induced 1							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(155;2.34e-05)|GBM - Glioblastoma multiforme(68;0.0246)		TATAAAATTGTAAAAAAAAAAA	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	53882486	53882487	+	IGR	INS	-	AGGT	AGGT	rs146360144	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53882486_53882487insAGGT								POM121L12 (777869 upstream) : HPVC1 (386430 downstream)																							ggaaggaaggaaggagggaagg	0.153													5	3	---	---	---	---	
STAG3L2	442582	broad.mit.edu	37	7	74300804	74300804	+	Intron	DEL	A	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74300804delA	uc003ubj.3	-						STAG3L2_uc011kfj.1_Intron	NM_001025202	NP_001020373	P0CL84	ST3L2_HUMAN	STAG3-like							nucleus	binding				0						CTTCATACTTAAAAAAAAAAA	0.458													5	4	---	---	---	---	
DPY19L2P2	349152	broad.mit.edu	37	7	102815705	102815705	+	3'UTR	DEL	G	-	-	rs7796853		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102815705delG	uc003vbh.3	-	21					DPY19L2P2_uc003vbg.3_RNA|DPY19L2P2_uc010lit.2_RNA	NR_003561				RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0						ATCAAGttttgtttttttttt	0.199													4	2	---	---	---	---	
WNT2	7472	broad.mit.edu	37	7	116932347	116932348	+	Intron	INS	-	CA	CA	rs148453352	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116932347_116932348insCA	uc003viz.2	-						WNT2_uc003vja.2_Intron	NM_003391	NP_003382	P09544	WNT2_HUMAN	wingless-type MMTV integration site family						atrial cardiac muscle tissue morphogenesis|canonical Wnt receptor signaling pathway|cardiac epithelial to mesenchymal transition|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|dorsal/ventral axis specification|iris morphogenesis|labyrinthine layer blood vessel development|lens development in camera-type eye|lung induction|mammary gland epithelium development|neuron differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of fibroblast proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, calcium modulating pathway	cytoplasm|extracellular space|proteinaceous extracellular matrix	cytokine activity|frizzled binding|frizzled-2 binding|signal transducer activity			breast(2)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	7	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		CCAACcacactcacacacacac	0.292													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	119121961	119121962	+	IGR	DEL	AT	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119121961_119121962delAT								None (None upstream) : KCND2 (791760 downstream)																							gcctgtacccataaaaccccag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	128162823	128162824	+	IGR	DEL	GT	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128162823_128162824delGT								METTL2B (19846 upstream) : FLJ45340 (118471 downstream)																							CTGTTTTTTGgtgtgtgtgtgt	0.069													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	49297743	49297743	+	IGR	DEL	A	-	-	rs140564135		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49297743delA								UBE2V2 (323291 upstream) : EFCAB1 (325608 downstream)																							CGGAGGCAGGAAAAAAAAAAG	0.428													6	3	---	---	---	---	
C8orf84	157869	broad.mit.edu	37	8	73982364	73982365	+	Intron	INS	-	T	T	rs138332692	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73982364_73982365insT	uc003xzf.2	-							NM_153225	NP_694957	Q8IVN8	RPESP_HUMAN	RPE-spondin precursor						immune response	extracellular region	polysaccharide binding|scavenger receptor activity				0						TGTCAATCACCTTTAAGGTTTC	0.431													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	96977957	96977964	+	IGR	DEL	AGGGAAGG	-	-	rs67336860		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96977957_96977964delAGGGAAGG								C8orf37 (696520 upstream) : GDF6 (176596 downstream)																							gaaggaaggaagggaaggaaggaaggaa	0.125													3	3	---	---	---	---	
TOP1MT	116447	broad.mit.edu	37	8	144405960	144405962	+	Intron	DEL	GCA	-	-	rs62524733	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144405960_144405962delGCA	uc003yxz.2	-						TOP1MT_uc011lkd.1_Intron|TOP1MT_uc011lke.1_Intron|TOP1MT_uc010mfb.2_Intron|TOP1MT_uc011lkf.1_Intron|TOP1MT_uc010mfd.1_Intron	NM_052963	NP_443195	Q969P6	TOP1M_HUMAN	mitochondrial topoisomerase I precursor						DNA topological change	chromosome|mitochondrial nucleoid	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	cacaccacacgcacaagtgcaca	0.059													3	3	---	---	---	---	
DOCK8	81704	broad.mit.edu	37	9	400063	400064	+	Intron	INS	-	CCA	CCA	rs56372695		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:400063_400064insCCA	uc003zgf.2	+						DOCK8_uc010mgu.2_Intron|DOCK8_uc010mgv.2_Intron|DOCK8_uc010mgw.1_Intron|DOCK8_uc003zgk.2_Intron	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8						blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		caccacctccttcaccatcacc	0.000													4	2	---	---	---	---	
CD274	29126	broad.mit.edu	37	9	5455895	5455896	+	Intron	INS	-	T	T	rs139454534	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5455895_5455896insT	uc003zje.2	+						C9orf46_uc003zjd.2_Intron|CD274_uc011lmb.1_Intron|CD274_uc010mhn.2_5'Flank|CD274_uc003zjf.2_5'Flank	NM_014143	NP_054862	Q9NZQ7	PD1L1_HUMAN	CD274 molecule precursor						cell proliferation|cell surface receptor linked signaling pathway|immune response|T cell costimulation	endomembrane system|integral to membrane	receptor activity			lung(1)|central_nervous_system(1)	2	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000742)|Lung(218;0.111)		CTTTTAGTAACTTTTTTCACTT	0.351			T	CIITA	PMBL|Hodgkin Lymphona|								3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	17554183	17554184	+	IGR	INS	-	TTCC	TTCC	rs71331495		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17554183_17554184insTTCC								CNTLN (50268 upstream) : SH3GL2 (24769 downstream)																							tctctctctctttccttccttc	0.000													3	3	---	---	---	---	
DAB2IP	153090	broad.mit.edu	37	9	124406453	124406455	+	Intron	DEL	AAG	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124406453_124406455delAAG	uc004bln.2	+							NM_032552	NP_115941	Q5VWQ8	DAB2P_HUMAN	disabled homolog 2 interacting protein isoform						activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2						ttgtctaaaaaagaagaagaaga	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	63557400	63557401	+	IGR	INS	-	GC	GC			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63557400_63557401insGC								C10orf107 (31311 upstream) : ARID5B (104042 downstream)																							TGCACTTGCGTGcacacacaca	0.455													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	63557424	63557425	+	IGR	DEL	CC	-	-	rs28645298	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63557424_63557425delCC								C10orf107 (31335 upstream) : ARID5B (104018 downstream)																							cacacacacacCCCATGTCAGG	0.446													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	67367656	67367657	+	IGR	DEL	TC	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67367656_67367657delTC								ANXA2P3 (781022 upstream) : CTNNA3 (312068 downstream)																							cttccttctttctctatatctc	0.000													4	4	---	---	---	---	
C10orf76	79591	broad.mit.edu	37	10	103609835	103609836	+	Intron	INS	-	TC	TC	rs148630843	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103609835_103609836insTC	uc009xwy.1	-						C10orf76_uc009xwx.1_Intron	NM_024541	NP_078817	Q5T2E6	CJ076_HUMAN	hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		TGGGACCACTTTCTCTCTCTCT	0.272													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	59066259	59066262	+	IGR	DEL	GAAA	-	-	rs55644813		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59066259_59066262delGAAA								MPEG1 (85765 upstream) : OR5AN1 (65670 downstream)																							ggaaagaaaggaaagaaagagaga	0.000													5	4	---	---	---	---	
ADRBK1	156	broad.mit.edu	37	11	67034245	67034246	+	Frame_Shift_Del	DEL	CG	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67034245_67034246delCG	uc009yrn.1	+	1	341_342	c.75_76delCG	c.(73-78)GCCGCGfs	p.A25fs	ADRBK1_uc009yrm.1_Frame_Shift_Del_p.A25fs	NM_001619	NP_001610	P25098	ARBK1_HUMAN	beta-adrenergic receptor kinase 1	25_26	N-terminal.				activation of phospholipase C activity|cardiac muscle contraction|desensitization of G-protein coupled receptor protein signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of striated muscle contraction|negative regulation of the force of heart contraction by chemical signal|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of catecholamine secretion|tachykinin receptor signaling pathway	cytosol|soluble fraction	alpha-2A adrenergic receptor binding|ATP binding|beta-adrenergic receptor kinase activity|Edg-2 lysophosphatidic acid receptor binding|G-protein coupled receptor kinase activity|signal transducer activity			large_intestine(1)	1			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	CCACGCCGGCCGCGCGCGCCAG	0.515													4	2	---	---	---	---	
INTS4	92105	broad.mit.edu	37	11	77692786	77692789	+	Intron	DEL	TTTA	-	-	rs71930315		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77692786_77692789delTTTA	uc001oys.2	-						INTS4_uc001oyt.2_Intron|INTS4_uc001oyu.1_Intron|INTS4_uc001oyv.1_Intron	NM_033547	NP_291025	Q96HW7	INT4_HUMAN	integrator complex subunit 4						snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			ACAGCTTTCTtttatttatttatt	0.152													4	2	---	---	---	---	
CACNA1C	775	broad.mit.edu	37	12	2547459	2547460	+	Intron	INS	-	TGA	TGA			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2547459_2547460insTGA	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	ggtaatgatggtggtggtggtg	0.000													1	5	---	---	---	---	
VDR	7421	broad.mit.edu	37	12	48253630	48253649	+	Intron	DEL	TTCCTTCCTTCCTTCCTTCT	-	-	rs60761635		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48253630_48253649delTTCCTTCCTTCCTTCCTTCT	uc001rqm.2	-						VDR_uc001rql.2_Intron|VDR_uc001rqn.2_Intron|VDR_uc010slq.1_Intron	NM_001017535	NP_001017535	P11473	VDR_HUMAN	vitamin D (1,25-dihydroxyvitamin D3) receptor						decidualization|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	tttcccttccttccttccttccttccttctttccttcctt	0.036													4	2	---	---	---	---	
RASSF9	9182	broad.mit.edu	37	12	86199850	86199851	+	Intron	INS	-	T	T	rs149030946	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86199850_86199851insT	uc001taf.1	-							NM_005447	NP_005438	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family						endosome transport|protein targeting|signal transduction	cytosol|endosome|trans-Golgi network transport vesicle membrane	protein binding|transporter activity			ovary(1)	1						TGAGAGAGGCATTTTTTTtctg	0.163													5	3	---	---	---	---	
HNF1A	6927	broad.mit.edu	37	12	121428470	121428483	+	Intron	DEL	AAGGTAGGAAAGGG	-	-	rs56368260	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121428470_121428483delAAGGTAGGAAAGGG	uc001tzg.2	+						HNF1A_uc001tze.1_Intron|HNF1A_uc001tzf.2_Intron|HNF1A_uc010szn.1_Intron	NM_000545	NP_000536	P20823	HNF1A_HUMAN	hepatic nuclear factor-1-alpha						glucose homeostasis|glucose import|insulin secretion|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|renal glucose absorption	cytoplasm|nucleus|protein complex	DNA binding|protein dimerization activity|protein heterodimerization activity|protein homodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			liver(92)|large_intestine(15)|endometrium(6)|breast(2)|lung(1)	116	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					aaagggaggaaaggtaggaaagggaggaaggaag	0.033									Hepatic_Adenoma_Familial_Clustering_of				5	3	---	---	---	---	
NCOR2	9612	broad.mit.edu	37	12	124818537	124818538	+	Intron	DEL	TG	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124818537_124818538delTG	uc010tay.1	-						NCOR2_uc010taz.1_Intron|NCOR2_uc010tax.1_Intron	NM_006312	NP_006303	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 1						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		cgggtgtgcatgtgtgtgtgtg	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	131962167	131962168	+	IGR	INS	-	ATA	ATA	rs148457819	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131962167_131962168insATA								LOC116437 (264692 upstream) : SFRS8 (233467 downstream)																							tggtaatggtggtgatgatggt	0.000													4	2	---	---	---	---	
EPSTI1	94240	broad.mit.edu	37	13	43543057	43543057	+	Intron	DEL	T	-	-	rs66750351		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43543057delT	uc001uyw.1	-						EPSTI1_uc001uyx.1_Intron	NM_001002264	NP_001002264	Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 isoform 1											ovary(1)	1		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		AAAAAAAAAATacacacacac	0.308													5	3	---	---	---	---	
SEC14L5	9717	broad.mit.edu	37	16	5055864	5055865	+	Intron	INS	-	AA	AA			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5055864_5055865insAA	uc002cye.2	+							NM_014692	NP_055507	O43304	S14L5_HUMAN	SEC14-like 5							integral to membrane|intracellular	transporter activity				0						gactccgtctcaaaaaaaaaaa	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	54535782	54535785	+	IGR	DEL	GAAA	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54535782_54535785delGAAA								IRX3 (215404 upstream) : IRX5 (429326 downstream)																							agaaaggaaggaaagaaggaagga	0.039													6	3	---	---	---	---	
DNAH9	1770	broad.mit.edu	37	17	11597927	11597930	+	Intron	DEL	CTTT	-	-	rs12946303		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11597927_11597930delCTTT	uc002gne.2	+						DNAH9_uc010coo.2_Intron	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		AGctttcttgctttcttgctttct	0.245													4	3	---	---	---	---	
ELAC2	60528	broad.mit.edu	37	17	12901544	12901545	+	Intron	INS	-	A	A	rs140011002	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12901544_12901545insA	uc002gnz.3	-						ELAC2_uc002gnu.3_Intron|ELAC2_uc002gnv.3_Intron|ELAC2_uc002gnw.3_Intron|ELAC2_uc002gnx.3_Intron|ELAC2_uc010vvo.1_Intron|ELAC2_uc010vvp.1_Intron|ELAC2_uc010vvq.1_Intron|ELAC2_uc010vvr.1_Intron	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2 isoform 1						tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0						ATTCCCAGGGTAAAGTTTGCTA	0.337									Hereditary_Prostate_Cancer				4	2	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21205359	21205364	+	Intron	DEL	GGGGCT	-	-	rs74998514		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21205359_21205364delGGGGCT	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CGTCGGAGAGggggctggggctgggg	0.583													10	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	28894612	28894612	+	IGR	DEL	T	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28894612delT								TBC1D29 (4105 upstream) : LRRC37B2 (8871 downstream)																							TCATTTGATCTTTTCCTGAGT	0.567													4	2	---	---	---	---	
CCDC46	201134	broad.mit.edu	37	17	63747018	63747018	+	Intron	DEL	A	-	-	rs75469128		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63747018delA	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron|CCDC46_uc002jfk.2_Intron	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)			CTTAAAAAGCAAAAAAAAAAA	0.343													6	4	---	---	---	---	
NAPG	8774	broad.mit.edu	37	18	10548536	10548537	+	Intron	INS	-	T	T	rs1662154		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10548536_10548537insT	uc002kon.2	+						NAPG_uc010wzr.1_Intron|NAPG_uc002koo.2_Intron|NAPG_uc002kop.2_Intron	NM_003826	NP_003817	Q99747	SNAG_HUMAN	N-ethylmaleimide-sensitive factor attachment						cellular membrane fusion|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein complex assembly|protein stabilization	membrane|membrane fraction|mitochondrion	protein binding				0						TGTTTTACACCTTTTTTTTTTT	0.361													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	60753943	60753946	+	IGR	DEL	TTCC	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60753943_60753946delTTCC								PHLPP1 (106278 upstream) : BCL2 (36633 downstream)																							cttcctttctttccttccttcctt	0.147													4	3	---	---	---	---	
TMPRSS9	360200	broad.mit.edu	37	19	2405705	2405705	+	Intron	DEL	T	-	-	rs113589749		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2405705delT	uc010xgx.1	+						TMPRSS9_uc002lvv.1_Intron	NM_182973	NP_892018	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9						proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2				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)		GAGGGCAttcttttttttttt	0.214													4	3	---	---	---	---	
PIP5K1C	23396	broad.mit.edu	37	19	3642656	3642657	+	Intron	INS	-	A	A	rs139835481	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3642656_3642657insA	uc002lyj.1	-						PIP5K1C_uc010xhq.1_Intron|PIP5K1C_uc010xhr.1_Intron	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type						axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		TGTTTTAAGTTAAAAAAAAAAC	0.475													4	2	---	---	---	---	
RFX2	5990	broad.mit.edu	37	19	6013624	6013624	+	Intron	DEL	G	-	-			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6013624delG	uc002meb.2	-						RFX2_uc002mec.2_Intron	NM_000635	NP_000626	P48378	RFX2_HUMAN	regulatory factor X2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			breast(4)|ovary(1)|skin(1)	6						ttgacctcctgggatcaagtg	0.015													4	2	---	---	---	---	
LPHN1	22859	broad.mit.edu	37	19	14274277	14274278	+	Intron	INS	-	GA	GA			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14274277_14274278insGA	uc010xnn.1	-						LPHN1_uc010xno.1_Intron|uc002myf.2_Intron	NM_001008701	NP_001008701	O94910	LPHN1_HUMAN	latrophilin 1 isoform 1 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(2)|lung(2)|central_nervous_system(1)	5						gcgagagggaggagagagagag	0.465													3	3	---	---	---	---	
ZNF492	57615	broad.mit.edu	37	19	22838450	22838453	+	Intron	DEL	TTAT	-	-	rs35989436		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22838450_22838453delTTAT	uc002nqw.3	+							NM_020855	NP_065906	Q9P255	ZN492_HUMAN	zinc finger protein 492						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				aactttttacttatttgtcttcaa	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	53833023	53833024	+	IGR	INS	-	T	T	rs112929393		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53833023_53833024insT								BIRC8 (38148 upstream) : ZNF845 (3978 downstream)																							TCAGAAAAttcttttttttttt	0.203													9	5	---	---	---	---	
PTK6	5753	broad.mit.edu	37	20	62164170	62164170	+	Intron	DEL	C	-	-	rs142590975		TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62164170delC	uc002yfg.2	-						PTK6_uc011aay.1_Intron|PTK6_uc011aaz.1_5'UTR	NM_005975	NP_005966	Q13882	PTK6_HUMAN	PTK6 protein tyrosine kinase 6							cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			stomach(1)|kidney(1)	2	all_cancers(38;2.51e-11)		Epithelial(9;1.5e-08)|all cancers(9;8.67e-08)|BRCA - Breast invasive adenocarcinoma(10;6.43e-06)			AGACCTCCTGCCCCCGACAGG	0.706													3	4	---	---	---	---	
GGT5	2687	broad.mit.edu	37	22	24640263	24640264	+	Intron	INS	-	CA	CA	rs146390000	by1000genomes	TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24640263_24640264insCA	uc002zzo.3	-						GGT5_uc002zzp.3_Intron|GGT5_uc002zzr.3_Intron|GGT5_uc002zzq.3_Intron|GGT5_uc011ajm.1_Intron|GGT5_uc011ajn.1_Intron	NM_004121	NP_004112	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5 isoform b						glutathione biosynthetic process|hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	integral to membrane|plasma membrane	acyltransferase activity|gamma-glutamyltransferase activity			ovary(2)|skin(1)	3						CAGTGCACGTGcacacacacac	0.322													3	3	---	---	---	---	
RFPL3	10738	broad.mit.edu	37	22	32752978	32752979	+	5'Flank	INS	-	G	G			TCGA-CJ-4882-01A-02D-1429-08	TCGA-CJ-4882-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32752978_32752979insG	uc003amj.2	+						RFPL3_uc010gwn.2_Intron	NM_001098535	NP_001092005	O75679	RFPL3_HUMAN	ret finger protein-like 3 isoform 1								zinc ion binding			ovary(1)	1						GGCTGGCCTGTGGGTGGGCGAG	0.624													8	5	---	---	---	---	
