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
PAFAH2	5051	broad.mit.edu	37	1	26310492	26310492	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26310492A>G	uc001bld.3	-	6	677	c.497T>C	c.(496-498)ATC>ACC	p.I166T	PAFAH2_uc001ble.3_Missense_Mutation_p.I166T	NM_000437	NP_000428	Q99487	PAFA2_HUMAN	platelet-activating factor acetylhydrolase 2	166					lipid catabolic process	cytoplasm	1-alkyl-2-acetylglycerophosphocholine esterase activity|phospholipid binding			ovary(2)	2		Colorectal(325;3.47e-05)|Lung NSC(340;6.23e-05)|all_lung(284;9.48e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-25)|Colorectal(126;3.57e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00717)|READ - Rectum adenocarcinoma(331;0.0649)		ACGGAAAGGGATCCATTCCTC	0.527													6	484	---	---	---	---	PASS
DOCK7	85440	broad.mit.edu	37	1	62973695	62973695	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62973695C>A	uc001daq.2	-	35	4421	c.4387G>T	c.(4387-4389)GAT>TAT	p.D1463Y	DOCK7_uc001dan.2_Missense_Mutation_p.D1324Y|DOCK7_uc001dao.2_Missense_Mutation_p.D1324Y|DOCK7_uc001dap.2_Missense_Mutation_p.D1441Y|DOCK7_uc001dam.2_Missense_Mutation_p.D643Y|DOCK7_uc010oov.1_Missense_Mutation_p.D202Y	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1472					activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2						AGGTTTCCATCAATCAGTGCT	0.294													45	121	---	---	---	---	PASS
SLC16A4	9122	broad.mit.edu	37	1	110906399	110906399	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110906399T>C	uc001dzo.1	-	9	1635	c.1453A>G	c.(1453-1455)AGT>GGT	p.S485G	SLC16A4_uc009wfs.1_Missense_Mutation_p.S437G|SLC16A4_uc001dzp.1_Missense_Mutation_p.S317G|SLC16A4_uc010ovy.1_Missense_Mutation_p.S423G|SLC16A4_uc001dzq.1_Missense_Mutation_p.S255G|SLC16A4_uc010ovz.1_Silent_p.T381T	NM_004696	NP_004687	O15374	MOT5_HUMAN	solute carrier family 16, member 4	485	Cytoplasmic (Potential).					integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity			ovary(3)	3		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	CAGGTCAGACTGTTTTTCCAT	0.378													60	140	---	---	---	---	PASS
CASQ2	845	broad.mit.edu	37	1	116243998	116243998	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116243998G>C	uc001efx.3	-	11	1328	c.1064C>G	c.(1063-1065)GCT>GGT	p.A355G	CASQ2_uc010owu.1_Missense_Mutation_p.A284G	NM_001232	NP_001223	O14958	CASQ2_HUMAN	cardiac calsequestrin 2 precursor	355					heart development|striated muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		CAGCTCCTCAGCAGTTGGAAG	0.368													30	97	---	---	---	---	PASS
NOTCH2	4853	broad.mit.edu	37	1	120462002	120462002	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120462002G>T	uc001eik.2	-	31	5970	c.5714C>A	c.(5713-5715)GCC>GAC	p.A1905D		NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	1905	Cytoplasmic (Potential).|ANK 2.				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTTGTCCTGGGCATTGGCATC	0.567			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				38	112	---	---	---	---	PASS
ADAR	103	broad.mit.edu	37	1	154574246	154574246	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154574246A>G	uc001ffh.2	-	2	1072	c.872T>C	c.(871-873)CTT>CCT	p.L291P	ADAR_uc001ffj.2_Missense_Mutation_p.L291P|ADAR_uc001ffi.2_Missense_Mutation_p.L291P|ADAR_uc001ffk.2_5'UTR|ADAR_uc001ffl.1_5'UTR	NM_001111	NP_001102	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific isoform a	291					adenosine to inosine editing|gene silencing by RNA|mRNA modification|mRNA processing|type I interferon-mediated signaling pathway	cytoplasm|nucleolus|nucleoplasm	DNA binding|double-stranded RNA adenosine deaminase activity|metal ion binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		TAAAAACTCAAGAGGATCTTC	0.468													81	172	---	---	---	---	PASS
KRTCAP2	200185	broad.mit.edu	37	1	155145437	155145437	+	Intron	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155145437A>G	uc001fho.2	-						RAG1AP1_uc010pey.1_Intron|KRTCAP2_uc001fhp.1_Intron|TRIM46_uc009wpe.1_RNA|TRIM46_uc010pez.1_5'Flank|TRIM46_uc001fhq.2_5'Flank|TRIM46_uc001fhr.2_5'Flank|TRIM46_uc001fhs.1_5'Flank|TRIM46_uc001fht.1_5'Flank|TRIM46_uc010pfa.1_5'Flank|TRIM46_uc001fhu.1_5'Flank|TRIM46_uc009wpg.1_5'Flank|TRIM46_uc009wpf.2_5'Flank|TRIM46_uc001fhv.3_5'Flank|TRIM46_uc001fhw.1_5'Flank	NM_173852	NP_776251	Q8N6L1	KTAP2_HUMAN	keratinocyte associated protein 2							integral to membrane					0	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.18e-10)|all cancers(21;8.39e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CGGGCAGATCAGCCGGTCCGG	0.692													3	7	---	---	---	---	PASS
SEMA4A	64218	broad.mit.edu	37	1	156127886	156127886	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156127886A>G	uc001fnl.2	+	4	430	c.326A>G	c.(325-327)AAA>AGA	p.K109R	SEMA4A_uc009wrq.2_Missense_Mutation_p.K109R|SEMA4A_uc001fnm.2_Missense_Mutation_p.K109R|SEMA4A_uc001fnn.2_Missense_Mutation_p.K10R|SEMA4A_uc001fno.2_Missense_Mutation_p.K109R	NM_022367	NP_071762	Q9H3S1	SEM4A_HUMAN	semaphorin B precursor	109	Sema.|Extracellular (Potential).				axon guidance	integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)					AGTGACAGAAAAAAGAGTGAA	0.517													12	43	---	---	---	---	PASS
ETV3	2117	broad.mit.edu	37	1	157105442	157105442	+	Silent	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157105442G>A	uc001fqr.2	-	3	394	c.105C>T	c.(103-105)ATC>ATT	p.I35I	ETV3_uc001fqt.2_Silent_p.I35I	NM_001145312	NP_001138784	P41162	ETV3_HUMAN	ets variant gene 3 isoform 1	35	ETS.						sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(266;0.158)	Prostate(1639;0.174)				GCCACAGCTGGATCTGCCGGG	0.522													43	113	---	---	---	---	PASS
ATP1A4	480	broad.mit.edu	37	1	160151511	160151511	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160151511A>T	uc001fve.3	+	19	3253	c.2774A>T	c.(2773-2775)CAA>CTA	p.Q925L	ATP1A4_uc001fvf.3_RNA|ATP1A4_uc001fvg.2_Missense_Mutation_p.Q428L|ATP1A4_uc001fvh.2_Missense_Mutation_p.Q61L	NM_144699	NP_653300	Q13733	AT1A4_HUMAN	Na+/K+ -ATPase alpha 4 subunit isoform 1	925	Helical; (Potential).				ATP biosynthetic process|ATP hydrolysis coupled proton transport|regulation of cellular pH|sperm motility	sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(2)|skin(2)	4	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TTCACATGCCAAACGGCCTTT	0.507													38	122	---	---	---	---	PASS
ATP1B1	481	broad.mit.edu	37	1	169096631	169096631	+	RNA	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169096631A>G	uc001gfs.1	+	4		c.673A>G			uc010plp.1_5'Flank			P05026	AT1B1_HUMAN	Synthetic construct DNA, clone: pF1KB8186, Homo sapiens ATP1B1 gene for ATPase, Na+/K+ transporting, beta 1 polypeptide, without stop codon, in Flexi system.						ATP biosynthetic process|blood coagulation|leukocyte migration	sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	all_hematologic(923;0.208)					ACCGAGTTCTAGGCTTCAAAC	0.343													3	131	---	---	---	---	PASS
FAM5B	57795	broad.mit.edu	37	1	177249817	177249817	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177249817T>C	uc001glf.2	+	8	1817	c.1505T>C	c.(1504-1506)TTT>TCT	p.F502S	FAM5B_uc001glg.2_Missense_Mutation_p.F397S	NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B	502						extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6						CTGGAAAACTTTCTTGGGCTG	0.577													32	65	---	---	---	---	PASS
C1orf14	81626	broad.mit.edu	37	1	182908433	182908433	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182908433A>C	uc001gpu.2	-	5	1239	c.954T>G	c.(952-954)ATT>ATG	p.I318M	C1orf14_uc001gpv.2_Missense_Mutation_p.I199M|C1orf14_uc010pnz.1_Missense_Mutation_p.I176M|C1orf14_uc001gpw.2_Missense_Mutation_p.I38M	NM_030933	NP_112195	Q9BZQ2	SHP1L_HUMAN	chromosome 1 open reading frame 14	390	Potential.										0				Colorectal(1306;1.64e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00267)		TCTGATACTCAATGAGCTCGA	0.378													40	111	---	---	---	---	PASS
GPATCH2	55105	broad.mit.edu	37	1	217665062	217665062	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217665062T>C	uc001hlf.1	-	8	1333	c.1237A>G	c.(1237-1239)AGA>GGA	p.R413G	GPATCH2_uc009xdq.1_RNA	NM_018040	NP_060510	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	413						intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		TTGTGTCCTCTTTCAGCTCGA	0.313													52	142	---	---	---	---	PASS
EPHX1	2052	broad.mit.edu	37	1	226027665	226027665	+	Silent	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226027665G>A	uc001hpk.2	+	6	938	c.858G>A	c.(856-858)AAG>AAA	p.K286K	EPHX1_uc001hpl.2_Silent_p.K286K	NM_001136018	NP_001129490	P07099	HYEP_HUMAN	epoxide hydrolase 1	286					aromatic compound catabolic process|response to toxin	endoplasmic reticulum membrane|integral to membrane|microsome	cis-stilbene-oxide hydrolase activity|epoxide hydrolase activity			ovary(3)|lung(1)	4	Breast(184;0.197)					ACCCCGTCAAGGAGAAGGTAT	0.567													77	155	---	---	---	---	PASS
PCNXL2	80003	broad.mit.edu	37	1	233363106	233363106	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233363106C>G	uc001hvl.2	-	10	2605	c.2370G>C	c.(2368-2370)CAG>CAC	p.Q790H	PCNXL2_uc009xfu.2_Intron|PCNXL2_uc009xfv.1_Intron|PCNXL2_uc001hvq.1_Missense_Mutation_p.Q89H	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	790						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				CTTCCAGATCCTGACTCACAT	0.338													8	106	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237586481	237586481	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237586481A>T	uc001hyl.1	+	12	1058	c.938A>T	c.(937-939)AAC>ATC	p.N313I		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	313	Cytoplasmic (By similarity).|MIR 4.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GAAGACAAAAACCTTCTACTC	0.413													12	168	---	---	---	---	PASS
AHCTF1	25909	broad.mit.edu	37	1	247061603	247061603	+	Silent	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247061603G>T	uc001ibu.1	-	11	1537	c.1530C>A	c.(1528-1530)CTC>CTA	p.L510L	AHCTF1_uc001ibv.1_Silent_p.L519L|AHCTF1_uc009xgs.1_5'UTR	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	510	Necessary for cytoplasmic localization (By similarity).				cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			TGAGTTCATTGAGTGATGGAC	0.343													49	158	---	---	---	---	PASS
EIF2AK2	5610	broad.mit.edu	37	2	37366825	37366825	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37366825T>G	uc010ynh.1	-	6	1022	c.465A>C	c.(463-465)CAA>CAC	p.Q155H	EIF2AK2_uc010fab.1_Missense_Mutation_p.Q155H|EIF2AK2_uc010yng.1_Missense_Mutation_p.Q155H|EIF2AK2_uc010fac.2_Missense_Mutation_p.Q155H|EIF2AK2_uc010fad.2_Missense_Mutation_p.Q155H	NM_002759	NP_002750	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha	155	DRBM 2.				evasion by virus of host immune response|modulation by virus of host cellular process|negative regulation of osteoblast proliferation|protein autophosphorylation|response to virus|viral infectious cycle	cytosol	ATP binding|double-stranded RNA binding|eukaryotic translation initiation factor 2alpha kinase activity|protein binding|protein phosphatase type 2A regulator activity			ovary(2)|lung(2)|pancreas(1)	5		all_hematologic(82;0.248)				TAGCGGCCAATTGTTTTGCTT	0.328													22	284	---	---	---	---	PASS
CNRIP1	25927	broad.mit.edu	37	2	68544212	68544212	+	Intron	SNP	G	C	C	rs72904278	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68544212G>C	uc002sek.3	-						CNRIP1_uc002sej.3_Intron|CNRIP1_uc002sel.3_Intron|CNRIP1_uc010fdd.1_Missense_Mutation_p.S136C	NM_015463	NP_056278	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1								protein binding			liver(1)	1						TTCTTACAGAGAGATAGTGAT	0.433													61	111	---	---	---	---	PASS
ELMOD3	84173	broad.mit.edu	37	2	85598666	85598666	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85598666G>T	uc002spf.3	+	11	1253	c.588G>T	c.(586-588)TGG>TGT	p.W196C	ELMOD3_uc010fgg.2_Intron|ELMOD3_uc002spg.3_Missense_Mutation_p.W196C|ELMOD3_uc002sph.3_Missense_Mutation_p.W196C|ELMOD3_uc010ysn.1_Missense_Mutation_p.W196C|ELMOD3_uc010yso.1_RNA|ELMOD3_uc010ysp.1_Intron	NM_001135021	NP_001128493	Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3 isoform b	196	ELMO.				phagocytosis	cytoskeleton				ovary(2)	2						GAAACCACTGGGAGGACCTGG	0.537													47	150	---	---	---	---	PASS
ARID5A	10865	broad.mit.edu	37	2	97217964	97217964	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97217964C>A	uc002swe.2	+	7	1799	c.1699C>A	c.(1699-1701)CTT>ATT	p.L567I	ARID5A_uc010yuq.1_Missense_Mutation_p.L515I|ARID5A_uc002swf.2_Missense_Mutation_p.L403I|ARID5A_uc002swg.2_Missense_Mutation_p.L515I	NM_212481	NP_997646	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A	567					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding				0						CCGCCACAGACTTTGCCCGGC	0.657													59	141	---	---	---	---	PASS
ST6GAL2	84620	broad.mit.edu	37	2	107460175	107460175	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107460175C>T	uc002tdq.2	-	2	378	c.259G>A	c.(259-261)GGT>AGT	p.G87S	ST6GAL2_uc002tdr.2_Missense_Mutation_p.G87S|ST6GAL2_uc002tds.3_Missense_Mutation_p.G87S	NM_001142351	NP_001135823	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide	87	Lumenal (Potential).				growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(4)|skin(1)	11						TGAAAGGAACCGGCTGGGTGG	0.642													49	99	---	---	---	---	PASS
DBI	1622	broad.mit.edu	37	2	120129921	120129921	+	3'UTR	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120129921G>T	uc002tlv.2	+	4					DBI_uc010yyh.1_3'UTR|DBI_uc010yyi.1_3'UTR|DBI_uc010yyj.1_RNA|DBI_uc010yyk.1_3'UTR|DBI_uc010yyl.1_3'UTR|DBI_uc010yym.1_3'UTR|DBI_uc010yyn.1_3'UTR|DBI_uc002tlw.2_3'UTR|DBI_uc010yyo.1_RNA|DBI_uc002tlx.2_3'UTR	NM_001079862	NP_001073331	P07108	ACBP_HUMAN	diazepam binding inhibitor isoform 3						transport		benzodiazepine receptor binding|fatty-acyl-CoA binding				0						ACTGTGCCATGTGTTTATCCT	0.408													20	69	---	---	---	---	PASS
FAM123C	205147	broad.mit.edu	37	2	131521736	131521736	+	Silent	SNP	A	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131521736A>T	uc002trw.2	+	2	2281	c.2091A>T	c.(2089-2091)CCA>CCT	p.P697P	FAM123C_uc010fmv.2_Silent_p.P697P|FAM123C_uc010fms.1_Silent_p.P697P|FAM123C_uc010fmt.1_Silent_p.P697P|FAM123C_uc010fmu.1_Silent_p.P697P	NM_152698	NP_689911	Q8N944	F123C_HUMAN	hypothetical protein LOC205147	697										pancreas(2)|ovary(1)	3	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.13)		CATGGCCTCCAAGGCAAGACA	0.642													12	31	---	---	---	---	PASS
GALNT3	2591	broad.mit.edu	37	2	166606342	166606342	+	Silent	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166606342A>G	uc010fph.1	-	10	2076	c.1689T>C	c.(1687-1689)CAT>CAC	p.H563H		NM_004482	NP_004473	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	563	Ricin B-type lectin.|Lumenal (Potential).				protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	Golgi cisterna membrane|integral to membrane|membrane fraction|nucleus|perinuclear region of cytoplasm	calcium ion binding|manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(2)|ovary(1)	3						CTTGAGCAGCATGAAGACATA	0.443													6	355	---	---	---	---	PASS
SCN9A	6335	broad.mit.edu	37	2	167160593	167160593	+	Intron	SNP	T	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167160593T>A	uc010fpl.2	-						SCN9A_uc002udr.1_Intron|SCN9A_uc002uds.1_Silent_p.A83A|SCN9A_uc002udt.1_Silent_p.A83A	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)	ATGTTCTCAATGCTGAGACAT	0.423													37	87	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170103247	170103247	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170103247T>A	uc002ues.2	-	21	3371	c.3158A>T	c.(3157-3159)GAT>GTT	p.D1053V	LRP2_uc010zdf.1_Missense_Mutation_p.D916V	NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	1053	LDL-receptor class A 8.|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)	ATCACTGTTATCATGACAATC	0.428													142	362	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179490104	179490104	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179490104C>T	uc010zfg.1	-	190	36964	c.36740G>A	c.(36739-36741)GGA>GAA	p.G12247E	TTN_uc010zfh.1_Missense_Mutation_p.G5942E|TTN_uc010zfi.1_Missense_Mutation_p.G5875E|TTN_uc010zfj.1_Missense_Mutation_p.G5750E	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	13174							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)			ATGAACTTTTCCTTCTGAACG	0.353													107	314	---	---	---	---	PASS
CRYGB	1419	broad.mit.edu	37	2	209007637	209007637	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209007637G>T	uc002vcp.3	-	3	286	c.253C>A	c.(253-255)CAC>AAC	p.H85N		NM_005210	NP_005201	P07316	CRGB_HUMAN	crystallin, gamma B	85	Connecting peptide.				visual perception		structural constituent of eye lens				0				Epithelial(149;0.0641)|LUSC - Lung squamous cell carcinoma(261;0.0703)|Lung(261;0.132)		GCGCCAGAGTGCTGGAGTGGC	0.483													83	201	---	---	---	---	PASS
HJURP	55355	broad.mit.edu	37	2	234754423	234754423	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234754423T>A	uc002vvg.2	-	6	512	c.446A>T	c.(445-447)AAA>ATA	p.K149I	HJURP_uc010znd.1_Missense_Mutation_p.K88I|HJURP_uc010zne.1_Intron	NM_018410	NP_060880	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	149					cell cycle|CenH3-containing nucleosome assembly at centromere|centromeric core chromatin assembly|chromosome segregation|regulation of DNA binding|regulation of protein complex assembly	condensed chromosome kinetochore|cytoplasm|nucleolus|nucleoplasm	DNA binding|histone binding			ovary(1)	1		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		GGTCAAGTATTTCCTTCTTAA	0.343													47	107	---	---	---	---	PASS
COL6A3	1293	broad.mit.edu	37	2	238280464	238280464	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238280464C>A	uc002vwl.2	-	9	4481	c.4196G>T	c.(4195-4197)AGC>ATC	p.S1399I	COL6A3_uc002vwo.2_Missense_Mutation_p.S1193I|COL6A3_uc010znj.1_Missense_Mutation_p.S792I|COL6A3_uc002vwq.2_Missense_Mutation_p.S1193I|COL6A3_uc002vwr.2_Missense_Mutation_p.S992I	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1399	VWFA 7.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity	p.S1399S(1)		ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CTGCTCCAGGCTGGGCAGCTC	0.597													41	142	---	---	---	---	PASS
OGG1	4968	broad.mit.edu	37	3	9792055	9792055	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9792055C>A	uc003bsi.2	+	1	428	c.85C>A	c.(85-87)CCT>ACT	p.P29T	OGG1_uc003bsh.2_Missense_Mutation_p.P29T|OGG1_uc003bsj.2_Missense_Mutation_p.P29T|OGG1_uc003bsk.2_Missense_Mutation_p.P29T|OGG1_uc003bsl.2_Missense_Mutation_p.P29T|OGG1_uc003bsm.2_Missense_Mutation_p.P29T|OGG1_uc003bsn.2_Missense_Mutation_p.P29T|OGG1_uc003bso.2_Missense_Mutation_p.P29T|OGG1_uc003bsp.1_5'Flank|OGG1_uc010hcm.1_5'Flank|OGG1_uc003bsq.1_5'Flank|OGG1_uc003bsr.1_5'Flank	NM_002542	NP_002533	O15527	OGG1_HUMAN	8-oxoguanine DNA-glycosylase 1 isoform 1a	29					depurination|nucleotide-excision repair|regulation of protein import into nucleus, translocation|regulation of transcription, DNA-dependent|response to oxidative stress|response to radiation	mitochondrion|nuclear matrix|nuclear speck	damaged DNA binding|endonuclease activity|oxidized purine base lesion DNA N-glycosylase activity|protein binding				0	Medulloblastoma(99;0.227)					CATCCCGTGCCCTCGCTCTGA	0.652								BER_DNA_glycosylases					23	28	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10183725	10183725	+	Missense_Mutation	SNP	C	T	T	rs5030826		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183725C>T	uc003bvc.2	+	1	407	c.194C>T	c.(193-195)TCG>TTG	p.S65L	VHL_uc003bvd.2_Missense_Mutation_p.S65L	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	65			S -> L (in VHLD; type I).|S -> A (in pheochromocytoma).|S -> W (in VHLD; type I).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.S65*(8)|p.S65L(8)|p.S65S(2)|p.S65W(2)|p.S65fs*2(2)|p.S65P(1)|p.E52_S65del(1)|p.S65fs*92(1)|p.R60fs*35(1)|p.S65>Q(1)|p.S65_N67del(1)|p.P61fs*61(1)|p.R64fs*63(1)|p.V62fs*1(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GTGCTGCGCTCGGTGAACTCG	0.721		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				3	4	---	---	---	---	PASS
SCN11A	11280	broad.mit.edu	37	3	38962724	38962724	+	Silent	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38962724G>T	uc011ays.1	-	6	934	c.735C>A	c.(733-735)GCC>GCA	p.A245A		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	245	I.				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)	AGCGTAGCAAGGCCCCCACGA	0.542													46	74	---	---	---	---	PASS
FAM19A4	151647	broad.mit.edu	37	3	68788346	68788346	+	Silent	SNP	G	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68788346G>C	uc003dnh.1	-	5	734	c.291C>G	c.(289-291)TCC>TCG	p.S97S	FAM19A4_uc003dni.1_Silent_p.S97S	NM_182522	NP_872328	Q96LR4	F19A4_HUMAN	family with sequence similarity 19 (chemokine	97						extracellular region				skin(2)	2		Lung NSC(201;0.0198)		BRCA - Breast invasive adenocarcinoma(55;1.38e-05)|Epithelial(33;0.000124)|LUSC - Lung squamous cell carcinoma(21;0.0248)|KIRC - Kidney renal clear cell carcinoma(39;0.0729)|Kidney(39;0.0904)		GAATCACAATGGAAGCTGGAA	0.408													88	150	---	---	---	---	PASS
FOXP1	27086	broad.mit.edu	37	3	71247084	71247084	+	Intron	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71247084C>G	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron|FOXP1_uc003dos.2_Missense_Mutation_p.V106L	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|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|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GGCTGACACACAGGTCCACTC	0.443			T	PAX5	ALL								10	126	---	---	---	---	PASS
POLQ	10721	broad.mit.edu	37	3	121263752	121263752	+	Silent	SNP	T	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121263752T>C	uc003eee.3	-	2	294	c.165A>G	c.(163-165)GGA>GGG	p.G55G		NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	55					DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		GCTTGCATTCTCCTTTTAGGA	0.358								DNA_polymerases_(catalytic_subunits)					13	145	---	---	---	---	PASS
UROC1	131669	broad.mit.edu	37	3	126216954	126216954	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126216954C>T	uc003eiz.1	-	14	1410	c.1378G>A	c.(1378-1380)GAC>AAC	p.D460N	UROC1_uc010hsi.1_Missense_Mutation_p.D520N	NM_144639	NP_653240	Q96N76	HUTU_HUMAN	urocanase domain containing 1 isoform 1	460					histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)		ACCGCCAGGTCCTGGGGGTCC	0.642													77	233	---	---	---	---	PASS
MBD4	8930	broad.mit.edu	37	3	129150269	129150269	+	3'UTR	SNP	T	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129150269T>G	uc003emh.1	-	8					uc003emg.2_5'Flank|MBD4_uc003emi.1_3'UTR|MBD4_uc003emj.1_3'UTR|MBD4_uc003emk.1_3'UTR	NM_003925	NP_003916	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4						depyrimidination	nucleoplasm	DNA N-glycosylase activity|endodeoxyribonuclease activity|protein binding|satellite DNA binding			ovary(1)|lung(1)	2						GCTGGAAAGGTGGTTGGTTGT	0.373								BER_DNA_glycosylases					14	56	---	---	---	---	PASS
MFN1	55669	broad.mit.edu	37	3	179096586	179096586	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179096586C>A	uc003fjs.2	+	14	1772	c.1646C>A	c.(1645-1647)TCA>TAA	p.S549*	MFN1_uc010hxb.2_RNA|MFN1_uc003fjt.2_Nonsense_Mutation_p.S577*|MFN1_uc010hxc.2_Intron	NM_033540	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	549	Cytoplasmic (Potential).				mitochondrial fusion	integral to membrane|mitochondrial outer membrane	GTP binding|GTPase activity			ovary(2)|large_intestine(1)	3	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			CTAGGATTATCAGAGCCTATC	0.358													30	90	---	---	---	---	PASS
MCCC1	56922	broad.mit.edu	37	3	182759359	182759359	+	Silent	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182759359C>G	uc003fle.2	-	11	1400	c.1263G>C	c.(1261-1263)CGG>CGC	p.R421R	MCCC1_uc010hxi.2_RNA|MCCC1_uc011bqo.1_RNA|MCCC1_uc003flf.2_Silent_p.R304R|MCCC1_uc003flg.2_Silent_p.R312R|MCCC1_uc011bqp.1_Silent_p.R374R	NM_020166	NP_064551	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	421	Biotin carboxylation.				biotin metabolic process|leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	CTTTACCTTGCCGTACTCCAG	0.418													48	144	---	---	---	---	PASS
EIF4G1	1981	broad.mit.edu	37	3	184049812	184049812	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184049812A>G	uc003fnp.2	+	32	4754	c.4556A>G	c.(4555-4557)CAG>CGG	p.Q1519R	EIF4G1_uc003fnt.2_Missense_Mutation_p.Q1230R|EIF4G1_uc003fnq.2_Missense_Mutation_p.Q1432R|EIF4G1_uc003fnr.2_Missense_Mutation_p.Q1355R|EIF4G1_uc010hxx.2_Missense_Mutation_p.Q1526R|EIF4G1_uc003fns.2_Missense_Mutation_p.Q1479R|EIF4G1_uc010hxy.2_Missense_Mutation_p.Q1526R|EIF4G1_uc003fnv.3_Missense_Mutation_p.Q1520R|EIF4G1_uc003fnu.3_Missense_Mutation_p.Q1519R|EIF4G1_uc003fnw.2_Missense_Mutation_p.Q1526R|EIF4G1_uc003fnx.2_Missense_Mutation_p.Q1324R|EIF4G1_uc003fny.3_Missense_Mutation_p.Q1323R|EIF4G1_uc003foa.2_Missense_Mutation_p.Q191R	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	1519	W2.|EIF4A-binding.				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGTGACGAGCAGAAGGAGCTA	0.587													28	75	---	---	---	---	PASS
OSTalpha	200931	broad.mit.edu	37	3	195954575	195954575	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195954575G>A	uc003fwd.2	+	4	530	c.329G>A	c.(328-330)CGT>CAT	p.R110H	OSTalpha_uc010iac.1_5'UTR|OSTalpha_uc003fwe.2_5'Flank	NM_152672	NP_689885	Q86UW1	OSTA_HUMAN	organic solute transporter alpha	110						integral to membrane|plasma membrane	transporter activity			ovary(1)	1	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;8.83e-25)|all cancers(36;8.38e-23)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;7.51e-07)|Lung(62;1.06e-06)	GBM - Glioblastoma multiforme(46;0.00202)		TGGATCCCTCGTTCCCTGGTG	0.652													36	111	---	---	---	---	PASS
MFSD7	84179	broad.mit.edu	37	4	677418	677418	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:677418C>T	uc003gay.2	-	7	1033	c.976G>A	c.(976-978)GCC>ACC	p.A326T	MFSD7_uc003gaw.2_Missense_Mutation_p.A68T|MFSD7_uc003gax.2_Missense_Mutation_p.A325T|MFSD7_uc003gaz.2_Missense_Mutation_p.A207T|MFSD7_uc003gba.2_Missense_Mutation_p.A229T|MFSD7_uc003gbb.1_Missense_Mutation_p.A261T	NM_032219	NP_115595	Q6UXD7	MFSD7_HUMAN	major facilitator superfamily domain containing	326	Helical; (Potential).				transmembrane transport	integral to membrane					0						GGCACGCAGGCCAGAGAGAAC	0.657													8	28	---	---	---	---	PASS
ATP10D	57205	broad.mit.edu	37	4	47559972	47559972	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47559972A>T	uc003gxk.1	+	12	2280	c.2116A>T	c.(2116-2118)AAT>TAT	p.N706Y	ATP10D_uc003gxl.1_Intron	NM_020453	NP_065186	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	706	Cytoplasmic (Potential).				ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3						AGGCCTCCTGAATGGCAAGGC	0.597													26	81	---	---	---	---	PASS
FRYL	285527	broad.mit.edu	37	4	48566087	48566087	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48566087C>G	uc003gyh.1	-	31	4079	c.3474G>C	c.(3472-3474)TTG>TTC	p.L1158F	FRYL_uc003gyk.2_Missense_Mutation_p.L1158F|FRYL_uc003gyi.1_Missense_Mutation_p.L47F	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	1158					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						GCTCCAGTAACAACGTAACTG	0.512													39	97	---	---	---	---	PASS
TECRL	253017	broad.mit.edu	37	4	65274893	65274893	+	Silent	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65274893G>A	uc003hcv.2	-	1	286	c.177C>T	c.(175-177)CAC>CAT	p.H59H	TECRL_uc003hcw.2_Silent_p.H59H	NM_001010874	NP_001010874	Q5HYJ1	TECRL_HUMAN	steroid 5 alpha-reductase 2-like 2	59					lipid metabolic process	cytoplasm|integral to membrane	oxidoreductase activity, acting on the CH-CH group of donors				0						CAATCTCAAAGTGAGTCGTTT	0.313													8	83	---	---	---	---	PASS
SLC4A4	8671	broad.mit.edu	37	4	72316908	72316908	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72316908G>T	uc003hfy.2	+	11	1329	c.1212G>T	c.(1210-1212)AAG>AAT	p.K404N	SLC4A4_uc010iic.2_Missense_Mutation_p.K404N|SLC4A4_uc010iib.2_Missense_Mutation_p.K404N|SLC4A4_uc003hfz.2_Missense_Mutation_p.K404N|SLC4A4_uc003hgc.3_Missense_Mutation_p.K360N|SLC4A4_uc010iid.2_5'UTR|SLC4A4_uc003hga.2_Missense_Mutation_p.K282N|SLC4A4_uc003hgb.3_Missense_Mutation_p.K360N	NM_001098484	NP_001091954	Q9Y6R1	S4A4_HUMAN	solute carrier family 4, sodium bicarbonate	404	Cytoplasmic (Potential).					basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)			TGCTTAGAAAGAATATGTACT	0.443													5	83	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79432725	79432725	+	Intron	SNP	T	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79432725T>G	uc003hlb.2	+						FRAS1_uc003hlc.1_3'UTR	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						CTTTGTGTGTTTCCCAGGACA	0.393													3	6	---	---	---	---	PASS
THAP9	79725	broad.mit.edu	37	4	83838940	83838940	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83838940C>G	uc003hnt.2	+	5	1694	c.1575C>G	c.(1573-1575)AAC>AAG	p.N525K	THAP9_uc003hns.1_Missense_Mutation_p.N381K|THAP9_uc003hnu.1_RNA|THAP9_uc003hnv.2_Missense_Mutation_p.N242K	NM_024672	NP_078948	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	525							DNA binding|metal ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	5		Hepatocellular(203;0.114)				ATAGTAGGAACTGTTATGGAA	0.338													83	230	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	4	120116717	120116717	+	Missense_Mutation	SNP	C	A	A	rs149257591	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120116717C>A	uc011cgi.1	-	3	309	c.254G>T	c.(253-255)TGT>TTT	p.C85F						SubName: Full=cDNA FLJ40807 fis, clone TRACH2009268;																		TTTGCAATTACAGTCATCTGG	0.348													3	17	---	---	---	---	PASS
ANKRD50	57182	broad.mit.edu	37	4	125631599	125631599	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125631599A>C	uc003ifg.3	-	1	334	c.68T>G	c.(67-69)TTT>TGT	p.F23C	ANKRD50_uc011cgo.1_Intron|ANKRD50_uc010inw.2_Missense_Mutation_p.F23C	NM_020337	NP_065070	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	23										central_nervous_system(1)	1						CCTACAGTAAAACTGCTTCCC	0.423													98	233	---	---	---	---	PASS
NR3C2	4306	broad.mit.edu	37	4	149356735	149356735	+	Silent	SNP	T	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149356735T>G	uc003ilj.3	-	2	1612	c.1278A>C	c.(1276-1278)CCA>CCC	p.P426P	NR3C2_uc003ilk.3_Silent_p.P426P|NR3C2_uc010iph.2_RNA	NM_000901	NP_000892	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	426	Modulating.				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	endoplasmic reticulum membrane|nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			large_intestine(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Desoxycorticosterone Pivalate(DB01134)|Eplerenone(DB00700)|Fludrocortisone(DB00687)|Spironolactone(DB00421)	CTTGCTTTATTGGTACTGAGA	0.383													65	181	---	---	---	---	PASS
GUSBP1	728411	broad.mit.edu	37	5	21459810	21459810	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21459810C>A	uc010iub.2	+	2	129	c.49C>A	c.(49-51)CCG>ACG	p.P17T	GUSBP1_uc011cnn.1_RNA|GUSBP1_uc003jgh.3_RNA|GUSBP1_uc003jgf.3_Missense_Mutation_p.P17T|GUSBP1_uc003jgg.3_RNA	NR_027028				SubName: Full=Putative uncharacterized protein GUSBL2;												0						CGCATCGGGACCGGACCCGCA	0.647											OREG0016459	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	19	70	---	---	---	---	PASS
CDH6	1004	broad.mit.edu	37	5	31299715	31299715	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31299715A>T	uc003jhe.1	+	5	1114	c.788A>T	c.(787-789)GAC>GTC	p.D263V	CDH6_uc003jhd.1_Missense_Mutation_p.D263V	NM_004932	NP_004923	P55285	CADH6_HUMAN	cadherin 6, type 2 preproprotein	263	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|skin(2)|large_intestine(1)	7						GATGTCAACGACAACCCTCCC	0.433													32	133	---	---	---	---	PASS
ESM1	11082	broad.mit.edu	37	5	54275124	54275124	+	3'UTR	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54275124G>A	uc003jpk.2	-	3					ESM1_uc010ivt.2_3'UTR	NM_007036	NP_008967	Q9NQ30	ESM1_HUMAN	endothelial cell-specific molecule 1 isoform a						angiogenesis|regulation of cell growth	extracellular region	growth factor activity|insulin-like growth factor binding				0		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.116)	Lung(15;0.23)			GAACAATCACGAAAATAGAGC	0.418													6	221	---	---	---	---	PASS
MAP3K1	4214	broad.mit.edu	37	5	56160679	56160679	+	Nonsense_Mutation	SNP	T	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56160679T>G	uc003jqw.3	+	4	1454	c.953T>G	c.(952-954)TTA>TGA	p.L318*		NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase	318					cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		AGACTGTACTTACTGCAGCAG	0.512													35	105	---	---	---	---	PASS
CTXN3	613212	broad.mit.edu	37	5	126993520	126993520	+	3'UTR	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126993520C>A	uc003kul.3	+	3					CTXN3_uc003kum.3_3'UTR	NM_001048252	NP_001041717	Q4LDR2	CTXN3_HUMAN	cortexin 3							integral to membrane					0		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0128)|COAD - Colon adenocarcinoma(49;0.0234)|OV - Ovarian serous cystadenocarcinoma(64;0.038)		GGTGAGGATTCCCTTTATTTA	0.428													13	36	---	---	---	---	PASS
CDX1	1044	broad.mit.edu	37	5	149563073	149563073	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149563073C>G	uc003lrq.2	+	3	724	c.628C>G	c.(628-630)CGC>GGC	p.R210G		NM_001804	NP_001795	P47902	CDX1_HUMAN	caudal type homeobox 1	210	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGCAAAGGAGCGCAAAGTGAA	0.612													12	35	---	---	---	---	PASS
FAM153B	202134	broad.mit.edu	37	5	175528095	175528095	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175528095C>T	uc003mdk.2	+	11	665	c.608C>T	c.(607-609)TCT>TTT	p.S203F		NM_001079529	NP_001072997	P0C7A2	F153B_HUMAN	hypothetical protein LOC202134	203										ovary(1)	1	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		CAGACAGTCTCTGAGGAAGCC	0.458													22	399	---	---	---	---	PASS
ADAMTS2	9509	broad.mit.edu	37	5	178771139	178771139	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178771139C>G	uc003mjw.2	-	2	163	c.163G>C	c.(163-165)GAG>CAG	p.E55Q	ADAMTS2_uc011dgm.1_Missense_Mutation_p.E55Q	NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	55					collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		AGGATGCGCTCCGCTCCGTGC	0.726													6	9	---	---	---	---	PASS
CANX	821	broad.mit.edu	37	5	179149818	179149818	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179149818C>A	uc003mkk.2	+	11	1373	c.1196C>A	c.(1195-1197)CCC>CAC	p.P399H	CANX_uc011dgp.1_Missense_Mutation_p.P434H|CANX_uc003mkl.2_Missense_Mutation_p.P399H|CANX_uc011dgq.1_Missense_Mutation_p.P291H	NM_001746	NP_001737	P27824	CALX_HUMAN	calnexin precursor	399	4 X approximate repeats.|P domain (Extended arm) (By similarity).|2-4.|Lumenal (Potential).				post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein secretion	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane|melanosome	calcium ion binding|sugar binding|unfolded protein binding				0	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)	ATCTGGAAACCCAGGAAAATA	0.363													22	78	---	---	---	---	PASS
ZKSCAN3	80317	broad.mit.edu	37	6	28329128	28329128	+	Silent	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28329128C>T	uc003nle.3	+	3	646	c.430C>T	c.(430-432)CTG>TTG	p.L144L	ZKSCAN3_uc010jrc.2_Silent_p.L144L|ZKSCAN3_uc003nlf.3_5'UTR	NM_024493	NP_077819	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	144					positive regulation of transcription, DNA-dependent|viral reproduction	nucleus	chromatin binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2						GGGGCAAGAACTGCTCTGTTG	0.398													6	140	---	---	---	---	PASS
BAT1	7919	broad.mit.edu	37	6	31507024	31507024	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31507024A>G	uc003ntt.2	-	3	870	c.239T>C	c.(238-240)ATT>ACT	p.I80T	BAT1_uc003nts.2_Missense_Mutation_p.I80T|BAT1_uc011dnn.1_Intron|BAT1_uc003ntu.2_Missense_Mutation_p.I80T|BAT1_uc003ntv.2_Missense_Mutation_p.I80T|BAT1_uc003ntw.2_Missense_Mutation_p.I80T|BAT1_uc003ntx.2_Missense_Mutation_p.I80T|BAT1_uc011dno.1_Intron|BAT1_uc011dnp.1_Intron|SNORD117_uc003nty.1_5'Flank|BAT1_uc011dnq.1_RNA	NM_004640	NP_004631	Q13838	DX39B_HUMAN	HLA-B associated transcript 1	80	Helicase ATP-binding.				intronless viral mRNA export from host nucleus|RNA secondary structure unwinding|spliceosome assembly	nuclear speck|spliceosomal complex|transcription export complex	ATP binding|ATP-dependent protein binding|ATP-dependent RNA helicase activity|identical protein binding|U4 snRNA binding|U6 snRNA binding				0						CATTCCCAGAATGGCCTGAGG	0.517													59	150	---	---	---	---	PASS
PTK7	5754	broad.mit.edu	37	6	43107181	43107181	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43107181G>T	uc003oub.1	+	10	1734	c.1536G>T	c.(1534-1536)CAG>CAT	p.Q512H	PTK7_uc003ouc.1_Missense_Mutation_p.Q512H|PTK7_uc003oud.1_Intron|PTK7_uc003oue.1_Intron|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Missense_Mutation_p.Q520H|PTK7_uc010jyj.1_Intron	NM_002821	NP_002812	Q13308	PTK7_HUMAN	PTK7 protein tyrosine kinase 7 isoform a	512	Ig-like C2-type 6.|Extracellular (Potential).				actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration	cell-cell junction|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			ovary(2)|large_intestine(1)	3			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			AGCCACAGCAGTGCATGGAGT	0.597													27	68	---	---	---	---	PASS
ENPP3	5169	broad.mit.edu	37	6	131995388	131995388	+	Silent	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131995388A>G	uc003qcu.3	+	9	1076	c.729A>G	c.(727-729)GAA>GAG	p.E243E	ENPP3_uc010kfn.1_RNA|ENPP3_uc011ecc.1_Silent_p.E209E|ENPP3_uc010kfo.1_RNA|ENPP3_uc010kfp.1_RNA|ENPP3_uc010kfq.2_RNA|ENPP3_uc003qcv.2_Silent_p.E243E	NM_005021	NP_005012	O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	243	Extracellular (Potential).|Phosphodiesterase.				immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)|skin(1)	4	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		CTTCAAAGGAACAAAATAATC	0.393													38	85	---	---	---	---	PASS
MIR550-1	693133	broad.mit.edu	37	7	30329467	30329467	+	RNA	SNP	T	C	C	rs71528599		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30329467T>C	hsa-mir-550-1|MI0003600	+			c.58T>C			ZNRF2_uc003tat.2_Intron																	0						TGTTGTAAGATAGTGTCTTAC	0.478													9	143	---	---	---	---	PASS
PHTF2	57157	broad.mit.edu	37	7	77538203	77538203	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77538203G>A	uc003ugs.3	+	7	665	c.539G>A	c.(538-540)GGA>GAA	p.G180E	PHTF2_uc003ugo.3_Missense_Mutation_p.G142E|PHTF2_uc003ugp.2_Missense_Mutation_p.G142E|PHTF2_uc003ugq.3_Missense_Mutation_p.G142E|PHTF2_uc010ldv.2_Missense_Mutation_p.G142E|PHTF2_uc003ugr.3_Missense_Mutation_p.G146E|PHTF2_uc003ugt.3_Missense_Mutation_p.G146E|PHTF2_uc003ugu.3_Missense_Mutation_p.G142E|PHTF2_uc003ugv.2_Missense_Mutation_p.G5E|PHTF2_uc010ldw.1_Missense_Mutation_p.G5E	NM_001127357	NP_001120829	Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	180					regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1						CTGCTCCTGGGAACTGTGCAT	0.428													6	103	---	---	---	---	PASS
PON3	5446	broad.mit.edu	37	7	94989187	94989187	+	3'UTR	SNP	G	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94989187G>C	uc003unt.2	-	9					PON1_uc011kih.1_Intron	NM_000940	NP_000931	Q15166	PON3_HUMAN	paraoxonase 3						aromatic compound catabolic process|carboxylic acid catabolic process|response to external stimulus	extracellular space	aryldialkylphosphatase activity|arylesterase activity|metal ion binding|protein homodimerization activity			ovary(1)	1	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)			TCACTGGTTGGTGTTTGCTAT	0.333													4	16	---	---	---	---	PASS
PTPRZ1	5803	broad.mit.edu	37	7	121650685	121650685	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121650685C>G	uc003vjy.2	+	12	1980	c.1585C>G	c.(1585-1587)CAC>GAC	p.H529D	PTPRZ1_uc003vjz.2_Missense_Mutation_p.H529D|PTPRZ1_uc011knt.1_5'UTR	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	529	Extracellular (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						ACTGCCACCTCACACTGTGGA	0.408													54	101	---	---	---	---	PASS
MKLN1	4289	broad.mit.edu	37	7	131163553	131163553	+	Intron	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131163553G>A	uc011kpm.1	+						MKLN1_uc011kpl.1_Intron|MKLN1_uc010lmh.2_3'UTR|MKLN1_uc003vqs.2_Intron|MKLN1_uc003vqu.2_Intron	NM_013255	NP_037387	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)					ATGAGCAAATGAAGTTTCAAG	0.358													33	72	---	---	---	---	PASS
ACTR3B	57180	broad.mit.edu	37	7	152550641	152550641	+	Silent	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152550641A>G	uc003wle.1	+	11	1257	c.1140A>G	c.(1138-1140)GGA>GGG	p.G380G	ACTR3B_uc003wlf.1_Intron|ACTR3B_uc003wlg.1_Silent_p.G292G|ACTR3B_uc011kvp.1_Silent_p.G292G	NM_020445	NP_065178	Q9P1U1	ARP3B_HUMAN	actin-related protein 3-beta isoform 1	380					regulation of actin filament polymerization	cell projection|cytoplasm|cytoskeleton	actin binding|ATP binding				0		all_hematologic(28;0.0592)|Prostate(32;0.191)	OV - Ovarian serous cystadenocarcinoma(82;0.0287)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0434)		TGTGGTTCGGAGGCTCCATGC	0.572													4	58	---	---	---	---	PASS
NCAPG2	54892	broad.mit.edu	37	7	158447311	158447311	+	Silent	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158447311G>T	uc003wnv.1	-	22	2867	c.2722C>A	c.(2722-2724)CGG>AGG	p.R908R	NCAPG2_uc010lqu.1_Silent_p.R700R|NCAPG2_uc003wnw.1_RNA|NCAPG2_uc003wnx.1_Silent_p.R908R|NCAPG2_uc011kwe.1_Silent_p.R908R|NCAPG2_uc011kwc.1_Silent_p.R409R|NCAPG2_uc011kwd.1_Silent_p.R351R	NM_017760	NP_060230	Q86XI2	CNDG2_HUMAN	leucine zipper protein 5	908					cell division|chromosome condensation|mitosis	nucleus	methylated histone residue binding			ovary(1)|breast(1)|kidney(1)	3	Ovarian(565;0.152)	all_cancers(7;3.44e-11)|all_epithelial(9;3.05e-05)|all_hematologic(28;0.014)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.187)|STAD - Stomach adenocarcinoma(7;0.18)		CCAAGACTCCGCTGTAAGAGT	0.463													94	315	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	8	12428040	12428040	+	Intron	SNP	C	A	A	rs4115597	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12428040C>A	uc003wvy.3	-						uc003wvz.1_RNA|uc003wwa.2_RNA					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		GATAAATTGGCAAACCTTTTC	0.398													9	34	---	---	---	---	PASS
MSR1	4481	broad.mit.edu	37	8	16026114	16026114	+	Silent	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16026114G>T	uc003wwz.2	-	4	681	c.483C>A	c.(481-483)ACC>ACA	p.T161T	MSR1_uc010lsu.2_Silent_p.T179T|MSR1_uc003wxa.2_Silent_p.T161T|MSR1_uc003wxb.2_Silent_p.T161T|MSR1_uc011kxz.1_Intron	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1	161	Extracellular (Potential).				cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		AGGAAAACAAGGTACTTAGCT	0.388													6	251	---	---	---	---	PASS
SULF1	23213	broad.mit.edu	37	8	70514054	70514054	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70514054C>G	uc010lza.1	+	10	1768	c.1051C>G	c.(1051-1053)CCA>GCA	p.P351A	SULF1_uc003xyd.2_Missense_Mutation_p.P351A|SULF1_uc003xye.2_Missense_Mutation_p.P351A|SULF1_uc003xyf.2_Missense_Mutation_p.P351A|SULF1_uc003xyg.2_Missense_Mutation_p.P351A|SULF1_uc003xyh.1_RNA	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor	351					apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			AAGTGTAGAACCAGGATCAAT	0.403													115	320	---	---	---	---	PASS
INTS8	55656	broad.mit.edu	37	8	95861709	95861709	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95861709A>C	uc003yhb.2	+	11	1406	c.1280A>C	c.(1279-1281)AAT>ACT	p.N427T	INTS8_uc003yha.1_Missense_Mutation_p.N427T|INTS8_uc011lgq.1_RNA|INTS8_uc011lgr.1_RNA|INTS8_uc010mba.2_Missense_Mutation_p.N254T	NM_017864	NP_060334	Q75QN2	INT8_HUMAN	integrator complex subunit 8	427					snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)					AGATCAGTAAATTTAGAAAAA	0.239													49	165	---	---	---	---	PASS
EFR3A	23167	broad.mit.edu	37	8	132956999	132956999	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132956999T>G	uc003yte.2	+	3	296	c.95T>G	c.(94-96)CTT>CGT	p.L32R		NM_015137	NP_055952	Q14156	EFR3A_HUMAN	EFR3 homolog A	32						plasma membrane	binding			ovary(3)|breast(1)|central_nervous_system(1)	5	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			TAGGATGGCCTTGTGAAAACT	0.343													14	21	---	---	---	---	PASS
ALDH1B1	219	broad.mit.edu	37	9	38395753	38395753	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38395753G>T	uc004aay.2	+	2	120	c.8G>T	c.(7-9)CGC>CTC	p.R3L		NM_000692	NP_000683	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1B1 precursor	3					carbohydrate metabolic process	mitochondrial matrix|nucleus	aldehyde dehydrogenase (NAD) activity			skin(1)	1				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)	NADH(DB00157)	AGCATGCTGCGCTTCCTGGCA	0.622													11	100	---	---	---	---	PASS
MAMDC2	256691	broad.mit.edu	37	9	72758526	72758526	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72758526C>A	uc004ahm.2	+	9	1812	c.1195C>A	c.(1195-1197)CTC>ATC	p.L399I	MAMDC2_uc004ahn.2_RNA	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor	399	MAM 3.					endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2						CATTGGAAGGCTCTATGGGCC	0.408													4	164	---	---	---	---	PASS
TRPM6	140803	broad.mit.edu	37	9	77435329	77435329	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77435329T>G	uc004ajl.1	-	9	1263	c.1025A>C	c.(1024-1026)CAG>CCG	p.Q342P	TRPM6_uc004ajk.1_Missense_Mutation_p.Q337P|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Missense_Mutation_p.Q342P|TRPM6_uc010mpd.1_Missense_Mutation_p.Q342P|TRPM6_uc010mpe.1_Intron	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	342	Cytoplasmic (Potential).				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						CTCTTTCACCTGAGGTCGCAG	0.448													24	93	---	---	---	---	PASS
RASEF	158158	broad.mit.edu	37	9	85605307	85605307	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85605307G>A	uc004amo.1	-	16	2377	c.2116C>T	c.(2116-2118)CGA>TGA	p.R706*		NM_152573	NP_689786	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	706					protein transport|small GTPase mediated signal transduction	perinuclear region of cytoplasm	calcium ion binding|GTP binding			upper_aerodigestive_tract(1)|lung(1)|breast(1)	3						AAACTTTACCGAGCAAGGTGC	0.383													4	140	---	---	---	---	PASS
KIF27	55582	broad.mit.edu	37	9	86518027	86518027	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86518027C>A	uc004ana.2	-	4	1550	c.1406G>T	c.(1405-1407)GGA>GTA	p.G469V	KIF27_uc010mpw.2_Missense_Mutation_p.G469V|KIF27_uc010mpx.2_Missense_Mutation_p.G469V	NM_017576	NP_060046	Q86VH2	KIF27_HUMAN	kinesin family member 27	469					cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5						ATGCTGTGGTCCTTCTTCCAG	0.403													32	106	---	---	---	---	PASS
C9orf5	23731	broad.mit.edu	37	9	111855820	111855820	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111855820T>G	uc004bdt.3	-	4	883	c.851A>C	c.(850-852)AAC>ACC	p.N284T	C9orf5_uc004bds.3_RNA|C9orf5_uc004bdr.3_Missense_Mutation_p.N284T	NM_032012	NP_114401	Q9H330	CI005_HUMAN	hypothetical protein LOC23731	284						integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)		GATGGCCAAGTTTGCCAGAGT	0.453													48	136	---	---	---	---	PASS
EPB41L4B	54566	broad.mit.edu	37	9	111979310	111979310	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111979310G>C	uc004bdz.1	-	16	1820	c.1525C>G	c.(1525-1527)CAG>GAG	p.Q509E		NM_019114	NP_061987	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	509	His-rich.					cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|skin(1)	3						tgctgatgctggtgctggtgg	0.453													38	87	---	---	---	---	PASS
PTPN3	5774	broad.mit.edu	37	9	112172526	112172526	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112172526G>A	uc004bed.2	-	15	1595	c.1483C>T	c.(1483-1485)CAG>TAG	p.Q495*	PTPN3_uc004beb.2_Nonsense_Mutation_p.Q364*|PTPN3_uc004bec.2_Nonsense_Mutation_p.Q319*|PTPN3_uc010mtu.2_RNA|PTPN3_uc011lwg.1_Nonsense_Mutation_p.Q450*|PTPN3_uc011lwh.1_Nonsense_Mutation_p.Q341*|PTPN3_uc011lwd.1_5'UTR|PTPN3_uc011lwe.1_Nonsense_Mutation_p.Q208*|PTPN3_uc011lwf.1_Nonsense_Mutation_p.Q163*	NM_002829	NP_002820	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type	495					negative regulation of membrane protein ectodomain proteolysis|negative regulation of mitotic cell cycle	cytoplasm|cytoskeleton|internal side of plasma membrane	ATPase binding|cytoskeletal protein binding|phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(3)	3						CAGTAGTACTGGCTGGCGTCC	0.587													59	90	---	---	---	---	PASS
AKNA	80709	broad.mit.edu	37	9	117129973	117129973	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117129973C>T	uc004biq.3	-	5	1713	c.1578G>A	c.(1576-1578)TGG>TGA	p.W526*	AKNA_uc004bio.3_5'UTR|AKNA_uc004bip.3_Nonsense_Mutation_p.W445*|AKNA_uc004bir.3_Nonsense_Mutation_p.W526*|AKNA_uc004bis.3_Nonsense_Mutation_p.W526*|AKNA_uc010mve.2_Nonsense_Mutation_p.W407*|AKNA_uc004biu.1_Nonsense_Mutation_p.W267*|AKNA_uc004biv.1_Nonsense_Mutation_p.W526*	NM_030767	NP_110394	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	526					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6						GAGCTGATGGCCACCCTGGAA	0.587													4	107	---	---	---	---	PASS
PAPPA	5069	broad.mit.edu	37	9	118982390	118982390	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118982390A>T	uc004bjn.2	+	5	2474	c.2093A>T	c.(2092-2094)GAT>GTT	p.D698V	PAPPA_uc011lxp.1_Missense_Mutation_p.D393V|PAPPA_uc011lxq.1_Intron	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A	698					cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9						CCACCTATAGATGGCCATTTC	0.557													84	195	---	---	---	---	PASS
NEK6	10783	broad.mit.edu	37	9	127055176	127055176	+	Intron	SNP	A	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127055176A>C	uc004bog.2	+						NEK6_uc004bof.2_Intron|NEK6_uc004boh.2_5'UTR|NEK6_uc010mwj.2_Intron|NEK6_uc010mwk.2_Intron|NEK6_uc004boi.2_Intron	NM_014397	NP_055212	Q9HC98	NEK6_HUMAN	NIMA-related kinase 6 isoform 2						apoptosis|cell division|chromosome segregation|mitosis|peptidyl-serine phosphorylation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of mitotic metaphase/anaphase transition	cytoplasm|nucleus	ATP binding|kinesin binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity|signal transducer activity			ovary(2)|kidney(1)	3						caggctgtggagctgggagtg	0.000													2	5	---	---	---	---	PASS
ZER1	10444	broad.mit.edu	37	9	131514950	131514950	+	Splice_Site	SNP	A	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131514950A>C	uc004bwa.1	-	5	1356	c.923_splice	c.e5+1	p.S308_splice		NM_006336	NP_006327	Q7Z7L7	ZER1_HUMAN	zyg-11 homolog B (C. elegans)-like						ATP hydrolysis coupled proton transport|regulation of ubiquitin-protein ligase activity	Cul2-RING ubiquitin ligase complex|vacuolar proton-transporting V-type ATPase, V1 domain	protein binding|proton-transporting ATPase activity, rotational mechanism|ubiquitin-protein ligase activity			ovary(1)	1						CTGGGGCCCCACCTGGTCTGC	0.393													4	32	---	---	---	---	PASS
PRDM12	59335	broad.mit.edu	37	9	133542139	133542139	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133542139C>T	uc004bzt.1	+	2	428	c.368C>T	c.(367-369)GCC>GTC	p.A123V		NM_021619	NP_067632	Q9H4Q4	PRD12_HUMAN	PR domain containing 12	123	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534)		OV - Ovarian serous cystadenocarcinoma(145;0.000344)		CGCGTGATCGCCCCGGAGCAC	0.677													41	122	---	---	---	---	PASS
ABL1	25	broad.mit.edu	37	9	133750263	133750263	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133750263C>T	uc004bzw.2	+	7	1097	c.1094C>T	c.(1093-1095)GCT>GTT	p.A365V	ABL1_uc004bzv.2_Missense_Mutation_p.A384V	NM_005157	NP_005148	P00519	ABL1_HUMAN	c-abl oncogene 1, receptor tyrosine kinase	365	Protein kinase.				actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)	AGAGATCTTGCTGCCCGAAAC	0.517			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL								39	133	---	---	---	---	PASS
TUBBP5	643224	broad.mit.edu	37	9	141070935	141070935	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141070935C>T	uc004com.2	+	4	599	c.338C>T	c.(337-339)GCC>GTC	p.A113V	TUBBP5_uc010ncq.2_3'UTR					RecName: Full=Putative tubulin beta-4q chain;												0						CCCTACAACGCCACCCTCTCA	0.517													5	104	---	---	---	---	PASS
TUBBP5	643224	broad.mit.edu	37	9	141071110	141071110	+	Silent	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141071110A>G	uc004com.2	+	4	774	c.513A>G	c.(511-513)CCA>CCG	p.P171P	TUBBP5_uc010ncq.2_3'UTR					RecName: Full=Putative tubulin beta-4q chain;												0						TGCGCTTCCCAGGCCAGCTGA	0.597													7	98	---	---	---	---	PASS
YME1L1	10730	broad.mit.edu	37	10	27437893	27437893	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27437893G>A	uc001iti.2	-	2	292	c.110C>T	c.(109-111)TCA>TTA	p.S37L	YME1L1_uc001itj.2_Missense_Mutation_p.S37L|YME1L1_uc010qdl.1_Missense_Mutation_p.S37L|YME1L1_uc009xkv.2_RNA|YME1L1_uc001itk.1_Missense_Mutation_p.S37L	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1	37					protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1						TTGAGAAACTGACACTCCACT	0.403													121	278	---	---	---	---	PASS
KIAA0913	23053	broad.mit.edu	37	10	75556685	75556685	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75556685T>C	uc009xrl.2	+	16	3204	c.3172T>C	c.(3172-3174)TCA>CCA	p.S1058P	KIAA0913_uc001jve.2_Missense_Mutation_p.S1063P|KIAA0913_uc001jvf.2_Missense_Mutation_p.S1058P|KIAA0913_uc001jvh.2_RNA|KIAA0913_uc001jvi.2_Missense_Mutation_p.S493P|KIAA0913_uc010qkr.1_Missense_Mutation_p.S481P|KIAA0913_uc001jvj.2_Missense_Mutation_p.S481P|KIAA0913_uc009xrn.1_5'Flank	NM_015037	NP_055852	A7E2V4	K0913_HUMAN	hypothetical protein LOC23053	1058							zinc ion binding			breast(1)	1	Prostate(51;0.0112)					ACCACTGACCTCAGGCTCTGC	0.642													53	90	---	---	---	---	PASS
LOC650623	650623	broad.mit.edu	37	10	81443821	81443821	+	RNA	SNP	C	G	G	rs150975459	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81443821C>G	uc010qlu.1	+	1		c.1091C>G				NR_027512				Homo sapiens BEN domain containing 3 pseudogene (LOC650623), non-coding RNA.												0						GCAGCACCATCGCCTCAGACC	0.612													3	60	---	---	---	---	PASS
PTEN	5728	broad.mit.edu	37	10	89692779	89692779	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89692779A>G	uc001kfb.2	+	6	1294	c.263A>G	c.(262-264)TAT>TGT	p.Y88C		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	88	Phosphatase tensin-type.				activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.Y88C(5)|p.R55fs*1(4)|p.?(2)|p.Y27fs*1(2)|p.Y88fs*3(2)|p.Y27_N212>Y(2)|p.Y88N(1)|p.Y88H(1)|p.Q87_P96del(1)|p.Y88S(1)|p.N82_P95del(1)|p.F56fs*2(1)		endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		GTTGCACAATATCCTTTTGAA	0.338		31	D|Mis|N|F|S		glioma| prostate|endometrial	harmartoma|glioma| prostate|endometrial			Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)			5	193	---	---	---	---	PASS
CYP2C19	1557	broad.mit.edu	37	10	96580386	96580386	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96580386A>C	uc010qnz.1	+	6	953	c.953A>C	c.(952-954)GAG>GCG	p.E318A	CYP2C19_uc010qny.1_Missense_Mutation_p.E296A	NM_000769	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C,	318					exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	(S)-limonene 6-monooxygenase activity|(S)-limonene 7-monooxygenase activity|4-hydroxyacetophenone monooxygenase activity|electron carrier activity|enzyme binding|heme binding|oxygen binding|steroid hydroxylase activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Adinazolam(DB00546)|Aminophenazone(DB01424)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Arformoterol(DB01274)|Bortezomib(DB00188)|Carisoprodol(DB00395)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Desipramine(DB01151)|Desloratadine(DB00967)|Diclofenac(DB00586)|Diltiazem(DB00343)|Efavirenz(DB00625)|Esomeprazole(DB00736)|Famotidine(DB00927)|Felbamate(DB00949)|Finasteride(DB01216)|Flunitrazepam(DB01544)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Guanfacine(DB01018)|Imipramine(DB00458)|Indomethacin(DB00328)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Loratadine(DB00455)|Melatonin(DB01065)|Mephenytoin(DB00532)|Methadone(DB00333)|Methylphenobarbital(DB00849)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nilutamide(DB00665)|Norgestrel(DB00506)|Omeprazole(DB00338)|Oxcarbazepine(DB00776)|Pantoprazole(DB00213)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Quinidine(DB00908)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ritonavir(DB00503)|Selegiline(DB01037)|Sertraline(DB01104)|Temazepam(DB00231)|Teniposide(DB00444)|Terfenadine(DB00342)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tolbutamide(DB01124)|Topiramate(DB00273)|Tranylcypromine(DB00752)|Troglitazone(DB00197)|Troleandomycin(DB01361)|Voriconazole(DB00582)	AAGCACCCAGAGGTCACAGGT	0.453													60	155	---	---	---	---	PASS
ADAM12	8038	broad.mit.edu	37	10	127843806	127843806	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127843806C>A	uc001ljk.2	-	4	742	c.329G>T	c.(328-330)CGA>CTA	p.R110L	ADAM12_uc010qul.1_Missense_Mutation_p.R110L|ADAM12_uc001ljm.2_Missense_Mutation_p.R110L|ADAM12_uc001ljn.2_Missense_Mutation_p.R110L|ADAM12_uc001ljl.3_Missense_Mutation_p.R110L	NM_003474	NP_003465	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12 isoform 1	110					cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		CGTGTAATTTCGAGCGAGGGA	0.438													4	174	---	---	---	---	PASS
KRTAP5-4	387267	broad.mit.edu	37	11	1643006	1643006	+	Silent	SNP	G	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1643006G>C	uc009ycy.1	-	3	543	c.456C>G	c.(454-456)GGC>GGG	p.G152G		NM_001012709	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	166	9 X 4 AA repeats of C-C-X-P.					keratin filament					0		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCCCCTTGGAGCCCCCACAGG	0.682													9	63	---	---	---	---	PASS
OR52L1	338751	broad.mit.edu	37	11	6007950	6007950	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6007950G>A	uc001mcd.2	-	1	266	c.211C>T	c.(211-213)CCA>TCA	p.P71S		NM_001005173	NP_001005173	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L,	71	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|pancreas(1)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCAAGGATGGGTCCATCCAG	0.527													7	52	---	---	---	---	PASS
SBF2	81846	broad.mit.edu	37	11	9983423	9983423	+	Intron	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9983423A>G	uc001mib.2	-						SBF2_uc001mif.3_Intron|SBF2_uc001mih.3_Silent_p.Y176Y	NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		AAGAACTGATATATTGGTAAT	0.294													21	37	---	---	---	---	PASS
MRGPRX4	117196	broad.mit.edu	37	11	18194722	18194722	+	5'UTR	SNP	T	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18194722T>G	uc001mnv.1	+	1						NM_054032	NP_473373	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4							integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1						tacggcagggtggtggggaga	0.209													12	57	---	---	---	---	PASS
QSER1	79832	broad.mit.edu	37	11	32955024	32955024	+	Silent	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32955024C>T	uc001mty.2	+	4	2100	c.1833C>T	c.(1831-1833)ATC>ATT	p.I611I	QSER1_uc001mtz.1_Silent_p.I372I|QSER1_uc001mua.2_Silent_p.I116I	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	611										ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)					AGAGTGTAATCAGAAGTAATT	0.383													53	185	---	---	---	---	PASS
APIP	51074	broad.mit.edu	37	11	34916607	34916607	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34916607G>T	uc001mvs.2	-	2	216	c.108C>A	c.(106-108)TAC>TAA	p.Y36*	APIP_uc010reo.1_Nonsense_Mutation_p.Y53*	NM_015957	NP_057041	Q96GX9	MTNB_HUMAN	APAF1 interacting protein	36					apoptosis|L-methionine salvage	cytoplasm	identical protein binding|metal ion binding|methylthioribulose 1-phosphate dehydratase activity				0	all_epithelial(35;0.161)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.000425)			AGCCTAAATGGTAAAACTGTT	0.403													5	252	---	---	---	---	PASS
SSRP1	6749	broad.mit.edu	37	11	57099755	57099755	+	Splice_Site	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57099755C>G	uc001njt.2	-	8	1140	c.873_splice	c.e8-1	p.E291_splice		NM_003146	NP_003137	Q08945	SSRP1_HUMAN	structure specific recognition protein 1						DNA repair|DNA replication|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	chromosome|cytoplasm|nucleoplasm	DNA binding|protein binding			ovary(2)	2						CACTTCTTCCCTACAAAGAAA	0.527													4	157	---	---	---	---	PASS
CLP1	10978	broad.mit.edu	37	11	57428611	57428611	+	Nonsense_Mutation	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57428611C>G	uc001nkw.2	+	3	1120	c.981C>G	c.(979-981)TAC>TAG	p.Y327*	CLP1_uc010rjw.1_Nonsense_Mutation_p.Y263*|CLP1_uc009yml.2_Nonsense_Mutation_p.Y327*	NM_006831	NP_006822	Q92989	CLP1_HUMAN	ATP/GTP-binding protein isoform 1	327					mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|siRNA loading onto RISC involved in RNA interference|targeting of mRNA for destruction involved in RNA interference|termination of RNA polymerase II transcription|tRNA splicing, via endonucleolytic cleavage and ligation	nucleoplasm|tRNA-intron endonuclease complex	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity			ovary(1)	1						TGAAAATCTACAAAGTTGGGG	0.463													4	336	---	---	---	---	PASS
KLC2	64837	broad.mit.edu	37	11	66030378	66030378	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66030378A>G	uc010rov.1	+	5	866	c.623A>G	c.(622-624)TAC>TGC	p.Y208C	KLC2_uc010row.1_Missense_Mutation_p.Y208C|KLC2_uc009yra.2_Missense_Mutation_p.Y208C|KLC2_uc001ohb.2_Missense_Mutation_p.Y208C|KLC2_uc010rox.1_Missense_Mutation_p.Y131C|KLC2_uc001ohc.2_Missense_Mutation_p.Y208C|KLC2_uc001ohd.2_Missense_Mutation_p.Y131C|KLC2_uc001ohe.1_Missense_Mutation_p.Y69C	NM_001134775	NP_001128247	Q9H0B6	KLC2_HUMAN	kinesin light chain 2 isoform 1	208	TPR 1.				blood coagulation	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0						GTGATCCAATACGCCTCACAG	0.647													3	157	---	---	---	---	PASS
BBS1	582	broad.mit.edu	37	11	66282106	66282106	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66282106C>T	uc001oij.1	+	4	401	c.389C>T	c.(388-390)CCT>CTT	p.P130L	BBS1_uc001oii.1_Missense_Mutation_p.P167L|BBS1_uc010rpf.1_RNA|BBS1_uc010rpg.1_Missense_Mutation_p.P130L|BBS1_uc001oik.1_Missense_Mutation_p.P54L|BBS1_uc001oil.1_Missense_Mutation_p.P130L	NM_024649	NP_078925	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	130					nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1						CCCCAATTGCCTCCAAATCCT	0.512									Bardet-Biedl_syndrome				7	225	---	---	---	---	PASS
KIAA1731	85459	broad.mit.edu	37	11	93454688	93454688	+	Intron	SNP	G	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93454688G>C	uc009ywb.1	+						KIAA1731_uc001pdu.1_Intron|SCARNA9_uc001pdv.2_RNA|KIAA1731_uc001pdw.1_5'Flank	NM_033395	NP_203753	Q9C0D2	K1731_HUMAN	hypothetical protein LOC85459							centrosome					0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TGCTTTCTGAGATCTGCTTTT	0.368													55	153	---	---	---	---	PASS
DYNC2H1	79659	broad.mit.edu	37	11	103093809	103093809	+	Nonsense_Mutation	SNP	T	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103093809T>G	uc001pho.2	+	59	9491	c.9347T>G	c.(9346-9348)TTA>TGA	p.L3116*	DYNC2H1_uc001phn.1_Nonsense_Mutation_p.L3116*|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3116	Potential.|Stalk (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CAGGCAGGATTAGAATCGTAA	0.328													19	26	---	---	---	---	PASS
TTC12	54970	broad.mit.edu	37	11	113230094	113230094	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113230094G>T	uc001pnu.2	+	17	1561	c.1456G>T	c.(1456-1458)GAG>TAG	p.E486*	TTC12_uc001pnv.2_Nonsense_Mutation_p.E492*|TTC12_uc001pnw.2_RNA|TTC12_uc001pnx.2_Nonsense_Mutation_p.E336*	NM_017868	NP_060338	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	486							binding			pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		GGCCAGGTGTGAGGAGGATGT	0.478													48	141	---	---	---	---	PASS
ANKK1	255239	broad.mit.edu	37	11	113270032	113270032	+	Silent	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113270032C>T	uc001pny.2	+	8	1435	c.1341C>T	c.(1339-1341)CTC>CTT	p.L447L		NM_178510	NP_848605	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	447	ANK 3.						ATP binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|ovary(1)|breast(1)	8		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		CGCGCCTGCTCCTGGACCACG	0.602													9	8	---	---	---	---	PASS
LOC100288778	100288778	broad.mit.edu	37	12	88651	88651	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88651A>G	uc010scy.1	+	6	715	c.160A>G	c.(160-162)AGC>GGC	p.S54G	LOC100288778_uc010scz.1_RNA|LOC100288778_uc010sdb.1_RNA|LOC100288778_uc010sdc.1_RNA|LOC100288778_uc010sdd.1_Missense_Mutation_p.S54G|LOC100288778_uc010sde.1_Missense_Mutation_p.S54G|LOC100288778_uc010sdf.1_Missense_Mutation_p.S54G|LOC100288778_uc010sdg.1_Missense_Mutation_p.S54G|LOC100288778_uc010sdh.1_RNA					SubName: Full=Actin nucleation promoting factor; Flags: Fragment;												0						TGACCTGCCCAGCATTGCCAA	0.587													3	39	---	---	---	---	PASS
WNK1	65125	broad.mit.edu	37	12	862733	862733	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:862733T>A	uc001qio.3	+	1	509	c.2T>A	c.(1-3)ATG>AAG	p.M1K	WNK1_uc001qin.2_Missense_Mutation_p.M1K|WNK1_uc001qip.3_Missense_Mutation_p.M1K	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1					intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GAACCGACCATGTCTGGCGGC	0.682													11	33	---	---	---	---	PASS
APOBEC1	339	broad.mit.edu	37	12	7802168	7802168	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7802168A>G	uc001qtb.2	-	5	720	c.686T>C	c.(685-687)ATA>ACA	p.I229T	APOBEC1_uc001qtc.2_Missense_Mutation_p.I184T|APOBEC1_uc010sgf.1_Missense_Mutation_p.I229T	NM_001644	NP_001635	P41238	ABEC1_HUMAN	apolipoprotein B mRNA editing enzyme	229					cytidine to uridine editing|DNA demethylation|lipid metabolic process|mRNA modification|mRNA processing|negative regulation of methylation-dependent chromatin silencing	nucleoplasm	cytidine deaminase activity|RNA binding|zinc ion binding				0						AGAAGGATGTATCAGCCCTGT	0.403													45	92	---	---	---	---	PASS
A2M	2	broad.mit.edu	37	12	9225307	9225307	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9225307G>T	uc001qvk.1	-	30	4030	c.3917C>A	c.(3916-3918)CCA>CAA	p.P1306Q	A2M_uc001qvj.1_Missense_Mutation_p.P348Q|A2M_uc009zgk.1_Missense_Mutation_p.P1156Q	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	1306					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	AGGCAGCTCTGGCAATGAGAC	0.527													85	238	---	---	---	---	PASS
DDX12	440081	broad.mit.edu	37	12	9573258	9573258	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9573258C>A	uc010sgs.1	-	21	2250	c.2055G>T	c.(2053-2055)ATG>ATT	p.M685I	DDX12_uc001qvx.3_5'Flank|DDX12_uc001qvy.1_5'Flank	NM_004400	NP_004391			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 12												0						CCACCTCGTCCATCTaaggaa	0.473													21	90	---	---	---	---	PASS
LETMD1	25875	broad.mit.edu	37	12	51442117	51442117	+	5'UTR	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51442117C>G	uc001rxm.2	+	1					LETMD1_uc010smz.1_5'UTR|LETMD1_uc010sna.1_5'UTR|LETMD1_uc001rxl.2_5'UTR|LETMD1_uc009zlv.2_RNA|LETMD1_uc001rxs.2_5'UTR|LETMD1_uc009zlw.2_5'UTR|LETMD1_uc001rxn.2_5'UTR|LETMD1_uc001rxo.2_RNA|LETMD1_uc001rxp.2_5'UTR|LETMD1_uc001rxq.2_5'UTR|LETMD1_uc001rxr.2_RNA|LETMD1_uc001rxt.2_5'Flank	NM_015416	NP_056231	Q6P1Q0	LTMD1_HUMAN	LETM1 domain containing 1 isoform 1							integral to membrane|mitochondrial outer membrane	protein binding			central_nervous_system(2)	2						AACCTCTTCTCTCCCGCTTCT	0.582											OREG0021818	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	263	---	---	---	---	PASS
NACA	4666	broad.mit.edu	37	12	57114669	57114669	+	Intron	SNP	G	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57114669G>C	uc001slz.2	-						NACA_uc001sly.2_Intron|NACA_uc009zoy.1_Missense_Mutation_p.H215Q|NACA_uc001smc.2_Intron|NACA_uc001sma.2_Missense_Mutation_p.H215Q|NACA_uc001smb.2_Intron|NACA_uc010squ.1_Intron	NM_001113201	NP_001106672	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha						interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1						GAGTCACACAGTGGTAAGGAA	0.488			T	BCL6	NHL								99	221	---	---	---	---	PASS
CSRP2	1466	broad.mit.edu	37	12	77259966	77259966	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77259966A>C	uc001syl.1	-	2	158	c.75T>G	c.(73-75)TGT>TGG	p.C25W		NM_001321	NP_001312	Q16527	CSRP2_HUMAN	cysteine and glycine-rich protein 2	25	LIM zinc-binding 1.				multicellular organismal development	nucleus	zinc ion binding			ovary(1)	1						TCCTGCCATCACACTGCACCT	0.502													3	120	---	---	---	---	PASS
KCTD10	83892	broad.mit.edu	37	12	109889372	109889372	+	3'UTR	SNP	G	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109889372G>C	uc001toi.1	-	7					KCTD10_uc001toh.1_RNA|KCTD10_uc009zvi.1_3'UTR|KCTD10_uc001toj.1_3'UTR|KCTD10_uc001tok.1_3'UTR	NM_031954	NP_114160	Q9H3F6	BACD3_HUMAN	potassium channel tetramerisation domain						proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination	Cul3-RING ubiquitin ligase complex|cytoplasm|nucleus|voltage-gated potassium channel complex	voltage-gated potassium channel activity				0						GGGGCGGTGAGAGGAGGGCGG	0.657													5	53	---	---	---	---	PASS
COQ5	84274	broad.mit.edu	37	12	120954469	120954469	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120954469C>T	uc001tyn.2	-	3	495	c.475G>A	c.(475-477)GAA>AAA	p.E159K	COQ5_uc001tyo.2_Missense_Mutation_p.E78K|COQ5_uc010szj.1_Intron	NM_032314	NP_115690	Q5HYK3	COQ5_HUMAN	coenzyme Q5 homolog, methyltransferase	159					ubiquinone biosynthetic process	mitochondrion	methyltransferase activity			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AAGGAATCTTCTTCATTCTGG	0.458													174	367	---	---	---	---	PASS
GPR133	283383	broad.mit.edu	37	12	131616270	131616270	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131616270G>T	uc001uit.3	+	21	2735	c.2176G>T	c.(2176-2178)GTC>TTC	p.V726F	GPR133_uc010tbm.1_Missense_Mutation_p.V758F|GPR133_uc009zyo.2_Missense_Mutation_p.V8F|GPR133_uc009zyp.2_RNA	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor	726	Helical; Name=5; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		TCTTGTGCAGGTCAACATTGG	0.587													27	61	---	---	---	---	PASS
HSPH1	10808	broad.mit.edu	37	13	31729705	31729705	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31729705C>G	uc001utj.2	-	3	650	c.252G>C	c.(250-252)AAG>AAC	p.K84N	HSPH1_uc001utk.2_Missense_Mutation_p.K84N|HSPH1_uc010aaw.2_Missense_Mutation_p.K84N|HSPH1_uc001utl.2_Missense_Mutation_p.K86N|HSPH1_uc010tds.1_Missense_Mutation_p.K86N|HSPH1_uc010tdt.1_RNA|HSPH1_uc010aax.1_Missense_Mutation_p.K86N|HSPH1_uc010aay.1_Missense_Mutation_p.K86N	NM_006644	NP_006635	Q92598	HS105_HUMAN	heat shock 105kD	84					positive regulation of MHC class I biosynthetic process|positive regulation of NK T cell activation|response to unfolded protein	cytoplasm|extracellular region	ATP binding				0		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		TCAAGTTTTCCTTCTCCTTTT	0.348													54	160	---	---	---	---	PASS
N4BP2L2	10443	broad.mit.edu	37	13	33110320	33110320	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33110320A>G	uc001uuk.3	-	2	1023	c.845T>C	c.(844-846)CTT>CCT	p.L282P	N4BP2L2_uc010abe.1_Intron|N4BP2L2_uc010tdz.1_Intron|N4BP2L2_uc001uul.1_Missense_Mutation_p.L282P|N4BP2L2_uc001uum.2_5'Flank	NM_014887	NP_055702	Q92802	N42L2_HUMAN	phosphonoformate immuno-associated protein 5	282											0		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		CAAACTGGGAAGAGGGGGACC	0.388													41	120	---	---	---	---	PASS
POU4F1	5457	broad.mit.edu	37	13	79177468	79177468	+	5'UTR	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79177468G>A	uc001vkv.2	-	1					uc001vku.1_Intron	NM_006237	NP_006228	Q01851	PO4F1_HUMAN	POU domain, class 4, transcription factor 1						axonogenesis|regulation of transcription from RNA polymerase II promoter|synapse assembly	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.129)		TCATCGTGGCGGCTTGGCATG	0.562													26	73	---	---	---	---	PASS
CHD8	57680	broad.mit.edu	37	14	21884050	21884050	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21884050C>T	uc001was.1	-	6	990	c.896G>A	c.(895-897)CGC>CAC	p.R299H	CHD8_uc001war.1_Missense_Mutation_p.R195H	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	578					ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		CTTAACTTGGCGGTTTGAGCG	0.378													5	366	---	---	---	---	PASS
RHOJ	57381	broad.mit.edu	37	14	63757822	63757822	+	3'UTR	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63757822G>T	uc001xgb.1	+	5						NM_020663	NP_065714	Q9H4E5	RHOJ_HUMAN	ras homolog gene family, member J precursor						actin cytoskeleton organization|regulation of cell shape|regulation of small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity				0				OV - Ovarian serous cystadenocarcinoma(108;0.00326)|all cancers(60;0.031)|BRCA - Breast invasive adenocarcinoma(234;0.119)		AGCCAAAAAGGAGGGCACGAC	0.577													15	22	---	---	---	---	PASS
C14orf166B	145497	broad.mit.edu	37	14	77292838	77292838	+	5'UTR	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77292838C>G	uc001xsx.2	+	1					C14orf166B_uc010asn.1_5'UTR|C14orf166B_uc001xsw.2_RNA|C14orf166B_uc010aso.1_RNA|C14orf166B_uc010tvg.1_RNA	NM_194287	NP_919263	Q0VAA2	CN16B_HUMAN	hypothetical protein LOC145497												0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)		GGGTCAAATTCATGCACATCC	0.557													5	7	---	---	---	---	PASS
SNW1	22938	broad.mit.edu	37	14	78184796	78184796	+	Silent	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78184796A>G	uc001xuf.2	-	13	1353	c.1326T>C	c.(1324-1326)GAT>GAC	p.D442D	SNW1_uc010tvm.1_Silent_p.D367D|SNW1_uc010asu.2_Silent_p.D280D|SNW1_uc010tvn.1_Silent_p.D442D	NM_012245	NP_036377	Q13573	SNW1_HUMAN	SKI-interacting protein	442					negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|regulation of transcription from RNA polymerase II promoter	catalytic step 2 spliceosome|nucleoplasm	Notch binding			ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		TCTGGGCCATATCTTTACCAC	0.418													40	168	---	---	---	---	PASS
EML5	161436	broad.mit.edu	37	14	89202708	89202708	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89202708C>G	uc001xxg.2	-	8	1235	c.1049G>C	c.(1048-1050)AGG>ACG	p.R350T		NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like	350	WD 7.					cytoplasm|microtubule				ovary(3)	3						ATTTGCTTACCTGACCGAACG	0.318													42	131	---	---	---	---	PASS
KIAA1409	57578	broad.mit.edu	37	14	94129061	94129061	+	Splice_Site	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94129061G>A	uc001ybv.1	+	39	6371	c.6288_splice	c.e39+1	p.K2096_splice	KIAA1409_uc001ybs.1_Splice_Site_p.K2074_splice	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578							integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		TTTCACTAAGGTAAGCAAGCT	0.423													15	34	---	---	---	---	PASS
BCL11B	64919	broad.mit.edu	37	14	99640573	99640573	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99640573C>T	uc001yga.2	-	4	2867	c.2600G>A	c.(2599-2601)AGC>AAC	p.S867N	BCL11B_uc001ygb.2_Missense_Mutation_p.S796N	NM_138576	NP_612808	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B isoform 1	867	C2H2-type 6.					nucleus	zinc ion binding			central_nervous_system(8)|large_intestine(1)|lung(1)	10		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		CTCCAGGGTGCTGTAGACGCT	0.537			T	TLX3	T-ALL								9	72	---	---	---	---	PASS
HSP90AA1	3320	broad.mit.edu	37	14	102552583	102552583	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102552583G>C	uc001yku.3	-	2	323	c.133C>G	c.(133-135)CTG>GTG	p.L45V	HSP90AA1_uc001ykv.3_Missense_Mutation_p.L167V|HSP90AA1_uc001ykw.1_5'UTR|HSP90AA1_uc001ykx.1_Missense_Mutation_p.L34V	NM_005348	NP_005339	P07900	HS90A_HUMAN	heat shock 90kDa protein 1, alpha isoform 2	45					axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction	cytosol|melanosome|plasma membrane	ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding			ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1)	7					Rifabutin(DB00615)	AGCTCTCTCAGAAAGATCTCT	0.418													29	83	---	---	---	---	PASS
MKRN3	7681	broad.mit.edu	37	15	23811293	23811293	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23811293T>A	uc001ywh.3	+	1	840	c.364T>A	c.(364-366)TCT>ACT	p.S122T	MKRN3_uc001ywi.2_Intron|MKRN3_uc010ayi.1_Missense_Mutation_p.S122T	NM_005664	NP_005655	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	122	C3H1-type 1.					ribonucleoprotein complex	ligase activity|nucleic acid binding|zinc ion binding			lung(6)|large_intestine(2)|ovary(2)	10		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		GCACGACCTTTCTGGTCGGAA	0.597													45	123	---	---	---	---	PASS
MTMR10	54893	broad.mit.edu	37	15	31234125	31234125	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31234125C>G	uc001zfh.1	-	16	1980	c.1882G>C	c.(1882-1884)GAG>CAG	p.E628Q	MTMR15_uc001zff.2_3'UTR|MTMR15_uc001zfe.2_3'UTR|MTMR10_uc010ubk.1_Missense_Mutation_p.E42Q|MTMR10_uc001zfg.1_Missense_Mutation_p.E209Q|MTMR10_uc010azx.1_Missense_Mutation_p.E380Q|MTMR10_uc001zfi.1_3'UTR	NM_017762	NP_060232	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	628	Myotubularin phosphatase.						phosphatase activity			ovary(1)	1		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		AAATACTGCTCCGTATCACTG	0.433													11	394	---	---	---	---	PASS
RAD51	5888	broad.mit.edu	37	15	41022091	41022091	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41022091A>T	uc001zmi.3	+	9	1114	c.815A>T	c.(814-816)CAA>CTA	p.Q272L	RAD51_uc010bbw.2_Intron|RAD51_uc010bbx.2_Missense_Mutation_p.Q273L|RAD51_uc001zmk.3_RNA|RAD51_uc001zml.3_Missense_Mutation_p.Q273L	NM_002875	NP_002866	Q06609	RAD51_HUMAN	RAD51 homolog protein isoform 1	272					DNA recombinase assembly|DNA unwinding involved in replication|mitotic recombination|positive regulation of DNA ligation|protein homooligomerization|reciprocal meiotic recombination	mitochondrial matrix|nucleus|perinuclear region of cytoplasm|PML body	ATP binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|protein C-terminus binding|single-stranded DNA binding|single-stranded DNA-dependent ATPase activity				0		all_cancers(109;1.19e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.45e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000421)|COAD - Colon adenocarcinoma(120;0.163)		GTGGTAGCTCAAGTGGATGGA	0.448								Homologous_recombination					56	116	---	---	---	---	PASS
CYP19A1	1588	broad.mit.edu	37	15	51514629	51514629	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51514629G>A	uc001zyz.3	-	6	796	c.545C>T	c.(544-546)TCG>TTG	p.S182L	CYP19A1_uc001zza.3_Missense_Mutation_p.S182L|CYP19A1_uc001zzb.2_Missense_Mutation_p.S182L|CYP19A1_uc001zzd.2_Missense_Mutation_p.S182L|CYP19A1_uc010bey.1_Missense_Mutation_p.S182L	NM_031226	NP_112503	P11511	CP19A_HUMAN	cytochrome P450, family 19	182					estrogen biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|membrane fraction	aromatase activity|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(3)	3				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Diethylstilbestrol(DB00255)|Exemestane(DB00990)|Letrozole(DB01006)|Testolactone(DB00894)|Testosterone(DB00624)	CACATAGCCCGATTCATTGGT	0.522													28	61	---	---	---	---	PASS
VPS13C	54832	broad.mit.edu	37	15	62204143	62204143	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62204143A>G	uc002agz.2	-	63	8685	c.8611T>C	c.(8611-8613)TTT>CTT	p.F2871L	VPS13C_uc002aha.2_Missense_Mutation_p.F2828L|VPS13C_uc002ahb.1_Missense_Mutation_p.F2871L|VPS13C_uc002ahc.1_Missense_Mutation_p.F2828L|VPS13C_uc002ahd.1_Missense_Mutation_p.F248L	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	2871					protein localization					ovary(2)	2						ATGGTACAAAAGGGAGTCAGG	0.373													3	182	---	---	---	---	PASS
PDIA2	64714	broad.mit.edu	37	16	336870	336870	+	Silent	SNP	T	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:336870T>A	uc002cgn.1	+	15	2566	c.1458T>A	c.(1456-1458)ACT>ACA	p.T486T	PDIA2_uc010bqt.1_Silent_p.T331T|PDIA2_uc002cgo.1_Silent_p.T486T	NM_006849	NP_006840	Q13087	PDIA2_HUMAN	protein disulfide isomerase A2 precursor	486	Thioredoxin 2.				apoptosis|cell redox homeostasis|glycerol ether metabolic process|protein folding|protein retention in ER lumen|response to hypoxia	endoplasmic reticulum lumen	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity|steroid binding			central_nervous_system(1)|skin(1)	2		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				ACCTGGAGACTTTCTCCAAGT	0.647													11	22	---	---	---	---	PASS
AXIN1	8312	broad.mit.edu	37	16	396564	396564	+	Silent	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:396564G>A	uc002cgp.1	-	2	639	c.462C>T	c.(460-462)GGC>GGT	p.G154G	AXIN1_uc002cgq.1_Silent_p.G154G	NM_003502	NP_003493	O15169	AXIN1_HUMAN	axin 1 isoform a	154	RGS.				activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			breast(1)|liver(1)	2		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				GGGACACGATGCCATTGTTAT	0.552											OREG0003698	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	55	141	---	---	---	---	PASS
GSPT1	2935	broad.mit.edu	37	16	11971401	11971401	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11971401C>T	uc002dbr.2	-	10	1078	c.1051G>A	c.(1051-1053)GTA>ATA	p.V351I	GSPT1_uc002dbu.2_Missense_Mutation_p.V488I|GSPT1_uc002dbt.2_Missense_Mutation_p.V489I|GSPT1_uc010bux.2_Missense_Mutation_p.V351I	NM_001130007	NP_001123479	P15170	ERF3A_HUMAN	G1 to S phase transition 1 isoform 3	351					G1/S transition of mitotic cell cycle|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|protein methylation	intracellular	GTP binding|GTPase activity|protein binding|translation release factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						TCAGTCTCTACATCATCGGAA	0.393													16	51	---	---	---	---	PASS
MYH11	4629	broad.mit.edu	37	16	15797782	15797782	+	3'UTR	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15797782G>T	uc002ddy.2	-	41					MYH11_uc002ddv.2_3'UTR|MYH11_uc002ddw.2_3'UTR|MYH11_uc002ddx.2_3'UTR|MYH11_uc010bvg.2_3'UTR|NDE1_uc010uzy.1_Intron|NDE1_uc002dds.2_Intron	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15						TTGTTGTTGGGTTTTTTTTGT	0.403			T	CBFB	AML								23	152	---	---	---	---	PASS
OGFOD1	55239	broad.mit.edu	37	16	56485531	56485531	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56485531G>C	uc002ejb.2	+	1	108	c.7G>C	c.(7-9)GGG>CGG	p.G3R	OGFOD1_uc002ejc.2_Intron|NUDT21_uc002eja.2_5'Flank	NM_018233	NP_060703	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase	3							iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			skin(1)	1					Vitamin C(DB00126)	AGAGATGAATGGGAAGCGGCC	0.572													51	169	---	---	---	---	PASS
DUS2L	54920	broad.mit.edu	37	16	68071947	68071947	+	Silent	SNP	T	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68071947T>A	uc002evi.2	+	3	170	c.21T>A	c.(19-21)TCT>TCA	p.S7S	DUS2L_uc002evj.2_Silent_p.S7S|DUS2L_uc010vkk.1_Silent_p.S7S|DUS2L_uc010cez.2_5'UTR	NM_017803	NP_060273	Q9NX74	DUS2L_HUMAN	dihydrouridine synthase 2-like, SMM1 homolog	7					tRNA processing	endoplasmic reticulum	double-stranded RNA binding|flavin adenine dinucleotide binding|tRNA dihydrouridine synthase activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0131)|Epithelial(162;0.0564)		ATAGCCTCTCTCTGTGTTACC	0.423													65	174	---	---	---	---	PASS
RPH3AL	9501	broad.mit.edu	37	17	169255	169255	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:169255C>T	uc002frd.1	-	3	351	c.307G>A	c.(307-309)GGC>AGC	p.G103S	RPH3AL_uc010vpy.1_Missense_Mutation_p.G103S|RPH3AL_uc002fre.1_Missense_Mutation_p.G103S|RPH3AL_uc002frf.1_Missense_Mutation_p.G103S|RPH3AL_uc010cjl.1_Missense_Mutation_p.G103S	NM_006987	NP_008918	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)	103	RabBD.|FYVE-type.				exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		CCCAGGAAGCCCAGCACCTCC	0.642													16	37	---	---	---	---	PASS
ABR	29	broad.mit.edu	37	17	915255	915255	+	Intron	SNP	G	C	C	rs113364180		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:915255G>C	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc010vqf.1_Intron|ABR_uc010vqg.1_Intron|ABR_uc002fsg.2_Intron|ABR_uc002fsh.1_Intron|ABR_uc002fsf.2_Missense_Mutation_p.C181W	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		TGGGTGGAGGGCAGCCCCCAC	0.662													8	50	---	---	---	---	PASS
SCARF1	8578	broad.mit.edu	37	17	1540015	1540015	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1540015G>A	uc002fsz.1	-	10	1671	c.1621C>T	c.(1621-1623)CCA>TCA	p.P541S	SCARF1_uc002fsy.1_Silent_p.C528C|SCARF1_uc002fta.1_RNA|SCARF1_uc010cjv.1_Missense_Mutation_p.P455S	NM_003693	NP_003684	Q14162	SREC_HUMAN	scavenger receptor class F, member 1 isoform 1	541	Pro/Ser-rich.|Cytoplasmic (Potential).				cell adhesion|neuron remodeling|positive regulation of axon regeneration|receptor-mediated endocytosis	integral to membrane	low-density lipoprotein particle binding|scavenger receptor activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TCTTGGGGTGGCACACAGTAG	0.577													5	135	---	---	---	---	PASS
CAMTA2	23125	broad.mit.edu	37	17	4872277	4872277	+	Splice_Site	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4872277C>T	uc002gah.1	-	22	3579	c.3471_splice	c.e22-1	p.K1157_splice	SPAG7_uc002gad.2_5'Flank|SPAG7_uc002gae.2_5'Flank|SPAG7_uc002gaf.2_5'Flank|CAMTA2_uc010cku.1_Intron|CAMTA2_uc002gag.1_Splice_Site_p.K1156_splice|CAMTA2_uc002gai.1_Splice_Site_p.K1152_splice	NM_015099	NP_055914	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2						cardiac muscle hypertrophy in response to stress|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	calmodulin binding|chromatin binding|histone deacetylase binding|transcription factor binding			ovary(1)	1						AAAGGAGCCTCTGGTGAAAGA	0.577													32	70	---	---	---	---	PASS
PMP22	5376	broad.mit.edu	37	17	15142905	15142905	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15142905T>C	uc002goj.2	-	3	251	c.202A>G	c.(202-204)ACC>GCC	p.T68A	PMP22_uc002gok.2_Missense_Mutation_p.T68A|PMP22_uc002gol.2_Missense_Mutation_p.T68A	NM_153322	NP_696997	Q01453	PMP22_HUMAN	peripheral myelin protein 22	68	Helical; (By similarity).				peripheral nervous system development|synaptic transmission	integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0884)|BRCA - Breast invasive adenocarcinoma(8;4.92e-06)		AGGATCATGGTGGCCTGGACA	0.562													31	56	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	18333107	18333107	+	RNA	SNP	G	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18333107G>C	uc010vxz.1	+	4		c.929G>C								Homo sapiens cDNA FLJ61294 complete cds, highly similar to Keratin, type I cytoskeletal 17.																		AGCAGTATGAGAAGATGGCAG	0.622													20	52	---	---	---	---	PASS
TANC2	26115	broad.mit.edu	37	17	61498351	61498351	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61498351G>A	uc002jal.3	+	25	5031	c.5008G>A	c.(5008-5010)GAT>AAT	p.D1670N	TANC2_uc010wpe.1_3'UTR|TANC2_uc002jao.3_Missense_Mutation_p.D781N	NM_025185	NP_079461	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and	1670							binding			ovary(2)	2						AATCGTAGGGGATGGAAGGCC	0.542													44	129	---	---	---	---	PASS
GNA13	10672	broad.mit.edu	37	17	63010386	63010386	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63010386T>G	uc002jfc.2	-	4	1332	c.1123A>C	c.(1123-1125)ATG>CTG	p.M375L	GNA13_uc010wqh.1_Missense_Mutation_p.M280L	NM_006572	NP_006563	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein),	375					activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase D activity|cellular component movement|platelet activation|Rho protein signal transduction	brush border membrane|heterotrimeric G-protein complex|melanosome	D5 dopamine receptor binding|G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|signal transducer activity|type 1 angiotensin receptor binding				0						CACTGTAGCATAAGCTGCTTG	0.373													24	69	---	---	---	---	PASS
RECQL5	9400	broad.mit.edu	37	17	73657711	73657711	+	Silent	SNP	A	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73657711A>T	uc010dgl.2	-	5	1005	c.849T>A	c.(847-849)GGT>GGA	p.G283G	RECQL5_uc010dgk.2_Silent_p.G256G|RECQL5_uc002jpb.1_Silent_p.G283G|RECQL5_uc002joz.3_Silent_p.G283G|RECQL5_uc002jpa.3_Silent_p.G283G	NM_004259	NP_004250	O94762	RECQ5_HUMAN	RecQ protein-like 5 isoform 1	283	Helicase C-terminal.				DNA recombination|DNA repair	cytoplasm|nuclear membrane|nucleolus|nucleoplasm	ATP binding|ATP-dependent helicase activity|DNA helicase activity|nucleic acid binding			kidney(3)	3	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			TGGCGTTCACACCCCTGCAGC	0.537								Other_identified_genes_with_known_or_suspected_DNA_repair_function					47	134	---	---	---	---	PASS
AZI1	22994	broad.mit.edu	37	17	79169644	79169644	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79169644C>A	uc002jzp.1	-	16	2216	c.2016G>T	c.(2014-2016)CAG>CAT	p.Q672H	AZI1_uc002jzm.1_Missense_Mutation_p.Q99H|AZI1_uc002jzn.1_Missense_Mutation_p.Q669H|AZI1_uc002jzo.1_Missense_Mutation_p.Q669H|AZI1_uc010wum.1_Missense_Mutation_p.Q672H|AZI1_uc002jzq.2_5'Flank	NM_014984	NP_055799	Q9UPN4	AZI1_HUMAN	5-azacytidine induced 1 isoform a	672					cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centrosome|cytosol|intracellular membrane-bounded organelle				central_nervous_system(2)|large_intestine(1)|ovary(1)	4	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCAGCTCGTGCTGCGCCTGTG	0.647													12	117	---	---	---	---	PASS
EMILIN2	84034	broad.mit.edu	37	18	2890714	2890714	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2890714A>G	uc002kln.2	+	4	748	c.589A>G	c.(589-591)ACG>GCG	p.T197A		NM_032048	NP_114437	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2 precursor	197	Potential.				cell adhesion	collagen	extracellular matrix constituent conferring elasticity|protein binding			skin(2)|ovary(1)	3				READ - Rectum adenocarcinoma(2;0.1)		ACTCACAAGGACGGTTCTTGA	0.522													33	126	---	---	---	---	PASS
LAMA1	284217	broad.mit.edu	37	18	6941968	6941968	+	3'UTR	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6941968C>T	uc002knm.2	-	63					LAMA1_uc002knk.2_3'UTR|LAMA1_uc002knl.2_3'UTR|LAMA1_uc010wzj.1_3'UTR	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor						axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TCCCCAGAAACACTTAACCTG	0.353													19	66	---	---	---	---	PASS
NOL4	8715	broad.mit.edu	37	18	31432719	31432719	+	3'UTR	SNP	A	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31432719A>C	uc010dmi.2	-	11					NOL4_uc010xbs.1_3'UTR|NOL4_uc002kxr.3_3'UTR|NOL4_uc010xbt.1_3'UTR|NOL4_uc010dmh.2_3'UTR|NOL4_uc010xbu.1_3'UTR|NOL4_uc002kxt.3_3'UTR	NM_003787	NP_003778	O94818	NOL4_HUMAN	nucleolar protein 4							nucleolus	RNA binding			ovary(3)	3						CTGTGCAGTAAGACCAGAAGT	0.398													3	24	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	8994508	8994508	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8994508A>G	uc002mkp.2	-	64	41588	c.41384T>C	c.(41383-41385)CTC>CCC	p.L13795P	MUC16_uc010dwi.2_RNA|MUC16_uc010dwj.2_Missense_Mutation_p.L612P|MUC16_uc010xki.1_RNA	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	13797	Extracellular (Potential).|SEA 12.|ANK 1.			Missing (in Ref. 3; AAK74120).	cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GGTGAAGTTGAGGGTGAATAG	0.463													3	150	---	---	---	---	PASS
ATP13A1	57130	broad.mit.edu	37	19	19767887	19767887	+	Silent	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19767887C>A	uc002nnh.3	-	5	850	c.822G>T	c.(820-822)GTG>GTT	p.V274V	ATP13A1_uc002nnf.3_5'Flank|ATP13A1_uc002nng.2_Silent_p.V156V	NM_020410	NP_065143	Q9HD20	AT131_HUMAN	ATPase type 13A1	274	Extracellular (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(3)|large_intestine(2)|central_nervous_system(1)	6						CCTCGAACGCCACCAGCATGG	0.587													4	8	---	---	---	---	PASS
CEBPG	1054	broad.mit.edu	37	19	33870405	33870405	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33870405C>T	uc002nup.2	+	2	549	c.260C>T	c.(259-261)GCA>GTA	p.A87V		NM_001806	NP_001797	P53567	CEBPG_HUMAN	CCAAT/enhancer binding protein gamma	87					B cell differentiation|enucleate erythrocyte differentiation|liver development|natural killer cell mediated cytotoxicity|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of DNA binding|positive regulation of DNA repair|positive regulation of interferon-gamma biosynthetic process|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding				0	Esophageal squamous(110;0.137)					AAGCAGAAAGCACAAGACACA	0.448													11	40	---	---	---	---	PASS
ZNF30	90075	broad.mit.edu	37	19	35434752	35434752	+	Silent	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35434752G>T	uc010edp.1	+	5	1260	c.882G>T	c.(880-882)GGG>GGT	p.G294G	ZNF30_uc002nxf.2_Silent_p.G213G|ZNF30_uc010edq.1_Silent_p.G295G|ZNF30_uc010edr.1_Silent_p.G295G	NM_194325	NP_919306	P17039	ZNF30_HUMAN	zinc finger protein 30 isoform b	294	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		AAGAATGTGGGAAGGCCTTTA	0.463													4	131	---	---	---	---	PASS
GRAMD1A	57655	broad.mit.edu	37	19	35501012	35501012	+	Silent	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35501012G>T	uc010xse.1	+	5	479	c.342G>T	c.(340-342)CTG>CTT	p.L114L	GRAMD1A_uc002nxi.1_Silent_p.L201L|GRAMD1A_uc002nxk.2_Silent_p.L107L|GRAMD1A_uc002nxl.2_5'UTR|GRAMD1A_uc010xsf.1_Silent_p.L119L	NM_020895	NP_065946	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A isoform 1	114	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)			CCTGCGCCCTGCAGCGTGAGA	0.652													56	152	---	---	---	---	PASS
NPHS1	4868	broad.mit.edu	37	19	36340513	36340513	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36340513A>C	uc002oby.2	-	6	651	c.651T>G	c.(649-651)TGT>TGG	p.C217W		NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	217	Ig-like C2-type 2.|Extracellular (Potential).				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)|skin(1)	5	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TAGACGCCTCACAGACCAGCA	0.542													41	104	---	---	---	---	PASS
HNRNPL	3191	broad.mit.edu	37	19	39327271	39327271	+	3'UTR	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39327271C>A	uc010xul.1	-	13					HNRNPL_uc010ege.1_Intron|HNRNPL_uc002ojj.1_Intron|HNRNPL_uc002ojo.1_3'UTR|HNRNPL_uc002ojk.2_3'UTR|HNRNPL_uc002ojl.2_3'UTR|HNRNPL_uc010xum.1_3'UTR	NM_001533	NP_001524	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L						nuclear mRNA splicing, via spliceosome	cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding|transcription regulatory region DNA binding				0	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			aaaaGGAATACAAGATCTTTT	0.363													11	72	---	---	---	---	PASS
LIPE	3991	broad.mit.edu	37	19	42930516	42930516	+	Silent	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42930516G>A	uc002otr.2	-	1	1063	c.786C>T	c.(784-786)TTC>TTT	p.F262F	uc010eif.1_Intron|uc002ott.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron|LIPE_uc002ots.1_5'Flank	NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase	262					cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)				ATTTTCCTTTGAAGCCTAGCT	0.488													19	233	---	---	---	---	PASS
SULT2A1	6822	broad.mit.edu	37	19	48385434	48385434	+	Silent	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48385434A>G	uc002phr.2	-	3	519	c.379T>C	c.(379-381)TTG>CTG	p.L127L		NM_003167	NP_003158	Q06520	ST2A1_HUMAN	bile-salt sulfotransferase 2A1	127	PAPS.				3'-phosphoadenosine 5'-phosphosulfate metabolic process|bile acid catabolic process|cellular lipid metabolic process|digestion|sulfation|xenobiotic metabolic process	cytosol	bile-salt sulfotransferase activity			ovary(1)|pancreas(1)	2		all_cancers(25;3.02e-09)|all_lung(116;6.48e-07)|all_epithelial(76;7.35e-07)|Lung NSC(112;1.56e-06)|all_neural(266;0.0146)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000254)|all cancers(93;0.000545)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.0552)		CCAGACACCAAAACATCTCTG	0.338													57	161	---	---	---	---	PASS
MED25	81857	broad.mit.edu	37	19	50322611	50322611	+	Intron	SNP	T	G	G	rs1640512	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50322611T>G	uc002ppw.1	+						MED25_uc010ybe.1_Intron|MED25_uc010enl.1_3'UTR	NM_030973	NP_112235	Q71SY5	MED25_HUMAN	mediator complex subunit 25						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm				ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		CGTGAATGAGTGATGGCTTGG	0.572													3	33	---	---	---	---	PASS
MYH14	79784	broad.mit.edu	37	19	50753042	50753042	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50753042C>G	uc002prr.1	+	13	1641	c.1594C>G	c.(1594-1596)CTC>GTC	p.L532V	MYH14_uc010enu.1_Missense_Mutation_p.L540V|MYH14_uc002prq.1_Missense_Mutation_p.L540V	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2	532	Myosin head-like.				axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		CGACTTTGGCCTCGACCTGCA	0.547													46	141	---	---	---	---	PASS
NLRP4	147945	broad.mit.edu	37	19	56369055	56369055	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56369055A>G	uc002qmd.3	+	3	718	c.296A>G	c.(295-297)TAT>TGT	p.Y99C	NLRP4_uc002qmf.2_Missense_Mutation_p.Y24C|NLRP4_uc010etf.2_5'UTR	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	99				Y -> H (in Ref. 4; AAL88672).			ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		ACAAAGACCTATCAAGCTCAC	0.423													23	78	---	---	---	---	PASS
MCM8	84515	broad.mit.edu	37	20	5948539	5948539	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5948539A>G	uc002wmi.2	+	10	1468	c.1091A>G	c.(1090-1092)AAT>AGT	p.N364S	MCM8_uc002wmj.2_Missense_Mutation_p.N348S|MCM8_uc002wmk.2_Missense_Mutation_p.N364S|MCM8_uc002wml.2_Missense_Mutation_p.N364S|MCM8_uc010gbp.2_Missense_Mutation_p.N364S|MCM8_uc002wmm.2_5'Flank	NM_032485	NP_115874	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	364					cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1						TCTATTAGTAATAGCAAAGGA	0.328													7	218	---	---	---	---	PASS
RIMS4	140730	broad.mit.edu	37	20	43386410	43386410	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43386410C>T	uc002xms.2	-	4	352	c.352G>A	c.(352-354)GAT>AAT	p.D118N	RIMS4_uc010ggu.2_Missense_Mutation_p.D119N	NM_182970	NP_892015	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4	118	C2.				exocytosis|neurotransmitter transport	cell junction|synapse				ovary(4)|central_nervous_system(1)	5		Myeloproliferative disorder(115;0.0122)				ATCTCCACATCCCCTGGAAGA	0.567													44	106	---	---	---	---	PASS
TMPRSS15	5651	broad.mit.edu	37	21	19698767	19698767	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19698767A>T	uc002ykw.2	-	16	1934	c.1903T>A	c.(1903-1905)TAT>AAT	p.Y635N		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	635	Extracellular (Potential).				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8						CCCAAGTGATAGCCAGTAGTA	0.418													107	247	---	---	---	---	PASS
CCT8	10694	broad.mit.edu	37	21	30442596	30442596	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30442596T>A	uc002ynb.2	-	2	222	c.123A>T	c.(121-123)CAA>CAT	p.Q41H	CCT8_uc011acp.1_Missense_Mutation_p.Q22H|CCT8_uc002yna.2_5'UTR|CCT8_uc002ync.2_Missense_Mutation_p.Q41H|CCT8_uc010glm.2_Missense_Mutation_p.Q41H|CCT8_uc011acq.1_5'UTR	NM_006585	NP_006576	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	41					'de novo' posttranslational protein folding	aggresome|cytosol|intermediate filament cytoskeleton|microtubule organizing center	ATP binding|ATPase activity, coupled|unfolded protein binding				0						TACGAGTGGTTTGGGCAAGCT	0.348													36	86	---	---	---	---	PASS
KRTAP19-6	337973	broad.mit.edu	37	21	31913932	31913932	+	3'UTR	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31913932A>G	uc002yok.1	-	1						NM_181612	NP_853643	Q3LI70	KR196_HUMAN	keratin associated protein 19-6							intermediate filament					0						GCTGAAGCATACGGGCAAGAT	0.428													5	218	---	---	---	---	PASS
CCDC116	164592	broad.mit.edu	37	22	21989453	21989453	+	Silent	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21989453C>T	uc002zve.2	+	4	1194	c.1101C>T	c.(1099-1101)CGC>CGT	p.R367R	CCDC116_uc011aih.1_Silent_p.R367R	NM_152612	NP_689825	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	367										ovary(1)|skin(1)	2	Colorectal(54;0.105)					CTTCCCCCCGCCCCACAGTCT	0.612													22	57	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22661478	22661478	+	RNA	SNP	T	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22661478T>G	uc011aim.1	+	28		c.1702T>G			LOC96610_uc011aiq.1_RNA|LOC96610_uc011aip.1_RNA|LOC96610_uc010gto.2_RNA					Parts of antibodies, mostly variable regions.												0						CAGATGCGTCTGAAGAAACAT	0.488													3	129	---	---	---	---	PASS
CHCHD10	400916	broad.mit.edu	37	22	24108075	24108075	+	3'UTR	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24108075G>T	uc002zxw.2	-	4						NM_213720	NP_998885	Q8WYQ3	CHC10_HUMAN	coiled-coil-helix-coiled-coil-helix domain							mitochondrion					0						TATCTGTGGGGTGAGAAACCT	0.532													10	22	---	---	---	---	PASS
DERL3	91319	broad.mit.edu	37	22	24176989	24176989	+	3'UTR	SNP	C	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24176989C>G	uc002zyh.2	-	7					DERL3_uc002zyk.3_3'UTR|DERL3_uc002zyi.2_3'UTR|DERL3_uc002zyj.2_3'UTR	NM_001002862	NP_001002862	Q96Q80	DERL3_HUMAN	derlin 3 isoform 2						endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process	integral to endoplasmic reticulum membrane	protein binding			ovary(1)	1						AGGAACAGCCCTAACCCTGCT	0.622													20	46	---	---	---	---	PASS
BAIAP2L2	80115	broad.mit.edu	37	22	38506582	38506582	+	5'UTR	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38506582G>T	uc003auw.2	-	1						NM_025045	NP_079321	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2						filopodium assembly|signal transduction		cytoskeletal adaptor activity|SH3 domain binding			pancreas(1)	1	Melanoma(58;0.045)					GGTGGCGATGGCACAGCCGGG	0.647													11	20	---	---	---	---	PASS
SBF1	6305	broad.mit.edu	37	22	50903133	50903133	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50903133A>G	uc003blh.2	-	14	1661	c.1466T>C	c.(1465-1467)GTA>GCA	p.V489A	SBF1_uc011arx.1_Missense_Mutation_p.V153A|SBF1_uc003bli.2_Missense_Mutation_p.V490A	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1	489					protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		GGGCCTCTGTACCTTGTGCAT	0.701													36	93	---	---	---	---	PASS
BEND2	139105	broad.mit.edu	37	X	18221887	18221887	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18221887G>T	uc004cyj.3	-	5	795	c.641C>A	c.(640-642)TCA>TAA	p.S214*	BEND2_uc010nfb.2_Nonsense_Mutation_p.S214*	NM_153346	NP_699177	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2	214										ovary(3)|kidney(1)|central_nervous_system(1)	5						TAATGAACTTGAGGAGACAAT	0.473													5	296	---	---	---	---	PASS
CDKL5	6792	broad.mit.edu	37	X	18622812	18622812	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18622812G>A	uc004cym.2	+	12	2021	c.1768G>A	c.(1768-1770)GAA>AAA	p.E590K	CDKL5_uc004cyn.2_Missense_Mutation_p.E590K	NM_003159	NP_003150	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	590					neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)					TGCACCTCACGAATCTTTTTC	0.498													83	336	---	---	---	---	PASS
TFE3	7030	broad.mit.edu	37	X	48900725	48900725	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48900725C>A	uc004dmb.3	-	1	266	c.28G>T	c.(28-30)GAT>TAT	p.D10Y	TFE3_uc004dmc.3_5'UTR|TFE3_uc004dme.1_RNA	NM_006521	NP_006512	P19532	TFE3_HUMAN	transcription factor E3	10					humoral immune response|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding		ASPSCR1/TFE3(161)|PRCC/TFE3(25)|SFPQ/TFE3(6)|NONO/TFE3(2)|CLTC/TFE3(2)	soft_tissue(120)|kidney(76)|central_nervous_system(1)	197						TCTACGCCATCCCGAGCTGGT	0.721			T	SFPQ|ASPSCR1|PRCC|NONO|CLTC	papillary renal|alveolar soft part sarcoma|renal								3	9	---	---	---	---	PASS
MAGEE1	57692	broad.mit.edu	37	X	75650469	75650469	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75650469G>T	uc004ecm.1	+	1	2353	c.2146G>T	c.(2146-2148)GAA>TAA	p.E716*		NM_020932	NP_065983	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	716						dendrite|nucleus|perinuclear region of cytoplasm|postsynaptic membrane				breast(3)|ovary(1)|pancreas(1)|skin(1)	6						CTTTTTTGAGGAAGCTGCTGC	0.512													25	39	---	---	---	---	PASS
PCDH11X	27328	broad.mit.edu	37	X	91873325	91873325	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91873325C>A	uc004efk.1	+	7	4275	c.3430C>A	c.(3430-3432)CTC>ATC	p.L1144I	PCDH11X_uc004efl.1_Missense_Mutation_p.L1134I|PCDH11X_uc004efo.1_Missense_Mutation_p.L1107I|PCDH11X_uc010nmv.1_3'UTR|PCDH11X_uc004efm.1_Missense_Mutation_p.L1136I|PCDH11X_uc004efn.1_Missense_Mutation_p.L1126I	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	1144	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						TCAAGAATGTCTCATCTATGG	0.468													11	30	---	---	---	---	PASS
ARMCX6	54470	broad.mit.edu	37	X	100871360	100871360	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100871360G>T	uc004ehx.2	-	3	596	c.251C>A	c.(250-252)ACT>AAT	p.T84N	ARMCX6_uc004ehy.2_Missense_Mutation_p.T84N	NM_019007	NP_061880	Q7L4S7	ARMX6_HUMAN	armadillo repeat containing, X-linked 6	84						integral to membrane					0						CCTGTCCTCAGTGCCACCTGG	0.488													68	176	---	---	---	---	PASS
ARMCX5	64860	broad.mit.edu	37	X	101857826	101857826	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101857826A>T	uc004ejg.2	+	6	1638	c.757A>T	c.(757-759)ACC>TCC	p.T253S	ARMCX5_uc004ejh.2_Missense_Mutation_p.T253S	NM_022838	NP_073749	Q6P1M9	ARMX5_HUMAN	armadillo repeat containing, X-linked 5	253							binding			ovary(1)	1						CCTGGTTGAGACCTTGATTGA	0.468													72	215	---	---	---	---	PASS
ALG13	79868	broad.mit.edu	37	X	110964871	110964871	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110964871T>A	uc011msy.1	+	12	1401	c.1367T>A	c.(1366-1368)GTG>GAG	p.V456E	ALG13_uc011msx.1_Missense_Mutation_p.V352E|ALG13_uc011msz.1_Missense_Mutation_p.V378E|ALG13_uc011mta.1_Missense_Mutation_p.V352E|ALG13_uc011mtb.1_Missense_Mutation_p.V352E			Q9NP73	ALG13_HUMAN	SubName: Full=Asparagine-linked glycosylation 13 homolog (S. cerevisiae);	456					dolichol-linked oligosaccharide biosynthetic process|lipid glycosylation|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane	carbohydrate binding|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity			lung(1)	1						CCCTATAAGGTGCTCAAAGCC	0.368													11	35	---	---	---	---	PASS
HTR2C	3358	broad.mit.edu	37	X	113965887	113965887	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113965887G>C	uc004epu.1	+	4	948	c.220G>C	c.(220-222)GTG>CTG	p.V74L	HTR2C_uc010nqc.1_Missense_Mutation_p.V74L|HTR2C_uc004epv.1_Missense_Mutation_p.V74L	NM_000868	NP_000859	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C	74	Helical; Name=1; (By similarity).				cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)	CAACATCCTTGTGATCATGGC	0.443													79	198	---	---	---	---	PASS
LONRF3	79836	broad.mit.edu	37	X	118108850	118108850	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118108850G>T	uc004eqw.2	+	1	138	c.107G>T	c.(106-108)GGC>GTC	p.G36V	LONRF3_uc004eqx.2_Missense_Mutation_p.G36V|LONRF3_uc004eqy.2_RNA|LONRF3_uc004eqz.2_5'Flank	NM_001031855	NP_001027026	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger	36					proteolysis		ATP-dependent peptidase activity|protein binding|zinc ion binding			breast(1)|central_nervous_system(1)	2						GTAGACATGGGCCCCCACCCA	0.647													14	12	---	---	---	---	PASS
GRIA3	2892	broad.mit.edu	37	X	122318320	122318320	+	5'UTR	SNP	T	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122318320T>C	uc004etq.3	+	1					GRIA3_uc004etr.3_5'UTR|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_5'Flank|GRIA3_uc010nqs.1_5'UTR	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform						glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)	TTCTTTTTCTTTTTCTATTAT	0.512													30	69	---	---	---	---	PASS
SLC25A14	9016	broad.mit.edu	37	X	129499386	129499386	+	Intron	SNP	C	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129499386C>T	uc004evn.1	+						SLC25A14_uc011mut.1_3'UTR|SLC25A14_uc011muu.1_3'UTR|SLC25A14_uc010nrg.2_3'UTR|SLC25A14_uc004evo.1_Intron|SLC25A14_uc004evp.1_Intron|SLC25A14_uc004evq.1_Intron|SLC25A14_uc004evr.1_Intron	NM_003951	NP_003942	O95258	UCP5_HUMAN	solute carrier family 25, member 14 isoform						aerobic respiration|mitochondrial transport	integral to plasma membrane|mitochondrial inner membrane	binding			ovary(1)	1						TAGATTGTAACGAAAGGCCAA	0.388													3	16	---	---	---	---	PASS
TFDP3	51270	broad.mit.edu	37	X	132351883	132351883	+	Silent	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132351883G>A	uc004exb.1	-	1	494	c.405C>T	c.(403-405)GGC>GGT	p.G135G		NM_016521	NP_057605	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	135	Potential.					transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					CGACCAGCTCGCCCACCACTT	0.552													41	93	---	---	---	---	PASS
GABRE	2564	broad.mit.edu	37	X	151123262	151123262	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151123262A>T	uc004ffi.2	-	9	1486	c.1432T>A	c.(1432-1434)TAC>AAC	p.Y478N	GABRE_uc011myd.1_RNA	NM_004961	NP_004952	P78334	GBRE_HUMAN	gamma-aminobutyric acid (GABA) A receptor,	478	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)					TCCAGGCGGTAGACATGGATG	0.517													17	58	---	---	---	---	PASS
IRAK1	3654	broad.mit.edu	37	X	153278674	153278674	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153278674G>T	uc004fjs.1	-	12	1829	c.1750C>A	c.(1750-1752)CAG>AAG	p.Q584K	IRAK1_uc004fjr.1_Missense_Mutation_p.Q554K|IRAK1_uc004fjt.1_Missense_Mutation_p.Q505K|IRAK1_uc010nur.2_Intron	NM_001569	NP_001560	P51617	IRAK1_HUMAN	interleukin-1 receptor-associated kinase 1	584					activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|lipopolysaccharide-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|protein autophosphorylation|protein oligomerization|regulation of cytokine-mediated signaling pathway|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|transmembrane receptor protein serine/threonine kinase signaling pathway	cytosol|endosome membrane|interleukin-1 receptor complex	ATP binding|NF-kappaB-inducing kinase activity|protein binding|protein heterodimerization activity|protein homodimerization activity|ubiquitin-protein ligase activity			lung(5)|ovary(2)|breast(1)|central_nervous_system(1)	9	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCCACGGGCTGGTTGGGGCCT	0.682													14	37	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	3327	3327	+	5'Flank	SNP	A	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:3327A>G	uc004coq.3	-						uc004cos.3_RNA|uc011mfh.1_5'Flank					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		GCCAACCTCCTACTCCTCATT	0.269													16	1	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	3915	3915	+	RNA	SNP	G	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:3915G>A	uc004cos.3	+	2		c.2208G>A			uc011mfh.1_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP47.																		CTTGCCGAAGGGGAGTCCGAA	0.483													10	4	---	---	---	---	PASS
MTOR	2475	broad.mit.edu	37	1	11175117	11175117	+	Intron	DEL	A	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11175117delA	uc001asd.2	-						MTOR_uc001asc.2_Intron	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated						cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						AAGACAACTTaaaaaaaaaaa	0.333													4	2	---	---	---	---	
MYOM3	127294	broad.mit.edu	37	1	24439878	24439881	+	5'Flank	DEL	TCCT	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24439878_24439881delTCCT	uc001bin.3	-						MYOM3_uc001bio.2_5'Flank	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3											skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		cctccccccctccttccttccttc	0.000													6	4	---	---	---	---	
IL28RA	163702	broad.mit.edu	37	1	24515726	24515730	+	5'Flank	DEL	TTTTC	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24515726_24515730delTTTTC	uc001bis.2	-						IL28RA_uc001bir.2_5'Flank|IL28RA_uc001bit.2_5'Flank|IL28RA_uc001biu.2_5'Flank|IL28RA_uc001biv.2_5'Flank	NM_170743	NP_734464	Q8IU57	I28RA_HUMAN	interleukin 28 receptor, alpha isoform 1						cytokine-mediated signaling pathway|negative regulation of cell proliferation|regulation of defense response to virus by host	interleukin-28 receptor complex	protein binding|receptor activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00117)|all_lung(284;0.00151)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.21e-24)|Colorectal(126;6.61e-08)|COAD - Colon adenocarcinoma(152;3.56e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00918)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.185)		cttccttcttttttctctctctttc	0.000													4	2	---	---	---	---	
TRIT1	54802	broad.mit.edu	37	1	40312703	40312703	+	Intron	DEL	T	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40312703delT	uc010oiz.1	-						TRIT1_uc001cec.3_Intron|TRIT1_uc001ced.3_Intron|TRIT1_uc001cee.3_Intron|TRIT1_uc001cef.3_Intron|TRIT1_uc001ceg.3_Intron|TRIT1_uc001ceh.3_Intron|TRIT1_uc009vvv.2_Intron|TRIT1_uc001cei.3_Intron|TRIT1_uc001ceq.2_Intron|TRIT1_uc001cek.2_Intron|TRIT1_uc009vvx.2_Intron|TRIT1_uc001cel.2_Intron|TRIT1_uc001cem.2_Intron|TRIT1_uc001cen.2_Intron|TRIT1_uc001ceo.2_Intron|TRIT1_uc001cep.2_Intron	NM_017646	NP_060116	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1 precursor						tRNA processing	mitochondrion	ATP binding|metal ion binding|tRNA dimethylallyltransferase activity			ovary(1)	1	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			ATGCAAATAATTTTTTTTTTT	0.388													5	3	---	---	---	---	
CCT3	7203	broad.mit.edu	37	1	156294585	156294586	+	Intron	INS	-	T	T	rs148501476	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156294585_156294586insT	uc001fol.1	-						CCT3_uc001fom.1_Intron|CCT3_uc001fon.1_Intron|CCT3_uc010phj.1_Intron|CCT3_uc010phk.1_Intron|CCT3_uc010phl.1_Intron	NM_005998	NP_005989	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 isoform a						'de novo' posttranslational protein folding	cytoskeleton|cytosol|plasma membrane	ATP binding|unfolded protein binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)					tgcccaactaattttttgtatt	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	161716342	161716343	+	IGR	INS	-	C	C			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161716342_161716343insC								FCRLB (18410 upstream) : DUSP12 (3238 downstream)																							cttccttccgtcttccttccat	0.035													5	3	---	---	---	---	
DARS2	55157	broad.mit.edu	37	1	173798342	173798343	+	Intron	INS	-	GT	GT	rs140033629	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173798342_173798343insGT	uc001gjh.1	+							NM_018122	NP_060592	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial						tRNA aminoacylation for protein translation	mitochondrial matrix|nucleus	aspartate-tRNA ligase activity|ATP binding|nucleic acid binding			central_nervous_system(2)	2					L-Aspartic Acid(DB00128)	ATATACATTCAgtgtgtgtgtg	0.347													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	212092219	212092219	+	IGR	DEL	A	-	-	rs67437821		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212092219delA								LPGAT1 (88105 upstream) : INTS7 (22479 downstream)																							agaaagaaagaaaagaaagaa	0.040													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228090032	228090033	+	IGR	DEL	GT	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228090032_228090033delGT								PRSS38 (55863 upstream) : WNT9A (19132 downstream)																							Ctgtctgtgagtgtgtgtgtgt	0.208													3	4	---	---	---	---	
PCNXL2	80003	broad.mit.edu	37	1	233135199	233135200	+	Intron	DEL	TT	-	-	rs137857886		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233135199_233135200delTT	uc001hvl.2	-						PCNXL2_uc001hvk.1_Intron|PCNXL2_uc001hvm.1_Intron	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				tttctttttctttttttttttt	0.218													5	3	---	---	---	---	
HS1BP3	64342	broad.mit.edu	37	2	20846171	20846171	+	Intron	DEL	C	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20846171delC	uc002rdw.1	-						HS1BP3_uc002rdx.2_Intron|HS1BP3_uc002rdy.2_Intron	NM_022460	NP_071905	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3						cell communication		phosphatidylinositol binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGAATTATACCCCAATCCAT	0.597													4	2	---	---	---	---	
SLC30A6	55676	broad.mit.edu	37	2	32429880	32429881	+	Intron	INS	-	T	T	rs71407425		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32429880_32429881insT	uc002roe.1	+						SLC30A6_uc002rof.1_Intron|SLC30A6_uc010ymw.1_Intron|SLC30A6_uc010ezr.1_Intron|SLC30A6_uc002rog.1_Intron|SLC30A6_uc010ezs.1_Intron|SLC30A6_uc002roh.1_Intron	NM_017964	NP_060434	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter),							Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					tttaattttaattttttttttt	0.124													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64893259	64893259	+	IGR	DEL	A	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64893259delA								SERTAD2 (12213 upstream) : SLC1A4 (322320 downstream)																							AACTTAAAATAAAAAAAAAAA	0.269													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105294791	105294792	+	IGR	DEL	CA	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105294791_105294792delCA								LOC150568 (165577 upstream) : POU3F3 (177177 downstream)																							GCCACACACGCACACACACACA	0.535													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	122067665	122067666	+	IGR	DEL	GT	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122067665_122067666delGT								TFCP2L1 (24887 upstream) : CLASP1 (27688 downstream)																							CCACATGAACgtgtgtgtgtgt	0.401													4	2	---	---	---	---	
LRP1B	53353	broad.mit.edu	37	2	141526600	141526601	+	Intron	INS	-	T	T	rs141193186	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141526600_141526601insT	uc002tvj.1	-							NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ATTTTACTTGATTTTTTTTTCA	0.272										TSP Lung(27;0.18)			3	4	---	---	---	---	
ZAK	51776	broad.mit.edu	37	2	174131419	174131419	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174131419delC	uc002uhz.2	+	20	2544	c.2344delC	c.(2344-2346)CCCfs	p.P782fs	uc002uib.2_Intron	NM_016653	NP_057737	Q9NYL2	MLTK_HUMAN	MLK-related kinase isoform 1	782					activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation	cytoplasm|nucleus	ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			lung(3)|stomach(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.176)			CAGGCCATCTCCCGCCAAAAC	0.483													24	16	---	---	---	---	
KCTD18	130535	broad.mit.edu	37	2	201355433	201355433	+	Intron	DEL	T	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201355433delT	uc002uvs.2	-						KCTD18_uc002uvt.2_Intron	NM_152387	NP_689600	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1						AACAGAAAGGTTTTGGTCAAG	0.388													32	14	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	107973477	107973480	+	IGR	DEL	GTGT	-	-	rs35038126		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107973477_107973480delGTGT								IFT57 (32060 upstream) : HHLA2 (41913 downstream)																							ttttatgtgcgtgtgtgtgtgtgt	0.029													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	121673368	121673371	+	IGR	DEL	TTCC	-	-	rs112836162		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121673368_121673371delTTCC								SLC15A2 (10334 upstream) : ILDR1 (32800 downstream)																							atttttatggttccttccttcctt	0.005													6	3	---	---	---	---	
IL1RAP	3556	broad.mit.edu	37	3	190240130	190240133	+	Intron	DEL	CCTC	-	-	rs72210196		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190240130_190240133delCCTC	uc003fsm.1	+						IL1RAP_uc003fsk.2_Intron|IL1RAP_uc003fsl.2_Intron|IL1RAP_uc010hzf.2_Intron|IL1RAP_uc010hzg.1_Intron|IL1RAP_uc003fsn.1_Intron|IL1RAP_uc003fso.1_Intron|IL1RAP_uc003fsp.1_Intron|IL1RAP_uc003fsq.2_Intron	NM_002182	NP_002173	Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein isoform						inflammatory response|innate immune response|protein complex assembly	extracellular region|integral to plasma membrane				ovary(1)	1	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		ttccttccttcctccctccctccc	0.000													5	4	---	---	---	---	
SLIT2	9353	broad.mit.edu	37	4	20619357	20619357	+	Intron	DEL	A	-	-	rs71653889		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20619357delA	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						agaaaaagtgaaaaaaaaaaa	0.303													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	165403237	165403240	+	IGR	DEL	AGGC	-	-	rs67048987	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165403237_165403240delAGGC								MARCH1 (98035 upstream) : TRIM61 (472360 downstream)																							gaaggaaggaaggcaggcaggcag	0.147													4	4	---	---	---	---	
CTNNA1	1495	broad.mit.edu	37	5	138253221	138253224	+	Intron	DEL	TTTA	-	-	rs66467400		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138253221_138253224delTTTA	uc003ldh.2	+						CTNNA1_uc011cyx.1_Intron|CTNNA1_uc011cyy.1_Intron|CTNNA1_uc003ldi.2_Intron|CTNNA1_uc003ldj.2_Intron|CTNNA1_uc003ldl.2_Intron	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1						adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TAGTACAGTTTTTATTTGTTTTAT	0.314													6	3	---	---	---	---	
RASGEF1C	255426	broad.mit.edu	37	5	179528352	179528352	+	3'UTR	DEL	G	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179528352delG	uc003mlq.2	-	13					RASGEF1C_uc003mlr.2_3'UTR|RASGEF1C_uc003mlp.3_3'UTR	NM_175062	NP_778232	Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity			ovary(1)	1	all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGGCCACTGTGGGGGGGGGGG	0.672													0	7	---	---	---	---	
BTN3A2	11118	broad.mit.edu	37	6	26373817	26373819	+	Intron	DEL	AAA	-	-	rs71863965		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26373817_26373819delAAA	uc010jqh.1	+						BTN3A2_uc003nho.1_Intron|BTN3A2_uc003nhp.2_Intron|BTN3A2_uc011dkd.1_Intron|BTN3A2_uc011dke.1_Intron|BTN3A2_uc010jqi.1_Intron	NM_007047	NP_008978	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2 precursor							integral to membrane					0						TTCTCTCTAGaaaaaaaaaaaaa	0.404													4	3	---	---	---	---	
CENPQ	55166	broad.mit.edu	37	6	49456585	49456585	+	Intron	DEL	T	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49456585delT	uc003ozh.1	+							NM_018132	NP_060602	Q7L2Z9	CENPQ_HUMAN	centromere protein Q						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2	Lung NSC(77;0.0128)					gcattatttcttttttttttt	0.000													4	2	---	---	---	---	
C6orf204	387119	broad.mit.edu	37	6	118801233	118801234	+	Intron	DEL	CA	-	-	rs143503840		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118801233_118801234delCA	uc003pxz.1	-							NM_001042475	NP_001035940	Q5SZL2	CF204_HUMAN	chromosome 6 open reading frame 204 isoform a							centrosome				breast(1)	1		all_cancers(87;0.0814)|all_epithelial(87;0.115)		GBM - Glioblastoma multiforme(226;0.0114)|all cancers(137;0.035)|OV - Ovarian serous cystadenocarcinoma(136;0.0618)		TGATTTGGGTCACACACGTATA	0.252													2	4	---	---	---	---	
CARD11	84433	broad.mit.edu	37	7	2955091	2955091	+	Intron	DEL	C	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2955091delC	uc003smv.2	-							NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11						positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CCCGGCAAAGCCAGACCTTGT	0.582			Mis		DLBCL								18	15	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57659644	57659644	+	IGR	DEL	G	-	-	rs111399871		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57659644delG								ZNF716 (126379 upstream) : None (None downstream)																							CATGTTTTTTGTGTTTTTCTT	0.353													10	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64722027	64722028	+	IGR	INS	-	A	A	rs34277183		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64722027_64722028insA								INTS4L1 (27428 upstream) : ZNF92 (116740 downstream)																							agactctgtctaaaaaaaaaaa	0.178													4	2	---	---	---	---	
AUTS2	26053	broad.mit.edu	37	7	70249760	70249760	+	Intron	DEL	C	-	-	rs71991976		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70249760delC	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron|AUTS2_uc011keg.1_Intron	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		aaaaaaaaaaCACACATTTTC	0.423													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	71952879	71952880	+	IGR	INS	-	A	A			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71952879_71952880insA								CALN1 (40743 upstream) : TYW1B (70849 downstream)																							gaaaagaaaagaaagaaagaaa	0.000													4	3	---	---	---	---	
PUS7	54517	broad.mit.edu	37	7	105146865	105146865	+	Intron	DEL	T	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105146865delT	uc003vcx.2	-						PUS7_uc010lji.2_Intron|PUS7_uc003vcy.2_Intron|PUS7_uc003vcz.1_Intron	NM_019042	NP_061915	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 homolog						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1						ATGGAGTTAAttttttttttc	0.134													9	5	---	---	---	---	
JHDM1D	80853	broad.mit.edu	37	7	139826263	139826263	+	Intron	DEL	A	-	-	rs79442932		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139826263delA	uc003vvm.2	-							NM_030647	NP_085150	Q6ZMT4	KDM7_HUMAN	jumonji C domain containing histone demethylase						midbrain development|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1	Melanoma(164;0.0142)					ATTTGAGATTAAAAAAAAAAA	0.284													4	2	---	---	---	---	
RBM33	155435	broad.mit.edu	37	7	155534923	155534923	+	Intron	DEL	C	-	-	rs35396377		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155534923delC	uc010lqk.1	+						RBM33_uc011kvv.1_Intron	NM_053043	NP_444271	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33								nucleotide binding|RNA binding			ovary(1)	1	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		TCACCTGGGTCTTTTTTTTTT	0.308													4	2	---	---	---	---	
TUSC3	7991	broad.mit.edu	37	8	15531507	15531510	+	Intron	DEL	ACAC	-	-	rs113421840		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15531507_15531510delACAC	uc003wwt.2	+						TUSC3_uc003wwr.2_Intron|TUSC3_uc003wws.2_Intron|TUSC3_uc003wwu.2_Intron|TUSC3_uc003wwv.2_Intron|TUSC3_uc003www.2_Intron|TUSC3_uc003wwx.2_Intron|TUSC3_uc003wwy.2_Intron	NM_006765	NP_006756	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3 isoform a						cell redox homeostasis|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				ovary(2)|central_nervous_system(1)	3				Colorectal(111;0.113)		ACATGTGCATACACACACACACAC	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	135331910	135331935	+	IGR	DEL	CCAGGGAGAGGGTGTGAGGGGTCAAT	-	-	rs13271339		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135331910_135331935delCCAGGGAGAGGGTGTGAGGGGTCAAT								ST3GAL1 (747727 upstream) : ZFAT (158098 downstream)																							CCACAGCAGCCCAGGGAGAGGGTGTGAGGGGTCAATCCAGGGAGAG	0.345													5	3	---	---	---	---	
TSNARE1	203062	broad.mit.edu	37	8	143337251	143337252	+	Intron	INS	-	CAT	CAT			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143337251_143337252insCAT	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					atcaccaccaccaccaccactg	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	144493044	144493046	+	IGR	DEL	ATA	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144493044_144493046delATA								RHPN1 (26655 upstream) : MAFA (18469 downstream)																							gatgatggtgatagtgatggtgg	0.000													4	2	---	---	---	---	
KDM4C	23081	broad.mit.edu	37	9	6990364	6990364	+	Intron	DEL	G	-	-	rs77778821		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6990364delG	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1						TTTTTTTTTTGTAGTTTGTTT	0.333													15	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	83786171	83786172	+	IGR	DEL	GT	-	-	rs67478186		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83786171_83786172delGT								None (None upstream) : TLE1 (412428 downstream)																							AGTAGTAGTAgtgtgtgtgtgt	0.267													4	2	---	---	---	---	
FANCC	2176	broad.mit.edu	37	9	98056650	98056652	+	Intron	DEL	TAC	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98056650_98056652delTAC	uc004avh.2	-						FANCC_uc004avi.3_Intron|FANCC_uc010mrm.1_Intron|FANCC_uc011lul.1_Intron	NM_000136	NP_000127	Q00597	FANCC_HUMAN	Fanconi anemia, complementation group C						protein complex assembly	cytosol|nucleoplasm	protein binding			kidney(1)	1		Acute lymphoblastic leukemia(62;0.138)				ACGGACTTCTTACTCGCAGATAC	0.448			D|Mis|N|F|S			AML|leukemia		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				93	52	---	---	---	---	
SLC35D2	11046	broad.mit.edu	37	9	99130723	99130723	+	Intron	DEL	T	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99130723delT	uc004awc.2	-						SLC35D2_uc010msd.2_Intron|SLC35D2_uc010mse.2_Intron|SLC35D2_uc010msf.2_Intron|SLC35D2_uc004awd.2_Intron|SLC35D2_uc004awe.2_Intron	NM_007001	NP_008932	Q76EJ3	S35D2_HUMAN	solute carrier family 35, member D2							Golgi membrane|integral to membrane	nucleotide-sugar transmembrane transporter activity				0		Acute lymphoblastic leukemia(62;0.0167)				catttaattcttttttttttt	0.090													8	4	---	---	---	---	
LPPR1	54886	broad.mit.edu	37	9	104086507	104086507	+	3'UTR	DEL	T	-	-	rs148907009		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104086507delT	uc004bbb.2	+	8					LPPR1_uc011lvi.1_3'UTR|LPPR1_uc004bbc.2_3'UTR|LPPR1_uc010mtc.2_3'UTR	NM_207299	NP_997182	Q8TBJ4	LPPR1_HUMAN	plasticity related gene 3							integral to membrane	catalytic activity				0						CTTGCCCTGATTTTTTTTTTT	0.294													4	2	---	---	---	---	
OR13C5	138799	broad.mit.edu	37	9	107361898	107361899	+	5'Flank	INS	-	GAAT	GAAT	rs139149858	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107361898_107361899insGAAT	uc011lvp.1	-							NM_001004482	NP_001004482	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)|skin(1)	4						gagagggaagggaatgaatgaa	0.030													4	4	---	---	---	---	
ASTN2	23245	broad.mit.edu	37	9	119545564	119545579	+	Intron	DEL	CCTTCCTTCCTTCCTC	-	-	rs34143636		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119545564_119545579delCCTTCCTTCCTTCCTC	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9						ttccttccttccttccttccttcctccctccctccc	0.153													8	5	---	---	---	---	
C5	727	broad.mit.edu	37	9	123780857	123780868	+	Intron	DEL	AAGGAAGGAAGG	-	-	rs144743782	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123780857_123780868delAAGGAAGGAAGG	uc004bkv.2	-						C5_uc010mvm.1_Intron|C5_uc010mvn.1_Intron	NM_001735	NP_001726	P01031	CO5_HUMAN	complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)	ACCAAAaagaaaggaaggaaggaaggaaggaa	0.009													3	5	---	---	---	---	
DDX31	64794	broad.mit.edu	37	9	135500888	135500889	+	Intron	INS	-	A	A	rs75372078		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135500888_135500889insA	uc004cbq.1	-						DDX31_uc010mzu.1_Intron	NM_022779	NP_073616	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		CAAAGACGAGGAAAAAAAAAAA	0.441													5	4	---	---	---	---	
LARP4B	23185	broad.mit.edu	37	10	910364	910364	+	Intron	DEL	A	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:910364delA	uc001ifs.1	-							NM_015155	NP_055970	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B								nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3						GTTCaaaattaaaaaaaaaaa	0.388													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	6820659	6820659	+	5'Flank	DEL	G	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6820659delG	uc001ijm.2	+											Homo sapiens cDNA FLJ36835 fis, clone ASTRO2010996.																		gaaggtaggtgggggggggga	0.100													4	2	---	---	---	---	
GATA3	2625	broad.mit.edu	37	10	8106275	8106275	+	Intron	DEL	T	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8106275delT	uc001ika.2	+						GATA3_uc001ijz.2_Intron	NM_002051	NP_002042	P23771	GATA3_HUMAN	GATA binding protein 3 isoform 2						aortic valve morphogenesis|blood coagulation|canonical Wnt receptor signaling pathway involved in metanephric kidney development|cardiac right ventricle morphogenesis|cell fate determination|cellular response to interferon-alpha|cellular response to interleukin-4|cellular response to tumor necrosis factor|defense response|ear development|lymphocyte migration|male gonad development|mesenchymal to epithelial transition|mesonephros development|negative regulation of cell cycle|negative regulation of cell motility|negative regulation of cell proliferation involved in mesonephros development|negative regulation of endothelial cell apoptosis|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation|negative regulation of inflammatory response|negative regulation of mammary gland epithelial cell proliferation|nephric duct formation|norepinephrine biosynthetic process|pharyngeal system development|phosphatidylinositol 3-kinase cascade|positive regulation of endothelial cell migration|positive regulation of interleukin-13 secretion|positive regulation of interleukin-4 production|positive regulation of interleukin-5 secretion|positive regulation of protein kinase B signaling cascade|positive regulation of T cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription regulatory region DNA binding|positive regulation of ureteric bud formation|regulation of cellular response to X-ray|regulation of cytokine biosynthetic process|regulation of nephron tubule epithelial cell differentiation|response to estrogen stimulus|response to virus|sympathetic nervous system development|T cell receptor signaling pathway|TOR signaling cascade|ureteric bud formation|uterus development|ventricular septum development	nuclear chromatin|nucleolus|nucleoplasm	core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|E-box binding|HMG box domain binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription coactivator activity|transcription factor binding|zinc ion binding			breast(17)|ovary(3)|central_nervous_system(2)	22						cttcttcttcttttttttttt	0.313			F|N|S		breast		HDR syndrome (HYPOPARATHYROIDISM|SENSORINEURAL DEAFNESS|AND RENAL DISEASE)						4	3	---	---	---	---	
FAM190B	54462	broad.mit.edu	37	10	86130950	86130950	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86130950delA	uc001kdh.1	+	2	336	c.142delA	c.(142-144)AAAfs	p.K48fs	FAM190B_uc001kdg.1_Frame_Shift_Del_p.K48fs|FAM190B_uc010qmd.1_Frame_Shift_Del_p.K48fs	NM_018999	NP_061872	Q9H7U1	F190B_HUMAN	granule cell antiserum positive 14	48										ovary(3)|skin(1)	4						TAGTAATGTCAAAAGTTACAT	0.353													106	53	---	---	---	---	
VTI1A	143187	broad.mit.edu	37	10	114215425	114215428	+	Intron	DEL	CCTT	-	-	rs57381306		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114215425_114215428delCCTT	uc001kzy.2	+						VTI1A_uc001kzz.2_Intron	NM_145206	NP_660207	Q96AJ9	VTI1A_HUMAN	SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		tcccttcctcccttccttccttcc	0.127													4	2	---	---	---	---	
SEC23IP	11196	broad.mit.edu	37	10	121668424	121668427	+	Intron	DEL	CAGT	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121668424_121668427delCAGT	uc001leu.1	+						SEC23IP_uc010qtc.1_Intron	NM_007190	NP_009121	Q9Y6Y8	S23IP_HUMAN	Sec23-interacting protein p125						Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding			ovary(3)	3		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		ATATGTTAACCAGTCAGGAAATGA	0.338													11	5	---	---	---	---	
ARMS2	387715	broad.mit.edu	37	10	124214600	124214601	+	Intron	INS	-	GT	GT	rs144224550	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124214600_124214601insGT	uc001lgi.2	+							NM_001099667	NP_001093137	P0C7Q2	ARMS2_HUMAN	age-related maculopathy susceptibility 2						retina homeostasis	mitochondrion|photoreceptor inner segment				ovary(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				attctggagtggtgccctgcag	0.134													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	26174005	26174006	+	IGR	INS	-	AAAG	AAAG			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26174005_26174006insAAAG								None (None upstream) : ANO3 (36823 downstream)																							aaggaaaaagaaaagaaaggaa	0.139													5	4	---	---	---	---	
C11orf41	25758	broad.mit.edu	37	11	33565649	33565649	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33565649delC	uc001mup.3	+	1	1773	c.1649delC	c.(1648-1650)ACCfs	p.T550fs	C11orf41_uc001mun.1_Frame_Shift_Del_p.T550fs	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	550						integral to membrane				ovary(2)	2						CTTTTGCTAACCTCACCAGGA	0.463													132	57	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	42010411	42010412	+	IGR	INS	-	AAGG	AAGG	rs1828897		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42010411_42010412insAAGG								LRRC4C (529088 upstream) : None (None downstream)																							aagaaaaaagaaaggaaggaag	0.168													4	5	---	---	---	---	
TRIM48	79097	broad.mit.edu	37	11	55032958	55032958	+	Intron	DEL	A	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55032958delA	uc010rid.1	+							NM_024114	NP_077019	Q8IWZ4	TRI48_HUMAN	tripartite motif-containing 48							intracellular	zinc ion binding				0						AGTGAAACAGAAGAAATGCCA	0.428													4	8	---	---	---	---	
POLD3	10714	broad.mit.edu	37	11	74336917	74336918	+	Intron	DEL	TG	-	-	rs150373223	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74336917_74336918delTG	uc001ovf.1	+						POLD3_uc009yua.1_Intron	NM_006591	NP_006582	Q15054	DPOD3_HUMAN	DNA-directed DNA polymerase delta 3						base-excision repair|DNA strand elongation involved in DNA replication|DNA synthesis involved in DNA repair|mismatch repair|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	delta DNA polymerase complex|nucleoplasm	DNA-directed DNA polymerase activity|protein binding			kidney(2)|ovary(1)	3	Breast(11;3.21e-06)					TGTGCCTAGTtgtgtgtgtgtg	0.272													4	2	---	---	---	---	
SLCO2B1	11309	broad.mit.edu	37	11	74836994	74836994	+	Intron	DEL	A	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74836994delA	uc010rrp.1	+									O94956	SO2B1_HUMAN	Homo sapiens mRNA for KIAA0880 protein, partial cds.						sodium-independent organic anion transport	integral to membrane	sodium-independent organic anion transmembrane transporter activity			ovary(1)|breast(1)	2					Ergoloid mesylate(DB01049)	gcatgtaaggaaggaggcgag	0.000													4	2	---	---	---	---	
OVCH1	341350	broad.mit.edu	37	12	29597359	29597361	+	Intron	DEL	AAA	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29597359_29597361delAAA	uc001rix.1	-							NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					GGTTTCACTGAAAATTTTCTCCG	0.384													4	2	---	---	---	---	
XPOT	11260	broad.mit.edu	37	12	64816642	64816646	+	Intron	DEL	CACTG	-	-	rs151118213		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64816642_64816646delCACTG	uc001ssb.2	+							NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin						intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)		atgactgcgccactgcactccagcc	0.078													5	5	---	---	---	---	
FRS2	10818	broad.mit.edu	37	12	69966175	69966178	+	Intron	DEL	TTAC	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69966175_69966178delTTAC	uc001suy.2	+						FRS2_uc001suz.2_Intron|FRS2_uc009zrj.2_Intron|FRS2_uc009zrk.2_Intron	NM_006654	NP_006645	Q8WU20	FRS2_HUMAN	fibroblast growth factor receptor substrate 2						activation of MAPKK activity|activation of phospholipase C activity|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|transmembrane receptor protein tyrosine phosphatase signaling pathway	endomembrane system|endosome|integral to plasma membrane|membrane fraction	fibroblast growth factor receptor binding|insulin receptor binding|phosphatase activator activity|transmembrane receptor protein tyrosine kinase adaptor activity			prostate(1)|kidney(1)	2	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			TGTTTGTAAATTACTTTTGTAGTG	0.353													19	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80764205	80764206	+	Intron	DEL	TT	-	-	rs150207533		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80764205_80764206delTT	uc009zsg.1	+						uc001szd.2_Intron					RecName: Full=Uncharacterized protein C12orf64;																		TTAGATAAACTTAGGGTCATTT	0.262													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80765684	80765686	+	Intron	DEL	GAA	-	-	rs56017107		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80765684_80765686delGAA	uc009zsg.1	+						uc001szd.2_Intron					RecName: Full=Uncharacterized protein C12orf64;																		ATTTTTCTATGAAGGCTTTGTGG	0.246													10	9	---	---	---	---	
SART3	9733	broad.mit.edu	37	12	108929135	108929136	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108929135_108929136insT	uc001tmz.1	-	12	1790_1791	c.1555_1556insA	c.(1555-1557)AGAfs	p.R519fs	SART3_uc001tmy.1_Frame_Shift_Ins_p.R45fs|SART3_uc009zux.1_Frame_Shift_Ins_p.R131fs|SART3_uc010swx.1_Frame_Shift_Ins_p.R483fs|SART3_uc010swy.1_Frame_Shift_Ins_p.R405fs|SART3_uc010swz.1_Frame_Shift_Ins_p.R519fs|SART3_uc001tna.1_RNA	NM_014706	NP_055521	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T	519	HAT 8.				RNA processing	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding			pancreas(1)	1						GATCAGTTACCTTTCCAGGTTG	0.520									Porokeratosis				305	133	---	---	---	---	
TRPV4	59341	broad.mit.edu	37	12	110238216	110238217	+	Intron	INS	-	CAAGTT	CAAGTT	rs148721750	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110238216_110238217insCAAGTT	uc001tpj.1	-						TRPV4_uc001tpg.1_Intron|TRPV4_uc001tph.1_Intron|TRPV4_uc001tpi.1_Intron|TRPV4_uc001tpk.1_Intron|TRPV4_uc001tpl.1_Intron	NM_021625	NP_067638	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel,						actin cytoskeleton reorganization|actin filament organization|calcium ion import|cell death|cell volume homeostasis|cell-cell junction assembly|cellular hypotonic response|cortical microtubule organization|elevation of cytosolic calcium ion concentration|microtubule polymerization|negative regulation of neuron projection development|osmosensory signaling pathway|positive regulation of microtubule depolymerization|response to mechanical stimulus	cortical actin cytoskeleton|filopodium|focal adhesion|growth cone|integral to membrane|lamellipodium|ruffle membrane	actin filament binding|alpha-tubulin binding|beta-tubulin binding|calcium channel activity|calmodulin binding|microtubule binding|protein binding|protein kinase C binding|SH2 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						gtccatggtactcccCATGGCA	0.302													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	116095687	116095691	+	IGR	DEL	TTCTT	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116095687_116095691delTTCTT								TBX3 (973718 upstream) : MED13L (300692 downstream)																							cctcctcctcttcttctccttcttc	0.059													4	2	---	---	---	---	
DCLK1	9201	broad.mit.edu	37	13	36559035	36559036	+	Intron	DEL	CA	-	-	rs146313847		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36559035_36559036delCA	uc001uvf.2	-							NM_004734	NP_004725	O15075	DCLK1_HUMAN	doublecortin-like kinase 1						cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		CGTGCGCATGcacacacacaca	0.530													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	64528002	64528002	+	IGR	DEL	T	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64528002delT								OR7E156P (211301 upstream) : None (None downstream)																							ccttccttccttccttccttc	0.000													4	2	---	---	---	---	
GABRG3	2567	broad.mit.edu	37	15	27633294	27633305	+	Intron	DEL	AAGGAAGGAAGA	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27633294_27633305delAAGGAAGGAAGA	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)		gagggtaaggaaggaaggaagaaaggaaggaa	0.000													3	3	---	---	---	---	
RPAP1	26015	broad.mit.edu	37	15	41814089	41814089	+	Intron	DEL	A	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41814089delA	uc001zod.2	-						RPAP1_uc001zoc.2_Intron	NM_015540	NP_056355	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1							nucleus	DNA binding|DNA-directed RNA polymerase activity			large_intestine(1)	1		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CTGCAGACAGAAAAGCAGGGA	0.592													42	22	---	---	---	---	
TCF12	6938	broad.mit.edu	37	15	57574602	57574603	+	Intron	INS	-	T	T			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57574602_57574603insT	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron|TCF12_uc002aee.2_Intron|TCF12_uc010bft.2_Intron|TCF12_uc010ugo.1_Intron|TCF12_uc010ugp.1_Intron|TCF12_uc010ugq.1_Intron	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		TAATTCATAACTTAAAACCATA	0.371			T	TEC	extraskeletal myxoid chondrosarcoma								85	45	---	---	---	---	
OSTBETA	123264	broad.mit.edu	37	15	65344105	65344106	+	Intron	INS	-	AAAC	AAAC	rs140336932	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65344105_65344106insAAAC	uc002aog.2	+						OSTBETA_uc002aoh.2_Intron	NM_178859	NP_849190	Q86UW2	OSTB_HUMAN	organic solute transporter beta							integral to membrane|plasma membrane					0						CAAGCTGTTaaaaacaaacaaa	0.465													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	90686999	90686999	+	IGR	DEL	A	-	-	rs10553548		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90686999delA								IDH2 (41291 upstream) : SEMA4B (41153 downstream)																							CCCATCCTAGAAAAAAAAAAA	0.333													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	15251607	15251610	+	IGR	DEL	CTCA	-	-	rs57571688		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15251607_15251610delCTCA								PDXDC1 (18412 upstream) : MPV17L (238001 downstream)																							cacacacactctcacacacacaca	0.392													4	2	---	---	---	---	
RBBP6	5930	broad.mit.edu	37	16	24574316	24574317	+	Intron	INS	-	G	G	rs141208600	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24574316_24574317insG	uc002dmh.2	+						RBBP6_uc010vcb.1_Intron|RBBP6_uc002dmi.2_Intron|RBBP6_uc010bxr.2_Intron|RBBP6_uc002dmk.2_Intron	NM_006910	NP_008841	Q7Z6E9	RBBP6_HUMAN	retinoblastoma-binding protein 6 isoform 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	chromosome|nucleolus|ubiquitin ligase complex	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|pancreas(1)	4				GBM - Glioblastoma multiforme(48;0.0518)		CTTCTTAAGGAGGTCCTTCATT	0.332													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	25031511	25031512	+	IGR	INS	-	GGAAGGAA	GGAAGGAA	rs7498498	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25031511_25031512insGGAAGGAA								ARHGAP17 (4836 upstream) : LCMT1 (91535 downstream)																							gaaggaaggacggaaggaagga	0.144													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	34858398	34858400	+	IGR	DEL	TTC	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34858398_34858400delTTC								LOC146481 (143431 upstream) : None (None downstream)																							cttctttcttttctctttctttc	0.005													4	2	---	---	---	---	
CPNE2	221184	broad.mit.edu	37	16	57159645	57159647	+	Intron	DEL	TTA	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57159645_57159647delTTA	uc002eks.1	+						CPNE2_uc010cct.1_Intron|CPNE2_uc010ccu.1_Intron|CPNE2_uc002ekt.1_Intron	NM_152727	NP_689940	Q96FN4	CPNE2_HUMAN	copine II											central_nervous_system(1)|skin(1)	2		all_neural(199;0.224)				TCAGACCATCTTATTGTGGGGAG	0.384													15	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	57454612	57454615	+	IGR	DEL	AAGG	-	-	rs113613565		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57454612_57454615delAAGG								CCL17 (4638 upstream) : CIAPIN1 (7472 downstream)																							aagaaaaagaaaggaaggaaggaa	0.000													4	2	---	---	---	---	
ADAMTS18	170692	broad.mit.edu	37	16	77359570	77359570	+	Intron	DEL	A	-	-	rs112943550		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77359570delA	uc002ffc.3	-						ADAMTS18_uc010chc.1_Intron|ADAMTS18_uc002ffe.1_Intron	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18						GGTATCTTATAGGGGGAAAAA	0.373													4	2	---	---	---	---	
CMIP	80790	broad.mit.edu	37	16	81712240	81712241	+	Intron	INS	-	C	C	rs142187160	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81712240_81712241insC	uc002fgp.2	+						CMIP_uc002fgq.1_Intron|CMIP_uc010vnq.1_Intron|CMIP_uc002fgr.1_Intron	NM_198390	NP_938204	Q8IY22	CMIP_HUMAN	c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0						TGCTGTGAGTgccccccccgcg	0.545													10	6	---	---	---	---	
HSDL1	83693	broad.mit.edu	37	16	84165089	84165092	+	Intron	DEL	TCTA	-	-	rs36192181	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84165089_84165092delTCTA	uc002fhk.2	-						HSDL1_uc010vnv.1_Intron	NM_031463	NP_113651	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1 isoform a							mitochondrion	oxidoreductase activity|protein binding				0						ACAGTTTCAGtctatctatctatc	0.206													4	2	---	---	---	---	
PLSCR3	57048	broad.mit.edu	37	17	7307104	7307105	+	Intron	DEL	CC	-	-	rs71383487		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7307104_7307105delCC	uc002ggr.1	-						PLSCR3_uc010cmg.1_Intron|C17orf61_uc002ggs.2_Intron	NM_020360	NP_065093	Q9NRY6	PLS3_HUMAN	phospholipid scramblase 3						phospholipid scrambling	integral to membrane|plasma membrane	calcium ion binding|calcium-dependent protein binding|phospholipid scramblase activity|SH3 domain binding				0		Prostate(122;0.173)				AGAAAGGGCACCCCCCCCCCCG	0.624													5	4	---	---	---	---	
NF1	4763	broad.mit.edu	37	17	29587624	29587624	+	Intron	DEL	G	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29587624delG	uc002hgg.2	+						NF1_uc002hgh.2_Intron|NF1_uc002hgi.1_Intron	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(3)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TTTTTACTTTGCATCTTCTTG	0.303			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			65	34	---	---	---	---	
TMEM132E	124842	broad.mit.edu	37	17	32965276	32965276	+	3'UTR	DEL	C	-	-	rs71921875		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32965276delC	uc002hif.2	+	10						NM_207313	NP_997196	Q6IEE7	T132E_HUMAN	transmembrane protein 132E precursor							integral to membrane				central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(366;0.231)		GTAGCAGGGACCCCCCCCCCC	0.647											OREG0024325	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	10	5	---	---	---	---	
HOXB5	3215	broad.mit.edu	37	17	46671172	46671173	+	5'Flank	INS	-	G	G			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46671172_46671173insG	uc002inr.2	-							NM_002147	NP_002138	P09067	HXB5_HUMAN	homeobox B5							nucleus	sequence-specific DNA binding				0						CGGCCAAATATGGGGGGGGGGT	0.470											OREG0024519	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	2	4	---	---	---	---	
FTSJ3	117246	broad.mit.edu	37	17	61898808	61898808	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61898808delA	uc002jbz.2	-	15	1870	c.1792delT	c.(1792-1794)TCTfs	p.S598fs	FTSJ3_uc002jca.2_Frame_Shift_Del_p.S598fs	NM_017647	NP_060117	Q8IY81	RRMJ3_HUMAN	FtsJ homolog 3	598					RNA methylation|rRNA processing	nucleolus	methyltransferase activity|nucleic acid binding			ovary(1)	1						GTCCCCGAAGAAGCCTCTGTT	0.527													151	72	---	---	---	---	
TBC1D16	125058	broad.mit.edu	37	17	77958419	77958420	+	Intron	INS	-	GAAGGAAG	GAAGGAAG	rs9900976	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77958419_77958420insGAAGGAAG	uc002jxj.2	-							NM_019020	NP_061893	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16							intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			agggagggagtgaaggaaggaa	0.089													10	5	---	---	---	---	
L3MBTL4	91133	broad.mit.edu	37	18	6322509	6322510	+	Intron	INS	-	A	A	rs143247312	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6322509_6322510insA	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron	NM_173464	NP_775735	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)				aggaaagaaggaaaaaaaaaac	0.000													6	4	---	---	---	---	
FHOD3	80206	broad.mit.edu	37	18	34349098	34349098	+	Intron	DEL	G	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34349098delG	uc002kzt.1	+						FHOD3_uc002kzs.1_Intron|FHOD3_uc010dmz.1_Intron|FHOD3_uc010dnb.1_Intron	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CACTAGCTCTGGGGCTTTAAC	0.498													12	8	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17777677	17777678	+	Intron	DEL	AC	-	-	rs71336631		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17777677_17777678delAC	uc002nhd.2	-							NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						GGAGAGAAAGACACACACACAC	0.282													2	5	---	---	---	---	
ZNF100	163227	broad.mit.edu	37	19	21910934	21910934	+	Intron	DEL	A	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21910934delA	uc002nqi.2	-						ZNF100_uc002nqh.2_Intron	NM_173531	NP_775802	Q8IYN0	ZN100_HUMAN	zinc finger protein 100						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						ATATAAATGTAAAAAAAAAAA	0.313													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	31670636	31670638	+	IGR	DEL	GGT	-	-	rs139984397		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31670636_31670638delGGT								DKFZp566F0947 (29327 upstream) : TSHZ3 (95215 downstream)																							gatgatggtaggtggtggtggtg	0.015													5	3	---	---	---	---	
CABP5	56344	broad.mit.edu	37	19	48546793	48546794	+	Intron	INS	-	CTT	CTT			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48546793_48546794insCTT	uc002phu.1	-							NM_019855	NP_062829	Q9NP86	CABP5_HUMAN	calcium binding protein 5						signal transduction	cytoplasm	calcium ion binding			skin(1)	1		all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058)		accaccaccaccatcatcacca	0.149													4	2	---	---	---	---	
VRK3	51231	broad.mit.edu	37	19	50485050	50485051	+	Intron	INS	-	AC	AC	rs150610662	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50485050_50485051insAC	uc002prg.2	-						VRK3_uc002prh.1_Intron|VRK3_uc002pri.1_Intron|VRK3_uc010ens.2_Intron|VRK3_uc010ybl.1_Intron|VRK3_uc010ybm.1_Intron|VRK3_uc002prj.1_3'UTR|VRK3_uc002prk.1_3'UTR	NM_016440	NP_057524	Q8IV63	VRK3_HUMAN	vaccinia related kinase 3 isoform 1							nucleus	ATP binding|protein kinase activity			stomach(1)|skin(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)		cacacacacagacacacacaca	0.297													2	4	---	---	---	---	
NLRP12	91662	broad.mit.edu	37	19	54304349	54304349	+	Intron	DEL	A	-	-	rs35326804		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54304349delA	uc002qch.3	-						NLRP12_uc010eqw.2_Intron|NLRP12_uc002qci.3_Intron|NLRP12_uc002qcj.3_Intron|NLRP12_uc002qck.3_Intron|NLRP12_uc010eqx.2_Intron	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform						negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		tgggagtctCAAAAAAAAAAA	0.244													4	2	---	---	---	---	
SLC24A3	57419	broad.mit.edu	37	20	19203427	19203428	+	Intron	INS	-	CCTTCCTT	CCTTCCTT	rs147696601	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19203427_19203428insCCTTCCTT	uc002wrl.2	+							NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1						tcccctccctcccttccttcct	0.119													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	50563356	50563357	+	IGR	DEL	GT	-	-	rs111578894		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50563356_50563357delGT								SALL4 (144308 upstream) : ZFP64 (137194 downstream)																							GGGAACATGGgtgtgtgtgtgt	0.134													3	3	---	---	---	---	
CTCFL	140690	broad.mit.edu	37	20	56083440	56083440	+	Intron	DEL	T	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56083440delT	uc010gix.1	-						CTCFL_uc010giw.1_Intron|CTCFL_uc002xym.2_Intron|CTCFL_uc010giz.1_Intron|CTCFL_uc010giy.1_Intron|CTCFL_uc010gja.1_Intron|CTCFL_uc010gjb.1_Intron|CTCFL_uc010gjc.1_Intron|CTCFL_uc010gjd.1_Intron|CTCFL_uc010gje.2_Intron|CTCFL_uc010gjf.2_Intron|CTCFL_uc010gjg.2_Intron|CTCFL_uc010gjh.1_Intron|CTCFL_uc010gji.1_Intron|CTCFL_uc010gjj.1_Intron|CTCFL_uc010giu.2_Intron|CTCFL_uc010giv.2_Intron	NM_080618	NP_542185	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor-like protein						cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|skin(1)	4	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			TGGATTGTCCTTTTTTTTTTT	0.338													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	20151725	20151726	+	IGR	INS	-	ACC	ACC	rs138268702	by1000genomes	TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20151725_20151726insACC								ZDHHC8 (16196 upstream) : LOC150197 (42129 downstream)																							ccaccatcactaccaccaccac	0.025													4	3	---	---	---	---	
APOBEC3H	164668	broad.mit.edu	37	22	39497573	39497579	+	Intron	DEL	TGGGGGT	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39497573_39497579delTGGGGGT	uc011aoh.1	+						APOBEC3H_uc011aoi.1_5'Flank|APOBEC3H_uc003axa.3_5'Flank	NM_181773	NP_861438	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic						DNA cytosine deamination|negative regulation of retroviral genome replication|negative regulation of transposition	cytoplasm|nucleus	cytidine deaminase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Melanoma(58;0.04)					TGGCAggggctgggggttgggggttgg	0.271													10	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	930724	930725	+	IGR	INS	-	GGAA	GGAA			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:930724_930725insGGAA								SHOX (310579 upstream) : CRLF2 (384162 downstream)																							aaaaaaGTGGGggaaggaagga	0.129													6	3	---	---	---	---	
HDAC8	55869	broad.mit.edu	37	X	71687925	71687926	+	Intron	DEL	GC	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71687925_71687926delGC	uc004eau.2	-						HDAC8_uc011mqe.1_Intron|HDAC8_uc011mqf.1_Intron|HDAC8_uc011mqg.1_Intron|HDAC8_uc011mqh.1_Intron|HDAC8_uc010nlk.1_Intron	NM_018486	NP_060956	Q9BY41	HDAC8_HUMAN	histone deacetylase 8						chromatin assembly or disassembly|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|nuclear chromosome	histone deacetylase activity (H3-K16 specific)|metal ion binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|transcription factor binding				0	Renal(35;0.156)				Vorinostat(DB02546)	TGTACATAGTGCAAACTTCAAA	0.396													13	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	82254422	82254422	+	IGR	DEL	A	-	-			TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82254422delA								None (None upstream) : POU3F4 (508847 downstream)																							AGTTTCTCAGAAAAAAAAAAA	0.368													5	3	---	---	---	---	
MCF2	4168	broad.mit.edu	37	X	138688111	138688112	+	Intron	DEL	TA	-	-	rs112656536		TCGA-CJ-4920-01A-01D-1429-08	TCGA-CJ-4920-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138688111_138688112delTA	uc004fau.2	-						MCF2_uc004fav.2_Intron|MCF2_uc011mwl.1_Intron|MCF2_uc010nsh.1_Intron|MCF2_uc011mwm.1_Intron|MCF2_uc011mwn.1_Intron|MCF2_uc004faw.2_Intron|MCF2_uc011mwo.1_Intron	NM_005369	NP_005360	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|membrane|membrane fraction	protein binding|Rho guanyl-nucleotide exchange factor activity			lung(1)|pleura(1)	2	Acute lymphoblastic leukemia(192;0.000127)					GAATAAAAACTATATATATATA	0.218													4	2	---	---	---	---	
