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
MST1P2	11209	broad.mit.edu	37	1	16974549	16974549	+	RNA	SNP	C	G	G			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974549C>G	uc009vow.2	+	5		c.1359C>G			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_RNA|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						GGGCTGAGTGCAGCGCCTGCT	0.692													3	62	---	---	---	---	PASS
KIAA0754	643314	broad.mit.edu	37	1	39879328	39879328	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39879328G>A	uc009vvt.1	+	1	4153	c.3391G>A	c.(3391-3393)GCC>ACC	p.A1131T	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc010oiu.1_Intron	NM_015038	NP_055853	O94854	K0754_HUMAN	hypothetical protein LOC643314	995	Ala-rich.|10.										0	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AGAGGAGCCCGCCTCCCCAGC	0.711													3	15	---	---	---	---	PASS
EIF2B3	8891	broad.mit.edu	37	1	45363078	45363078	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45363078G>C	uc001cmt.1	-	6	732	c.605C>G	c.(604-606)GCC>GGC	p.A202G	EIF2B3_uc001cmu.1_Missense_Mutation_p.A202G|EIF2B3_uc001cmv.1_Missense_Mutation_p.A202G|EIF2B3_uc001cmw.2_Missense_Mutation_p.A202G	NM_020365	NP_065098	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B,	202					negative regulation of translational initiation in response to stress|oligodendrocyte development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	nucleotidyltransferase activity|protein binding|translation initiation factor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					GTAGAGGTGGGCATCCACAAG	0.388													7	32	---	---	---	---	PASS
CELSR2	1952	broad.mit.edu	37	1	109816711	109816711	+	3'UTR	SNP	T	C	C			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109816711T>C	uc001dxa.3	+	34						NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2						dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|lung(3)|skin(1)	8		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		TCCCTTCCCTTCCCCAGCCGC	0.587													10	63	---	---	---	---	PASS
MFSD4	148808	broad.mit.edu	37	1	205549915	205549915	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205549915C>A	uc001hcv.3	+	3	642	c.556C>A	c.(556-558)CAT>AAT	p.H186N	MFSD4_uc010prk.1_Intron|MFSD4_uc010prl.1_RNA|MFSD4_uc010prm.1_Missense_Mutation_p.H131N	NM_181644	NP_857595	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing	186					transmembrane transport	integral to membrane				skin(2)|central_nervous_system(1)	3	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			CCACCTGTTCCATGTCTCCAG	0.617													4	92	---	---	---	---	PASS
PARP1	142	broad.mit.edu	37	1	226549151	226549151	+	3'UTR	SNP	C	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226549151C>A	uc001hqd.3	-	23						NM_001618	NP_001609	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase family, member 1						cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nuclear envelope|nucleolus|transcription factor complex	DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding			lung(3)|ovary(2)|breast(2)|skin(2)|upper_aerodigestive_tract(1)	10	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		GACTCGGCTACCTCTCCCAAT	0.478								Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA					7	46	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237801684	237801684	+	Silent	SNP	C	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237801684C>T	uc001hyl.1	+	45	6940	c.6820C>T	c.(6820-6822)CTG>TTG	p.L2274L		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2274	Cytoplasmic (By similarity).|4 X approximate repeats.				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)			TGGTTGTGGACTGCAAAGTTG	0.413													8	248	---	---	---	---	PASS
SH3BP5L	80851	broad.mit.edu	37	1	249107303	249107303	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249107303C>A	uc001iew.1	-	6	1148	c.596G>T	c.(595-597)CGG>CTG	p.R199L	SH3BP5L_uc010pzp.1_Missense_Mutation_p.R92L|SH3BP5L_uc010pzq.1_Missense_Mutation_p.R167L|SH3BP5L_uc001iev.1_Missense_Mutation_p.R80L	NM_030645	NP_085148	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	199	Potential.										0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			TTGGCACAGCCGAGTCACTCG	0.637													2	5	---	---	---	---	PASS
NLRC4	58484	broad.mit.edu	37	2	32475161	32475161	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32475161A>T	uc002roi.2	-	4	2018	c.1772T>A	c.(1771-1773)ATC>AAC	p.I591N	NLRC4_uc002roj.1_Missense_Mutation_p.I591N|NLRC4_uc010ezt.1_Intron	NM_021209	NP_067032	Q9NPP4	NLRC4_HUMAN	caspase recruitment domain protein 12	591	LRR 3.				activation of caspase activity|defense response to bacterium|detection of bacterium|interleukin-1 beta secretion|positive regulation of apoptosis	cytoplasm	ATP binding|magnesium ion binding|protein homodimerization activity			ovary(3)|large_intestine(1)|lung(1)|skin(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GTAATCGGGGATGTTCCCTGA	0.408													6	245	---	---	---	---	PASS
LTBP1	4052	broad.mit.edu	37	2	33172887	33172887	+	Splice_Site	SNP	T	C	C			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33172887T>C	uc002ros.2	+	1	494	c.494_splice	c.e1+2	p.G165_splice		NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GCTGCAGGGGTAAgcccacac	0.517													2	9	---	---	---	---	PASS
CNRIP1	25927	broad.mit.edu	37	2	68520911	68520911	+	3'UTR	SNP	C	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68520911C>A	uc002sek.3	-	3					CNRIP1_uc002sej.3_Intron|CNRIP1_uc002sem.1_RNA|CNRIP1_uc002sel.3_RNA	NM_015463	NP_056278	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1								protein binding			liver(1)	1						AATGGTGTGGCATGCCTTGTT	0.433													9	32	---	---	---	---	PASS
THNSL2	55258	broad.mit.edu	37	2	88478453	88478453	+	Silent	SNP	G	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88478453G>A	uc002ssz.3	+	5	876	c.723G>A	c.(721-723)CAG>CAA	p.Q241Q	THNSL2_uc002ssv.2_RNA|THNSL2_uc002ssw.3_Silent_p.Q241Q|THNSL2_uc002ssx.3_Silent_p.Q209Q|THNSL2_uc002sta.3_Silent_p.Q83Q|THNSL2_uc002ssy.3_Silent_p.Q241Q|THNSL2_uc010fhe.2_Silent_p.Q83Q	NM_018271	NP_060741	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2	241					threonine biosynthetic process		threonine synthase activity			ovary(1)	1						CTTACTTCCAGTGTACGCCAT	0.552													10	447	---	---	---	---	PASS
ANAPC1	64682	broad.mit.edu	37	2	112551673	112551673	+	Silent	SNP	G	A	A	rs141030655	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112551673G>A	uc002thi.2	-	37	4747	c.4500C>T	c.(4498-4500)TCC>TCT	p.S1500S		NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	1500	PC 3.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2						CATTAGGTGCGGACAAATAAG	0.279													4	23	---	---	---	---	PASS
ATG4B	23192	broad.mit.edu	37	2	242611547	242611547	+	Intron	SNP	G	A	A	rs34859751	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242611547G>A	uc002wbv.2	+						ATG4B_uc002wbu.2_3'UTR|ATG4B_uc002wbw.2_Intron|ATG4B_uc010zox.1_Intron|ATG4B_uc010zoy.1_Intron|ATG4B_uc010fzp.2_Intron|ATG4B_uc010zoz.1_Intron|ATG4B_uc002wby.2_Intron	NM_013325	NP_037457	Q9Y4P1	ATG4B_HUMAN	APG4 autophagy 4 homolog B isoform a						autophagic vacuole assembly|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)		AAGGGCCCTTGACTCACACCC	0.587													3	2	---	---	---	---	PASS
ULK4	54986	broad.mit.edu	37	3	41939929	41939929	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41939929T>A	uc003ckv.3	-	14	1544	c.1343A>T	c.(1342-1344)TAT>TTT	p.Y448F	ULK4_uc003ckw.2_Missense_Mutation_p.Y448F|ULK4_uc003ckx.1_Missense_Mutation_p.Y448F	NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4	448							ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CCTACCTGAATATGTTGGTAG	0.274													8	212	---	---	---	---	PASS
ULK4	54986	broad.mit.edu	37	3	41939933	41939933	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41939933T>C	uc003ckv.3	-	14	1540	c.1339A>G	c.(1339-1341)ACA>GCA	p.T447A	ULK4_uc003ckw.2_Missense_Mutation_p.T447A|ULK4_uc003ckx.1_Missense_Mutation_p.T447A	NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4	447							ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CCTGAATATGTTGGTAGATGC	0.279													8	214	---	---	---	---	PASS
CP	1356	broad.mit.edu	37	3	148905905	148905905	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148905905A>C	uc003ewy.3	-	10	2051	c.1798T>G	c.(1798-1800)TTT>GTT	p.F600V	CP_uc011bnr.1_RNA|CP_uc003ewx.3_Missense_Mutation_p.F381V|CP_uc003ewz.2_Missense_Mutation_p.F600V|CP_uc010hvf.1_Missense_Mutation_p.F326V	NM_000096	NP_000087	P00450	CERU_HUMAN	ceruloplasmin precursor	600	Plastocyanin-like 4.|F5/8 type A 2.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	GCAGTTGTAAACATTCTAATA	0.343													6	261	---	---	---	---	PASS
ETV5	2119	broad.mit.edu	37	3	185797681	185797681	+	Missense_Mutation	SNP	G	A	A	rs141531791		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185797681G>A	uc003fpz.2	-	7	822	c.575C>T	c.(574-576)GCG>GTG	p.A192V	ETV5_uc003fpy.2_Missense_Mutation_p.A234V	NM_004454	NP_004445	P41161	ETV5_HUMAN	ets variant gene 5 (ets-related molecule)	192					cellular response to oxidative stress	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			TCGGGGGACCGCAAATGTTTG	0.607			T	TMPRSS2|SCL45A3	Prostate 								4	123	---	---	---	---	PASS
TMEM14B	81853	broad.mit.edu	37	6	10756854	10756854	+	3'UTR	SNP	C	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10756854C>T	uc003mzk.3	+	6					SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jor.2_3'UTR|TMEM14B_uc010jos.1_Intron	NM_030969	NP_112231	Q9NUH8	TM14B_HUMAN	transmembrane protein 14B isoform a							integral to membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)				TTGCATCTGACATTTTACCTA	0.373													3	24	---	---	---	---	PASS
DAXX	1616	broad.mit.edu	37	6	33287900	33287900	+	Silent	SNP	C	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33287900C>T	uc003oec.2	-	5	1557	c.1353G>A	c.(1351-1353)GAG>GAA	p.E451E	ZBTB22_uc003oeb.2_5'Flank|ZBTB22_uc010juu.2_5'Flank|DAXX_uc011drd.1_Silent_p.E376E|DAXX_uc011dre.1_Silent_p.E463E|DAXX_uc003oed.2_Silent_p.E451E	NM_001350	NP_001341	Q9UER7	DAXX_HUMAN	death-domain associated protein isoform a	451	Asp/Glu-rich (acidic).|Potential.|Necessary for interaction with USP7.				activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent	chromosome, centromeric region|cytosol|nucleolus|PML body	androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding			pancreas(18)|ovary(2)|skin(2)|prostate(1)	23						cttcttcttcctcctcctcct	0.254			Mis|F|N		Pancreatic neuroendocrine tumors								3	91	---	---	---	---	PASS
GABRR2	2570	broad.mit.edu	37	6	89974189	89974189	+	Missense_Mutation	SNP	G	A	A	rs149245573	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89974189G>A	uc003pnb.2	-	8	1111	c.1103C>T	c.(1102-1104)GCG>GTG	p.A368V	GABRR2_uc011dzx.1_Missense_Mutation_p.A244V	NM_002043	NP_002034	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 2	368	Helical; (Potential).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity				0		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)		GTTGACAGCCGCATACTCCAG	0.597													3	53	---	---	---	---	PASS
ADCY1	107	broad.mit.edu	37	7	45744119	45744119	+	Silent	SNP	C	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45744119C>A	uc003tne.3	+	17	2739	c.2721C>A	c.(2719-2721)CTC>CTA	p.L907L		NM_021116	NP_066939	Q08828	ADCY1_HUMAN	adenylate cyclase 1	907	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	AAACAAAGCTCATGGAAAAAG	0.498													6	134	---	---	---	---	PASS
PEX1	5189	broad.mit.edu	37	7	92147136	92147136	+	Silent	SNP	G	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92147136G>A	uc003uly.2	-	5	789	c.693C>T	c.(691-693)AAC>AAT	p.N231N	PEX1_uc011khr.1_Silent_p.N23N|PEX1_uc010ley.2_Silent_p.N231N|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_RNA	NM_000466	NP_000457	O43933	PEX1_HUMAN	peroxin1	231					microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TCTCTGACTCGTTTTCATTAG	0.363													6	147	---	---	---	---	PASS
PILRB	29990	broad.mit.edu	37	7	99965285	99965285	+	3'UTR	SNP	T	C	C	rs705866	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99965285T>C	uc003uuk.2	+	18					PILRB_uc003uul.2_3'UTR|PILRB_uc003uun.2_3'UTR	NM_013440	NP_038468	Q9UKJ0	PILRB_HUMAN	paired immunoglobulin-like type 2 receptor beta						activation of transmembrane receptor protein tyrosine kinase activity	integral to plasma membrane	protein binding|receptor activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					gggggctgtttattatagcag	0.179													2	1	---	---	---	---	PASS
ZNF282	8427	broad.mit.edu	37	7	148892653	148892653	+	5'UTR	SNP	C	G	G			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148892653C>G	uc003wfm.2	+	1					ZNF282_uc011kun.1_5'UTR|ZNF282_uc003wfn.2_5'Flank|ZNF282_uc003wfo.2_5'Flank	NM_003575	NP_003566	Q9UDV7	ZN282_HUMAN	zinc finger protein 282						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)		TCTCCCTGGCCGACCCGAGCG	0.667													3	20	---	---	---	---	PASS
CHMP7	91782	broad.mit.edu	37	8	23114023	23114023	+	Silent	SNP	C	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23114023C>T	uc003xdc.2	+	5	1356	c.708C>T	c.(706-708)GAC>GAT	p.D236D	CHMP7_uc011kzs.1_RNA|CHMP7_uc003xdd.2_Silent_p.D126D|CHMP7_uc003xde.2_Silent_p.D94D	NM_152272	NP_689485	Q8WUX9	CHMP7_HUMAN	CHMP family, member 7	236					cellular membrane organization|late endosome to vacuole transport	cytosol|ESCRT III complex	protein transporter activity				0		Prostate(55;0.0513)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		CAGTCAATGACGTAGATGTTG	0.502													5	299	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68413572	68413572	+	RNA	SNP	C	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68413572C>T	uc004aex.2	+	1		c.127C>T								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		CCAGTGGCGCCGGATCTAGGA	0.567													2	4	---	---	---	---	PASS
FAM75C1	441452	broad.mit.edu	37	9	90535283	90535283	+	Missense_Mutation	SNP	T	C	C	rs118048695	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90535283T>C	uc010mqi.2	+	4	490	c.461T>C	c.(460-462)ATG>ACG	p.M154T	FAM75C1_uc004apq.3_Missense_Mutation_p.M137T	NM_001145124	NP_001138596			family with sequence similarity 75, member C1												0						CATGAGCCTATGGAAGATGCT	0.582													5	298	---	---	---	---	PASS
FAM75C1	441452	broad.mit.edu	37	9	90535290	90535290	+	Silent	SNP	T	C	C	rs55701842	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90535290T>C	uc010mqi.2	+	4	497	c.468T>C	c.(466-468)GAT>GAC	p.D156D	FAM75C1_uc004apq.3_Silent_p.D139D	NM_001145124	NP_001138596			family with sequence similarity 75, member C1												0						CTATGGAAGATGCTGCTCCCA	0.592													5	302	---	---	---	---	PASS
MRPL50	54534	broad.mit.edu	37	9	104152773	104152773	+	Missense_Mutation	SNP	T	C	C	rs75793839		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104152773T>C	uc004bbe.2	-	2	497	c.452A>G	c.(451-453)AAT>AGT	p.N151S	MRPL50_uc011lvj.1_Intron	NM_019051	NP_061924	Q8N5N7	RM50_HUMAN	mitochondrial ribosomal protein L50	151						mitochondrion|ribosome					0		Acute lymphoblastic leukemia(62;0.0559)				GATTTTCAAATTGGGGGGCAG	0.398													6	170	---	---	---	---	PASS
MRPL50	54534	broad.mit.edu	37	9	104152775	104152775	+	Silent	SNP	G	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104152775G>A	uc004bbe.2	-	2	495	c.450C>T	c.(448-450)CCC>CCT	p.P150P	MRPL50_uc011lvj.1_Intron	NM_019051	NP_061924	Q8N5N7	RM50_HUMAN	mitochondrial ribosomal protein L50	150						mitochondrion|ribosome					0		Acute lymphoblastic leukemia(62;0.0559)				TTTTCAAATTGGGGGGCAGAT	0.403													6	172	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	56287578	56287578	+	Silent	SNP	G	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56287578G>T	uc001jju.1	-	3	546	c.151C>A	c.(151-153)CGG>AGG	p.R51R	PCDH15_uc010qhq.1_Silent_p.R56R|PCDH15_uc010qhr.1_Silent_p.R51R|PCDH15_uc010qhs.1_Silent_p.R56R|PCDH15_uc010qht.1_Silent_p.R51R|PCDH15_uc010qhu.1_Silent_p.R51R|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Silent_p.R51R|PCDH15_uc010qhw.1_Silent_p.R51R|PCDH15_uc010qhx.1_Silent_p.R51R|PCDH15_uc010qhy.1_Silent_p.R56R|PCDH15_uc010qhz.1_Silent_p.R51R|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Silent_p.R51R	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	51	Cadherin 1.|Extracellular (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				TTACCATTCCGACTTTCTTCA	0.343										HNSCC(58;0.16)			6	123	---	---	---	---	PASS
KRTAP5-6	440023	broad.mit.edu	37	11	1718464	1718464	+	5'UTR	SNP	T	C	C			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1718464T>C	uc001lua.2	+	1						NM_001012416	NP_001012416	Q6L8G9	KRA56_HUMAN	keratin associated protein 5-6							keratin filament					0		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCACCCTCAATCCACCAGAAC	0.637													7	253	---	---	---	---	PASS
TSG101	7251	broad.mit.edu	37	11	18524118	18524118	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18524118G>T	uc001mor.2	-	7	681	c.555C>A	c.(553-555)TAC>TAA	p.Y185*	TSG101_uc001mos.1_Nonsense_Mutation_p.Y133*|TSG101_uc009yhs.1_RNA	NM_006292	NP_006283	Q99816	TS101_HUMAN	tumor susceptibility gene 101	185					cell division|cellular membrane organization|endosome transport|interspecies interaction between organisms|non-lytic virus budding|protein transport|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	early endosome|late endosome membrane|multivesicular body|nucleolus|plasma membrane	calcium-dependent protein binding|DNA binding|transcription corepressor activity|ubiquitin binding|ubiquitin protein ligase binding				0						GACAGCCTGGGTAACCACTAA	0.428													6	14	---	---	---	---	PASS
SPRYD5	84767	broad.mit.edu	37	11	55653591	55653591	+	Intron	SNP	T	G	G			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55653591T>G	uc010rip.1	+						SPRYD5_uc010riq.1_5'UTR	NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN	SPRY domain containing 5							intracellular	zinc ion binding				0		all_epithelial(135;0.226)				TTCGTGGCTGTTTTGCAGGAG	0.398													14	43	---	---	---	---	PASS
PDE2A	5138	broad.mit.edu	37	11	72301503	72301503	+	Missense_Mutation	SNP	G	A	A	rs341047	byFrequency	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72301503G>A	uc010rrc.1	-	8	914	c.671C>T	c.(670-672)ACC>ATC	p.T224I	PDE2A_uc001oso.2_Missense_Mutation_p.T203I|PDE2A_uc010rra.1_Missense_Mutation_p.T217I|PDE2A_uc001osn.2_Intron|PDE2A_uc010rrb.1_Missense_Mutation_p.T215I|PDE2A_uc010rrd.1_Missense_Mutation_p.T109I	NM_002599	NP_002590	O00408	PDE2A_HUMAN	phosphodiesterase 2A isoform 1	224					platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)	GTCGCGGTCGGTGTACGCCGC	0.736													8	9	---	---	---	---	PASS
NARS2	79731	broad.mit.edu	37	11	78277317	78277317	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78277317T>C	uc001ozi.2	-	4	750	c.374A>G	c.(373-375)GAT>GGT	p.D125G	NARS2_uc010rsq.1_5'UTR	NM_024678	NP_078954	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial	125					asparaginyl-tRNA aminoacylation	mitochondrial matrix	asparagine-tRNA ligase activity|ATP binding|nucleic acid binding			ovary(2)	2	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	GATGGGGAAATCCTGCCAATA	0.363													13	59	---	---	---	---	PASS
IL10RA	3587	broad.mit.edu	37	11	117864125	117864125	+	Silent	SNP	G	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117864125G>A	uc001prv.2	+	4	614	c.537G>A	c.(535-537)ACG>ACA	p.T179T	IL10RA_uc010rxl.1_Silent_p.T159T|IL10RA_uc010rxm.1_Silent_p.T159T|IL10RA_uc010rxn.1_Silent_p.T30T|IL10RA_uc001prw.2_Silent_p.T30T	NM_001558	NP_001549	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha precursor	179	Extracellular (Potential).					integral to membrane|plasma membrane	interleukin-10 receptor activity			ovary(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		GAAACTTCACGGTATGGGGTT	0.562													3	83	---	---	---	---	PASS
RECQL	5965	broad.mit.edu	37	12	21623127	21623127	+	3'UTR	SNP	A	G	G	rs143505576	byFrequency	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21623127A>G	uc001rex.2	-	16					RECQL_uc001rey.2_3'UTR|PYROXD1_uc001rew.2_3'UTR|PYROXD1_uc009ziq.2_3'UTR|PYROXD1_uc009zir.2_3'UTR	NM_032941	NP_116559	P46063	RECQ1_HUMAN	RecQ protein-like						DNA recombination|DNA repair|DNA replication	nucleus	ATP binding|ATP-dependent 3'-5' DNA helicase activity|DNA strand annealing activity|protein binding			ovary(1)|lung(1)	2						TAACATTCATATCAGGCATCA	0.299								Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					3	136	---	---	---	---	PASS
P2RX4	5025	broad.mit.edu	37	12	121671496	121671496	+	3'UTR	SNP	G	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121671496G>A	uc001tzr.2	+	12					P2RX4_uc009zxc.2_3'UTR|P2RX4_uc001tzs.2_3'UTR|P2RX4_uc009zxb.2_RNA|P2RX4_uc010szt.1_3'UTR	NM_002560	NP_002551	Q99571	P2RX4_HUMAN	purinergic receptor P2X4						endothelial cell activation|negative regulation of cardiac muscle hypertrophy|positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling|positive regulation of nitric oxide biosynthetic process|positive regulation of prostaglandin secretion|regulation of apoptosis|regulation of blood pressure|regulation of sodium ion transport|relaxation of cardiac muscle|response to ATP|response to fluid shear stress|sensory perception of pain|tissue homeostasis	cell junction|perinuclear region of cytoplasm	cadherin binding|copper ion binding|extracellular ATP-gated cation channel activity|protein homodimerization activity|purinergic nucleotide receptor activity|receptor binding|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TTCCCCAGCAGCTCCTGTGTG	0.557													2	3	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22932283	22932283	+	Intron	SNP	G	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22932283G>T	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wds.1_Intron|uc001wdv.3_Intron|uc001wdx.3_Intron|uc001wdz.3_3'UTR|uc010tms.1_Intron|uc010ajt.2_3'UTR|uc010aju.1_Intron|uc001wea.3_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																		ATGTAACTGTGGACAAATCAT	0.443													3	58	---	---	---	---	PASS
CPSF2	53981	broad.mit.edu	37	14	92608697	92608697	+	Splice_Site	SNP	T	C	C			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92608697T>C	uc001yah.1	+	8	1086	c.849_splice	c.e8+2	p.Q283_splice		NM_017437	NP_059133	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		AAGTCCCAGGTTTGTTCTCAT	0.383													5	286	---	---	---	---	PASS
LOC646214	646214	broad.mit.edu	37	15	21938316	21938316	+	RNA	SNP	A	C	C	rs111913251	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21938316A>C	uc010tzj.1	-	1		c.2424T>G				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						aaacctgacaaaaacaagaaa	0.010													4	18	---	---	---	---	PASS
CDAN1	146059	broad.mit.edu	37	15	43022880	43022880	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43022880A>C	uc001zql.2	-	14	2207	c.2090T>G	c.(2089-2091)GTG>GGG	p.V697G	CDAN1_uc001zqj.2_RNA|CDAN1_uc001zqk.2_Missense_Mutation_p.W23G	NM_138477	NP_612486	Q8IWY9	CDAN1_HUMAN	codanin 1	697						integral to membrane	protein binding			ovary(2)	2		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		GAGAAACTCCACCAGCCAGGG	0.637													6	41	---	---	---	---	PASS
CSPG4	1464	broad.mit.edu	37	15	75980335	75980335	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75980335C>A	uc002baw.2	-	3	3164	c.3071G>T	c.(3070-3072)AGC>ATC	p.S1024I		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4 precursor	1024	Interaction with COL5A1 (By similarity).|Extracellular (Potential).|Gly/Ser-rich (glycosaminoglycan attachment domain).|CSPG 6.|Interaction with COL6A2 (By similarity).				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3						GAAGATCCGGCTGATGGTCTG	0.657													4	118	---	---	---	---	PASS
GOLGA6L5	374650	broad.mit.edu	37	15	85055872	85055872	+	RNA	SNP	C	T	T	rs62029638	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85055872C>T	uc002bkm.2	-	6		c.688G>A				NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						CTCCTGTTCACGTAGCCTCTC	0.547													6	10	---	---	---	---	PASS
ATP2C2	9914	broad.mit.edu	37	16	84402275	84402275	+	Silent	SNP	G	C	C	rs62048787	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84402275G>C	uc002fhx.2	+	1	143	c.54G>C	c.(52-54)GGG>GGC	p.G18G	ATP2C2_uc010chj.2_Silent_p.G18G	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	18	Cytoplasmic (Potential).				ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2						TCTCGGGCGGGGGCCGCCAGT	0.706													3	9	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9075833	9075833	+	Silent	SNP	C	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9075833C>T	uc002mkp.2	-	3	11817	c.11613G>A	c.(11611-11613)GAG>GAA	p.E3871E		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	3872	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						ATTTTTCTTTCTCATTCCAGG	0.448													8	100	---	---	---	---	PASS
PBX4	80714	broad.mit.edu	37	19	19675795	19675795	+	Missense_Mutation	SNP	G	A	A	rs139542458		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19675795G>A	uc002nmy.2	-	6	873	c.872C>T	c.(871-873)ACG>ATG	p.T291M	PBX4_uc010xqz.1_RNA|PBX4_uc010xra.1_Missense_Mutation_p.T126M	NM_025245	NP_079521	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4	291							sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|ovary(1)	2						CCCAACTTCCGTGGTATCCAC	0.527													9	377	---	---	---	---	PASS
CYP2B6	1555	broad.mit.edu	37	19	41497274	41497274	+	Missense_Mutation	SNP	C	T	T	rs8192709	byFrequency	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41497274C>T	uc002opr.1	+	1	71	c.64C>T	c.(64-66)CGC>TGC	p.R22C	CYP2A7_uc002opo.2_Intron	NM_000767	NP_000758	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B,	22					cellular ketone metabolic process|exogenous drug catabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|skin(1)	2			LUSC - Lung squamous cell carcinoma(20;0.00322)		Bupropion(DB01156)|Butalbital(DB00241)|Carbamazepine(DB00564)|Clopidogrel(DB00758)|Cyclophosphamide(DB00531)|Efavirenz(DB00625)|Ifosfamide(DB01181)|Memantine(DB01043)|Meperidine(DB00454)|Mephenytoin(DB00532)|Methadone(DB00333)|Methylphenobarbital(DB00849)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicotine(DB00184)|Orphenadrine(DB01173)|Phenytoin(DB00252)|Propofol(DB00818)|Ritonavir(DB00503)|Selegiline(DB01037)|Sertraline(DB01104)|Ticlopidine(DB00208)|Troleandomycin(DB01361)	CCTGGTTCAGCGCCACCCTAA	0.592													15	491	---	---	---	---	PASS
NSFL1C	55968	broad.mit.edu	37	20	1433675	1433675	+	Splice_Site	SNP	C	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1433675C>T	uc002wfc.2	-	6	1595	c.647_splice	c.e6+1	p.G216_splice	NSFL1C_uc002wfd.2_Splice_Site_p.G105_splice|NSFL1C_uc002wfe.2_Splice_Site_p.G185_splice|NSFL1C_uc002wff.2_Splice_Site|NSFL1C_uc010gag.2_Translation_Start_Site	NM_016143	NP_057227	Q9UNZ2	NSF1C_HUMAN	p47 protein isoform a							chromosome|Golgi stack|nucleus	lipid binding|protein binding				0						TTTTCACTCACCCTCTGCGGA	0.453													7	354	---	---	---	---	PASS
SLC4A11	83959	broad.mit.edu	37	20	3209652	3209652	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3209652A>C	uc002wig.2	-	16	2120	c.2072T>G	c.(2071-2073)GTG>GGG	p.V691G	SLC4A11_uc010zqe.1_Missense_Mutation_p.V718G|SLC4A11_uc002wih.2_RNA|SLC4A11_uc010zqf.1_Missense_Mutation_p.V675G	NM_032034	NP_114423	Q8NBS3	S4A11_HUMAN	solute carrier family 4 member 11	691	Membrane (bicarbonate transporter).				cellular cation homeostasis|fluid transport|phosphoenolpyruvate-dependent sugar phosphotransferase system	basolateral plasma membrane|integral to membrane	bicarbonate transmembrane transporter activity|borate transmembrane transporter activity|hydrogen ion channel activity|inorganic anion exchanger activity|sodium channel activity|sugar:hydrogen symporter activity			ovary(1)	1						AGTGCCCTTCACCAGCCTGCA	0.667													8	25	---	---	---	---	PASS
RAE1	8480	broad.mit.edu	37	20	55948583	55948583	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55948583C>T	uc002xyg.2	+	9	1036	c.695C>T	c.(694-696)GCC>GTC	p.A232V	RAE1_uc010gis.1_Missense_Mutation_p.A185V|RAE1_uc010git.1_Missense_Mutation_p.A232V|RAE1_uc002xyh.2_Missense_Mutation_p.A232V|RAE1_uc002xyi.2_Missense_Mutation_p.A232V	NM_003610	NP_003601	P78406	RAE1L_HUMAN	RAE1 (RNA export 1, S.pombe) homolog	232					carbohydrate metabolic process|glucose transport|mRNA export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|cytoskeleton|nuclear outer membrane|nuclear pore	microtubule binding|RNA binding				0	Lung NSC(12;0.00263)|all_lung(29;0.00828)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;3.7e-14)|Epithelial(14;1.07e-09)|all cancers(14;1.11e-08)			ACTGGTTTTGCCCTGGGAAGT	0.398													4	137	---	---	---	---	PASS
C21orf70	85395	broad.mit.edu	37	21	46387079	46387079	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46387079C>A	uc002zgl.2	+	4	501	c.483C>A	c.(481-483)AGC>AGA	p.S161R	C21orf70_uc002zgm.2_Missense_Mutation_p.S146R	NM_058190	NP_478070	Q9NSI2	CU070_HUMAN	hypothetical protein LOC85395	161											0				Colorectal(79;0.248)		AGGCTGGCAGCCGGCGCCAAG	0.716													3	22	---	---	---	---	PASS
MORC2	22880	broad.mit.edu	37	22	31322760	31322760	+	3'UTR	SNP	T	G	G			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31322760T>G	uc003aje.1	-	27						NM_014941	NP_055756	Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2								ATP binding|zinc ion binding			ovary(1)|pancreas(1)	2						GAGGGGCAGGTGGGCAGGGGA	0.552													15	24	---	---	---	---	PASS
XRCC6	2547	broad.mit.edu	37	22	42057337	42057337	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42057337C>T	uc003bao.1	+	12	1595	c.1525C>T	c.(1525-1527)CCC>TCC	p.P509S	XRCC6_uc003bap.1_Missense_Mutation_p.P468S|XRCC6_uc011apc.1_Missense_Mutation_p.P459S|XRCC6_uc003baq.1_Missense_Mutation_p.P509S|XRCC6_uc003bar.1_Missense_Mutation_p.P509S|XRCC6_uc003bas.1_Missense_Mutation_p.P459S	NM_001469	NP_001460	P12956	XRCC6_HUMAN	ATP-dependent DNA helicase II, 70 kDa subunit	509					DNA ligation|double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|provirus integration|telomere maintenance|transcription, DNA-dependent	DNA-dependent protein kinase-DNA ligase 4 complex|Ku70:Ku80 complex|membrane fraction|nuclear telomere cap complex|transcription factor complex	5'-deoxyribose-5-phosphate lyase activity|ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|transcription regulatory region DNA binding			skin(2)|ovary(1)|lung(1)|kidney(1)	5						TTTTCTAGTGCCCAAGGTTGA	0.473								Direct_reversal_of_damage|NHEJ					7	250	---	---	---	---	PASS
MAGEB6	158809	broad.mit.edu	37	X	26212305	26212305	+	Silent	SNP	T	G	G	rs4997767	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26212305T>G	uc004dbr.2	+	2	491	c.342T>G	c.(340-342)TCT>TCG	p.S114S	MAGEB6_uc010ngc.1_Intron	NM_173523	NP_775794	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	114	Ser-rich.									ovary(3)	3						CCACTGGCTCTCCTGATGCAG	0.537													3	75	---	---	---	---	PASS
XIST	7503	broad.mit.edu	37	X	73066367	73066367	+	RNA	SNP	T	C	C			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73066367T>C	uc004ebm.1	-	1		c.6222A>G				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0						AGTAGGACCTTATTCACATGG	0.448													6	127	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	3243	3243	+	5'Flank	SNP	A	G	G			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:3243A>G	uc004coq.3	-						uc004cos.3_RNA|uc011mfh.1_5'Flank					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		taagatggcagagcccggtaa	0.289													3	8	---	---	---	---	PASS
KIF1B	23095	broad.mit.edu	37	1	10436893	10436894	+	3'UTR	DEL	AC	-	-	rs111663673		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10436893_10436894delAC	uc001aqx.3	+	49					KIF1B_uc001aqw.3_3'UTR|KIF1B_uc001aqy.2_Intron|KIF1B_uc001aqz.2_Intron|KIF1B_uc001ara.2_Intron|KIF1B_uc001arb.2_Intron	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		ATGTTTTTAAacacacacacac	0.297													4	2	---	---	---	---	
ANKRD13C	81573	broad.mit.edu	37	1	70728658	70728659	+	Intron	INS	-	AG	AG	rs150975244	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70728658_70728659insAG	uc001dex.3	-						ANKRD13C_uc009wbk.2_Intron	NM_030816	NP_110443	Q8N6S4	AN13C_HUMAN	ankyrin repeat domain 13C						protein retention in ER lumen|regulation of anoikis|regulation of receptor biosynthetic process	endoplasmic reticulum membrane|perinuclear region of cytoplasm	receptor binding				0						CAAGAACCAGAAGAATTCAAAT	0.302													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	78886740	78886741	+	IGR	INS	-	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78886740_78886741insT								MGC27382 (51595 upstream) : PTGFR (69987 downstream)																							ttccttccttctttccttcctt	0.010													4	3	---	---	---	---	
CNTN2	6900	broad.mit.edu	37	1	205034852	205034853	+	Intron	INS	-	TGGCCTGCTGCACTGGTCAGGGCCGGTGGTC	TGGCCTGCTGCACTGGTCAGGGCCGGTGGTC	rs143128501	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205034852_205034853insTGGCCTGCTGCACTGGTCAGGGCCGGTGGTC	uc001hbr.2	+						CNTN2_uc001hbq.1_Intron|CNTN2_uc001hbs.2_Intron	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor						axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CTCATGTCTCATGGCCTGCTGC	0.589													61	7	---	---	---	---	
RAB3GAP2	25782	broad.mit.edu	37	1	220387075	220387075	+	Intron	DEL	G	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220387075delG	uc010puk.1	-						RAB3GAP2_uc001hmf.2_Intron|RAB3GAP2_uc001hmg.2_Intron|RAB3GAP2_uc010pum.1_Intron	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)		aggaggagttggggggggggg	0.174													4	2	---	---	---	---	
PCNXL2	80003	broad.mit.edu	37	1	233424551	233424552	+	Intron	DEL	TT	-	-	rs10558976		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233424551_233424552delTT	uc001hvl.2	-							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)				AAAGATGCCCtttttttttttt	0.356													7	4	---	---	---	---	
HEATR1	55127	broad.mit.edu	37	1	236732199	236732200	+	Intron	INS	-	C	C	rs76883267		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236732199_236732200insC	uc001hyd.1	-						HEATR1_uc009xgh.1_Intron	NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28						rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			aaaaaaaaacaaaaaaaaaaaa	0.262													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	12293381	12293382	+	Intron	INS	-	TCCC	TCCC			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12293381_12293382insTCCC	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																		ccttccctccttccttccttcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	34041837	34041838	+	IGR	INS	-	CCTCC	CCTCC	rs141683394	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34041837_34041838insCCTCC								MYADML (88553 upstream) : None (None downstream)																							tcttctcttctcctcccctccc	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	58479808	58479808	+	IGR	DEL	A	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58479808delA								FANCL (11293 upstream) : None (None downstream)																							TTTGtaaattaaaaaaaaaaa	0.234													9	4	---	---	---	---	
ALMS1P	200420	broad.mit.edu	37	2	73900214	73900214	+	Intron	DEL	A	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73900214delA	uc010yrl.1	+							NR_003683				RecName: Full=Putative ALMS1-like protein;												0						CCCTACATGTAGGGAGAAGAA	0.557													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	132586331	132586332	+	IGR	INS	-	C	C			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132586331_132586332insC								C2orf27B (27097 upstream) : NCRNA00164 (318832 downstream)																							CGCACCTCGCGCCCAGCAGGTT	0.698													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	146656726	146656727	+	IGR	INS	-	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146656726_146656727insT								None (None upstream) : PABPC1P2 (687898 downstream)																							tttcttttttctttttttttcc	0.149													4	2	---	---	---	---	
OTOS	150677	broad.mit.edu	37	2	241078958	241078960	+	Intron	DEL	GAA	-	-	rs10526200		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241078958_241078960delGAA	uc002vyv.2	-							NM_148961	NP_683764	Q8NHW6	OTOSP_HUMAN	otospiralin precursor							extracellular region					0		all_epithelial(40;2.79e-15)|Breast(86;3.04e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|Hepatocellular(293;0.148)|all_hematologic(139;0.158)|Melanoma(123;0.16)		Epithelial(32;2.56e-30)|all cancers(36;7.18e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.37e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.07e-06)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)|Colorectal(34;0.019)|COAD - Colon adenocarcinoma(134;0.141)		GGAGACAGAGGAAGAAGAAGAAG	0.581													5	3	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41939887	41939888	+	Intron	DEL	AG	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41939887_41939888delAG	uc003ckv.3	-						ULK4_uc003ckw.2_Intron|ULK4_uc003ckx.1_Intron	NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CTGTATACAAAGAGTCTACATG	0.302													196	8	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52668452	52668454	+	Intron	DEL	AAA	-	-	rs79463946		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52668452_52668454delAAA	uc003des.2	-						PBRM1_uc003dex.2_Intron|PBRM1_uc003deq.2_Intron|PBRM1_uc003der.2_Intron|PBRM1_uc003det.2_Intron|PBRM1_uc003deu.2_Intron|PBRM1_uc003dev.2_Intron|PBRM1_uc003dew.2_Intron|PBRM1_uc010hmk.1_Intron|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_Intron|PBRM1_uc003dfb.1_Intron	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		actccgtctcaaaaaaaaaaaaa	0.103			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								3	3	---	---	---	---	
CCDC80	151887	broad.mit.edu	37	3	112329033	112329034	+	Intron	INS	-	A	A	rs146699705		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112329033_112329034insA	uc003dzf.2	-						CCDC80_uc011bhv.1_Intron|CCDC80_uc003dzg.2_Intron|CCDC80_uc003dzh.1_Intron	NM_199512	NP_955806	Q76M96	CCD80_HUMAN	steroid-sensitive protein 1 precursor											ovary(2)	2						TCTGTGCCCAGAAAAAAAAAAA	0.361													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152446726	152446727	+	IGR	INS	-	TTCCTTCCCTCCTTCC	TTCCTTCCCTCCTTCC			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152446726_152446727insTTCCTTCCCTCCTTCC								MBNL1 (263158 upstream) : P2RY1 (106009 downstream)																							ACAGTTTttctttccttccttc	0.173													5	4	---	---	---	---	
RBM47	54502	broad.mit.edu	37	4	40438223	40438224	+	Intron	INS	-	C	C	rs142373140		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40438223_40438224insC	uc003gvc.2	-						RBM47_uc003gvd.2_Intron|RBM47_uc003gve.2_Intron|RBM47_uc011bys.1_Intron	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a							nucleus	nucleotide binding|RNA binding			breast(3)	3						aaacaaacaaaaaaaAACCTTA	0.208													3	3	---	---	---	---	
CHIC2	26511	broad.mit.edu	37	4	54876121	54876122	+	3'UTR	INS	-	A	A	rs145864126	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54876121_54876122insA	uc003haj.1	-	6					PDGFRA_uc003haa.2_Intron	NM_012110	NP_036242	Q9UKJ5	CHIC2_HUMAN	cysteine-rich hydrophobic domain 2							plasma membrane	protein binding			central_nervous_system(1)	1	all_cancers(7;0.0193)|all_neural(26;0.0209)|Lung NSC(11;0.0281)|Glioma(25;0.08)		LUSC - Lung squamous cell carcinoma(32;0.00216)			TGCGGTTATTTaaaaaaaaaac	0.317			T	ETV6	AML								8	4	---	---	---	---	
SMARCAD1	56916	broad.mit.edu	37	4	95202130	95202133	+	Intron	DEL	AGTT	-	-	rs34519004		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95202130_95202133delAGTT	uc003htc.3	+						SMARCAD1_uc003htb.3_Intron|SMARCAD1_uc003htd.3_Intron|SMARCAD1_uc010ila.2_Intron|SMARCAD1_uc011cdw.1_Intron	NM_020159	NP_064544	Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated						chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		AACAATAGAAAGTTAGTAGACTGT	0.304													4	7	---	---	---	---	
SCLT1	132320	broad.mit.edu	37	4	130003740	130003740	+	Intron	DEL	A	-	-	rs67888649		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130003740delA	uc003igp.2	-						SCLT1_uc003igq.2_Intron|SCLT1_uc010iob.1_Intron|SCLT1_uc003igr.2_Intron|SCLT1_uc003igs.2_Intron|SCLT1_uc003igt.3_Intron	NM_144643	NP_653244	Q96NL6	SCLT1_HUMAN	sodium channel associated protein 1							centrosome				ovary(3)|lung(1)|central_nervous_system(1)	5						TGCCAAAGTGAAAAAAATAAC	0.313													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	9971301	9971302	+	IGR	DEL	TG	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9971301_9971302delTG								LOC285692 (67365 upstream) : FAM173B (255136 downstream)																							TTTTTTCTTTtgtgtgtgtgtg	0.262													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	55028949	55028956	+	IGR	DEL	TCCTTCCT	-	-	rs7380931		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55028949_55028956delTCCTTCCT								SLC38A9 (20395 upstream) : DDX4 (4889 downstream)																							ttctctttcctccttccttccttccttc	0.000													4	2	---	---	---	---	
ARRDC3	57561	broad.mit.edu	37	5	90669429	90669430	+	Intron	INS	-	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90669429_90669430insA	uc003kjz.2	-							NM_020801	NP_065852	Q96B67	ARRD3_HUMAN	arrestin domain containing 3						signal transduction	cytoplasm	protein binding			ovary(1)|breast(1)	2		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)		ATAACATTAAGAAAAAAAAATG	0.297													131	7	---	---	---	---	
LEAP2	116842	broad.mit.edu	37	5	132209165	132209168	+	5'Flank	DEL	TCAC	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132209165_132209168delTCAC	uc003kyc.2	+						LEAP2_uc003kyb.1_5'Flank	NM_052971	NP_443203	Q969E1	LEAP2_HUMAN	liver-expressed antimicrobial peptide 2						defense response to bacterium	extracellular region					0		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGCAACACAATCACTCAAAGTCCA	0.466													2	7	---	---	---	---	
FLT4	2324	broad.mit.edu	37	5	180051227	180051227	+	Intron	DEL	G	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180051227delG	uc003mma.3	-						FLT4_uc003mlz.3_Intron|FLT4_uc003mmb.1_Intron|FLT4_uc011dgy.1_Intron	NM_002020	NP_002011	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4 isoform 2						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)	GGACTTTGGTGtttttttttt	0.313									Congenital_Hereditary_Lymphedema				4	2	---	---	---	---	
HLA-DRB5	3127	broad.mit.edu	37	6	32547921	32547922	+	Intron	INS	-	AGAC	AGAC			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32547921_32547922insAGAC	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obo.1_Intron|uc010jub.1_5'Flank|HLA-DRB1_uc003obp.3_Intron|HLA-DRB1_uc011dqb.1_Intron	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						aacctcttgtaagaaaagttct	0.074													8	4	---	---	---	---	
EFHC1	114327	broad.mit.edu	37	6	52344223	52344224	+	Intron	DEL	TT	-	-	rs55987008		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52344223_52344224delTT	uc003pap.3	+						EFHC1_uc011dwv.1_Intron|EFHC1_uc011dww.1_Intron	NM_018100	NP_060570	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1							axoneme|neuronal cell body	calcium ion binding|protein C-terminus binding			ovary(2)|skin(1)	3	Lung NSC(77;0.109)					AATTAAACTCTTAAGTTGATTG	0.337													14	7	---	---	---	---	
RNF217	154214	broad.mit.edu	37	6	125346722	125346723	+	Intron	INS	-	AGGG	AGGG	rs140086309	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125346722_125346723insAGGG	uc003pzs.2	+						RNF217_uc003pzr.2_Intron|RNF217_uc003pzt.2_Intron	NM_152553	NP_689766	Q8TC41	RN217_HUMAN	ring finger protein 217						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0162)		gaaaagaaggaagggagggagg	0.257													4	2	---	---	---	---	
C7orf28B	221960	broad.mit.edu	37	7	6839053	6839054	+	Intron	INS	-	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6839053_6839054insT	uc003sqx.1	-						C7orf28B_uc011jxd.1_Intron	NM_198097	NP_932765	P86791	CCZ1_HUMAN	hypothetical protein LOC221960							lysosomal membrane					0		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)		CTAGGCAAGAAttttttttttt	0.144													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	22902264	22902265	+	IGR	DEL	GT	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22902264_22902265delGT								SNORD93 (5960 upstream) : FAM126A (78622 downstream)																							CCTGATCTTAgtgtgtgtgtgt	0.153													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	30535931	30535932	+	IGR	INS	-	AC	AC			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30535931_30535932insAC								NOD1 (17538 upstream) : GGCT (307 downstream)																							GCTTATTTTATacacacacaca	0.020													4	2	---	---	---	---	
TBX20	57057	broad.mit.edu	37	7	35288459	35288460	+	Intron	DEL	AG	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35288459_35288460delAG	uc011kas.1	-							NM_001077653	NP_001071121	Q9UMR3	TBX20_HUMAN	T-box transcription factor TBX20							nucleus	DNA binding			central_nervous_system(1)	1						TCCTCCTGACAGAGAGAGAGAG	0.421													123	7	---	---	---	---	
GTF2IRD1	9569	broad.mit.edu	37	7	73974113	73974114	+	Intron	INS	-	T	T	rs112974956		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73974113_73974114insT	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						CCCTGCCtttcttttttttttt	0.312													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	75788111	75788112	+	IGR	INS	-	AAA	AAA	rs144835429	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75788111_75788112insAAA								MDH2 (92183 upstream) : SRRM3 (43104 downstream)																							acaacaacaacaacaaAATAAA	0.114													3	3	---	---	---	---	
SLC26A4	5172	broad.mit.edu	37	7	107338764	107338764	+	Intron	DEL	T	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107338764delT	uc003vep.2	+						SLC26A4_uc011kmb.1_Intron|SLC26A4_uc011kmc.1_Intron|SLC26A4_uc011kmd.1_Intron	NM_000441	NP_000432	O43511	S26A4_HUMAN	pendrin						regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7						GCTGAATGTCttttttttttt	0.214									Pendred_syndrome				6	4	---	---	---	---	
PPP1R3A	5506	broad.mit.edu	37	7	113519968	113519968	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113519968delT	uc010ljy.1	-	4	1210	c.1179delA	c.(1177-1179)AAAfs	p.K393fs		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	393					glycogen metabolic process	integral to membrane				lung(9)|ovary(9)|pancreas(7)|skin(6)|breast(2)|prostate(1)	34						CTGAGGAATATTTTTCATTGC	0.393													413	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	142461091	142461093	+	Intron	DEL	AAG	-	-	rs148616464	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142461091_142461093delAAG	uc011krr.1	+						uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Intron|TRY6_uc011ksn.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																		ATCCAAAAATAAGAAGAAGCTTG	0.443													4	2	---	---	---	---	
ARHGEF10	9639	broad.mit.edu	37	8	1806393	1806393	+	Intron	DEL	A	-	-	rs11331147		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1806393delA	uc003wpr.2	+						ARHGEF10_uc003wpq.1_Intron|ARHGEF10_uc003wps.2_Intron|ARHGEF10_uc003wpt.2_5'Flank|ARHGEF10_uc010lrd.1_5'Flank|ARHGEF10_uc003wpu.2_5'Flank	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10						centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		tccccaggtgagtccccaggt	0.154													2	4	---	---	---	---	
EPHX2	2053	broad.mit.edu	37	8	27382586	27382587	+	Intron	DEL	TG	-	-	rs71553863		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27382586_27382587delTG	uc003xfu.2	+						EPHX2_uc010lut.1_Intron|EPHX2_uc010luu.2_Intron|EPHX2_uc010luv.2_Intron|EPHX2_uc003xfv.2_Intron|EPHX2_uc010luw.2_Intron	NM_001979	NP_001970	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic						aromatic compound catabolic process|cellular calcium ion homeostasis|drug metabolic process|inflammatory response|positive regulation of vasodilation|reactive oxygen species metabolic process|regulation of blood pressure|response to toxin|xenobiotic metabolic process	cytosol|focal adhesion|Golgi apparatus|nucleolus|peroxisome|soluble fraction	epoxide hydrolase activity|metal ion binding|protein homodimerization activity			ovary(1)	1		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)	Tamoxifen(DB00675)	GTATGTGTACtgtgtgtgtgtg	0.302													4	2	---	---	---	---	
TG	7038	broad.mit.edu	37	8	134129131	134129131	+	Intron	DEL	A	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134129131delA	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		ggggaaagttaaaaaaaaaaa	0.055													2	4	---	---	---	---	
SUGT1P1	441394	broad.mit.edu	37	9	33449647	33449647	+	Intron	DEL	A	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33449647delA	uc010mjq.1	-						AQP3_uc003zsv.1_5'Flank|AQP3_uc003zsx.2_5'Flank|AQP3_uc010mju.2_5'Flank	NR_003667				Homo sapiens suppressor of G2 allele of SKP1 pseudogene (S. cerevisiae) (SUGT1P), non-coding RNA.												0						actccatctcaaaaaaaaaaa	0.224													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68413562	68413563	+	RNA	INS	-	G	G	rs71256949		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68413562_68413563insG	uc004aex.2	+	1		c.117_118insG								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		TTCAGCTCCCCCAGTGGCGCCG	0.535													5	3	---	---	---	---	
PANK1	53354	broad.mit.edu	37	10	91353292	91353292	+	Intron	DEL	A	-	-	rs3215821		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91353292delA	uc001kgp.1	-						PANK1_uc001kgn.1_Intron|PANK1_uc001kgo.1_Intron|PANK1_uc009xtu.1_Intron|uc001kgq.1_5'Flank|MIR107_hsa-mir-107|MI0000114_5'Flank	NM_148977	NP_683878	Q8TE04	PANK1_HUMAN	pantothenate kinase 1 isoform alpha						coenzyme A biosynthetic process|pantothenate metabolic process	cytosol|nucleus	ATP binding|pantothenate kinase activity				0					Bezafibrate(DB01393)	ATGGGGGGGGAAAATTAATGC	0.378													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	125014051	125014052	+	IGR	INS	-	CAC	CAC			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125014051_125014052insCAC								BUB3 (89165 upstream) : GPR26 (411819 downstream)																							caccaccatcacaccaccacca	0.000													4	2	---	---	---	---	
JAKMIP3	282973	broad.mit.edu	37	10	133961636	133961637	+	Intron	INS	-	TGAACA	TGAACA	rs141683861	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133961636_133961637insTGAACA	uc001lkx.3	+						JAKMIP3_uc009yba.1_Intron	NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		ACACAAAGCCCtgaacatgaac	0.495													4	3	---	---	---	---	
SLC22A18	5002	broad.mit.edu	37	11	2940338	2940360	+	Intron	DEL	GGCACTTTCCACACCAGGGATAC	-	-	rs143592360		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2940338_2940360delGGCACTTTCCACACCAGGGATAC	uc001lwx.2	+						SLC22A18_uc001lwy.2_Intron|SLC22A18_uc001lwz.2_Intron	NM_183233	NP_899056	Q96BI1	S22AI_HUMAN	tumor suppressing subtransferable candidate 5						excretion|organic cation transport	apical plasma membrane|cytoplasmic part|integral to membrane|nuclear envelope	drug:hydrogen antiporter activity|symporter activity|ubiquitin protein ligase binding			central_nervous_system(2)|ovary(1)	3		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		ccacacgagaggcactttccacaccagggatacggcagaatcc	0.157													6	3	---	---	---	---	
FAR1	84188	broad.mit.edu	37	11	13722198	13722199	+	Intron	INS	-	TCT	TCT	rs137872059	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13722198_13722199insTCT	uc001mld.2	+						FAR1_uc009ygp.2_Intron	NM_032228	NP_115604	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1						ether lipid biosynthetic process	integral to membrane|peroxisomal matrix|peroxisomal membrane	protein binding			ovary(1)|skin(1)	2						TAAAAGAATTCTCTTCTTCTTC	0.317													5	4	---	---	---	---	
EIF3M	10480	broad.mit.edu	37	11	32609951	32609958	+	Intron	DEL	AAAAAAAG	-	-	rs71463359		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32609951_32609958delAAAAAAAG	uc001mtu.2	+						EIF3M_uc010ref.1_Intron	NM_006360	NP_006351	Q7L2H7	EIF3M_HUMAN	eukaryotic translation initiation factor 3,							eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)|breast(1)|skin(1)	3	Breast(20;0.109)					aaaaaaaaaaaaaaaaagaaaCCACATC	0.149													7	5	---	---	---	---	
UBASH3B	84959	broad.mit.edu	37	11	122597059	122597060	+	Intron	INS	-	C	C	rs7113307	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122597059_122597060insC	uc001pyi.3	+							NM_032873	NP_116262	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing,							cytoplasm|nucleus	protein tyrosine phosphatase activity			central_nervous_system(1)	1		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		ttcttcttcttttttttttttt	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	124144175	124144175	+	IGR	DEL	T	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124144175delT								OR8G2 (47865 upstream) : OR8D1 (35562 downstream)																							CCATCATTCCTTTTTTTTTTT	0.413													4	2	---	---	---	---	
FOXRED1	55572	broad.mit.edu	37	11	126146771	126146772	+	Intron	INS	-	A	A			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126146771_126146772insA	uc001qdi.2	+						FOXRED1_uc010sbn.1_Intron|FOXRED1_uc010sbo.1_Intron|FOXRED1_uc010sbp.1_Intron|FOXRED1_uc010sbq.1_Intron|FOXRED1_uc001qdj.2_Intron|FOXRED1_uc010sbr.1_Intron|FOXRED1_uc001qdk.2_Intron	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing							integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)		aactccatctcaaaaaaaaaaa	0.183													4	2	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	5693305	5693306	+	Intron	INS	-	CCG	CCG	rs140461271	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5693305_5693306insCCG	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						ACACCCCCCCCCCGCCGCAAGA	0.475													4	2	---	---	---	---	
ELK3	2004	broad.mit.edu	37	12	96635204	96635205	+	Intron	INS	-	TG	TG	rs138999912	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96635204_96635205insTG	uc001teo.1	+							NM_005230	NP_005221	P41970	ELK3_HUMAN	ELK3 protein						negative regulation of transcription, DNA-dependent|signal transduction	mitochondrion	protein binding|purine-rich negative regulatory element binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	all_cancers(2;0.00173)					AGTGGAGCGTTtgtgtgtgtgt	0.302													4	2	---	---	---	---	
GNPTAB	79158	broad.mit.edu	37	12	102159644	102159648	+	Intron	DEL	AAACA	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102159644_102159648delAAACA	uc001tit.2	-							NM_024312	NP_077288	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase						cell differentiation	Golgi membrane|integral to membrane|nucleus	metal ion binding|transcription factor binding|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity			ovary(1)|skin(1)	2						TGCTTGGTCCaaacaaaacaaaaca	0.278													4	2	---	---	---	---	
RNF34	80196	broad.mit.edu	37	12	121840527	121840527	+	Intron	DEL	T	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121840527delT	uc001ual.1	+						RNF34_uc010szw.1_Intron|RNF34_uc001uak.1_Intron|RNF34_uc001uam.1_Intron	NM_025126	NP_079402	Q969K3	RNF34_HUMAN	ring finger protein 34 isoform 2						apoptosis	endomembrane system|membrane|nuclear speck	ligase activity|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)		TTCCTTTTCCTTTTTTTTTCT	0.338													203	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	20160421	20160428	+	IGR	DEL	GTGTGTGT	-	-	rs72109454		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20160421_20160428delGTGTGTGT								TPTE2 (24707 upstream) : MPHOSPH8 (47452 downstream)																							TATTTGAAGCgtgtgtgtgtgtgtgtgt	0.346													3	4	---	---	---	---	
TGDS	23483	broad.mit.edu	37	13	95228830	95228830	+	Intron	DEL	A	-	-	rs116036564	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95228830delA	uc001vlw.2	-						TGDS_uc001vlx.2_Intron	NM_014305	NP_055120	O95455	TGDS_HUMAN	TDP-glucose 4,6-dehydratase						cellular metabolic process		coenzyme binding|dTDP-glucose 4,6-dehydratase activity|protein binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)					GTATATATTTAAAAAAAAAAA	0.348													4	2	---	---	---	---	
ANKRD10	55608	broad.mit.edu	37	13	111545198	111545199	+	Intron	INS	-	GT	GT	rs147785874	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111545198_111545199insGT	uc001vrn.2	-						ANKRD10_uc001vrm.2_Intron|ANKRD10_uc001vro.1_3'UTR|ANKRD10_uc001vrp.1_3'UTR	NM_017664	NP_060134	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10											central_nervous_system(1)	1	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)			CCTTTTGTTAAGTCCCATCTTC	0.465													5	4	---	---	---	---	
KIAA0586	9786	broad.mit.edu	37	14	58915352	58915353	+	Intron	INS	-	G	G	rs3825623		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58915352_58915353insG	uc001xdv.3	+						KIAA0586_uc010trr.1_Intron|KIAA0586_uc001xdt.3_Intron|KIAA0586_uc001xdu.3_Intron|KIAA0586_uc010trs.1_Intron|KIAA0586_uc010trt.1_Intron|KIAA0586_uc010tru.1_Intron	NM_014749	NP_055564	E9PGW8	E9PGW8_HUMAN	talpid3 protein											ovary(1)	1						ttttataaaacaatttttttaa	0.203													4	3	---	---	---	---	
RHOJ	57381	broad.mit.edu	37	14	63757404	63757404	+	Intron	DEL	A	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63757404delA	uc001xgb.1	+							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)		acaaaaatacaaaaaaaaaaa	0.229													6	3	---	---	---	---	
POTEB	339010	broad.mit.edu	37	15	22077310	22077310	+	Intron	DEL	A	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22077310delA	uc010tzr.1	-						POTEB_uc010tzq.1_Intron	NM_207355	NP_997238	Q6S5H4	POTEB_HUMAN	protein expressed in prostate, ovary, testis,												0						TTTTTTTTTTAAAAAGCATTA	0.239													9	4	---	---	---	---	
OTUD7A	161725	broad.mit.edu	37	15	31779270	31779271	+	Intron	INS	-	G	G			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31779270_31779271insG	uc001zfq.2	-						OTUD7A_uc001zfr.2_Intron	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A							cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		TGGGTATGGCTGGGGTGGGCGG	0.649													4	2	---	---	---	---	
CASC5	57082	broad.mit.edu	37	15	40921694	40921706	+	Intron	DEL	TTTTTTTTTTTTT	-	-	rs71104709		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40921694_40921706delTTTTTTTTTTTTT	uc010bbs.1	+						CASC5_uc010bbt.1_Intron	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		ttgccttttcttttttttttttttttttttttt	0.103													4	3	---	---	---	---	
SOLH	6650	broad.mit.edu	37	16	600778	600779	+	Intron	INS	-	C	C	rs146137561	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:600778_600779insC	uc002chi.2	+						SOLH_uc002chj.2_5'Flank	NM_005632	NP_005623	O75808	CAN15_HUMAN	small optic lobes						proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)	2		Hepatocellular(780;0.00335)				CCGGTGAGGGTCCCGGTCGGTG	0.757													2	4	---	---	---	---	
METRN	79006	broad.mit.edu	37	16	767426	767427	+	3'UTR	INS	-	G	G	rs147270224	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:767426_767427insG	uc002cjd.2	+	4					uc010bra.1_5'Flank	NM_024042	NP_076947	Q9UJH8	METRN_HUMAN	meteorin, glial cell differentiation regulator												0		Hepatocellular(780;0.00335)				GGAGGGAGGGTGGGCCCACTGC	0.658													3	3	---	---	---	---	
MLST8	64223	broad.mit.edu	37	16	2255805	2255805	+	Intron	DEL	G	-	-	rs3214648		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2255805delG	uc002coz.2	+						MLST8_uc002coy.2_Intron|MLST8_uc002cpa.2_Intron|MLST8_uc002cpb.2_Intron|MLST8_uc010uvx.1_Intron|MLST8_uc002cpc.2_Intron|MLST8_uc002cpd.2_Intron|MLST8_uc002cpe.2_5'UTR|MLST8_uc010uvy.1_5'UTR|MLST8_uc002cpg.2_5'UTR|MLST8_uc002cph.2_RNA|MLST8_uc002cpf.2_5'UTR	NM_022372	NP_071767	Q9BVC4	LST8_HUMAN	G protein beta subunit-like						insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|T cell costimulation	cytosol	protein binding				0						CTGCGGAGGTGGGGGGGGGAC	0.512													11	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	69120426	69120427	+	IGR	DEL	TG	-	-	rs72137501		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69120426_69120427delTG								TMCO7 (1343 upstream) : HAS3 (19040 downstream)																							TTCTATATTAtgtgtgtgtgtg	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	13023052	13023059	+	IGR	DEL	CCTTCCTT	-	-	rs113469843		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13023052_13023059delCCTTCCTT								ELAC2 (101693 upstream) : HS3ST3A1 (375947 downstream)																							cctctttTTCccttccttccttccttcc	0.038													4	3	---	---	---	---	
ETV4	2118	broad.mit.edu	37	17	41607375	41607376	+	Intron	DEL	AG	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41607375_41607376delAG	uc002idw.2	-						ETV4_uc002idv.2_Intron|ETV4_uc010wih.1_Intron|ETV4_uc010czh.2_Intron|ETV4_uc010wii.1_Intron|ETV4_uc002idx.2_Intron|ETV4_uc010wij.1_Intron	NM_001986	NP_001977	P43268	ETV4_HUMAN	ets variant gene 4 (E1A enhancer binding						positive regulation of transcription, DNA-dependent	nucleolus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/ETV4(6)	bone(4)|soft_tissue(2)|ovary(1)	7		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)		ATGAGACCCCAGAGAGTCCAGA	0.614			T	EWSR1|TMPRSS2|DDX5|KLK2|CANT1	Ewing sarcoma|Prostate carcinoma								146	12	---	---	---	---	
DHX40P1	653645	broad.mit.edu	37	17	58090680	58090681	+	Intron	INS	-	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58090680_58090681insT	uc002iyf.2	-						uc010wor.1_5'Flank	NR_002924				Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 40 pseudogene, mRNA (cDNA clone IMAGE:5170263).												0						ACTCTGAATGATTTTTTTTTTT	0.455													4	2	---	---	---	---	
BPTF	2186	broad.mit.edu	37	17	65905565	65905565	+	Intron	DEL	T	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65905565delT	uc002jgf.2	+						BPTF_uc002jge.2_Intron	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor						brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			GACCTTTGTCTTTTTTTTTTT	0.299													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	77876983	77876984	+	IGR	INS	-	CTTC	CTTC	rs12943230	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77876983_77876984insCTTC								CBX4 (63770 upstream) : TBC1D16 (36837 downstream)																							ttccttccttcctttctttctt	0.000													5	3	---	---	---	---	
B3GNTL1	146712	broad.mit.edu	37	17	81005899	81005902	+	Intron	DEL	TCTC	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:81005899_81005902delTCTC	uc002kgg.1	-						B3GNTL1_uc002kgf.1_Intron	NM_001009905	NP_001009905	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal								transferase activity, transferring glycosyl groups			ovary(1)|pancreas(1)	2	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			ttcCtctctttctctctctctttc	0.034													0	6	---	---	---	---	
MYO5B	4645	broad.mit.edu	37	18	47501149	47501150	+	Intron	INS	-	CA	CA	rs146410387	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47501149_47501150insCA	uc002leb.2	-						MYO5B_uc002lec.1_Intron	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB						protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)		GCAGTCTCTCTcacacacacac	0.426													5	5	---	---	---	---	
ANO8	57719	broad.mit.edu	37	19	17434121	17434122	+	3'UTR	DEL	TG	-	-	rs72194730		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17434121_17434122delTG	uc002ngf.2	-	18					ANO8_uc010eap.2_RNA	NM_020959	NP_066010	Q9HCE9	ANO8_HUMAN	anoctamin 8							chloride channel complex	chloride channel activity			ovary(3)	3						TCGCCTGTTCtgtgtgtgtgtg	0.312													4	2	---	---	---	---	
SLC5A5	6528	broad.mit.edu	37	19	17991503	17991504	+	Intron	INS	-	CAAAA	CAAAA	rs144134876	by1000genomes	TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17991503_17991504insCAAAA	uc002nhr.3	+							NM_000453	NP_000444	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium iodide						cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4						agatcttttctcaaaacaaaac	0.005													9	5	---	---	---	---	
PTPRH	5794	broad.mit.edu	37	19	55717861	55717862	+	Intron	INS	-	T	T	rs72044547		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55717861_55717862insT	uc002qjq.2	-						PTPRH_uc010esv.2_Intron|PTPRH_uc002qjs.2_Intron	NM_002842	NP_002833	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H						apoptosis	cytoplasm|integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		ctactttttaatttttttgtag	0.020													4	2	---	---	---	---	
VSTM2L	128434	broad.mit.edu	37	20	36572311	36572311	+	Intron	DEL	C	-	-	rs33961791		TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36572311delC	uc002xhk.3	+							NM_080607	NP_542174	Q96N03	VTM2L_HUMAN	V-set and transmembrane domain containing 2 like											ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)				GATCTTGGGACCCCCCCCCCC	0.418													9	4	---	---	---	---	
CHD6	84181	broad.mit.edu	37	20	40120107	40120107	+	Intron	DEL	A	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40120107delA	uc002xka.1	-						CHD6_uc002xkd.2_Intron	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6						chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)				GTGGCTGGCCAAAAAAAAAAG	0.348													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	49068649	49068650	+	IGR	INS	-	GAAG	GAAG			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49068649_49068650insGAAG								CEBPB (259437 upstream) : PTPN1 (58241 downstream)																							aaggaaggaaggaaaggaagga	0.054													4	2	---	---	---	---	
TNRC6B	23112	broad.mit.edu	37	22	40502242	40502242	+	Intron	DEL	T	-	-			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40502242delT	uc003aym.2	+							NM_001024843	NP_001020014	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 3						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0						CGAGGTTGTCTTTTTTTTTTT	0.234													8	5	---	---	---	---	
IL3RA	3563	broad.mit.edu	37	X	1501563	1501564	+	3'UTR	INS	-	T	T			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1501563_1501564insT	uc004cps.2	+	12					IL3RA_uc011mhd.1_3'UTR	NM_002183	NP_002174	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	TGATAAAGTGATTTTTTTTTTT	0.426													4	2	---	---	---	---	
P2RY8	286530	broad.mit.edu	37	X	1585603	1585604	+	Intron	INS	-	CCTC	CCTC			TCGA-CH-5789-01	TCGA-CH-5789-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1585603_1585604insCCTC	uc004cpz.2	-							NM_178129	NP_835230	Q86VZ1	P2RY8_HUMAN	G-protein coupled purinergic receptor P2Y8							integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(5)	5		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GCCTGCTGTCtcctccctccct	0.356			T	CRLF2	B-ALL|Downs associated ALL								7	4	---	---	---	---	
