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
WDR8	49856	broad.mit.edu	37	1	3549909	3549909	+	Intron	SNP	G	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3549909G>T	uc001ako.2	-						WDR8_uc001akn.3_Intron|WDR8_uc010nzi.1_3'UTR	NM_017818	NP_060288	Q9P2S5	WRP73_HUMAN	WD repeat domain 8							centrosome	protein binding				0	all_cancers(77;0.0128)|all_epithelial(69;0.00526)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;4.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;4.16e-22)|GBM - Glioblastoma multiforme(42;1.05e-14)|Colorectal(212;1.19e-05)|BRCA - Breast invasive adenocarcinoma(365;2.67e-05)|COAD - Colon adenocarcinoma(227;5.82e-05)|Kidney(185;0.000364)|KIRC - Kidney renal clear cell carcinoma(229;0.00223)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		TCTGGACAACGAGGAATCTTG	0.358													46	122	---	---	---	---	PASS
MFAP2	4237	broad.mit.edu	37	1	17303611	17303611	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17303611G>C	uc001azw.2	-	3	253	c.120C>G	c.(118-120)GAC>GAG	p.D40E	MFAP2_uc001azx.2_Missense_Mutation_p.D39E|MFAP2_uc001azy.2_Missense_Mutation_p.D40E|MFAP2_uc010ocl.1_Missense_Mutation_p.D39E	NM_002403	NP_002394	P55001	MFAP2_HUMAN	microfibrillar-associated protein 2 isoform a	40						microfibril					0		Colorectal(325;3.46e-05)|Breast(348;0.000118)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000538)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|COAD - Colon adenocarcinoma(227;1.07e-05)|BRCA - Breast invasive adenocarcinoma(304;3.04e-05)|Kidney(64;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00544)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		TACCGATCTGGTCGCTATAGT	0.647													16	39	---	---	---	---	PASS
GRHL3	57822	broad.mit.edu	37	1	24666207	24666207	+	Silent	SNP	C	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24666207C>G	uc001biy.2	+	8	1063	c.1017C>G	c.(1015-1017)GCC>GCG	p.A339A	GRHL3_uc001bix.2_Silent_p.A334A|GRHL3_uc001biz.2_Silent_p.A241A	NM_021180	NP_067003	Q8TE85	GRHL3_HUMAN	sister-of-mammalian grainyhead protein isoform	334					regulation of actin cytoskeleton organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		AGGAGGTGGCCTATAATGCAC	0.527													80	348	---	---	---	---	PASS
TMEM39B	55116	broad.mit.edu	37	1	32557586	32557586	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32557586G>T	uc010ogv.1	+	6	1047	c.901G>T	c.(901-903)GCC>TCC	p.A301S	TMEM39B_uc010ogt.1_RNA|TMEM39B_uc010ogu.1_Missense_Mutation_p.A174S|TMEM39B_uc001bue.3_Missense_Mutation_p.A302S|TMEM39B_uc001buf.3_Missense_Mutation_p.A102S|TMEM39B_uc010ogw.1_Missense_Mutation_p.A102S	NM_018056	NP_060526	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	301	Helical; (Potential).					integral to membrane					0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				CTACTATGTGGCCTTTGTGCC	0.572													6	48	---	---	---	---	PASS
GJB3	2707	broad.mit.edu	37	1	35251229	35251229	+	3'UTR	SNP	G	C	C	rs476220	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35251229G>C	uc001bxx.2	+	2					GJB3_uc001bxy.2_3'UTR|GJB3_uc001bxz.3_3'UTR|uc010ohs.1_5'Flank	NM_024009	NP_076872	O75712	CXB3_HUMAN	connexin 31						cell communication	connexon complex|integral to membrane	gap junction channel activity				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				CATGCAGGGCGGTGTGGCAGG	0.562													4	13	---	---	---	---	PASS
FGGY	55277	broad.mit.edu	37	1	59978033	59978033	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59978033G>T	uc001czi.3	+	7	933	c.721G>T	c.(721-723)GAG>TAG	p.E241*	FGGY_uc001czg.2_Nonsense_Mutation_p.E129*|FGGY_uc001czh.2_RNA|FGGY_uc009wac.2_Nonsense_Mutation_p.E241*|FGGY_uc001czj.3_Nonsense_Mutation_p.E241*|FGGY_uc001czk.3_Nonsense_Mutation_p.E129*|FGGY_uc001czl.3_Nonsense_Mutation_p.E153*	NM_018291	NP_060761	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	241					carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)					GCTCACACCAGAGGCAGCAAG	0.478													4	120	---	---	---	---	PASS
PIGK	10026	broad.mit.edu	37	1	77627328	77627328	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77627328G>T	uc001dhk.2	-	7	698	c.653C>A	c.(652-654)CCT>CAT	p.P218H	PIGK_uc010orj.1_Missense_Mutation_p.P142H|PIGK_uc009wbx.2_Missense_Mutation_p.P124H|PIGK_uc001dhl.1_Missense_Mutation_p.P218H	NM_005482	NP_005473	Q92643	GPI8_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	218	Lumenal (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation|protein thiol-disulfide exchange|proteolysis	GPI-anchor transamidase complex	cysteine-type endopeptidase activity|GPI-anchor transamidase activity|protein binding			ovary(2)|pancreas(1)	3						CATTATGTTAGGAGAATAAAA	0.378													51	127	---	---	---	---	PASS
SASS6	163786	broad.mit.edu	37	1	100571393	100571393	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100571393G>T	uc001dsu.2	-	13	1616	c.1475C>A	c.(1474-1476)CCT>CAT	p.P492H	SASS6_uc009wdz.2_Missense_Mutation_p.P325H	NM_194292	NP_919268	Q6UVJ0	SAS6_HUMAN	spindle assembly abnormal protein 6	492					centriole replication	centriole				upper_aerodigestive_tract(1)|ovary(1)	2		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		AGTAGTAGAAGGTCCCAATAC	0.363													36	78	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152287246	152287246	+	Intron	SNP	G	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152287246G>T	uc001ezu.1	-						uc001ezv.2_RNA	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin						keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AAGTCACAGAGGGAGACTGCA	0.368									Ichthyosis				18	72	---	---	---	---	PASS
SPRR3	6707	broad.mit.edu	37	1	152976121	152976121	+	3'UTR	SNP	C	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152976121C>A	uc001fax.3	+	3					SPRR3_uc001faz.3_3'UTR|SPRR3_uc001fay.2_3'UTR	NM_005416	NP_005407	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3						keratinization|peptide cross-linking|wound healing	cytoplasm	protein binding|structural molecule activity			skin(1)	1	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ATTGTCACCCCAAGCCATAGT	0.428													4	2	---	---	---	---	PASS
DISC1	27185	broad.mit.edu	37	1	231829671	231829671	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231829671T>A	uc001huz.2	+	2	220	c.167T>A	c.(166-168)TTC>TAC	p.F56Y	TSNAX-DISC1_uc010pwe.1_Missense_Mutation_p.F11Y|TSNAX-DISC1_uc010pwf.1_Missense_Mutation_p.F11Y|TSNAX-DISC1_uc010pwg.1_Missense_Mutation_p.F45Y|TSNAX-DISC1_uc010pwh.1_Missense_Mutation_p.F11Y|TSNAX-DISC1_uc010pwi.1_Missense_Mutation_p.F11Y|TSNAX-DISC1_uc010pwj.1_Missense_Mutation_p.F45Y|TSNAX-DISC1_uc010pwk.1_Missense_Mutation_p.F45Y|TSNAX-DISC1_uc010pwl.1_RNA|DISC1_uc010pwo.1_Missense_Mutation_p.F56Y|DISC1_uc010pwp.1_Missense_Mutation_p.F56Y|DISC1_uc010pwq.1_Missense_Mutation_p.F56Y|DISC1_uc010pwr.1_Missense_Mutation_p.F56Y|DISC1_uc010pws.1_Missense_Mutation_p.F56Y|DISC1_uc010pwt.1_Missense_Mutation_p.F56Y|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_RNA|DISC1_uc010pww.1_Missense_Mutation_p.F56Y|DISC1_uc010pwx.1_RNA|DISC1_uc010pwy.1_RNA|DISC1_uc010pwz.1_RNA|DISC1_uc010pxa.1_RNA|DISC1_uc001huy.2_Missense_Mutation_p.F56Y|DISC1_uc010pxb.1_Missense_Mutation_p.F56Y|DISC1_uc010pxc.1_Missense_Mutation_p.F56Y|DISC1_uc010pxd.1_5'UTR|DISC1_uc010pxe.1_Missense_Mutation_p.F56Y|DISC1_uc009xfr.2_Missense_Mutation_p.F11Y|DISC1_uc010pxf.1_Missense_Mutation_p.F56Y|DISC1_uc010pxg.1_Missense_Mutation_p.F56Y|DISC1_uc010pxh.1_Missense_Mutation_p.F56Y|DISC1_uc010pxi.1_RNA|DISC1_uc010pxj.1_5'UTR|DISC1_uc010pxk.1_RNA|DISC1_uc010pxl.1_RNA|DISC1_uc010pxm.1_Missense_Mutation_p.F56Y|DISC1_uc010pxn.1_5'UTR|DISC1_uc001hva.2_Missense_Mutation_p.F56Y|DISC1_uc010pwm.1_Missense_Mutation_p.F56Y|DISC1_uc001hux.1_Missense_Mutation_p.F56Y|DISC1_uc001hvc.3_Missense_Mutation_p.F56Y|DISC1_uc010pwn.1_Missense_Mutation_p.F56Y	NM_018662	NP_061132	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1 isoform L	56	Interaction with MAP1A.				microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)				GGGATCGGGTTCCTTTCCCCA	0.662													11	45	---	---	---	---	PASS
TEKT4	150483	broad.mit.edu	37	2	95537442	95537442	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95537442C>A	uc002stw.1	+	1	211	c.118C>A	c.(118-120)CTG>ATG	p.L40M	uc002stv.1_Intron|TEKT4_uc010fhr.1_RNA	NM_144705	NP_653306	Q8WW24	TEKT4_HUMAN	tektin 4	40					cell projection organization|microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(1)|breast(1)|skin(1)	3						CTCCAAGTACCTGCTGGAGGA	0.677													21	74	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	96568655	96568655	+	Intron	SNP	A	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96568655A>T	uc002sva.1	-						uc002suz.1_5'UTR|uc002svb.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		TTTTCTCCATACTTTTTTCCT	0.279													4	28	---	---	---	---	PASS
RANBP2	5903	broad.mit.edu	37	2	109384514	109384514	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109384514G>T	uc002tem.3	+	20	7645	c.7519G>T	c.(7519-7521)GCA>TCA	p.A2507S		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	2507					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						AACACCAAAAGCAGTGGTTTC	0.393													10	561	---	---	---	---	PASS
ORC4L	5000	broad.mit.edu	37	2	148693265	148693265	+	Silent	SNP	A	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148693265A>T	uc002twi.2	-	14	1260	c.1125T>A	c.(1123-1125)GCT>GCA	p.A375A	ORC4L_uc002twj.2_Silent_p.A375A|ORC4L_uc010zbo.1_Silent_p.A301A|ORC4L_uc010zbp.1_Silent_p.A158A|ORC4L_uc010fnr.2_Missense_Mutation_p.F321I|ORC4L_uc010zbq.1_Silent_p.A291A|ORC4L_uc002twk.2_Silent_p.A375A|ORC4L_uc002twl.1_RNA	NM_181741	NP_859525	O43929	ORC4_HUMAN	origin recognition complex subunit 4	375					cell cycle checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	ATP binding|DNA replication origin binding|nucleoside-triphosphatase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.0963)|COAD - Colon adenocarcinoma(177;0.203)		AGTGTTCAAAAGCCTGAAAGA	0.398													47	194	---	---	---	---	PASS
DNAJC10	54431	broad.mit.edu	37	2	183601013	183601013	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183601013C>T	uc002uow.1	+	11	1302	c.887C>T	c.(886-888)ACC>ATC	p.T296I	DNAJC10_uc002uox.1_RNA|DNAJC10_uc002uoy.1_RNA|DNAJC10_uc002uoz.1_Intron|DNAJC10_uc010fro.1_Intron	NM_018981	NP_061854	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10	296					apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|ER-associated protein catabolic process|glycerol ether metabolic process|negative regulation of protein phosphorylation|protein folding|response to endoplasmic reticulum stress	endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|extracellular region	ATPase activator activity|ATPase binding|chaperone binding|electron carrier activity|heat shock protein binding|misfolded protein binding|protein disulfide oxidoreductase activity|unfolded protein binding			ovary(1)|large_intestine(1)|breast(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			GACTGTGCCACCCAGGATAAC	0.358													32	165	---	---	---	---	PASS
SGOL2	151246	broad.mit.edu	37	2	201397829	201397829	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201397829T>C	uc002uvw.2	+	2	244	c.131T>C	c.(130-132)CTA>CCA	p.L44P	SGOL2_uc002uvv.3_Missense_Mutation_p.L44P|SGOL2_uc010zhd.1_Missense_Mutation_p.L44P|SGOL2_uc010zhe.1_Missense_Mutation_p.L44P	NM_152524	NP_689737	Q562F6	SGOL2_HUMAN	shugoshin-like 2 isoform 1	44					cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding			ovary(2)|skin(2)	4						ACAAAAATACTAAGTAAGTGC	0.274													5	250	---	---	---	---	PASS
FRMD4B	23150	broad.mit.edu	37	3	69230660	69230660	+	Silent	SNP	G	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69230660G>A	uc003dnv.2	-	21	2531	c.2241C>T	c.(2239-2241)ACC>ACT	p.T747T	FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnu.2_Silent_p.T399T|FRMD4B_uc011bga.1_Silent_p.T591T	NM_015123	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	747						cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		AATAGGGGCCGGTAACTGGTG	0.493													4	127	---	---	---	---	PASS
CEP97	79598	broad.mit.edu	37	3	101450513	101450513	+	Intron	SNP	C	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101450513C>G	uc003dvk.1	+						CEP97_uc010hpm.1_Intron|CEP97_uc011bhf.1_Intron|CEP97_uc003dvl.1_Intron|CEP97_uc003dvm.1_5'UTR	NM_024548	NP_078824	Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa							centrosome|nucleus	protein binding			ovary(2)	2						agagttggaccagaagatcat	0.104													4	4	---	---	---	---	PASS
TRAT1	50852	broad.mit.edu	37	3	108572551	108572551	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108572551C>A	uc003dxi.1	+	6	532	c.388C>A	c.(388-390)CAT>AAT	p.H130N	TRAT1_uc010hpx.1_Missense_Mutation_p.H93N	NM_016388	NP_057472	Q6PIZ9	TRAT1_HUMAN	T-cell receptor interacting molecule	130	Cytoplasmic (Potential).				cellular defense response|negative regulation of receptor recycling|negative regulation of transport|positive regulation of calcium-mediated signaling|positive regulation of T cell receptor signaling pathway|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	phosphatidylinositol-4,5-bisphosphate 3-kinase activity|transmembrane receptor protein tyrosine kinase adaptor activity			skin(1)	1						ACAGAATACTCATTTCTCAGA	0.463													45	93	---	---	---	---	PASS
GATA2	2624	broad.mit.edu	37	3	128199926	128199926	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128199926T>G	uc003ekm.3	-	7	1814	c.1379A>C	c.(1378-1380)CAC>CCC	p.H460P	GATA2_uc003ekn.3_Missense_Mutation_p.H446P|GATA2_uc003eko.2_Missense_Mutation_p.H460P	NM_001145661	NP_001139133	P23769	GATA2_HUMAN	GATA binding protein 2 isoform 1	460					blood coagulation|negative regulation of fat cell differentiation|negative regulation of fat cell proliferation|negative regulation of neural precursor cell proliferation|negative regulation of Notch signaling pathway|phagocytosis|positive regulation of angiogenesis|positive regulation of phagocytosis|positive regulation of transcription from RNA polymerase II promoter	nucleoplasm	C2H2 zinc finger domain binding|chromatin binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(13)|lung(1)|skin(1)	15				GBM - Glioblastoma multiforme(114;0.173)		GGAGGAGGGGTGGATGGGCGT	0.687			Mis		AML(CML blast transformation)								6	18	---	---	---	---	PASS
DHX36	170506	broad.mit.edu	37	3	154022915	154022915	+	Silent	SNP	T	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154022915T>A	uc003ezy.3	-	7	1017	c.936A>T	c.(934-936)ACA>ACT	p.T312T	DHX36_uc010hvq.2_Silent_p.T312T|DHX36_uc003ezz.3_Silent_p.T312T	NM_020865	NP_065916	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	312	Helicase ATP-binding.					cytoplasm|nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			GGATGATTCCTGTTGTACAGT	0.338													34	80	---	---	---	---	PASS
SH3TC1	54436	broad.mit.edu	37	4	8217896	8217896	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8217896G>T	uc003gkv.3	+	6	641	c.540G>T	c.(538-540)TTG>TTT	p.L180F	SH3TC1_uc003gkw.3_Missense_Mutation_p.L104F|SH3TC1_uc003gkx.3_RNA	NM_018986	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	180							binding			large_intestine(2)|pancreas(1)	3						GGCTGCTCTTGCCCAGTGAGG	0.602													14	27	---	---	---	---	PASS
C4orf37	285555	broad.mit.edu	37	4	98902354	98902354	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98902354C>T	uc003htt.1	-	6	818	c.728G>A	c.(727-729)AGT>AAT	p.S243N		NM_174952	NP_777612	Q8N412	CD037_HUMAN	hypothetical protein LOC285555	243											0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)		TCGAACAGCACTTTGACCAAA	0.383													102	252	---	---	---	---	PASS
TACR3	6870	broad.mit.edu	37	4	104512654	104512654	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104512654G>T	uc003hxe.1	-	4	1218	c.1075C>A	c.(1075-1077)CTG>ATG	p.L359M		NM_001059	NP_001050	P29371	NK3R_HUMAN	tachykinin receptor 3	359	Helical; Name=7; (Potential).					integral to plasma membrane	tachykinin receptor activity			ovary(3)|lung(2)|breast(1)|skin(1)	7		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		CTTTTATTCAGACAGCAGTAG	0.398													38	137	---	---	---	---	PASS
FAT4	79633	broad.mit.edu	37	4	126328192	126328192	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126328192C>T	uc003ifj.3	+	3	5465	c.5465C>T	c.(5464-5466)TCC>TTC	p.S1822F	FAT4_uc011cgp.1_Missense_Mutation_p.S120F	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	1822	Cadherin 17.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						GGTCTTCAGTCCTCGGATATG	0.468													81	209	---	---	---	---	PASS
LMNB1	4001	broad.mit.edu	37	5	126171999	126171999	+	3'UTR	SNP	T	C	C	rs1051643	byFrequency	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126171999T>C	uc003kud.1	+	11					LMNB1_uc010jdb.1_RNA|LMNB1_uc011cxb.1_3'UTR	NM_005573	NP_005564	P20700	LMNB1_HUMAN	lamin B1						cellular component disassembly involved in apoptosis	lamin filament|nuclear inner membrane	protein binding|structural molecule activity			kidney(1)|central_nervous_system(1)	2		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)		TATGGTAATCTTTACCTGTAT	0.353													4	215	---	---	---	---	PASS
SLC35A4	113829	broad.mit.edu	37	5	139947164	139947164	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139947164G>T	uc003lgg.1	+	3	1138	c.410G>T	c.(409-411)CGC>CTC	p.R137L	APBB3_uc003lgd.1_5'Flank|APBB3_uc003lge.1_5'Flank|APBB3_uc003lgf.1_5'Flank|APBB3_uc010jfp.1_5'Flank|APBB3_uc011czi.1_5'Flank|APBB3_uc010jfr.1_5'Flank|SLC35A4_uc003lgh.1_Missense_Mutation_p.R137L	NM_080670	NP_542401	Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	137	Leu-rich.					Golgi membrane|integral to membrane	sugar:hydrogen symporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCCGGCACCGCCTCTCTGTG	0.592													26	21	---	---	---	---	PASS
RSPH9	221421	broad.mit.edu	37	6	43613007	43613007	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43613007T>C	uc003ovw.1	+	1	198	c.172T>C	c.(172-174)TAC>CAC	p.Y58H	RSPH9_uc003ovx.1_Missense_Mutation_p.Y58H	NM_152732	NP_689945	Q9H1X1	RSPH9_HUMAN	radial spoke head 9 homolog	58					cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton				upper_aerodigestive_tract(1)|skin(1)	2						CGCCGATTACTACATCGCGCA	0.642									Kartagener_syndrome				28	62	---	---	---	---	PASS
SNX14	57231	broad.mit.edu	37	6	86258029	86258029	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86258029A>G	uc003pkr.2	-	9	1050	c.857T>C	c.(856-858)CTA>CCA	p.L286P	SNX14_uc003pkp.2_Missense_Mutation_p.L149P|SNX14_uc003pkq.2_5'UTR|SNX14_uc011dzg.1_Missense_Mutation_p.L234P|SNX14_uc003pks.2_Missense_Mutation_p.L242P|SNX14_uc003pkt.2_Missense_Mutation_p.L286P	NM_153816	NP_722523	Q9Y5W7	SNX14_HUMAN	sorting nexin 14 isoform a	286	PXA.				cell communication|protein transport	integral to membrane	phosphatidylinositol binding|signal transducer activity				0		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		TGGATCAGCTAGGAAATCCAA	0.204													24	85	---	---	---	---	PASS
SLC22A16	85413	broad.mit.edu	37	6	110763477	110763477	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110763477C>T	uc003puf.2	-	4	1220	c.1153G>A	c.(1153-1155)GGC>AGC	p.G385S	SLC22A16_uc003pue.2_Missense_Mutation_p.G366S	NM_033125	NP_149116	Q86VW1	S22AG_HUMAN	solute carrier family 22, member 16	385					acid secretion|cell differentiation|multicellular organismal development|single fertilization|sperm motility|spermatogenesis	integral to membrane	carnitine transporter activity			ovary(1)	1		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)		TATTCATTGCCTCCTAAGTTA	0.388													28	73	---	---	---	---	PASS
PKD1L1	168507	broad.mit.edu	37	7	47869026	47869026	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47869026T>G	uc003tny.1	-	44	6732	c.6732A>C	c.(6730-6732)GAA>GAC	p.E2244D	C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_5'Flank	NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	2244	Cytoplasmic (Potential).				cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11						TTTTTACTTTTTCAACCTCGC	0.413													35	99	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82584331	82584331	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82584331C>T	uc003uhx.2	-	5	6227	c.5938G>A	c.(5938-5940)GAA>AAA	p.E1980K	PCLO_uc003uhv.2_Missense_Mutation_p.E1980K	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1911					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						AATCCATTTTCTTCTTCTTGC	0.373													8	347	---	---	---	---	PASS
RBM28	55131	broad.mit.edu	37	7	127979814	127979814	+	Silent	SNP	G	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127979814G>A	uc003vmp.2	-	2	265	c.150C>T	c.(148-150)GTC>GTT	p.V50V	RBM28_uc011koj.1_Intron|RBM28_uc011kok.1_5'UTR	NM_018077	NP_060547	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	50	RRM 1.				mRNA processing|RNA splicing	Golgi apparatus|nucleolus|spliceosomal complex	nucleotide binding|RNA binding			ovary(2)	2						TTGAAAAAGTGACATAGCCAA	0.483													36	82	---	---	---	---	PASS
AKR1B15	441282	broad.mit.edu	37	7	134261744	134261744	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134261744T>G	uc011kpr.1	+	10	1154	c.855T>G	c.(853-855)AAT>AAG	p.N285K	AKR1B15_uc011kps.1_Missense_Mutation_p.N257K	NM_001080538	NP_001074007	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	285							oxidoreductase activity			ovary(1)	1						TCCAGAGGAATGTGACAGTGA	0.488													58	136	---	---	---	---	PASS
PTPRN2	5799	broad.mit.edu	37	7	157475557	157475557	+	Missense_Mutation	SNP	C	G	G	rs144004975		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157475557C>G	uc003wno.2	-	13	1982	c.1861G>C	c.(1861-1863)GTC>CTC	p.V621L	PTPRN2_uc003wnp.2_Missense_Mutation_p.V604L|PTPRN2_uc003wnq.2_Missense_Mutation_p.V592L|PTPRN2_uc003wnr.2_Missense_Mutation_p.V583L|PTPRN2_uc011kwa.1_Missense_Mutation_p.V644L	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	621	Helical; (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GCGAGGGAGACCAGGGTGAGC	0.587													32	86	---	---	---	---	PASS
UBR5	51366	broad.mit.edu	37	8	103293614	103293614	+	Silent	SNP	A	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103293614A>G	uc003ykr.1	-	41	5863	c.5830T>C	c.(5830-5832)TTG>CTG	p.L1944L	UBR5_uc003yks.1_Silent_p.L1944L	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	1944					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			ACATGCTTCAATGAGCAAACA	0.398													4	214	---	---	---	---	PASS
DPYS	1807	broad.mit.edu	37	8	105456595	105456595	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105456595A>G	uc003yly.3	-	4	803	c.674T>C	c.(673-675)GTG>GCG	p.V225A		NM_001385	NP_001376	Q14117	DPYS_HUMAN	dihydropyrimidinase	225					protein homotetramerization|pyrimidine nucleoside catabolic process|thymine catabolic process|uracil catabolic process	cytosol	dihydropyrimidinase activity|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CTCTGCCTCCACTGCCTCTGG	0.542													27	77	---	---	---	---	PASS
APBA1	320	broad.mit.edu	37	9	72131197	72131197	+	Silent	SNP	G	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72131197G>A	uc004ahh.2	-	2	1206	c.930C>T	c.(928-930)CGC>CGT	p.R310R		NM_001163	NP_001154	Q02410	APBA1_HUMAN	amyloid beta A4 precursor protein-binding,	310	Pro-rich.|Munc-18-1 binding.				axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1						ggctgtcggggcgacccccgg	0.343													4	9	---	---	---	---	PASS
SMC5	23137	broad.mit.edu	37	9	72897437	72897437	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72897437A>C	uc004ahr.2	+	7	1036	c.919A>C	c.(919-921)ACA>CCA	p.T307P		NM_015110	NP_055925	Q8IY18	SMC5_HUMAN	SMC5 protein	307	Potential.				DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3						GATTCCTGTAACATGTCGAAT	0.363													36	114	---	---	---	---	PASS
C9orf84	158401	broad.mit.edu	37	9	114490023	114490023	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114490023C>T	uc004bfr.2	-	11	1667	c.1532G>A	c.(1531-1533)GGC>GAC	p.G511D	C9orf84_uc011lwt.1_RNA|C9orf84_uc004bfq.2_Missense_Mutation_p.G472D|C9orf84_uc010mug.2_Missense_Mutation_p.G457D	NM_173521	NP_775792	Q5VXU9	CI084_HUMAN	hypothetical protein LOC158401 isoform 1	511										ovary(2)	2						TTGTTTTTTGCCATGTTCAAA	0.338													6	311	---	---	---	---	PASS
ST6GALNAC4	27090	broad.mit.edu	37	9	130678760	130678760	+	5'UTR	SNP	T	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130678760T>G	uc004bss.2	-	2					ST6GALNAC4_uc004bst.2_Intron	NM_175039	NP_778204	Q9H4F1	SIA7D_HUMAN	sialyltransferase 7D isoform a						glycolipid metabolic process|protein glycosylation	integral to Golgi membrane|nucleus|soluble fraction	(alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity				0						TGGGAAGGGGTGGGAGCCGGG	0.607													7	46	---	---	---	---	PASS
FAM188A	80013	broad.mit.edu	37	10	15879243	15879243	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15879243A>G	uc001iod.1	-	6	757	c.536T>C	c.(535-537)TTT>TCT	p.F179S	FAM188A_uc001ioe.1_Missense_Mutation_p.F6S|FAM188A_uc001iof.1_Missense_Mutation_p.F179S	NM_024948	NP_079224	Q9H8M7	F188A_HUMAN	chromosome 10 open reading frame 97	179					apoptosis	nucleus	calcium ion binding			ovary(1)	1						CAATACTCCAAATTTATTTCC	0.333													71	232	---	---	---	---	PASS
C11orf41	25758	broad.mit.edu	37	11	33566837	33566837	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33566837C>T	uc001mup.3	+	2	2549	c.2425C>T	c.(2425-2427)CCT>TCT	p.P809S	C11orf41_uc001mun.1_Missense_Mutation_p.P809S	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	803						integral to membrane				ovary(2)	2						TGCTGTCCTTCCTGCTGCATC	0.562													11	31	---	---	---	---	PASS
GPR84	53831	broad.mit.edu	37	12	54757201	54757201	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54757201C>A	uc001sfu.2	-	2	525	c.435G>T	c.(433-435)TGG>TGT	p.W145C		NM_020370	NP_065103	Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	145	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			breast(2)	2						CGCCCACAACCCAGGTGCTCA	0.577													3	38	---	---	---	---	PASS
ELK3	2004	broad.mit.edu	37	12	96640767	96640767	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96640767C>A	uc001teo.1	+	3	536	c.257C>A	c.(256-258)TCT>TAT	p.S86Y		NM_005230	NP_005221	P41970	ELK3_HUMAN	ELK3 protein	86					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)					AAGTTTGTCTCTTTCCCGGAG	0.527													19	70	---	---	---	---	PASS
LOC374491	374491	broad.mit.edu	37	13	25168432	25168432	+	RNA	SNP	T	C	C	rs149337771	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25168432T>C	uc001upm.2	+	10		c.1104T>C			LOC374491_uc001upn.2_RNA|LOC374491_uc001upo.2_RNA					Homo sapiens mRNA; cDNA DKFZp434J0717 (from clone DKFZp434J0717).												0						TTGAAACAGCTGGTGTATTAA	0.373													3	47	---	---	---	---	PASS
NHLRC3	387921	broad.mit.edu	37	13	39613761	39613761	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39613761T>C	uc001uxc.2	+	3	620	c.298T>C	c.(298-300)TGG>CGG	p.W100R	C13orf23_uc001uwy.2_5'Flank|C13orf23_uc001uwz.2_5'Flank|NHLRC3_uc001uxa.1_Missense_Mutation_p.W100R|NHLRC3_uc001uxb.1_Missense_Mutation_p.W100R|NHLRC3_uc001uxd.2_Missense_Mutation_p.W100R|NHLRC3_uc001uxe.2_5'UTR	NM_001012754	NP_001012772	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3 isoform a	100						extracellular region				skin(1)	1		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		CCTACGAGCCTGGAATTATAC	0.388													4	173	---	---	---	---	PASS
MYH7	4625	broad.mit.edu	37	14	23894489	23894489	+	Splice_Site	SNP	A	T	T	rs111726379		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23894489A>T	uc001wjx.2	-	21	2529	c.2423_splice	c.e21+1	p.R808_splice		NM_000257	NP_000248	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta						adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis	focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(3)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		GAGATCTCTCACCTACGTTCC	0.552													30	56	---	---	---	---	PASS
C14orf156	81892	broad.mit.edu	37	14	78182158	78182158	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78182158T>C	uc001xue.3	+	3	230	c.200T>C	c.(199-201)TTT>TCT	p.F67S		NM_031210	NP_112487	Q9GZT3	SLIRP_HUMAN	SRA stem-loop-interacting RNA-binding protein	67	RRM.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	nucleotide binding|RNA binding				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0276)		TGGGTTCAGTTTTCTTCAGAA	0.343													3	88	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	29110458	29110458	+	Intron	SNP	T	C	C	rs151074589	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29110458T>C	uc010vct.1	-						RRN3P2_uc002dsf.3_RNA|RRN3P2_uc002dsg.3_RNA|RRN3P2_uc010vdn.1_RNA					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		GAATTTTGAGTGGATAGTGAT	0.328													3	104	---	---	---	---	PASS
FUS	2521	broad.mit.edu	37	16	31202907	31202907	+	3'UTR	SNP	A	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31202907A>G	uc002ebf.2	+	15					FUS_uc002ebh.2_3'UTR|FUS_uc002ebg.2_3'UTR|FUS_uc002ebi.2_3'UTR|FUS_uc002ebj.2_3'UTR	NM_004960	NP_004951	P35637	FUS_HUMAN	fusion (involved in t(12;16) in malignant						cell death|nuclear mRNA splicing, via spliceosome	nucleoplasm	DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding		FUS/DDIT3(623)|FUS/ERG(163)|FUS/CREB3L2(158)|FUS/CREB3L1(6)|FUS/ATF1(4)|FUS/FEV(2)	soft_tissue(791)|haematopoietic_and_lymphoid_tissue(153)|bone(12)|breast(2)	958		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		TTCCCATTAAAAGTGACCATT	0.398			T	DDIT3|ERG|FEV|ATF1|CREB3L2|CREB3L1	liposarcoma|AML|Ewing sarcoma|angiomatoid fibrous histiocytoma|fibromyxoid sarcoma								2	11	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													3	20	---	---	---	---	PASS
PKD1L2	114780	broad.mit.edu	37	16	81208318	81208318	+	Intron	SNP	C	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81208318C>T	uc002fgh.1	-						PKD1L2_uc002fgg.1_Intron|PKD1L2_uc002fgi.2_Intron|PKD1L2_uc002fgj.2_Intron|PKD1L2_uc002fgk.1_Missense_Mutation_p.V71M|PKD1L2_uc002fgl.1_Missense_Mutation_p.V185M	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a						neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						CAGCTTCCCACGGGTACCTTC	0.592													3	9	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	90161902	90161902	+	3'UTR	SNP	A	G	G	rs6500471	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90161902A>G	uc002fqp.2	+	3					uc002fqq.2_3'UTR					Homo sapiens, Similar to tubulin, beta, 2, clone IMAGE:4873024, mRNA.																		ATATGTTCCAAGACCCTAAAA	0.537													4	73	---	---	---	---	PASS
MLX	6945	broad.mit.edu	37	17	40723622	40723622	+	3'UTR	SNP	C	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40723622C>T	uc002iag.2	+	8					MLX_uc002iaf.2_3'UTR|MLX_uc002iah.2_3'UTR	NM_170607	NP_733752	Q9UH92	MLX_HUMAN	transcription factor-like protein 4 isoform						energy reserve metabolic process|negative regulation of transcription, DNA-dependent|positive regulation of cellular metabolic process	cytoplasm|nucleus	DNA binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding				0		all_cancers(22;4.26e-05)|Breast(137;0.000153)|all_epithelial(22;0.00148)		BRCA - Breast invasive adenocarcinoma(366;0.129)		GCTTTACTGACCGGTTCTTGG	0.537													69	177	---	---	---	---	PASS
SLC25A39	51629	broad.mit.edu	37	17	42397274	42397274	+	3'UTR	SNP	C	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42397274C>A	uc002ign.2	-	12					SLC25A39_uc002igm.2_3'UTR|SLC25A39_uc002igo.2_3'UTR|SLC25A39_uc010wiw.1_3'UTR|SLC25A39_uc010czu.2_3'UTR	NM_001143780	NP_001137252	Q9BZJ4	S2539_HUMAN	solute carrier family 25, member 39 isoform a						heme biosynthetic process|transport	integral to membrane|mitochondrial inner membrane				upper_aerodigestive_tract(1)	1		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		AAACAAGCCCCCTCCCTCAGT	0.642													3	11	---	---	---	---	PASS
DSC3	1825	broad.mit.edu	37	18	28574307	28574307	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28574307C>A	uc002kwj.3	-	16	2680	c.2525G>T	c.(2524-2526)CGC>CTC	p.R842L	DSC3_uc002kwi.3_3'UTR	NM_001941	NP_001932	Q14574	DSC3_HUMAN	desmocollin 3 isoform Dsc3a preproprotein	842	Cytoplasmic (Potential).				homophilic cell adhesion|protein stabilization	desmosome|integral to membrane|membrane fraction	calcium ion binding|gamma-catenin binding			ovary(2)|skin(2)	4			OV - Ovarian serous cystadenocarcinoma(10;0.125)			GGATGGCATGCGGTCTTCATT	0.313													3	102	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9068085	9068085	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9068085G>A	uc002mkp.2	-	3	19565	c.19361C>T	c.(19360-19362)GCG>GTG	p.A6454V		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	6456	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						CTGTGATGTCGCCCTATGAGG	0.498													7	318	---	---	---	---	PASS
LILRA2	11027	broad.mit.edu	37	19	55086976	55086976	+	Silent	SNP	C	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55086976C>T	uc002qgg.3	+	5	998	c.909C>T	c.(907-909)TCC>TCT	p.S303S	LILRA2_uc010ern.2_Silent_p.S303S|LILRA2_uc002qgf.2_Silent_p.S303S|LILRA2_uc010yfe.1_Silent_p.S303S|LILRA2_uc010yff.1_Silent_p.S291S|LILRA2_uc010ero.2_Silent_p.S291S|LILRA2_uc010yfg.1_Intron	NM_001130917	NP_001124389	Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor,	303	Ig-like C2-type 3.|Extracellular (Potential).				defense response	integral to membrane	antigen binding|receptor activity			ovary(1)	1				GBM - Glioblastoma multiforme(193;0.0963)		ACCTCTCCTCCGAGTGGTCGG	0.672													28	95	---	---	---	---	PASS
ADIG	149685	broad.mit.edu	37	20	37214721	37214721	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37214721C>A	uc002xjb.1	+	2	230	c.174C>A	c.(172-174)AGC>AGA	p.S58R		NM_001018082	NP_001018092	Q0VDE8	ADIG_HUMAN	small adipocyte factor 1	58					brown fat cell differentiation|positive regulation of fat cell differentiation|white fat cell differentiation	cytoplasm|integral to membrane|nucleus					0		Myeloproliferative disorder(115;0.00878)				AGCCCTGGAGCAAAGGCCCAG	0.582													5	20	---	---	---	---	PASS
GMEB2	26205	broad.mit.edu	37	20	62221522	62221522	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62221522C>T	uc002yfp.1	-	9	1992	c.1513G>A	c.(1513-1515)GCA>ACA	p.A505T	GMEB2_uc002yfo.1_Missense_Mutation_p.A427T|GMEB2_uc002yfq.1_Missense_Mutation_p.A505T	NM_012384	NP_036516	Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding	505					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|metal ion binding				0	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			GCAGCCCCTGCGGGCACTGTC	0.697													3	48	---	---	---	---	PASS
DSCAM	1826	broad.mit.edu	37	21	41385099	41385099	+	Silent	SNP	G	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41385099G>A	uc002yyq.1	-	33	6353	c.5901C>T	c.(5899-5901)GCC>GCT	p.A1967A	DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1967	Cytoplasmic (Potential).			HRPGDLIHLPPYLRMDFLLNRGGPGTSRDLSLGQACLEPQK SRTLKRPTVLEPIPMEAASSASSTREGQSWQPGAVATLPQR EGAELGQAAKMSSSQESLLDSRGHLKGNNPYAKSYTLV -> IGQVTSYICLHTLEWTFC (in Ref. 1; AAC17966).	cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				ATGTGGCCACGGCCCCCGGCT	0.652													5	27	---	---	---	---	PASS
SBF1	6305	broad.mit.edu	37	22	50892988	50892988	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50892988C>A	uc003blh.2	-	36	5191	c.4996G>T	c.(4996-4998)GAC>TAC	p.D1666Y	SBF1_uc003ble.2_Missense_Mutation_p.D130Y|SBF1_uc003blf.2_Missense_Mutation_p.D142Y|SBF1_uc011arx.1_Missense_Mutation_p.D1304Y	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1	1640					protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		GGGCAGCTGTCGTAACAGGGC	0.692													3	113	---	---	---	---	PASS
HTATSF1	27336	broad.mit.edu	37	X	135594070	135594070	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135594070T>G	uc004ezw.2	+	10	2588	c.2166T>G	c.(2164-2166)GAT>GAG	p.D722E	HTATSF1_uc004ezx.2_Missense_Mutation_p.D722E	NM_001163280	NP_001156752	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	722	Asp/Glu-rich (acidic).|Mediates interaction with the P-TEFb complex.				regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|viral genome replication	nucleus	nucleotide binding|protein binding|RNA binding			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)					ACGATTCTGATGAGAGGGGGA	0.438													5	282	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	5050112	5050113	+	IGR	DEL	TC	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5050112_5050113delTC								AJAP1 (206262 upstream) : NPHP4 (872757 downstream)																							aggccttctgtctctctctctc	0.000													3	3	---	---	---	---	
PADI1	29943	broad.mit.edu	37	1	17561705	17561709	+	Intron	DEL	GAGGA	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17561705_17561709delGAGGA	uc001bah.1	+						PADI1_uc010oco.1_Intron|PADI1_uc010ocp.1_Intron|PADI1_uc010ocq.1_Intron	NM_013358	NP_037490	Q9ULC6	PADI1_HUMAN	peptidylarginine deiminase type I						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity				0		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	gggagggagggaggaagggaaggaa	0.015													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	44672874	44672875	+	IGR	INS	-	A	A			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44672874_44672875insA								KLF17 (72067 upstream) : DMAP1 (6250 downstream)																							ccctgtctcagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
C1orf177	163747	broad.mit.edu	37	1	55285655	55285656	+	Intron	INS	-	TTTT	TTTT			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55285655_55285656insTTTT	uc001cyb.3	+						C1orf177_uc001cya.3_Intron	NM_001110533	NP_001104003	Q3ZCV2	CA177_HUMAN	hypothetical protein LOC163747 isoform 2												0						ttctttttctctctttcttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	100288464	100288466	+	IGR	DEL	ACC	-	-	rs79614284		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100288464_100288466delACC								FRRS1 (57115 upstream) : AGL (27174 downstream)																							tacctcctctacctcctctacct	0.059													6	3	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	148011136	148011137	+	Intron	INS	-	T	T	rs148901736	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148011136_148011137insT	uc001eqf.2	-						LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc001eqx.2_Intron|NBPF14_uc001eqq.2_Intron|NBPF14_uc010pad.1_Intron|NBPF14_uc001eqs.1_Intron	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						CATGGCTAACGTAAGGAAGAGT	0.416													6	4	---	---	---	---	
ZNF687	57592	broad.mit.edu	37	1	151262327	151262328	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151262327_151262328insC	uc001exq.2	+	6	2906_2907	c.2808_2809insC	c.(2806-2811)GAGCCCfs	p.E936fs	ZNF687_uc009wmo.2_Frame_Shift_Ins_p.E936fs|ZNF687_uc009wmp.2_Frame_Shift_Ins_p.E936fs	NM_020832	NP_065883	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	936_937					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding			central_nervous_system(3)|ovary(1)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GCTCCCCTGAGCCCCCCCGTCC	0.649													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16134251	16134258	+	IGR	DEL	CTTCCTTC	-	-	rs71938919		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16134251_16134258delCTTCCTTC								MYCN (47123 upstream) : FAM49A (599643 downstream)																							ttctttctttcttccttccttccttcct	0.029													4	3	---	---	---	---	
ALMS1	7840	broad.mit.edu	37	2	73830582	73830582	+	Intron	DEL	A	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73830582delA	uc002sje.1	+						ALMS1_uc002sjf.1_Intron|ALMS1_uc002sjh.1_3'UTR	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1						G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9						TATGGCACTGAAAAAAAAAAA	0.353													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	98248130	98248131	+	IGR	INS	-	AAGC	AAGC			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98248130_98248131insAAGC								ANKRD36B (41702 upstream) : COX5B (14390 downstream)																							cAgaaagaaagaaggaaggaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	105135748	105135749	+	IGR	INS	-	G	G	rs113745795	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105135748_105135749insG								LOC150568 (6534 upstream) : POU3F3 (336220 downstream)																							AGAGAGAGAGagaaggaaggaa	0.163													4	2	---	---	---	---	
DPP10	57628	broad.mit.edu	37	2	116593691	116593694	+	Intron	DEL	GTGA	-	-	rs145523243	byFrequency	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116593691_116593694delGTGA	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						gtgtgtgtgtgtgAGatatatata	0.245													4	2	---	---	---	---	
LCT	3938	broad.mit.edu	37	2	136587400	136587401	+	Intron	INS	-	GTGTGT	GTGTGT	rs137885947	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136587400_136587401insGTGTGT	uc002tuu.1	-							NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein						carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|skin(2)|pancreas(1)|lung(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.169)		GGAATGAGAAAgtgtgtgtgtg	0.416													8	4	---	---	---	---	
ITGA4	3676	broad.mit.edu	37	2	182344708	182344708	+	Intron	DEL	T	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182344708delT	uc002unu.2	+						ITGA4_uc010zfl.1_Intron	NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor						blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)	CTTCTCTGGCTTTTTTTTTTT	0.318													10	5	---	---	---	---	
C2orf60	129450	broad.mit.edu	37	2	200803934	200803935	+	Intron	DEL	TC	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200803934_200803935delTC	uc002uvi.3	-						C2orf60_uc002uvj.3_Intron|C2orf60_uc002uvk.3_Intron|C2orf60_uc010fss.2_Intron	NM_001039693	NP_001034782	A2RUC4	TYW5_HUMAN	hypothetical protein LOC129450						wybutosine biosynthetic process		iron ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein homodimerization activity|tRNA binding				0						tctctatctttctctctctctc	0.153													4	2	---	---	---	---	
SCN11A	11280	broad.mit.edu	37	3	38991560	38991560	+	Intron	DEL	A	-	-	rs60219362		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38991560delA	uc011ays.1	-							NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha						response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)	ccccacccccacccccccccc	0.413													1	5	---	---	---	---	
BAP1	8314	broad.mit.edu	37	3	52436397	52436397	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52436397delC	uc003ddx.2	-	17	2212	c.2097delG	c.(2095-2097)CGGfs	p.R699fs	BAP1_uc003ddw.2_RNA|BAP1_uc010hmg.2_RNA|BAP1_uc010hmh.2_RNA	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	699	Interaction with BRCA1.				monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	p.Q694fs*14(1)		pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CTTGGCGCCGCCGCACGGAGA	0.657			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								4	2	---	---	---	---	
C3orf63	23272	broad.mit.edu	37	3	56662794	56662794	+	Intron	DEL	T	-	-	rs35779948		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56662794delT	uc003did.3	-						C3orf63_uc003dib.3_Intron|C3orf63_uc003dic.3_Intron|C3orf63_uc003die.3_Intron	NM_015224	NP_056039	Q9UK61	CC063_HUMAN	retinoblastoma-associated protein 140 isoform b											ovary(3)|kidney(1)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.0126)|Kidney(284;0.0147)		CATCAAATCCttttttttttt	0.159													4	2	---	---	---	---	
BFSP2	8419	broad.mit.edu	37	3	133156474	133156477	+	Intron	DEL	AAAG	-	-	rs141969388		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133156474_133156477delAAAG	uc003epn.1	+						uc003epo.2_Intron	NM_003571	NP_003562	Q13515	BFSP2_HUMAN	phakinin						response to stimulus|visual perception	cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens				0						agaaagagaaaaagaaagaagaga	0.108													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	152434376	152434379	+	IGR	DEL	CCTT	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152434376_152434379delCCTT								MBNL1 (250808 upstream) : P2RY1 (118357 downstream)																							ccttcctttcccttccttccttcc	0.103													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	186204359	186204360	+	Intron	INS	-	G	G	rs111354223		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186204359_186204360insG	uc003fqd.1	-											Homo sapiens cDNA FLJ32735 fis, clone TESTI2001229.																		gaaggaaggaaggacagactac	0.000													6	3	---	---	---	---	
PDS5A	23244	broad.mit.edu	37	4	39847505	39847506	+	Intron	INS	-	A	A	rs79426492		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39847505_39847506insA	uc003guv.3	-						PDS5A_uc010ifo.2_Intron	NM_001100399	NP_001093869	Q29RF7	PDS5A_HUMAN	PDS5, regulator of cohesion maintenance, homolog						cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0						GAAGTCCTATTaaaaaaaaaaa	0.252													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	53661752	53661765	+	IGR	DEL	AAGAAAGAGAGAGA	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53661752_53661765delAAGAAAGAGAGAGA								KIAA0114 (81447 upstream) : RASL11B (66730 downstream)																							ggaaggaaggaagaaagagagagaaagaaagaga	0.000													3	3	---	---	---	---	
THAP6	152815	broad.mit.edu	37	4	76446792	76446793	+	Intron	DEL	AA	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76446792_76446793delAA	uc003him.2	+						THAP6_uc010iis.1_Intron|THAP6_uc003hin.2_Intron|THAP6_uc011cbm.1_Intron|THAP6_uc010iiu.1_Intron|THAP6_uc003hio.1_Intron|THAP6_uc010iiv.2_Intron	NM_144721	NP_653322	Q8TBB0	THAP6_HUMAN	THAP domain containing 6							microtubule cytoskeleton	DNA binding|metal ion binding				0			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			AAGTTCTTTTAAAATTATCTGG	0.208													4	4	---	---	---	---	
SHROOM3	57619	broad.mit.edu	37	4	77439725	77439728	+	Intron	DEL	TGCT	-	-	rs71659329		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77439725_77439728delTGCT	uc011cbx.1	+							NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)			ccttcTtgcctgcttgcctgcctg	0.127													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	135393585	135393586	+	IGR	INS	-	AAGG	AAGG	rs144776837	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135393585_135393586insAAGG								PABPC4L (270682 upstream) : None (None downstream)																							agaaggaaggaaaggaaggaag	0.040													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	179208518	179208519	+	IGR	INS	-	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179208518_179208519insT								LOC285501 (296615 upstream) : None (None downstream)																							CCTTTATCTGCTTAAAAAAAAA	0.366													4	2	---	---	---	---	
NDUFS6	4726	broad.mit.edu	37	5	1801427	1801428	+	5'Flank	INS	-	G	G	rs150444980	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1801427_1801428insG	uc003jcy.2	+						MRPL36_uc003jcx.3_5'Flank	NM_004553	NP_004544	O75380	NDUS6_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 6,						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	electron carrier activity|NADH dehydrogenase (ubiquinone) activity			central_nervous_system(1)	1					NADH(DB00157)	GCGCTCCCCGCCCCCAGGGCGA	0.644													5	5	---	---	---	---	
FAM151B	167555	broad.mit.edu	37	5	79797492	79797493	+	Intron	DEL	TA	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79797492_79797493delTA	uc003kgv.1	+						FAM151B_uc010jal.1_Intron	NM_205548	NP_991111	Q6UXP7	F151B_HUMAN	hypothetical protein LOC167555												0		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)		tctatctatctatatatatata	0.054													9	4	---	---	---	---	
PAM	5066	broad.mit.edu	37	5	102284025	102284025	+	Intron	DEL	A	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102284025delA	uc003knw.2	+						PAM_uc003kns.2_Intron|PAM_uc003knt.2_Intron|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Intron	NM_000919	NP_000910	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase						peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	CTGTTTTTCCAAAACAGTCAT	0.289													45	24	---	---	---	---	
PCDHGA10	56106	broad.mit.edu	37	5	140852548	140852548	+	Intron	DEL	A	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140852548delA	uc003lkl.1	+						PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron	NM_018913	NP_061736	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			agtgaaactcaaaaaaaaaaa	0.050													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	75468290	75468291	+	IGR	INS	-	AAGG	AAGG	rs71685977		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75468290_75468291insAAGG								CD109 (930250 upstream) : COL12A1 (325752 downstream)																							aggaagaaagaaagaaagaaag	0.173													5	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152004276	152004279	+	Intron	DEL	GAGG	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152004276_152004279delGAGG	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		aaggaaagaagagggaggaaggaa	0.039			N		medulloblastoma								6	4	---	---	---	---	
XKR6	286046	broad.mit.edu	37	8	11058892	11058892	+	5'Flank	DEL	C	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11058892delC	uc003wtk.1	-							NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		ggagggacggcgggggggggg	0.249													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	67458184	67458187	+	IGR	DEL	GGAA	-	-	rs60180673		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67458184_67458187delGGAA								C8orf46 (27427 upstream) : MYBL1 (16224 downstream)																							agggagggagggaaggaaggaagg	0.074													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	6051612	6051614	+	IGR	DEL	GAG	-	-	rs111817505		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6051612_6051614delGAG								RANBP6 (35972 upstream) : IL33 (164193 downstream)																							ggaggaggaagaggaggaggagg	0.010													4	2	---	---	---	---	
FRMPD1	22844	broad.mit.edu	37	9	37736882	37736883	+	Intron	DEL	GC	-	-	rs151329428		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37736882_37736883delGC	uc004aag.1	+						FRMPD1_uc004aah.1_Intron|FRMPD1_uc011lqm.1_Intron|FRMPD1_uc011lqn.1_Intron	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1							cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		gtgtatgtgtgCGCACACACAC	0.376													3	4	---	---	---	---	
TRPM6	140803	broad.mit.edu	37	9	77427483	77427483	+	Intron	DEL	A	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77427483delA	uc004ajl.1	-						TRPM6_uc004ajk.1_Intron|TRPM6_uc010mpb.1_Intron|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,						response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						GTGGGTACAGAAAAAAAAAAA	0.159													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	138016546	138016549	+	IGR	DEL	AAAC	-	-	rs71979181		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138016546_138016549delAAAC								OLFM1 (3515 upstream) : KIAA0649 (355099 downstream)																							agaaagaaagaaacaaagaaagaa	0.083													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	2220808	2220809	+	IGR	INS	-	CCTC	CCTC	rs145929531	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2220808_2220809insCCTC								ADARB2 (441090 upstream) : PFKP (888943 downstream)																							cttccttccttccctccttcct	0.198													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	27620447	27620448	+	IGR	INS	-	TT	TT	rs142562667	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27620447_27620448insTT								LOC387646 (79212 upstream) : PTCHD3 (66669 downstream)																							ACTCAGGCTTCTTTCCGCCAAG	0.465													5	3	---	---	---	---	
PCGF6	84108	broad.mit.edu	37	10	105086164	105086164	+	Intron	DEL	C	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105086164delC	uc001kwt.2	-						PCGF6_uc001kwu.2_Intron|PCGF6_uc009xxk.2_Intron|PCGF6_uc009xxl.2_Intron|PCGF6_uc009xxm.2_Intron	NM_001011663	NP_001011663	Q9BYE7	PCGF6_HUMAN	polycomb group ring finger 6 isoform a						negative regulation of transcription, DNA-dependent	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			kidney(1)	1		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;2.57e-09)|all cancers(201;7.21e-08)|BRCA - Breast invasive adenocarcinoma(275;0.205)		aaaaaaaaaaCAATGTCTACA	0.159													4	2	---	---	---	---	
TCF7L2	6934	broad.mit.edu	37	10	114724571	114724572	+	Intron	INS	-	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114724571_114724572insG	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		gtggtggtggtggGGGGGGGTT	0.238													4	2	---	---	---	---	
TCERG1L	256536	broad.mit.edu	37	10	133055212	133055215	+	Intron	DEL	GAAG	-	-	rs141999228		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133055212_133055215delGAAG	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		ggaagagaaagaaggaaggaagga	0.000													7	6	---	---	---	---	
DRD4	1815	broad.mit.edu	37	11	640341	640342	+	Intron	INS	-	G	G			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:640341_640342insG	uc001lqp.1	+							NM_000797	NP_000788	P21917	DRD4_HUMAN	dopamine receptor D4						activation of MAPK activity|adult locomotory behavior|arachidonic acid secretion|behavioral fear response|behavioral response to cocaine|behavioral response to ethanol|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of cAMP biosynthetic process|negative regulation of protein secretion|positive regulation of sodium:hydrogen antiporter activity|regulation of dopamine metabolic process|regulation of inhibitory postsynaptic membrane potential|response to amphetamine|response to histamine|social behavior	integral to plasma membrane	dopamine D4 receptor activity|drug binding|potassium channel regulator activity|SH3 domain binding				0		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.36e-28)|Epithelial(43;2.59e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Apomorphine(DB00714)|Clozapine(DB00363)|Olanzapine(DB00334)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Ropinirole(DB00268)|Thiethylperazine(DB00372)|Ziprasidone(DB00246)	GGAGGAGAGGAGGGGGGGGGTA	0.733													4	2	---	---	---	---	
NUP98	4928	broad.mit.edu	37	11	3723472	3723473	+	Intron	DEL	AC	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3723472_3723473delAC	uc001lyh.2	-						NUP98_uc001lyi.2_Intron|NUP98_uc001lyg.2_Intron	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1						carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		agactcaaaaaCACACACACAC	0.099			T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								4	2	---	---	---	---	
SBF2	81846	broad.mit.edu	37	11	10313241	10313246	+	Intron	DEL	ACACAG	-	-	rs10580039		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10313241_10313246delACACAG	uc001mib.2	-							NM_030962	NP_112224	Q86WG5	MTMRD_HUMAN	SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		acacacacacacacagactccatgta	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	44336453	44336454	+	IGR	INS	-	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44336453_44336454insT								ALX4 (4737 upstream) : CD82 (250687 downstream)																							cttttccttccttccttccttc	0.025													6	3	---	---	---	---	
TECTA	7007	broad.mit.edu	37	11	121005034	121005035	+	Intron	INS	-	CA	CA	rs140288404	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121005034_121005035insCA	uc010rzo.1	+							NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor						cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		aaaaCCAacaccacacacacac	0.153													4	2	---	---	---	---	
NTM	50863	broad.mit.edu	37	11	131971479	131971480	+	Intron	DEL	TA	-	-	rs67623623		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131971479_131971480delTA	uc001qgp.2	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgo.2_Intron|NTM_uc001qgq.2_Intron	NM_016522	NP_057606	Q9P121	NTRI_HUMAN	neurotrimin isoform 1						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						tgtgtgtgtgtatgtttgaatg	0.297													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48661151	48661166	+	IGR	DEL	CTTCCTTCCTTCCTTT	-	-	rs12810981	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48661151_48661166delCTTCCTTCCTTCCTTT								OR10AD1 (64076 upstream) : H1FNT (61597 downstream)																							tccttccttccttccttccttcctttcttccttcct	0.093													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	107320643	107320644	+	IGR	INS	-	TTCCTTCC	TTCCTTCC	rs142740419	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107320643_107320644insTTCCTTCC								RIC8B (37551 upstream) : C12orf23 (28900 downstream)																							tcctttcttctttccttccttc	0.000													4	2	---	---	---	---	
GPR81	27198	broad.mit.edu	37	12	123150159	123150160	+	Intron	INS	-	TC	TC	rs113852766	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123150159_123150160insTC	uc001ucw.1	-							NM_032554		Q9BXC0	HCAR1_HUMAN	G protein-coupled receptor 81						response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)		ttctttctttgtctctctctct	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	19985459	19985461	+	IGR	DEL	TGG	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19985459_19985461delTGG								LOC100101938 (66346 upstream) : TPTE2 (11560 downstream)																							atgtttctgttggtgatggatgg	0.192													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	31652509	31652516	+	IGR	DEL	AAGGAAGA	-	-	rs148041842	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31652509_31652516delAAGGAAGA								C13orf26 (103358 upstream) : HSPH1 (58249 downstream)																							ggaaggaaggaaggaagaaagaaagaaa	0.192													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	97657697	97657698	+	IGR	DEL	AC	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97657697_97657698delAC								OXGR1 (11093 upstream) : MBNL2 (216876 downstream)																							AGCATTGTGTacacacacacac	0.322													5	3	---	---	---	---	
LGMN	5641	broad.mit.edu	37	14	93184931	93184931	+	Intron	DEL	A	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93184931delA	uc001yav.2	-						LGMN_uc001yat.2_Intron|LGMN_uc001yau.2_Intron|LGMN_uc001yaw.2_Intron|LGMN_uc010aul.2_Intron|LGMN_uc001yax.2_Intron|LGMN_uc001yay.2_Intron	NM_001008530	NP_001008530	Q99538	LGMN_HUMAN	legumain preproprotein						hormone biosynthetic process|negative regulation of neuron apoptosis|vitamin D metabolic process	lysosome	cysteine-type endopeptidase activity|protein serine/threonine kinase activity			skin(1)	1		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		aaataataataaaaaaaaaaa	0.184													4	2	---	---	---	---	
IQGAP1	8826	broad.mit.edu	37	15	90982386	90982387	+	Intron	INS	-	A	A	rs72328066		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90982386_90982387insA	uc002bpl.1	+							NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1						energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TCATGTAAACTAAAAAAAAAAA	0.228													4	2	---	---	---	---	
DECR2	26063	broad.mit.edu	37	16	460579	460579	+	Intron	DEL	T	-	-	rs11315123		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:460579delT	uc002chb.2	+						DECR2_uc002chc.2_Intron|DECR2_uc010bqv.2_Intron|DECR2_uc002chd.2_Intron|DECR2_uc002che.1_Intron	NM_020664	NP_065715	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2							peroxisome	2,4-dienoyl-CoA reductase (NADPH) activity|binding				0		Hepatocellular(16;0.00015)				GGCCTCCCCCTGACGGCCGCC	0.781													6	4	---	---	---	---	
C1QTNF8	390664	broad.mit.edu	37	16	1143444	1143445	+	Intron	DEL	AC	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1143444_1143445delAC	uc010uuw.1	-							NM_207419	NP_997302	P60827	C1QT8_HUMAN	C1q and tumor necrosis factor related protein 8							collagen				skin(1)	1		Hepatocellular(780;0.00369)				acacacacagacacacacacac	0.485													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	27088704	27088705	+	IGR	INS	-	CTTT	CTTT	rs143025532	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27088704_27088705insCTTT								C16orf82 (8218 upstream) : JMJD5 (126102 downstream)																							ctccttccttccttccttcctt	0.000													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	58925845	58925850	+	IGR	DEL	ACACAT	-	-	rs58628573		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58925845_58925850delACACAT								GOT2 (157599 upstream) : None (None downstream)																							acacacacacacacatacataacatc	0.078													4	2	---	---	---	---	
CLEC18C	283971	broad.mit.edu	37	16	70072983	70072984	+	Intron	INS	-	T	T			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70072983_70072984insT	uc002exy.2	+						PDXDC2_uc002eyb.2_RNA|PDXDC2_uc002eyc.2_Intron	NM_182619	NP_872425	Q8NCF0	CL18C_HUMAN	secretory protein LOC348174 precursor							extracellular region	sugar binding				0						GTTGCTTCAAGTTTTTTTTTTT	0.376													4	2	---	---	---	---	
TNFSF12-TNFSF13	407977	broad.mit.edu	37	17	7451480	7451481	+	5'Flank	INS	-	CTTT	CTTT			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7451480_7451481insCTTT	uc002ghi.1	+						TNFSF12_uc002ghg.2_5'Flank|TNFSF12_uc002ghh.2_5'Flank	NM_172089	NP_742086	Q8IZK7	Q8IZK7_HUMAN	TNFSF12-TNFSF13 protein						immune response	extracellular space|membrane	cytokine activity|tumor necrosis factor receptor binding				0		Prostate(122;0.157)				ttccttccttccttccttcctt	0.010													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	9669678	9669681	+	IGR	DEL	CTCT	-	-	rs72084350		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9669678_9669681delCTCT								USP43 (36677 upstream) : DHRS7C (5075 downstream)																							tccttccttcctctctctctctct	0.108													3	4	---	---	---	---	
MYH3	4621	broad.mit.edu	37	17	10544823	10544825	+	Intron	DEL	GTC	-	-	rs111338270		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10544823_10544825delGTC	uc002gmq.1	-							NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,						muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(2)|pancreas(1)	7						ATTTAACTCTGTCtttttttttt	0.133													3	3	---	---	---	---	
MPRIP	23164	broad.mit.edu	37	17	17064775	17064776	+	Intron	INS	-	C	C	rs72535824		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17064775_17064776insC	uc002gqu.1	+						MPRIP_uc002gqv.1_Intron|MPRIP_uc002gqw.1_Intron	NM_201274	NP_958431	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase-Rho interacting protein							cytoplasm|cytoskeleton	actin binding				0						CTGAGCAGGGGTGTCTCCCAGG	0.569													4	2	---	---	---	---	
KCNJ12	3768	broad.mit.edu	37	17	21312637	21312638	+	Intron	INS	-	TGT	TGT	rs143247012		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21312637_21312638insTGT	uc002gyv.1	+							NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily						blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	aggagACTTGGTGTGGGGCATC	0.312										Prostate(3;0.18)			6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	53285938	53285939	+	IGR	INS	-	GAAG	GAAG	rs143873127	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53285938_53285939insGAAG								STXBP4 (44489 upstream) : HLF (56382 downstream)																							gagggagggaagaaggaaggaa	0.163													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	68974494	68974497	+	IGR	DEL	AGGA	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68974494_68974497delAGGA								KCNJ2 (798313 upstream) : None (None downstream)																							ggagggagggaggaaggaaggaag	0.000													6	4	---	---	---	---	
CLUL1	27098	broad.mit.edu	37	18	646498	646501	+	Intron	DEL	ACAC	-	-	rs72441948		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:646498_646501delACAC	uc002kkp.2	+						CLUL1_uc010wys.1_Intron|CLUL1_uc002kkq.2_Intron	NM_014410	NP_055225	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal) precursor						cell death	extracellular region				ovary(2)	2						agatagatagacacacacacacac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	41181708	41181709	+	IGR	INS	-	GGCAGGCT	GGCAGGCT	rs140205752	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41181708_41181709insGGCAGGCT								SYT4 (324093 upstream) : None (None downstream)																							gaaggaaggaaggctggcttac	0.000													7	5	---	---	---	---	
MRO	83876	broad.mit.edu	37	18	48341575	48341593	+	Intron	DEL	TGAAGTAAAAAGTGTCCTT	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48341575_48341593delTGAAGTAAAAAGTGTCCTT	uc002lew.3	-						MRO_uc010xdn.1_Intron|MRO_uc010dpa.2_Intron|MRO_uc010dpb.2_Intron|MRO_uc010dpc.2_Intron|MRO_uc002lex.3_Intron	NM_031939	NP_114145	Q9BYG7	MSTRO_HUMAN	maestro isoform a							nucleolus	binding				0		Colorectal(6;0.0596)		Colorectal(21;0.082)		GGCATAATTGTGAAGTAAAAAGTGTCCTTTCTAAATGAG	0.393													10	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	6288378	6288379	+	IGR	DEL	GT	-	-	rs149989824	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6288378_6288379delGT								MLLT1 (8419 upstream) : ACER1 (18131 downstream)																							gtgcgcacgcgtgtgtgtgtgt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	8230721	8230722	+	IGR	INS	-	GAAAGGG	GAAAGGG			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8230721_8230722insGAAAGGG								FBN3 (18340 upstream) : LASS4 (43495 downstream)																							gaaggaaggaaagaaaggaagg	0.153													3	3	---	---	---	---	
ZNF420	147923	broad.mit.edu	37	19	37617892	37617893	+	Intron	INS	-	TAT	TAT	rs143864812	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37617892_37617893insTAT	uc002ofl.2	+							NM_144689	NP_653290	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGAAAGGTAGGTATTATATGTC	0.262													5	5	---	---	---	---	
NLRP7	199713	broad.mit.edu	37	19	55452576	55452576	+	Intron	DEL	A	-	-	rs111382825		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55452576delA	uc002qih.3	-						NLRP7_uc002qig.3_Intron|NLRP7_uc002qii.3_Intron|NLRP7_uc010esk.2_Intron|NLRP7_uc010esl.2_Intron	NM_206828	NP_996611	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7								ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)		ctaaaaatacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
RBBP9	10741	broad.mit.edu	37	20	18476307	18476307	+	Intron	DEL	G	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18476307delG	uc002wqy.2	-							NM_006606	NP_006597	O75884	RBBP9_HUMAN	retinoblastoma binding protein 9							cytoplasm|nucleus	hydrolase activity			haematopoietic_and_lymphoid_tissue(1)	1						aaaaaaAAAAGAATTTTCTAT	0.209													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11106330	11106331	+	IGR	INS	-	AC	AC	rs469434	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11106330_11106331insAC								BAGE (7393 upstream) : None (None downstream)																							taaatatatatacacacacaca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	11124357	11124368	+	IGR	DEL	TCTTCTTCTTCT	-	-	rs10211962	by1000genomes	TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11124357_11124368delTCTTCTTCTTCT								BAGE (25420 upstream) : None (None downstream)																							ctcctcctcctcttcttcttcttcttcttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	18842473	18842473	+	Intron	DEL	G	-	-	rs66618606		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18842473delG	uc010grj.1	+						uc002zoe.2_RNA					Homo sapiens mRNA; cDNA DKFZp434K191 (from clone DKFZp434K191).																		AGCTGCTGGTGGGGAGGTCTT	0.647													6	4	---	---	---	---	
PPARA	5465	broad.mit.edu	37	22	46570088	46570089	+	Intron	DEL	AG	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46570088_46570089delAG	uc003bgw.1	+						PPARA_uc003bgx.1_Intron|PPARA_uc010hab.1_Intron|PPARA_uc003bgy.1_Intron|PPARA_uc003bgz.1_Intron|PPARA_uc003bha.2_5'Flank|PPARA_uc003bhb.1_5'Flank	NM_005036	NP_005027	Q07869	PPARA_HUMAN	peroxisome proliferative activated receptor,						fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641)	gaaggaagaaagagagagagag	0.000													5	3	---	---	---	---	
XG	7499	broad.mit.edu	37	X	2683418	2683425	+	Intron	DEL	GGAAGGAA	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2683418_2683425delGGAAGGAA	uc011mhg.1	+						XG_uc010ndb.2_Intron|XG_uc004cqp.2_Intron	NM_175569	NP_780778	P55808	XG_HUMAN	XG glycoprotein isoform 1 precursor							integral to membrane|plasma membrane				ovary(1)	1		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				agggagggagggaaggaaggaaggaagg	0.135													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	21844464	21844464	+	IGR	DEL	A	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21844464delA								SMPX (68234 upstream) : MBTPS2 (13192 downstream)																							cctgtctcagaaaaaaaaaaa	0.065													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	37759371	37759372	+	IGR	DEL	AC	-	-	rs113389448		TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37759371_37759372delAC								DYNLT3 (52482 upstream) : CXorf27 (90698 downstream)																							acacacaaagacacacacacac	0.168													4	3	---	---	---	---	
MSN	4478	broad.mit.edu	37	X	64952923	64952923	+	Intron	DEL	A	-	-			TCGA-BP-5174-01A-01D-1429-08	TCGA-BP-5174-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64952923delA	uc004dwf.2	+							NM_002444	NP_002435	P26038	MOES_HUMAN	moesin						leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking	apical plasma membrane|cytoskeleton|extrinsic to membrane|microvillus membrane|nucleolus	cell adhesion molecule binding|receptor binding|structural constituent of cytoskeleton		MSN/ALK(6)	haematopoietic_and_lymphoid_tissue(6)|ovary(3)|lung(1)	10						tatttattttaaaaaaaaaaa	0.234			T	ALK	ALCL								9	4	---	---	---	---	
