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
TAS1R3	83756	broad.mit.edu	37	1	1267928	1267928	+	Silent	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1267928G>A	uc010nyk.1	+	3	1017	c.1017G>A	c.(1015-1017)AAG>AAA	p.K339K		NM_152228	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3 precursor	339	Extracellular (Potential).				detection of chemical stimulus involved in sensory perception of sweet taste|sensory perception of umami taste	plasma membrane	protein heterodimerization activity|taste receptor activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)	Aspartame(DB00168)	AGTACGTGAAGACGCACCTGG	0.697													10	63	---	---	---	---	PASS
MTOR	2475	broad.mit.edu	37	1	11217230	11217230	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11217230C>A	uc001asd.2	-	30	4569	c.4448G>T	c.(4447-4449)TGC>TTC	p.C1483F		NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	1483	FAT.				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						GGCCTCGAGGCAGCGCATGCG	0.527													13	305	---	---	---	---	PASS
PLEKHM2	23207	broad.mit.edu	37	1	16058448	16058448	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16058448A>C	uc010obo.1	+	17	2757	c.2530A>C	c.(2530-2532)ATT>CTT	p.I844L		NM_015164	NP_055979	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M	844	Interaction with sifA.|PH.				Golgi organization	cytoplasm	kinesin binding			ovary(1)	1		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		CTTCCAGGTCATTCTCTCCGA	0.667													4	24	---	---	---	---	PASS
EPHA8	2046	broad.mit.edu	37	1	22902868	22902868	+	Silent	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22902868C>T	uc001bfx.1	+	3	443	c.318C>T	c.(316-318)CGC>CGT	p.R106R	EPHA8_uc001bfw.2_Silent_p.R106R	NM_020526	NP_065387	P29322	EPHA8_HUMAN	ephrin receptor EphA8 isoform 1 precursor	106	Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TTACCCTGCGCGACTGCAACA	0.622													7	85	---	---	---	---	PASS
EXTL1	2134	broad.mit.edu	37	1	26357724	26357724	+	Silent	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26357724C>T	uc001blf.2	+	5	2070	c.1203C>T	c.(1201-1203)CCC>CCT	p.P401P		NM_004455	NP_004446	Q92935	EXTL1_HUMAN	exostoses-like 1	401	Lumenal (Potential).				skeletal system development	integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|protein binding			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		CCACAAGCCCCCAGGACTTCC	0.587													31	113	---	---	---	---	PASS
MANEAL	149175	broad.mit.edu	37	1	38261312	38261312	+	Intron	SNP	G	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38261312G>C	uc001cby.2	+						MANEAL_uc001cbx.2_Intron|MANEAL_uc001cbz.2_5'UTR	NM_001113482	NP_001106954	Q5VSG8	MANEL_HUMAN	mannosidase, endo-alpha-like isoform 3							Golgi membrane|integral to membrane	hydrolase activity				0	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CAGGTTTTTAGGAACCATTTT	0.552													5	32	---	---	---	---	PASS
S1PR1	1901	broad.mit.edu	37	1	101705772	101705772	+	3'UTR	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101705772C>T	uc001dud.2	+	2					S1PR1_uc009weg.2_3'UTR	NM_001400	NP_001391	P21453	S1PR1_HUMAN	sphingosine-1-phosphate receptor 1						cell adhesion	integral to membrane	lysosphingolipid and lysophosphatidic acid receptor activity			ovary(2)|lung(1)	3						CTCTGGGCTTCGACTGCTGCC	0.562													6	15	---	---	---	---	PASS
CDKL4	344387	broad.mit.edu	37	2	39405846	39405846	+	3'UTR	SNP	C	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39405846C>G	uc002rrm.2	-	8					CDKL4_uc010fal.1_Missense_Mutation_p.V328L	NM_001009565	NP_001009565	Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4							cytoplasm	ATP binding|cyclin-dependent protein kinase activity			ovary(1)	1		all_hematologic(82;0.248)				TTCCTTTGTACCTGGCAGATC	0.433													8	17	---	---	---	---	PASS
PPM1B	5495	broad.mit.edu	37	2	44457414	44457414	+	Intron	SNP	A	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44457414A>T	uc002rtt.2	+						PPM1B_uc002rtu.2_3'UTR|PPM1B_uc002rtv.2_Intron|PPM1B_uc002rtw.2_Intron|PPM1B_uc002rtx.2_Intron	NM_002706	NP_002697	O75688	PPM1B_HUMAN	protein phosphatase 1B isoform 1						protein dephosphorylation	protein serine/threonine phosphatase complex	magnesium ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			kidney(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				GTAAGAATTGATATTTAATAA	0.254													4	34	---	---	---	---	PASS
EXOC6B	23233	broad.mit.edu	37	2	72945362	72945362	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72945362C>A	uc010fep.2	-	6	677	c.539G>T	c.(538-540)TGC>TTC	p.C180F	EXOC6B_uc002sij.2_Missense_Mutation_p.C180F	NM_015189	NP_056004	Q9Y2D4	EXC6B_HUMAN	SEC15-like 2	180					protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2						CATCACCTTGCAGAATCGATA	0.428													5	148	---	---	---	---	PASS
LRRTM4	80059	broad.mit.edu	37	2	76975919	76975919	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76975919C>T	uc002snr.2	-	4	2090	c.1675G>A	c.(1675-1677)GAA>AAA	p.E559K	LRRTM4_uc002snq.2_Missense_Mutation_p.E559K	NM_001134745	NP_001128217	Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	559	Cytoplasmic (Potential).					integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)		CCGGGGCTTTCGTCCTGCTCT	0.592													9	154	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90078038	90078038	+	RNA	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90078038G>A	uc010fhm.2	+	14		c.1428G>A								Parts of antibodies, mostly variable regions.																		TTGTGTTGACGCAGTCTCCAG	0.502													8	162	---	---	---	---	PASS
GCC2	9648	broad.mit.edu	37	2	109113518	109113518	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109113518C>G	uc002tec.2	+	21	4889	c.4735C>G	c.(4735-4737)CTT>GTT	p.L1579V	GCC2_uc002ted.2_Missense_Mutation_p.L1478V	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	1579	Mediates interaction with RAB6A.|Potential.|Mediates interaction with RAB9A.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1						AAACGGCCTGCTTCGGGAAAC	0.448													87	221	---	---	---	---	PASS
THSD7B	80731	broad.mit.edu	37	2	138033572	138033572	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138033572T>A	uc002tva.1	+	11	2383	c.2383T>A	c.(2383-2385)TGT>AGT	p.C795S	THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Missense_Mutation_p.C685S	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		CAGTGAAGCCTGTGGAAAGGG	0.398													7	62	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179558720	179558720	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179558720G>T	uc010zfg.1	-	115	27934	c.27710C>A	c.(27709-27711)ACA>AAA	p.T9237K	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.T5898K|TTN_uc010fre.1_Missense_Mutation_p.T348K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	10164							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATCTTCTTTGTATGCACAGC	0.373													9	30	---	---	---	---	PASS
STT3B	201595	broad.mit.edu	37	3	31658488	31658488	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31658488G>C	uc011axe.1	+	7	1044	c.1044G>C	c.(1042-1044)GAG>GAC	p.E348D	STT3B_uc010hft.1_Missense_Mutation_p.E348D|STT3B_uc003cer.1_Missense_Mutation_p.E348D|STT3B_uc003cet.2_Missense_Mutation_p.E99D	NM_178862	NP_849193	Q8TCJ2	STT3B_HUMAN	source of immunodominant MHC-associated	348					protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding				0						CAAAACAAGAGTTCCAGACCC	0.398													60	297	---	---	---	---	PASS
OR5H1	26341	broad.mit.edu	37	3	97851850	97851850	+	Silent	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97851850G>A	uc011bgt.1	+	1	309	c.309G>A	c.(307-309)TCG>TCA	p.S103S		NM_001005338	NP_001005338	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H,	103	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2						AGTTTTTTTCGTTTGCAATCA	0.388													10	468	---	---	---	---	PASS
KIAA2018	205717	broad.mit.edu	37	3	113374665	113374665	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113374665G>T	uc003eam.2	-	7	6275	c.5864C>A	c.(5863-5865)TCT>TAT	p.S1955Y	KIAA2018_uc003eal.2_Missense_Mutation_p.S1899Y	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717	1955					regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3						ATGAGACACAGATGGATGTGG	0.537													26	52	---	---	---	---	PASS
IGSF11	152404	broad.mit.edu	37	3	118621704	118621704	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118621704C>T	uc003ebw.2	-	7	1206	c.959G>A	c.(958-960)CGA>CAA	p.R320Q	IGSF11_uc011biv.1_Missense_Mutation_p.R292Q|IGSF11_uc003ebx.2_Missense_Mutation_p.R296Q|IGSF11_uc003eby.2_Missense_Mutation_p.R319Q|IGSF11_uc003ebz.2_Missense_Mutation_p.R295Q|IGSF11_uc010hqs.2_Missense_Mutation_p.R319Q	NM_001015887	NP_001015887	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11 isoform b	320	Cytoplasmic (Potential).				cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0						GCTCCAGTATCGACTGTTGTA	0.458													48	174	---	---	---	---	PASS
TSC22D2	9819	broad.mit.edu	37	3	150176367	150176367	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150176367G>A	uc003exv.2	+	4	2637	c.2287G>A	c.(2287-2289)GCA>ACA	p.A763T	TSC22D2_uc003exw.2_RNA|TSC22D2_uc003exx.2_Missense_Mutation_p.A739T	NM_014779	NP_055594	O75157	T22D2_HUMAN	TSC22 domain family, member 2	763							sequence-specific DNA binding transcription factor activity			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			AGCAGTGATAGCACAGCCTCC	0.443													4	133	---	---	---	---	PASS
PIK3CA	5290	broad.mit.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	G	G	rs121913279		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178952085A>G	uc003fjk.2	+	21	3297	c.3140A>G	c.(3139-3141)CAT>CGT	p.H1047R		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	1047	PI3K/PI4K.		H -> L (in cancer).|H -> R (in KERSEB; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane).|H -> Y (in cancer).		epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.H1047R(1269)|p.H1047L(152)|p.H1047Y(31)|p.H1047Q(3)|p.H1047T(1)		breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			AATGATGCACATCATGGTGGC	0.378	H1047R(BT20_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(MCAS_OVARY)|H1047R(HCC1954_BREAST)|H1047R(RKO_LARGE_INTESTINE)|H1047L(EFM19_BREAST)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(CAL29_URINARY_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(T47D_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(SKOV3_OVARY)|H1047R(MDAMB453_BREAST)	57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			4	112	---	---	---	---	PASS
DRD5	1816	broad.mit.edu	37	4	9784913	9784913	+	Silent	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9784913C>T	uc003gmb.3	+	1	1656	c.1260C>T	c.(1258-1260)CCC>CCT	p.P420P		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	420	Cytoplasmic (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane				skin(1)	1					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)	CCGTTACCCCCGGCAACCGGG	0.547													18	98	---	---	---	---	PASS
CENPC1	1060	broad.mit.edu	37	4	68380078	68380078	+	Silent	SNP	A	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68380078A>G	uc003hdd.1	-	8	1341	c.1158T>C	c.(1156-1158)GCT>GCC	p.A386A	CENPC1_uc010ihj.1_RNA|CENPC1_uc010ihk.1_RNA|CENPC1_uc010ihm.1_Silent_p.A386A	NM_001812	NP_001803	Q03188	CENPC_HUMAN	centromere protein C 1	386					mitotic prometaphase	condensed chromosome kinetochore|condensed nuclear chromosome, centromeric region|cytosol	DNA binding			urinary_tract(1)|lung(1)	2						CACCTATCAAAGCATAACTTG	0.333													28	51	---	---	---	---	PASS
ADH1B	125	broad.mit.edu	37	4	100239948	100239948	+	Silent	SNP	G	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100239948G>C	uc003hus.3	-	2	198	c.114C>G	c.(112-114)CGC>CGG	p.R38R	ADH1A_uc011ceg.1_Intron|ADH1B_uc003hut.3_5'UTR|ADH1B_uc011ceh.1_5'UTR|ADH1B_uc011cei.1_5'UTR	NM_000668	NP_000659	P00325	ADH1B_HUMAN	class I alcohol dehydrogenase, beta subunit	38					ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase activity, zinc-dependent|zinc ion binding			ovary(1)|breast(1)	2				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Fomepizole(DB01213)|NADH(DB00157)	TCACCTTAATGCGAACTTCAT	0.348													13	114	---	---	---	---	PASS
NPNT	255743	broad.mit.edu	37	4	106819134	106819134	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106819134C>T	uc003hya.2	+	2	353	c.148C>T	c.(148-150)CGC>TGC	p.R50C	NPNT_uc011cfc.1_Missense_Mutation_p.R50C|NPNT_uc011cfd.1_Missense_Mutation_p.R50C|NPNT_uc011cfe.1_Missense_Mutation_p.R50C|NPNT_uc010ilt.1_Missense_Mutation_p.R50C|NPNT_uc011cff.1_Missense_Mutation_p.R50C|NPNT_uc010ilu.1_5'UTR	NM_001033047	NP_001028219	Q6UXI9	NPNT_HUMAN	nephronectin precursor	50					cell differentiation	membrane	calcium ion binding			skin(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		GGGCTGGGCTCGCCAGTCTTG	0.522													14	42	---	---	---	---	PASS
COL25A1	84570	broad.mit.edu	37	4	109783657	109783657	+	Silent	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109783657C>T	uc003hze.1	-	21	1728	c.1197G>A	c.(1195-1197)AAG>AAA	p.K399K	COL25A1_uc003hzg.2_Silent_p.K399K|COL25A1_uc003hzd.2_RNA|COL25A1_uc003hzf.2_Intron	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1	399	Extracellular (Potential).|Collagen-like 5.					collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		GGTTACTGACCTTTGACCCCT	0.368													69	375	---	---	---	---	PASS
IRF2	3660	broad.mit.edu	37	4	185310135	185310135	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185310135C>T	uc003iwf.3	-	9	1027	c.827G>A	c.(826-828)GGC>GAC	p.G276D		NM_002199	NP_002190	P14316	IRF2_HUMAN	interferon regulatory factor 2	276					blood coagulation|cell proliferation|interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	focal adhesion|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		GGACGCCATGCCGGGCAGCAG	0.552													6	245	---	---	---	---	PASS
ZCCHC9	84240	broad.mit.edu	37	5	80600797	80600797	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80600797G>T	uc003khj.2	+	2	354	c.221G>T	c.(220-222)GGA>GTA	p.G74V	RNU5E_uc011cto.1_Intron|ZCCHC9_uc003khk.3_Missense_Mutation_p.G74V|ZCCHC9_uc003khi.2_Missense_Mutation_p.G74V	NM_001131035	NP_001124507	Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	74							nucleic acid binding|zinc ion binding			ovary(1)	1		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		GATGTGAATGGATTCATGGAA	0.363													18	81	---	---	---	---	PASS
DMXL1	1657	broad.mit.edu	37	5	118484562	118484562	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118484562A>G	uc003ksd.2	+	18	3221	c.3040A>G	c.(3040-3042)AAT>GAT	p.N1014D	DMXL1_uc010jcl.1_Missense_Mutation_p.N1014D	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1	1014										ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		CACGTCAAAGAATGGAAAAAT	0.398													135	169	---	---	---	---	PASS
TIFAB	497189	broad.mit.edu	37	5	134784962	134784962	+	3'UTR	SNP	C	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134784962C>A	uc003law.3	-	2					C5orf20_uc003lav.2_5'Flank	NM_001099221	NP_001092691	Q6ZNK6	TIFAB_HUMAN	TIFA-related protein TIFAB												0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CATGATGCAGCTCAAGTATTT	0.502													3	13	---	---	---	---	PASS
BRD8	10902	broad.mit.edu	37	5	137502346	137502346	+	Silent	SNP	A	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137502346A>T	uc003lcf.1	-	10	913	c.858T>A	c.(856-858)ACT>ACA	p.T286T	BRD8_uc003lcc.1_Intron|BRD8_uc011cyl.1_Silent_p.T65T|BRD8_uc003lcg.2_Silent_p.T359T|BRD8_uc003lci.2_Intron|BRD8_uc003lch.2_Intron|BRD8_uc011cym.1_Silent_p.T270T|BRD8_uc010jer.1_Intron|BRD8_uc011cyn.1_Silent_p.T245T	NM_139199	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8 isoform 2	286					cell surface receptor linked signaling pathway|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription from RNA polymerase II promoter	mitochondrion|NuA4 histone acetyltransferase complex	sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TGGCAACAGTAGTGAAGGAAG	0.502													29	39	---	---	---	---	PASS
FAT2	2196	broad.mit.edu	37	5	150925180	150925180	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150925180G>C	uc003lue.3	-	9	5521	c.5508C>G	c.(5506-5508)TTC>TTG	p.F1836L	GM2A_uc011dcs.1_Intron	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	1836	Extracellular (Potential).|Cadherin 16.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CACAGAATTGGAAAGAGGGCA	0.448													28	171	---	---	---	---	PASS
STK10	6793	broad.mit.edu	37	5	171481605	171481605	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171481605C>G	uc003mbo.1	-	17	2920	c.2620G>C	c.(2620-2622)GAG>CAG	p.E874Q		NM_005990	NP_005981	O94804	STK10_HUMAN	serine/threonine kinase 10	874	Gln-rich.|Potential.						ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ATGTTGCTCTCACACTGCGCC	0.627													23	200	---	---	---	---	PASS
DTNBP1	84062	broad.mit.edu	37	6	15627643	15627643	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15627643C>A	uc003nbm.2	-	5	457	c.286G>T	c.(286-288)GAG>TAG	p.E96*	DTNBP1_uc003nbl.2_Nonsense_Mutation_p.E15*|DTNBP1_uc003nbn.2_RNA|DTNBP1_uc003nbo.2_RNA|DTNBP1_uc003nbp.2_Nonsense_Mutation_p.E96*|DTNBP1_uc010jph.2_Nonsense_Mutation_p.E83*	NM_032122	NP_115498	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1 isoform a	96	Potential.				actin cytoskeleton reorganization|cellular membrane organization|neuron projection morphogenesis|post-Golgi vesicle-mediated transport|regulation of dopamine receptor signaling pathway	axon part|BLOC-1 complex|cell junction|dendritic spine|endoplasmic reticulum membrane|endosome membrane|growth cone|melanosome membrane|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|synaptic vesicle membrane|synaptosome	identical protein binding				0	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			TCTTGCAGCTCCACGAGGCTT	0.488									Hermansky-Pudlak_syndrome				12	62	---	---	---	---	PASS
CCHCR1	54535	broad.mit.edu	37	6	31124616	31124616	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31124616G>T	uc003nsr.3	-	3	245	c.122C>A	c.(121-123)CCA>CAA	p.P41Q	CCHCR1_uc011dne.1_Missense_Mutation_p.P41Q|CCHCR1_uc003nsq.3_Intron|CCHCR1_uc003nsp.3_Missense_Mutation_p.P130Q|CCHCR1_uc010jsk.1_Missense_Mutation_p.P41Q|TCF19_uc003nss.2_5'Flank|TCF19_uc003nst.2_5'Flank	NM_019052	NP_061925	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1 isoform	41					cell differentiation|multicellular organismal development	cytoplasm|nucleus	protein binding			skin(1)	1						TTGATGGCCTGGGGGTTGGAC	0.597													4	130	---	---	---	---	PASS
ATF6B	1388	broad.mit.edu	37	6	32095464	32095464	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32095464G>C	uc003nzn.2	-	2	188	c.155C>G	c.(154-156)CCG>CGG	p.P52R	ATF6B_uc003nzo.2_Missense_Mutation_p.P49R|ATF6B_uc011dpg.1_5'UTR|ATF6B_uc011dph.1_Missense_Mutation_p.P52R	NM_004381	NP_004372	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta isoform	52	Cytoplasmic (Potential).|Transcription activation.				response to unfolded protein|signal transduction	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						ATCCTGCTCCGGGCAACGGAA	0.572													10	99	---	---	---	---	PASS
TINAG	27283	broad.mit.edu	37	6	54185464	54185464	+	Intron	SNP	A	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54185464A>G	uc003pcj.2	+						TINAG_uc003pci.2_3'UTR|TINAG_uc010jzt.2_Intron	NM_014464	NP_055279	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen						cell adhesion|immune response|Malpighian tubule morphogenesis|proteolysis	basement membrane	cysteine-type endopeptidase activity|nucleotide binding|polysaccharide binding|scavenger receptor activity			ovary(3)|central_nervous_system(1)	4	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			GTGGCACAGAACTGAGTTCTA	0.323													17	98	---	---	---	---	PASS
TAAR1	134864	broad.mit.edu	37	6	132967028	132967028	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132967028C>T	uc003qdm.1	-	1	115	c.115G>A	c.(115-117)GTT>ATT	p.V39I		NM_138327	NP_612200	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	39	Helical; Name=1; (Potential).					plasma membrane					0	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00616)|GBM - Glioblastoma multiforme(226;0.0154)	Amphetamine(DB00182)	AGATTGCCAACGAGTGTGGTC	0.383													20	274	---	---	---	---	PASS
CNKSR3	154043	broad.mit.edu	37	6	154743778	154743778	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154743778C>T	uc003qpy.2	-	9	1312	c.807G>A	c.(805-807)TGG>TGA	p.W269*		NM_173515	NP_775786	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	269	PDZ.				negative regulation of ERK1 and ERK2 cascade|negative regulation of peptidyl-serine phosphorylation|positive regulation of sodium ion transport	cytoplasm|membrane				ovary(2)|breast(1)|skin(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		TTTTCAGCTGCCATCCCACCT	0.463													28	140	---	---	---	---	PASS
MAP3K4	4216	broad.mit.edu	37	6	161513128	161513128	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161513128G>T	uc003qtn.2	+	13	3364	c.3222G>T	c.(3220-3222)ATG>ATT	p.M1074I	MAP3K4_uc010kkc.1_Missense_Mutation_p.M1074I|MAP3K4_uc003qto.2_Missense_Mutation_p.M1074I|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_Missense_Mutation_p.M527I|MAP3K4_uc003qtp.2_Missense_Mutation_p.M64I	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1074					activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		GGAAGTGGATGAATTATGTCC	0.398													52	283	---	---	---	---	PASS
ABCA13	154664	broad.mit.edu	37	7	48556330	48556330	+	Silent	SNP	T	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48556330T>A	uc003toq.2	+	52	13675	c.13650T>A	c.(13648-13650)ACT>ACA	p.T4550T	ABCA13_uc010kys.1_Silent_p.T1625T|ABCA13_uc010kyt.1_RNA|ABCA13_uc010kyu.1_Silent_p.T280T	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	4550	Helical; (Potential).				transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10						GATATGCAACTCTTCCATGGA	0.289													50	332	---	---	---	---	PASS
OR2AE1	81392	broad.mit.edu	37	7	99474267	99474267	+	Silent	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99474267C>T	uc003usc.1	-	1	390	c.390G>A	c.(388-390)CTG>CTA	p.L130L		NM_001005276	NP_001005276	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE,	130	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					CAGCATAGCGCAGTGGATGAC	0.493													7	132	---	---	---	---	PASS
CNOT4	4850	broad.mit.edu	37	7	135080392	135080392	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135080392T>C	uc003vsv.1	-	9	1430	c.1123A>G	c.(1123-1125)ACA>GCA	p.T375A	CNOT4_uc003vss.2_Missense_Mutation_p.T372A|CNOT4_uc011kpz.1_Missense_Mutation_p.T372A|CNOT4_uc003vst.2_Missense_Mutation_p.T375A|CNOT4_uc003vsu.1_Missense_Mutation_p.T372A|CNOT4_uc011kpy.1_Missense_Mutation_p.T375A	NM_001008225	NP_001008226	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	375					nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding				0						ATACCTGATGTGAAGAGGCTC	0.433													71	209	---	---	---	---	PASS
UBE3C	9690	broad.mit.edu	37	7	157049683	157049683	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157049683G>A	uc010lqs.2	+	22	3338	c.3026G>A	c.(3025-3027)CGC>CAC	p.R1009H	UBE3C_uc003wni.3_Missense_Mutation_p.R372H	NM_014671	NP_055486	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	1009	HECT.				protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		GAAGAAAAGCGCAAACTGCTG	0.423													28	184	---	---	---	---	PASS
PTPRN2	5799	broad.mit.edu	37	7	157985057	157985057	+	Missense_Mutation	SNP	C	T	T	rs137877535		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157985057C>T	uc003wno.2	-	5	632	c.511G>A	c.(511-513)GCC>ACC	p.A171T	PTPRN2_uc003wnp.2_Missense_Mutation_p.A154T|PTPRN2_uc003wnq.2_Missense_Mutation_p.A171T|PTPRN2_uc003wnr.2_Missense_Mutation_p.A133T|PTPRN2_uc011kwa.1_Missense_Mutation_p.A194T	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	171	Extracellular (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)		TGGGTCCTGGCGAGCACGTCT	0.697													10	54	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	3216686	3216686	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3216686G>A	uc011kwk.1	-	21	3685	c.3295C>T	c.(3295-3297)CCA>TCA	p.P1099S	CSMD1_uc011kwj.1_Missense_Mutation_p.P491S|CSMD1_uc003wqe.2_Missense_Mutation_p.P255S	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	1099	Sushi 6.|Extracellular (Potential).					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		ACACACCTTGGCAGAGGTGCA	0.592													6	97	---	---	---	---	PASS
PSKH2	85481	broad.mit.edu	37	8	87060713	87060713	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87060713G>T	uc011lfy.1	-	3	1136	c.1136C>A	c.(1135-1137)TCG>TAG	p.S379*		NM_033126	NP_149117	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	379							ATP binding|protein serine/threonine kinase activity			stomach(2)|lung(2)|ovary(1)	5			STAD - Stomach adenocarcinoma(118;0.129)			AGACAGTGGCGATTCTACTAT	0.433													22	138	---	---	---	---	PASS
PABPC1	26986	broad.mit.edu	37	8	101719135	101719135	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101719135A>T	uc003yjs.1	-	10	1931	c.1427T>A	c.(1426-1428)GTC>GAC	p.V476D	PABPC1_uc011lhc.1_Missense_Mutation_p.V444D|PABPC1_uc011lhd.1_Missense_Mutation_p.V431D|PABPC1_uc003yjt.1_Missense_Mutation_p.V473D|PABPC1_uc003yju.2_Intron	NM_002568	NP_002559	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	476					mRNA polyadenylation|mRNA stabilization|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|translation	catalytic step 2 spliceosome|cytosol	nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity				0	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TGTTGACATGACTCGTGGAAC	0.393													15	77	---	---	---	---	PASS
MTSS1	9788	broad.mit.edu	37	8	125565825	125565825	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125565825C>T	uc003yrk.2	-	14	2210	c.1676G>A	c.(1675-1677)CGA>CAA	p.R559Q	NDUFB9_uc011lim.1_Intron|MTSS1_uc003yrh.2_Missense_Mutation_p.R208Q|MTSS1_uc011lin.1_Missense_Mutation_p.R333Q|MTSS1_uc011lio.1_Missense_Mutation_p.R449Q|MTSS1_uc003yri.2_Missense_Mutation_p.R277Q|MTSS1_uc003yrj.2_Missense_Mutation_p.R534Q|MTSS1_uc003yrl.2_Missense_Mutation_p.R563Q	NM_014751	NP_055566	O43312	MTSS1_HUMAN	metastasis suppressor 1	559					actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			GAACATCCGTCGGTAGGACTG	0.557													9	38	---	---	---	---	PASS
MORN5	254956	broad.mit.edu	37	9	124936889	124936889	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124936889G>A	uc004blw.2	+	4	484	c.422G>A	c.(421-423)CGC>CAC	p.R141H	MORN5_uc011lyn.1_Missense_Mutation_p.R141H|MORN5_uc011lyo.1_3'UTR	NM_198469	NP_940871	Q5VZ52	MORN5_HUMAN	MORN repeat containing 5	141											0						TATAGGAACCGCTTTCTAAGA	0.458													12	142	---	---	---	---	PASS
LAMC3	10319	broad.mit.edu	37	9	133911651	133911651	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133911651G>A	uc004caa.1	+	4	1006	c.908G>A	c.(907-909)CGC>CAC	p.R303H		NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	303	Laminin EGF-like 1.				cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GACTGTGAGCGCTGCCTGCCC	0.687													10	51	---	---	---	---	PASS
NEURL	9148	broad.mit.edu	37	10	105330649	105330649	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105330649C>A	uc001kxh.2	+	2	516	c.106C>A	c.(106-108)CCC>ACC	p.P36T		NM_004210	NP_004201	O76050	NEU1A_HUMAN	neuralized-like	36					nervous system development	perinuclear region of cytoplasm	zinc ion binding				0				Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)		GGGCCCCTTCCCCGTCACTTC	0.652													51	242	---	---	---	---	PASS
FAM160B1	57700	broad.mit.edu	37	10	116595310	116595310	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116595310G>T	uc001lcb.2	+	4	644	c.309G>T	c.(307-309)ATG>ATT	p.M103I	FAM160B1_uc001lcc.2_Missense_Mutation_p.M103I	NM_020940	NP_065991	Q5W0V3	F16B1_HUMAN	hypothetical protein LOC57700 isoform a	103										lung(1)	1						CTCCGGGAATGAAACAGCAGG	0.423													5	96	---	---	---	---	PASS
OSBPL5	114879	broad.mit.edu	37	11	3109495	3109495	+	Silent	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3109495G>A	uc001lxk.2	-	22	2738	c.2580C>T	c.(2578-2580)TCC>TCT	p.S860S	OSBPL5_uc010qxq.1_Silent_p.S771S|OSBPL5_uc009ydw.2_Silent_p.S792S|OSBPL5_uc001lxl.2_Silent_p.S792S|OSBPL5_uc001lxj.2_Silent_p.S314S	NM_020896	NP_065947	Q9H0X9	OSBL5_HUMAN	oxysterol-binding protein-like protein 5 isoform	860					cholesterol metabolic process|cholesterol transport|Golgi to plasma membrane transport	cytosol	oxysterol binding|protein binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GCAGGAACCAGGATCGGGGGC	0.642													4	44	---	---	---	---	PASS
PPFIBP2	8495	broad.mit.edu	37	11	7663540	7663540	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7663540C>T	uc001mfj.3	+	17	1917	c.1529C>T	c.(1528-1530)ACT>ATT	p.T510I	PPFIBP2_uc010rbb.1_Missense_Mutation_p.T433I|PPFIBP2_uc001mfk.1_Intron|PPFIBP2_uc010rbc.1_Missense_Mutation_p.T444I|PPFIBP2_uc010rbd.1_Missense_Mutation_p.T352I|PPFIBP2_uc010rbe.1_Missense_Mutation_p.T398I|PPFIBP2_uc001mfl.3_Missense_Mutation_p.T367I|PPFIBP2_uc009yfj.1_Missense_Mutation_p.T154I	NM_003621	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2	510					cell communication|DNA integration	intracellular	DNA binding|integrase activity|protein binding			ovary(2)|breast(2)	4				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		ATCCGAAGAACTCAGTCAGGA	0.542													26	88	---	---	---	---	PASS
CTNND1	1500	broad.mit.edu	37	11	57573944	57573944	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57573944T>C	uc001nmc.3	+	11	2459	c.1888T>C	c.(1888-1890)TCC>CCC	p.S630P	CTNND1_uc001nlh.1_Missense_Mutation_p.S630P|CTNND1_uc001nlu.3_Intron|CTNND1_uc001nlt.3_Intron|CTNND1_uc001nls.3_Intron|CTNND1_uc001nlw.3_Intron|CTNND1_uc001nmf.3_Missense_Mutation_p.S630P|CTNND1_uc001nmd.3_Missense_Mutation_p.S576P|CTNND1_uc001nlk.3_Missense_Mutation_p.S576P|CTNND1_uc001nme.3_Intron|CTNND1_uc001nll.3_Intron|CTNND1_uc001nmg.3_Intron|CTNND1_uc001nlj.3_Intron|CTNND1_uc001nlr.3_Intron|CTNND1_uc001nlp.3_Intron|CTNND1_uc001nlx.3_Missense_Mutation_p.S307P|CTNND1_uc001nlz.3_Missense_Mutation_p.S307P|CTNND1_uc009ymn.2_Intron|CTNND1_uc001nlm.3_Intron|CTNND1_uc001nly.3_Intron|CTNND1_uc001nmb.3_Intron|CTNND1_uc001nma.3_Intron|CTNND1_uc001nmi.3_Missense_Mutation_p.S529P|CTNND1_uc001nmh.3_Intron|CTNND1_uc001nlq.3_Missense_Mutation_p.S529P|CTNND1_uc001nln.3_Intron|CTNND1_uc001nli.3_Intron|CTNND1_uc001nlo.3_Intron|CTNND1_uc001nlv.3_Intron	NM_001085458	NP_001078927	O60716	CTND1_HUMAN	catenin, delta 1 isoform 1ABC	630	Nuclear localization signal (By similarity).				adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)				TGAGTGGTTCTCCAGAGGTGA	0.413													6	18	---	---	---	---	PASS
POLD4	57804	broad.mit.edu	37	11	67119428	67119428	+	3'UTR	SNP	A	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67119428A>G	uc001okm.2	-	4					LOC100130987_uc010rpo.1_Intron|POLD4_uc001okn.2_RNA|POLD4_uc001oko.2_RNA|POLD4_uc001okp.1_3'UTR	NM_021173	NP_066996	Q9HCU8	DPOD4_HUMAN	DNA-directed DNA polymerase delta 4						base-excision repair|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	DNA-directed DNA polymerase activity|protein binding				0			BRCA - Breast invasive adenocarcinoma(15;3.08e-06)			TTGGGTGGTGAGCAAGAGAGC	0.602											OREG0021126	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	13	---	---	---	---	PASS
JRKL	8690	broad.mit.edu	37	11	96124831	96124831	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96124831G>T	uc009ywu.2	+	2	1270	c.1018G>T	c.(1018-1020)GCA>TCA	p.A340S	CCDC82_uc001pfx.3_5'Flank|CCDC82_uc009ywr.2_5'Flank|CCDC82_uc009ywt.1_5'Flank|JRKL_uc001pfy.2_Missense_Mutation_p.A340S	NM_003772	NP_003763	Q9Y4A0	JERKL_HUMAN	jerky homolog-like	340	DDE.				central nervous system development|regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)		BRCA - Breast invasive adenocarcinoma(274;0.148)		AAATTATCGTGCAGGTCTTCT	0.254													10	95	---	---	---	---	PASS
CNTN5	53942	broad.mit.edu	37	11	99942549	99942549	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99942549C>A	uc001pga.2	+	12	1751	c.1412C>A	c.(1411-1413)GCT>GAT	p.A471D	CNTN5_uc009ywv.1_Missense_Mutation_p.A471D|CNTN5_uc001pfz.2_Missense_Mutation_p.A471D|CNTN5_uc001pgb.2_Missense_Mutation_p.A397D	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	471	Ig-like C2-type 4.				cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		TACGCTAGTGCTGAGCTGAAG	0.338													8	25	---	---	---	---	PASS
GALNT8	26290	broad.mit.edu	37	12	4848328	4848328	+	Splice_Site	SNP	G	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4848328G>T	uc001qne.1	+	3	602	c.510_splice	c.e3-1	p.R170_splice		NM_017417	NP_059113	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(1)|skin(1)	4						GTCTCTTATAGATGTCTTCGG	0.358													6	103	---	---	---	---	PASS
KCNA5	3741	broad.mit.edu	37	12	5154474	5154474	+	Silent	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5154474C>T	uc001qni.2	+	1	1390	c.1161C>T	c.(1159-1161)GGC>GGT	p.G387G		NM_002234	NP_002225	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related	387	Poly-Gly.					Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(2)|breast(2)	4						GAGGAGGCGGCCAGAATGGGC	0.627													7	86	---	---	---	---	PASS
KRT18	3875	broad.mit.edu	37	12	53344268	53344268	+	Intron	SNP	T	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53344268T>G	uc001sbe.2	+						KRT18_uc009zmn.1_Intron|KRT18_uc001sbf.1_5'UTR|KRT18_uc001sbg.2_Intron|KRT18_uc009zmo.2_Intron|KRT8_uc009zml.1_5'Flank|KRT8_uc009zmm.1_5'Flank	NM_199187	NP_954657	P05783	K1C18_HUMAN	keratin 18						anatomical structure morphogenesis|cell cycle|Golgi to plasma membrane CFTR protein transport|interspecies interaction between organisms|negative regulation of apoptosis	centriolar satellite|keratin filament|perinuclear region of cytoplasm	protein binding|structural molecule activity			skin(1)	1						GCTGGGTCAGTTAGGGGCTCA	0.502													49	100	---	---	---	---	PASS
PAH	5053	broad.mit.edu	37	12	103240687	103240687	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103240687C>A	uc001tjq.1	-	10	1427	c.955G>T	c.(955-957)GAA>TAA	p.E319*		NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase	319					catecholamine biosynthetic process|L-phenylalanine catabolic process|neurotransmitter biosynthetic process	cytosol	phenylalanine 4-monooxygenase activity			ovary(4)	4					Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Levodopa(DB01235)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GCGAGCTTTTCAATGTATTCA	0.488													46	123	---	---	---	---	PASS
OAS1	4938	broad.mit.edu	37	12	113346530	113346530	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113346530C>A	uc001tud.2	+	2	476	c.370C>A	c.(370-372)CCA>ACA	p.P124T	OAS1_uc010syn.1_Missense_Mutation_p.P123T|OAS1_uc010syo.1_Missense_Mutation_p.P123T|OAS1_uc001tub.2_Missense_Mutation_p.P124T|OAS1_uc001tuc.2_Missense_Mutation_p.P124T|OAS1_uc009zwf.2_Missense_Mutation_p.P123T	NM_016816	NP_058132	P00973	OAS1_HUMAN	2',5'-oligoadenylate synthetase 1 isoform 1	124	Necessary for binding to dsRNA.				interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	endoplasmic reticulum|microsome|mitochondrion|nucleus	ATP binding|nucleotidyltransferase activity|RNA binding			ovary(2)	2						GGTCCAGGCTCCACGCTGGGG	0.577													21	153	---	---	---	---	PASS
MTUS2	23281	broad.mit.edu	37	13	29599346	29599346	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29599346G>T	uc001usl.3	+	1	599	c.541G>T	c.(541-543)GAA>TAA	p.E181*		NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a	171						cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0						TGACAATGAGGAACTGAGGAG	0.532													14	109	---	---	---	---	PASS
CCNA1	8900	broad.mit.edu	37	13	37014312	37014312	+	Silent	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37014312C>T	uc001uvr.3	+	6	1440	c.1090C>T	c.(1090-1092)CTG>TTG	p.L364L	CCNA1_uc010teo.1_Silent_p.L320L|CCNA1_uc010abq.2_Silent_p.L320L|CCNA1_uc010abp.2_Silent_p.L320L|CCNA1_uc001uvs.3_Silent_p.L363L|CCNA1_uc010abr.2_RNA	NM_003914	NP_003905	P78396	CCNA1_HUMAN	cyclin A1 isoform a	364					cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis	cytosol|microtubule cytoskeleton|nucleoplasm	protein kinase binding			lung(2)|skin(2)|ovary(1)	5		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		GACTGAGAACCTGGCTAAGGT	0.458													22	131	---	---	---	---	PASS
STRN3	29966	broad.mit.edu	37	14	31376115	31376115	+	Nonsense_Mutation	SNP	A	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31376115A>T	uc001wqu.2	-	14	2072	c.1856T>A	c.(1855-1857)TTG>TAG	p.L619*	STRN3_uc001wqv.2_Nonsense_Mutation_p.L535*|STRN3_uc010tpj.1_RNA	NM_001083893	NP_001077362	Q13033	STRN3_HUMAN	nuclear autoantigen isoform 1	619	WD 3.				negative regulation of estrogen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus	cytoplasm|dendrite|Golgi apparatus|neuronal cell body|nucleoplasm|nucleus|plasma membrane|protein complex	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		AATACATGGCAATTTTTCTTG	0.323													17	132	---	---	---	---	PASS
FLRT2	23768	broad.mit.edu	37	14	86089519	86089519	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86089519T>C	uc001xvr.2	+	2	2428	c.1661T>C	c.(1660-1662)GTG>GCG	p.V554A	FLRT2_uc010atd.2_Missense_Mutation_p.V554A	NM_013231	NP_037363	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	554	Helical; (Potential).				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)		GTGATATTTGTGCTGGTGGTC	0.587													16	169	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34137144	34137144	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34137144G>A	uc001zhi.2	+	93	13448	c.13378G>A	c.(13378-13380)GCG>ACG	p.A4460T	RYR3_uc010bar.2_Missense_Mutation_p.A4455T	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	4460					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AGAGGAAGAAGCGATGGTATT	0.473													41	75	---	---	---	---	PASS
AQR	9716	broad.mit.edu	37	15	35149171	35149171	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35149171C>T	uc001ziv.2	-	35	4461	c.4280G>A	c.(4279-4281)CGT>CAT	p.R1427H		NM_014691	NP_055506	O60306	AQR_HUMAN	aquarius	1427						catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		AGTTTCTTGACGGCAGCTGGT	0.498													9	113	---	---	---	---	PASS
LOXL1	4016	broad.mit.edu	37	15	74239485	74239485	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74239485A>G	uc002awc.1	+	4	1763	c.1427A>G	c.(1426-1428)CAC>CGC	p.H476R	LOXL1_uc002awd.1_5'Flank	NM_005576	NP_005567	Q08397	LOXL1_HUMAN	lysyl oxidase-like 1 preproprotein	476	Lysyl-oxidase like.				protein deamination	extracellular space	copper ion binding				0						GCCGAGGGCCACAAGGCCAGT	0.587													9	63	---	---	---	---	PASS
CSPG4	1464	broad.mit.edu	37	15	75974707	75974707	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75974707G>A	uc002baw.2	-	8	4970	c.4877C>T	c.(4876-4878)CCC>CTC	p.P1626L		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4 precursor	1626	Extracellular (Potential).|Cysteine-containing.|Neurite growth inhibition (By similarity).|CSPG 11.				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3						GCCTAGCTGGGGGCCCCGCAC	0.672													5	90	---	---	---	---	PASS
CHRNA3	1136	broad.mit.edu	37	15	78889071	78889071	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78889071G>T	uc002bec.2	-	6	1579	c.1393C>A	c.(1393-1395)CAA>AAA	p.Q465K	CHRNA3_uc002bea.2_RNA|CHRNA3_uc002beb.2_Intron|CHRNA3_uc010blg.1_RNA	NM_000743	NP_000734	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3	465	Cytoplasmic (Potential).				activation of transmembrane receptor protein tyrosine kinase activity|behavioral response to nicotine|locomotory behavior|regulation of acetylcholine secretion|regulation of dendrite morphogenesis|regulation of excitatory postsynaptic membrane potential|regulation of smooth muscle contraction|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|dendrite|neuronal cell body|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic density|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			central_nervous_system(3)|ovary(1)	4						CAATCATCTTGAATCTGCAAA	0.378													4	66	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	62996	62996	+	Intron	SNP	A	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62996A>G	uc010utx.1	+						uc010bqm.2_RNA					Homo sapiens mRNA for DEAD/H box polypeptide 11 like 10 (DDX11L10 gene).																		TGTTGGCCTGAATCTGAGCCC	0.567													2	9	---	---	---	---	PASS
A2BP1	54715	broad.mit.edu	37	16	7703894	7703894	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7703894G>A	uc002cys.2	+	12	1823	c.835G>A	c.(835-837)GTG>ATG	p.V279M	A2BP1_uc010buf.1_Missense_Mutation_p.V279M|A2BP1_uc002cyr.1_Missense_Mutation_p.V278M|A2BP1_uc002cyt.2_Missense_Mutation_p.V252M|A2BP1_uc010uxz.1_Missense_Mutation_p.V322M|A2BP1_uc010uya.1_Missense_Mutation_p.V236M|A2BP1_uc002cyv.1_Missense_Mutation_p.V279M|A2BP1_uc010uyb.1_Missense_Mutation_p.V279M|A2BP1_uc002cyw.2_Missense_Mutation_p.V299M|A2BP1_uc002cyy.2_Missense_Mutation_p.V299M|A2BP1_uc002cyx.2_Missense_Mutation_p.V299M|A2BP1_uc010uyc.1_Missense_Mutation_p.V272M	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4	279					mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)		CGGTCGCACCGTGTACAACAC	0.627													4	24	---	---	---	---	PASS
MAP1LC3B	81631	broad.mit.edu	37	16	87436734	87436734	+	3'UTR	SNP	G	T	T	rs115646842	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87436734G>T	uc002fjx.2	+	4					MAP1LC3B_uc010chs.2_RNA	NM_022818	NP_073729	Q9GZQ8	MLP3B_HUMAN	microtubule-associated proteins 1A/1B light						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|endomembrane system|microtubule	protein binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0249)		TTCTAGAATTGTTTAAACCCT	0.413													6	123	---	---	---	---	PASS
ZC3H18	124245	broad.mit.edu	37	16	88697620	88697620	+	Silent	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88697620G>A	uc002fky.2	+	18	2975	c.2775G>A	c.(2773-2775)CTG>CTA	p.L925L	ZC3H18_uc010voz.1_Silent_p.L949L|ZC3H18_uc010chw.2_RNA|ZC3H18_uc002fkz.2_Silent_p.L195L	NM_144604	NP_653205	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	925	Potential.					nucleus	nucleic acid binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CCAGCACGCTGTCTCGGCGGG	0.652													13	37	---	---	---	---	PASS
FLJ36000	284124	broad.mit.edu	37	17	21904083	21904083	+	RNA	SNP	C	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21904083C>A	uc002gza.2	+	1		c.22C>A				NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						ctgacctctccacggggtcca	0.000													4	26	---	---	---	---	PASS
LRRC37A4	55073	broad.mit.edu	37	17	43587708	43587708	+	Intron	SNP	A	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43587708A>G	uc002ije.2	-						uc010wjp.1_RNA					Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						AACAACCACCATCTCCAAATC	0.348													3	91	---	---	---	---	PASS
MYST2	11143	broad.mit.edu	37	17	47895315	47895315	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47895315A>G	uc002ipm.2	+	9	1223	c.1097A>G	c.(1096-1098)TAT>TGT	p.Y366C	MYST2_uc002ipl.1_Missense_Mutation_p.Y336C|MYST2_uc010wma.1_Missense_Mutation_p.Y227C|MYST2_uc010wmb.1_Missense_Mutation_p.Y256C|MYST2_uc010wmc.1_Missense_Mutation_p.Y197C|MYST2_uc010wmd.1_Missense_Mutation_p.Y210C|MYST2_uc010wme.1_Missense_Mutation_p.Y180C|MYST2_uc010wmf.1_Missense_Mutation_p.Y31C|MYST2_uc010wmg.1_Intron	NM_007067	NP_008998	O95251	MYST2_HUMAN	MYST histone acetyltransferase 2	366	C2HC-type.				DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	histone acetyltransferase activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3						GGACGTCTCTATATGTGTGAA	0.438													33	92	---	---	---	---	PASS
TRIM37	4591	broad.mit.edu	37	17	57105859	57105859	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57105859C>T	uc002iwy.3	-	19	2618	c.2174G>A	c.(2173-2175)GGA>GAA	p.G725E	TRIM37_uc002iwz.3_Missense_Mutation_p.G725E|TRIM37_uc002ixa.3_Missense_Mutation_p.G603E|TRIM37_uc010woc.1_Missense_Mutation_p.G691E	NM_001005207	NP_001005207	O94972	TRI37_HUMAN	tripartite motif-containing 37 protein	725						perinuclear region of cytoplasm|peroxisome	ligase activity|protein binding|zinc ion binding			lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1)	7	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					GTTTTCAGTTCCACATGCAGC	0.438									Mulibrey_Nanism				7	155	---	---	---	---	PASS
TBX4	9496	broad.mit.edu	37	17	59560318	59560318	+	Nonsense_Mutation	SNP	C	A	A	rs149749116		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59560318C>A	uc002izi.2	+	8	1124	c.1079C>A	c.(1078-1080)TCG>TAG	p.S360*	TBX4_uc010ddo.2_Nonsense_Mutation_p.S361*|TBX4_uc010woy.1_Nonsense_Mutation_p.S361*	NM_018488	NP_060958	P57082	TBX4_HUMAN	T-box 4	360					leg morphogenesis|skeletal system morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)	2						GCCCCCTCTTCGGTGGGGGAG	0.552													3	57	---	---	---	---	PASS
CD300C	10871	broad.mit.edu	37	17	72537599	72537599	+	3'UTR	SNP	G	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72537599G>T	uc002jky.1	-	4						NM_006678	NP_006669	Q08708	CLM6_HUMAN	CD300C antigen precursor						cellular defense response	integral to plasma membrane	transmembrane receptor activity				0						ACAGGGAAAAGGCTGAAGGAG	0.602													14	53	---	---	---	---	PASS
AFG3L2	10939	broad.mit.edu	37	18	12353008	12353008	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12353008C>T	uc002kqz.1	-	10	1427	c.1314G>A	c.(1312-1314)ATG>ATA	p.M438I		NM_006796	NP_006787	Q9Y4W6	AFG32_HUMAN	AFG3 ATPase family gene 3-like 2	438					cell death|protein catabolic process|proteolysis	integral to membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0					Adenosine triphosphate(DB00171)	ACTCACCATCCATCTCCACCA	0.353													6	148	---	---	---	---	PASS
POTEC	388468	broad.mit.edu	37	18	14513663	14513663	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14513663C>T	uc010dln.2	-	10	1985	c.1531G>A	c.(1531-1533)GAG>AAG	p.E511K	POTEC_uc010xaj.1_RNA	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2	511	Potential.									skin(3)	3						GAAAATACCTCAGAATTCATT	0.269													5	135	---	---	---	---	PASS
PIK3C3	5289	broad.mit.edu	37	18	39567803	39567803	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39567803A>T	uc002lap.2	+	5	617	c.559A>T	c.(559-561)ATG>TTG	p.M187L	PIK3C3_uc010xcl.1_Missense_Mutation_p.M124L	NM_002647	NP_002638	Q8NEB9	PK3C3_HUMAN	catalytic phosphatidylinositol 3-kinase 3	187					cell cycle|cytokinesis|fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	midbody|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|protein binding	p.M187K(1)		lung(8)|ovary(1)|breast(1)	10						ACAAGGACACATGGTGAAAGT	0.308										TSP Lung(28;0.18)			32	97	---	---	---	---	PASS
S1PR4	8698	broad.mit.edu	37	19	3179921	3179921	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3179921C>A	uc002lxg.2	+	1	1156	c.1131C>A	c.(1129-1131)AGC>AGA	p.S377R		NM_003775	NP_003766	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4 precursor	377	Cytoplasmic (By similarity).				activation of phospholipase C activity|elevation of cytosolic calcium ion concentration|immune response	integral to plasma membrane	lipid binding|lysosphingolipid and lysophosphatidic acid receptor activity			lung(1)|skin(1)	2						CCCTGTCCAGCATCTCCAGCG	0.647													12	123	---	---	---	---	PASS
PIP5K1C	23396	broad.mit.edu	37	19	3651895	3651895	+	Silent	SNP	C	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3651895C>A	uc002lyj.1	-	8	1113	c.1056G>T	c.(1054-1056)GCG>GCT	p.A352A	PIP5K1C_uc010xhq.1_Silent_p.A352A|PIP5K1C_uc010xhr.1_Silent_p.A352A	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type	352	PIPK.				axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		TGGAGTAGAGCGCCTTCTGGC	0.706													5	70	---	---	---	---	PASS
PTPRS	5802	broad.mit.edu	37	19	5219380	5219380	+	Silent	SNP	C	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5219380C>G	uc002mbv.2	-	23	4098	c.3864G>C	c.(3862-3864)GGG>GGC	p.G1288G	PTPRS_uc002mbu.1_Silent_p.G857G|PTPRS_uc010xin.1_Silent_p.G857G|PTPRS_uc002mbw.2_Silent_p.G1266G|PTPRS_uc002mbx.2_Silent_p.G861G|PTPRS_uc002mby.2_Silent_p.G857G	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	1288	Helical; (Potential).				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)		CCAGCACAGGCCCGATCACCC	0.502													22	72	---	---	---	---	PASS
FAM125A	93343	broad.mit.edu	37	19	17535839	17535839	+	3'UTR	SNP	A	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17535839A>C	uc002ngo.1	+	9					FAM125A_uc002ngp.1_3'UTR|FAM125A_uc002ngq.1_3'UTR	NM_138401	NP_612410	Q96EY5	F125A_HUMAN	family with sequence similarity 125, member A						protein transport	late endosome membrane|microtubule organizing center|nucleus	SH3 domain binding				0						CCCTTACTCCACCTCCCCGCC	0.657											OREG0025346	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	56	---	---	---	---	PASS
KIAA0892	23383	broad.mit.edu	37	19	19459978	19459978	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19459978G>A	uc002nmk.3	+	15	1412	c.1373G>A	c.(1372-1374)CGA>CAA	p.R458Q	KIAA0892_uc002nml.3_Missense_Mutation_p.R63Q|KIAA0892_uc010ecd.2_Missense_Mutation_p.R63Q|KIAA0892_uc010ece.2_Missense_Mutation_p.R34Q	NM_015329	NP_056144	Q9Y6X3	SCC4_HUMAN	hypothetical protein LOC23383 precursor	458					cell division|maintenance of mitotic sister chromatid cohesion	chromatin|nucleoplasm|SMC loading complex	protein N-terminus binding				0						CACTGCCTCCGAGCAGCCGCC	0.582													19	71	---	---	---	---	PASS
C19orf2	8725	broad.mit.edu	37	19	30477203	30477203	+	Silent	SNP	T	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30477203T>C	uc002nsr.2	+	4	276	c.246T>C	c.(244-246)CCT>CCC	p.P82P	C19orf2_uc002nsq.2_Silent_p.P64P|C19orf2_uc002nss.2_Silent_p.P42P|C19orf2_uc002nst.2_Silent_p.P6P	NM_003796	NP_003787	O94763	RMP_HUMAN	RPB5-mediating protein isoform a	82					protein folding|regulation of transcription from RNA polymerase II promoter|response to virus	DNA-directed RNA polymerase II, core complex|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)|kidney(1)	2	Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)	Hepatocellular(1079;0.137)|Renal(1328;0.228)	STAD - Stomach adenocarcinoma(5;5.36e-06)|Lung(7;0.0144)|LUAD - Lung adenocarcinoma(5;0.115)	STAD - Stomach adenocarcinoma(1328;0.18)		CATTTGGCCCTTTTGCCTTCA	0.363													4	206	---	---	---	---	PASS
SBSN	374897	broad.mit.edu	37	19	36014289	36014289	+	3'UTR	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36014289C>T	uc002oae.1	-	5					SBSN_uc002oad.1_3'UTR	NM_198538	NP_940940	Q6UWP8	SBSN_HUMAN	suprabasin isoform 2 precursor							extracellular region				ovary(1)	1	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			AGTTTATTCACAAATCCCAGT	0.517													11	19	---	---	---	---	PASS
RPL18	6141	broad.mit.edu	37	19	49119434	49119434	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49119434C>T	uc002pjq.1	-	5	356	c.323G>A	c.(322-324)CGG>CAG	p.R108Q	FAM83E_uc002pjn.2_5'Flank|RPL18_uc002pjp.1_Missense_Mutation_p.R56Q|RPL18_uc010xzs.1_3'UTR	NM_000979	NP_000970	Q07020	RL18_HUMAN	ribosomal protein L18	108					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.89e-05)|all cancers(93;0.00011)|GBM - Glioblastoma multiforme(486;0.0061)|Epithelial(262;0.0154)		GCTGCGGGCCCGGCTGGTCAC	0.672													26	53	---	---	---	---	PASS
PREX1	57580	broad.mit.edu	37	20	47258752	47258752	+	Silent	SNP	C	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47258752C>A	uc002xtw.1	-	29	3752	c.3729G>T	c.(3727-3729)CGG>CGT	p.R1243R	PREX1_uc002xtv.1_Silent_p.R540R	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	1243					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CTTCGAAAGCCCGGCTCATGA	0.577													8	57	---	---	---	---	PASS
CTCFL	140690	broad.mit.edu	37	20	56089655	56089655	+	Silent	SNP	G	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56089655G>A	uc010gix.1	-	6	1985	c.1323C>T	c.(1321-1323)AGC>AGT	p.S441S	CTCFL_uc010giw.1_Silent_p.S441S|CTCFL_uc002xym.2_Silent_p.S441S|CTCFL_uc010giz.1_Silent_p.S29S|CTCFL_uc010giy.1_Silent_p.S111S|CTCFL_uc010gja.1_Intron|CTCFL_uc010gjb.1_Silent_p.S441S|CTCFL_uc010gjc.1_Silent_p.S441S|CTCFL_uc010gjd.1_Silent_p.S441S|CTCFL_uc010gje.2_Silent_p.S441S|CTCFL_uc010gjf.2_Silent_p.S236S|CTCFL_uc010gjg.2_Silent_p.S173S|CTCFL_uc010gjh.1_Intron|CTCFL_uc010gji.1_Silent_p.S236S|CTCFL_uc010gjj.1_Silent_p.S441S	NM_080618	NP_542185	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor-like protein	441	C2H2-type 7.				cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|skin(1)	4	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			CACGTAGGTCGCTTTTCCGTG	0.483											OREG0026065	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	97	217	---	---	---	---	PASS
TPTE	7179	broad.mit.edu	37	21	11014952	11014952	+	RNA	SNP	A	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11014952A>T	uc002yis.1	-	7		c.1494T>A						P56180	TPTE_HUMAN	Homo sapiens putative tyrosine phosphatase mRNA, complete cds.						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CACATTGTCTACATTGCAGAA	0.333													5	64	---	---	---	---	PASS
KRTAP12-1	353332	broad.mit.edu	37	21	46101688	46101688	+	3'UTR	SNP	C	T	T	rs2838621	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46101688C>T	uc002zfv.2	-	1					C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_181686	NP_859014	P59990	KR121_HUMAN	keratin associated protein 12-1							keratin filament				skin(2)	2						AGGACTCATCCAGGGAGTGTA	0.527													3	64	---	---	---	---	PASS
PI4KAP1	728233	broad.mit.edu	37	22	20385733	20385733	+	RNA	SNP	A	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20385733A>G	uc010gse.1	-	12		c.1968T>C			PI4KAP1_uc010gsf.1_RNA|PI4KAP1_uc010gsg.1_RNA|PI4KAP1_uc010gsh.1_RNA|PI4KAP1_uc002zsc.3_RNA					Homo sapiens cDNA FLJ11279 fis, clone PLACE1009444, highly similar to PHOSPHATIDYLINOSITOL 4-KINASE ALPHA (EC 2.7.1.67).												0						TACTTCAAGAACTTGATTGTC	0.537													3	37	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	25627838	25627838	+	IGR	SNP	C	G	G			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25627838C>G								CRYBB2 (2 upstream) : IGLL3 (86050 downstream)																							TGCAACTTGTCTGCTGTGGGT	0.388													7	14	---	---	---	---	PASS
SULT4A1	25830	broad.mit.edu	37	22	44237743	44237743	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44237743A>C	uc003bee.1	-	2	355	c.239T>G	c.(238-240)ATG>AGG	p.M80R	SULT4A1_uc003bed.1_Missense_Mutation_p.M1R|SULT4A1_uc003bef.1_RNA|SULT4A1_uc011aqb.1_Intron	NM_014351	NP_055166	Q9BR01	ST4A1_HUMAN	sulfotransferase family 4A, member 1	80					3'-phosphoadenosine 5'-phosphosulfate metabolic process|steroid metabolic process|xenobiotic metabolic process	cytosol	sulfotransferase activity				0		Ovarian(80;0.024)|all_neural(38;0.0416)		Colorectal(1;0.00242)|READ - Rectum adenocarcinoma(1;0.0419)		GTCGATGTTCATCAAGCCGAT	0.637													14	39	---	---	---	---	PASS
ACR	49	broad.mit.edu	37	22	51178394	51178394	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51178394T>C	uc003bnh.3	+	3	566	c.554T>C	c.(553-555)ATA>ACA	p.I185T	uc003bng.2_5'Flank|ACR_uc010hbh.1_Missense_Mutation_p.I185T	NM_001097	NP_001088	P10323	ACRO_HUMAN	acrosin precursor	185	Peptidase S1.				acrosome matrix dispersal|activation of adenylate cyclase activity	acrosomal matrix|protein complex	amidase activity|copper ion binding|DNA binding|drug binding|fucose binding|mannose binding|protein binding|serine-type endopeptidase activity|zinc ion binding				0		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;1.1e-06)|LUAD - Lung adenocarcinoma(64;0.247)		TGGGGATATATAGAAGAGAAA	0.617													21	106	---	---	---	---	PASS
GNL3L	54552	broad.mit.edu	37	X	54585053	54585053	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54585053C>T	uc004dth.1	+	15	1770	c.1631C>T	c.(1630-1632)GCC>GTC	p.A544V	GNL3L_uc004dti.2_RNA	NM_019067	NP_061940	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3	544					ribosome biogenesis	nucleolus	GTP binding			ovary(1)	1						CTGGCATCTGCCCTGAAAAAT	0.542													7	23	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	5454794	5454795	+	IGR	INS	-	AAGG	AAGG			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5454794_5454795insAAGG								AJAP1 (610944 upstream) : NPHP4 (468075 downstream)																							gagaggaagaaaaggaaggaag	0.000													3	3	---	---	---	---	
EYA3	2140	broad.mit.edu	37	1	28316444	28316445	+	Intron	DEL	TA	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28316444_28316445delTA	uc001bpi.1	-						EYA3_uc010ofs.1_Intron|EYA3_uc010oft.1_Intron|EYA3_uc001bpj.2_Intron|EYA3_uc001bpk.1_Intron|EYA3_uc010ofu.1_Intron	NM_001990	NP_001981	Q99504	EYA3_HUMAN	eyes absent 3						anatomical structure morphogenesis|double-strand break repair|histone dephosphorylation|multicellular organismal development|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|transcription, DNA-dependent|visual perception	cytoplasm	metal ion binding|protein binding|protein tyrosine phosphatase activity			ovary(2)|skin(1)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)		TGAGTATGTTtatatatatata	0.272													4	2	---	---	---	---	
FAM63A	55793	broad.mit.edu	37	1	150971006	150971007	+	Intron	INS	-	T	T	rs113138449		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150971006_150971007insT	uc001ewf.2	-						FAM63A_uc001ewc.2_Intron|FAM63A_uc010pcm.1_Intron|FAM63A_uc001ewd.2_Intron|FAM63A_uc001ewe.2_Intron|FAM63A_uc010pcn.1_Intron|FAM63A_uc001ewg.2_Intron	NM_018379	NP_001156731	Q8N5J2	FA63A_HUMAN	hypothetical protein LOC55793 isoform 1								protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			aatgtttggtatttttttagta	0.000													7	4	---	---	---	---	
RHOU	58480	broad.mit.edu	37	1	228873641	228873641	+	Intron	DEL	T	-	-	rs35672194		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228873641delT	uc001htf.2	+							NM_021205	NP_067028	Q7L0Q8	RHOU_HUMAN	ras homolog gene family, member U						regulation of small GTPase mediated signal transduction	cell projection|cytosol|focal adhesion|Golgi membrane|podosome	GTP binding|metal ion binding|protein binding				0	Breast(184;0.162)	Prostate(94;0.183)				AGGGGCCAGGTTATTGGCCGG	0.542													5	5	---	---	---	---	
THADA	63892	broad.mit.edu	37	2	43808704	43808704	+	Intron	DEL	A	-	-	rs74506936		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43808704delA	uc002rsw.3	-						THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc002rsz.2_Intron|THADA_uc002rta.2_Intron|THADA_uc002rtb.1_Intron|THADA_uc002rtc.3_Intron|THADA_uc002rtd.2_Intron	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				aaaagaaaagaaaaaaaaaaa	0.194													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	113480938	113480939	+	Intron	INS	-	CACACA	CACACA			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113480938_113480939insCACACA	uc002tid.2	+											RecName: Full=5'-nucleotidase domain-containing protein 4;																		GGGTacacatgcacacacacac	0.436													4	2	---	---	---	---	
RBMS1	5937	broad.mit.edu	37	2	161282846	161282847	+	Intron	INS	-	AAGG	AAGG	rs138498508	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161282846_161282847insAAGG	uc002ubo.2	-						RBMS1_uc002ubn.2_Intron|RBMS1_uc002ubi.3_Intron|RBMS1_uc002ubm.2_Intron|RBMS1_uc002ubp.2_Intron|RBMS1_uc010fox.2_Intron	NM_016836	NP_058520	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting						DNA replication|RNA processing	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding|single-stranded DNA binding				0						ggaaggaaggaaaggaaggaag	0.099													4	2	---	---	---	---	
ITPR1	3708	broad.mit.edu	37	3	4715262	4715273	+	Intron	DEL	TTTGTTTGTTTG	-	-	rs112871347		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4715262_4715273delTTTGTTTGTTTG	uc003bqa.2	+						ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc010hcb.1_Intron	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN	inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)		GTTTTTGGTTtttgtttgtttgtttgtttgtt	0.137													3	4	---	---	---	---	
DCLK3	85443	broad.mit.edu	37	3	36762771	36762772	+	Intron	INS	-	AC	AC	rs139147686	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36762771_36762772insAC	uc003cgi.2	-							NM_033403	NP_208382	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3							cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			lung(3)|large_intestine(2)|breast(1)|skin(1)|ovary(1)|kidney(1)	9						AAACACAATAAacacacacaca	0.381													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	182178993	182178993	+	IGR	DEL	A	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182178993delA								SOX2OT (719990 upstream) : ATP11B (332298 downstream)																							attactctacacttttttttt	0.000													4	2	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195494399	195494401	+	Intron	DEL	TCG	-	-	rs71743942	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195494399_195494401delTCG	uc011bto.1	-						MUC4_uc003fuz.2_Intron|MUC4_uc003fva.2_Intron|MUC4_uc003fvb.2_Intron|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Intron|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a						cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		accaccaccatcgccaccaccat	0.000													4	2	---	---	---	---	
IQCG	84223	broad.mit.edu	37	3	197665189	197665189	+	Intron	DEL	A	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197665189delA	uc003fyo.2	-						IQCG_uc003fyn.2_Intron|IQCG_uc003fyp.2_Intron|IQCG_uc003fyq.3_Intron	NM_001134435	NP_001127907	Q9H095	IQCG_HUMAN	IQ motif containing G												0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)		actccatctcaaaaaaaaaaa	0.159													3	3	---	---	---	---	
STK32B	55351	broad.mit.edu	37	4	5102357	5102358	+	Intron	INS	-	TC	TC	rs142745949	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5102357_5102358insTC	uc003gih.1	+						STK32B_uc010ida.1_Intron	NM_018401	NP_060871	Q9NY57	ST32B_HUMAN	serine/threonine kinase 32B								ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						ttttctttctttctctttcttt	0.000													1	6	---	---	---	---	
ANK2	287	broad.mit.edu	37	4	114135113	114135114	+	Intron	INS	-	A	A	rs36076544		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114135113_114135114insA	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc003ibc.2_Intron|ANK2_uc011cgb.1_Intron	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1						axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ttttatttatttttttttttta	0.173													4	2	---	---	---	---	
WWC2	80014	broad.mit.edu	37	4	184091939	184091941	+	Intron	DEL	CTC	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184091939_184091941delCTC	uc010irx.2	+							NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2											ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		taaccttgaactcctcaagtgat	0.010													0	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	105353468	105353471	+	IGR	DEL	TCCT	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105353468_105353471delTCCT								RAB9BP1 (917670 upstream) : None (None downstream)																							cctccccttctccttccttccttc	0.093													4	3	---	---	---	---	
RAPGEF6	51735	broad.mit.edu	37	5	130983109	130983110	+	Intron	INS	-	TT	TT	rs114314479		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130983109_130983110insTT	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.1_Intron	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TCTACAGCGTCTTTTTTttttt	0.158													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	141270157	141270168	+	IGR	DEL	CTTCCTTCCTTC	-	-	rs71830412		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141270157_141270168delCTTCCTTCCTTC								PCDH1 (12213 upstream) : KIAA0141 (33217 downstream)																							ggtaaattttcttccttccttccttccttcct	0.000													3	3	---	---	---	---	
ODZ2	57451	broad.mit.edu	37	5	167182463	167182464	+	Intron	INS	-	A	A	rs138021443	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167182463_167182464insA	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)		TATTTCACCAGaaaaaaaaaat	0.277													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	26205347	26205347	+	IGR	DEL	T	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26205347delT								HIST1H4E (99 upstream) : HIST1H2BG (11081 downstream)																							TTTTCAGCCGTTTTTTTTTTT	0.373													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	30345852	30345852	+	IGR	DEL	A	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30345852delA								TRIM39 (31220 upstream) : HLA-E (111419 downstream)																							ggaaggaaggaaggaaggaag	0.060													4	2	---	---	---	---	
LOC100132354	100132354	broad.mit.edu	37	6	43872656	43872659	+	Intron	DEL	TTCC	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43872656_43872659delTTCC	uc011dvm.1	+							NR_024478				Homo sapiens cDNA FLJ38229 fis, clone FCBBF2004256.												0						Attccttcctttccttccttcctt	0.240													6	3	---	---	---	---	
PRIM2	5558	broad.mit.edu	37	6	57191021	57191022	+	Intron	INS	-	G	G	rs148099435	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57191021_57191022insG	uc003pdx.2	+						PRIM2_uc003pdv.1_3'UTR|PRIM2_uc003pdw.2_Intron	NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		CTAGAAGAAAAGGACTCCTTAA	0.342													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	75560075	75560075	+	IGR	DEL	T	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75560075delT								None (None upstream) : COL12A1 (233968 downstream)																							TACGTGTTGCTTTTTTTTTTT	0.373													5	3	---	---	---	---	
MDN1	23195	broad.mit.edu	37	6	90489787	90489788	+	Intron	INS	-	A	A			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90489787_90489788insA	uc003pnn.1	-						MDN1_uc003pno.1_Intron	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		gacttcgtctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
TUBE1	51175	broad.mit.edu	37	6	112400624	112400625	+	Intron	INS	-	A	A	rs111683493		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112400624_112400625insA	uc003pvq.2	-						TUBE1_uc003pvr.2_Intron	NM_016262	NP_057346	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1						centrosome cycle|microtubule-based movement|protein polymerization	microtubule|pericentriolar material	GTP binding|GTPase activity|structural constituent of cytoskeleton			ovary(1)	1		all_cancers(87;0.0101)|all_hematologic(75;0.000258)|Colorectal(196;0.0466)|all_epithelial(87;0.1)		all cancers(137;0.0217)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0636)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		GGGCTTACATTAaaaaaaaaaa	0.262													4	3	---	---	---	---	
MOXD1	26002	broad.mit.edu	37	6	132705439	132705442	+	Intron	DEL	CCTC	-	-	rs78267317		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132705439_132705442delCCTC	uc003qdf.2	-							NM_015529	NP_056344	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1 isoform 2						catecholamine metabolic process	endoplasmic reticulum membrane|integral to membrane	copper ion binding|dopamine beta-monooxygenase activity			ovary(1)	1	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		ctccttccttcctccctccctccc	0.064													3	5	---	---	---	---	
SHPRH	257218	broad.mit.edu	37	6	146242677	146242677	+	Intron	DEL	T	-	-	rs146207931		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146242677delT	uc003qlf.2	-						SHPRH_uc003qld.2_Intron|SHPRH_uc003qle.2_Intron|SHPRH_uc003qlg.1_Intron|SHPRH_uc003qlh.2_Intron|SHPRH_uc003qli.1_Intron	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a						DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		ATTTGGCCAGTTTTTTTTTTT	0.303													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	157691443	157691445	+	IGR	DEL	CCT	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157691443_157691445delCCT								ARID1B (161042 upstream) : C6orf35 (18610 downstream)																							caccaccatccctaccaccacca	0.005													3	3	---	---	---	---	
GET4	51608	broad.mit.edu	37	7	932269	932292	+	Intron	DEL	TGGGTGTATGTGCAAGTGTAGACA	-	-	rs66553046	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:932269_932292delTGGGTGTATGTGCAAGTGTAGACA	uc003sjl.1	+						GET4_uc003sjj.1_Intron	NM_015949	NP_057033	Q7L5D6	GET4_HUMAN	hypothetical protein LOC51608						tail-anchored membrane protein insertion into ER membrane|transport	BAT3 complex	protein binding				0						ggtagctgtgtgggtgtatgtgCAAGTGTAGACATGGCGTGGGG	0.272													4	2	---	---	---	---	
STK31	56164	broad.mit.edu	37	7	23923265	23923268	+	Intron	DEL	TCCT	-	-	rs36198206		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23923265_23923268delTCCT	uc003swv.1	+									Q9BXU1	STK31_HUMAN	SubName: Full=Putative uncharacterized protein STK31;								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						ATTAGCTCGCtccttccttccttc	0.181													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	102016084	102016085	+	Intron	DEL	TA	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102016084_102016085delTA	uc003uzd.1	+						uc003uze.1_Intron|PRKRIP1_uc003uzf.2_Intron|PRKRIP1_uc003uzg.2_Intron|PRKRIP1_uc011kkq.1_5'Flank	NM_001003686	NP_001003686			SubName: Full=Putative uncharacterized protein PMS2L3;																		atatatattttatatatatata	0.178													5	4	---	---	---	---	
TBXAS1	6916	broad.mit.edu	37	7	139604857	139604858	+	Intron	DEL	TC	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139604857_139604858delTC	uc011kqv.1	+						TBXAS1_uc003vvh.2_Intron|TBXAS1_uc010lne.2_Intron|TBXAS1_uc011kqu.1_Intron|TBXAS1_uc003vvi.2_Intron|TBXAS1_uc003vvj.2_Intron|TBXAS1_uc011kqw.1_Intron|TBXAS1_uc011kqx.1_Intron	NM_001130966	NP_001124438	P24557	THAS_HUMAN	thromboxane A synthase 1, platelet isoform						hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)					tttctttctttctctctctctc	0.000													6	4	---	---	---	---	
C9orf5	23731	broad.mit.edu	37	9	111882356	111882356	+	5'Flank	DEL	A	-	-	rs113896695		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111882356delA	uc004bdt.3	-						C9orf5_uc004bdr.3_5'Flank	NM_032012	NP_114401	Q9H330	CI005_HUMAN	hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)		CCCGAAGGGGAAATGGGGAAA	0.607													6	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	138016485	138016486	+	IGR	INS	-	AAGA	AAGA	rs147997959	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138016485_138016486insAAGA								OLFM1 (3454 upstream) : KIAA0649 (355162 downstream)																							agaaaagaaagaagaaagaaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42388292	42388292	+	IGR	DEL	G	-	-	rs72505277		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42388292delG								None (None upstream) : LOC441666 (439023 downstream)																							aacatcgaatggaatcgaatg	0.000													1	8	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	57298572	57298572	+	Intron	DEL	C	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57298572delC	uc001jjv.1	-							NM_001142770	NP_001136242	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD2-2 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				ttccttccttcctttccttcc	0.000										HNSCC(58;0.16)			3	3	---	---	---	---	
NFKB2	4791	broad.mit.edu	37	10	104158972	104158973	+	Intron	INS	-	A	A	rs76894719		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104158972_104158973insA	uc001kvb.2	+						NFKB2_uc001kva.2_Intron|NFKB2_uc001kvd.2_Intron|NFKB2_uc009xxc.2_Intron	NM_001077494	NP_001070962	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	Bcl3/NF-kappaB2 complex|cytosol|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			lung(3)	3		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)		aactccgtctcaaaaaaaaaaa	0.262			T	IGH@	B-NHL								4	2	---	---	---	---	
GPR123	84435	broad.mit.edu	37	10	134906251	134906252	+	Intron	INS	-	AGGA	AGGA			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134906251_134906252insAGGA	uc001llx.3	+						GPR123_uc001llw.2_Intron	NM_001083909	NP_001077378	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123							integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		GAGAAATagggagggaggaagg	0.203													4	3	---	---	---	---	
ABCC8	6833	broad.mit.edu	37	11	17452093	17452093	+	Intron	DEL	G	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17452093delG	uc001mnc.2	-							NM_000352	NP_000343	Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C, member 8						carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)	gctcaacaCTGGTTTTTTTTT	0.239													7	7	---	---	---	---	
KCTD14	65987	broad.mit.edu	37	11	77728498	77728498	+	Intron	DEL	T	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77728498delT	uc001oyw.3	-							NM_023930	NP_076419	Q9BQ13	KCD14_HUMAN	potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1e-24)			gggggtgggcttttttttttt	0.000													4	2	---	---	---	---	
SFRS2IP	9169	broad.mit.edu	37	12	46339320	46339321	+	Intron	DEL	TT	-	-	rs138186962		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46339320_46339321delTT	uc001rox.2	-						SFRS2IP_uc001roy.1_Intron	NM_004719	NP_004710	Q99590	SCAFB_HUMAN	splicing factor, arginine/serine-rich 2,						spliceosome assembly	nucleus	protein binding|zinc ion binding				0	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.209)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.1)		TATCTCAGTCtttttttttttt	0.153													4	2	---	---	---	---	
TSPAN8	7103	broad.mit.edu	37	12	71631431	71631432	+	Intron	DEL	AC	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71631431_71631432delAC	uc001swk.1	-							NM_004616	NP_004607	P19075	TSN8_HUMAN	transmembrane 4 superfamily member 3						protein glycosylation	integral to membrane|lysosome	signal transducer activity			skin(2)|lung(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)			GTCCAGGTAAacacacacacac	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	127326820	127326823	+	IGR	DEL	GAAA	-	-	rs72236683		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127326820_127326823delGAAA								LOC100128554 (369490 upstream) : None (None downstream)																							aggaaggaaggAAAGAAGAAAAAA	0.181													3	3	---	---	---	---	
NBEA	26960	broad.mit.edu	37	13	36003937	36003938	+	Intron	INS	-	GT	GT	rs60362511		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36003937_36003938insGT	uc001uvb.2	+						NBEA_uc010abi.2_Intron	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		gagtccccaaCgtgtgtgtgtg	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	54592074	54592094	+	IGR	DEL	AAAGGAAGGAAGGAAGGCAAG	-	-	rs140720075		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54592074_54592094delAAAGGAAGGAAGGAAGGCAAG								OLFM4 (965888 upstream) : MIR1297 (294013 downstream)																							gaaggaaagaaaaggaaggaaggaaggcaagaaaggaagag	0.000													6	3	---	---	---	---	
MYO16	23026	broad.mit.edu	37	13	109859336	109859337	+	3'UTR	DEL	GT	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109859336_109859337delGT	uc001vqt.1	+	35					MYO16_uc010agk.1_3'UTR	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			ATGAGATCCCgtgtgtgtgtgt	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	44690412	44690419	+	IGR	DEL	GAAGGAAG	-	-	rs72383008		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44690412_44690419delGAAGGAAG								None (None upstream) : FSCB (282936 downstream)																							GTAGAAAGAAgaaggaaggaaggaagga	0.014													3	3	---	---	---	---	
GOLGA8G	283768	broad.mit.edu	37	15	28771709	28771709	+	Intron	DEL	G	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28771709delG	uc001zbu.2	-						GOLGA8G_uc001zbt.3_Intron|GOLGA8G_uc001zbv.2_Intron|GOLGA8F_uc010uah.1_Intron|uc002cdz.2_5'Flank	NM_001012420	NP_001012420			golgi autoantigen, golgin subfamily a, 8G												0		all_lung(180;1.98e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;4.69e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0201)|GBM - Glioblastoma multiforme(186;0.0503)|Lung(196;0.171)		aaaaaaaaaagaaaagaaaag	0.483													18	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84946555	84946556	+	RNA	INS	-	TT	TT	rs71453238		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84946555_84946556insTT	uc002bke.1	-	1		c.662_663insAA								Homo sapiens cDNA FLJ34196 fis, clone FCBBF3019437.																		CGAAGGGAGGAttttttttttt	0.515													4	2	---	---	---	---	
AP3S2	10239	broad.mit.edu	37	15	90402631	90402632	+	Intron	INS	-	TTTT	TTTT	rs144636370	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90402631_90402632insTTTT	uc002boq.3	-						AP3S2_uc002bos.3_Intron|AP3S2_uc010bns.2_Intron|AP3S2_uc002bor.3_Intron|AP3S2_uc010bnt.2_Intron	NM_005829	NP_005820	P59780	AP3S2_HUMAN	adaptor-related protein complex 3, sigma 2						intracellular protein transport|vesicle-mediated transport	cytoplasmic vesicle membrane|Golgi apparatus|membrane coat	protein transporter activity				0	Lung NSC(78;0.0181)|all_lung(78;0.0384)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.223)			ttctttctttcttttttttttt	0.000													4	2	---	---	---	---	
VWA3A	146177	broad.mit.edu	37	16	22149613	22149614	+	Intron	DEL	TG	-	-	rs66986818		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22149613_22149614delTG	uc010vbq.1	+						VWA3A_uc010bxd.2_Intron|VWA3A_uc010bxc.2_Intron	NM_173615	NP_775886	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A							extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)		TCCCTCCTGCtgtgtgtgtgtg	0.505													4	2	---	---	---	---	
GNAO1	2775	broad.mit.edu	37	16	56374466	56374475	+	Intron	DEL	CTGCCCCCAC	-	-	rs75150348		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56374466_56374475delCTGCCCCCAC	uc002eit.3	+						GNAO1_uc002eiu.3_Intron	NM_138736	NP_620073	P09471	GNAO_HUMAN	guanine nucleotide binding protein, alpha						dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|muscle contraction	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			lung(1)|breast(1)	2		all_neural(199;0.159)				AGTGACCTCACTGCCCCCACCTGGGGCCAG	0.538													5	5	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2888572	2888573	+	Intron	DEL	TG	-	-	rs146159488		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2888572_2888573delTG	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						TAAACAGTGATGTTTTTTTTTT	0.391													3	5	---	---	---	---	
SNF8	11267	broad.mit.edu	37	17	47013382	47013383	+	Intron	INS	-	TTTGT	TTTGT	rs140139274	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47013382_47013383insTTTGT	uc002ioj.2	-						SNF8_uc002iok.2_Intron	NM_007241	NP_009172	Q96H20	SNF8_HUMAN	EAP30 subunit of ELL complex						cellular membrane organization|endosome transport|protein transport|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytosol|late endosome membrane|transcription factor complex	transcription factor binding				0						cTTATTTTTTGTTTGTTTTTTG	0.168													6	5	---	---	---	---	
MALT1	10892	broad.mit.edu	37	18	56363569	56363570	+	Intron	INS	-	T	T			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56363569_56363570insT	uc002lhm.1	+						MALT1_uc002lhn.1_Intron	NM_006785	NP_006776	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma						activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway	CBM complex|cytosol|nucleus|perinuclear region of cytoplasm	cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity			ovary(2)|lung(1)|central_nervous_system(1)	4						TGTGACTTTAAttttttttttt	0.307			T	BIRC3	MALT								15	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	57522454	57522459	+	IGR	DEL	CTTTCT	-	-	rs149419421	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57522454_57522459delCTTTCT								CCBE1 (157810 upstream) : PMAIP1 (44733 downstream)																							tccttccttcctttctctttctttct	0.141													4	3	---	---	---	---	
LGI4	163175	broad.mit.edu	37	19	35632205	35632206	+	Intron	INS	-	A	A	rs11455343		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35632205_35632206insA	uc002nxy.1	-						FXYD1_uc002nyc.2_Intron|FXYD1_uc002nyd.2_Intron|FXYD7_uc010xsp.1_5'Flank|FXYD7_uc002nye.1_5'Flank|FXYD7_uc002nyf.1_5'Flank	NM_139284	NP_644813	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4							extracellular region				pancreas(1)	1	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			tccctagcccccctctccctgg	0.059													4	3	---	---	---	---	
C19orf48	84798	broad.mit.edu	37	19	51302473	51302474	+	Intron	INS	-	AAG	AAG	rs139236217	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51302473_51302474insAAG	uc002ptf.2	-						C19orf48_uc002pte.2_Intron|C19orf48_uc002ptg.2_Intron|SNORD88B_uc010eoc.1_5'Flank	NM_199249	NP_954857	Q6RUI8	CS048_HUMAN	multidrug resistance-related protein											ovary(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00531)|GBM - Glioblastoma multiforme(134;0.0145)		ACAGGGTTACTAAGGTTAATGA	0.604													4	3	---	---	---	---	
C20orf194	25943	broad.mit.edu	37	20	3278997	3278997	+	Intron	DEL	T	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3278997delT	uc002wii.2	-						C20orf194_uc002wij.3_Intron|C20orf194_uc002wik.2_Intron	NM_001009984	NP_001009984	Q5TEA3	CT194_HUMAN	hypothetical protein LOC25943												0						AATAAAAGGAttttttttttg	0.164													4	2	---	---	---	---	
TOX2	84969	broad.mit.edu	37	20	42556283	42556287	+	Intron	DEL	CCCTT	-	-			TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42556283_42556287delCCCTT	uc010ggo.2	+						TOX2_uc002xle.3_Intron|TOX2_uc010ggp.2_Intron	NM_001098797	NP_001092267	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			ttccttcctccccttcccttccctt	0.054													6	3	---	---	---	---	
SLC13A3	64849	broad.mit.edu	37	20	45228952	45228953	+	Intron	INS	-	GGAAGGAA	GGAAGGAA	rs144741251	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45228952_45228953insGGAAGGAA	uc002xsf.1	-						SLC13A3_uc010ghn.1_Intron|SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010zxx.1_Intron	NM_022829	NP_073740	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	gaaagaaagagggaaggaagga	0.000													4	3	---	---	---	---	
IL10RB	3588	broad.mit.edu	37	21	34660753	34660754	+	Intron	INS	-	AGGGAAGTCTG	AGGGAAGTCTG	rs138463621	by1000genomes	TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34660753_34660754insAGGGAAGTCTG	uc002yrk.1	+						IL10RB_uc002yrl.1_Intron	NM_000628	NP_000619	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta precursor						immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0						GTAACCATGTCAGGTGAAGGAA	0.436													4	2	---	---	---	---	
CELSR1	9620	broad.mit.edu	37	22	46877682	46877682	+	Intron	DEL	T	-	-	rs112110956		TCGA-CJ-4907-01A-01D-1429-08	TCGA-CJ-4907-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46877682delT	uc003bhw.1	-							NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1						central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		TTTCTAAAtcttttttttttt	0.274													4	2	---	---	---	---	
