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
H6PD	9563	broad.mit.edu	37	1	9323628	9323628	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9323628G>A	uc001apt.2	+	5	1349	c.1076G>A	c.(1075-1077)GGC>GAC	p.G359D		NM_004285	NP_004276	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase precursor	359	Glucose 1-dehydrogenase.					endoplasmic reticulum lumen	6-phosphogluconolactonase activity|glucose 1-dehydrogenase|glucose-6-phosphate dehydrogenase activity|NADP binding				0	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)	NADH(DB00157)	CTGATGTCTGGCAAAGCCTTG	0.602													4	132	---	---	---	---	PASS
NBPF3	84224	broad.mit.edu	37	1	21795329	21795329	+	Silent	SNP	C	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21795329C>G	uc001ber.2	+	3	632	c.282C>G	c.(280-282)CTC>CTG	p.L94L	NBPF3_uc001bes.2_Silent_p.L38L|NBPF3_uc009vqb.2_Silent_p.L94L|NBPF3_uc010odm.1_Intron	NM_032264	NP_115640	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	94						cytoplasm				upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TCAGAAACCTCAAACAGAAAT	0.473											OREG0013205	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	44	100	---	---	---	---	PASS
HSPG2	3339	broad.mit.edu	37	1	22214000	22214000	+	Missense_Mutation	SNP	C	T	T	rs148693072	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22214000C>T	uc001bfj.2	-	8	911	c.871G>A	c.(871-873)GCA>ACA	p.A291T	HSPG2_uc009vqd.2_Missense_Mutation_p.A291T|HSPG2_uc009vqe.1_Silent_p.P189P	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	291	LDL-receptor class A 2.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)	TTGCGGCATGCGGCCTCCTGG	0.667													4	85	---	---	---	---	PASS
ZBTB40	9923	broad.mit.edu	37	1	22816881	22816881	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22816881A>C	uc001bft.2	+	3	951	c.440A>C	c.(439-441)GAA>GCA	p.E147A	ZBTB40_uc001bfu.2_Missense_Mutation_p.E147A|ZBTB40_uc009vqi.1_Missense_Mutation_p.E147A	NM_001083621	NP_001077090	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	147					bone mineralization|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		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;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		CCTCAAGTAGAAATCCTTTCA	0.537													54	229	---	---	---	---	PASS
EYA3	2140	broad.mit.edu	37	1	28339697	28339697	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28339697A>C	uc001bpi.1	-	9	859	c.694T>G	c.(694-696)TTA>GTA	p.L232V	EYA3_uc010ofs.1_Missense_Mutation_p.L179V|EYA3_uc010oft.1_Missense_Mutation_p.L186V|EYA3_uc001bpj.2_Missense_Mutation_p.L186V|EYA3_uc001bpk.1_RNA|EYA3_uc010ofu.1_RNA	NM_001990	NP_001981	Q99504	EYA3_HUMAN	eyes absent 3	232					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)		GTTGCTGCTAATGTGGTGCTC	0.522													5	231	---	---	---	---	PASS
RRAGC	64121	broad.mit.edu	37	1	39318113	39318113	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39318113C>A	uc001ccq.2	-	4	711	c.689G>T	c.(688-690)AGT>ATT	p.S230I	RRAGC_uc010oim.1_Missense_Mutation_p.S196I|RRAGC_uc001ccr.2_Missense_Mutation_p.S152I	NM_022157	NP_071440	Q9HB90	RRAGC_HUMAN	Ras-related GTP binding C	230					apoptosis|cell growth|cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade|RNA splicing|small GTPase mediated signal transduction|transcription, DNA-dependent	lysosome|nucleus	GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein heterodimerization activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)				CACCACCTTACTAAAGGCTTC	0.318													13	285	---	---	---	---	PASS
CCDC76	54482	broad.mit.edu	37	1	100606486	100606486	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100606486G>A	uc001dsv.2	+	7	599	c.580G>A	c.(580-582)GGA>AGA	p.G194R	CCDC76_uc010ouf.1_RNA|CCDC76_uc009wea.2_Missense_Mutation_p.G194R	NM_019083	NP_061956	Q9NUP7	TRM13_HUMAN	coiled-coil domain containing 76	194					tRNA processing		metal ion binding|methyltransferase activity			ovary(1)	1		all_epithelial(167;0.000542)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.0814)|all cancers(265;0.133)|COAD - Colon adenocarcinoma(174;0.146)|Lung(183;0.194)		AGCGGGAAAGGGAAAATTATC	0.358													18	90	---	---	---	---	PASS
PI4KB	5298	broad.mit.edu	37	1	151278725	151278725	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151278725G>A	uc001ext.2	-	5	1712	c.1297C>T	c.(1297-1299)CCC>TCC	p.P433S	PI4KB_uc001exr.2_Missense_Mutation_p.P445S|PI4KB_uc001exs.2_Missense_Mutation_p.P418S|PI4KB_uc001exu.2_Missense_Mutation_p.P418S|PI4KB_uc010pcw.1_Missense_Mutation_p.P101S	NM_002651	NP_002642	Q9UBF8	PI4KB_HUMAN	catalytic phosphatidylinositol 4-kinase beta	433					phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|receptor-mediated endocytosis	endosome|Golgi apparatus|mitochondrial outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum membrane	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			ovary(2)|skin(2)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CCACATTCGGGCAAGTTTTCT	0.527													4	131	---	---	---	---	PASS
APCS	325	broad.mit.edu	37	1	159558512	159558512	+	3'UTR	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159558512C>T	uc001ftv.2	+	2						NM_001639	NP_001630	P02743	SAMP_HUMAN	serum amyloid P component precursor						acute-phase response|chaperone-mediated protein complex assembly|protein folding	extracellular space	metal ion binding|sugar binding|unfolded protein binding			ovary(1)|breast(1)	2	all_hematologic(112;0.0429)					CTTGACTCAACGAGAGCACTT	0.438													8	71	---	---	---	---	PASS
F5	2153	broad.mit.edu	37	1	169510307	169510307	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169510307G>C	uc001ggg.1	-	13	4166	c.4021C>G	c.(4021-4023)CCA>GCA	p.P1341A		NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	1341	2-18.|35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.				cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)	CTGAGTTCTGGAGAGAGGTTT	0.527													68	248	---	---	---	---	PASS
LHX9	56956	broad.mit.edu	37	1	197898314	197898314	+	Silent	SNP	G	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197898314G>T	uc001guk.1	+	5	1556	c.1119G>T	c.(1117-1119)GTG>GTT	p.V373V	LHX9_uc001gui.1_Silent_p.V364V|LHX9_uc001guj.1_Intron	NM_020204	NP_064589	Q9NQ69	LHX9_HUMAN	LIM homeobox 9 isoform 1	373					motor axon guidance|negative regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1						TCACTGTAGTGACATCCGTGA	0.502													4	127	---	---	---	---	PASS
TIMM17A	10440	broad.mit.edu	37	1	201924654	201924654	+	5'UTR	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201924654G>A	uc001gxc.2	+	1						NM_006335	NP_006326	Q99595	TI17A_HUMAN	translocase of inner mitochondrial membrane 17						protein targeting to mitochondrion	integral to membrane|mitochondrial inner membrane presequence translocase complex	P-P-bond-hydrolysis-driven protein transmembrane transporter activity				0						TTGGAGTCAAGATGGAGGAGT	0.612													5	83	---	---	---	---	PASS
TARBP1	6894	broad.mit.edu	37	1	234565044	234565044	+	Silent	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234565044G>A	uc001hwd.2	-	17	2898	c.2898C>T	c.(2896-2898)TGC>TGT	p.C966C		NM_005646	NP_005637	Q13395	TARB1_HUMAN	TAR RNA binding protein 1	966					regulation of transcription from RNA polymerase II promoter|RNA processing	nucleus	RNA binding|RNA methyltransferase activity			ovary(2)|skin(1)	3	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			AAGACTCTATGCAGAGTGATT	0.338													7	106	---	---	---	---	PASS
C2orf71	388939	broad.mit.edu	37	2	29294985	29294985	+	Missense_Mutation	SNP	C	T	T	rs138261370	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29294985C>T	uc002rmt.1	-	1	2143	c.2143G>A	c.(2143-2145)GCC>ACC	p.A715T		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	715					response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1						GTGGCCTTGGCAGCCTCACTG	0.527													4	143	---	---	---	---	PASS
PTCD3	55037	broad.mit.edu	37	2	86359530	86359530	+	Silent	SNP	A	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86359530A>G	uc002sqw.2	+	17	1422	c.1356A>G	c.(1354-1356)CAA>CAG	p.Q452Q	PTCD3_uc002sqx.1_Silent_p.Q42Q	NM_017952	NP_060422	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3 precursor	452						mitochondrion	protein binding			ovary(1)	1						GACCTGATCAACATCGTAATT	0.408													54	170	---	---	---	---	PASS
EIF5B	9669	broad.mit.edu	37	2	99978267	99978267	+	Silent	SNP	T	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99978267T>A	uc002tab.2	+	4	1087	c.903T>A	c.(901-903)ACT>ACA	p.T301T		NM_015904	NP_056988	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	301					regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(2)|pancreas(1)	3						AAGCAGAGACTCCCACAGCTG	0.388													7	171	---	---	---	---	PASS
BARD1	580	broad.mit.edu	37	2	215657073	215657073	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215657073C>G	uc002veu.2	-	3	447	c.312G>C	c.(310-312)ATG>ATC	p.M104I	BARD1_uc010zjm.1_Intron	NM_000465	NP_000456	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	104	Interaction with BRCA1.				cell cycle arrest|DNA repair|negative regulation of apoptosis|negative regulation of mRNA 3'-end processing|negative regulation of protein export from nucleus|positive regulation of apoptosis|positive regulation of protein catabolic process|protein K6-linked ubiquitination|regulation of phosphorylation|tissue homeostasis	BRCA1-A complex|BRCA1-BARD1 complex|cytoplasm	kinase binding|protein heterodimerization activity|protein homodimerization activity|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AAAGTTGAATCATGCTGTCCA	0.383									Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				14	103	---	---	---	---	PASS
BOD1L	259282	broad.mit.edu	37	4	13605566	13605566	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13605566C>A	uc003gmz.1	-	10	3075	c.2958G>T	c.(2956-2958)AAG>AAT	p.K986N	BOD1L_uc010idr.1_Missense_Mutation_p.K323N	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	986	Lys-rich.						DNA binding			ovary(5)|breast(1)	6						GACTAGAATCCTTCTGTGTAC	0.398													32	389	---	---	---	---	PASS
SNCA	6622	broad.mit.edu	37	4	90743427	90743427	+	Silent	SNP	A	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90743427A>G	uc003hsq.2	-	4	535	c.276T>C	c.(274-276)ACT>ACC	p.T92T	SNCA_uc010ikt.2_Silent_p.T78T|SNCA_uc003hso.2_Silent_p.T92T|SNCA_uc003hsp.2_Silent_p.T92T|SNCA_uc003hsr.2_Silent_p.T92T	NM_001146054	NP_001139526	P37840	SYUA_HUMAN	alpha-synuclein isoform NACP140	92				Missing: Reduces polymerization into amyloid fibrils.	activation of caspase activity|anti-apoptosis|negative regulation of dopamine uptake|negative regulation of exocytosis|negative regulation of histone acetylation|negative regulation of microtubule polymerization|negative regulation of monooxygenase activity|negative regulation of norepinephrine uptake|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of serotonin uptake|negative regulation of thrombin receptor signaling pathway|negative regulation of transporter activity|positive regulation of endocytosis|positive regulation of inositol phosphate biosynthetic process|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein serine/threonine kinase activity|positive regulation of receptor recycling|positive regulation of release of sequestered calcium ion into cytosol|receptor internalization|regulation of phospholipase activity|response to interferon-gamma|response to interleukin-1|response to iron(II) ion|response to lipopolysaccharide|response to magnesium ion|synaptic vesicle endocytosis	actin cytoskeleton|axon|cell cortex|cell junction|cytosol|fibril|growth cone|nucleus|synapse	alpha-tubulin binding|calcium ion binding|caspase inhibitor activity|dynein binding|ferrous iron binding|histone binding|Hsp70 protein binding|kinesin binding|magnesium ion binding|phosphoprotein binding|tau protein binding|zinc ion binding				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.42e-05)	Melatonin(DB01065)	TGACAAAGCCAGTGGCTGCTG	0.498													38	104	---	---	---	---	PASS
GAB1	2549	broad.mit.edu	37	4	144336751	144336751	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144336751G>T	uc003ije.2	+	2	553	c.194G>T	c.(193-195)TGT>TTT	p.C65F	GAB1_uc003ijd.2_Missense_Mutation_p.C65F|GAB1_uc011chq.1_5'UTR	NM_002039	NP_002030	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1 isoform b	65	PH.				cell proliferation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway	cytosol	SH3/SH2 adaptor activity			breast(2)|lung(1)|skin(1)	4	all_hematologic(180;0.158)					TTAAATTTATGTCAACAAGTA	0.338													24	81	---	---	---	---	PASS
GPM6A	2823	broad.mit.edu	37	4	176622807	176622807	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176622807G>A	uc003iuf.2	-	2	953	c.149C>T	c.(148-150)GCG>GTG	p.A50V	GPM6A_uc011ckj.1_Missense_Mutation_p.A43V|GPM6A_uc003iug.2_Missense_Mutation_p.A50V|GPM6A_uc003iuh.2_Missense_Mutation_p.A39V	NM_201591	NP_963885	P51674	GPM6A_HUMAN	glycoprotein M6A isoform 2	50	Extracellular (Potential).					cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		TCCAGAAAGCGCTTCATGACC	0.488													25	225	---	---	---	---	PASS
NNT	23530	broad.mit.edu	37	5	43619222	43619222	+	Splice_Site	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43619222G>A	uc003joe.2	+	5	942	c.687_splice	c.e5+1	p.K229_splice	NNT_uc003jof.2_Splice_Site_p.K229_splice	NM_012343	NP_036475	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase						tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)	TCCAGCTAAGGTAGGTACAAC	0.299													26	45	---	---	---	---	PASS
ERCC8	1161	broad.mit.edu	37	5	60183321	60183321	+	Silent	SNP	G	A	A	rs141898557		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60183321G>A	uc003jsm.3	-	11	1138	c.1068C>T	c.(1066-1068)TGC>TGT	p.C356C	ERCC8_uc003jsk.2_RNA|ERCC8_uc003jsl.3_Silent_p.C298C|ERCC8_uc011cqp.1_Silent_p.C203C	NM_000082	NP_000073	Q13216	ERCC8_HUMAN	excision repair cross-complementing rodent	356	WD 5.				positive regulation of DNA repair|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein polyubiquitination|response to oxidative stress|response to UV|response to UV|transcription-coupled nucleotide-excision repair	Cul4A-RING ubiquitin ligase complex|nuclear matrix|nucleoplasm|nucleotide-excision repair complex|soluble fraction	protein binding|protein complex binding				0		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)				CCAGAATGTTGCAGTCTCTGC	0.348								Direct_reversal_of_damage|NER					11	150	---	---	---	---	PASS
ZFYVE16	9765	broad.mit.edu	37	5	79770584	79770584	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79770584C>G	uc003kgr.3	+	18	4698	c.4396C>G	c.(4396-4398)CTG>GTG	p.L1466V	ZFYVE16_uc003kgq.3_Missense_Mutation_p.L1466V|ZFYVE16_uc003kgs.3_Missense_Mutation_p.L1466V|ZFYVE16_uc003kgt.3_Missense_Mutation_p.L554V|ZFYVE16_uc003kgu.3_Missense_Mutation_p.L218V	NM_001105251	NP_001098721	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	1466					BMP signaling pathway|endosome transport|protein targeting to lysosome|regulation of endocytosis|vesicle organization	early endosome membrane	1-phosphatidylinositol binding|metal ion binding|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|protein transporter activity				0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		GTGCCCTCACCTGAAAACTCT	0.363													9	146	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	90052865	90052865	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90052865C>T	uc003kju.2	+	57	11923	c.11827C>T	c.(11827-11829)CGG>TGG	p.R3943W	GPR98_uc003kjt.2_Missense_Mutation_p.R1649W|GPR98_uc003kjv.2_Missense_Mutation_p.R1543W	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	3943	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TCCTGTAGTCCGGCTGGCTGG	0.453													4	156	---	---	---	---	PASS
LOC100133050	100133050	broad.mit.edu	37	5	99715528	99715528	+	RNA	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99715528C>T	uc011cuw.1	-	4		c.382G>A				NR_027503				Homo sapiens glucuronidase, beta pseudogene (LOC100133050), non-coding RNA.												0						AGCGGACAGTCGAAGCCCTTC	0.607													3	17	---	---	---	---	PASS
NRG2	9542	broad.mit.edu	37	5	139422020	139422020	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139422020G>A	uc003lex.1	-	1	860	c.635C>T	c.(634-636)GCC>GTC	p.A212V	NRG2_uc003lev.1_Missense_Mutation_p.A212V|NRG2_uc003lew.1_Missense_Mutation_p.A212V|NRG2_uc003ley.1_Missense_Mutation_p.A212V	NM_004883	NP_004874	O14511	NRG2_HUMAN	neuregulin 2 isoform 1	212	Extracellular (Potential).				embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCGAGGGGGGCAAAGGCCGT	0.572													3	26	---	---	---	---	PASS
LOC222699	222699	broad.mit.edu	37	6	28185441	28185441	+	RNA	SNP	A	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28185441A>G	uc011dla.1	-	1		c.1267T>C				NR_002936				Homo sapiens pp14762 mRNA, complete cds.												0						AGCACCACGGACTGGAACGGT	0.473													5	9	---	---	---	---	PASS
OR2B3	442184	broad.mit.edu	37	6	29054943	29054943	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29054943A>G	uc003nlx.2	-	1	148	c.83T>C	c.(82-84)TTT>TCT	p.F28S		NM_001005226	NP_001005226			olfactory receptor, family 2, subfamily B,											skin(1)	1						CAGGACCACAAAAAGGGGCAT	0.408													38	70	---	---	---	---	PASS
LOC442308	442308	broad.mit.edu	37	7	55714466	55714466	+	RNA	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55714466C>T	uc010kzj.2	+	1		c.1155C>T				NR_003598				Homo sapiens similar to tubulin, beta 5 (LOC442308), non-coding RNA.												0						GAGCAGTTCACTGCCATGTTC	0.532													10	40	---	---	---	---	PASS
MOSPD3	64598	broad.mit.edu	37	7	100211278	100211278	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100211278C>A	uc003uvq.2	+	4	662	c.460C>A	c.(460-462)CCA>ACA	p.P154T	MOSPD3_uc003uvr.2_Missense_Mutation_p.P154T|MOSPD3_uc003uvs.2_Missense_Mutation_p.P154T|MOSPD3_uc003uvt.2_Missense_Mutation_p.P144T	NM_001040097	NP_001035186	O75425	MSPD3_HUMAN	motile sperm domain containing 3 isoform a	154						integral to membrane	structural molecule activity			ovary(2)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					AGCGCCTCGCCCAGGGCCTCC	0.622													17	71	---	---	---	---	PASS
MLL5	55904	broad.mit.edu	37	7	104753636	104753636	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104753636C>A	uc003vcm.2	+	27	5967	c.5433C>A	c.(5431-5433)TTC>TTA	p.F1811L	MLL5_uc010ljc.2_Missense_Mutation_p.F1811L|MLL5_uc010ljf.1_RNA|MLL5_uc010ljg.2_Missense_Mutation_p.F545L	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5	1811	Pro-rich.				cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3						CTTCAGGGTTCTGTCCTCATC	0.552													4	98	---	---	---	---	PASS
LAMB1	3912	broad.mit.edu	37	7	107569729	107569729	+	Intron	SNP	A	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107569729A>G	uc003vew.2	-						LAMB1_uc003vev.2_Intron|LAMB1_uc003veu.2_Missense_Mutation_p.L39P	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor						axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TTTAAAGAATAGCCTTCCTGA	0.333													13	36	---	---	---	---	PASS
RBM33	155435	broad.mit.edu	37	7	155559381	155559381	+	Intron	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155559381G>A	uc010lqk.1	+						RBM33_uc011kvv.1_Missense_Mutation_p.G946E|RBM33_uc003wmg.2_Intron	NM_053043	NP_444271	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33								nucleotide binding|RNA binding			ovary(1)	1	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		CTGTGCCACGGGTAGTTGTGT	0.493													2	5	---	---	---	---	PASS
SGCZ	137868	broad.mit.edu	37	8	13948107	13948107	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13948107G>A	uc003wwq.2	-	8	1444	c.784C>T	c.(784-786)CCA>TCA	p.P262S	SGCZ_uc010lss.2_Missense_Mutation_p.P215S	NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta	249	Extracellular (Potential).				cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		GAGCCAGTTGGTAGATTTCCC	0.398													6	118	---	---	---	---	PASS
BMP1	649	broad.mit.edu	37	8	22054158	22054158	+	Intron	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22054158C>T	uc003xbg.2	+						BMP1_uc003xba.2_Intron|BMP1_uc003xbb.2_Intron|BMP1_uc003xbe.2_RNA|BMP1_uc003xbc.2_Intron|BMP1_uc003xbd.2_Intron|BMP1_uc003xbf.2_Intron|BMP1_uc011kzc.1_Intron|BMP1_uc003xbh.2_Intron|BMP1_uc003xbi.2_Intron	NM_006129	NP_006120	P13497	BMP1_HUMAN	bone morphogenetic protein 1 isoform 3						cartilage condensation|cell differentiation|lipid metabolic process|lipoprotein metabolic process|ossification|positive regulation of cartilage development|proteolysis	extracellular space	calcium ion binding|cytokine activity|growth factor activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)	3				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		GGCAGGGGCTCCCCGCAGACG	0.637													5	50	---	---	---	---	PASS
TG	7038	broad.mit.edu	37	8	134034366	134034366	+	Missense_Mutation	SNP	G	A	A	rs121912650		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134034366G>A	uc003ytw.2	+	40	7048	c.7007G>A	c.(7006-7008)CGA>CAA	p.R2336Q	TG_uc010mdw.2_Missense_Mutation_p.R1095Q|TG_uc011ljb.1_Missense_Mutation_p.R705Q|TG_uc011ljc.1_Missense_Mutation_p.R469Q	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	2336			R -> Q (in TDH3).		hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GCCAGCTACCGAGTGGGTGTC	0.602													9	127	---	---	---	---	PASS
ACTL7B	10880	broad.mit.edu	37	9	111618041	111618041	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111618041C>T	uc004bdi.2	-	1	235	c.170G>A	c.(169-171)GGC>GAC	p.G57D		NM_006686	NP_006677	Q9Y614	ACL7B_HUMAN	actin-like 7B	57						actin cytoskeleton|cytoplasm	structural constituent of cytoskeleton			pancreas(1)	1						GTACTGGGAGCCCAGGTCGAT	0.667													13	163	---	---	---	---	PASS
C9orf98	158067	broad.mit.edu	37	9	135602886	135602886	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135602886A>T	uc004cbu.1	-	12	1713	c.1157T>A	c.(1156-1158)ATG>AAG	p.M386K	C9orf98_uc010mzx.1_RNA|C9orf98_uc004cbv.1_Missense_Mutation_p.M182K	NM_152572	NP_689785	Q96MA6	KAD8_HUMAN	putative adenylate kinase-like protein C9orf98	386	Adenylate kinase.					cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity				0				OV - Ovarian serous cystadenocarcinoma(145;4.89e-06)|Epithelial(140;0.00016)		CAGCCGCTCCATGATGGAATC	0.388													32	104	---	---	---	---	PASS
WAC	51322	broad.mit.edu	37	10	28878669	28878669	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28878669A>G	uc001iuf.2	+	5	471	c.386A>G	c.(385-387)TAT>TGT	p.Y129C	WAC_uc001iud.2_Missense_Mutation_p.Y84C|WAC_uc001iue.2_Intron|WAC_uc009xlb.2_Missense_Mutation_p.Y84C|WAC_uc001iug.2_Missense_Mutation_p.Y129C|WAC_uc001iuh.2_Missense_Mutation_p.Y84C	NM_016628	NP_057712	Q9BTA9	WAC_HUMAN	WW domain-containing adapter with a coiled-coil	129	WW.				cell cycle checkpoint|histone H2B conserved C-terminal lysine ubiquitination|histone monoubiquitination|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nuclear speck	chromatin binding|RNA polymerase II core binding			large_intestine(1)|ovary(1)	2						TTTAAGCCTTATGATTCTGCA	0.308													9	160	---	---	---	---	PASS
C10orf82	143379	broad.mit.edu	37	10	118424435	118424435	+	Missense_Mutation	SNP	G	A	A	rs145415319		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118424435G>A	uc001lcr.2	-	4	353	c.298C>T	c.(298-300)CTC>TTC	p.L100F	C10orf82_uc001lcs.1_3'UTR	NM_144661	NP_653262	Q8WW14	CJ082_HUMAN	hypothetical protein LOC143379	100											0				all cancers(201;0.0143)		GGCTCCTGGAGAGGTTTCTTT	0.493													6	194	---	---	---	---	PASS
OR52B4	143496	broad.mit.edu	37	11	4388662	4388662	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4388662C>A	uc010qye.1	-	1	864	c.864G>T	c.(862-864)ATG>ATT	p.M288I		NM_001005161	NP_001005161	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B,	288	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGGATTCAGCATAGGTGGAG	0.428													4	86	---	---	---	---	PASS
PPP1R14B	26472	broad.mit.edu	37	11	64013926	64013926	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64013926A>G	uc001nza.2	-	1	488	c.220T>C	c.(220-222)TGG>CGG	p.W74R		NM_138689	NP_619634	Q96C90	PP14B_HUMAN	protein phosphatase 1 regulatory subunit 14B	74	Potential.				regulation of phosphorylation	cytoplasm	protein phosphatase inhibitor activity				0						TCCAGGATCCACTCCTCTAGG	0.672													4	13	---	---	---	---	PASS
CWC15	51503	broad.mit.edu	37	11	94704596	94704596	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94704596A>C	uc001pfd.3	-	3	310	c.187T>G	c.(187-189)TTG>GTG	p.L63V	CWC15_uc009ywl.1_Missense_Mutation_p.L63V|KDM4D_uc001pfe.2_5'Flank	NM_016403	NP_057487	Q9P013	CWC15_HUMAN	CWC15 homolog	63	Potential.				nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome	protein binding|RNA binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CTTTCTTCCAACTCTCTCCTG	0.413													6	40	---	---	---	---	PASS
ATM	472	broad.mit.edu	37	11	108170468	108170468	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108170468T>G	uc001pkb.1	+	34	5418	c.5033T>G	c.(5032-5034)GTG>GGG	p.V1678G	ATM_uc009yxr.1_Missense_Mutation_p.V1678G|ATM_uc001pke.1_Missense_Mutation_p.V330G|ATM_uc001pkg.1_Missense_Mutation_p.V35G	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	1678					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		TTGGGAGAAGTGGGTCCTATA	0.353			D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			58	161	---	---	---	---	PASS
CDON	50937	broad.mit.edu	37	11	125850957	125850957	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125850957T>A	uc009zbw.2	-	17	3391	c.3263A>T	c.(3262-3264)CAT>CTT	p.H1088L	CDON_uc001qdb.3_Missense_Mutation_p.H465L|CDON_uc001qdc.3_Missense_Mutation_p.H1088L	NM_016952	NP_058648	Q4KMG0	CDON_HUMAN	surface glycoprotein, Ig superfamily member	1088	Cytoplasmic (Potential).				cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|skin(2)|breast(1)	6	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		CACTAGATGATGAGGATGTTC	0.463													6	121	---	---	---	---	PASS
KRT73	319101	broad.mit.edu	37	12	53012201	53012201	+	Silent	SNP	G	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53012201G>T	uc001sas.2	-	1	143	c.108C>A	c.(106-108)GGC>GGA	p.G36G		NM_175068	NP_778238	Q86Y46	K2C73_HUMAN	keratin 73	36	Head.|Gly-rich.					keratin filament	structural molecule activity			large_intestine(2)|ovary(2)|skin(2)	6				BRCA - Breast invasive adenocarcinoma(357;0.189)		TGAGCCCTTTGCCCCCTGCTC	0.642													21	106	---	---	---	---	PASS
GDF11	10220	broad.mit.edu	37	12	56142619	56142619	+	Nonsense_Mutation	SNP	C	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56142619C>G	uc001shq.2	+	2	732	c.695C>G	c.(694-696)TCA>TGA	p.S232*	GDF11_uc010spv.1_Nonsense_Mutation_p.S232*	NM_005811	NP_005802	O95390	GDF11_HUMAN	growth differentiation factor 11 precursor	232					growth|mesoderm development|skeletal system development	extracellular space	cytokine activity|growth factor activity			kidney(1)	1						CACTCACGCTCAGGCCATTGG	0.597													6	25	---	---	---	---	PASS
ANKS1B	56899	broad.mit.edu	37	12	99223072	99223072	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99223072G>T	uc001tge.1	-	19	3363	c.2946C>A	c.(2944-2946)TAC>TAA	p.Y982*	ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Nonsense_Mutation_p.Y279*|ANKS1B_uc010svd.1_5'UTR|ANKS1B_uc001tgd.1_Intron|ANKS1B_uc009ztq.2_5'UTR|ANKS1B_uc010sve.1_5'UTR|ANKS1B_uc001tgh.3_5'UTR|ANKS1B_uc001tgi.2_Nonsense_Mutation_p.Y208*|ANKS1B_uc009ztr.2_Intron|ANKS1B_uc001tgj.2_Intron|ANKS1B_uc009ztp.2_5'UTR|ANKS1B_uc010svf.1_5'UTR|ANKS1B_uc001tgg.3_Intron|ANKS1B_uc010svg.1_Intron|ANKS1B_uc009zts.1_Nonsense_Mutation_p.Y208*	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a	982						Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		CACCAGTGGTGTAAGTGCTTT	0.438													9	172	---	---	---	---	PASS
PAN3	255967	broad.mit.edu	37	13	28840980	28840980	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28840980G>T	uc001urz.2	+	9	1110	c.1102G>T	c.(1102-1104)GAT>TAT	p.D368Y	PAN3_uc010tdo.1_Missense_Mutation_p.D514Y|PAN3_uc001ury.2_Missense_Mutation_p.D202Y|PAN3_uc001urx.2_Missense_Mutation_p.D314Y	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease	514	Protein kinase.|Interaction with PAN2.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		AAACAGCAAAGATGATCTGCC	0.378													10	134	---	---	---	---	PASS
N4BP2L2	10443	broad.mit.edu	37	13	33110883	33110883	+	Silent	SNP	A	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33110883A>G	uc001uuk.3	-	2	460	c.282T>C	c.(280-282)ATT>ATC	p.I94I	N4BP2L2_uc010abe.1_Intron|N4BP2L2_uc010tdz.1_Intron|N4BP2L2_uc001uul.1_Silent_p.I94I|N4BP2L2_uc001uum.2_5'Flank	NM_014887	NP_055702	Q92802	N42L2_HUMAN	phosphonoformate immuno-associated protein 5	94											0		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		CAATGGATTCAATAACATCTG	0.383													15	384	---	---	---	---	PASS
ARHGEF7	8874	broad.mit.edu	37	13	111862226	111862226	+	Silent	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111862226G>A	uc001vrs.2	+	5	658	c.408G>A	c.(406-408)GGG>GGA	p.G136G	ARHGEF7_uc001vrr.2_Silent_p.G115G|ARHGEF7_uc001vrt.2_Silent_p.G86G|ARHGEF7_uc010tjn.1_Intron|ARHGEF7_uc001vru.1_5'UTR|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_5'UTR|ARHGEF7_uc001vrx.3_5'UTR|ARHGEF7_uc010tjo.1_Silent_p.G33G	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c	136					apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CAGACATCGGGCTGGGGAGTG	0.522													32	434	---	---	---	---	PASS
SEC23A	10484	broad.mit.edu	37	14	39554995	39554995	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39554995C>T	uc001wup.1	-	7	1022	c.799G>A	c.(799-801)GCA>ACA	p.A267T	SEC23A_uc010tqa.1_Missense_Mutation_p.A129T|SEC23A_uc010tqb.1_Missense_Mutation_p.A238T|SEC23A_uc010tqc.1_Missense_Mutation_p.A129T	NM_006364	NP_006355	Q15436	SC23A_HUMAN	SEC23-related protein A	267					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|Golgi membrane|smooth endoplasmic reticulum membrane	protein binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		ATGGAAAGTGCCACCCCAGAG	0.388													4	204	---	---	---	---	PASS
FSCB	84075	broad.mit.edu	37	14	44973940	44973940	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44973940C>G	uc001wvn.2	-	1	2560	c.2251G>C	c.(2251-2253)GCT>CCT	p.A751P		NM_032135	NP_115511	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	751						cilium				lung(3)|breast(3)|ovary(2)|central_nervous_system(1)	9				GBM - Glioblastoma multiforme(112;0.128)		TCTACCAGAGCCTCATCTTCA	0.468													12	136	---	---	---	---	PASS
ZFYVE1	53349	broad.mit.edu	37	14	73490808	73490808	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73490808C>T	uc001xnm.2	-	2	1049	c.409G>A	c.(409-411)GAG>AAG	p.E137K	ZFYVE1_uc010arj.2_Missense_Mutation_p.E137K	NM_021260	NP_067083	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1 isoform 1	137						endoplasmic reticulum|Golgi stack|perinuclear region of cytoplasm	1-phosphatidylinositol binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|zinc ion binding			skin(1)	1		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		TTGGTCTCCTCATCCATCTCT	0.463													6	302	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106054130	106054130	+	Intron	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106054130G>A	uc010tyt.1	-						uc001yrs.2_RNA|uc001yrt.2_Missense_Mutation_p.A136V					Parts of antibodies, mostly variable regions.												0						CGTGAGGTTCGCTTCTGAACC	0.637													4	18	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106110177	106110177	+	RNA	SNP	G	C	C			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106110177G>C	uc010tyt.1	-	3642		c.61074C>G			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_RNA					Parts of antibodies, mostly variable regions.												0						CGGGGTCTTCGTGGCTCACGT	0.602													4	200	---	---	---	---	PASS
TGM5	9333	broad.mit.edu	37	15	43552495	43552495	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43552495C>T	uc001zrd.1	-	3	199	c.191G>A	c.(190-192)GGA>GAA	p.G64E	TGM5_uc001zre.1_Intron	NM_201631	NP_963925	O43548	TGM5_HUMAN	transglutaminase 5 isoform 1	64					epidermis development|peptide cross-linking	cytoplasm	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(1)	1		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	TGGCAGCGGTCCTAGGAGGGA	0.647													12	50	---	---	---	---	PASS
NARG2	79664	broad.mit.edu	37	15	60741078	60741078	+	Silent	SNP	T	C	C			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60741078T>C	uc002agp.2	-	10	2323	c.2088A>G	c.(2086-2088)GGA>GGG	p.G696G	NARG2_uc002ago.2_Silent_p.G559G|NARG2_uc002agq.3_Silent_p.G364G	NM_024611	NP_078887	Q659A1	NARG2_HUMAN	NMDA receptor regulated 2 isoform a	696						nucleus				ovary(1)|lung(1)	2						CAGAAGGCCATCCAGATTTCG	0.388													5	113	---	---	---	---	PASS
PLEKHO2	80301	broad.mit.edu	37	15	65157582	65157582	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65157582C>T	uc002anv.2	+	6	1102	c.968C>T	c.(967-969)GCC>GTC	p.A323V	PLEKHO2_uc010bgz.2_5'UTR|PLEKHO2_uc002anw.2_Missense_Mutation_p.A273V	NM_025201	NP_079477	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O	323	Pro-rich.									ovary(1)|lung(1)	2						AAACTGAAAGCCTCCATGGGT	0.602													23	81	---	---	---	---	PASS
ITGA11	22801	broad.mit.edu	37	15	68642956	68642956	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68642956T>A	uc002ari.2	-	9	1146	c.1059A>T	c.(1057-1059)GAA>GAT	p.E353D	ITGA11_uc010bib.2_Missense_Mutation_p.E353D	NM_001004439	NP_001004439	Q9UKX5	ITA11_HUMAN	integrin, alpha 11 precursor	353	Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)	ATTGCTTACCTTCCAGGCTGA	0.502													24	78	---	---	---	---	PASS
LOC100134368	100134368	broad.mit.edu	37	16	436725	436725	+	Intron	SNP	C	A	A	rs143645242	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:436725C>A	uc002cgw.1	+						uc002cgx.3_Missense_Mutation_p.T12N	NR_024453				Homo sapiens cDNA clone IMAGE:3636396, partial cds.												0						aaaaaaaaaaccaaaaaaaaa	0.284													4	13	---	---	---	---	PASS
TIGD7	91151	broad.mit.edu	37	16	3350367	3350367	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3350367G>A	uc002cus.2	-	1	1034	c.248C>T	c.(247-249)GCG>GTG	p.A83V	ZNF263_uc002cur.2_3'UTR|TIGD7_uc010btj.1_RNA	NM_033208	NP_149985	Q6NT04	TIGD7_HUMAN	tigger transposable element derived 7	83	HTH CENPB-type.				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0						CATGTAGACCGCATCATCTAC	0.502													4	209	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													3	14	---	---	---	---	PASS
VAC14	55697	broad.mit.edu	37	16	70818692	70818692	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70818692T>C	uc002ezm.2	-	4	731	c.473A>G	c.(472-474)GAC>GGC	p.D158G	VAC14_uc010cfw.2_5'UTR|VAC14_uc002ezn.2_5'UTR	NM_018052	NP_060522	Q08AM6	VAC14_HUMAN	Vac14 homolog	158					interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity			pancreas(1)|skin(1)	2		Ovarian(137;0.0699)				TAAAAGGCGGTCTAGGAGCTC	0.498													8	192	---	---	---	---	PASS
ADAMTS18	170692	broad.mit.edu	37	16	77387747	77387747	+	Silent	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77387747C>T	uc002ffc.3	-	10	1916	c.1497G>A	c.(1495-1497)AAG>AAA	p.K499K	ADAMTS18_uc010chc.1_Silent_p.K87K|ADAMTS18_uc002ffe.1_Silent_p.K195K	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	499	Disintegrin.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18						GTCCTGCTTGCTTGGGCTCAT	0.423													15	250	---	---	---	---	PASS
RAI1	10743	broad.mit.edu	37	17	17699836	17699836	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17699836A>G	uc002grm.2	+	3	4043	c.3574A>G	c.(3574-3576)AGC>GGC	p.S1192G	RAI1_uc002grn.1_Missense_Mutation_p.S1192G	NM_030665	NP_109590	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1192						cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)|skin(1)	2				READ - Rectum adenocarcinoma(1115;0.0276)		GGTCTCCAGCAGCCCCCAGAA	0.657													19	52	---	---	---	---	PASS
SPAG5	10615	broad.mit.edu	37	17	26912593	26912593	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26912593G>A	uc002hbq.2	-	8	1911	c.1819C>T	c.(1819-1821)CGG>TGG	p.R607W	SGK494_uc010waq.1_Intron	NM_006461	NP_006452	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	607	Potential.				cell division|mitosis|phosphatidylinositol-mediated signaling|spindle organization	condensed chromosome kinetochore|cytoplasm|spindle pole	protein binding			central_nervous_system(1)	1	Lung NSC(42;0.00431)					CTGAATTCCCGCATGGATGCT	0.537													6	286	---	---	---	---	PASS
SLFN13	146857	broad.mit.edu	37	17	33767432	33767432	+	3'UTR	SNP	A	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33767432A>G	uc002hjk.1	-	4					SLFN13_uc010wch.1_3'UTR|SLFN13_uc002hjl.2_3'UTR|SLFN13_uc010ctt.2_3'UTR|SLFN13_uc002hjm.2_3'UTR	NM_144682	NP_653283	Q68D06	SLN13_HUMAN	schlafen family member 13							intracellular	ATP binding			ovary(1)|breast(1)	2				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		tgctgaaaagagttgggggag	0.000													2	7	---	---	---	---	PASS
SLFN12L	342615	broad.mit.edu	37	17	33802445	33802445	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33802445G>T	uc002hjn.2	-	5	2230	c.1351C>A	c.(1351-1353)CAT>AAT	p.H451N		NM_001145027	NP_001138499			schlafen family member 12-like											ovary(1)	1						AGTCCTTCATGTTGTGAGAAC	0.393													8	52	---	---	---	---	PASS
TADA2A	6871	broad.mit.edu	37	17	35836946	35836946	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35836946C>A	uc002hnt.2	+	16	1348	c.1191C>A	c.(1189-1191)TAC>TAA	p.Y397*	TADA2A_uc002hnv.2_Nonsense_Mutation_p.Y397*|TADA2A_uc002hnw.2_Nonsense_Mutation_p.Y296*|TADA2A_uc010cvb.2_Nonsense_Mutation_p.Y193*	NM_001488	NP_001479	O75478	TAD2A_HUMAN	transcriptional adaptor 2A isoform a	397	SWIRM.				histone H3 acetylation|transcription from RNA polymerase II promoter	chromosome|PCAF complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|zinc ion binding			breast(3)|skin(1)	4						ATTTAGAATACAAATCTGCTC	0.398													18	204	---	---	---	---	PASS
KRT17	3872	broad.mit.edu	37	17	39779138	39779138	+	Intron	SNP	G	C	C			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39779138G>C	uc002hxh.2	-						JUP_uc010wfs.1_Intron|KRT17_uc010wft.1_3'UTR	NM_000422	NP_000413	Q04695	K1C17_HUMAN	keratin 17						epidermis development	cytoplasm|intermediate filament	protein binding|structural constituent of cytoskeleton			ovary(1)|skin(1)	2		Breast(137;0.000307)				CTGGGGTCAGGAGGGGTACCC	0.622									Steatocystoma_Multiplex				5	31	---	---	---	---	PASS
SDK2	54549	broad.mit.edu	37	17	71398278	71398278	+	Silent	SNP	C	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71398278C>A	uc010dfm.2	-	19	2487	c.2487G>T	c.(2485-2487)CTG>CTT	p.L829L	SDK2_uc002jjt.3_5'UTR|SDK2_uc010dfn.2_Silent_p.L508L	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2	829	Fibronectin type-III 3.|Extracellular (Potential).				cell adhesion	integral to membrane				ovary(2)	2						CCCAGGCGATCAGCTGCGGAG	0.612													3	53	---	---	---	---	PASS
DYM	54808	broad.mit.edu	37	18	46906085	46906085	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46906085C>G	uc002ldi.1	-	4	602	c.237G>C	c.(235-237)AAG>AAC	p.K79N	DYM_uc010xdf.1_Intron	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin	79						Golgi apparatus					0						AAAGGAAGACCTTAATTAGTG	0.313													56	180	---	---	---	---	PASS
ZNF407	55628	broad.mit.edu	37	18	72345031	72345031	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72345031C>A	uc002llw.2	+	1	2113	c.2056C>A	c.(2056-2058)CCT>ACT	p.P686T	ZNF407_uc010xfc.1_Missense_Mutation_p.P686T|ZNF407_uc010dqu.1_Missense_Mutation_p.P686T|ZNF407_uc002llu.2_Missense_Mutation_p.P685T	NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1	686					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TCAGGAAGAACCTCTGAAGTC	0.383													18	50	---	---	---	---	PASS
ZNRF4	148066	broad.mit.edu	37	19	5456615	5456615	+	Silent	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5456615C>T	uc002mca.3	+	1	1190	c.1113C>T	c.(1111-1113)GAC>GAT	p.D371D		NM_181710	NP_859061	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4 precursor	371	Cytoplasmic (Potential).					integral to membrane	zinc ion binding			large_intestine(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		GCTTCAGGGACGAGGACCCCT	0.682													5	90	---	---	---	---	PASS
ZFP112	7771	broad.mit.edu	37	19	44833686	44833686	+	Silent	SNP	A	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44833686A>G	uc010ejj.2	-	5	755	c.642T>C	c.(640-642)AGT>AGC	p.S214S	ZFP112_uc002ozc.3_Silent_p.S208S|ZFP112_uc010xwy.1_Silent_p.S231S|ZFP112_uc010xwz.1_Silent_p.S213S	NM_001083335	NP_001076804	Q9UJU3	ZF112_HUMAN	zinc finger protein 228 isoform 1	214					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)	5						GTGAGAGCCAACTGACACTGT	0.358													13	200	---	---	---	---	PASS
SLC1A5	6510	broad.mit.edu	37	19	47278747	47278747	+	3'UTR	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47278747G>A	uc002pfs.2	-	8					SLC1A5_uc010xyh.1_3'UTR|SLC1A5_uc002pfq.2_3'UTR|SLC1A5_uc002pfr.2_3'UTR	NM_005628	NP_005619	Q15758	AAAT_HUMAN	solute carrier family 1 member 5 isoform 1						cellular nitrogen compound metabolic process	integral to plasma membrane|melanosome|membrane fraction	neutral amino acid transmembrane transporter activity|protein binding|receptor activity|sodium:dicarboxylate symporter activity				0		all_epithelial(76;0.00314)|Ovarian(192;0.0798)|all_neural(266;0.107)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000882)|Epithelial(262;0.0211)|GBM - Glioblastoma multiforme(486;0.0341)	L-Asparagine(DB00174)|L-Glutamine(DB00130)	CAGCAGGGCAGGGAAGGTCCC	0.597													30	180	---	---	---	---	PASS
HAS1	3036	broad.mit.edu	37	19	52219536	52219536	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52219536C>T	uc002pxo.1	-	4	1069	c.1034G>A	c.(1033-1035)CGC>CAC	p.R345H	HAS1_uc010epc.1_Intron|HAS1_uc010epd.1_Missense_Mutation_p.R310H|HAS1_uc002pxn.1_Missense_Mutation_p.R352H|HAS1_uc002pxp.1_Missense_Mutation_p.R344H	NM_001523	NP_001514	Q92839	HAS1_HUMAN	hyaluronan synthase 1	345	Cytoplasmic (Potential).				cell adhesion	integral to plasma membrane	hyaluronan synthase activity|protein binding			ovary(1)|pancreas(1)	2		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GCTGAGCATGCGGTTGGTGAG	0.522													4	97	---	---	---	---	PASS
NLRP8	126205	broad.mit.edu	37	19	56459316	56459316	+	Silent	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56459316C>T	uc002qmh.2	+	1	119	c.48C>T	c.(46-48)TCC>TCT	p.S16S	NLRP8_uc010etg.2_Silent_p.S16S	NM_176811	NP_789781	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	16						cytoplasm	ATP binding			ovary(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|kidney(1)	13		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CCTTTTCATCCTCCTCCACTC	0.512													16	201	---	---	---	---	PASS
TRIM28	10155	broad.mit.edu	37	19	59057138	59057138	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59057138C>G	uc002qtg.1	+	3	750	c.461C>G	c.(460-462)ACT>AGT	p.T154S	TRIM28_uc010eut.1_Intron|TRIM28_uc002qth.1_5'Flank	NM_005762	NP_005753	Q13263	TIF1B_HUMAN	tripartite motif-containing 28 protein	154	RBCC domain.|B box-type 1; atypical.				epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	nucleoplasm	chromo shadow domain binding|ligase activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		CAGTGCTGCACTAGCTGTGAG	0.527													15	60	---	---	---	---	PASS
PISD	23761	broad.mit.edu	37	22	32044095	32044095	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32044095G>A	uc003alm.3	-	3	320	c.313C>T	c.(313-315)CAC>TAC	p.H105Y	PISD_uc003aln.3_Missense_Mutation_p.H105Y	NM_014338	NP_055153	Q9UG56	PISD_HUMAN	phosphatidylserine decarboxylase	105					phospholipid biosynthetic process	mitochondrion	phosphatidylserine decarboxylase activity			central_nervous_system(2)|ovary(1)	3					Phosphatidylserine(DB00144)	ACCTCCCAGTGACCAGCAAGT	0.517													9	29	---	---	---	---	PASS
ELFN2	114794	broad.mit.edu	37	22	37770332	37770332	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37770332C>T	uc003asq.3	-	3	2029	c.1243G>A	c.(1243-1245)GTG>ATG	p.V415M		NM_052906	NP_443138	Q5R3F8	LRFN6_HUMAN	leucine rich repeat containing 62	415	Helical; (Potential).					cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)					CAGTAGTACACGGCTCCCAGC	0.607													10	113	---	---	---	---	PASS
YY2	404281	broad.mit.edu	37	X	21875491	21875491	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21875491A>G	uc011mjp.1	+	1	889	c.889A>G	c.(889-891)AAG>GAG	p.K297E	MBTPS2_uc004dae.2_Intron|MBTPS2_uc010nfr.2_Intron|YY2_uc010nfq.2_Missense_Mutation_p.K515E|MBTPS2_uc004dab.2_Intron	NM_206923	NP_996806	O15391	TYY2_HUMAN	YY2 transcription factor	297	Mediates transcriptional repression.|C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	DNA binding|zinc ion binding			breast(1)|skin(1)	2						TGAGAGCTCAAAGCTGAGACG	0.532													8	473	---	---	---	---	PASS
CACNA1F	778	broad.mit.edu	37	X	49066823	49066823	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49066823G>A	uc004dnb.2	-	39	4621	c.4559C>T	c.(4558-4560)ACG>ATG	p.T1520M	CACNA1F_uc010nip.2_Missense_Mutation_p.T1509M	NM_005183	NP_005174	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type,	1520	Cytoplasmic (Potential).				axon guidance|detection of light stimulus involved in visual perception	voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			breast(3)|ovary(1)|kidney(1)|skin(1)	6					Verapamil(DB00661)	GAATGTCACCGTCCCATCTGA	0.537													9	187	---	---	---	---	PASS
EFNB1	1947	broad.mit.edu	37	X	68059559	68059559	+	Silent	SNP	C	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68059559C>T	uc004dxd.3	+	3	1239	c.459C>T	c.(457-459)TGC>TGT	p.C153C	EFNB1_uc004dxe.2_Silent_p.C153C	NM_004429	NP_004420	P98172	EFNB1_HUMAN	ephrin-B1 precursor	153	Extracellular (Potential).		C -> Y (in CFNS).|C -> S (in CFNS).		cell adhesion|cell-cell signaling	integral to plasma membrane|soluble fraction|synapse	ephrin receptor binding				0						GCGGTGTGTGCCGCACACGCA	0.562													3	55	---	---	---	---	PASS
ERCC6L	54821	broad.mit.edu	37	X	71425351	71425351	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71425351G>T	uc004eaq.1	-	2	3363	c.3266C>A	c.(3265-3267)TCT>TAT	p.S1089Y	PIN4_uc004eao.1_Intron|ERCC6L_uc004eap.1_Missense_Mutation_p.S966Y	NM_017669	NP_060139	Q2NKX8	ERC6L_HUMAN	excision repair protein ERCC6-like	1089					cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol	ATP binding|DNA binding|helicase activity|protein binding			ovary(3)	3	Renal(35;0.156)					AGATCTTCTAGAGTTCATAGA	0.413													4	175	---	---	---	---	PASS
GPR174	84636	broad.mit.edu	37	X	78427406	78427406	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78427406G>T	uc004edg.1	+	1	938	c.902G>T	c.(901-903)AGA>ATA	p.R301I		NM_032553	NP_115942	Q9BXC1	GP174_HUMAN	putative purinergic receptor FKSG79	301	Cytoplasmic (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(1)|central_nervous_system(1)	2						GAGTTCCGAAGACGGCTTTCA	0.403										HNSCC(63;0.18)			8	161	---	---	---	---	PASS
HNRNPH2	3188	broad.mit.edu	37	X	100668409	100668409	+	3'UTR	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100668409G>A	uc004ehm.2	+	2					HNRNPH2_uc004ehn.2_3'UTR	NM_019597	NP_062543	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2						nuclear mRNA splicing, via spliceosome	actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding				0						GGGATGTTTAGTATATCCAGT	0.358													11	68	---	---	---	---	PASS
GUCY2F	2986	broad.mit.edu	37	X	108631719	108631719	+	Silent	SNP	T	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108631719T>A	uc004eod.3	-	15	3231	c.2955A>T	c.(2953-2955)TCA>TCT	p.S985S	GUCY2F_uc011msq.1_RNA	NM_001522	NP_001513	P51841	GUC2F_HUMAN	guanylate cyclase 2F precursor	985	Guanylate cyclase.|Cytoplasmic (Potential).				intracellular signal transduction|receptor guanylyl cyclase signaling pathway|visual perception	integral to plasma membrane|nuclear outer membrane	ATP binding|GTP binding|guanylate cyclase activity|protein kinase activity|receptor activity			lung(4)|breast(3)|central_nervous_system(1)	8						GGTTATTACCTGAGTGAAGGC	0.458													11	296	---	---	---	---	PASS
MAGEC2	51438	broad.mit.edu	37	X	141291503	141291503	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:141291503G>C	uc004fbu.1	-	3	619	c.271C>G	c.(271-273)CCT>GCT	p.P91A		NM_016249	NP_057333	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	91	Ser-rich.					cytoplasm|nucleus				breast(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)					ccctgtggaggaccctgtgga	0.413										HNSCC(46;0.14)			3	78	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15257	15257	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15257G>A	uc004coy.2	+	1	497	c.422G>A	c.(421-423)AGA>AAA	p.R141K	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		GCTACTCAGTAGACAGTCCCA	0.458											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	16	10	---	---	---	---	PASS
ATP13A2	23400	broad.mit.edu	37	1	17323366	17323367	+	Intron	INS	-	G	G	rs140594331	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17323366_17323367insG	uc001baa.2	-						ATP13A2_uc001bab.2_Intron|ATP13A2_uc001bac.2_Intron|ATP13A2_uc009vpa.1_Intron|ATP13A2_uc001bad.1_Intron	NM_022089	NP_071372	Q9NQ11	AT132_HUMAN	ATPase type 13A2 isoform 1						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		agaccccagatggggggcaact	0.178													3	3	---	---	---	---	
TBX15	6913	broad.mit.edu	37	1	119435952	119435952	+	Intron	DEL	G	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119435952delG	uc001ehl.1	-						TBX15_uc009whj.1_Intron	NM_152380	NP_689593	Q96SF7	TBX15_HUMAN	T-box 15							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|pancreas(1)	2	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		aaagaaagaagaaagaaggaa	0.000													2	4	---	---	---	---	
IGSF9	57549	broad.mit.edu	37	1	159896866	159896867	+	3'UTR	INS	-	CA	CA	rs138111490	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159896866_159896867insCA	uc001fur.2	-	21					IGSF9_uc001fuq.2_3'UTR|CCDC19_uc001ful.2_5'Flank|TAGLN2_uc001fun.1_5'Flank|TAGLN2_uc001fuo.1_5'Flank|TAGLN2_uc010piy.1_5'Flank|IGSF9_uc001fup.2_3'UTR	NM_001135050	NP_001128522	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9 isoform a							cell junction|integral to membrane|synapse				ovary(2)|central_nervous_system(2)|large_intestine(1)	5	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			GTAAAAAACTTcacacacacac	0.317													1	5	---	---	---	---	
RGS7	6000	broad.mit.edu	37	1	241384294	241384295	+	Intron	INS	-	AAGAAAGA	AAGAAAGA	rs12039594	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241384294_241384295insAAGAAAGA	uc001hyv.2	-						RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			aggaaggaaggaagagagagag	0.015													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	18676774	18676774	+	IGR	DEL	C	-	-	rs72118019		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18676774delC								KCNS3 (562550 upstream) : NT5C1B (59217 downstream)																							cttccttcctcccCTTCCCCT	0.050													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89867324	89867328	+	IGR	DEL	CACTG	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89867324_89867328delCACTG								FLJ40330 (761199 upstream) : None (None downstream)																							cattccattccactgcattccattc	0.000													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92307360	92307360	+	IGR	DEL	T	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92307360delT								FKSG73 (176866 upstream) : None (None downstream)																							gagttgaacctttcttttgag	0.000													7	5	---	---	---	---	
MYO7B	4648	broad.mit.edu	37	2	128394875	128394876	+	Intron	INS	-	A	A	rs139192837	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128394875_128394876insA	uc002top.2	+						MYO7B_uc002tos.1_Frame_Shift_Ins_p.P322fs|MYO7B_uc002tot.2_Intron	NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB							apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CTCTGACCCCCCCGTCCCCTGT	0.624													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	151040355	151040356	+	IGR	DEL	TG	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151040355_151040356delTG								MMADHC (596025 upstream) : RND3 (284356 downstream)																							GAGAGGGCTAtgtgtgtgtgtg	0.312													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	241580301	241580304	+	IGR	DEL	TCCC	-	-	rs111676100		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241580301_241580304delTCCC								GPR35 (9626 upstream) : AQP12B (35532 downstream)																							cctccttccttccctgacctacct	0.000													7	5	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191562	10191563	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191562_10191563insG	uc003bvc.2	+	3	768_769	c.555_556insG	c.(553-558)TACGAAfs	p.Y185fs	VHL_uc003bvd.2_Frame_Shift_Ins_p.Y144fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	185_186			E -> K (in VHLD; type I).|Missing (in VHLD).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.Y185fs*17(4)|p.Y185*(2)|p.E186*(2)|p.E186fs*14(1)|p.Y185fs*1(1)|p.S183*(1)|p.Y185fs*11(1)|p.Y185Y(1)|p.Y185fs*29(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GGTCGCTCTACGAAGATCTGGA	0.515		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				31	27	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	75264910	75264912	+	IGR	DEL	AAA	-	-	rs35563675		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75264910_75264912delAAA								CNTN3 (694567 upstream) : FAM86D (205793 downstream)																							TGATGACCCCaaaaaaaaaaaaa	0.296													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	7372639	7372647	+	IGR	DEL	CTCCACCAT	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7372639_7372647delCTCCACCAT								PAPD7 (615478 upstream) : ADCY2 (23696 downstream)																							ccaccaccacctccaccatcaccaccacc	0.000													5	3	---	---	---	---	
C6orf167	253714	broad.mit.edu	37	6	97717991	97717991	+	Intron	DEL	A	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97717991delA	uc003ppb.2	-						C6orf167_uc011eaf.1_Intron|C6orf167_uc010kcn.1_5'UTR|C6orf167_uc010kco.1_Intron|C6orf167_uc003ppc.2_Intron	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714						double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)		ACCACTATTCAAAAGCTCAGG	0.234													6	3	---	---	---	---	
AKD1	221264	broad.mit.edu	37	6	109818530	109818535	+	Intron	DEL	CACACA	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109818530_109818535delCACACA	uc003ptn.2	-						AKD1_uc011eas.1_Intron	NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	adenylate kinase domain containing 1 isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1						agtgcttgttcacacacacacacaca	0.000													4	4	---	---	---	---	
AGR3	155465	broad.mit.edu	37	7	16919728	16919729	+	Intron	INS	-	TTCT	TTCT	rs3052033		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16919728_16919729insTTCT	uc003sts.2	-							NM_176813	NP_789783	Q8TD06	AGR3_HUMAN	breast cancer membrane protein 11 precursor							extracellular region					0	Lung NSC(10;0.0376)|all_lung(11;0.0721)|all_epithelial(12;0.202)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)		tccttccttccttctttccttc	0.074													4	2	---	---	---	---	
OSBPL3	26031	broad.mit.edu	37	7	24907957	24907959	+	Intron	DEL	AGT	-	-	rs146459843	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24907957_24907959delAGT	uc003sxf.2	-						OSBPL3_uc003sxd.2_Intron|OSBPL3_uc003sxe.2_Intron|OSBPL3_uc003sxg.2_Intron|OSBPL3_uc003sxh.2_Intron|OSBPL3_uc003sxi.2_Intron	NM_015550	NP_056365	Q9H4L5	OSBL3_HUMAN	oxysterol-binding protein-like protein 3 isoform						lipid transport		lipid binding|protein binding			skin(1)	1						aaaaaaaaaaagtgtgtgtgtgt	0.074													3	3	---	---	---	---	
SHFM1	7979	broad.mit.edu	37	7	96339292	96339292	+	5'Flank	DEL	T	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96339292delT	uc003uoi.2	-						SHFM1_uc010lfn.1_5'Flank	NM_006304	NP_006295	P60896	DSS1_HUMAN	split hand/foot malformation type 1						proteolysis	proteasome complex	peptidase activity|protein binding				0	all_cancers(62;4.24e-09)|all_epithelial(64;5.59e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0353)|Lung NSC(181;0.0987)					GTAGAGGTGAttttttttttt	0.458								Direct_reversal_of_damage|Homologous_recombination					4	2	---	---	---	---	
PXDNL	137902	broad.mit.edu	37	8	52520415	52520418	+	Intron	DEL	AGGA	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52520415_52520418delAGGA	uc003xqu.3	-							NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				aaaggaagagaggaaggaaggaag	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	55279007	55279008	+	IGR	DEL	GT	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55279007_55279008delGT								MRPL15 (217933 upstream) : SOX17 (91487 downstream)																							tgtgtgtgtagtgtgtgtgtgG	0.416													4	2	---	---	---	---	
PVT1	5820	broad.mit.edu	37	8	129015214	129015215	+	Intron	INS	-	CTTC	CTTC			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129015214_129015215insCTTC	uc010mdq.2	+						PVT1_uc003ysl.2_Intron	NR_003367				Homo sapiens Pvt1 oncogene (non-protein coding), mRNA (cDNA clone IMAGE:5517530), with apparent retained intron.												0						cctccctccctcttccttcctt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68420735	68420735	+	IGR	DEL	A	-	-	rs150487532		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68420735delA								FAM27B (626546 upstream) : MIR1299 (581504 downstream)																							CAGGTGTTGCAGAAACTGGGC	0.363													4	2	---	---	---	---	
PCSK5	5125	broad.mit.edu	37	9	78506444	78506445	+	Intron	DEL	TA	-	-	rs62559211		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78506444_78506445delTA	uc004ajz.2	+						PCSK5_uc004ajy.2_Intron|PCSK5_uc004aka.2_Intron	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3						CGCGCGCGCGTacgcacacaca	0.500													5	3	---	---	---	---	
FRMD3	257019	broad.mit.edu	37	9	86094655	86094656	+	Intron	INS	-	AAG	AAG			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86094655_86094656insAAG	uc004ams.1	-						FRMD3_uc004amr.1_Intron	NM_174938	NP_777598	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2						ggaaagaaagaaaaagaaaaga	0.005													4	2	---	---	---	---	
OR13C5	138799	broad.mit.edu	37	9	107361899	107361902	+	5'Flank	DEL	GAAT	-	-	rs10541505		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107361899_107361902delGAAT	uc011lvp.1	-							NM_001004482	NP_001004482	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)|skin(1)	4						agagggaagggaatgaatgaatga	0.029													4	2	---	---	---	---	
NR6A1	2649	broad.mit.edu	37	9	127360949	127360949	+	Intron	DEL	C	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127360949delC	uc004bor.1	-						NR6A1_uc004boq.1_Intron|NR6A1_uc010mwq.1_Intron	NM_033334	NP_201591	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1						cell proliferation|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	transcription factor complex	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3						aaaaaaaaaacaaggaaggga	0.274													4	2	---	---	---	---	
GATA3	2625	broad.mit.edu	37	10	8106259	8106265	+	Intron	DEL	TCTTTTC	-	-	rs60280763		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8106259_8106265delTCTTTTC	uc001ika.2	+						GATA3_uc001ijz.2_Intron	NM_002051	NP_002042	P23771	GATA3_HUMAN	GATA binding protein 3 isoform 2						aortic valve morphogenesis|blood coagulation|canonical Wnt receptor signaling pathway involved in metanephric kidney development|cardiac right ventricle morphogenesis|cell fate determination|cellular response to interferon-alpha|cellular response to interleukin-4|cellular response to tumor necrosis factor|defense response|ear development|lymphocyte migration|male gonad development|mesenchymal to epithelial transition|mesonephros development|negative regulation of cell cycle|negative regulation of cell motility|negative regulation of cell proliferation involved in mesonephros development|negative regulation of endothelial cell apoptosis|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation|negative regulation of inflammatory response|negative regulation of mammary gland epithelial cell proliferation|nephric duct formation|norepinephrine biosynthetic process|pharyngeal system development|phosphatidylinositol 3-kinase cascade|positive regulation of endothelial cell migration|positive regulation of interleukin-13 secretion|positive regulation of interleukin-4 production|positive regulation of interleukin-5 secretion|positive regulation of protein kinase B signaling cascade|positive regulation of T cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription regulatory region DNA binding|positive regulation of ureteric bud formation|regulation of cellular response to X-ray|regulation of cytokine biosynthetic process|regulation of nephron tubule epithelial cell differentiation|response to estrogen stimulus|response to virus|sympathetic nervous system development|T cell receptor signaling pathway|TOR signaling cascade|ureteric bud formation|uterus development|ventricular septum development	nuclear chromatin|nucleolus|nucleoplasm	core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|E-box binding|HMG box domain binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription coactivator activity|transcription factor binding|zinc ion binding			breast(17)|ovary(3)|central_nervous_system(2)	22						tttctttctttcttttcttcttcttct	0.329			F|N|S		breast		HDR syndrome (HYPOPARATHYROIDISM|SENSORINEURAL DEAFNESS|AND RENAL DISEASE)						6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	34220055	34220056	+	IGR	INS	-	TTCCTTCCTTCC	TTCCTTCCTTCC			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34220055_34220056insTTCCTTCCTTCC								NRP1 (596049 upstream) : PARD3 (180042 downstream)																							AGATAAGTGGAttccttccttc	0.188													4	3	---	---	---	---	
PCDH15	65217	broad.mit.edu	37	10	55721844	55721845	+	Intron	INS	-	T	T	rs145641930	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55721844_55721845insT	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 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)				AATCAATGAAGTATCTCTACTA	0.287										HNSCC(58;0.16)			2	4	---	---	---	---	
SLC16A9	220963	broad.mit.edu	37	10	61444172	61444172	+	Intron	DEL	A	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61444172delA	uc010qig.1	-							NM_194298	NP_919274	Q7RTY1	MOT9_HUMAN	solute carrier family 16 (monocarboxylic acid						urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3						TCCTAAAGTGAAAAAAAAAAA	0.323													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65874223	65874224	+	IGR	INS	-	GTGTGTGTGTGTGT	GTGTGTGTGTGTGT	rs113836467		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65874223_65874224insGTGTGTGTGTGTGT								REEP3 (492252 upstream) : ANXA2P3 (711061 downstream)																							ATCATCGTGGGgtgtgtgtgtg	0.347													4	2	---	---	---	---	
TET1	80312	broad.mit.edu	37	10	70381974	70381989	+	Intron	DEL	CCTTCCCTCCTTCCTC	-	-	rs12777015	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70381974_70381989delCCTTCCCTCCTTCCTC	uc001jok.3	+							NM_030625	NP_085128	Q8NFU7	TET1_HUMAN	CXXC finger 6						DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9						ttccttccttccttccctccttcctcccttccctcc	0.000													4	2	---	---	---	---	
SFXN4	119559	broad.mit.edu	37	10	120914415	120914415	+	Intron	DEL	T	-	-	rs34654417		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120914415delT	uc001leb.2	-						SFXN4_uc001ldy.2_Intron|SFXN4_uc001ldz.2_Intron|SFXN4_uc001lea.2_Intron	NM_213649	NP_998814	Q6P4A7	SFXN4_HUMAN	sideroflexin 4						iron ion homeostasis	integral to membrane|mitochondrial membrane	cation transmembrane transporter activity			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		atgcCCCATCTTATCAGGGGG	0.239													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	6265816	6265821	+	IGR	DEL	ACACAC	-	-	rs72008342		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6265816_6265821delACACAC								CNGA4 (109 upstream) : CCKBR (15145 downstream)																							ACTTACCAGTacacacacacacacac	0.374													4	2	---	---	---	---	
SPON1	10418	broad.mit.edu	37	11	14252331	14252334	+	Intron	DEL	TTCA	-	-	rs62745561		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14252331_14252334delTTCA	uc001mle.2	+							NM_006108	NP_006099	Q9HCB6	SPON1_HUMAN	spondin 1, extracellular matrix protein						cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding				0				Epithelial(150;0.00898)		ccttccttccttcattttttcGTG	0.142													4	2	---	---	---	---	
KIF18A	81930	broad.mit.edu	37	11	28116025	28116025	+	Intron	DEL	A	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28116025delA	uc001msc.2	-							NM_031217	NP_112494	Q8NI77	KI18A_HUMAN	kinesin family member 18A						blood coagulation|microtubule depolymerization|microtubule-based movement|mitotic metaphase plate congression|mitotic prometaphase|protein transport	caveola|cytosol|kinetochore microtubule|microtubule organizing center|nucleus|ruffle	actin binding|ATP binding|microtubule plus-end binding|plus-end-directed microtubule motor activity|tubulin-dependent ATPase activity|ubiquitin binding			ovary(2)	2						ttgccaaagtaaaaaAAAAAA	0.095													4	2	---	---	---	---	
EFCAB4B	84766	broad.mit.edu	37	12	3806236	3806239	+	Intron	DEL	GGTG	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3806236_3806239delGGTG	uc001qmj.2	-						EFCAB4B_uc010sen.1_Intron|EFCAB4B_uc010seo.1_Intron	NM_032680	NP_116069	Q9BSW2	EFC4B_HUMAN	EF-hand calcium binding domain 4B isoform c						activation of store-operated calcium channel activity|store-operated calcium entry	cytoplasm	calcium ion binding|protein binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			AAGTGGGTGTGGTGGGTTGGAGTG	0.480													4	3	---	---	---	---	
C12orf54	121273	broad.mit.edu	37	12	48882278	48882279	+	Intron	INS	-	AC	AC	rs139492148	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48882278_48882279insAC	uc001rrr.2	+						C12orf54_uc009zky.1_Intron	NM_152319	NP_689532	Q6X4T0	CL054_HUMAN	hypothetical protein LOC121273												0						AAAAAAAAAAAGAAAGAAAGAA	0.218													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	30984754	30984755	+	IGR	INS	-	AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA	AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA	rs68107497		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30984754_30984755insAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA								LOC100188949 (36718 upstream) : HMGB1 (48126 downstream)																							aagaaaGAGAGaggaaggaagg	0.084													5	3	---	---	---	---	
FAM155A	728215	broad.mit.edu	37	13	108373458	108373461	+	Intron	DEL	ACAC	-	-	rs146577775		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108373458_108373461delACAC	uc001vql.2	-							NM_001080396	NP_001073865	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1						AGATCTCAATacacacacacacac	0.289													4	2	---	---	---	---	
PSMC1	5700	broad.mit.edu	37	14	90731688	90731688	+	Intron	DEL	A	-	-	rs34260220		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90731688delA	uc001xyf.2	+						PSMC1_uc001xyg.2_Intron|PSMC1_uc001xyh.2_Intron|PSMC1_uc010twh.1_Intron	NM_002802	NP_002793	P62191	PRS4_HUMAN	proteasome 26S ATPase subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding				0		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)		atactgatgGAAAAAAAAAAA	0.065													4	2	---	---	---	---	
CCDC78	124093	broad.mit.edu	37	16	773292	773292	+	Intron	DEL	C	-	-	rs67977308		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:773292delC	uc002cjg.2	-						CCDC78_uc002cjf.2_Intron|CCDC78_uc002cji.3_3'UTR|CCDC78_uc002cjj.3_3'UTR|CCDC78_uc002cjh.2_Intron	NM_001031737	NP_001026907	A2IDD5	CCD78_HUMAN	coiled-coil domain containing 78											central_nervous_system(1)	1		Hepatocellular(780;0.0218)				GAGGCATGGGCCCCCCCCGTG	0.687													4	3	---	---	---	---	
OTOA	146183	broad.mit.edu	37	16	21725687	21725688	+	Intron	DEL	TT	-	-	rs170017		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21725687_21725688delTT	uc002djh.2	+						uc002diq.3_Intron|OTOA_uc010vbj.1_Intron|OTOA_uc002dji.2_Intron|OTOA_uc010vbk.1_Intron	NM_144672	NP_653273	Q7RTW8	OTOAN_HUMAN	otoancorin isoform 1						sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(48;0.0414)		tctctctttctttctctctctt	0.000													3	3	---	---	---	---	
NDRG4	65009	broad.mit.edu	37	16	58543844	58543845	+	Intron	DEL	AC	-	-	rs35165953		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58543844_58543845delAC	uc002eno.2	+						NDRG4_uc002enk.2_Intron|NDRG4_uc002enm.2_Intron|NDRG4_uc010vif.1_Intron|NDRG4_uc010cdk.2_Intron|NDRG4_uc010vig.1_Intron|NDRG4_uc010vih.1_Intron|NDRG4_uc010vii.1_Intron|NDRG4_uc002enp.2_Intron|NDRG4_uc002enq.1_Intron	NM_022910	NP_075061	Q9ULP0	NDRG4_HUMAN	NDRG family member 4 isoform 1						cell differentiation|cell growth|multicellular organismal development|response to stress	cytoplasm				skin(1)	1						acacacacagacacacacacac	0.470													5	4	---	---	---	---	
C16orf70	80262	broad.mit.edu	37	16	67165084	67165084	+	Intron	DEL	T	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67165084delT	uc002erc.2	+						C16orf70_uc002erd.2_Intron|C16orf70_uc002ere.1_Intron	NM_025187	NP_079463	Q9BSU1	CP070_HUMAN	lin-10											ovary(2)	2		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		TTGGTAATAGttttttttttt	0.174													8	4	---	---	---	---	
USP6	9098	broad.mit.edu	37	17	5047791	5047792	+	Intron	INS	-	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5047791_5047792insT	uc002gau.1	+						USP6_uc002gav.1_Intron|USP6_uc010ckz.1_Intron	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6						protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5						AAATACTTCTCTTTTTTTTTTT	0.297			T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								2	4	---	---	---	---	
AOC3	8639	broad.mit.edu	37	17	41006869	41006869	+	Intron	DEL	T	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41006869delT	uc002ibv.2	+							NM_003734	NP_003725	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3 precursor						amine metabolic process|cell adhesion|inflammatory response	cell surface|integral to membrane|plasma membrane	aliphatic-amine oxidase activity|aminoacetone:oxygen oxidoreductase(deaminating) activity|copper ion binding|phenethylamine:oxygen oxidoreductase (deaminating) activity|primary amine oxidase activity|protein homodimerization activity|quinone binding|tryptamine:oxygen oxidoreductase (deaminating) activity			central_nervous_system(2)|ovary(1)|skin(1)	4		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	tttcttttccttttttttttt	0.269													4	2	---	---	---	---	
UBTF	7343	broad.mit.edu	37	17	42284469	42284469	+	3'UTR	DEL	T	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42284469delT	uc002igb.2	-	20					UBTF_uc002igc.2_3'UTR|UBTF_uc010czs.2_3'UTR|UBTF_uc002igd.2_3'UTR|UBTF_uc010czt.2_3'UTR	NM_014233	NP_055048	P17480	UBF1_HUMAN	upstream binding transcription factor, RNA						positive regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm	DNA binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CCCCACCGTATTTTTTTTTTT	0.562													4	2	---	---	---	---	
HOXB7	3217	broad.mit.edu	37	17	46685066	46685066	+	3'UTR	DEL	T	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46685066delT	uc002inv.2	-	2					HOXB6_uc002ins.1_5'Flank|HOXB6_uc010dbh.1_5'Flank	NM_004502	NP_004493	P09629	HXB7_HUMAN	homeobox B7							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						TTAAATAGGGttttttttttg	0.264													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	46754509	46754512	+	IGR	DEL	CCTT	-	-	rs143755906		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46754509_46754512delCCTT								MIR196A1 (44588 upstream) : PRAC (44580 downstream)																							ttccttcctcccttccttccttcc	0.005													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	15005568	15005568	+	IGR	DEL	G	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15005568delG								ANKRD30B (152831 upstream) : LOC644669 (307987 downstream)																							CGTCCCTGGCGGGGGTTGTGT	0.672													4	2	---	---	---	---	
ADAMTSL5	339366	broad.mit.edu	37	19	1509662	1509665	+	Intron	DEL	GAGA	-	-	rs112785977	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1509662_1509665delGAGA	uc002ltd.2	-						ADAMTSL5_uc010dsl.2_Intron|ADAMTSL5_uc010xgq.1_Intron	NM_213604	NP_998769	Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5 precursor							proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gaagggaagggagaaagggaagga	0.250													4	2	---	---	---	---	
IL27RA	9466	broad.mit.edu	37	19	14153066	14153066	+	Intron	DEL	T	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14153066delT	uc002mxx.2	+							NM_004843	NP_004834	Q6UWB1	I27RA_HUMAN	class I cytokine receptor precursor						cell surface receptor linked signaling pathway|immune response	integral to plasma membrane	transmembrane receptor activity				0						taatcccagctactcaggagg	0.000													5	3	---	---	---	---	
ANKRD27	84079	broad.mit.edu	37	19	33132674	33132675	+	Intron	DEL	TT	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33132674_33132675delTT	uc002ntn.1	-						ANKRD27_uc002nto.1_Intron	NM_032139	NP_115515	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)						early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)	5	Esophageal squamous(110;0.137)					TTACTTCTtctttttttttttt	0.163													4	2	---	---	---	---	
LRP3	4037	broad.mit.edu	37	19	33697768	33697768	+	Intron	DEL	G	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33697768delG	uc010edh.2	+						LRP3_uc002nuk.3_Intron	NM_002333	NP_002324	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein						receptor-mediated endocytosis	coated pit|integral to membrane	receptor activity			pancreas(2)|ovary(1)	3	Esophageal squamous(110;0.137)					ATGGCCAGGTGGGGGGGGTGG	0.701													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	44624572	44624595	+	IGR	DEL	TCCTTCCTTCCTTCCTTCCTTCCC	-	-	rs149904626	by1000genomes	TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44624572_44624595delTCCTTCCTTCCTTCCTTCCTTCCC								ZNF335 (23739 upstream) : MMP9 (12952 downstream)																							cttccttccttccttccttccttccttccttccctccttccttc	0.107													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	44756425	44756431	+	IGR	DEL	ACCACCA	-	-			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44756425_44756431delACCACCA								CRYAA (163512 upstream) : SIK1 (77967 downstream)																							caccatcaccaccaccaccaccatcac	0.000													3	4	---	---	---	---	
MYO18B	84700	broad.mit.edu	37	22	26272012	26272013	+	Intron	DEL	TA	-	-	rs56708676		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26272012_26272013delTA	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12						tgtgtgtgtgtatgtgtTTTAA	0.376													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	504749	504750	+	IGR	INS	-	CCTT	CCTT			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:504749_504750insCCTT								PPP2R3B (157122 upstream) : SHOX (80329 downstream)																							ttccttccttcccttcctccct	0.059													4	2	---	---	---	---	
DYNLT3	6990	broad.mit.edu	37	X	37699977	37699978	+	Intron	DEL	AC	-	-	rs111598091		TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37699977_37699978delAC	uc004dds.2	-							NM_006520	NP_006511	P51808	DYLT3_HUMAN	dynein, light chain, Tctex-type 3						cell division|mitosis|regulation of mitotic cell cycle|transport	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|nucleus|plasma membrane	motor activity				0						ATATATATATacacacacacac	0.158													5	4	---	---	---	---	
GNL3L	54552	broad.mit.edu	37	X	54585146	54585147	+	Intron	INS	-	T	T			TCGA-CJ-4904-01A-02D-1429-08	TCGA-CJ-4904-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54585146_54585147insT	uc004dth.1	+						GNL3L_uc004dti.2_Intron	NM_019067	NP_061940	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3						ribosome biogenesis	nucleolus	GTP binding			ovary(1)	1						ATCTTTTTTTGTTTTTTTTTTC	0.262													5	3	---	---	---	---	
