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
MTOR	2475	broad.mit.edu	37	1	11188078	11188078	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11188078C>G	uc001asd.2	-	43	6137	c.6016G>C	c.(6016-6018)GTC>CTC	p.V2006L	MTOR_uc001asc.2_Missense_Mutation_p.V211L	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	2006					cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						GCCTGCTGGACCAGGGTGTTG	0.552													71	111	---	---	---	---	PASS
MTOR	2475	broad.mit.edu	37	1	11188100	11188100	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11188100C>G	uc001asd.2	-	43	6115	c.5994G>C	c.(5992-5994)ATG>ATC	p.M1998I	MTOR_uc001asc.2_Missense_Mutation_p.M203I	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	1998					cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						TGTGCTCACACATGTTCTTCA	0.562													17	213	---	---	---	---	PASS
PRAMEF17	391004	broad.mit.edu	37	1	13716890	13716890	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13716890C>T	uc009vnz.1	+	2	407	c.377C>T	c.(376-378)CCA>CTA	p.P126L		NM_001099851	NP_001093321	Q5VTA0	PRA17_HUMAN	PRAME family member 17	126											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;9.86e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|COAD - Colon adenocarcinoma(227;0.000502)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TCCTGCTCCCCAGAGGCCATG	0.527													4	198	---	---	---	---	PASS
AGMAT	79814	broad.mit.edu	37	1	15906637	15906637	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15906637C>T	uc001awv.1	-	3	619	c.476G>A	c.(475-477)GGT>GAT	p.G159D	DNAJC16_uc001awu.2_Intron	NM_024758	NP_079034	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase) precursor	159					putrescine biosynthetic process|spermidine biosynthetic process	mitochondrion	agmatinase activity|metal ion binding			skin(1)	1		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		GTGATCTCCACCTGCAAAGAG	0.328													5	402	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16945570	16945570	+	RNA	SNP	A	G	G	rs28552760	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16945570A>G	uc010ocf.1	-	4		c.587T>C			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						TGACAGCGCCATCTTCTCAGA	0.622													7	115	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974549	16974549	+	RNA	SNP	C	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974549C>G	uc009vow.2	+	5		c.1359C>G			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_RNA|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						GGGCTGAGTGCAGCGCCTGCT	0.692													5	101	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16975495	16975495	+	RNA	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16975495T>C	uc010och.1	+	9		c.1776T>C			MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						CTTGCGGAATTGGTGAGGCAC	0.612													6	31	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19407977	19407977	+	Silent	SNP	G	A	A	rs138176260		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19407977G>A	uc001bbi.2	-	103	15103	c.15099C>T	c.(15097-15099)GAC>GAT	p.D5033D	UBR4_uc001bbf.2_Translation_Start_Site|UBR4_uc010ocv.1_Silent_p.D556D|UBR4_uc009vph.2_Silent_p.D667D|UBR4_uc010ocw.1_Silent_p.D697D|UBR4_uc001bbg.2_Silent_p.D744D|UBR4_uc001bbh.2_Silent_p.D742D	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	5033					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AGTAGGGCCCGTCCACTTCAA	0.552													56	132	---	---	---	---	PASS
SRRM1	10250	broad.mit.edu	37	1	24993365	24993365	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24993365C>T	uc001bjm.2	+	13	1912	c.1688C>T	c.(1687-1689)CCC>CTC	p.P563L	SRRM1_uc010oel.1_Missense_Mutation_p.P575L|SRRM1_uc009vrh.1_Missense_Mutation_p.P536L|SRRM1_uc009vri.1_Missense_Mutation_p.P492L|SRRM1_uc010oem.1_RNA	NM_005839	NP_005830	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	563	Pro-rich.|Necessary for speckles and matrix localization.|Arg-rich.|Ser-rich.				mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nuclear matrix|nuclear speck	DNA binding|protein binding|RNA binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		TCTCCTTCTCCCGCCCCTCCT	0.522													17	34	---	---	---	---	PASS
GJA9	81025	broad.mit.edu	37	1	39341703	39341703	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39341703T>C	uc001cct.1	-	2	349	c.68A>G	c.(67-69)AAG>AGG	p.K23R	RRAGC_uc001ccr.2_5'Flank|MYCBP_uc001ccs.2_5'Flank	NM_030772	NP_110399	P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	23	Helical; (Potential).				cell communication	connexon complex|integral to membrane					0	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			GAGCCAGATCTTTCCAATCAT	0.458													4	90	---	---	---	---	PASS
ZMPSTE24	10269	broad.mit.edu	37	1	40735718	40735718	+	Silent	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40735718T>C	uc001cfg.2	+	5	757	c.546T>C	c.(544-546)TCT>TCC	p.S182S		NM_005857	NP_005848	O75844	FACE1_HUMAN	zinc metallopeptidase STE24	182	Helical; (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane	metal ion binding|metalloexopeptidase activity				0	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			TGCCTGTGTCTTCACTTCTAC	0.333													7	656	---	---	---	---	PASS
MMACHC	25974	broad.mit.edu	37	1	45974519	45974519	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45974519C>T	uc009vxv.2	+	4	630	c.481C>T	c.(481-483)CGA>TGA	p.R161*	MMACHC_uc001cny.2_RNA	NM_015506	NP_056321	Q9Y4U1	MMAC_HUMAN	methylmalonic aciduria (cobalamin deficiency)	161			R -> Q (in MMACHC).|R -> G (in MMACHC).				cobalamin binding				0	Acute lymphoblastic leukemia(166;0.155)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTTTGCCATCCGAGGGGTAGT	0.572													4	169	---	---	---	---	PASS
ATPAF1	64756	broad.mit.edu	37	1	47124388	47124388	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47124388A>G	uc001cqh.2	-	3	502	c.397T>C	c.(397-399)TCT>CCT	p.S133P	ATPAF1_uc001cqg.2_5'UTR|ATPAF1_uc009vyk.2_5'UTR|ATPAF1_uc010omg.1_Missense_Mutation_p.S45P|ATPAF1_uc001cqi.2_Missense_Mutation_p.S133P|KIAA0494_uc010omh.1_Silent_p.S417S	NM_022745	NP_073582	Q5TC12	ATPF1_HUMAN	ATP synthase mitochondrial F1 complex assembly	133					protein complex assembly	mitochondrion	protein binding				0	Acute lymphoblastic leukemia(166;0.155)					CTGTTCACAGACTGTTTCCCC	0.353													5	221	---	---	---	---	PASS
CYP4X1	260293	broad.mit.edu	37	1	47512217	47512217	+	Silent	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47512217T>C	uc001cqt.2	+	9	1402	c.1152T>C	c.(1150-1152)ATT>ATC	p.I384I	CYP4X1_uc001cqr.2_Silent_p.I383I|CYP4X1_uc001cqs.2_Silent_p.I319I	NM_178033	NP_828847	Q8N118	CP4X1_HUMAN	cytochrome P450, family 4, subfamily X,	384						endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)|skin(1)	2						TCCCGTCCATTTCCAGAGATC	0.512													5	274	---	---	---	---	PASS
ZYG11B	79699	broad.mit.edu	37	1	53287358	53287358	+	3'UTR	SNP	T	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53287358T>G	uc001cuj.2	+	14					ZYG11B_uc010onj.1_3'UTR|ZYG11B_uc009vzh.2_3'UTR	NM_024646	NP_078922	Q9C0D3	ZY11B_HUMAN	zyg-11 homolog B								protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4						TTGGTCCATTTGGAATATCTT	0.413													7	40	---	---	---	---	PASS
RPL5	6125	broad.mit.edu	37	1	93298416	93298416	+	Intron	SNP	T	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93298416T>G	uc001doz.2	+						RPL5_uc001dpa.2_Intron|RPL5_uc001dpb.2_5'UTR	NM_000969	NP_000960	P46777	RL5_HUMAN	ribosomal protein L5						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	5S rRNA binding|protein binding|structural constituent of ribosome				0		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)		TTGTGGCAGGTAATTTAGGCT	0.448													6	9	---	---	---	---	PASS
DENND2D	79961	broad.mit.edu	37	1	111730264	111730264	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111730264T>C	uc001eak.1	-	12	1579	c.1379A>G	c.(1378-1380)AAG>AGG	p.K460R	DENND2D_uc001eal.1_Missense_Mutation_p.K457R	NM_024901	NP_079177	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	460										ovary(1)	1		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		CTTCTGTTTCTTCTGTTCCTC	0.413													7	742	---	---	---	---	PASS
NRAS	4893	broad.mit.edu	37	1	115251227	115251227	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115251227G>A	uc009wgu.2	-	5	753	c.499C>T	c.(499-501)CGA>TGA	p.R167*	NRAS_uc001efh.3_Nonsense_Mutation_p.R57*	NM_002524	NP_002515	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	167	Hypervariable region.				activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity			haematopoietic_and_lymphoid_tissue(1008)|skin(956)|thyroid(334)|large_intestine(62)|NS(60)|soft_tissue(32)|lung(31)|upper_aerodigestive_tract(25)|urinary_tract(12)|liver(10)|adrenal_gland(9)|autonomic_ganglia(8)|testis(8)|central_nervous_system(8)|prostate(8)|breast(7)|biliary_tract(6)|ovary(6)|stomach(5)|pancreas(5)|endometrium(2)|kidney(2)|cervix(2)|eye(1)	2607	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTTTCATTCGGTACTGGCGT	0.403		50	Mis		melanoma|MM|AML|thyroid				Noonan_syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)			5	632	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142806254	142806254	+	Intron	SNP	A	G	G	rs114813183	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142806254A>G	uc001eiw.1	+						uc001ejb.2_Intron|uc001ejd.1_Intron|uc001ejc.2_RNA					Homo sapiens PNAS-130 mRNA, complete cds.																		CATTTTGCATAAACTGTGTGT	0.353													65	524	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144618201	144618201	+	Missense_Mutation	SNP	T	C	C	rs61809737		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144618201T>C	uc009wig.1	+	6	474	c.398T>C	c.(397-399)CTG>CCG	p.L133P	NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Missense_Mutation_p.L64P|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Missense_Mutation_p.L64P|NBPF9_uc010oyg.1_Missense_Mutation_p.L98P|NBPF9_uc009wii.1_5'UTR	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	133						cytoplasm					0						CTCCTCACTCTGGATGAGCCG	0.567													38	60	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144621522	144621522	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144621522A>C	uc009wig.1	+	9	930	c.854A>C	c.(853-855)GAG>GCG	p.E285A	NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Missense_Mutation_p.E285A|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Missense_Mutation_p.E216A|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Missense_Mutation_p.E216A|NBPF9_uc010oyg.1_Missense_Mutation_p.E250A|NBPF9_uc009wii.1_Missense_Mutation_p.E14A	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	285						cytoplasm					0						GAGAAGGCAGAGATGAACATT	0.488													5	117	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144621526	144621526	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144621526G>A	uc009wig.1	+	9	934	c.858G>A	c.(856-858)ATG>ATA	p.M286I	NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Missense_Mutation_p.M286I|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Missense_Mutation_p.M217I|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Missense_Mutation_p.M217I|NBPF9_uc010oyg.1_Missense_Mutation_p.M251I|NBPF9_uc009wii.1_Missense_Mutation_p.M15I	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	286						cytoplasm					0						AGGCAGAGATGAACATTCTAG	0.502													5	123	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144815953	144815953	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144815953A>G	uc009wig.1	+	12	1400	c.1324A>G	c.(1324-1326)AAT>GAT	p.N442D	NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Missense_Mutation_p.N442D|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF9_uc009wii.1_Missense_Mutation_p.N171D|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|NBPF9_uc001elp.2_Missense_Mutation_p.N102D	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	442	NBPF 2.					cytoplasm					0						CAACGATGACAATGAAGATGT	0.423													24	245	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144815968	144815968	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144815968G>A	uc009wig.1	+	12	1415	c.1339G>A	c.(1339-1341)GTT>ATT	p.V447I	NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Missense_Mutation_p.V447I|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF9_uc009wii.1_Missense_Mutation_p.V176I|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|NBPF9_uc001elp.2_Missense_Mutation_p.V107I	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	447	NBPF 2.					cytoplasm					0						AGATGTTCAAGTTGAGGTGGC	0.423													21	227	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144828583	144828583	+	Silent	SNP	G	A	A	rs28712116	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144828583G>A	uc009wig.1	+	23	2704	c.2628G>A	c.(2626-2628)TTG>TTA	p.L876L	NBPF9_uc010oxn.1_Silent_p.L774L|NBPF9_uc010oxo.1_Silent_p.L801L|NBPF9_uc010oxr.1_Silent_p.L903L|NBPF9_uc010oxt.1_Silent_p.L691L|NBPF9_uc001ekg.1_Silent_p.L203L|NBPF9_uc001ekk.1_Silent_p.L447L|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Silent_p.L203L|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|NBPF9_uc001elp.2_Silent_p.L536L|uc001elr.3_5'Flank	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	876	NBPF 7.					cytoplasm					0						CTGAAGTCTTGCAGGACTCAC	0.468													18	327	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144828683	144828683	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144828683C>G	uc009wig.1	+	23	2804	c.2728C>G	c.(2728-2730)CAG>GAG	p.Q910E	NBPF9_uc010oxn.1_Missense_Mutation_p.Q808E|NBPF9_uc010oxo.1_Missense_Mutation_p.Q835E|NBPF9_uc010oxr.1_Missense_Mutation_p.Q937E|NBPF9_uc010oxt.1_Missense_Mutation_p.Q725E|NBPF9_uc001ekg.1_Missense_Mutation_p.Q237E|NBPF9_uc001ekk.1_Missense_Mutation_p.Q481E|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Missense_Mutation_p.Q237E|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|NBPF9_uc001elp.2_Missense_Mutation_p.Q570E|uc001elr.3_5'Flank	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	910	NBPF 7.					cytoplasm					0						ATTTGAGGAACAGCACATCAG	0.438													8	384	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144828688	144828688	+	Silent	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144828688C>T	uc009wig.1	+	23	2809	c.2733C>T	c.(2731-2733)CAC>CAT	p.H911H	NBPF9_uc010oxn.1_Silent_p.H809H|NBPF9_uc010oxo.1_Silent_p.H836H|NBPF9_uc010oxr.1_Silent_p.H938H|NBPF9_uc010oxt.1_Silent_p.H726H|NBPF9_uc001ekg.1_Silent_p.H238H|NBPF9_uc001ekk.1_Silent_p.H482H|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Silent_p.H238H|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|NBPF9_uc001elp.2_Silent_p.H571H|uc001elr.3_5'Flank	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	911	NBPF 7.					cytoplasm					0						AGGAACAGCACATCAGCTTCG	0.433													8	383	---	---	---	---	PASS
NBPF9	400818	broad.mit.edu	37	1	144828807	144828807	+	3'UTR	SNP	A	G	G	rs76022554		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144828807A>G	uc009wig.1	+	23					NBPF9_uc010oxn.1_3'UTR|NBPF9_uc010oxo.1_3'UTR|NBPF9_uc010oxr.1_3'UTR|NBPF9_uc010oxt.1_3'UTR|NBPF9_uc001ekg.1_3'UTR|NBPF9_uc001ekk.1_3'UTR|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_3'UTR|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|NBPF9_uc001elp.2_3'UTR|uc001elr.3_5'Flank	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818							cytoplasm					0						AAGCCGAGAGATGTCATTCCT	0.473													11	189	---	---	---	---	PASS
SEC22B	9554	broad.mit.edu	37	1	145115858	145115858	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145115858T>C	uc001eml.1	+	7	757	c.617T>C	c.(616-618)TTA>TCA	p.L206S	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron	NM_004892	NP_004883	O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B	206	Helical; Anchor for type IV membrane protein; (Potential).				ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane|melanosome	protein binding				0						TTCATCATGTTAATAGTGTAT	0.418													33	458	---	---	---	---	PASS
BCL9	607	broad.mit.edu	37	1	147091273	147091273	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147091273G>A	uc001epq.2	+	8	2052	c.1312G>A	c.(1312-1314)GTA>ATA	p.V438I	BCL9_uc010ozr.1_Missense_Mutation_p.V364I	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	438	Pro-rich.				Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)					ACATAGAGATGTACCCTTTTC	0.547			T	IGH@|IGL@	B-ALL								3	41	---	---	---	---	PASS
NBPF14	25832	broad.mit.edu	37	1	148004472	148004472	+	3'UTR	SNP	G	A	A	rs3961381		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148004472G>A	uc001eqq.2	-	22					LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqf.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron|NBPF14_uc010pab.1_3'UTR|NBPF14_uc010pac.1_3'UTR	NM_015383	NP_056198	Q5TI25	NBPFE_HUMAN	hypothetical protein LOC25832							cytoplasm				ovary(1)	1	all_hematologic(923;0.032)					AAATGGAACTGTACTTTCATT	0.488													5	96	---	---	---	---	PASS
NBPF14	25832	broad.mit.edu	37	1	148004475	148004475	+	3'UTR	SNP	C	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148004475C>G	uc001eqq.2	-	22					LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqf.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron|NBPF14_uc010pab.1_3'UTR|NBPF14_uc010pac.1_3'UTR	NM_015383	NP_056198	Q5TI25	NBPFE_HUMAN	hypothetical protein LOC25832							cytoplasm				ovary(1)	1	all_hematologic(923;0.032)					TGGAACTGTACTTTCATTCAA	0.493													10	97	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	148891580	148891580	+	RNA	SNP	A	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148891580A>T	uc009wkv.1	+	9		c.882A>T								Homo sapiens cDNA, FLJ17483.																		GAATCAGGGAAGACTCAGTTA	0.358													126	464	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	148891643	148891643	+	RNA	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148891643A>G	uc009wkv.1	+	9		c.945A>G								Homo sapiens cDNA, FLJ17483.																		CCAAAACTGAAATTGAAGATT	0.423													174	522	---	---	---	---	PASS
FCGR1A	2209	broad.mit.edu	37	1	149763191	149763191	+	3'UTR	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149763191G>A	uc001esp.3	+	6					HIST2H2BF_uc010pbj.1_Intron|FCGR1A_uc009wlg.2_RNA	NM_000566	NP_000557	P12314	FCGR1_HUMAN	Fc fragment of IgG, high affinity Ia, receptor						interferon-gamma-mediated signaling pathway|phagocytosis, engulfment	integral to membrane|plasma membrane	IgG binding|receptor activity|receptor signaling protein activity			ovary(1)	1	Breast(34;0.0124)|all_hematologic(923;0.127)				Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Methyl aminolevulinate(DB00992)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Porfimer(DB00707)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CTCATGGTATGTAACTCTTAA	0.438													3	35	---	---	---	---	PASS
FLG2	388698	broad.mit.edu	37	1	152330075	152330075	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152330075G>A	uc001ezw.3	-	3	260	c.187C>T	c.(187-189)CGA>TGA	p.R63*	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	63	S-100-like (By similarity).|EF-hand 2.|Potential.						calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCATGATCTCGATCCAGCATA	0.448													25	239	---	---	---	---	PASS
CD247	919	broad.mit.edu	37	1	167404498	167404498	+	Intron	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167404498C>T	uc001gei.3	-						CD247_uc001gej.3_Intron|CD247_uc001gek.2_Silent_p.P158P	NM_198053	NP_932170	P20963	CD3Z_HUMAN	T-cell receptor zeta chain isoform 1 precursor						interspecies interaction between organisms|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytoplasm|integral to membrane	protein homodimerization activity|transmembrane receptor activity				0			LUSC - Lung squamous cell carcinoma(543;0.236)			gcccttcctccggagccctcc	0.095													8	36	---	---	---	---	PASS
C1orf49	84066	broad.mit.edu	37	1	178492550	178492550	+	3'UTR	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178492550A>G	uc001glw.1	+	9					C1orf49_uc001glv.1_Intron	NM_032126	NP_115502	Q5T0J7	CA049_HUMAN	hypothetical protein LOC84066							microtubule cytoskeleton					0						attcccaccaacagtgtacaa	0.109													5	46	---	---	---	---	PASS
CACNA1S	779	broad.mit.edu	37	1	201036117	201036117	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201036117G>A	uc001gvv.2	-	20	2782	c.2555C>T	c.(2554-2556)ACG>ATG	p.T852M		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	852	III.|Helical; Name=S2 of repeat III; (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	TCCGTAGGTCGTCATCTGGGG	0.582													13	113	---	---	---	---	PASS
PTPN14	5784	broad.mit.edu	37	1	214656164	214656164	+	Intron	SNP	A	G	G	rs58782956		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214656164A>G	uc001hkk.1	-						PTPN14_uc010pty.1_Intron|uc010ptz.1_RNA	NM_005401	NP_005392	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		TTAAAAGAGGACAGGTTTGGC	0.388													16	146	---	---	---	---	PASS
HHIPL2	79802	broad.mit.edu	37	1	222705449	222705449	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222705449G>T	uc001hnh.1	-	6	1640	c.1582C>A	c.(1582-1584)CTT>ATT	p.L528I		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2 precursor	528					carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0185)		AAAGCCATAAGTCGACTAGAC	0.438													30	112	---	---	---	---	PASS
ABCB10	23456	broad.mit.edu	37	1	229654001	229654001	+	Silent	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229654001T>C	uc001htp.3	-	13	2185	c.2142A>G	c.(2140-2142)AAA>AAG	p.K714K		NM_012089	NP_036221	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B, member 10	714	Mitochondrial intermembrane (Potential).|ABC transporter.|Mitochondrial matrix (Potential).					integral to mitochondrial membrane|mitochondrial inner membrane	ATP binding|oligopeptide-transporting ATPase activity			breast(2)	2	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				GCTCTTCATGTTTTCCATATT	0.343													6	439	---	---	---	---	PASS
ZP4	57829	broad.mit.edu	37	1	238045723	238045723	+	Nonstop_Mutation	SNP	T	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238045723T>A	uc001hym.2	-	12	1622	c.1622A>T	c.(1621-1623)TAA>TTA	p.*541L	LOC100130331_uc010pyc.1_Intron	NM_021186	NP_067009	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4 preproprotein	541					acrosomal vesicle exocytosis|negative regulation of binding of sperm to zona pellucida|positive regulation of acrosome reaction|positive regulation of humoral immune response|positive regulation of protein kinase activity|positive regulation of T cell proliferation|protein kinase A signaling cascade|protein kinase C signaling cascade	integral to membrane|intracellular|plasma membrane|proteinaceous extracellular matrix	acrosin binding|receptor activity			ovary(2)|skin(1)	3	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			ACTCTGGTTTTATTGACACAT	0.428													101	224	---	---	---	---	PASS
OR2M1P	388762	broad.mit.edu	37	1	248285997	248285997	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248285997G>C	uc001idy.1	+	1	560	c.560G>C	c.(559-561)GGT>GCT	p.G187A		NR_002141				RecName: Full=Olfactory receptor 2M5;												0						TATGGAGCAGGTTTGTTCATG	0.517													6	231	---	---	---	---	PASS
PUM2	23369	broad.mit.edu	37	2	20451396	20451396	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20451396T>A	uc002rds.1	-	20	3168	c.3145A>T	c.(3145-3147)AAT>TAT	p.N1049Y	PUM2_uc002rdq.1_Missense_Mutation_p.N428Y|PUM2_uc002rdt.1_Missense_Mutation_p.N1049Y|PUM2_uc002rdr.2_Missense_Mutation_p.N909Y|PUM2_uc010yjy.1_Missense_Mutation_p.N970Y|PUM2_uc002rdu.1_Missense_Mutation_p.N1049Y|PUM2_uc010yjz.1_Missense_Mutation_p.N988Y	NM_015317	NP_056132	Q8TB72	PUM2_HUMAN	pumilio homolog 2	1051					regulation of translation	perinuclear region of cytoplasm|stress granule	protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCGGGCTATTCTTCAAATAA	0.373													121	594	---	---	---	---	PASS
PUM2	23369	broad.mit.edu	37	2	20451397	20451397	+	Silent	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20451397C>T	uc002rds.1	-	20	3167	c.3144G>A	c.(3142-3144)AAG>AAA	p.K1048K	PUM2_uc002rdq.1_Silent_p.K427K|PUM2_uc002rdt.1_Silent_p.K1048K|PUM2_uc002rdr.2_Silent_p.K908K|PUM2_uc010yjy.1_Silent_p.K969K|PUM2_uc002rdu.1_Silent_p.K1048K|PUM2_uc010yjz.1_Silent_p.K987K	NM_015317	NP_056132	Q8TB72	PUM2_HUMAN	pumilio homolog 2	1050					regulation of translation	perinuclear region of cytoplasm|stress granule	protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCGGGCTATTCTTCAAATAAT	0.378													121	593	---	---	---	---	PASS
LTBP1	4052	broad.mit.edu	37	2	33526653	33526653	+	Silent	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33526653T>C	uc002ros.2	+	22	3426	c.3426T>C	c.(3424-3426)TCT>TCC	p.S1142S	LTBP1_uc002rot.2_Silent_p.S816S|LTBP1_uc002rou.2_Silent_p.S815S|LTBP1_uc002rov.2_Silent_p.S762S|LTBP1_uc010ymz.1_Silent_p.S815S|LTBP1_uc010yna.1_Silent_p.S762S|LTBP1_uc010ynb.1_Silent_p.S81S	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	1141	EGF-like 10; calcium-binding (Potential).				negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				CTGAGGGCTCTTTTCAATGTG	0.428													6	385	---	---	---	---	PASS
DHX57	90957	broad.mit.edu	37	2	39085938	39085938	+	Silent	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39085938G>A	uc002rrf.2	-	6	1551	c.1452C>T	c.(1450-1452)GAC>GAT	p.D484D	DHX57_uc002rre.2_Translation_Start_Site|DHX57_uc002rrg.2_Silent_p.D484D	NM_198963	NP_945314	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	484							ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)				GTGCAGGACCGTCATCCTCAT	0.378													4	279	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61416094	61416094	+	Silent	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61416094T>C	uc002sbe.2	-	79	10006	c.9984A>G	c.(9982-9984)CAA>CAG	p.Q3328Q	USP34_uc002sbd.2_Silent_p.Q130Q	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	3328					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			AGTTTCTCTGTTGCAGACAAG	0.433													7	697	---	---	---	---	PASS
MPHOSPH10	10199	broad.mit.edu	37	2	71360677	71360677	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71360677G>T	uc002sht.1	+	2	1091	c.739G>T	c.(739-741)GGG>TGG	p.G247W	MPHOSPH10_uc010feb.1_Missense_Mutation_p.G247W	NM_005791	NP_005782	O00566	MPP10_HUMAN	M-phase phosphoprotein 10	247					RNA splicing, via transesterification reactions|rRNA processing	chromosome|nucleolus|small nucleolar ribonucleoprotein complex	protein binding			skin(2)|ovary(1)	3						TGAAGATGAAGGGGGACTGTT	0.333													21	189	---	---	---	---	PASS
VAMP8	8673	broad.mit.edu	37	2	85809036	85809036	+	3'UTR	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85809036A>G	uc002spt.3	+	3					VAMP5_uc002spu.1_5'Flank	NM_003761	NP_003752	Q9BV40	VAMP8_HUMAN	vesicle-associated membrane protein 8						post-Golgi vesicle-mediated transport	early endosome|integral to membrane|membrane fraction|plasma membrane|secretory granule membrane					0						AAAAAGAGAGATGGACTGTGG	0.562													3	11	---	---	---	---	PASS
FLJ40330	645784	broad.mit.edu	37	2	89100619	89100619	+	RNA	SNP	C	T	T	rs75347118		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89100619C>T	uc010fhg.2	+	13		c.1059C>T			FLJ40330_uc010fhh.2_RNA|FLJ40330_uc010fhi.1_RNA	NR_015424				Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						TCAACAGCAACTGGATGATGC	0.303													19	116	---	---	---	---	PASS
FLJ40330	645784	broad.mit.edu	37	2	89102230	89102230	+	Intron	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89102230G>T	uc010fhg.2	+						FLJ40330_uc010fhh.2_RNA|FLJ40330_uc010fhi.1_Intron	NR_015424				Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0						ATAACATCAGGTAGCTGTGAG	0.318													7	160	---	---	---	---	PASS
ANKRD36B	57730	broad.mit.edu	37	2	98201858	98201858	+	Silent	SNP	A	G	G	rs2442304		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98201858A>G	uc010yvc.1	-	2	445	c.165T>C	c.(163-165)ACT>ACC	p.T55T	ANKRD36B_uc010yve.1_RNA|ANKRD36B_uc010fif.2_RNA	NM_025190	NP_079466	Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B	55	ANK 2.										0						AATGTAGGGCAGTCCTGTGAG	0.428													7	120	---	---	---	---	PASS
RGPD3	653489	broad.mit.edu	37	2	107040985	107040985	+	Silent	SNP	T	C	C	rs140856347	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107040985T>C	uc010ywi.1	-	20	3495	c.3438A>G	c.(3436-3438)CGA>CGG	p.R1146R		NM_001144013	NP_001137485	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	1146	RanBD1 1.				intracellular transport		binding			ovary(1)	1						TTGCTGCCAATCGCTCTAGTT	0.463													8	67	---	---	---	---	PASS
RGPD4	285190	broad.mit.edu	37	2	108487877	108487877	+	Silent	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108487877T>C	uc010ywk.1	+	20	3499	c.3417T>C	c.(3415-3417)GAT>GAC	p.D1139D	RGPD4_uc002tdu.2_Silent_p.D326D|RGPD4_uc010ywl.1_RNA	NM_182588	NP_872394	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1139	RanBD1 1.				intracellular transport		binding			skin(2)	2						ATTTCTCTGATGGTGATGCCA	0.438													7	79	---	---	---	---	PASS
LIMS1	3987	broad.mit.edu	37	2	109293101	109293101	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109293101C>T	uc002teg.2	+	7	804	c.685C>T	c.(685-687)CAT>TAT	p.H229Y	LIMS1_uc002tef.2_Missense_Mutation_p.H241Y|LIMS1_uc002teh.2_Missense_Mutation_p.H229Y|LIMS1_uc002tei.2_Missense_Mutation_p.H229Y|LIMS1_uc002tej.2_Missense_Mutation_p.H266Y|LIMS1_uc002tek.3_Missense_Mutation_p.H291Y	NM_004987	NP_004978	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1	229	LIM zinc-binding 4.				cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0						CTTTCTTGGACATCGCCATTA	0.348													28	237	---	---	---	---	PASS
KIF5C	3800	broad.mit.edu	37	2	149861937	149861937	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149861937C>T	uc010zbu.1	+	22	2772	c.2404C>T	c.(2404-2406)CGG>TGG	p.R802W	KIF5C_uc002tws.1_RNA|KIF5C_uc002twu.1_Missense_Mutation_p.R84W	NM_004522	NP_004513	O60282	KIF5C_HUMAN	kinesin family member 5C	802					microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)		GCACAACCTTCGGAAACTCTT	0.418													26	337	---	---	---	---	PASS
COBLL1	22837	broad.mit.edu	37	2	165584536	165584536	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165584536T>C	uc010zcw.1	-	6	887	c.763A>G	c.(763-765)ACA>GCA	p.T255A	COBLL1_uc002ucp.2_Missense_Mutation_p.T202A|COBLL1_uc002ucq.2_Missense_Mutation_p.T202A|COBLL1_uc010zcx.1_Missense_Mutation_p.T248A|COBLL1_uc002ucs.1_RNA	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	240										ovary(2)|pancreas(1)	3						AGAGATTTTGTCAAGTCAAGA	0.363													6	365	---	---	---	---	PASS
HOXD3	3232	broad.mit.edu	37	2	177033940	177033940	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177033940G>C	uc002ukt.1	+	2	274	c.98G>C	c.(97-99)GGC>GCC	p.G33A		NM_006898	NP_008829	P31249	HXD3_HUMAN	homeobox D3	33					anterior/posterior pattern formation|cartilage development|cell-matrix adhesion|embryonic skeletal system morphogenesis|Notch signaling pathway|positive regulation of gene expression|positive regulation of neuron differentiation|thyroid gland development		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)		GGAGGCTATGGCTACAGCAAA	0.552													46	110	---	---	---	---	PASS
HOXD3	3232	broad.mit.edu	37	2	177033941	177033941	+	Silent	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177033941C>T	uc002ukt.1	+	2	275	c.99C>T	c.(97-99)GGC>GGT	p.G33G		NM_006898	NP_008829	P31249	HXD3_HUMAN	homeobox D3	33					anterior/posterior pattern formation|cartilage development|cell-matrix adhesion|embryonic skeletal system morphogenesis|Notch signaling pathway|positive regulation of gene expression|positive regulation of neuron differentiation|thyroid gland development		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)		GAGGCTATGGCTACAGCAAAA	0.557													46	108	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179394839	179394839	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179394839A>G	uc010zfg.1	-	308	98899	c.98675T>C	c.(98674-98676)ATT>ACT	p.I32892T	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.I26587T|TTN_uc010zfi.1_Missense_Mutation_p.I26520T|TTN_uc010zfj.1_Missense_Mutation_p.I26395T|TTN_uc002umq.2_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	33819							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCCTTGTGTAATGGCCTGTAG	0.308													7	473	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179437576	179437576	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179437576A>G	uc010zfg.1	-	275	65803	c.65579T>C	c.(65578-65580)ATT>ACT	p.I21860T	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.I15555T|TTN_uc010zfi.1_Missense_Mutation_p.I15488T|TTN_uc010zfj.1_Missense_Mutation_p.I15363T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	22787							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATCCAGTTCAATTTCTGGAGG	0.498													25	282	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179449638	179449638	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179449638C>T	uc010zfg.1	-	259	57250	c.57026G>A	c.(57025-57027)TGC>TAC	p.C19009Y	uc002umo.2_RNA|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.C12704Y|TTN_uc010zfi.1_Missense_Mutation_p.C12637Y|TTN_uc010zfj.1_Missense_Mutation_p.C12512Y	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	19936							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGACAGGGAGCAAGCATCAGC	0.498													29	35	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179583621	179583621	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179583621T>A	uc010zfg.1	-	81	20798	c.20574A>T	c.(20572-20574)AGA>AGT	p.R6858S	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.R3519S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	7785							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAGGGGTGCCTCTGATGACAC	0.488													8	332	---	---	---	---	PASS
TMEM169	92691	broad.mit.edu	37	2	216960605	216960605	+	5'UTR	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216960605A>G	uc010zjr.1	+	3					TMEM169_uc010zjs.1_5'UTR|TMEM169_uc002vfw.2_5'UTR|TMEM169_uc002vfv.3_5'UTR	NM_001142310	NP_001135782	Q96HH4	TM169_HUMAN	transmembrane protein 169							integral to membrane				ovary(1)	1		Renal(323;0.0651)		Epithelial(149;6.44e-06)|all cancers(144;0.000398)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCATCTAGGAAGAAGTTCTGT	0.453													4	31	---	---	---	---	PASS
OBSL1	23363	broad.mit.edu	37	2	220428159	220428159	+	Silent	SNP	C	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220428159C>A	uc010fwk.2	-	7	2655	c.2598G>T	c.(2596-2598)CTG>CTT	p.L866L	OBSL1_uc010zli.1_5'Flank|OBSL1_uc010fwl.1_Silent_p.L341L|OBSL1_uc002vmi.2_Silent_p.L866L|OBSL1_uc002vmj.2_Silent_p.L453L	NM_015311	NP_056126	O75147	OBSL1_HUMAN	obscurin-like 1	866	Ig-like 6.				cardiac myofibril assembly	intercalated disc|M band|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity				0		Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		GGGTGGCGGGCAGCACCAGGC	0.657													15	43	---	---	---	---	PASS
PSMD1	5707	broad.mit.edu	37	2	231927232	231927232	+	Silent	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231927232C>T	uc002vrn.1	+	4	278	c.147C>T	c.(145-147)TAC>TAT	p.Y49Y	PSMD1_uc002vrm.1_Silent_p.Y49Y|PSMD1_uc010fxu.1_Intron	NM_002807	NP_002798	Q99460	PSMD1_HUMAN	proteasome 26S non-ATPase subunit 1	49					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|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding			ovary(1)|skin(1)	2		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)	AGGTTTTATACGAAGATGAAG	0.398													5	459	---	---	---	---	PASS
RBM44	375316	broad.mit.edu	37	2	238733023	238733023	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238733023C>T	uc002vxi.3	+	10	2545	c.2413C>T	c.(2413-2415)CAA>TAA	p.Q805*		NM_001080504	NP_001073973	Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	804							nucleotide binding|RNA binding			ovary(4)	4		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		ACAGGGAAATCAAGTAGAACA	0.428													112	197	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191485	10191485	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191485G>T	uc003bvc.2	+	3	691	c.478G>T	c.(478-480)GAG>TAG	p.E160*	VHL_uc003bvd.2_Nonsense_Mutation_p.E119*	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	160	Interaction with Elongin BC complex.				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.E160K(5)|p.E160fs*10(3)|p.E160fs*14(2)|p.E160*(2)|p.E160fs*9(1)|p.K159fs*13(1)|p.E160del(1)|p.L158fs*6(1)|p.E160fs*13(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)		TACTCTGAAAGAGCGATGCCT	0.502		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				46	80	---	---	---	---	PASS
EOMES	8320	broad.mit.edu	37	3	27760303	27760303	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27760303T>G	uc003cdx.2	-	4	1240	c.1240A>C	c.(1240-1242)AAT>CAT	p.N414H	EOMES_uc003cdy.3_Missense_Mutation_p.N414H|EOMES_uc010hfn.2_Missense_Mutation_p.N414H|EOMES_uc011axc.1_Missense_Mutation_p.N119H	NM_005442	NP_005433	O95936	EOMES_HUMAN	eomesodermin	414	T-box.				CD8-positive, alpha-beta T cell differentiation involved in immune response|cell differentiation involved in embryonic placenta development|endoderm formation|mesoderm formation|mesodermal to mesenchymal transition involved in gastrulation|positive regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|breast(1)	4						GAGGGCTCATTCAAGTCCTCC	0.443													125	157	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52702662	52702662	+	Splice_Site	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52702662C>T	uc003des.2	-	3	249	c.237_splice	c.e3-1	p.R79_splice	PBRM1_uc003dex.2_Splice_Site|PBRM1_uc003deq.2_Splice_Site_p.R79_splice|PBRM1_uc003der.2_Splice_Site_p.R79_splice|PBRM1_uc003det.2_Splice_Site_p.R79_splice|PBRM1_uc003deu.2_Splice_Site_p.R79_splice|PBRM1_uc003dev.2_Splice_Site|PBRM1_uc003dew.2_Splice_Site_p.R79_splice|PBRM1_uc010hmk.1_Splice_Site_p.R79_splice|PBRM1_uc003dey.2_Splice_Site_p.R79_splice|PBRM1_uc003dez.1_Splice_Site_p.R79_splice|PBRM1_uc003dfb.1_Splice_Site	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TGGTTGATTTCTGttataatt	0.289			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								60	74	---	---	---	---	PASS
PDZRN3	23024	broad.mit.edu	37	3	73432856	73432856	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73432856C>A	uc003dpl.1	-	10	2957	c.2861G>T	c.(2860-2862)CGC>CTC	p.R954L	PDZRN3_uc011bgh.1_Missense_Mutation_p.R611L|PDZRN3_uc010hoe.1_Missense_Mutation_p.R652L|PDZRN3_uc011bgf.1_Missense_Mutation_p.R671L|PDZRN3_uc011bgg.1_Missense_Mutation_p.R674L	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	954							ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		CATGCCGCTGCGCTCTTCCCG	0.657													5	24	---	---	---	---	PASS
KIAA1524	57650	broad.mit.edu	37	3	108270037	108270037	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108270037C>T	uc003dxb.3	-	21	2946	c.2677G>A	c.(2677-2679)GGT>AGT	p.G893S		NM_020890	NP_065941	Q8TCG1	CIP2A_HUMAN	p90 autoantigen	893						cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3						ATTTTTCCACCACTTAAACTG	0.343													5	297	---	---	---	---	PASS
RAB43	339122	broad.mit.edu	37	3	128848936	128848936	+	Silent	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128848936G>A	uc003elo.1	-	11	1057	c.846C>T	c.(844-846)CTC>CTT	p.L282L	ISY1_uc010hsz.1_Silent_p.L102L|ISY1_uc003elp.1_Silent_p.L282L|ISY1_uc010hta.1_Silent_p.L304L	NM_020701	NP_065752	Q86YS6	RAB43_HUMAN	ISY1 splicing factor homolog	Error:Variant_position_missing_in_Q86YS6_after_alignment					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			lung(1)	1						AATACCCCAGGAGCCTTCTGG	0.577													67	166	---	---	---	---	PASS
MRPL3	11222	broad.mit.edu	37	3	131219363	131219363	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131219363A>C	uc003eoh.2	-	3	444	c.280T>G	c.(280-282)TCC>GCC	p.S94A	MRPL3_uc011blo.1_5'UTR|MRPL3_uc011blp.1_Missense_Mutation_p.S121A	NM_007208	NP_009139	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	94					translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome				0						ACTCTAAAGGAACCTGGCAAT	0.398													18	218	---	---	---	---	PASS
GPR149	344758	broad.mit.edu	37	3	154147408	154147408	+	5'UTR	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154147408C>T	uc003faa.2	-	1						NM_001038705	NP_001033794	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(6)	6			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			AAGACATTGTCCTTGGTCAAT	0.378													5	111	---	---	---	---	PASS
MFSD1	64747	broad.mit.edu	37	3	158539875	158539875	+	Silent	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158539875T>C	uc003fcl.1	+	11	1053	c.1023T>C	c.(1021-1023)ACT>ACC	p.T341T	MFSD1_uc003fcm.1_RNA|MFSD1_uc003fcn.1_Silent_p.T244T|MFSD1_uc011bow.1_Silent_p.T302T|MFSD1_uc011box.1_Silent_p.T268T	NM_022736	NP_073573	Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing	341	Helical; (Potential).				transmembrane transport	integral to membrane					0			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TAGCAGCCACTCTTGTGTCCC	0.512													6	283	---	---	---	---	PASS
MYNN	55892	broad.mit.edu	37	3	169496677	169496677	+	Missense_Mutation	SNP	T	C	C	rs139065735		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169496677T>C	uc003fft.2	+	3	817	c.388T>C	c.(388-390)TCT>CCT	p.S130P	MYNN_uc011bpm.1_Missense_Mutation_p.S16P|MYNN_uc003ffu.2_Missense_Mutation_p.S130P|MYNN_uc003ffv.2_5'UTR|MYNN_uc010hwo.2_Missense_Mutation_p.S130P|MYNN_uc003ffw.1_RNA	NM_018657	NP_061127	Q9NPC7	MYNN_HUMAN	myoneurin	130						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			TACAGAGATATCTAGTATTAC	0.343													4	93	---	---	---	---	PASS
ECT2	1894	broad.mit.edu	37	3	172520719	172520719	+	Silent	SNP	C	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172520719C>G	uc003fii.2	+	19	2100	c.1962C>G	c.(1960-1962)CCC>CCG	p.P654P	ECT2_uc010hwv.1_Silent_p.P685P|ECT2_uc003fih.2_Silent_p.P653P|ECT2_uc003fij.1_Silent_p.P654P|ECT2_uc003fik.1_Silent_p.P654P|ECT2_uc003fil.1_Silent_p.P685P|ECT2_uc003fim.1_5'UTR	NM_018098	NP_060568	Q9H8V3	ECT2_HUMAN	epithelial cell transforming sequence 2 oncogene	654	PH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|ovary(1)|skin(1)	4	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			GTGAGCACCCCTGTGACAGAG	0.373													6	282	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505791	195505791	+	Silent	SNP	A	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505791A>T	uc011bto.1	-	3	12736	c.12276T>A	c.(12274-12276)GGT>GGA	p.G4092G	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGCGTGACCTGTGGATG	0.587													6	108	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506005	195506005	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506005A>C	uc011bto.1	-	3	12522	c.12062T>G	c.(12061-12063)ATC>AGC	p.I4021S	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGGGATGGTGACAGG	0.587													6	130	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195506007	195506007	+	Silent	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195506007G>A	uc011bto.1	-	3	12520	c.12060C>T	c.(12058-12060)ACC>ACT	p.T4020T	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_5'Flank|MUC4_uc011btg.1_5'Flank|MUC4_uc011bth.1_5'Flank|MUC4_uc011bti.1_5'Flank|MUC4_uc011btj.1_5'Flank|MUC4_uc011btk.1_5'Flank|MUC4_uc011btl.1_5'Flank|MUC4_uc011btm.1_5'Flank|MUC4_uc011btn.1_5'Flank|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	915	Ser-rich.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGGGATGGTGACAGGAA	0.587													6	132	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195509182	195509182	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195509182G>T	uc011bto.1	-	3	9345	c.8885C>A	c.(8884-8886)CCT>CAT	p.P2962H	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGGTGACAGGAAGAGGGGT	0.597													8	44	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511918	195511918	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511918G>A	uc011bto.1	-	2	6993	c.6533C>T	c.(6532-6534)CCT>CTT	p.P2178L	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTCGGTGACAGGAAGAGAGGT	0.582													5	104	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511925	195511925	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511925A>G	uc011bto.1	-	2	6986	c.6526T>C	c.(6526-6528)TCT>CCT	p.S2176P	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGAGGTGGCGTGA	0.587													7	108	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195513539	195513539	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195513539C>G	uc011bto.1	-	2	5372	c.4912G>C	c.(4912-4914)GCT>CCT	p.A1638P	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AATGAGGAAGCATTGGTGACA	0.577													16	221	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195513540	195513540	+	Silent	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195513540A>G	uc011bto.1	-	2	5371	c.4911T>C	c.(4909-4911)AAT>AAC	p.N1637N	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ATGAGGAAGCATTGGTGACAG	0.577													17	220	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195513541	195513541	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195513541T>C	uc011bto.1	-	2	5370	c.4910A>G	c.(4909-4911)AAT>AGT	p.N1637S	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGCATTGGTGACAGG	0.577													16	218	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195515026	195515026	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195515026G>C	uc011bto.1	-	2	3885	c.3425C>G	c.(3424-3426)ACT>AGT	p.T1142S	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	1019	Repeat.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TACTGAGGAAGTGTCGGTGAC	0.567													8	147	---	---	---	---	PASS
TMEM128	85013	broad.mit.edu	37	4	4239697	4239697	+	Intron	SNP	C	A	A	rs116836858	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4239697C>A	uc003ghr.1	-						TMEM128_uc003ghq.1_Intron|TMEM128_uc003ghs.2_3'UTR|TMEM128_uc011bvv.1_Intron|TMEM128_uc011bvw.1_Intron	NM_032927	NP_116316	Q5BJH2	TM128_HUMAN	transmembrane protein 128							integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (64;0.166)		TTGACAACTCCAATATGCATC	0.323													18	99	---	---	---	---	PASS
FRYL	285527	broad.mit.edu	37	4	48622633	48622633	+	Intron	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48622633A>G	uc003gyh.1	-						FRYL_uc003gyk.2_Intron|FRYL_uc003gyl.1_Intron|FRYL_uc003gym.1_3'UTR	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1						TCCAGGTGAAACAGTGTAAAA	0.383													5	242	---	---	---	---	PASS
RASGEF1B	153020	broad.mit.edu	37	4	82378772	82378772	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82378772T>C	uc003hmi.1	-	3	325	c.181A>G	c.(181-183)ACA>GCA	p.T61A	RASGEF1B_uc003hmj.1_Missense_Mutation_p.T61A|RASGEF1B_uc010ijq.1_Intron|RASGEF1B_uc003hmk.2_Missense_Mutation_p.T61A	NM_152545	NP_689758	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	61	N-terminal Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0						AATATGTATGTTCTCTGCAGC	0.363													5	209	---	---	---	---	PASS
ANK2	287	broad.mit.edu	37	4	114279798	114279798	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114279798G>A	uc003ibe.3	+	38	10124	c.10024G>A	c.(10024-10026)GCA>ACA	p.A3342T	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_Missense_Mutation_p.A644T|ANK2_uc011cgb.1_Missense_Mutation_p.A3357T	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	3309					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GGCGGATGAAGCAAAACCAAA	0.473													4	325	---	---	---	---	PASS
MAP9	79884	broad.mit.edu	37	4	156289916	156289916	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156289916C>T	uc003ios.2	-	5	794	c.530G>A	c.(529-531)CGG>CAG	p.R177Q	MAP9_uc011cin.1_Missense_Mutation_p.R176Q|MAP9_uc010iqa.1_RNA|MAP9_uc003iot.1_Missense_Mutation_p.R176Q|MAP9_uc010iqb.1_Missense_Mutation_p.R104Q	NM_001039580	NP_001034669	Q49MG5	MAP9_HUMAN	aster-associated protein	177					cell division|mitosis	cytoplasm|microtubule|spindle				ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		ACTCCTTGGCCGAGGTGATGG	0.378													9	282	---	---	---	---	PASS
MAP9	79884	broad.mit.edu	37	4	156296103	156296103	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156296103T>C	uc003ios.2	-	3	410	c.146A>G	c.(145-147)GAC>GGC	p.D49G	MAP9_uc011cin.1_Missense_Mutation_p.D49G|MAP9_uc010iqa.1_RNA|MAP9_uc003iot.1_Missense_Mutation_p.D49G|MAP9_uc010iqb.1_5'UTR	NM_001039580	NP_001034669	Q49MG5	MAP9_HUMAN	aster-associated protein	49					cell division|mitosis	cytoplasm|microtubule|spindle				ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		CTCATCACTGTCAAAGTCATC	0.413													6	351	---	---	---	---	PASS
MLF1IP	79682	broad.mit.edu	37	4	185646151	185646151	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185646151A>G	uc003iwq.2	-	4	350	c.280T>C	c.(280-282)TCT>CCT	p.S94P	MLF1IP_uc003iwp.2_RNA|MLF1IP_uc003iwr.1_Missense_Mutation_p.S94P	NM_024629	NP_078905	Q71F23	CENPU_HUMAN	MLF1 interacting protein	94					CenH3-containing nucleosome assembly at centromere|interspecies interaction between organisms|mitotic prometaphase|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|condensed chromosome kinetochore|cytosol|nucleoplasm					0		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		GAAGAGAGAGACAGTCCACAA	0.353													10	655	---	---	---	---	PASS
MLF1IP	79682	broad.mit.edu	37	4	185652116	185652116	+	Silent	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185652116T>C	uc003iwq.2	-	2	124	c.54A>G	c.(52-54)AGA>AGG	p.R18R	MLF1IP_uc003iwp.2_RNA|MLF1IP_uc003iwr.1_Silent_p.R18R	NM_024629	NP_078905	Q71F23	CENPU_HUMAN	MLF1 interacting protein	18	Nuclear localization signal (Potential).				CenH3-containing nucleosome assembly at centromere|interspecies interaction between organisms|mitotic prometaphase|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|condensed chromosome kinetochore|cytosol|nucleoplasm					0		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		TCTTTGAACGTCTTGCGCTAT	0.323													5	220	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	89989964	89989964	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89989964T>C	uc003kju.2	+	33	7487	c.7391T>C	c.(7390-7392)TTC>TCC	p.F2464S	GPR98_uc003kjt.2_Missense_Mutation_p.F170S|GPR98_uc003kjv.2_Missense_Mutation_p.F64S	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	2464	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)		CCCCAGTGTTTCTGGATGACA	0.498													17	262	---	---	---	---	PASS
APC	324	broad.mit.edu	37	5	112175497	112175497	+	Silent	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112175497C>T	uc010jby.2	+	16	4586	c.4206C>T	c.(4204-4206)GCC>GCT	p.A1402A	APC_uc011cvt.1_Silent_p.A1384A|APC_uc003kpz.3_Silent_p.A1402A|APC_uc003kpy.3_Silent_p.A1402A|APC_uc010jbz.2_Silent_p.A1119A|APC_uc010jca.2_Silent_p.A702A	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli	1402	Ser-rich.				canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity	p.A1402fs*13(1)|p.Y1376fs*41(1)|p.?(1)|p.K1192fs*3(1)|p.I1401fs*2(1)|p.A1402fs*6(1)|p.S1400fs*5(1)		large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2515		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GTTCGATTGCCAGCTCCGTTC	0.473		12	D|Mis|N|F|S		colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS	colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS			Hereditary_Desmoid_Disease|Familial_Adenomatous_Polyposis|Turcot_syndrome	TSP Lung(16;0.13)			6	219	---	---	---	---	PASS
PCDHA6	56142	broad.mit.edu	37	5	140209499	140209499	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140209499C>T	uc003lho.2	+	1	1850	c.1823C>T	c.(1822-1824)TCG>TTG	p.S608L	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc011dab.1_Missense_Mutation_p.S608L	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	608	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGTGGCTTTCGTATGAGCTG	0.662													20	52	---	---	---	---	PASS
PCDHB11	56125	broad.mit.edu	37	5	140580140	140580140	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140580140T>C	uc003liy.2	+	1	793	c.793T>C	c.(793-795)TCA>CCA	p.S265P	PCDHB11_uc011daj.1_5'UTR	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	265	Extracellular (Potential).|Cadherin 3.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTTGATTGTCTCAGCTTGGGA	0.403													6	403	---	---	---	---	PASS
PCDHGA2	56113	broad.mit.edu	37	5	140719697	140719697	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140719697C>T	uc003ljk.1	+	1	1344	c.1159C>T	c.(1159-1161)CCC>TCC	p.P387S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Missense_Mutation_p.P387S	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	387	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGTTCACTCCCCGAGGATCT	0.428													4	173	---	---	---	---	PASS
JAKMIP2	9832	broad.mit.edu	37	5	146971180	146971180	+	3'UTR	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146971180A>G	uc003loq.1	-	21					JAKMIP2_uc011dbx.1_3'UTR|JAKMIP2_uc003lor.1_3'UTR|uc003lop.1_Intron	NM_014790	NP_055605	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein							Golgi apparatus				large_intestine(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTGGTGTAAACAATTTTGCC	0.368													6	493	---	---	---	---	PASS
MAT2B	27430	broad.mit.edu	37	5	162944783	162944783	+	Intron	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162944783T>C	uc003lzk.2	+						MAT2B_uc003lzj.2_Intron|MAT2B_uc003lzl.1_3'UTR|MAT2B_uc003lzm.2_Intron	NM_013283	NP_037415	Q9NZL9	MAT2B_HUMAN	methionine adenosyltransferase II, beta isoform						extracellular polysaccharide biosynthetic process|methylation|S-adenosylmethionine biosynthetic process|xenobiotic metabolic process	cytosol|methionine adenosyltransferase complex|nucleus	dTDP-4-dehydrorhamnose reductase activity|methionine adenosyltransferase regulator activity|protein binding			upper_aerodigestive_tract(1)	1	Renal(175;0.000281)	Medulloblastoma(196;0.0208)|all_neural(177;0.0765)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.027)|OV - Ovarian serous cystadenocarcinoma(192;0.0406)|Epithelial(171;0.0797)	L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	TGAACTTTGCTTGTATGCTGG	0.328													4	31	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	5	179079501	179079501	+	3'UTR	SNP	G	A	A	rs141365015	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179079501G>A	uc003mkj.1	+	1										RecName: Full=Putative uncharacterized protein LOC285679;																		CTGGAAATGCGTGTTCTAATG	0.562													5	239	---	---	---	---	PASS
SLC35B3	51000	broad.mit.edu	37	6	8422813	8422813	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8422813C>T	uc010joe.2	-	5	630	c.464G>A	c.(463-465)GGT>GAT	p.G155D	SLC35B3_uc003mya.2_Missense_Mutation_p.G123D|SLC35B3_uc003myc.2_Intron|SLC35B3_uc003myb.2_Missense_Mutation_p.G155D|SLC35B3_uc011did.1_Missense_Mutation_p.G155D|SLC35B3_uc003myd.2_RNA	NM_001142541	NP_001136013	Q9H1N7	S35B3_HUMAN	solute carrier family 35, member B3	155	Helical; (Potential).				transmembrane transport	Golgi membrane|integral to membrane					0	Ovarian(93;0.0569)					CCCCATAGTACCCACAGTTAG	0.373													37	353	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	6	9903622	9903622	+	Intron	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9903622T>C	uc003myg.1	-						uc010jog.1_Intron|uc003myh.1_Intron|uc003myi.2_RNA|uc003myj.1_Intron|uc003myk.1_RNA|uc003myn.2_Silent_p.R132R|uc010joi.1_Intron|uc010joh.1_RNA|uc011dif.1_Silent_p.R136R|uc011dig.1_Silent_p.R132R					Homo sapiens clone 958LR MRDS1 protein (MRDS1) mRNA, complete cds.																		GTTCTCCTTGTCTGCTCTCAT	0.333													7	653	---	---	---	---	PASS
HIST1H2BK	85236	broad.mit.edu	37	6	27114519	27114519	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27114519G>A	uc003nix.1	-	1	101	c.59C>T	c.(58-60)ACT>ATT	p.T20I	HIST1H2AH_uc003niz.2_5'Flank|hsa-mir-3143|MI0014167_5'Flank	NM_080593	NP_542160	O60814	H2B1K_HUMAN	histone cluster 1, H2bk	20					defense response to bacterium|nucleosome assembly	nucleosome|nucleus	DNA binding				0						CTGCGCCTTAGTCACGGCTTT	0.602													4	110	---	---	---	---	PASS
TCP11	6954	broad.mit.edu	37	6	35086049	35086049	+	Silent	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35086049A>G	uc003okd.2	-	10	1729	c.1548T>C	c.(1546-1548)GTT>GTC	p.V516V	TCP11_uc003ojz.1_Silent_p.V441V|TCP11_uc003oka.2_Silent_p.V441V|TCP11_uc003okb.2_Silent_p.V440V|TCP11_uc003okc.2_Silent_p.V440V|TCP11_uc011dsu.1_Silent_p.V498V|TCP11_uc011dsv.1_Silent_p.V465V|TCP11_uc011dsw.1_Silent_p.V470V	NM_001093728	NP_001087197	Q8WWU5	TCP11_HUMAN	t-complex 11 isoform 1	503					cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)|skin(2)	5						GACGCTATCAAACAGACTCCA	0.512													55	193	---	---	---	---	PASS
MEP1A	4224	broad.mit.edu	37	6	46766380	46766380	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46766380G>C	uc010jzh.1	+	4	225	c.183G>C	c.(181-183)TTG>TTC	p.L61F	MEP1A_uc011dwg.1_5'UTR|MEP1A_uc011dwh.1_Missense_Mutation_p.L89F|MEP1A_uc011dwi.1_5'UTR	NM_005588	NP_005579	Q16819	MEP1A_HUMAN	meprin A alpha precursor	61					digestion|proteolysis	extracellular space|integral to plasma membrane|soluble fraction	metalloendopeptidase activity|zinc ion binding			pancreas(2)|ovary(1)	3			Lung(136;0.192)			ACATCCTCTTGCAGGTGAGTA	0.463													5	154	---	---	---	---	PASS
KLHL31	401265	broad.mit.edu	37	6	53516418	53516418	+	Missense_Mutation	SNP	G	T	T	rs12204882		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53516418G>T	uc003pcb.3	-	3	2024	c.1883C>A	c.(1882-1884)TCT>TAT	p.S628Y	uc003pcc.1_5'UTR	NM_001003760	NP_001003760	Q9H511	KLH31_HUMAN	kelch repeat and BTB (POZ) domain containing 1	628					regulation of transcription, DNA-dependent|transcription, DNA-dependent					ovary(1)	1	Lung NSC(77;0.0158)					TGGCACAGAAGATACCGAACT	0.572											OREG0017507	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	18	30	---	---	---	---	PASS
PHF3	23469	broad.mit.edu	37	6	64421750	64421750	+	Silent	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64421750A>G	uc003pep.1	+	15	4292	c.4266A>G	c.(4264-4266)CCA>CCG	p.P1422P	PHF3_uc003pen.2_Silent_p.P1334P|PHF3_uc011dxs.1_Silent_p.P691P	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	1422					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			AAGACCTTCCAACAGCAGTTG	0.398													4	108	---	---	---	---	PASS
EYS	346007	broad.mit.edu	37	6	65300368	65300368	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65300368C>T	uc011dxu.1	-	26	5930	c.5392G>A	c.(5392-5394)GCA>ACA	p.A1798T	EYS_uc011dxt.1_Missense_Mutation_p.A710T	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	1798					response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6						GCTGGAGTTGCTGAAACTGTA	0.388													5	235	---	---	---	---	PASS
HGC6.3	100128124	broad.mit.edu	37	6	168376953	168376953	+	Missense_Mutation	SNP	A	C	C	rs2516607	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168376953A>C	uc010kks.1	-	1	667	c.380T>G	c.(379-381)GTA>GGA	p.V127G		NM_001129895	NP_001123367	Q9UM08	Q9UM08_HUMAN	hypothetical protein LOC100128124	127											0						GGGGGTCATTACCCCTGCAGT	0.642													6	50	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	39873374	39873374	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39873374C>A	uc010kxp.2	+	1	562	c.205C>A	c.(205-207)CTT>ATT	p.L69I						SubName: Full=Similar to sequence-specific single-stranded-DNA-binding protein;																		ATTTGGGGACCTTTACTGTGC	0.498													9	109	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	39894629	39894629	+	RNA	SNP	C	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39894629C>G	uc003thg.2	-	1		c.231G>C								full-length cDNA clone CS0DF025YB16 of Fetal brain of Homo sapiens (human).																		CTTCTAGTTCCATCTCCTGGT	0.537													7	201	---	---	---	---	PASS
ZNF138	7697	broad.mit.edu	37	7	64292314	64292314	+	3'UTR	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64292314T>C	uc011kdp.1	+	5					ZNF138_uc003ttg.2_Missense_Mutation_p.F175L|ZNF138_uc011kdq.1_Missense_Mutation_p.F206L|ZNF138_uc003tth.2_RNA|ZNF138_uc010kzs.2_Missense_Mutation_p.F200L	NM_001160183	NP_001153655	B4DFX2	B4DFX2_HUMAN	zinc finger protein 138 isoform 2						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding				0		Lung NSC(55;0.0795)|all_lung(88;0.18)				TGGAAAAGCCTTTCACCAATC	0.373													4	85	---	---	---	---	PASS
SPDYE7P	441251	broad.mit.edu	37	7	72334607	72334607	+	RNA	SNP	T	C	C	rs28493684	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72334607T>C	uc010lal.1	-	1		c.5049A>G				NR_003666				Homo sapiens speedy homolog E7 (Xenopus laevis), pseudogene (SPDYE7P), non-coding RNA.												0						CCAGCCCACCTGATTCCTCCC	0.592													42	184	---	---	---	---	PASS
NSUN5P2	260294	broad.mit.edu	37	7	72420448	72420448	+	Missense_Mutation	SNP	C	G	G	rs400282	byFrequency	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72420448C>G	uc003twn.2	-	7	852	c.140G>C	c.(139-141)TGG>TCG	p.W47S	POM121_uc010lam.1_3'UTR|NSUN5P2_uc003twl.2_RNA|NSUN5P2_uc003twm.2_Missense_Mutation_p.W47S|NSUN5P2_uc003two.2_Missense_Mutation_p.W47S|NSUN5P2_uc003twq.2_Missense_Mutation_p.W47S|NSUN5P2_uc010lan.1_5'UTR|NSUN5P2_uc003twp.2_Missense_Mutation_p.W47S	NM_032158	NP_115534			NOL1/NOP2/Sun domain family, member 5C isoform												0						CACAGGCATCCATGACATGGG	0.612													6	105	---	---	---	---	PASS
GATAD1	57798	broad.mit.edu	37	7	92083920	92083920	+	Silent	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92083920G>A	uc003ulx.1	+	4	819	c.540G>A	c.(538-540)GAG>GAA	p.E180E	GATAD1_uc011khq.1_RNA	NM_021167	NP_066990	Q8WUU5	GATD1_HUMAN	GATA zinc finger domain containing 1	180							sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(62;1.63e-10)|all_epithelial(64;8.33e-10)|Breast(17;0.00311)|all_lung(186;0.0498)|Lung NSC(181;0.0676)		STAD - Stomach adenocarcinoma(171;4.51e-05)|GBM - Glioblastoma multiforme(5;8.83e-05)|all cancers(6;0.000136)|Lung(22;0.123)|Epithelial(20;0.179)|LUSC - Lung squamous cell carcinoma(200;0.225)			AGTATTGCGAGAAGAGTGCAG	0.438													7	455	---	---	---	---	PASS
SAMD9	54809	broad.mit.edu	37	7	92734605	92734605	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92734605T>C	uc003umf.2	-	3	1062	c.806A>G	c.(805-807)AAC>AGC	p.N269S	SAMD9_uc003umg.2_Missense_Mutation_p.N269S	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	269						cytoplasm				ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			AAAATACTTGTTTATCATCAG	0.388													7	706	---	---	---	---	PASS
UPK3BL	100134938	broad.mit.edu	37	7	102279601	102279601	+	Silent	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102279601G>T	uc010lij.1	-	4	581	c.531C>A	c.(529-531)ACC>ACA	p.T177T	UPK3BL_uc003uzy.2_5'Flank|RASA4_uc011klb.1_5'UTR|RASA4_uc011kld.1_Intron|POLR2J2_uc003vai.2_RNA|POLR2J2_uc003vah.2_3'UTR	NM_001114403	NP_001107875	B0FP48	UPK3L_HUMAN	uroplakin-like protein	177	Extracellular (Potential).					integral to membrane					0						TGGACCACTTGGTTTCAGCCA	0.622													5	289	---	---	---	---	PASS
SLC26A4	5172	broad.mit.edu	37	7	107329537	107329537	+	Silent	SNP	G	A	A	rs140778437		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107329537G>A	uc003vep.2	+	9	1265	c.1041G>A	c.(1039-1041)TCG>TCA	p.S347S	SLC26A4_uc011kmb.1_5'Flank|SLC26A4_uc011kmc.1_5'Flank	NM_000441	NP_000432	O43511	S26A4_HUMAN	pendrin	347	Helical; (Potential).				regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7						GCTTGTTCTCGGAGATGCTGG	0.438									Pendred_syndrome				49	421	---	---	---	---	PASS
ZC3HC1	51530	broad.mit.edu	37	7	129662289	129662289	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129662289C>T	uc003vpi.2	-	9	1337	c.1310G>A	c.(1309-1311)GGC>GAC	p.G437D	ZC3HC1_uc003vph.2_Missense_Mutation_p.G281D|ZC3HC1_uc010lma.2_Missense_Mutation_p.G253D	NM_016478	NP_057562	Q86WB0	NIPA_HUMAN	zinc finger, C3HC type 1	437					cell division|mitosis	nucleus	protein kinase binding|zinc ion binding				0	Melanoma(18;0.0435)					GCTTTCTTTGCCAAGTGTGAT	0.522													5	435	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151921114	151921114	+	Nonsense_Mutation	SNP	A	T	T	rs4024337		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151921114A>T	uc003wla.2	-	20	3528	c.3309T>A	c.(3307-3309)TGT>TGA	p.C1103*	MLL3_uc003wkz.2_Nonsense_Mutation_p.C164*	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	1103	PHD-type 6.				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		CACATTGTCTACATTGCAGAA	0.338			N		medulloblastoma								6	251	---	---	---	---	PASS
CDCA2	157313	broad.mit.edu	37	8	25364809	25364809	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25364809C>T	uc003xep.1	+	15	3106	c.2627C>T	c.(2626-2628)GCC>GTC	p.A876V	PPP2R2A_uc003xek.2_Intron|CDCA2_uc011lae.1_3'UTR|CDCA2_uc003xeq.1_Missense_Mutation_p.A861V|CDCA2_uc003xer.1_Missense_Mutation_p.A539V	NM_152562	NP_689775	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	876					cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		TTGTCTGATGCCATTGAGCAA	0.393													23	57	---	---	---	---	PASS
PCMTD1	115294	broad.mit.edu	37	8	52758292	52758292	+	Silent	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52758292A>G	uc003xqx.3	-	3	680	c.339T>C	c.(337-339)CTT>CTC	p.L113L	PCMTD1_uc003xqw.3_Silent_p.L113L|PCMTD1_uc011ldn.1_5'UTR|PCMTD1_uc010lya.2_Intron|PCMTD1_uc011ldo.1_Silent_p.L113L	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)	113						cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)				CATCTGAATGAAGCTCAATCC	0.323													7	534	---	---	---	---	PASS
NKAIN3	286183	broad.mit.edu	37	8	63902748	63902748	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63902748G>T	uc010lyq.1	+	6	686	c.554G>T	c.(553-555)TGC>TTC	p.C185F		NM_173688	NP_775959	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3	185						integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)				ctgcaagtatgcaaacatctt	0.154													57	170	---	---	---	---	PASS
TOPORS	10210	broad.mit.edu	37	9	32542475	32542475	+	Missense_Mutation	SNP	C	T	T	rs149570596		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32542475C>T	uc003zrb.2	-	3	2215	c.2048G>A	c.(2047-2049)CGG>CAG	p.R683Q	TOPORS_uc003zrc.2_Missense_Mutation_p.R616Q	NM_005802	NP_005793	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich	683	Interaction with TOP1.|Arg-rich.|Interaction with p53/TP53.				DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		ATTTCTGCTCCGTGATCTTCT	0.393													4	289	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79323926	79323926	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79323926G>T	uc010mpk.2	-	8	3388	c.3264C>A	c.(3262-3264)TAC>TAA	p.Y1088*		NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	1088					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						TTGTTTCATTGTACAGTTGCA	0.517													7	565	---	---	---	---	PASS
ZNF484	83744	broad.mit.edu	37	9	95610732	95610732	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95610732A>G	uc004asu.1	-	5	486	c.337T>C	c.(337-339)TCC>CCC	p.S113P	ANKRD19_uc004asr.3_Intron|ZNF484_uc011lub.1_Missense_Mutation_p.S115P|ZNF484_uc010mrb.1_Missense_Mutation_p.S77P|ZNF484_uc004asv.1_Missense_Mutation_p.S77P	NM_031486	NP_113674	Q5JVG2	ZN484_HUMAN	zinc finger protein 484 isoform a	113					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TCTAAAATGGAATATGGGTCA	0.363													6	288	---	---	---	---	PASS
MED27	9442	broad.mit.edu	37	9	134735980	134735980	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134735980G>A	uc004cbe.1	-	8	903	c.881C>T	c.(880-882)CCG>CTG	p.P294L	MED27_uc004cbf.1_Missense_Mutation_p.P258L	NM_004269	NP_004260	Q6P2C8	MED27_HUMAN	mediator complex subunit 27	294					regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleolus|transcription factor complex	protein binding|transcription coactivator activity			skin(1)	1		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		CCTCCATGTCGGGGGAAGGCC	0.597													6	56	---	---	---	---	PASS
DHTKD1	55526	broad.mit.edu	37	10	12111026	12111026	+	5'UTR	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12111026G>T	uc001ild.3	+	1						NM_018706	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain						glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			CGGGACATCTGGTGAACATGG	0.697													3	24	---	---	---	---	PASS
PDSS1	23590	broad.mit.edu	37	10	27013021	27013021	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27013021C>A	uc001isv.2	+	8	846	c.800C>A	c.(799-801)ACC>AAC	p.T267N	PDSS1_uc001isw.2_Missense_Mutation_p.T267N	NM_014317	NP_055132	Q5T2R2	DPS1_HUMAN	prenyl diphosphate synthase, subunit 1	267		Polyprenyl diphosphate (By similarity).			isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	metal ion binding|protein heterodimerization activity				0						TTCAAGAAGACCGCCAGCCTG	0.393													5	226	---	---	---	---	PASS
PTCHD3	374308	broad.mit.edu	37	10	27702370	27702370	+	Silent	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27702370G>A	uc001itu.2	-	1	928	c.810C>T	c.(808-810)TAC>TAT	p.Y270Y		NM_001034842	NP_001030014	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	270					spermatid development	integral to membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|skin(1)	4						CCTGCCAGGCGTACAGGATCG	0.627													11	91	---	---	---	---	PASS
PARG	8505	broad.mit.edu	37	10	51093329	51093329	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51093329C>T	uc001jif.2	-	8	2011	c.1750G>A	c.(1750-1752)GCA>ACA	p.A584T	PARG_uc001jih.2_Missense_Mutation_p.A584T|PARG_uc001jig.2_Missense_Mutation_p.A170T|PARG_uc010qgv.1_Intron|PARG_uc009xoi.2_Intron|PARG_uc010qgw.1_Missense_Mutation_p.A475T|PARG_uc009xoj.2_Missense_Mutation_p.A135T|PARG_uc010qgx.1_Missense_Mutation_p.A502T	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	584					carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		TGAGCTTCTGCTTCTTCAAGT	0.318													9	466	---	---	---	---	PASS
ABCC2	1244	broad.mit.edu	37	10	101591884	101591884	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101591884C>T	uc001kqf.2	+	23	3393	c.3254C>T	c.(3253-3255)GCC>GTC	p.A1085V		NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),	1085	ABC transmembrane type-1 2.|Cytoplasmic (By similarity).					apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)	AACAGGTTTGCCGGCGTAAGT	0.438													4	132	---	---	---	---	PASS
NHLRC2	374354	broad.mit.edu	37	10	115636673	115636673	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115636673A>G	uc001lax.1	+	3	937	c.725A>G	c.(724-726)GAC>GGC	p.D242G		NM_198514	NP_940916	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	242	NHL 1.				cell redox homeostasis					ovary(1)	1				Epithelial(162;0.017)|all cancers(201;0.0187)		GTAATAGCAGACACTGGACAT	0.353													4	77	---	---	---	---	PASS
FRG2B	441581	broad.mit.edu	37	10	135439077	135439077	+	Silent	SNP	T	C	C	rs149978897	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135439077T>C	uc010qvg.1	-	4	416	c.363A>G	c.(361-363)TCA>TCG	p.S121S		NM_001080998	NP_001074467	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	121						nucleus					0		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		TTTTATTCAATGACAAGCTGC	0.517													6	104	---	---	---	---	PASS
MUC2	4583	broad.mit.edu	37	11	1093272	1093272	+	Silent	SNP	A	C	C	rs56230143		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1093272A>C	uc001lsx.1	+	31	12204	c.12177A>C	c.(12175-12177)ACA>ACC	p.T4059T		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4059						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	agaccccaacatcgacaccca	0.015													9	252	---	---	---	---	PASS
ZBED5	58486	broad.mit.edu	37	11	10875055	10875055	+	Missense_Mutation	SNP	T	C	C	rs1046297	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10875055T>C	uc009ygg.2	-	2	3255	c.1438A>G	c.(1438-1440)ATT>GTT	p.I480V	ZBED5_uc009ygh.2_Missense_Mutation_p.I480V|ZBED5_uc001mji.3_Missense_Mutation_p.I480V|ZBED5_uc001mjg.1_Intron	NM_021211	NP_067034	Q49AG3	ZBED5_HUMAN	zinc finger, BED-type containing 5	480							DNA binding|metal ion binding				0						ttagtaaaaatatctgcaaga	0.000													23	44	---	---	---	---	PASS
INSC	387755	broad.mit.edu	37	11	15222420	15222420	+	Silent	SNP	G	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15222420G>C	uc001mly.2	+	7	931	c.885G>C	c.(883-885)CGG>CGC	p.R295R	INSC_uc001mlz.2_Silent_p.R248R|INSC_uc001mma.2_Silent_p.R248R|INSC_uc010rcs.1_Silent_p.R283R|INSC_uc001mmb.2_Silent_p.R248R|INSC_uc001mmc.2_Intron	NM_001031853	NP_001027024	Q1MX18	INSC_HUMAN	inscuteable isoform a	295					cell differentiation|nervous system development	cytoplasm	binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)	5						ACAGTTTCCGGTGCTTGTACC	0.587													57	153	---	---	---	---	PASS
CKAP5	9793	broad.mit.edu	37	11	46837868	46837868	+	Silent	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46837868A>G	uc001ndi.1	-	4	449	c.339T>C	c.(337-339)TGT>TGC	p.C113C	CKAP5_uc009ylg.1_5'UTR|CKAP5_uc001ndj.1_Silent_p.C113C	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein	113					cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2						TGTACATAAGACAGATCTCTA	0.418													6	333	---	---	---	---	PASS
OR1S2	219958	broad.mit.edu	37	11	57970967	57970967	+	Silent	SNP	G	A	A	rs138762515	byFrequency	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57970967G>A	uc010rkb.1	-	1	687	c.687C>T	c.(685-687)TTC>TTT	p.F229F		NM_001004459	NP_001004459	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S,	229	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.0589)				AGACATAGGAGAAGAAGATGA	0.438													9	504	---	---	---	---	PASS
ARL2	402	broad.mit.edu	37	11	64786159	64786159	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64786159G>A	uc001och.3	+	3	387	c.293G>A	c.(292-294)CGC>CAC	p.R98H	ARL2_uc010rnu.1_Missense_Mutation_p.R98H|SNX15_uc001oci.3_5'UTR	NM_001667	NP_001658	P36404	ARL2_HUMAN	ADP-ribosylation factor-like 2	98					cell cycle|centrosome organization|maintenance of protein location in nucleus|negative regulation of GTPase activity|positive regulation of cell-substrate adhesion|positive regulation of microtubule polymerization|small GTPase mediated signal transduction|tight junction assembly|tubulin complex assembly	centrosome|lateral plasma membrane|mitochondrial intermembrane space|nucleus	GTP binding|GTPase activity|GTPase inhibitor activity|protein binding				0						GACCGCCAGCGCATGCAGGAC	0.617													5	46	---	---	---	---	PASS
DYNC2H1	79659	broad.mit.edu	37	11	103158285	103158285	+	Silent	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103158285A>G	uc001pho.2	+	75	11190	c.11046A>G	c.(11044-11046)AGA>AGG	p.R3682R	DYNC2H1_uc001phn.1_Silent_p.R3689R|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3682					cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AGGCGCTAAGACCGGACAGAT	0.333													6	350	---	---	---	---	PASS
ACRV1	56	broad.mit.edu	37	11	125546316	125546316	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125546316C>A	uc001qcs.2	-	3	878	c.611G>T	c.(610-612)CGT>CTT	p.R204L	ACRV1_uc001qck.2_Missense_Mutation_p.R115L|ACRV1_uc001qcl.2_Missense_Mutation_p.R134L|ACRV1_uc001qcm.2_Missense_Mutation_p.R60L|ACRV1_uc001qcn.2_Missense_Mutation_p.R149L|ACRV1_uc001qco.2_Missense_Mutation_p.R109L|ACRV1_uc001qcp.2_Intron|ACRV1_uc001qcq.2_Intron|ACRV1_uc001qcr.2_Missense_Mutation_p.R185L	NM_001612	NP_001603	P26436	ASPX_HUMAN	acrosomal vesicle protein 1 isoform a precursor	204					multicellular organismal development	acrosomal vesicle					0	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0179)|Lung NSC(97;0.0185)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0713)		TCCCTCTCCACGAAGACATTT	0.398													15	415	---	---	---	---	PASS
SLC2A3	6515	broad.mit.edu	37	12	8082243	8082243	+	Intron	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8082243C>T	uc001qtr.2	-						SLC2A3_uc001qts.2_3'UTR	NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		AAGTGAAATACTTTAAGACAC	0.254													4	101	---	---	---	---	PASS
SLC2A3	6515	broad.mit.edu	37	12	8082245	8082245	+	Intron	SNP	T	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8082245T>G	uc001qtr.2	-						SLC2A3_uc001qts.2_3'UTR	NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		GTGAAATACTTTAAGACACGT	0.254													5	107	---	---	---	---	PASS
PRB1	5542	broad.mit.edu	37	12	11506350	11506350	+	Silent	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11506350C>T	uc001qzw.1	-	4	724	c.687G>A	c.(685-687)CAG>CAA	p.Q229Q	PRB1_uc001qzu.1_Intron|PRB1_uc001qzv.1_Intron	NM_005039	NP_005030	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1 isoform 1	290	12.|15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-[PAQ]-Q-[GE]-[GD]- [NKS]-[KSQRN]-[PRQS]-[QS] [GPS]-[PQAR]- [PSR].		Missing (in clone CP-4).|Missing (in clone CP-5).			extracellular region					0			OV - Ovarian serous cystadenocarcinoma(49;0.185)			GACCTTGGGGCTGGTTGCCTC	0.602													12	56	---	---	---	---	PASS
PYROXD1	79912	broad.mit.edu	37	12	21621622	21621622	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21621622G>C	uc001rew.2	+	12	1564	c.1437G>C	c.(1435-1437)ATG>ATC	p.M479I	PYROXD1_uc009ziq.2_Missense_Mutation_p.M220I|PYROXD1_uc009zir.2_Missense_Mutation_p.M185I	NM_024854	NP_079130	Q8WU10	PYRD1_HUMAN	pyridine nucleotide-disulphide oxidoreductase	479							oxidoreductase activity			ovary(1)	1						TAAACCAAATGAATCTTTCAT	0.318													26	127	---	---	---	---	PASS
MYL6	4637	broad.mit.edu	37	12	56555235	56555235	+	3'UTR	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56555235C>T	uc001sjw.1	+	7					MYL6_uc001sjv.2_3'UTR|MYL6_uc001sjx.1_3'UTR|MYL6_uc010sqd.1_3'UTR|MYL6_uc001sjz.2_3'UTR|MYL6_uc010sqe.1_3'UTR	NM_021019	NP_066299	P60660	MYL6_HUMAN	myosin, light chain 6, alkali, smooth muscle and						axon guidance|muscle filament sliding|skeletal muscle tissue development	cytosol|unconventional myosin complex	actin-dependent ATPase activity|calcium ion binding|motor activity|structural constituent of muscle			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(18;0.0979)			CGTGCCTTTCCCTGTGTGAAT	0.512													4	177	---	---	---	---	PASS
PTPRB	5787	broad.mit.edu	37	12	70934675	70934675	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70934675C>T	uc001swb.3	-	21	4933	c.4903G>A	c.(4903-4905)GCT>ACT	p.A1635T	PTPRB_uc010sto.1_Missense_Mutation_p.A1545T|PTPRB_uc010stp.1_Missense_Mutation_p.A1545T|PTPRB_uc001swc.3_Missense_Mutation_p.A1853T|PTPRB_uc001swa.3_Missense_Mutation_p.A1765T	NM_002837	NP_002828	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1635	Helical; (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			GCAACAACAGCCACTAGCATG	0.418													5	330	---	---	---	---	PASS
KCNC2	3747	broad.mit.edu	37	12	75436883	75436883	+	3'UTR	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75436883G>T	uc001sxg.1	-	5					KCNC2_uc009zry.2_Intron|KCNC2_uc001sxe.2_Intron|KCNC2_uc001sxf.2_Intron|KCNC2_uc010stw.1_3'UTR	NM_139137	NP_631875	Q96PR1	KCNC2_HUMAN	Shaw-related voltage-gated potassium channel						energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(2)|pancreas(2)|skin(1)|lung(1)	6						TGGTTGTTTGGTTTACAAGAT	0.438													81	258	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88496844	88496844	+	Intron	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88496844C>T	uc001tar.2	-						CEP290_uc001taq.2_Translation_Start_Site|CEP290_uc001tat.2_Intron	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						TGGTCAAGCACTAGCCACTTT	0.299													9	25	---	---	---	---	PASS
IKBIP	121457	broad.mit.edu	37	12	99020061	99020061	+	Intron	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99020061C>T	uc001tfv.2	-						IKBIP_uc001tfw.2_Intron|IKBIP_uc001tfx.2_Missense_Mutation_p.D261N	NM_201612	NP_963906	Q70UQ0	IKIP_HUMAN	IKK interacting protein isoform 2						induction of apoptosis|response to X-ray	endoplasmic reticulum membrane|integral to membrane	protein binding				0						GGTTCGTAGTCGGAAAGTTTA	0.418													5	409	---	---	---	---	PASS
C12orf51	283450	broad.mit.edu	37	12	112717049	112717049	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112717049C>G	uc009zwc.2	-	3	506	c.488G>C	c.(487-489)GGT>GCT	p.G163A		NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						AGATGACAAACCACTTGTTCC	0.408													10	184	---	---	---	---	PASS
RAN	5901	broad.mit.edu	37	12	131357575	131357575	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131357575T>C	uc001uir.2	+	4	214	c.149T>C	c.(148-150)CTA>CCA	p.L50P	RAN_uc010tbk.1_5'UTR|RAN_uc010tbl.1_5'UTR|RAN_uc001uis.2_Missense_Mutation_p.L70P	NM_006325	NP_006316	P62826	RAN_HUMAN	ras-related nuclear protein	50					androgen receptor signaling pathway|cell division|DNA metabolic process|mitosis|mitotic spindle organization|positive regulation of transcription, DNA-dependent|protein export from nucleus|RNA export from nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|melanosome|nuclear pore|nucleoplasm	androgen receptor binding|chromatin binding|GTP binding|GTPase activity|transcription coactivator activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)		GTTCATCCCCTAGTGTTCCAC	0.468													6	390	---	---	---	---	PASS
FRY	10129	broad.mit.edu	37	13	32776165	32776165	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32776165G>T	uc001utx.2	+	30	4330	c.3834G>T	c.(3832-3834)ATG>ATT	p.M1278I	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	1278					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		AAATCTCCATGCAGCTCATGC	0.373													30	257	---	---	---	---	PASS
COG3	83548	broad.mit.edu	37	13	46054427	46054427	+	Splice_Site	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46054427T>C	uc001vak.2	+	4	650	c.549_splice	c.e4+2	p.Q183_splice	COG3_uc010tfu.1_Splice_Site|COG3_uc001vai.2_Splice_Site_p.Q183_splice|COG3_uc001vaj.1_Splice_Site_p.Q183_splice|COG3_uc010tfv.1_Splice_Site_p.Q20_splice|COG3_uc010aci.2_Splice_Site	NM_031431	NP_113619	Q96JB2	COG3_HUMAN	component of golgi transport complex 3						ER to Golgi vesicle-mediated transport|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein glycosylation|protein localization to organelle|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	cis-Golgi network|Golgi cisterna membrane|Golgi transport complex	protein binding|protein transporter activity			breast(1)|skin(1)	2		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		AAAGAACAGGTAATTTGGAGT	0.333													46	157	---	---	---	---	PASS
SLC7A8	23428	broad.mit.edu	37	14	23635685	23635685	+	Silent	SNP	C	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23635685C>A	uc001wiz.2	-	2	942	c.216G>T	c.(214-216)GTG>GTT	p.V72V	SLC7A8_uc010akj.2_Silent_p.V72V	NM_012244	NP_036376	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (cationic amino acid	72	Helical; (Potential).				blood coagulation|cellular amino acid metabolic process|leukocyte migration|metal ion homeostasis|response to toxin	basolateral plasma membrane|cytoplasm|integral to plasma membrane	neutral amino acid transmembrane transporter activity|organic cation transmembrane transporter activity|peptide antigen binding|protein binding|toxin transporter activity			ovary(1)	1	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	GAGCAAGGCCCACAGAACCAG	0.557													13	145	---	---	---	---	PASS
DHRS4	10901	broad.mit.edu	37	14	24435538	24435538	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24435538C>A	uc001wla.2	+	6	611	c.578C>A	c.(577-579)ACC>AAC	p.T193N	DHRS4_uc010aky.2_Intron|DHRS4_uc001wlb.2_Missense_Mutation_p.T159N|DHRS4_uc010akz.2_Intron|DHRS4_uc001wlc.3_Missense_Mutation_p.T193N|DHRS4L2_uc001wld.3_Intron|DHRS4L2_uc001wle.3_Intron	NM_021004	NP_066284	Q9BTZ2	DHRS4_HUMAN	peroxisomal short-chain alcohol dehydrogenase	193						mitochondrion|nuclear membrane|peroxisome	binding|carbonyl reductase (NADPH) activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CTGGGCCTGACCAAGACCCTG	0.502													10	282	---	---	---	---	PASS
ATG2B	55102	broad.mit.edu	37	14	96789012	96789012	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96789012T>G	uc001yfi.2	-	17	2966	c.2601A>C	c.(2599-2601)GAA>GAC	p.E867D		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	867										ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		CCTCTTCTTCTTCAGCTGCAA	0.408													74	387	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106134738	106134738	+	Intron	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106134738T>C	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001ysb.1_RNA					Parts of antibodies, mostly variable regions.												0						GAGTCCAGCATGGGAGGCGTG	0.587													30	129	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107183575	107183575	+	RNA	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107183575G>T	uc010tyt.1	-	29		c.1982C>A								Parts of antibodies, mostly variable regions.												0						GCCCCTTCCCGGGAGCCTGGC	0.552													5	72	---	---	---	---	PASS
JMJD7-PLA2G4B	8681	broad.mit.edu	37	15	42128715	42128715	+	5'Flank	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42128715C>T	uc010bco.2	+						JMJD7-PLA2G4B_uc001zon.2_Missense_Mutation_p.T223I|JMJD7-PLA2G4B_uc001zoo.3_Missense_Mutation_p.T223I|JMJD7-PLA2G4B_uc010bcn.2_Missense_Mutation_p.T223I|JMJD7-PLA2G4B_uc001zop.1_Missense_Mutation_p.T123I|JMJD7-PLA2G4B_uc001zoq.3_5'Flank	NM_001114633	NP_001108105	P0C869	PA24B_HUMAN	phospholipase A2, group IVB						arachidonic acid metabolic process|calcium-mediated signaling|glycerophospholipid catabolic process|inflammatory response|parturition	cytosol|early endosome membrane|extracellular region|mitochondrial membrane	calcium ion binding|calcium-dependent phospholipase A2 activity|calcium-dependent phospholipid binding|lysophospholipase activity			large_intestine(1)	1						GAAGAGGGCACCTTTAAGGTG	0.567													58	121	---	---	---	---	PASS
LOC645752	645752	broad.mit.edu	37	15	78208239	78208239	+	Silent	SNP	T	C	C	rs74587726	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78208239T>C	uc010bky.2	-	15	1694	c.930A>G	c.(928-930)GCA>GCG	p.A310A	LOC645752_uc010umq.1_5'Flank|uc002bcw.1_5'Flank|uc002bcx.1_5'Flank	NR_027024				SubName: Full=GOLGA6 protein; Flags: Fragment;												0						CCGTCCCATCTGCCTTCTCCT	0.597													34	147	---	---	---	---	PASS
AKAP13	11214	broad.mit.edu	37	15	86262436	86262436	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86262436A>G	uc002blv.1	+	23	6301	c.6131A>G	c.(6130-6132)GAG>GGG	p.E2044G	AKAP13_uc002blu.1_Missense_Mutation_p.E2048G|AKAP13_uc010bnf.1_Missense_Mutation_p.E665G|AKAP13_uc002blw.1_Missense_Mutation_p.E509G|AKAP13_uc002blx.1_Missense_Mutation_p.E289G	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	2044	Interaction with ESR1.|DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						TGTTTGGATGAGCTGATCAGT	0.468													6	305	---	---	---	---	PASS
OR4F15	390649	broad.mit.edu	37	15	102358604	102358604	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102358604C>T	uc010uts.1	+	1	215	c.215C>T	c.(214-216)GCA>GTA	p.A72V		NM_001001674	NP_001001674	Q8NGB8	O4F15_HUMAN	olfactory receptor, family 4, subfamily F,	72	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			ATTGATATGGCATTTTGCTCA	0.418													82	281	---	---	---	---	PASS
PRSS41	360226	broad.mit.edu	37	16	2849526	2849526	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2849526C>T	uc010uwi.1	+	3	536	c.536C>T	c.(535-537)CCG>CTG	p.P179L		NM_001135086	NP_001128558	Q7RTY9	PRS41_HUMAN	testis-specific serine protease 1 precursor	179	Peptidase S1.				proteolysis	anchored to membrane|plasma membrane	serine-type endopeptidase activity				0						GTGCACCGGCCGGACTGCTGG	0.597													35	80	---	---	---	---	PASS
MMP25	64386	broad.mit.edu	37	16	3100414	3100414	+	Silent	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3100414C>T	uc002cth.2	+	4	765	c.528C>T	c.(526-528)CGC>CGT	p.R176R	MMP25_uc002cti.1_Silent_p.R112R	NM_022468	NP_071913	Q9NPA2	MMP25_HUMAN	matrix metalloproteinase 25 preproprotein	176					inflammatory response|proteolysis	anchored to membrane|cell surface|plasma membrane|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0						ACTTTGCCCGCGCCTTCCACC	0.637													16	37	---	---	---	---	PASS
ERI2	112479	broad.mit.edu	37	16	20808364	20808364	+	3'UTR	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20808364G>A	uc010vbb.1	-	9					ERI2_uc002dht.3_3'UTR|ACSM3_uc002dhr.2_3'UTR|ACSM3_uc010vba.1_3'UTR|ERI2_uc002dhs.2_Intron|ERI2_uc010bwh.2_3'UTR|ERI2_uc010vbc.1_3'UTR|ERI2_uc002dhu.1_3'UTR	NM_001142725	NP_001136197	A8K979	ERI2_HUMAN	exoribonuclease 2 isoform 1							intracellular	exonuclease activity|nucleic acid binding|zinc ion binding			large_intestine(1)	1						ACCACAAGATGATGGAGAGGT	0.289													13	107	---	---	---	---	PASS
RRN3P3	100131998	broad.mit.edu	37	16	22441236	22441236	+	RNA	SNP	G	A	A	rs114681793	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22441236G>A	uc002dkp.2	-	5		c.1170C>T			RRN3P3_uc010vbu.1_RNA	NR_027460				Homo sapiens cDNA FLJ31180 fis, clone KIDNE2000266.												0						TGTTCCTCTCGATGATGGTGT	0.507													5	189	---	---	---	---	PASS
ATP2A1	487	broad.mit.edu	37	16	28913241	28913241	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28913241A>T	uc002dro.1	+	16	2342	c.2158A>T	c.(2158-2160)ATG>TTG	p.M720L	uc010vct.1_Intron|ATP2A1_uc002drn.1_Missense_Mutation_p.M720L|ATP2A1_uc002drp.1_Missense_Mutation_p.M595L	NM_173201	NP_775293	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, fast twitch 1 isoform	720	Cytoplasmic (By similarity).				apoptosis in response to endoplasmic reticulum stress|apoptotic mitochondrial changes|ATP biosynthetic process|calcium ion import|elevation of endoplasmic reticulum calcium ion concentration|elevation of mitochondrial calcium ion concentration|maintenance of mitochondrion location|negative regulation of striated muscle contraction|platelet activation|positive regulation of fast-twitch skeletal muscle fiber contraction|reduction of endoplasmic reticulum calcium ion concentration|relaxation of skeletal muscle|response to endoplasmic reticulum stress	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|H zone|I band|microsome|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum|sarcoplasmic reticulum membrane	ATP binding|ATP binding|calcium ion binding|calcium ion binding|calcium-transporting ATPase activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						TGGCATTGCCATGGGATCTGG	0.597													26	80	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	29415043	29415043	+	Translation_Start_Site	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29415043G>A	uc010vct.1	-	1	767	c.-14C>T	c.(-16--12)CACGT>CATGT		RUNDC2C_uc010bys.1_RNA					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																		CTGACTTTACGTGCTGCTGCA	0.577													9	163	---	---	---	---	PASS
COG4	25839	broad.mit.edu	37	16	70548368	70548368	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70548368G>C	uc002ezc.2	-	4	425	c.414C>G	c.(412-414)GAC>GAG	p.D138E	COG4_uc010cfu.2_RNA|COG4_uc002ezd.2_Missense_Mutation_p.D138E|COG4_uc002eze.2_5'UTR	NM_015386	NP_056201	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	134	Interacts with STX5.				Golgi organization|Golgi vesicle prefusion complex stabilization|protein transport|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0		Ovarian(137;0.0694)				AGAACTTCAGGTCCAAGATGT	0.448													63	191	---	---	---	---	PASS
PKD1L3	342372	broad.mit.edu	37	16	71977947	71977947	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71977947G>T	uc010vmm.1	-	24	3845	c.3845C>A	c.(3844-3846)ACT>AAT	p.T1282N		NM_181536	NP_853514			polycystin 1-like 3 precursor												0						AATATCTCCAGTCAGCTTGAA	0.398													7	776	---	---	---	---	PASS
YWHAE	7531	broad.mit.edu	37	17	1257637	1257637	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1257637C>T	uc002fsj.2	-	5	735	c.583G>A	c.(583-585)GCA>ACA	p.A195T	YWHAE_uc002fsk.2_Missense_Mutation_p.A173T|YWHAE_uc010vqh.1_RNA|YWHAE_uc010vqi.1_RNA	NM_006761	NP_006752	P62258	1433E_HUMAN	tyrosine 3/tryptophan 5 -monooxygenase	195					apoptosis|G2/M transition of mitotic cell cycle|induction of apoptosis by extracellular signals|interspecies interaction between organisms|intracellular signal transduction|nerve growth factor receptor signaling pathway	cytosol|melanosome	histone deacetylase binding|phosphoserine binding			lung(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(18;0.203)	UCEC - Uterine corpus endometrioid carcinoma (25;0.0887)		GCTGCTTTTGCCAACCTAAAG	0.348													4	214	---	---	---	---	PASS
PIK3R5	23533	broad.mit.edu	37	17	8784087	8784087	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8784087A>G	uc002glt.2	-	19	2579	c.2512T>C	c.(2512-2514)TGC>CGC	p.C838R	PIK3R5_uc010vuz.1_Missense_Mutation_p.C838R|PIK3R5_uc002glu.3_Missense_Mutation_p.C452R	NM_014308	NP_055123	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	838					platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5						GGCTTGTAGCACGGTGAGACC	0.652													5	114	---	---	---	---	PASS
MYH1	4619	broad.mit.edu	37	17	10404988	10404988	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10404988T>C	uc002gmo.2	-	26	3365	c.3271A>G	c.(3271-3273)ATG>GTG	p.M1091V	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1091	Potential.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21						AGACCGCTCATTTCAAACTCT	0.373													6	350	---	---	---	---	PASS
TEKT3	64518	broad.mit.edu	37	17	15222427	15222427	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15222427T>C	uc002gon.2	-	5	888	c.701A>G	c.(700-702)AAG>AGG	p.K234R		NM_031898	NP_114104	Q9BXF9	TEKT3_HUMAN	tektin 3	234					microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		CAAATGTAGCTTCATTCTTTC	0.308													6	411	---	---	---	---	PASS
CCDC144C	348254	broad.mit.edu	37	17	20254635	20254635	+	RNA	SNP	G	A	A	rs148192621	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20254635G>A	uc010cqy.1	+	8		c.1958G>A				NR_023380				Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.												0						AAATAGCCTCGGAGGATTGTG	0.368													7	506	---	---	---	---	PASS
FMNL1	752	broad.mit.edu	37	17	43323619	43323619	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43323619G>T	uc002iin.2	+	25	3333	c.3133G>T	c.(3133-3135)GAG>TAG	p.E1045*	FMNL1_uc002iiq.2_Nonsense_Mutation_p.E623*|FMNL1_uc010dag.2_RNA|LOC100133991_uc010dah.2_5'Flank	NM_005892	NP_005883	O95466	FMNL_HUMAN	formin-like 1	1045					actin cytoskeleton organization		actin binding|Rho GTPase binding			pancreas(1)	1						CCTCATCTCTGAGCTGAAACG	0.567													10	49	---	---	---	---	PASS
ARL17A	51326	broad.mit.edu	37	17	44630635	44630635	+	3'UTR	SNP	A	G	G	rs150521815	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44630635A>G	uc002iks.2	-	4					LRRC37A2_uc002ikn.1_Intron|ARL17A_uc002iko.3_Intron|LRRC37A2_uc002ikq.1_Intron	NM_001113738	NP_001107210	Q8IVW1	ARL17_HUMAN	hypothetical protein LOC51326 isoform a						protein transport|vesicle-mediated transport	Golgi apparatus	GTP binding				0						TACACAGCATACAATTCCTGT	0.239													25	149	---	---	---	---	PASS
TLK2	11011	broad.mit.edu	37	17	60637441	60637441	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60637441G>A	uc010ddp.2	+	10	1053	c.785G>A	c.(784-786)CGA>CAA	p.R262Q	TLK2_uc002izx.3_Missense_Mutation_p.R110Q|TLK2_uc002izz.3_Missense_Mutation_p.R262Q|TLK2_uc002jaa.3_Missense_Mutation_p.R230Q|TLK2_uc010wpd.1_Missense_Mutation_p.R230Q	NM_006852	NP_006843	Q86UE8	TLK2_HUMAN	tousled-like kinase 2 isoform A	262	Potential.		R -> Q.		cell cycle|chromatin modification|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|kidney(1)	2						TACAAGGAACGATTAAATAGA	0.358													6	380	---	---	---	---	PASS
NEDD4L	23327	broad.mit.edu	37	18	56033230	56033230	+	Splice_Site	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56033230G>A	uc002lgy.2	+	21	2108	c.1834_splice	c.e21-1	p.A612_splice	NEDD4L_uc002lgz.2_Splice_Site_p.A548_splice|NEDD4L_uc002lgx.2_Splice_Site_p.A592_splice|NEDD4L_uc010xee.1_Splice_Site_p.A491_splice|NEDD4L_uc002lhc.2_Splice_Site_p.A604_splice|NEDD4L_uc002lhd.2_Splice_Site_p.A491_splice|NEDD4L_uc002lhb.2_Splice_Site_p.A471_splice|NEDD4L_uc002lhe.2_Splice_Site_p.A584_splice|NEDD4L_uc002lhf.2_Splice_Site_p.A471_splice|NEDD4L_uc002lhg.2_Splice_Site_p.A491_splice|NEDD4L_uc002lhh.2_Splice_Site_p.A387_splice|NEDD4L_uc010dpn.2_5'Flank	NM_001144967	NP_001138439	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4						CTTTTGTGTAGGCTGATATCC	0.338													33	359	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9066942	9066942	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9066942A>G	uc002mkp.2	-	3	20708	c.20504T>C	c.(20503-20505)CTC>CCC	p.L6835P		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	6837	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						GCTAGGGGTGAGCAGTGAGGT	0.498													7	542	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9089241	9089241	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9089241A>C	uc002mkp.2	-	1	2778	c.2574T>G	c.(2572-2574)CAT>CAG	p.H858Q		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	858	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TAGTAAATAGATGAGTGGAAG	0.468													42	160	---	---	---	---	PASS
LPHN1	22859	broad.mit.edu	37	19	14268697	14268697	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14268697C>G	uc010xnn.1	-	14	2843	c.2547G>C	c.(2545-2547)GAG>GAC	p.E849D	LPHN1_uc010xno.1_Missense_Mutation_p.E844D|uc002myf.2_Intron	NM_001008701	NP_001008701	O94910	LPHN1_HUMAN	latrophilin 1 isoform 1 precursor	849	GPS.|Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(2)|lung(2)|central_nervous_system(1)	5						AGCTTACGATCTCACGGTGAG	0.622													14	80	---	---	---	---	PASS
CLEC17A	388512	broad.mit.edu	37	19	14707756	14707756	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14707756T>C	uc010dzn.1	+	9	591	c.514T>C	c.(514-516)TAC>CAC	p.Y172H	CLEC17A_uc002mzh.1_Missense_Mutation_p.Y155H|CLEC17A_uc010xnt.1_RNA|CLEC17A_uc010xnu.1_Missense_Mutation_p.Y172H|CLEC17A_uc010dzo.1_Missense_Mutation_p.Y172H			Q6ZS10	CL17A_HUMAN	SubName: Full=CLEC17A protein;	172	Cytoplasmic (Potential).					cell surface|integral to membrane	fucose binding|mannose binding|metal ion binding|receptor activity				0						GTGGATGGTGTACCTGTGTCT	0.582													6	402	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	19	22785425	22785425	+	RNA	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22785425G>A	uc002nqu.3	+	8		c.1514G>A								Homo sapiens cDNA FLJ60031 complete cds, moderately similar to Golgin subfamily A member 2.																		TGCAGCTGATGCAGGAAAAGG	0.577													3	24	---	---	---	---	PASS
ZNF566	84924	broad.mit.edu	37	19	36964349	36964349	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36964349C>T	uc002oea.3	-	3	103	c.21G>A	c.(19-21)ATG>ATA	p.M7I	ZNF566_uc010xte.1_Missense_Mutation_p.M7I|ZNF566_uc010xtf.1_Missense_Mutation_p.M7I|ZNF566_uc002oeb.3_Missense_Mutation_p.M7I|ZNF566_uc002oec.3_Intron|ZNF566_uc010xtg.1_Intron	NM_032838	NP_116227	Q969W8	ZN566_HUMAN	zinc finger protein 566 isoform 1	7	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.162)					CATCACTGAACATCACTGACT	0.378													5	437	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40363154	40363154	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40363154C>A	uc002omp.3	-	32	14924	c.14916G>T	c.(14914-14916)ATG>ATT	p.M4972I		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	4972	VWFD 12.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TGGGGATGGACATGAGGAGGT	0.627													9	17	---	---	---	---	PASS
MAP3K10	4294	broad.mit.edu	37	19	40704325	40704325	+	Silent	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40704325G>A	uc002ona.2	+	2	1014	c.726G>A	c.(724-726)ACG>ACA	p.T242T	MAP3K10_uc002onb.2_5'UTR	NM_002446	NP_002437	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase	242	Protein kinase.				activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway	cytoplasm	ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity			ovary(2)|lung(2)|skin(1)|pancreas(1)	6						TCGCAGACACGGTGCTCAAGA	0.637													3	80	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29632707	29632707	+	Intron	SNP	G	A	A	rs6057187		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29632707G>A	uc010ztl.1	+						FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010ztk.1_Silent_p.E96E					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						TTTTGCATGAGACGCTTCTGG	0.313													12	68	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29633900	29633900	+	Intron	SNP	A	G	G	rs60081496	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29633900A>G	uc010ztl.1	+						FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						TAAACAAGAGAACCAAATTGA	0.264													10	524	---	---	---	---	PASS
FRG1B	284802	broad.mit.edu	37	20	29633987	29633987	+	Intron	SNP	T	A	A	rs4006817		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29633987T>A	uc010ztl.1	+						FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						CTGAATAAAATATTCAGAGGA	0.308													21	336	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	21	10862643	10862643	+	IGR	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10862643C>T								None (None upstream) : TPTE (44100 downstream)																							TTGGAGGATCCTGTTTTTGGT	0.502													81	520	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11020869	11020869	+	3'UTR	SNP	G	A	A	rs9981999		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11020869G>A	uc002yit.1	-	10					TPTE_uc002yis.1_RNA	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CAGGCAAGTAGTCTTCCTTCT	0.358													22	223	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	22	18844888	18844888	+	RNA	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18844888A>G	uc002zoe.2	+	4		c.2142A>G			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		GCTCACGGAAATACAGCTTCA	0.587													6	62	---	---	---	---	PASS
PRAME	23532	broad.mit.edu	37	22	22899279	22899279	+	5'UTR	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22899279G>A	uc002zwf.2	-	2					LOC96610_uc011aim.1_Intron|PRAME_uc011air.1_5'Flank|PRAME_uc010gtr.2_5'UTR|PRAME_uc002zwg.2_5'UTR|PRAME_uc002zwh.2_5'UTR|PRAME_uc002zwi.2_5'UTR|PRAME_uc002zwj.2_5'UTR|PRAME_uc002zwk.2_5'UTR|LOC648691_uc011ais.1_5'Flank	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma						apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|regulation of growth|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding			central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		CTGGCCTCAGGACCTCCAACG	0.478													35	137	---	---	---	---	PASS
POM121L9P	29774	broad.mit.edu	37	22	24656904	24656904	+	RNA	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24656904C>T	uc002zzs.3	+	5		c.2184C>T				NR_003714				Homo sapiens mRNA; cDNA DKFZp434P211 (from clone DKFZp434P211).												0						GCTGTTTCAACGCCACCACCA	0.602													8	62	---	---	---	---	PASS
HPS4	89781	broad.mit.edu	37	22	26877723	26877723	+	Silent	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26877723G>T	uc003acl.2	-	2	665	c.6C>A	c.(4-6)GCC>GCA	p.A2A	HPS4_uc003aci.2_5'Flank|HPS4_uc003acj.2_5'Flank|HPS4_uc003ack.2_5'UTR|HPS4_uc003acn.2_5'UTR|HPS4_uc010gvd.1_Silent_p.A2A|HPS4_uc003aco.1_5'Flank|SRRD_uc003acp.3_5'Flank|SRRD_uc010gve.2_5'Flank	NM_022081	NP_071364	Q9NQG7	HPS4_HUMAN	light ear protein isoform a	2					lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting	lysosome|melanosome|membrane fraction|platelet dense granule	protein homodimerization activity				0						AGGTAGAGGTGGCCATCTACT	0.488									Hermansky-Pudlak_syndrome				10	594	---	---	---	---	PASS
CSNK1E	1454	broad.mit.edu	37	22	38776379	38776379	+	5'UTR	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38776379T>C	uc003avm.1	-	3					LOC400927_uc010gxm.2_RNA|LOC400927_uc011ans.1_RNA|LOC400927_uc011ant.1_RNA|LOC400927_uc003avr.1_RNA	NM_152221	NP_689407	P49674	KC1E_HUMAN	casein kinase 1 epsilon						DNA repair|G2/M transition of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|signal transduction	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Melanoma(58;0.045)					ACTCACCTTTTACTGATAGGT	0.388													18	412	---	---	---	---	PASS
MAGEB6	158809	broad.mit.edu	37	X	26212519	26212519	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26212519A>C	uc004dbr.2	+	2	705	c.556A>C	c.(556-558)ATT>CTT	p.I186L	MAGEB6_uc010ngc.1_5'UTR	NM_173523	NP_775794	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	186										ovary(3)	3						GAAAGCCATCATTTTTAAGCG	0.478													6	116	---	---	---	---	PASS
PRRG1	5638	broad.mit.edu	37	X	37312773	37312773	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37312773A>G	uc004ddn.2	+	5	809	c.556A>G	c.(556-558)ACA>GCA	p.T186A	PRRG1_uc004ddo.2_Missense_Mutation_p.T186A	NM_000950	NP_000941	O14668	TMG1_HUMAN	proline rich Gla (G-carboxyglutamic acid) 1	186	Cytoplasmic (Potential).					extracellular region|integral to plasma membrane	calcium ion binding			ovary(1)|breast(1)	2						GAGGAGTGAAACAGAACCTCA	0.532													5	249	---	---	---	---	PASS
GAGE12J	729396	broad.mit.edu	37	X	49179705	49179705	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49179705G>T	uc010nit.2	+	2	149	c.33G>T	c.(31-33)TGG>TGT	p.W11C	GAGE12J_uc004dnl.3_Missense_Mutation_p.W11C|GAGE10_uc010nis.2_Intron|GAGE12J_uc004dnk.3_Missense_Mutation_p.W11C	NM_001098406	NP_001091876	A6NER3	GG12J_HUMAN	G antigen 12J	11											0	Ovarian(276;0.236)					CCTATTATTGGCCTAGACCAA	0.443													5	244	---	---	---	---	PASS
STARD8	9754	broad.mit.edu	37	X	67936239	67936239	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67936239C>G	uc004dxa.2	+	4	395	c.23C>G	c.(22-24)TCG>TGG	p.S8W	STARD8_uc004dxb.2_Missense_Mutation_p.S88W|STARD8_uc004dxc.3_Missense_Mutation_p.S8W	NM_014725	NP_055540	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain	8					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion	GTPase activator activity			breast(3)|ovary(2)|pancreas(1)	6						AATTGTGCCTCGATGAAACTG	0.502													11	534	---	---	---	---	PASS
KLHL4	56062	broad.mit.edu	37	X	86924534	86924534	+	3'UTR	SNP	G	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86924534G>T	uc004efb.2	+	11					KLHL4_uc004efa.2_3'UTR	NM_019117	NP_061990	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 1							cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5						AAAAAACCCTGTGACTCTGGA	0.373													16	42	---	---	---	---	PASS
KIAA1210	57481	broad.mit.edu	37	X	118223222	118223222	+	Silent	SNP	A	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118223222A>G	uc004era.3	-	11	1971	c.1971T>C	c.(1969-1971)GCT>GCC	p.A657A		NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481	657										ovary(4)|skin(1)	5						CAGCTCCAGAAGCTGCATCTT	0.483													5	246	---	---	---	---	PASS
THOC2	57187	broad.mit.edu	37	X	122747970	122747970	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122747970T>C	uc004etu.2	-	34	4414	c.4382A>G	c.(4381-4383)GAC>GGC	p.D1461G	THOC2_uc010nqt.1_RNA|THOC2_uc004etw.1_Missense_Mutation_p.D282G	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN	THO complex 2	1461	Lys-rich.				intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding			ovary(3)	3						CCTTGACTTGTCCAAATCTTT	0.348													8	630	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	1913	1913	+	5'Flank	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:1913G>A	uc004coq.3	-						uc004cos.3_RNA					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		CCCCCGAAACCAGACGAGCTA	0.438													5	54	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	3010	3010	+	5'Flank	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:3010G>A	uc004coq.3	-						uc004cos.3_RNA|uc011mfh.1_5'Flank					Homo sapiens cDNA: FLJ22857 fis, clone KAT01615.																		TCAGGACATCCCGATGGTGCA	0.453													7	64	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	7805	7805	+	RNA	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:7805G>A	uc004cou.3	+	1		c.220G>A			uc011mfi.1_5'Flank|uc004cov.3_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP42.																		CCATCATCCTAGTCCTCATCG	0.463													7	91	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	9043	9043	+	RNA	SNP	C	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:9043C>T	uc011mfi.1	+	1		c.381C>T			uc004cov.3_5'Flank					Homo sapiens mRNA for OK/SW-CL.16, complete cds.																		TACTCATGCACCTAATTGGAA	0.443													3	71	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	9384	9384	+	RNA	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:9384G>A	uc011mfi.1	+	1		c.722G>A			uc004cov.3_5'Flank|uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens mRNA for OK/SW-CL.16, complete cds.																		AATGGTGGCGCGATGTAACAC	0.458													4	100	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15110	15110	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15110G>A	uc004coy.2	+	1	350	c.275G>A	c.(274-276)TGC>TAC	p.C92Y	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		TCCTCCTGCTTGCAACTATAG	0.453											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	7	83	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15784	15784	+	3'UTR	SNP	T	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15784T>C	uc004coy.2	+	1					uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		GTAAGCTACCCTTTTACCATC	0.403													6	89	---	---	---	---	PASS
CAMTA1	23261	broad.mit.edu	37	1	7805266	7805266	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7805266delT	uc001aoi.2	+						CAMTA1_uc001aok.3_Intron|CAMTA1_uc001aoj.2_Intron|CAMTA1_uc009vmf.2_Intron	NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TCTCCCATTATTTTTTTTACT	0.308													4	2	---	---	---	---	
RPA2	6118	broad.mit.edu	37	1	28223824	28223825	+	Intron	INS	-	T	T	rs150650563	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28223824_28223825insT	uc001bpe.1	-						RPA2_uc001bpd.1_Intron|RPA2_uc010ofp.1_Intron	NM_002946	NP_002937	P15927	RFA2_HUMAN	replication protein A2, 32kDa						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|regulation of double-strand break repair via homologous recombination|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor A complex|PML body	protein phosphatase binding|single-stranded DNA binding			skin(1)	1		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0429)|OV - Ovarian serous cystadenocarcinoma(117;3.62e-24)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;1.75e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00294)|STAD - Stomach adenocarcinoma(196;0.00308)|BRCA - Breast invasive adenocarcinoma(304;0.00613)|READ - Rectum adenocarcinoma(331;0.0649)		gctaagggacattaataatttt	0.188								Direct_reversal_of_damage|NER					9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	28300771	28300772	+	IGR	DEL	AG	-	-	rs34863997		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28300771_28300772delAG								XKR8 (6167 upstream) : EYA3 (47 downstream)																							GGATAAagacagagagagagag	0.223													6	3	---	---	---	---	
EYA3	2140	broad.mit.edu	37	1	28369364	28369364	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28369364delT	uc001bpi.1	-						EYA3_uc010ofs.1_Intron|EYA3_uc010oft.1_Intron|EYA3_uc001bpj.2_Intron|EYA3_uc001bpk.1_Intron|EYA3_uc010ofu.1_Intron	NM_001990	NP_001981	Q99504	EYA3_HUMAN	eyes absent 3						anatomical structure morphogenesis|double-strand break repair|histone dephosphorylation|multicellular organismal development|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|transcription, DNA-dependent|visual perception	cytoplasm	metal ion binding|protein binding|protein tyrosine phosphatase activity			ovary(2)|skin(1)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)		CCGCTCtttcttttttttttg	0.209													4	2	---	---	---	---	
C1orf94	84970	broad.mit.edu	37	1	34684572	34684577	+	3'UTR	DEL	ACACAT	-	-	rs3831264	byFrequency	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34684572_34684577delACACAT	uc001bxs.3	+	7					C1orf94_uc001bxt.2_3'UTR	NM_032884	NP_116273	Q6P1W5	CA094_HUMAN	hypothetical protein LOC84970 isoform b								protein binding				0		Myeloproliferative disorder(586;0.0393)				ACACACACACACACATGACCCTCATA	0.374													15	11	---	---	---	---	
MACF1	23499	broad.mit.edu	37	1	39834183	39834183	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39834183delT	uc010oiu.1	+						MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ttttcttttctttttttttga	0.179													4	3	---	---	---	---	
KDM4A	9682	broad.mit.edu	37	1	44159696	44159696	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44159696delC	uc001cjx.2	+	17	2573	c.2407delC	c.(2407-2409)CTGfs	p.L803fs	KDM4A_uc010oki.1_Intron	NM_014663	NP_055478	O75164	KDM4A_HUMAN	jumonji domain containing 2A	803					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleolus	histone demethylase activity (H3-K36 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1						TGTGGCAATTCTGGAAGCAAG	0.532													132	57	---	---	---	---	
AGL	178	broad.mit.edu	37	1	100358386	100358387	+	Intron	INS	-	TTCTT	TTCTT	rs146517912	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100358386_100358387insTTCTT	uc001dsi.1	+						AGL_uc001dsj.1_Intron|AGL_uc001dsk.1_Intron|AGL_uc001dsl.1_Intron|AGL_uc001dsm.1_Intron|AGL_uc001dsn.1_Intron	NM_000642	NP_000633	P35573	GDE_HUMAN	amylo-1,6-glucosidase,						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|isoamylase complex|nucleus	4-alpha-glucanotransferase activity|amylo-alpha-1,6-glucosidase activity|cation binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		TGGCTAGCTGATTCTTCATGTT	0.272													3	4	---	---	---	---	
NBPF7	343505	broad.mit.edu	37	1	120381686	120381687	+	Intron	INS	-	T	T	rs144031576	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120381686_120381687insT	uc010oxk.1	-							NM_001047980	NP_001041445	P0C2Y1	NBPF7_HUMAN	hypothetical protein LOC343505							cytoplasm				ovary(1)|skin(1)	2	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;3.66e-05)|Lung NSC(69;0.000192)|all_epithelial(167;0.0347)		Lung(183;0.0103)|LUSC - Lung squamous cell carcinoma(189;0.0544)		gtgattataTGGAGCACCTAGC	0.213													34	23	---	---	---	---	
NBPF7	343505	broad.mit.edu	37	1	120381687	120381688	+	Intron	INS	-	TGAGTCAC	TGAGTCAC	rs34302627		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120381687_120381688insTGAGTCAC	uc010oxk.1	-							NM_001047980	NP_001041445	P0C2Y1	NBPF7_HUMAN	hypothetical protein LOC343505							cytoplasm				ovary(1)|skin(1)	2	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;3.66e-05)|Lung NSC(69;0.000192)|all_epithelial(167;0.0347)		Lung(183;0.0103)|LUSC - Lung squamous cell carcinoma(189;0.0544)		tgattataTGGAGCACCTAGCT	0.218													42	23	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	142538778	142538779	+	IGR	INS	-	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142538778_142538779insT								None (None upstream) : None (None downstream)																							gcactccagcagggtgacagag	0.010													8	12	---	---	---	---	
VPS72	6944	broad.mit.edu	37	1	151157066	151157067	+	Intron	INS	-	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151157066_151157067insT	uc001exe.1	-						VPS72_uc001exf.1_Intron	NM_005997	NP_005988	Q15906	VPS72_HUMAN	transcription factor-like 1						chromatin modification|negative regulation of transcription from RNA polymerase II promoter	nucleus|protein complex	DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|pancreas(1)	2	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			Atttttttttcttttttttttt	0.129													5	3	---	---	---	---	
C1orf14	81626	broad.mit.edu	37	1	182873670	182873671	+	Intron	DEL	GT	-	-	rs71895744		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182873670_182873671delGT	uc001gpu.2	-						C1orf14_uc001gpv.2_Intron|C1orf14_uc010pnz.1_Intron|C1orf14_uc001gpw.2_Intron	NM_030933	NP_112195	Q9BZQ2	SHP1L_HUMAN	chromosome 1 open reading frame 14												0				Colorectal(1306;1.64e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00267)		CCCtgtgtgcgtgtgtgtgtgt	0.178													11	5	---	---	---	---	
NEK7	140609	broad.mit.edu	37	1	198248340	198248341	+	Intron	INS	-	AAGAGG	AAGAGG	rs145872676	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198248340_198248341insAAGAGG	uc001gun.3	+							NM_133494	NP_598001	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7							cytoplasm	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|lung(1)|ovary(1)	4						CAACTCTCTATTAGGTATAAGG	0.342													9	8	---	---	---	---	
NEK7	140609	broad.mit.edu	37	1	198248341	198248342	+	Intron	INS	-	ATAAG	ATAAG	rs75987902		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198248341_198248342insATAAG	uc001gun.3	+							NM_133494	NP_598001	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7							cytoplasm	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|lung(1)|ovary(1)	4						AACTCTCTATTAGGTATAAGGT	0.342													12	6	---	---	---	---	
PLXNA2	5362	broad.mit.edu	37	1	208224174	208224174	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208224174delA	uc001hgz.2	-							NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)		gccatgtcttaaaaaaaaaaa	0.194													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	228254475	228254475	+	IGR	DEL	T	-	-	rs58793961		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228254475delT								WNT3A (5514 upstream) : ARF1 (15886 downstream)																							tctctctctctTTTTTTTTTT	0.413													5	4	---	---	---	---	
MYT1L	23040	broad.mit.edu	37	2	1967126	1967126	+	Intron	DEL	G	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1967126delG	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		aagcacaggtggagtagattt	0.000													4	2	---	---	---	---	
CMPK2	129607	broad.mit.edu	37	2	7001234	7001235	+	Intron	DEL	CG	-	-	rs3085147		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7001234_7001235delCG	uc002qyo.2	-						CMPK2_uc010yis.1_Intron|CMPK2_uc010ewv.2_Intron	NM_207315	NP_997198	Q5EBM0	CMPK2_HUMAN	UMP-CMP kinase 2 precursor						dTDP biosynthetic process	mitochondrion	ATP binding|cytidylate kinase activity|thymidylate kinase activity|UMP kinase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					Tacacacacacgcacacacaca	0.198													23	23	---	---	---	---	
SMC6	79677	broad.mit.edu	37	2	17959442	17959443	+	Intron	DEL	TA	-	-	rs10535306	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17959442_17959443delTA	uc010exo.2	-						GEN1_uc002rct.2_Intron|GEN1_uc010yjs.1_Intron|GEN1_uc002rcu.2_Intron	NM_024624	NP_078900	Q96SB8	SMC6_HUMAN	SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					tagatatgtgtatatatatata	0.074													3	4	---	---	---	---	
DYSF	8291	broad.mit.edu	37	2	71845807	71845808	+	Intron	INS	-	GGT	GGT	rs138860021	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71845807_71845808insGGT	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron|DYSF_uc010yqy.1_Intron|DYSF_uc010yqz.1_Intron	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						tgtgtggtagagggatgtgagt	0.183													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89555603	89555604	+	Intron	DEL	AG	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89555603_89555604delAG	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		gaagcctggcagacaccccctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89924052	89924053	+	Intron	INS	-	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89924052_89924053insC	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		CATAACATAAACCCCCCAAGGA	0.510													40	19	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	91801336	91801337	+	IGR	INS	-	ATGT	ATGT	rs56344501		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91801336_91801337insATGT								None (None upstream) : LOC654342 (3855 downstream)																							catgactaccattagctcccac	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96610787	96610788	+	5'Flank	INS	-	A	A	rs148448972	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96610787_96610788insA	uc002sva.1	-						uc010yug.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		actctgtctacaaaaaataaga	0.104													132	109	---	---	---	---	
ANKRD36	375248	broad.mit.edu	37	2	97817803	97817807	+	Intron	DEL	CACTG	-	-	rs5832831		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97817803_97817807delCACTG	uc010yva.1	+						ANKRD36_uc010yuz.1_Intron|ANKRD36_uc010fic.2_Intron|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Intron	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36												0						gatcttggctcactgcagtttccat	0.024													66	45	---	---	---	---	
LONRF2	164832	broad.mit.edu	37	2	100906570	100906571	+	Intron	INS	-	AAAT	AAAT	rs139366121	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100906570_100906571insAAAT	uc002tal.3	-						LONRF2_uc010yvs.1_Intron	NM_198461	NP_940863	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger						proteolysis		ATP-dependent peptidase activity|zinc ion binding			large_intestine(1)|skin(1)	2						ccttgactcaaaaataaacaaa	0.124													9	4	---	---	---	---	
MYO7B	4648	broad.mit.edu	37	2	128341532	128341533	+	Intron	DEL	GT	-	-	rs150669299		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128341532_128341533delGT	uc002top.2	+							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)		AGGAGAGAGAGTGTGCAGGAAT	0.515													6	5	---	---	---	---	
SCN1A	6323	broad.mit.edu	37	2	166909122	166909123	+	Intron	INS	-	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166909122_166909123insA	uc010zcz.1	-						SCN1A_uc002udo.3_Intron|SCN1A_uc010fpk.2_Intron	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	CTAACATGGTGAAAAAAAAAAA	0.317													5	3	---	---	---	---	
TTN	7273	broad.mit.edu	37	2	179537655	179537655	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179537655delT	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron|TTN_uc010zfk.1_5'Flank|TTN_uc002una.1_Intron|TTN_uc010frf.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTGCCATTCTTTTTTTTTTC	0.303													7	4	---	---	---	---	
KCTD18	130535	broad.mit.edu	37	2	201362780	201362782	+	Intron	DEL	TCT	-	-	rs71715967		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201362780_201362782delTCT	uc002uvs.2	-						KCTD18_uc002uvt.2_Intron|KCTD18_uc002uvu.1_Intron	NM_152387	NP_689600	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1						TATTTTGATCTCTTTTTATCATA	0.276													5	6	---	---	---	---	
ORC2L	4999	broad.mit.edu	37	2	201778390	201778402	+	Intron	DEL	ACTTGGCAGATAC	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201778390_201778402delACTTGGCAGATAC	uc002uwr.2	-						ORC2L_uc010zhj.1_3'UTR	NM_006190	NP_006181	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2						cell cycle checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0						AAAAATATGTACTTGGCAGATACACATCCATAG	0.357													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	207275255	207275256	+	IGR	INS	-	CTGGTCTTG	CTGGTCTTG	rs138878079	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207275255_207275256insCTGGTCTTG								ZDBF2 (96107 upstream) : ADAM23 (33112 downstream)																							CACAGACCACCACCTTGAACCT	0.515													43	183	---	---	---	---	
PIKFYVE	200576	broad.mit.edu	37	2	209210976	209210986	+	Intron	DEL	CTACTTATGAT	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209210976_209210986delCTACTTATGAT	uc002vcz.2	+							NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type						cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding			ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1)	10						CAATGATTTACTACTTATGATCTCTGAAATA	0.270													36	24	---	---	---	---	
GIGYF2	26058	broad.mit.edu	37	2	233680614	233680614	+	Intron	DEL	A	-	-	rs151161298		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233680614delA	uc002vti.3	+						GIGYF2_uc010zmj.1_Intron|GIGYF2_uc002vtg.2_Intron|GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc010zml.1_Intron|GIGYF2_uc002vtq.3_Intron	NM_015575	NP_056390	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2 isoform b						cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		CTCTTCTCCCAAAAAAAAAAA	0.299													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	236144645	236144645	+	IGR	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236144645delT								SH3BP4 (180289 upstream) : AGAP1 (258091 downstream)																							aaaacatctctttttttagac	0.015													4	2	---	---	---	---	
GPC1	2817	broad.mit.edu	37	2	241403969	241403970	+	Intron	INS	-	CC	CC	rs111613058		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241403969_241403970insCC	uc002vyw.3	+							NM_002081	NP_002072	P35052	GPC1_HUMAN	glypican 1 precursor						axon guidance	anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		CGCCTGCGTGTGCGTGTCAACG	0.579													21	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	242912467	242912469	+	5'Flank	DEL	TGA	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242912467_242912469delTGA	uc002wcs.1	+											Homo sapiens cDNA FLJ40615 fis, clone THYMU2012882.																		agtgtggcgttgatgatgaggCG	0.261													1	5	---	---	---	---	
C3orf24	115795	broad.mit.edu	37	3	10146617	10146621	+	Intron	DEL	TTATT	-	-	rs113292025		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10146617_10146621delTTATT	uc003buz.2	-						C3orf24_uc003bva.1_Intron	NM_173472	NP_775743	Q96PS1	CC024_HUMAN	hypothetical protein LOC115795												0				OV - Ovarian serous cystadenocarcinoma(96;0.196)		ATATTAGTAAttattttattttatt	0.180													4	2	---	---	---	---	
LIMD1	8994	broad.mit.edu	37	3	45677635	45677636	+	Intron	INS	-	T	T	rs5848761		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45677635_45677636insT	uc003coq.2	+							NM_014240	NP_055055	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1						cytoplasmic mRNA processing body assembly|gene silencing by miRNA|multicellular organismal development|negative regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasmic mRNA processing body|nucleus|RNA-induced silencing complex	protein binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		TTCTCTTGTCCTGCAAGGAGCC	0.520													95	71	---	---	---	---	
LIMD1	8994	broad.mit.edu	37	3	45677639	45677639	+	Intron	DEL	A	-	-	rs5848762		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45677639delA	uc003coq.2	+							NM_014240	NP_055055	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1						cytoplasmic mRNA processing body assembly|gene silencing by miRNA|multicellular organismal development|negative regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasmic mRNA processing body|nucleus|RNA-induced silencing complex	protein binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		CTTGTCCTGCAAGGAGCCTGT	0.517													96	70	---	---	---	---	
ALS2CL	259173	broad.mit.edu	37	3	46728113	46728113	+	Intron	DEL	G	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46728113delG	uc003cqa.1	-						ALS2CL_uc003cqb.1_Intron|ALS2CL_uc003cqc.1_Intron	NM_147129	NP_667340	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like isoform 1						endosome organization|regulation of Rho protein signal transduction		GTPase activator activity|identical protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)|central_nervous_system(2)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		GCTTGGCCCTGGGCCCACGTG	0.627													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	76579395	76579396	+	IGR	INS	-	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76579395_76579396insC								ZNF717 (744725 upstream) : ROBO2 (509898 downstream)																							CAAAGTAATTTCCCCCTGGACT	0.455													4	2	---	---	---	---	
CP	1356	broad.mit.edu	37	3	148918731	148918731	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148918731delA	uc003ewy.3	-						CP_uc011bnr.1_Intron|CP_uc003ewx.3_Intron|CP_uc003ewz.2_Intron|CP_uc010hvf.1_Intron	NM_000096	NP_000087	P00450	CERU_HUMAN	ceruloplasmin precursor						cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	CACCGCTAGGAAAAAAAAAAG	0.418													9	4	---	---	---	---	
LPP	4026	broad.mit.edu	37	3	188103872	188103872	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188103872delA	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		ATAGGTGAACAAAAAAAAGTA	0.323			T	HMGA2|MLL|C12orf9	lipoma|leukemia								4	3	---	---	---	---	
LMLN	89782	broad.mit.edu	37	3	197765731	197765731	+	3'UTR	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197765731delT	uc011buo.1	+	16					LMLN_uc003fyt.2_3'UTR|LMLN_uc010iar.2_3'UTR|LMLN_uc010ias.2_3'UTR|LMLN_uc003fyu.2_3'UTR	NM_033029	NP_149018	Q96KR4	LMLN_HUMAN	leishmanolysin-like isoform 2						cell adhesion|cell division|mitosis|proteolysis	cytoplasm|membrane	metalloendopeptidase activity|zinc ion binding			skin(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		CCCAACCACCTTCATCAGCAA	0.313													5	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49160394	49160395	+	IGR	INS	-	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49160394_49160395insT								CWH43 (96301 upstream) : None (None downstream)																							gatgtaggtgcttttttctata	0.005													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	58808645	58808655	+	IGR	DEL	TTCCCACTAAT	-	-	rs77033843		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58808645_58808655delTTCCCACTAAT								IGFBP7 (832106 upstream) : None (None downstream)																							GGAATTGGGATTCCCACTAATGTATCTGTAT	0.289													4	4	---	---	---	---	
UGT2B4	7363	broad.mit.edu	37	4	70383369	70383369	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70383369delA	uc011cap.1	-							NM_021139	NP_066962	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2B4 precursor						estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(2)	2						TACTTACGTTAAAAATAAAGA	0.264													4	2	---	---	---	---	
TIFA	92610	broad.mit.edu	37	4	113198889	113198890	+	3'UTR	DEL	AC	-	-	rs5861096		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113198889_113198890delAC	uc003ial.2	-	2						NM_052864	NP_443096	Q96CG3	TIFA_HUMAN	TRAF-interacting protein with a								protein binding			breast(1)	1		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00172)		AAATGATAATACTGAATTCCAA	0.312													4	27	---	---	---	---	
USP53	54532	broad.mit.edu	37	4	120212605	120212608	+	Intron	DEL	TGTC	-	-	rs147775624		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120212605_120212608delTGTC	uc003ics.3	+						USP53_uc003icr.3_Intron|USP53_uc003icu.3_Intron	NM_019050	NP_061923	Q70EK8	UBP53_HUMAN	ubiquitin specific protease 53						ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			ovary(1)|breast(1)|kidney(1)|skin(1)	4						agtatctgattgtctgtttcaatc	0.118													5	5	---	---	---	---	
TLL1	7092	broad.mit.edu	37	4	166910815	166910816	+	Intron	INS	-	T	T	rs71604415		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166910815_166910816insT	uc003irh.1	+						TLL1_uc011cjn.1_Intron|TLL1_uc011cjo.1_Intron	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		Cattttattaattttttttttt	0.163													4	4	---	---	---	---	
AADAT	51166	broad.mit.edu	37	4	170987331	170987332	+	Intron	INS	-	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170987331_170987332insT	uc003isr.2	-						AADAT_uc003iss.2_Intron|AADAT_uc003ist.2_Intron	NM_016228	NP_057312	Q8N5Z0	AADAT_HUMAN	kynurenine aminotransferase II						2-oxoglutarate metabolic process|biosynthetic process|glutamate metabolic process|lysine catabolic process	mitochondrial matrix	2-aminoadipate transaminase activity|kynurenine-oxoglutarate transaminase activity|protein homodimerization activity				0		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	ATTTTTAGATCTTTTTTTTTTT	0.292													4	3	---	---	---	---	
HPGD	3248	broad.mit.edu	37	4	175443424	175443425	+	Intron	INS	-	T	T	rs146881598	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175443424_175443425insT	uc003itu.2	-						HPGD_uc003itv.2_Intron|HPGD_uc011ckf.1_Intron|HPGD_uc010irp.2_Intron|HPGD_uc010irq.2_Intron|HPGD_uc011ckg.1_Intron|HPGD_uc011ckh.1_Intron|HPGD_uc003itw.2_Intron|HPGD_uc003itx.2_Intron	NM_000860	NP_000851	P15428	PGDH_HUMAN	hydroxyprostaglandin dehydrogenase 15-(NAD)						female pregnancy|lipoxygenase pathway|negative regulation of cell cycle|parturition|prostaglandin metabolic process|transforming growth factor beta receptor signaling pathway	cytosol|nucleus	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|NAD+ binding|prostaglandin E receptor activity|protein homodimerization activity				0		Prostate(90;0.00763)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;2.6e-18)|Epithelial(43;4.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.23e-09)|GBM - Glioblastoma multiforme(59;0.00176)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.0253)	NADH(DB00157)	CGCGGCCTCCCTGTCTCCGCCA	0.644													7	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	856301	856302	+	IGR	DEL	CA	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:856301_856302delCA								ZDHHC11 (5200 upstream) : BRD9 (7549 downstream)																							GACCACGTACcacacacaccac	0.267													4	2	---	---	---	---	
MARCH6	10299	broad.mit.edu	37	5	10424069	10424069	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10424069delT	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						ATATATAACCTTTTTTTTTTT	0.214													15	7	---	---	---	---	
RAI14	26064	broad.mit.edu	37	5	34688211	34688216	+	Intron	DEL	GACAAA	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34688211_34688216delGACAAA	uc003jir.2	+						RAI14_uc010iur.2_Intron|RAI14_uc011coj.1_Intron|RAI14_uc010ius.1_Intron|RAI14_uc003jis.2_5'UTR|RAI14_uc003jit.2_Intron|RAI14_uc011cok.1_Intron	NM_015577	NP_056392	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14 isoform a							cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)					AAGAGACTTCGACAAAGACAGAAAAC	0.413													57	37	---	---	---	---	
KIF2A	3796	broad.mit.edu	37	5	61657534	61657535	+	Intron	INS	-	T	T	rs11418602		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61657534_61657535insT	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron|KIF2A_uc010iwq.2_Intron	NM_004520	NP_004511	O00139	KIF2A_HUMAN	kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		ATTCACaataattttttttttt	0.144													5	3	---	---	---	---	
KIF3A	11127	broad.mit.edu	37	5	132034740	132034740	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132034740delT	uc003kxo.2	-						KIF3A_uc003kxm.2_Intron|KIF3A_uc003kxn.2_Intron|KIF3A_uc011cxf.1_Intron|KIF3A_uc003kxp.2_Intron	NM_007054	NP_008985	Q9Y496	KIF3A_HUMAN	kinesin family member 3A						blood coagulation|organelle organization|plus-end-directed vesicle transport along microtubule	centrosome|cytosol|kinesin II complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|protein binding			pancreas(1)	1		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGGAATTTGATTTTTAATAAA	0.139													58	27	---	---	---	---	
SPINK5	11005	broad.mit.edu	37	5	147445109	147445114	+	Intron	DEL	CACACA	-	-	rs3036741		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147445109_147445114delCACACA	uc003lox.2	+						SPINK5_uc010jgq.1_Intron|SPINK5_uc010jgs.1_Intron|SPINK5_uc010jgr.2_Intron|SPINK5_uc003low.2_Intron|SPINK5_uc003loy.2_Intron	NM_006846	NP_006837	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5 isoform						anagen|epithelial cell differentiation|extracellular matrix organization|hair cell differentiation|negative regulation of angiogenesis|negative regulation of immune response|regulation of T cell differentiation	cell cortex|cytosol|endoplasmic reticulum membrane|extracellular region|lamellar body|perinuclear region of cytoplasm	serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)|breast(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCTCTCTCTcacacacacacacaca	0.252													14	25	---	---	---	---	
ARHGEF37	389337	broad.mit.edu	37	5	149006519	149006524	+	Intron	DEL	CAGTGG	-	-	rs150903273		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149006519_149006524delCAGTGG	uc003lra.1	+							NM_001001669	NP_001001669	A1IGU5	ARH37_HUMAN	hypothetical protein LOC389337						regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0						GTGGGCCCTtcagtggcagagttagg	0.398													12	14	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	156074655	156074661	+	Intron	DEL	AAATTGA	-	-	rs36045528		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156074655_156074661delAAATTGA	uc003lwd.3	+						SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTGAATACATAAATTGAAAGAGGTTGG	0.377													36	24	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	175336278	175336278	+	IGR	DEL	T	-	-	rs67243038		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175336278delT								CPLX2 (25255 upstream) : THOC3 (50258 downstream)																							ggctcccccctcttgccagcc	0.000													11	6	---	---	---	---	
GPLD1	2822	broad.mit.edu	37	6	24475278	24475278	+	Intron	DEL	G	-	-	rs77374467	byFrequency	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24475278delG	uc003ned.1	-						GPLD1_uc010jpr.1_Intron|GPLD1_uc010jps.1_Intron|GPLD1_uc003nee.2_Intron	NM_001503	NP_001494	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific							extracellular region	glycosylphosphatidylinositol phospholipase D activity			ovary(2)|kidney(1)	3						CTTTTAAAACGGTCAGGTTTT	0.373													40	31	---	---	---	---	
ZFP57	346171	broad.mit.edu	37	6	29642978	29642979	+	Intron	INS	-	AACTTGAA	AACTTGAA	rs143499124	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29642978_29642979insAACTTGAA	uc011dlw.1	-						ZFP57_uc003nnl.3_Intron	NM_001109809	NP_001103279	Q9NU63	ZFP57_HUMAN	zinc finger protein 57 homolog						DNA methylation involved in embryo development|regulation of gene expression by genetic imprinting|transcription, DNA-dependent		DNA binding|zinc ion binding			ovary(3)|skin(2)	5						CTTGGATCTTCAACTTGAAGTC	0.292													21	10	---	---	---	---	
HLA-G	3135	broad.mit.edu	37	6	29949173	29949174	+	Intron	INS	-	TG	TG	rs147954486	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29949173_29949174insTG	uc011dmb.1	+							NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4						CTCAGGCTGCAtgtgtgtgtgt	0.267													4	3	---	---	---	---	
CSNK2B	1460	broad.mit.edu	37	6	31635959	31635961	+	Intron	DEL	TAT	-	-	rs146750326	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31635959_31635961delTAT	uc003nvr.1	+						BAT4_uc003nvn.2_5'Flank|BAT4_uc003nvo.3_5'Flank|BAT4_uc003nvp.3_5'Flank|BAT4_uc003nvq.2_5'Flank|CSNK2B_uc010jta.1_3'UTR|CSNK2B_uc003nvs.1_Intron|LY6G5B_uc003nvt.1_5'Flank	NM_001320	NP_001311	P67870	CSK2B_HUMAN	casein kinase 2, beta polypeptide						adiponectin-mediated signaling pathway|axon guidance|cellular protein complex assembly|negative regulation of cell proliferation|regulation of DNA binding|Wnt receptor signaling pathway	cytosol|nucleus|protein kinase CK2 complex	identical protein binding|protein domain specific binding|protein kinase regulator activity|receptor binding|transcription factor binding				0						AATTCAGACCTATTCCAAAATGC	0.404													9	7	---	---	---	---	
CSNK2B	1460	broad.mit.edu	37	6	31635964	31635967	+	Intron	DEL	CAAA	-	-	rs34161953		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31635964_31635967delCAAA	uc003nvr.1	+						BAT4_uc003nvn.2_5'Flank|BAT4_uc003nvo.3_5'Flank|BAT4_uc003nvp.3_5'Flank|BAT4_uc003nvq.2_5'Flank|CSNK2B_uc010jta.1_3'UTR|CSNK2B_uc003nvs.1_Intron|LY6G5B_uc003nvt.1_5'Flank	NM_001320	NP_001311	P67870	CSK2B_HUMAN	casein kinase 2, beta polypeptide						adiponectin-mediated signaling pathway|axon guidance|cellular protein complex assembly|negative regulation of cell proliferation|regulation of DNA binding|Wnt receptor signaling pathway	cytosol|nucleus|protein kinase CK2 complex	identical protein binding|protein domain specific binding|protein kinase regulator activity|receptor binding|transcription factor binding				0						AGACCTATTCCAAAATGCGTTTCC	0.387													7	7	---	---	---	---	
HMGCLL1	54511	broad.mit.edu	37	6	55442034	55442042	+	Intron	DEL	ATAGAAAAA	-	-	rs59821254		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55442034_55442042delATAGAAAAA	uc003pcn.2	-						HMGCLL1_uc003pco.2_Intron|HMGCLL1_uc010jzx.2_Intron|HMGCLL1_uc011dxc.1_Intron|HMGCLL1_uc011dxd.1_Intron|HMGCLL1_uc011dxe.1_Intron|HMGCLL1_uc003pcp.2_Intron	NM_019036	NP_061909	Q8TB92	HMGC2_HUMAN	3-hydroxymethyl-3-methylglutaryl-Coenzyme A								hydroxymethylglutaryl-CoA lyase activity|metal ion binding			skin(2)|ovary(1)|pancreas(1)	4	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)			ttacgataagATAGAAAAAATCACAATTC	0.177													25	22	---	---	---	---	
MAP7	9053	broad.mit.edu	37	6	136861923	136861923	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136861923delA	uc003qgz.2	-						MAP7_uc010kgq.1_Intron|MAP7_uc003qha.1_Intron	NM_003980	NP_003971	Q14244	MAP7_HUMAN	microtubule-associated protein 7						establishment or maintenance of cell polarity|microtubule cytoskeleton organization|protein localization in plasma membrane|response to osmotic stress	basolateral plasma membrane|microtubule|microtubule associated complex|nucleus|perinuclear region of cytoplasm	receptor binding|structural molecule activity				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		ggggaattttaaaaacactgc	0.100													4	2	---	---	---	---	
LRP11	84918	broad.mit.edu	37	6	150173960	150173961	+	Intron	DEL	CT	-	-	rs142047967		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150173960_150173961delCT	uc003qng.2	-						LRP11_uc003qnh.1_Intron	NM_032832	NP_116221	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein							integral to membrane	receptor activity				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		TTGCTGCTCACTCTCAGCAGAA	0.421													4	3	---	---	---	---	
MTHFD1L	25902	broad.mit.edu	37	6	151286429	151286429	+	Intron	DEL	T	-	-	rs1625684	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151286429delT	uc003qob.2	+						MTHFD1L_uc011een.1_Intron|MTHFD1L_uc011eeo.1_Intron|MTHFD1L_uc003qoc.2_Intron	NM_015440	NP_056255	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+						folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		AAAAAAAAAATTTTTAAGTGT	0.199													5	3	---	---	---	---	
PARK2	5071	broad.mit.edu	37	6	161971723	161971724	+	Intron	INS	-	C	C	rs150609846	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161971723_161971724insC	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron|PARK2_uc011egf.1_Intron	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		gaggcgggtaggggtggggaca	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	170479260	170479265	+	IGR	DEL	CACACA	-	-	rs111264971		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170479260_170479265delCACACA								C6orf208 (276291 upstream) : LOC154449 (84157 downstream)																							CTCATGcacgcacacacacacacaca	0.320													18	12	---	---	---	---	
DPY19L1	23333	broad.mit.edu	37	7	35053485	35053486	+	Intron	DEL	TA	-	-	rs76882258		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35053485_35053486delTA	uc003tem.3	-							NM_015283	NP_056098	Q2PZI1	D19L1_HUMAN	dpy-19-like 1							integral to membrane					0						GTGAAAAAACTATGTATTTTCA	0.262													2	4	---	---	---	---	
ANLN	54443	broad.mit.edu	37	7	36465192	36465193	+	Intron	INS	-	ATTA	ATTA	rs148316707	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36465192_36465193insATTA	uc003tff.2	+						ANLN_uc011kaz.1_Intron|ANLN_uc003tfg.2_Intron|ANLN_uc010kxe.2_Intron	NM_018685	NP_061155	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein						cytokinesis|mitosis|regulation of exit from mitosis|septin ring assembly	actomyosin contractile ring|nucleus	actin binding			ovary(2)|skin(1)	3						cgtgagccactgctcccggcTA	0.099													14	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	39905848	39905849	+	IGR	INS	-	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39905848_39905849insC								LOC349114 (71627 upstream) : CDK13 (84110 downstream)																							ACGGTTCTGTTCTTTAGATTTT	0.332													4	2	---	---	---	---	
HECW1	23072	broad.mit.edu	37	7	43496232	43496236	+	Intron	DEL	AAGTT	-	-	rs3214630		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43496232_43496236delAAGTT	uc003tid.1	+						HECW1_uc011kbi.1_Intron	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						GGCGAGAGACAAGTTAAGCTTGAGT	0.390													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	56593316	56593317	+	IGR	DEL	TG	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56593316_56593317delTG								DKFZp434L192 (28339 upstream) : ZNF479 (594011 downstream)																							GCATAAATCTTGTGTGTGTGTG	0.361													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	62547646	62547646	+	IGR	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62547646delT								None (None upstream) : LOC643955 (204026 downstream)																							ATTTGTAGCAttttttttttg	0.179													4	5	---	---	---	---	
CCDC146	57639	broad.mit.edu	37	7	76922576	76922578	+	Intron	DEL	CAA	-	-	rs113826533		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76922576_76922578delCAA	uc003uga.2	+						CCDC146_uc010ldp.2_Intron|CCDC146_uc003ugc.2_Intron	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146											ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				TGCATTCAGGCAACCCACAGTTA	0.443													34	16	---	---	---	---	
PION	54103	broad.mit.edu	37	7	77006534	77006535	+	Intron	INS	-	A	A	rs145079993	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77006534_77006535insA	uc003ugf.2	-						PION_uc003ugg.1_Intron	NM_017439	NP_059135	A4D1B5	GSAP_HUMAN	pigeon homolog						beta-amyloid formation|regulation of proteolysis	trans-Golgi network	beta-amyloid binding			central_nervous_system(1)	1						accctgtctctaaaaaaaTTAA	0.119													30	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	85846236	85846236	+	IGR	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85846236delA								None (None upstream) : GRM3 (426994 downstream)																							ATCGCAGGCTAAAAGGAGAAG	0.373													4	2	---	---	---	---	
SPDYE2	441273	broad.mit.edu	37	7	102196082	102196083	+	Intron	INS	-	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102196082_102196083insC	uc011kkx.1	+						UPK3BL_uc003uzy.2_Intron|POLR2J3_uc003uzw.2_Intron|POLR2J3_uc011kkw.1_Intron|SPDYE2_uc003vaa.1_5'Flank	NM_001031618	NP_001026789	Q495Y8	SPDE2_HUMAN	speedy homolog E2												0						aacaacaacaaaaaaaaaaaaa	0.238													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	127841893	127841894	+	IGR	DEL	TT	-	-	rs151257847		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127841893_127841894delTT								SND1 (109235 upstream) : MIR129-1 (6031 downstream)																							TTCCTGTCTCTTATATTCTCAT	0.584													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	129792384	129792385	+	IGR	DEL	CA	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129792384_129792385delCA								KLHDC10 (18791 upstream) : TMEM209 (12170 downstream)																							cactgcagaccacacacacaca	0.099													3	3	---	---	---	---	
SVOPL	136306	broad.mit.edu	37	7	138356664	138356665	+	Intron	INS	-	A	A	rs77651439		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138356664_138356665insA	uc011kqh.1	-							NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	SVOP-like isoform 1							integral to membrane	transmembrane transporter activity				0						CCAACAGTGGCAGTGGTGAGAC	0.515													38	25	---	---	---	---	
SVOPL	136306	broad.mit.edu	37	7	138356730	138356731	+	Intron	INS	-	G	G	rs5887895		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138356730_138356731insG	uc011kqh.1	-							NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	SVOP-like isoform 1							integral to membrane	transmembrane transporter activity				0						CGCCCTCAGTTGCTGTGTTCAC	0.550													125	65	---	---	---	---	
ZC3HAV1	56829	broad.mit.edu	37	7	138763121	138763121	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138763121delA	uc003vun.2	-						ZC3HAV1_uc003vuo.2_Intron|ZC3HAV1_uc003vup.2_Intron	NM_020119	NP_064504	Q7Z2W4	ZCCHV_HUMAN	zinc finger antiviral protein isoform 1						response to virus	cytoplasm|nucleus	NAD+ ADP-ribosyltransferase activity|RNA binding|zinc ion binding			ovary(1)	1						atagttcctcaaaaaaaaaaa	0.000													6	4	---	---	---	---	
FAM160B2	64760	broad.mit.edu	37	8	21958843	21958844	+	Intron	INS	-	TCTT	TCTT	rs144156056	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21958843_21958844insTCTT	uc011kyx.1	+						FAM160B2_uc011kyy.1_Intron	NM_022749	NP_073586	Q86V87	F16B2_HUMAN	retinoic acid induced 16												0						cTGAGTTTTACTCTTTGGCCAC	0.347													19	15	---	---	---	---	
SORBS3	10174	broad.mit.edu	37	8	22426860	22426860	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22426860delT	uc003xbv.2	+						SORBS3_uc003xbw.3_Intron	NM_005775	NP_005766	O60504	VINEX_HUMAN	sorbin and SH3 domain containing 3 isoform 1						muscle contraction|positive regulation of stress fiber assembly	cytoskeleton|cytosol|nucleus	protein binding|structural constituent of cytoskeleton|vinculin binding				0		Prostate(55;0.0421)|Breast(100;0.102)		BRCA - Breast invasive adenocarcinoma(99;0.00566)|Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		CTAAAAACAGttttttttttt	0.294													5	3	---	---	---	---	
GSR	2936	broad.mit.edu	37	8	30546502	30546502	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30546502delT	uc003xih.1	-							NM_000637	NP_000628	P00390	GSHR_HUMAN	glutathione reductase precursor						cell redox homeostasis|nucleobase, nucleoside and nucleotide interconversion	cytosol|mitochondrion	electron carrier activity|glutathione-disulfide reductase activity			ovary(2)|pancreas(2)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Glutathione(DB00143)|NADH(DB00157)	aagagaaaaCTTTTTTTTTTA	0.164													4	2	---	---	---	---	
TCEA1	6917	broad.mit.edu	37	8	54886753	54886753	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54886753delA	uc003xru.2	-						TCEA1_uc003xrv.2_Intron|TCEA1_uc011ldw.1_Intron|TCEA1_uc010lyg.2_Intron	NM_006756	NP_006747	P23193	TCEA1_HUMAN	transcription elongation factor A 1 isoform 1						positive regulation of viral transcription|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	nucleoplasm	DNA binding|translation elongation factor activity|zinc ion binding				0		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)			TTCAAGCAAGAAAAAAAAAGT	0.259			T	PLAG1	salivary adenoma								7	4	---	---	---	---	
C8orf83	286144	broad.mit.edu	37	8	93899103	93899115	+	Intron	DEL	ACCATTTTTTGCC	-	-	rs59695699		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93899103_93899115delACCATTTTTTGCC	uc003yfk.3	-						C8orf83_uc003yfr.3_Intron|C8orf83_uc010map.2_Intron|C8orf83_uc003yfo.3_Intron|C8orf83_uc003yfn.3_Intron|C8orf83_uc003yfq.3_Intron|C8orf83_uc003yfl.3_Intron|C8orf83_uc003yfm.3_Intron	NR_015339		Q629K1	TRIQK_HUMAN	RecName: Full=UPF0599 protein C8orf83;							endoplasmic reticulum membrane|integral to membrane					0						CTTTTTGTTTACCATTTTTTGCCGTTAAGAAAC	0.305													14	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	103430535	103430535	+	IGR	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103430535delA								UBR5 (6040 upstream) : ODF1 (133313 downstream)																							AGGAGAATTCAAAAAAAAGCA	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44097478	44097479	+	IGR	INS	-	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44097478_44097479insC								FAM75A6 (466748 upstream) : FAM27C (892757 downstream)																							ATATCCAGCTTCCCCTCAAAAA	0.312													19	77	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	93513725	93513727	+	IGR	DEL	AAC	-	-	rs34140480		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93513725_93513727delAAC								DIRAS2 (108617 upstream) : SYK (50285 downstream)																							AAAATAAGCAAACAACTGCCAGG	0.478													21	18	---	---	---	---	
C9orf102	375748	broad.mit.edu	37	9	98678758	98678758	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98678758delT	uc004avt.3	+						C9orf102_uc010mrx.1_Intron|C9orf102_uc011lum.1_Intron|C9orf102_uc010mry.1_Intron|C9orf102_uc010mrz.2_Intron	NM_001010895	NP_001010895	Q5T890	RAD26_HUMAN	RAD26L hypothetical protein						DNA repair	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding				0		Acute lymphoblastic leukemia(62;0.0559)				TGTGGTCATATTTTTTTTTTC	0.358													5	4	---	---	---	---	
SVEP1	79987	broad.mit.edu	37	9	113163458	113163458	+	Intron	DEL	C	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113163458delC	uc010mtz.2	-						SVEP1_uc010mty.2_Intron	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						aaaaaacacacttTAATTATT	0.189													4	2	---	---	---	---	
PHF19	26147	broad.mit.edu	37	9	123622040	123622040	+	Intron	DEL	G	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123622040delG	uc004bks.1	-						PHF19_uc011lyf.1_Intron|PHF19_uc004bkr.2_Intron	NM_015651	NP_056466	Q5T6S3	PHF19_HUMAN	PHD finger protein 19 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)|breast(1)	2						GGCACGTGGAGGCCAAAAGTG	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	1196386	1196389	+	IGR	DEL	CACG	-	-	rs59098909	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1196386_1196389delCACG								WDR37 (18149 upstream) : NCRNA00200 (9319 downstream)																							cacgagcacacacgtgcacatgca	0.230													29	13	---	---	---	---	
AKR1C3	8644	broad.mit.edu	37	10	5112533	5112534	+	Intron	INS	-	C	C	rs148871056	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5112533_5112534insC	uc001ihr.2	+							NM_003739	NP_003730	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3						prostaglandin metabolic process	cytoplasm	aldo-keto reductase (NADP) activity|androsterone dehydrogenase (A-specific) activity|indanol dehydrogenase activity|prostaglandin-F synthase activity|testosterone 17-beta-dehydrogenase (NAD+) activity|testosterone 17-beta-dehydrogenase (NADP+) activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			skin(1)	1					Dimethyl sulfoxide(DB01093)|NADH(DB00157)	aaatgcacaaaaaagcaaagaa	0.000													9	6	---	---	---	---	
BMI1	648	broad.mit.edu	37	10	22616126	22616126	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22616126delT	uc001irh.2	+						BMI1_uc009xkg.2_Intron	NM_005180	NP_005171	P35226	BMI1_HUMAN	BMI1 polycomb ring finger oncogene						hemopoiesis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fibroblast proliferation|positive regulation of ubiquitin-protein ligase activity|segment specification|transcription, DNA-dependent	cytoplasm|nucleolus|PcG protein complex|ubiquitin ligase complex	RING-like zinc finger domain binding|zinc ion binding			ovary(1)|skin(1)	2						GATTTTAAGATTTTTTTTTCC	0.328													4	2	---	---	---	---	
SGMS1	259230	broad.mit.edu	37	10	52086760	52086761	+	Intron	INS	-	AAACTAGAACACAT	AAACTAGAACACAT	rs143456162	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52086760_52086761insAAACTAGAACACAT	uc001jje.2	-						SGMS1_uc010qhk.1_Intron|SGMS1_uc009xot.1_Intron	NM_147156	NP_671512	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1						apoptosis|cell growth|sphingomyelin biosynthetic process	endoplasmic reticulum|Golgi trans cisterna|integral to Golgi membrane|nucleus|plasma membrane	ceramide cholinephosphotransferase activity|kinase activity|sphingomyelin synthase activity			ovary(1)|kidney(1)	2						TTCCAACACACATTTCCCCAGT	0.436													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	94969501	94969502	+	IGR	DEL	AA	-	-	rs55900322	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94969501_94969502delAA								CYP26A1 (131860 upstream) : MYOF (96685 downstream)																							CCCCCCCcccaaaaaaaaaacc	0.218													13	6	---	---	---	---	
HPSE2	60495	broad.mit.edu	37	10	100503451	100503451	+	Intron	DEL	T	-	-	rs34603601		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100503451delT	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600	Q8WWQ2	HPSE2_HUMAN	heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		GCAAATGGTGTGTATTCACTA	0.363													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	103043479	103043482	+	IGR	DEL	CACA	-	-	rs140479707		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103043479_103043482delCACA								LBX1 (54762 upstream) : BTRC (70343 downstream)																							CCCCCACCACcacacacacacaca	0.382													5	3	---	---	---	---	
SLK	9748	broad.mit.edu	37	10	105761496	105761496	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105761496delT	uc001kxo.1	+						SLK_uc001kxp.1_Intron	NM_014720	NP_055535	Q9H2G2	SLK_HUMAN	serine/threonine kinase 2						apoptosis|nucleotide-excision repair	cytoplasm|plasma membrane	ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity			ovary(2)|stomach(2)|skin(2)|lung(1)|kidney(1)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TATATTTCCCttttttttgag	0.199													7	4	---	---	---	---	
CASC2	255082	broad.mit.edu	37	10	119816920	119816922	+	Intron	DEL	TCC	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119816920_119816922delTCC	uc001ldm.3	+						CASC2_uc009xzc.2_Intron|CASC2_uc009xza.2_Intron|CASC2_uc009xzb.2_Intron	NR_026939				Homo sapiens mRNA for IGM1 protein.												0						CTGTTCTGCTTCCTCCTCGTAAT	0.507													2	4	---	---	---	---	
ADAM12	8038	broad.mit.edu	37	10	127834032	127834041	+	Intron	DEL	CAGTGTAGCA	-	-	rs79929777	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127834032_127834041delCAGTGTAGCA	uc001ljk.2	-						ADAM12_uc010qul.1_Intron|ADAM12_uc001ljm.2_Intron|ADAM12_uc001ljn.2_Intron|ADAM12_uc001ljl.3_Intron	NM_003474	NP_003465	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12 isoform 1						cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		GAACTGGAGGCAGTGTAGCACAGCATATAG	0.267													2	9	---	---	---	---	
C11orf21	29125	broad.mit.edu	37	11	2321043	2321078	+	Intron	DEL	TGCACACACATCCACGTCTGCACACGCATCCACGCC	-	-	rs67461770	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2321043_2321078delTGCACACACATCCACGTCTGCACACGCATCCACGCC	uc001lvv.2	-						C11orf21_uc009ydj.2_Intron|TSPAN32_uc001lvx.1_5'Flank|TSPAN32_uc009ydk.1_5'Flank|TSPAN32_uc010qxk.1_5'Flank|TSPAN32_uc001lvy.1_5'Flank|TSPAN32_uc009ydl.1_5'Flank|TSPAN32_uc001lvz.1_5'Flank|TSPAN32_uc001lwb.1_5'Flank|TSPAN32_uc001lwc.1_5'Flank	NR_024621		Q9P2W6	CK021_HUMAN	RecName: Full=Uncharacterized protein C11orf21;							cytoplasm					0						cacatatgcatgcacacacatccacgtctgcacacgcatccacgcctgcacacgca	0.377													24	27	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	13001936	13001936	+	RNA	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13001936delA	uc001mkl.1	-	2		c.704delT			uc001mkm.1_RNA					Homo sapiens cDNA FLJ10570 fis, clone NT2RP2003117.																		AGTCAGAAATAAAACGTGAGC	0.428													4	2	---	---	---	---	
HPS5	11234	broad.mit.edu	37	11	18306690	18306690	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18306690delA	uc001mod.1	-						HPS5_uc001moe.1_Intron|HPS5_uc001mof.1_Intron	NM_181507	NP_852608	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 isoform a							cytosol				ovary(1)|pancreas(1)|skin(1)	3						AAGGCTATTTaaaaaaaaaaa	0.303									Hermansky-Pudlak_syndrome				5	4	---	---	---	---	
CSTF3	1479	broad.mit.edu	37	11	33163765	33163765	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33163765delA	uc001muh.2	-						CSTF3_uc001mui.2_Intron|CSTF3_uc001muj.2_Intron	NM_001326	NP_001317	Q12996	CSTF3_HUMAN	cleavage stimulation factor subunit 3 isoform 1						mRNA cleavage|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	protein binding|RNA binding				0						actcagagagaaaaaaaaaag	0.055													6	3	---	---	---	---	
AMBRA1	55626	broad.mit.edu	37	11	46450142	46450142	+	Intron	DEL	C	-	-	rs2864834	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46450142delC	uc010rgu.1	-						AMBRA1_uc010rgt.1_Intron|AMBRA1_uc009ylc.1_Intron|AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		tcttcttcttcttttttttTT	0.378													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	59980339	59980339	+	IGR	DEL	C	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59980339delC								MS4A6A (28200 upstream) : MS4A4A (67800 downstream)																							CTTACAACTTCCAAAGTCATT	0.338													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	79243131	79243131	+	IGR	DEL	T	-	-	rs72251115		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79243131delT								ODZ4 (91436 upstream) : None (None downstream)																							CATGAAAATGTTTTTTTTTGG	0.144													5	3	---	---	---	---	
PRSS23	11098	broad.mit.edu	37	11	86544047	86544047	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86544047delA	uc001pcc.1	+						uc001pcd.2_Intron			O95084	PRS23_HUMAN	Homo sapiens serine protease mRNA, complete cds.						proteolysis	extracellular region|nucleus	serine-type endopeptidase activity			central_nervous_system(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AAAGACTGAGAAAAAAAAAAA	0.418													4	2	---	---	---	---	
HEBP1	50865	broad.mit.edu	37	12	13141925	13141926	+	Intron	INS	-	A	A	rs140951661	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13141925_13141926insA	uc001rbd.2	-						HEBP1_uc001rbf.2_Intron	NM_015987	NP_057071	Q9NRV9	HEBP1_HUMAN	heme binding protein 1						circadian rhythm	extracellular region				breast(1)	1		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		ACTGCAGGGTTAAAAAAAAAAT	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	48566114	48566123	+	IGR	DEL	AAAACAAAAC	-	-	rs112856407		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48566114_48566123delAAAACAAAAC								ASB8 (14737 upstream) : C12orf68 (11243 downstream)																							ctccatctcaaaaacaaaacaaaacaaaac	0.119													5	3	---	---	---	---	
METTL7A	25840	broad.mit.edu	37	12	51324058	51324058	+	3'UTR	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51324058delT	uc001rxb.2	+	2					METTL7A_uc010smv.1_3'UTR	NM_014033	NP_054752	Q9H8H3	MET7A_HUMAN	methyltransferase like 7A precursor							endoplasmic reticulum|lipid particle|membrane	methyltransferase activity				0						TTGTTGTTGGttttttttttt	0.179													12	6	---	---	---	---	
DCD	117159	broad.mit.edu	37	12	55038760	55038760	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55038760delA	uc001sgj.2	-						DCD_uc009znt.2_Intron|DCD_uc009znu.2_Intron	NM_053283	NP_444513	P81605	DCD_HUMAN	dermcidin preproprotein						defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular region	protein binding			ovary(1)	1		Myeloproliferative disorder(1001;0.0255)				CAAGAGCAATAAAAAAAAAAG	0.453													11	5	---	---	---	---	
CPM	1368	broad.mit.edu	37	12	69252514	69252514	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69252514delT	uc001sup.2	-						CPM_uc001sur.2_Intron|CPM_uc001suq.2_Intron	NM_198320	NP_938079	P14384	CBPM_HUMAN	carboxypeptidase M precursor						anatomical structure morphogenesis|proteolysis	anchored to membrane|cytoplasm|nucleus|plasma membrane	metallocarboxypeptidase activity|zinc ion binding				0	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			ATTTTTGTGGTTTTTTTTTTT	0.323													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	70383058	70383059	+	IGR	DEL	GT	-	-	rs12425508	byFrequency	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70383058_70383059delGT								RAB3IP (166076 upstream) : CNOT2 (253718 downstream)																							CTGTCTCCTCgtgtgtgtgtgt	0.371													5	3	---	---	---	---	
PTPRB	5787	broad.mit.edu	37	12	70918054	70918054	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70918054delT	uc001swb.3	-						uc001svz.2_Intron|PTPRB_uc010sto.1_Intron|PTPRB_uc010stp.1_Intron|PTPRB_uc001swc.3_Intron|PTPRB_uc001swa.3_Intron	NM_002837	NP_002828	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B						angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			tgtctggctattttttttttt	0.000													8	4	---	---	---	---	
NAV3	89795	broad.mit.edu	37	12	78592703	78592704	+	Intron	INS	-	C	C	rs77713263	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78592703_78592704insC	uc001syp.2	+						NAV3_uc001syo.2_Intron|NAV3_uc010sub.1_Intron|NAV3_uc009zsf.2_Intron	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17						aaaaacaaaaaaaaaaaaaaag	0.287										HNSCC(70;0.22)			6	6	---	---	---	---	
PPFIA2	8499	broad.mit.edu	37	12	81741691	81741691	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81741691delT	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010sui.1_Intron|PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron|PPFIA2_uc010suf.1_Intron|PPFIA2_uc009zsh.2_Intron	NM_003625	NP_003616	B7Z663	B7Z663_HUMAN	PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6						TTTTTTCATCTTTTTTTTTTC	0.299													9	4	---	---	---	---	
STAB2	55576	broad.mit.edu	37	12	104086413	104086416	+	Intron	DEL	GAGA	-	-	rs71809816		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104086413_104086416delGAGA	uc001tjw.2	+							NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14						gcacgtgtgtgaGAGAGAGAGAGA	0.118													19	9	---	---	---	---	
HSP90B1	7184	broad.mit.edu	37	12	104333133	104333138	+	Intron	DEL	AACCTC	-	-	rs57480017		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104333133_104333138delAACCTC	uc001tkb.1	+						HSP90B1_uc010swg.1_Intron|HSP90B1_uc009zui.1_Intron	NM_003299	NP_003290	P14625	ENPL_HUMAN	heat shock protein 90kDa beta, member 1						actin rod assembly|anti-apoptosis|cellular response to ATP|ER-associated protein catabolic process|protein folding|protein transport|regulation of phosphoprotein phosphatase activity|response to hypoxia|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|melanosome|microsome|midbody|perinuclear region of cytoplasm	ATP binding|calcium ion binding|low-density lipoprotein particle receptor binding|protein phosphatase binding|RNA binding|unfolded protein binding|virion binding			ovary(2)|skin(1)	3					Rifabutin(DB00615)	ctcctaccctaacctcccaaagtgct	0.121													24	20	---	---	---	---	
HSP90B1	7184	broad.mit.edu	37	12	104333142	104333166	+	Intron	DEL	AAGTGCTAGGATTACAGGCGTGAGC	-	-	rs61295344		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104333142_104333166delAAGTGCTAGGATTACAGGCGTGAGC	uc001tkb.1	+						HSP90B1_uc010swg.1_Intron|HSP90B1_uc009zui.1_Intron	NM_003299	NP_003290	P14625	ENPL_HUMAN	heat shock protein 90kDa beta, member 1						actin rod assembly|anti-apoptosis|cellular response to ATP|ER-associated protein catabolic process|protein folding|protein transport|regulation of phosphoprotein phosphatase activity|response to hypoxia|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|melanosome|microsome|midbody|perinuclear region of cytoplasm	ATP binding|calcium ion binding|low-density lipoprotein particle receptor binding|protein phosphatase binding|RNA binding|unfolded protein binding|virion binding			ovary(2)|skin(1)	3					Rifabutin(DB00615)	taacctcccaaagtgctaggattacaggcgtgagccaccacaccA	0.173													30	20	---	---	---	---	
RFX4	5992	broad.mit.edu	37	12	107078795	107078796	+	Intron	INS	-	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107078795_107078796insT	uc001tlr.2	+						RFX4_uc010swv.1_Intron|RFX4_uc001tls.2_Intron|RFX4_uc001tlt.2_Intron|RFX4_uc001tlv.2_Intron|uc001tlu.3_5'Flank	NM_213594	NP_998759	Q33E94	RFX4_HUMAN	regulatory factor X4 isoform c						transcription, DNA-dependent	nucleus	DNA binding			upper_aerodigestive_tract(1)	1						CATCTGTATGATTTTGTGACTT	0.327													34	15	---	---	---	---	
CORO1C	23603	broad.mit.edu	37	12	109056094	109056094	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109056094delT	uc001tnj.2	-						CORO1C_uc009zva.2_Intron|CORO1C_uc010sxf.1_Intron	NM_014325	NP_055140	Q9ULV4	COR1C_HUMAN	coronin, actin binding protein, 1C isoform 1						actin cytoskeleton organization|phagocytosis|signal transduction	actin cytoskeleton	actin filament binding			skin(3)	3						TGTTAGGCGgttttttttttg	0.194													8	4	---	---	---	---	
MYO1H	283446	broad.mit.edu	37	12	109881160	109881161	+	Intron	INS	-	AC	AC	rs10545297		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109881160_109881161insAC	uc010sxo.1	+						MYO1H_uc010sxn.1_Intron			Q8N1T3	MYO1H_HUMAN	SubName: Full=cDNA FLJ54829, moderately similar to Myosin Ic; SubName: Full=Myosin IH, isoform CRA_a;							myosin complex	motor activity				0						tgtgtgtatatacacacacaca	0.099													7	4	---	---	---	---	
STARD13	90627	broad.mit.edu	37	13	33700058	33700059	+	Intron	INS	-	TTCAAATTAAATA	TTCAAATTAAATA	rs149849652	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33700058_33700059insTTCAAATTAAATA	uc001uuw.2	-						STARD13_uc001uuu.2_Intron|STARD13_uc001uuv.2_Intron|STARD13_uc001uux.2_Intron|STARD13_uc010tec.1_Intron	NM_178006	NP_821074	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GACATGTCTTGTTCAAATTAAA	0.416													4	3	---	---	---	---	
COG3	83548	broad.mit.edu	37	13	46060474	46060475	+	Intron	INS	-	GGAGA	GGAGA	rs113621277		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46060474_46060475insGGAGA	uc001vak.2	+						COG3_uc010tfu.1_Intron|COG3_uc001vai.2_Intron|COG3_uc001vaj.1_Intron|COG3_uc010tfv.1_Intron|COG3_uc010aci.2_Intron	NM_031431	NP_113619	Q96JB2	COG3_HUMAN	component of golgi transport complex 3						ER to Golgi vesicle-mediated transport|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein glycosylation|protein localization to organelle|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	cis-Golgi network|Golgi cisterna membrane|Golgi transport complex	protein binding|protein transporter activity			breast(1)|skin(1)	2		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		agacgggagacgggagagggag	0.163													44	21	---	---	---	---	
RB1	5925	broad.mit.edu	37	13	49033658	49033658	+	Intron	DEL	C	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49033658delC	uc001vcb.2	+							NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(6)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	tcataataaaccagtaaacat	0.124		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			22	11	---	---	---	---	
COL4A1	1282	broad.mit.edu	37	13	110861620	110861621	+	Intron	INS	-	AAAG	AAAG	rs114198011	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110861620_110861621insAAAG	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			tatagttagataTAGTGTTAAT	0.168													46	21	---	---	---	---	
SEC23A	10484	broad.mit.edu	37	14	39562235	39562235	+	Intron	DEL	T	-	-	rs80118032		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39562235delT	uc001wup.1	-						SEC23A_uc010tqa.1_Intron|SEC23A_uc010tqb.1_Intron|SEC23A_uc010tqc.1_5'Flank	NM_006364	NP_006355	Q15436	SC23A_HUMAN	SEC23-related protein A						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)		gcccagctaattttttttttg	0.000													8	6	---	---	---	---	
SYT16	83851	broad.mit.edu	37	14	62542323	62542323	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62542323delA	uc001xfu.1	+						SYT16_uc010tsd.1_Intron	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like											central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		GATGAACGGTaaaaaaaaaaa	0.284													4	2	---	---	---	---	
SYNE2	23224	broad.mit.edu	37	14	64408465	64408465	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64408465delA	uc001xgm.2	+	4	424	c.194delA	c.(193-195)CATfs	p.H65fs	SYNE2_uc001xgk.2_Frame_Shift_Del_p.H65fs|SYNE2_uc001xgl.2_Frame_Shift_Del_p.H65fs	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	65	CH 1.|Cytoplasmic (Potential).|Actin-binding.				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAAAAGGGGCATGTCCTCCTG	0.368													305	136	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	35530469	35530469	+	IGR	DEL	A	-	-	rs147841420		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35530469delA								LOC723972 (207 upstream) : ATPBD4 (132702 downstream)																							TTTTACTGCCAAAAAAAAAAA	0.433													8	4	---	---	---	---	
SPRED1	161742	broad.mit.edu	37	15	38641773	38641774	+	Intron	INS	-	TT	TT	rs61670754		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38641773_38641774insTT	uc001zka.3	+							NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain						inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		CTAATTAATAGATAGGTAAAGT	0.322									Legius_syndrome				37	30	---	---	---	---	
SPRED1	161742	broad.mit.edu	37	15	38641774	38641775	+	Intron	INS	-	AAT	AAT	rs34352434		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38641774_38641775insAAT	uc001zka.3	+							NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain						inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		TAATTAATAGATAGGTAAAGTT	0.317									Legius_syndrome				36	30	---	---	---	---	
SPRED1	161742	broad.mit.edu	37	15	38641777	38641778	+	Intron	INS	-	TA	TA	rs114258866	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38641777_38641778insTA	uc001zka.3	+							NM_152594	NP_689807	Q7Z699	SPRE1_HUMAN	sprouty-related protein 1 with EVH-1 domain						inactivation of MAPK activity|multicellular organismal development	caveola|nucleus	stem cell factor receptor binding			ovary(2)|lung(2)|skin(1)	5		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		TTAATAGATAGGTAAAGTTTTC	0.317									Legius_syndrome				18	30	---	---	---	---	
CASC5	57082	broad.mit.edu	37	15	40894859	40894860	+	Intron	INS	-	A	A			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40894859_40894860insA	uc010bbs.1	+						CASC5_uc010ucq.1_Intron|CASC5_uc001zme.2_Intron|CASC5_uc010bbt.1_Intron	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		taattttgtattttggtagaga	0.000													4	2	---	---	---	---	
SLC12A1	6557	broad.mit.edu	37	15	48526950	48526950	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48526950delA	uc001zwn.3	+						SLC12A1_uc010uew.1_Intron|SLC12A1_uc010bem.2_Intron|SLC12A1_uc010uex.1_Intron|SLC12A1_uc001zwq.3_Intron|SLC12A1_uc001zwr.3_Intron	NM_000338	NP_000329	Q13621	S12A1_HUMAN	sodium potassium chloride cotransporter 2						potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	actctgtctcaaaaaaaaaaa	0.139													9	4	---	---	---	---	
C15orf51	196968	broad.mit.edu	37	15	100340123	100340125	+	RNA	DEL	AGA	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100340123_100340125delAGA	uc010urx.1	-	4		c.802_804delTCT			C15orf51_uc010ury.1_RNA|uc002bvp.2_5'Flank|C15orf51_uc010urz.1_RNA|C15orf51_uc010bow.2_RNA|uc002bvt.1_5'Flank	NR_003260				Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288.												0						AGCAGCTCCGAGAAGATGAACTC	0.611													8	7	---	---	---	---	
TELO2	9894	broad.mit.edu	37	16	1557791	1557794	+	Intron	DEL	GTGA	-	-	rs12927760		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1557791_1557794delGTGA	uc002cly.2	+							NM_016111	NP_057195	Q9Y4R8	TELO2_HUMAN	TEL2, telomere maintenance 2, homolog							chromosome, telomeric region|cytoplasm|membrane|nucleus	protein binding				0		Hepatocellular(780;0.219)				gtgtgtgtgtgtgagagatgtgtc	0.250													10	5	---	---	---	---	
C16orf89	146556	broad.mit.edu	37	16	5112643	5112643	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5112643delA	uc010bud.2	-						ALG1_uc002cyj.2_Intron|C16orf89_uc002cyk.3_Intron	NM_152459	NP_689672	Q6UX73	CP089_HUMAN	hypothetical protein LOC146556 isoform 1							extracellular region				ovary(1)|skin(1)	2						TTGGAACAAGAAAAAAAAATG	0.478													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	17752828	17752829	+	IGR	INS	-	GGGTCTGTT	GGGTCTGTT	rs148020289	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17752828_17752829insGGGTCTGTT								XYLT1 (188090 upstream) : NOMO2 (758354 downstream)																							GCCCTGACTCCGGGTCTGTTTG	0.287													4	2	---	---	---	---	
DCTN5	84516	broad.mit.edu	37	16	23672834	23672835	+	Intron	INS	-	T	T	rs149908072	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23672834_23672835insT	uc002dly.1	+							NM_032486	NP_115875	Q9BTE1	DCTN5_HUMAN	dynactin 5							centrosome	transferase activity			upper_aerodigestive_tract(1)	1				GBM - Glioblastoma multiforme(48;0.0156)		gaggtcaggagtttgagaccag	0.035													4	7	---	---	---	---	
RBL2	5934	broad.mit.edu	37	16	53495454	53495454	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53495454delT	uc002ehi.3	+						RBL2_uc010vgv.1_Intron|RBL2_uc002ehj.2_Intron|RBL2_uc010vgw.1_Intron	NM_005611	NP_005602	Q08999	RBL2_HUMAN	retinoblastoma-like 2 (p130)						cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5						ACAAGAAAAGTTTTTTTTTTT	0.219													5	5	---	---	---	---	
PKD1L3	342372	broad.mit.edu	37	16	72003588	72003591	+	Intron	DEL	AGAG	-	-	rs71391428		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72003588_72003591delAGAG	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0						AAAAAAAAATAGAGAGAAAAAGTT	0.358													5	4	---	---	---	---	
PLCG2	5336	broad.mit.edu	37	16	81973807	81973808	+	Intron	INS	-	TGCA	TGCA	rs141767011	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81973807_81973808insTGCA	uc002fgt.2	+							NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2						intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8						TGGAGAGCAGGTGTACAGCCTG	0.470													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	88311126	88311133	+	IGR	DEL	GTGCACGG	-	-	rs149182560	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88311126_88311133delGTGCACGG								BANP (200203 upstream) : ZNF469 (182746 downstream)																							GTAGATATCAGTGCACGGTTAGTGCTGC	0.543													8	7	---	---	---	---	
PAFAH1B1	5048	broad.mit.edu	37	17	2575701	2575706	+	Intron	DEL	AAACCA	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2575701_2575706delAAACCA	uc002fuw.3	+						PAFAH1B1_uc010ckb.1_Intron|PAFAH1B1_uc010vqz.1_Intron	NM_000430	NP_000421	P43034	LIS1_HUMAN	platelet-activating factor acetylhydrolase,						acrosome assembly|actin cytoskeleton organization|adult locomotory behavior|brain morphogenesis|corpus callosum morphogenesis|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|hippocampus development|layer formation in cerebral cortex|learning or memory|lipid catabolic process|microtubule organizing center organization|mitotic prometaphase|neuroblast proliferation|neuromuscular process controlling balance|neuron migration|platelet activating factor metabolic process|regulation of Rho GTPase activity|retrograde axon cargo transport|synaptic transmission|vesicle transport along microtubule	astral microtubule|cell cortex|centrosome|cytosol|kinetochore|motile primary cilium|nuclear membrane|perinuclear region of cytoplasm	dynactin binding|heparin binding|microtubule binding|phospholipase binding|phosphoprotein binding|protein homodimerization activity			skin(1)	1						TTTTGTTTTTAAACCATTTGTACAGG	0.306													6	4	---	---	---	---	
RAP1GAP2	23108	broad.mit.edu	37	17	2703722	2703743	+	Intron	DEL	GGCTGTCCCGGGGACTCCTCCA	-	-	rs72122107		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2703722_2703743delGGCTGTCCCGGGGACTCCTCCA	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1						TGGTGGTTTGGGCTGTCCCGGGGACTCCTCCATACAGATGCT	0.595													39	20	---	---	---	---	
FBXO39	162517	broad.mit.edu	37	17	6690865	6690866	+	3'UTR	INS	-	TC	TC	rs4606762		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6690865_6690866insTC	uc010vtg.1	+	4					FBXO39_uc010cls.1_Intron	NM_153230	NP_694962	Q8N4B4	FBX39_HUMAN	F-box protein 39											ovary(1)|skin(1)	2						CCACTTTTTTTTTTTGTCAGCT	0.470													13	10	---	---	---	---	
FAM18B2	201158	broad.mit.edu	37	17	15406041	15406064	+	3'UTR	DEL	TCTCTTTCTCTCTCCTCTCTCCCG	-	-	rs149635358	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15406041_15406064delTCTCTTTCTCTCTCCTCTCTCCCG	uc002goq.2	-	6					CDRT4_uc010vvw.1_Intron|FAM18B2_uc010vvx.1_Intron	NM_145301	NP_660344	Q96ET8	F18B2_HUMAN	hypothetical protein LOC201158 isoform 1							integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0872)|BRCA - Breast invasive adenocarcinoma(8;0.0581)|READ - Rectum adenocarcinoma(1115;0.0967)		ctcctctctctctctttctctctcctctctcccgtctctttctc	0.241													9	14	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21217017	21217017	+	Intron	DEL	C	-	-	rs67245637		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21217017delC	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		ATACCTGGCTCCCTCCTCCCT	0.393													14	10	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21217021	21217022	+	Intron	DEL	CC	-	-	rs67362606		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21217021_21217022delCC	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CTGGCTCCCTCCTCCCTCCTTC	0.381													11	10	---	---	---	---	
AP2B1	163	broad.mit.edu	37	17	33998653	33998654	+	Intron	INS	-	T	T			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33998653_33998654insT	uc002hjr.2	+						AP2B1_uc002hjq.2_Intron|AP2B1_uc010wci.1_Intron|AP2B1_uc002hjs.2_Intron|AP2B1_uc002hjt.2_Intron|AP2B1_uc010ctv.2_Intron|AP2B1_uc010wcj.1_Intron	NM_001282	NP_001273	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|coated pit|cytosol|endocytic vesicle membrane|plasma membrane	clathrin binding|protein transporter activity			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		TCCTAAGAATATTGTAATTATG	0.292													4	4	---	---	---	---	
SAMD14	201191	broad.mit.edu	37	17	48202127	48202128	+	Intron	INS	-	CGCA	CGCA	rs71957766		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48202127_48202128insCGCA	uc002iqg.2	-						SAMD14_uc002iqe.2_5'Flank|SAMD14_uc002iqf.2_Intron	NM_174920	NP_777580	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14												0						ACGCGTGcacgcgcgcgcgcac	0.322													17	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	72559561	72559562	+	IGR	INS	-	CA	CA	rs151284939	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72559561_72559562insCA								CD300C (17279 upstream) : CD300LD (16549 downstream)																							acacctgctctcacacacacac	0.000													4	3	---	---	---	---	
KIAA0195	9772	broad.mit.edu	37	17	73487035	73487036	+	Intron	DEL	TT	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73487035_73487036delTT	uc002jnz.3	+						KIAA0195_uc010wsa.1_Intron|KIAA0195_uc010wsb.1_Intron	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772						ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCACCCCAACTTCGTGGTGCTC	0.564													27	13	---	---	---	---	
TSEN54	283989	broad.mit.edu	37	17	73513183	73513191	+	Intron	DEL	GCCCTCCCT	-	-	rs113075319		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73513183_73513191delGCCCTCCCT	uc002jof.1	+						CASKIN2_uc002joc.2_5'Flank|CASKIN2_uc002jod.2_5'Flank|TSEN54_uc002joe.1_Intron	NM_207346	NP_997229	Q7Z6J9	SEN54_HUMAN	tRNA splicing endonuclease 54 homolog						mRNA processing|tRNA splicing, via endonucleolytic cleavage and ligation	nucleolus				ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			ACCGGGGACCgccctccctgccctccctg	0.574													31	17	---	---	---	---	
DNAH17	8632	broad.mit.edu	37	17	76456444	76456447	+	Intron	DEL	GCAC	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76456444_76456447delGCAC	uc010dhp.1	-						DNAH17_uc002jvs.2_Intron					SubName: Full=DNAH17 variant protein; Flags: Fragment;											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			gtgcatgtatgcacgtgcatgagt	0.196													39	35	---	---	---	---	
SMCHD1	23347	broad.mit.edu	37	18	2772110	2772110	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2772110delT	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0						TTTCTGATAGTTTTTTTTTTA	0.279													4	3	---	---	---	---	
CHST9	83539	broad.mit.edu	37	18	24510893	24510897	+	Intron	DEL	TGGGG	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24510893_24510897delTGGGG	uc002kwd.2	-						C18orf16_uc002kwb.2_Intron|C18orf16_uc010xbm.1_Intron|CHST9_uc002kwc.2_Intron|CHST9_uc002kwe.2_Intron	NM_031422	NP_113610	Q7L1S5	CHST9_HUMAN	GalNAc-4-sulfotransferase 2						carbohydrate biosynthetic process|glycosaminoglycan metabolic process|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	extracellular region|Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			ovary(2)|skin(1)	3	all_lung(6;0.0145)|Ovarian(20;0.124)					AGAATATACAtggggtggggtgggg	0.278													4	3	---	---	---	---	
DSC3	1825	broad.mit.edu	37	18	28577109	28577110	+	Intron	INS	-	ATTC	ATTC			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28577109_28577110insATTC	uc002kwj.3	-						DSC3_uc002kwi.3_Intron	NM_001941	NP_001932	Q14574	DSC3_HUMAN	desmocollin 3 isoform Dsc3a preproprotein						homophilic cell adhesion|protein stabilization	desmosome|integral to membrane|membrane fraction	calcium ion binding|gamma-catenin binding			ovary(2)|skin(2)	4			OV - Ovarian serous cystadenocarcinoma(10;0.125)			TTCAACCTtttattcattcatt	0.158													19	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	74471546	74471546	+	IGR	DEL	T	-	-	rs35186190		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74471546delT								LOC284276 (199763 upstream) : ZNF236 (64570 downstream)																							CAGGCCAGACTTTTTTTTTTT	0.507													6	3	---	---	---	---	
FSD1	79187	broad.mit.edu	37	19	4306470	4306470	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4306470delT	uc002lzy.2	+						FSD1_uc010xie.1_Intron|FSD1_uc010xif.1_Intron|FSD1_uc002lzz.2_Intron	NM_024333	NP_077309	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing						cell division|mitosis	cleavage furrow|microtubule|microtubule organizing center|nucleus				skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		ACACtctctcttttttttttt	0.259													8	4	---	---	---	---	
MUC16	94025	broad.mit.edu	37	19	9080282	9080283	+	Intron	DEL	AG	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9080282_9080283delAG	uc002mkp.2	-							NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						aaagaaagaaagagaaagaaag	0.015													21	11	---	---	---	---	
OR7G3	390883	broad.mit.edu	37	19	9237801	9237802	+	5'Flank	DEL	TC	-	-	rs144625616		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9237801_9237802delTC	uc010xkl.1	-							NM_001001958	NP_001001958	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						tctttctctttctctctctttc	0.000													4	8	---	---	---	---	
ZNF121	7675	broad.mit.edu	37	19	9679048	9679048	+	Intron	DEL	T	-	-	rs34558756		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9679048delT	uc010xkp.1	-						ZNF121_uc010dwt.2_Intron|ZNF121_uc010xkq.1_Intron	NM_001008727	NP_001008727	P58317	ZN121_HUMAN	zinc finger protein 121						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						AACTTAGTAAttttttttttt	0.169													3	3	---	---	---	---	
PRDX2	7001	broad.mit.edu	37	19	12908143	12908143	+	Intron	DEL	T	-	-	rs112459805		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12908143delT	uc002mvd.2	-							NM_005809	NP_005800	P32119	PRDX2_HUMAN	peroxiredoxin 2 isoform a						anti-apoptosis|cell redox homeostasis|hydrogen peroxide catabolic process|removal of superoxide radicals		thioredoxin peroxidase activity				0						GTAttttttcttttttttttt	0.224													11	5	---	---	---	---	
UNC13A	23025	broad.mit.edu	37	19	17757078	17757079	+	Intron	INS	-	TGTT	TGTT	rs142508123	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17757078_17757079insTGTT	uc002nhd.2	-							NM_001080421	NP_001073890	Q9UPW8	UN13A_HUMAN	unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3						Ggttttttgtgtgtttgtttgt	0.272													7	4	---	---	---	---	
ZNF253	56242	broad.mit.edu	37	19	20003794	20003795	+	3'UTR	INS	-	TTT	TTT	rs149602365	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20003794_20003795insTTT	uc002noj.2	+	4					ZNF253_uc002nok.2_3'UTR|ZNF253_uc002nol.2_RNA	NM_021047	NP_066385	O75346	ZN253_HUMAN	zinc finger protein 253						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTCTCAATTCCtttttttttga	0.178													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54861176	54861177	+	IGR	INS	-	G	G			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54861176_54861177insG								LILRA4 (10755 upstream) : LAIR1 (4058 downstream)																							ATCCTGAGGGTGAATGGATGGA	0.569													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	54861178	54861179	+	IGR	INS	-	TGG	TGG	rs146571521	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54861178_54861179insTGG								LILRA4 (10757 upstream) : LAIR1 (4056 downstream)																							CCTGAGGGTGAATGGATGGAGG	0.579													8	4	---	---	---	---	
DDRGK1	65992	broad.mit.edu	37	20	3181262	3181263	+	Intron	INS	-	GT	GT	rs138231795	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3181262_3181263insGT	uc002wic.2	-						DDRGK1_uc010gaw.2_Intron|DDRGK1_uc010gax.1_Intron	NM_023935	NP_076424	Q96HY6	DDRGK_HUMAN	DDRGK domain containing 1 precursor							endoplasmic reticulum	protein binding				0						GCCATGAGTGCGTGTGTGTGTG	0.510													11	5	---	---	---	---	
SLC13A3	64849	broad.mit.edu	37	20	45192253	45192254	+	Intron	INS	-	A	A	rs59207395	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45192253_45192254insA	uc002xsf.1	-						SLC13A3_uc010ghn.1_Intron|SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010zxx.1_Intron|SLC13A3_uc002xse.1_5'UTR|SLC13A3_uc010ghm.1_Intron|SLC13A3_uc010zxv.1_Intron	NM_022829	NP_073740	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	CACAGCAagagggagagagaga	0.292													15	7	---	---	---	---	
NFATC2	4773	broad.mit.edu	37	20	50109844	50109845	+	Intron	INS	-	G	G	rs149346235	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50109844_50109845insG	uc002xwd.2	-						NFATC2_uc002xwc.2_Intron|NFATC2_uc010zyv.1_Intron|NFATC2_uc010zyw.1_Intron|NFATC2_uc010zyx.1_Intron|NFATC2_uc010zyy.1_Intron|NFATC2_uc010zyz.1_Intron|NFATC2_uc002xwe.2_Intron	NM_173091	NP_775114	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells,						B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)					gaaccagtggcgacacatagta	0.163													5	3	---	---	---	---	
NTSR1	4923	broad.mit.edu	37	20	61364993	61364994	+	Intron	INS	-	AAAG	AAAG	rs142862552	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61364993_61364994insAAAG	uc002ydf.2	+							NM_002531	NP_002522	P30989	NTR1_HUMAN	neurotensin receptor 1							endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	neurotensin receptor activity, G-protein coupled			skin(2)|lung(1)|central_nervous_system(1)	4	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)			aagagggagatagagaagagag	0.248													4	2	---	---	---	---	
CHODL	140578	broad.mit.edu	37	21	19638151	19638151	+	Intron	DEL	A	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19638151delA	uc002ykv.2	+						CHODL_uc002ykr.2_Intron|CHODL_uc002yks.2_Intron|CHODL_uc002ykt.2_Intron|CHODL_uc002yku.2_Intron	NM_024944	NP_079220	Q9H9P2	CHODL_HUMAN	chondrolectin precursor						muscle organ development	integral to membrane|perinuclear region of cytoplasm	sugar binding			upper_aerodigestive_tract(1)	1		all_epithelial(11;0.21)		Epithelial(23;0.000191)|all cancers(11;0.000827)|LUSC - Lung squamous cell carcinoma(23;0.00646)|Lung(58;0.0129)|OV - Ovarian serous cystadenocarcinoma(11;0.017)|COAD - Colon adenocarcinoma(22;0.03)|Colorectal(24;0.0917)		ATGGGAAAATATACTGCTGAG	0.333													24	13	---	---	---	---	
CHODL	140578	broad.mit.edu	37	21	19638152	19638153	+	Intron	INS	-	CTTC	CTTC	rs71329777		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19638152_19638153insCTTC	uc002ykv.2	+						CHODL_uc002ykr.2_Intron|CHODL_uc002yks.2_Intron|CHODL_uc002ykt.2_Intron|CHODL_uc002yku.2_Intron	NM_024944	NP_079220	Q9H9P2	CHODL_HUMAN	chondrolectin precursor						muscle organ development	integral to membrane|perinuclear region of cytoplasm	sugar binding			upper_aerodigestive_tract(1)	1		all_epithelial(11;0.21)		Epithelial(23;0.000191)|all cancers(11;0.000827)|LUSC - Lung squamous cell carcinoma(23;0.00646)|Lung(58;0.0129)|OV - Ovarian serous cystadenocarcinoma(11;0.017)|COAD - Colon adenocarcinoma(22;0.03)|Colorectal(24;0.0917)		TGGGAAAATATACTGCTGAGAG	0.332													26	13	---	---	---	---	
TRPM2	7226	broad.mit.edu	37	21	45824752	45824753	+	Intron	INS	-	TGA	TGA			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45824752_45824753insTGA	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						gacagtgactgtgatgatagtg	0.114													8	7	---	---	---	---	
C22orf43	51233	broad.mit.edu	37	22	23958900	23958900	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23958900delT	uc002zxf.2	-							NM_016449	NP_057533	Q6PGQ1	CV043_HUMAN	hypothetical protein LOC51233											skin(1)	1						ACAGCCCCTCTTCTCATAGCT	0.448													72	31	---	---	---	---	
MICALL1	85377	broad.mit.edu	37	22	38308653	38308653	+	Intron	DEL	T	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38308653delT	uc003aui.2	+							NM_033386	NP_203744	Q8N3F8	MILK1_HUMAN	molecule interacting with Rab13							cytoplasm|cytoskeleton	protein binding|zinc ion binding			breast(1)	1	Melanoma(58;0.045)					gaaatatttcttttttttttt	0.154													5	3	---	---	---	---	
MOV10L1	54456	broad.mit.edu	37	22	50572743	50572744	+	Intron	INS	-	ATTC	ATTC	rs67162661		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50572743_50572744insATTC	uc003bjj.2	+						MOV10L1_uc003bjk.3_Intron|MOV10L1_uc011arp.1_Intron|MOV10L1_uc011arq.1_Intron|MOV10L1_uc010hao.1_Intron	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1						germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)|skin(1)	3		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TCATAAATGTAATTTATGAATT	0.282													9	5	---	---	---	---	
MOV10L1	54456	broad.mit.edu	37	22	50572751	50572752	+	Intron	DEL	AA	-	-	rs67541620		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50572751_50572752delAA	uc003bjj.2	+						MOV10L1_uc003bjk.3_Intron|MOV10L1_uc011arp.1_Intron|MOV10L1_uc011arq.1_Intron|MOV10L1_uc010hao.1_Intron	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1						germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)|skin(1)	3		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GTAATTTATGAATTTTTACAGA	0.287													5	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	51406884	51406885	+	IGR	INS	-	C	C			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51406884_51406885insC								NUDT11 (167425 upstream) : GSPT2 (79612 downstream)																							ccaccttgactcccctacaatg	0.000													4	2	---	---	---	---	
TEX11	56159	broad.mit.edu	37	X	69944901	69944901	+	Intron	DEL	A	-	-	rs56663425	by1000genomes	TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69944901delA	uc004dyl.2	-						TEX11_uc004dyk.2_5'Flank|TEX11_uc004dym.2_Intron	NM_001003811	NP_001003811	Q8IYF3	TEX11_HUMAN	testis expressed sequence 11 isoform 1								protein binding			ovary(3)|breast(1)|skin(1)	5	Renal(35;0.156)					AGCTTTTTTTAAAAAAAAAAA	0.348													5	3	---	---	---	---	
FAM133A	286499	broad.mit.edu	37	X	92929496	92929496	+	Intron	DEL	G	-	-			TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:92929496delG	uc004efr.1	+						NAP1L3_uc004efq.2_5'Flank	NM_173698	NP_775969	Q8N9E0	F133A_HUMAN	hypothetical protein LOC286499												0						TGGGATGGGAGGGGGAATTTG	0.373													4	2	---	---	---	---	
MIR450B	100126302	broad.mit.edu	37	X	133675600	133675615	+	5'Flank	DEL	ACACACACACACACAA	-	-	rs67064887		TCGA-CJ-4644-01A-02D-1386-10	TCGA-CJ-4644-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133675600_133675615delACACACACACACACAA	hsa-mir-450b|MI0005531	-						MIR450A1_hsa-mir-450a-1|MI0001652_5'Flank|uc011mvl.1_5'Flank|MIR450A2_hsa-mir-450a-2|MI0003187_5'Flank|MIR542_hsa-mir-542|MI0003686_5'Flank																	0						acacacacacacacacacacacacaAAACCATGAAA	0.301													14	13	---	---	---	---	
