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
ATAD3B	83858	broad.mit.edu	37	1	1423280	1423280	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1423280C>T	uc001afv.2	+	12	1353	c.1252C>T	c.(1252-1254)CGG>TGG	p.R418W	ATAD3B_uc001afx.2_Missense_Mutation_p.R372W|ATAD3B_uc001afy.2_5'Flank	NM_031921	NP_114127	Q5T9A4	ATD3B_HUMAN	AAA-ATPase  TOB3	418							ATP binding|nucleoside-triphosphatase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CGCCTTCCTTCGGAAGCGAGC	0.622													13	68	---	---	---	---	PASS
NADK	65220	broad.mit.edu	37	1	1684482	1684482	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1684482G>A	uc009vkw.2	-	12	1323	c.1202C>T	c.(1201-1203)TCA>TTA	p.S401L	NADK_uc001aic.2_Missense_Mutation_p.S401L|NADK_uc001aid.3_Missense_Mutation_p.S401L|NADK_uc001aie.2_Missense_Mutation_p.S546L|NADK_uc010nyv.1_Missense_Mutation_p.S369L	NM_023018	NP_075394	O95544	NADK_HUMAN	NAD kinase	401					ATP metabolic process|NAD metabolic process|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|NAD+ kinase activity|protein binding				0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		CGGGTAGCATGAGGTAGTGAT	0.642													3	19	---	---	---	---	PASS
TNFRSF9	3604	broad.mit.edu	37	1	7995116	7995116	+	Silent	SNP	C	A	A	rs148554600	byFrequency	TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7995116C>A	uc001aot.2	-	6	629	c.501G>T	c.(499-501)CCG>CCT	p.P167P		NM_001561	NP_001552	Q07011	TNR9_HUMAN	tumor necrosis factor receptor superfamily,	167	Extracellular (Potential).				induction of apoptosis|negative regulation of cell proliferation	integral to plasma membrane	binding|receptor activity			large_intestine(1)|lung(1)|ovary(1)|skin(1)	4	Ovarian(185;0.0634)|all_lung(157;0.151)	all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649)		AGGATGCTCCCGGAGAGAGGT	0.542													3	85	---	---	---	---	PASS
PRAMEF6	440561	broad.mit.edu	37	1	13001218	13001218	+	Silent	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13001218G>C	uc001auq.2	-	3	551	c.465C>G	c.(463-465)CTC>CTG	p.L155L	PRAMEF5_uc001aur.2_Intron	NM_001010889	NP_001010889	Q5VXH4	PRAM6_HUMAN	PRAME family member 6	155											0	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TCCTGTTCTTGAGCCAAAGTT	0.483													36	456	---	---	---	---	PASS
EFHD2	79180	broad.mit.edu	37	1	15755247	15755247	+	3'UTR	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15755247C>T	uc001awh.2	+	4						NM_024329	NP_077305	Q96C19	EFHD2_HUMAN	EF-hand domain family, member D2							membrane raft					0		Renal(390;0.00145)|Breast(348;0.00173)|Colorectal(325;0.00215)|all_lung(284;0.00366)|Lung NSC(340;0.00395)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)|Hepatocellular(190;0.152)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.59e-07)|COAD - Colon adenocarcinoma(227;3.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000119)|KIRC - Kidney renal clear cell carcinoma(229;0.00251)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		CCGCCCTGCTCCGGCCCCAGT	0.597													3	9	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16945393	16945393	+	RNA	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16945393G>A	uc010ocf.1	-	4		c.764C>T			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						TGGGATGCTGGAAACCGCGGG	0.607													5	81	---	---	---	---	PASS
ARHGEF10L	55160	broad.mit.edu	37	1	17942532	17942532	+	Intron	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17942532C>T	uc001ban.2	+						ARHGEF10L_uc009vpe.1_Intron|ARHGEF10L_uc001bao.2_Intron|ARHGEF10L_uc001bap.2_Intron|ARHGEF10L_uc010ocr.1_Intron|ARHGEF10L_uc001baq.2_5'UTR|ARHGEF10L_uc010ocs.1_5'Flank|ARHGEF10L_uc001bar.2_5'Flank	NM_018125	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF)						regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GGGTGGCCCTCGGTAGCAGGC	0.647													24	79	---	---	---	---	PASS
HMGN2	3151	broad.mit.edu	37	1	26800477	26800477	+	Intron	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26800477G>C	uc001bmp.3	+						HMGN2_uc009vsk.2_Intron|HMGN2_uc001bmq.3_Missense_Mutation_p.E31D	NM_005517	NP_005508	P05204	HMGN2_HUMAN	high-mobility group nucleosomal binding domain						chromatin organization|regulation of transcription, DNA-dependent	chromatin|cytoplasm|nucleus	DNA binding|protein binding				0		all_cancers(24;1.9e-24)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.38e-49)|OV - Ovarian serous cystadenocarcinoma(117;5.38e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.026)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.153)|LUSC - Lung squamous cell carcinoma(448;0.227)		AGGAGGAGGAGAAACTTCTCT	0.418													5	16	---	---	---	---	PASS
ARID1A	8289	broad.mit.edu	37	1	27059204	27059204	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27059204C>T	uc001bmv.1	+	4	2214	c.1841C>T	c.(1840-1842)TCA>TTA	p.S614L	ARID1A_uc001bmt.1_Missense_Mutation_p.S614L|ARID1A_uc001bmu.1_Missense_Mutation_p.S614L|ARID1A_uc001bmw.1_Missense_Mutation_p.S231L	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	614					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CAGGCATCCTCAGCCCCCTCA	0.478			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								7	169	---	---	---	---	PASS
ARID1A	8289	broad.mit.edu	37	1	27059260	27059260	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27059260C>T	uc001bmv.1	+	4	2270	c.1897C>T	c.(1897-1899)CAG>TAG	p.Q633*	ARID1A_uc001bmt.1_Nonsense_Mutation_p.Q633*|ARID1A_uc001bmu.1_Nonsense_Mutation_p.Q633*|ARID1A_uc001bmw.1_Nonsense_Mutation_p.Q250*	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	633					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CCTGAGCCTTCAGTCAAGACC	0.488			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								14	170	---	---	---	---	PASS
RLF	6018	broad.mit.edu	37	1	40661404	40661404	+	Missense_Mutation	SNP	T	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40661404T>G	uc001cfc.3	+	4	606	c.575T>G	c.(574-576)ATT>AGT	p.I192S		NM_012421	NP_036553	Q13129	RLF_HUMAN	rearranged L-myc fusion	192					chromosome organization|DNA integration|DNA mediated transformation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			ovary(2)|pancreas(1)	3	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;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			CTTCTTAAAATTCTGTCTCAA	0.368													5	47	---	---	---	---	PASS
ECHDC2	55268	broad.mit.edu	37	1	53370432	53370432	+	Silent	SNP	C	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53370432C>G	uc001cup.3	-	7	834	c.588G>C	c.(586-588)CTG>CTC	p.L196L	ECHDC2_uc001cun.2_Silent_p.L119L|ECHDC2_uc001cuo.3_Silent_p.L165L|ECHDC2_uc010onk.1_Silent_p.L150L	NM_018281	NP_060751	Q86YB7	ECHD2_HUMAN	enoyl Coenzyme A hydratase domain containing 2	196					fatty acid metabolic process	mitochondrion	lyase activity			central_nervous_system(1)	1						CAGTTCCACTCAGTCGTCGGC	0.677													12	64	---	---	---	---	PASS
CD58	965	broad.mit.edu	37	1	117078842	117078842	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117078842G>C	uc001egm.2	-	3	494	c.373C>G	c.(373-375)CCA>GCA	p.P125A	CD58_uc001egn.2_RNA|CD58_uc010owy.1_Missense_Mutation_p.P125A|CD58_uc001ego.1_Intron|CD58_uc001egp.3_Missense_Mutation_p.P125A	NM_001779	NP_001770	P19256	LFA3_HUMAN	CD58 molecule isoform 1	125	Extracellular (Potential).				blood coagulation|cell-cell adhesion|leukocyte migration	anchored to membrane|integral to plasma membrane	protein binding				0	Lung SC(450;0.225)	all_cancers(81;0.000363)|all_lung(203;0.000118)|all_epithelial(167;0.000149)|Lung NSC(69;0.000577)		Lung(183;0.0086)|LUSC - Lung squamous cell carcinoma(189;0.0528)|Colorectal(144;0.0775)|all cancers(265;0.109)|Epithelial(280;0.118)|COAD - Colon adenocarcinoma(174;0.121)		GTGGGAGATGGAAGAGACTCT	0.358													5	36	---	---	---	---	PASS
NOTCH2	4853	broad.mit.edu	37	1	120612034	120612034	+	5'UTR	SNP	T	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120612034T>G	uc001eik.2	-	1					NOTCH2_uc001eil.2_5'UTR|NOTCH2_uc001eim.3_5'UTR	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTCGGTCGCCTCCTCCTccgc	0.622			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				3	4	---	---	---	---	PASS
NUDT17	200035	broad.mit.edu	37	1	145588986	145588986	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145588986C>T	uc001eoe.2	-	2	270	c.262G>A	c.(262-264)GAT>AAT	p.D88N	NBPF10_uc001emp.3_Intron|NUDT17_uc001eof.1_Missense_Mutation_p.D148N	NM_001012758	NP_001012776	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety	88							hydrolase activity|metal ion binding				0	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					ACACCTCGATCTGTGGGCAGC	0.637											OREG0013751	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	15	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	148891539	148891539	+	RNA	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148891539G>A	uc009wkv.1	+	9		c.841G>A								Homo sapiens cDNA, FLJ17483.																		ACCCACCCAAGACTTATACCC	0.368													11	138	---	---	---	---	PASS
GON4L	54856	broad.mit.edu	37	1	155720458	155720458	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155720458C>A	uc001flz.2	-	32	6740	c.6643G>T	c.(6643-6645)GAG>TAG	p.E2215*	MSTO2P_uc010pgp.1_RNA|GON4L_uc001flx.1_Nonsense_Mutation_p.E49*|GON4L_uc009wrg.1_RNA|GON4L_uc001fly.1_Nonsense_Mutation_p.E2214*|GON4L_uc009wrh.1_Nonsense_Mutation_p.E2214*|GON4L_uc001fma.1_Nonsense_Mutation_p.E2215*	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a	2215					regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					GCATCATCCTCATCCTCAGAG	0.512													3	13	---	---	---	---	PASS
KIF14	9928	broad.mit.edu	37	1	200571154	200571154	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200571154C>G	uc010ppk.1	-	11	2461	c.2022G>C	c.(2020-2022)ATG>ATC	p.M674I	KIF14_uc010ppj.1_Missense_Mutation_p.M183I	NM_014875	NP_055690	Q15058	KIF14_HUMAN	kinesin family member 14	674					microtubule-based movement	cytoplasm|microtubule|nucleus|spindle	ATP binding|microtubule motor activity|protein binding			breast(3)|ovary(2)|skin(2)	7						TCGTAGCAATCATTGCAGTTT	0.348													15	83	---	---	---	---	PASS
OBSCN	84033	broad.mit.edu	37	1	228547934	228547934	+	Intron	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228547934C>T	uc009xez.1	+						OBSCN_uc001hsn.2_Silent_p.H6447H|OBSCN_uc001hsr.1_Intron|OBSCN_uc009xfa.2_Silent_p.H109H	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				AGGACACACACAGCCTTGGGG	0.632													8	67	---	---	---	---	PASS
OR2L2	26246	broad.mit.edu	37	1	248202245	248202245	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248202245C>T	uc001idw.2	+	1	772	c.676C>T	c.(676-678)CGC>TGC	p.R226C	OR2L13_uc001ids.2_Intron	NM_001004686	NP_001004686	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L,	226	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			TGCTGTCTACCGCATGCACTC	0.488													33	191	---	---	---	---	PASS
ZNF512	84450	broad.mit.edu	37	2	27822539	27822539	+	Missense_Mutation	SNP	C	A	A	rs11539165		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27822539C>A	uc002rla.2	+	4	454	c.367C>A	c.(367-369)CTT>ATT	p.L123I	ZNF512_uc010ylv.1_Missense_Mutation_p.L44I|ZNF512_uc010ylw.1_Missense_Mutation_p.L122I|ZNF512_uc002rlb.2_Missense_Mutation_p.L44I|ZNF512_uc010ylx.1_Missense_Mutation_p.L44I|ZNF512_uc002rlc.2_Missense_Mutation_p.L44I|ZNF512_uc010yly.1_RNA|ZNF512_uc010ylz.1_Missense_Mutation_p.L44I	NM_032434	NP_115810	Q96ME7	ZN512_HUMAN	zinc finger protein 512	123					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					GAAGCATAAGCTTTATGGTAA	0.438													3	81	---	---	---	---	PASS
SMYD1	150572	broad.mit.edu	37	2	88409880	88409880	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88409880G>A	uc002ssr.2	+	10	1324	c.1322G>A	c.(1321-1323)CGG>CAG	p.R441Q	SMYD1_uc002ssq.1_Intron|SMYD1_uc002sss.2_Missense_Mutation_p.R137Q	NM_198274	NP_938015	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	441					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)|skin(1)	4						CAGGCCATGCGGGTGCAGACG	0.532													10	24	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	90078205	90078205	+	RNA	SNP	A	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90078205A>C	uc010fhm.2	+	14		c.1595A>C								Parts of antibodies, mostly variable regions.																		GGCATCCCAGACAGGTTCAGT	0.547													5	107	---	---	---	---	PASS
RGPD4	285190	broad.mit.edu	37	2	108496477	108496477	+	Missense_Mutation	SNP	A	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108496477A>C	uc010ywk.1	+	21	5060	c.4978A>C	c.(4978-4980)AGT>CGT	p.S1660R	RGPD4_uc002tdu.2_Missense_Mutation_p.S847R|RGPD4_uc010ywl.1_RNA	NM_182588	NP_872394	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1660					intracellular transport		binding			skin(2)	2						TCAGAAGCTCAGTTCCACCAC	0.408													4	195	---	---	---	---	PASS
RND3	390	broad.mit.edu	37	2	151326590	151326590	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151326590G>A	uc002txe.2	-	5	890	c.646C>T	c.(646-648)CGG>TGG	p.R216W	RND3_uc002txf.2_Missense_Mutation_p.R215W|RND3_uc002txg.2_Missense_Mutation_p.R216W|RND3_uc010zbv.1_Intron|RND3_uc010zbw.1_Missense_Mutation_p.R79W	NM_005168	NP_005159	P61587	RND3_HUMAN	ras homolog gene family, member E precursor	216					actin cytoskeleton organization|cell adhesion|small GTPase mediated signal transduction	Golgi membrane	GTP binding|GTPase activity			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.106)		TGTGAAATCCGCTTTGTGGCT	0.438													8	150	---	---	---	---	PASS
SPC25	57405	broad.mit.edu	37	2	169732631	169732631	+	Silent	SNP	A	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169732631A>G	uc002uel.2	-	5	533	c.402T>C	c.(400-402)TCT>TCC	p.S134S		NM_020675	NP_065726	Q9HBM1	SPC25_HUMAN	spindle pole body component 25	134	Potential.|Interaction with the N-terminus of SPBC24.				cell division|chromosome segregation|mitotic prometaphase|mitotic spindle organization	condensed chromosome kinetochore|cytosol|Ndc80 complex|nucleus	protein binding			central_nervous_system(1)	1						ACAAGTCTGCAGATTTCTGCA	0.284													3	40	---	---	---	---	PASS
RFTN2	130132	broad.mit.edu	37	2	198540158	198540158	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198540158C>T	uc002uuo.3	-	1	427	c.25G>A	c.(25-27)GAA>AAA	p.E9K		NM_144629	NP_653230	Q52LD8	RFTN2_HUMAN	raftlin family member 2	9						plasma membrane					0						TCAGGGTCTTCTAGCTTTCTA	0.423													74	189	---	---	---	---	PASS
HEG1	57493	broad.mit.edu	37	3	124728594	124728594	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124728594T>C	uc003ehs.3	-	8	3216	c.3148A>G	c.(3148-3150)AAA>GAA	p.K1050E	HEG1_uc011bke.1_Missense_Mutation_p.K1150E	NM_020733	NP_065784	Q9ULI3	HEG1_HUMAN	HEG homolog 1 precursor	1050	Extracellular (Potential).|EGF-like 2; calcium-binding (Potential).					extracellular region|integral to membrane	calcium ion binding			ovary(2)	2						ACCGGGCATTTGCAGATAAAG	0.428													9	41	---	---	---	---	PASS
STAG1	10274	broad.mit.edu	37	3	136088080	136088080	+	Silent	SNP	T	C	C	rs143784838	byFrequency	TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136088080T>C	uc003era.1	-	24	2707	c.2415A>G	c.(2413-2415)CAA>CAG	p.Q805Q	STAG1_uc003erb.1_Silent_p.Q805Q|STAG1_uc003erc.1_Silent_p.Q579Q	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	805					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						CTGTCATTAATTGGTGGCTGA	0.393													18	84	---	---	---	---	PASS
RBP2	5948	broad.mit.edu	37	3	139181129	139181129	+	Missense_Mutation	SNP	A	G	G	rs142756165		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139181129A>G	uc003eth.2	-	2	128	c.77T>C	c.(76-78)ATT>ACT	p.I26T		NM_004164	NP_004155	P50120	RET2_HUMAN	retinol binding protein 2, cellular	26					epidermis development|retinoid metabolic process|steroid metabolic process|vitamin A metabolic process	cytosol	retinal binding|retinol binding|transporter activity			skin(1)	1					Vitamin A(DB00162)	GGCAAAATCAATATCTGTTGG	0.428													19	114	---	---	---	---	PASS
MLF1	4291	broad.mit.edu	37	3	158314703	158314703	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158314703G>C	uc003fcb.2	+	3	385	c.248G>C	c.(247-249)AGA>ACA	p.R83T	MLF1_uc003fbz.2_Missense_Mutation_p.R58T|MLF1_uc003fca.2_Missense_Mutation_p.R58T|MLF1_uc003fbx.2_Missense_Mutation_p.R73T|MLF1_uc003fcc.2_Missense_Mutation_p.R114T|MLF1_uc003fby.2_Missense_Mutation_p.R9T|MLF1_uc010hvx.2_Missense_Mutation_p.R58T	NM_022443	NP_071888	P58340	MLF1_HUMAN	myeloid leukemia factor 1 isoform 1	83	Interaction with COPS3.				cell cycle arrest|myeloid progenitor cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein domain specific binding				0		Melanoma(1037;0.000458)|Prostate(884;0.0235)|all_neural(597;0.0299)	Lung(72;0.00199)|LUSC - Lung squamous cell carcinoma(72;0.00256)			TCAAATATGAGAAACTATATG	0.299			T	NPM1	AML								13	35	---	---	---	---	PASS
SLC2A2	6514	broad.mit.edu	37	3	170716012	170716012	+	Silent	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170716012G>A	uc003fhe.1	-	10	1653	c.1344C>T	c.(1342-1344)TTC>TTT	p.F448F	SLC2A2_uc003fhf.1_Silent_p.F275F|SLC2A2_uc011bpu.1_Silent_p.F321F	NM_000340	NP_000331	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose	448	Helical; Name=11; (Potential).				carbohydrate metabolic process|cellular lipid metabolic process|endocrine pancreas development|energy reserve metabolic process|regulation of insulin secretion	integral to plasma membrane|membrane fraction	D-glucose transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)			GAGCTACAATGAAATTGCAGG	0.458													16	88	---	---	---	---	PASS
SORBS2	8470	broad.mit.edu	37	4	186544867	186544867	+	Silent	SNP	C	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186544867C>A	uc003iyl.2	-	13	2562	c.1704G>T	c.(1702-1704)CGG>CGT	p.R568R	SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Silent_p.R668R|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cku.1_Intron|SORBS2_uc011ckv.1_Silent_p.R472R|SORBS2_uc003iyd.2_Intron|SORBS2_uc003iye.2_Intron|SORBS2_uc003iya.2_Intron|SORBS2_uc003iyb.2_Intron|SORBS2_uc003iyc.2_Intron|SORBS2_uc003iyg.2_Silent_p.R682R|SORBS2_uc003iyf.2_Intron|SORBS2_uc003iyo.1_Intron	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2	568						actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GGCAGCCTCGCCGGCCCCGAG	0.592													6	56	---	---	---	---	PASS
IRX1	79192	broad.mit.edu	37	5	3600733	3600733	+	Silent	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3600733C>T	uc003jde.2	+	3	1375	c.1323C>T	c.(1321-1323)CTC>CTT	p.L441L		NM_024337	NP_077313	P78414	IRX1_HUMAN	iroquois homeobox protein 1	441						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2						AGAGAGACCTCGTCCCCAGGC	0.617													10	141	---	---	---	---	PASS
TRIO	7204	broad.mit.edu	37	5	14359563	14359563	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14359563G>C	uc003jff.2	+	13	2320	c.2314G>C	c.(2314-2316)GAG>CAG	p.E772Q	TRIO_uc003jfg.2_RNA|TRIO_uc011cna.1_Missense_Mutation_p.E723Q|TRIO_uc003jfh.1_Missense_Mutation_p.E421Q	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	772					apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					GTCGCAGATGGAGGAGCTCTT	0.617													8	104	---	---	---	---	PASS
TRIM23	373	broad.mit.edu	37	5	64906836	64906836	+	Missense_Mutation	SNP	C	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64906836C>A	uc003jty.2	-	5	766	c.680G>T	c.(679-681)CGA>CTA	p.R227L	TRIM23_uc003jtw.2_Missense_Mutation_p.R227L|TRIM23_uc003jtx.2_Missense_Mutation_p.R227L	NM_001656	NP_001647	P36406	TRI23_HUMAN	ADP-ribosylation factor domain protein 1 isoform	227					interspecies interaction between organisms|small GTPase mediated signal transduction	Golgi membrane|lysosomal membrane	enzyme activator activity|GDP binding|GTP binding|GTPase activity|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|lung(1)	4		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		AATTGATGCTCGGATCTGATT	0.333													3	51	---	---	---	---	PASS
MAP1B	4131	broad.mit.edu	37	5	71493610	71493610	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71493610G>C	uc003kbw.3	+	5	4669	c.4428G>C	c.(4426-4428)AAG>AAC	p.K1476N	MAP1B_uc010iyw.1_Missense_Mutation_p.K1493N|MAP1B_uc010iyx.1_Missense_Mutation_p.K1350N|MAP1B_uc010iyy.1_Missense_Mutation_p.K1350N	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1476						microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		GCCAAGAAAAGAAAACTGATG	0.408													24	79	---	---	---	---	PASS
ARSB	411	broad.mit.edu	37	5	78076390	78076390	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78076390C>T	uc003kfq.2	-	8	2718	c.1432G>A	c.(1432-1434)GAT>AAT	p.D478N		NM_000046	NP_000037	P15848	ARSB_HUMAN	arylsulfatase B isoform 1 precursor	478					lysosomal transport|lysosome organization	lysosome	arylsulfatase activity|metal ion binding|N-acetylgalactosamine-4-sulfatase activity			upper_aerodigestive_tract(1)	1		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		GGGTCCCGATCAATATCAAAG	0.498													4	80	---	---	---	---	PASS
PAPD4	167153	broad.mit.edu	37	5	78964813	78964813	+	Silent	SNP	C	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78964813C>G	uc010jae.1	+	13	1588	c.1170C>G	c.(1168-1170)CTC>CTG	p.L390L	PAPD4_uc003kgb.2_Silent_p.L390L|PAPD4_uc010jaf.1_Silent_p.L390L|PAPD4_uc003kga.2_Silent_p.L386L|PAPD4_uc003kfz.2_Silent_p.L347L	NM_001114393	NP_001107865	Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	390	PAP-associated.				histone mRNA catabolic process|mRNA processing|RNA polyadenylation	cytoplasm	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity			ovary(1)	1		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		TTGGGGACCTCTTACTGGGCT	0.318													64	197	---	---	---	---	PASS
CKMT2	1160	broad.mit.edu	37	5	80561982	80561982	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80561982G>A	uc003khc.3	+	11	1407	c.1165G>A	c.(1165-1167)GAT>AAT	p.D389N	RNU5E_uc011cto.1_Intron|CKMT2_uc010jaq.2_Missense_Mutation_p.D389N|CKMT2_uc003khd.3_Missense_Mutation_p.D389N|uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NM_001825	NP_001816	P17540	KCRS_HUMAN	sarcomeric mitochondrial creatine kinase	389	Phosphagen kinase C-terminal.				creatine metabolic process|muscle contraction	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	GATAGTCATCGATGGAGTCAA	0.418													26	253	---	---	---	---	PASS
FER	2241	broad.mit.edu	37	5	108436173	108436173	+	Silent	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108436173C>T	uc003kop.1	+	17	2385	c.2001C>T	c.(1999-2001)GAC>GAT	p.D667D	FER_uc011cvg.1_Silent_p.D492D	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	667	Protein kinase.				intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		TTTCATTAGACGCTGCTGCTG	0.348													7	65	---	---	---	---	PASS
PCDHGA1	56114	broad.mit.edu	37	5	140710506	140710506	+	Silent	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140710506C>T	uc003lji.1	+	1	255	c.255C>T	c.(253-255)ATC>ATT	p.I85I	PCDHGA1_uc011dan.1_Silent_p.I85I	NM_018912	NP_061735	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1 isoform 1	85	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|breast(1)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGCTTGATCACCGCGCGCA	0.547													19	205	---	---	---	---	PASS
PCDHGA4	56111	broad.mit.edu	37	5	140736823	140736823	+	Missense_Mutation	SNP	G	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140736823G>T	uc003ljq.1	+	1	2056	c.2056G>T	c.(2056-2058)GAC>TAC	p.D686Y	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGB2_uc003ljs.1_5'Flank|PCDHGA4_uc003ljp.1_Missense_Mutation_p.D686Y|PCDHGB2_uc011dar.1_5'Flank	NM_018917	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4 isoform 1	686	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGACCCAGACGACTCGGGCCT	0.617													16	44	---	---	---	---	PASS
PCDHGB4	8641	broad.mit.edu	37	5	140769617	140769617	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140769617G>C	uc003lkc.1	+	1	2166	c.2166G>C	c.(2164-2166)TGG>TGC	p.W722C	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc011dav.1_Missense_Mutation_p.W722C	NM_003736	NP_003727	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4 isoform 1	722	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCCTCCTGGAGCTGCTTCC	0.572													42	293	---	---	---	---	PASS
HLA-H	3136	broad.mit.edu	37	6	29856977	29856977	+	3'UTR	SNP	T	G	G	rs116665472	by1000genomes	TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29856977T>G	uc010jro.2	+	3					HLA-G_uc011dmb.1_Intron|HLA-H_uc003nod.2_Intron					SubName: Full=cDNA FLJ52667, highly similar to HLA class I histocompatibility antigen, alpha chain H;												0						GTCCAGGCTGTTGTCTGGGTT	0.547													5	22	---	---	---	---	PASS
MDC1	9656	broad.mit.edu	37	6	30673687	30673687	+	Silent	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30673687C>T	uc003nrg.3	-	10	3713	c.3273G>A	c.(3271-3273)GAG>GAA	p.E1091E	MDC1_uc003nrf.3_Intron|MDC1_uc011dmp.1_Silent_p.E698E	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1091	Pro-rich.			Missing (in Ref. 2; CAH18685).	cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint	focal adhesion|nucleoplasm	FHA domain binding|protein C-terminus binding			breast(2)|ovary(1)|kidney(1)	4						ACAAGGGAGCCTCTGGAGCTT	0.527								Other_conserved_DNA_damage_response_genes					57	378	---	---	---	---	PASS
BAT1	7919	broad.mit.edu	37	6	31498940	31498940	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31498940G>A	uc003ntt.2	-	9	1643	c.1012C>T	c.(1012-1014)CGA>TGA	p.R338*	BAT1_uc003ntq.2_Nonsense_Mutation_p.R71*|BAT1_uc003ntr.2_Nonsense_Mutation_p.R145*|BAT1_uc003nts.2_Nonsense_Mutation_p.R338*|BAT1_uc011dnn.1_Nonsense_Mutation_p.R260*|BAT1_uc003ntu.2_Nonsense_Mutation_p.R338*|BAT1_uc003ntv.2_Nonsense_Mutation_p.R338*	NM_004640	NP_004631	Q13838	DX39B_HUMAN	HLA-B associated transcript 1	338	Helicase C-terminal.				intronless viral mRNA export from host nucleus|RNA secondary structure unwinding|spliceosome assembly	nuclear speck|spliceosomal complex|transcription export complex	ATP binding|ATP-dependent protein binding|ATP-dependent RNA helicase activity|identical protein binding|U4 snRNA binding|U6 snRNA binding				0						AGAATTCGTCGTTGAAAATCT	0.418													14	73	---	---	---	---	PASS
HSPA1B	3304	broad.mit.edu	37	6	31795567	31795567	+	5'UTR	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31795567G>A	uc003nxk.2	+	1						NM_005346	NP_005337	P08107	HSP71_HUMAN	heat shock 70kDa protein 1B						anti-apoptosis|mRNA catabolic process|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of inclusion body assembly|protein refolding|response to unfolded protein	cytosol|endoplasmic reticulum|inclusion body|mitochondrion|nuclear speck|perinuclear region of cytoplasm|ribonucleoprotein complex	ATP binding|protein binding involved in protein folding|protein N-terminus binding|receptor activity|ubiquitin protein ligase binding|unfolded protein binding			breast(1)	1						TTTCGAGAGTGACTCCCGCGG	0.642													3	4	---	---	---	---	PASS
GLO1	2739	broad.mit.edu	37	6	38649846	38649846	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38649846G>T	uc003ooc.2	-	5	530	c.408C>A	c.(406-408)TAC>TAA	p.Y136*		NM_006708	NP_006699	Q04760	LGUL_HUMAN	glyoxalase I	136					anti-apoptosis|carbohydrate metabolic process	cytoplasm	lactoylglutathione lyase activity|metal ion binding			ovary(1)	1					Glutathione(DB00143)	TACAAGCACTGTATACATCAG	0.403													19	122	---	---	---	---	PASS
SPACA1	81833	broad.mit.edu	37	6	88776067	88776067	+	3'UTR	SNP	T	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88776067T>C	uc003pmn.2	+	7						NM_030960	NP_112222	Q9HBV2	SACA1_HUMAN	sperm acrosome associated 1 precursor							integral to membrane					0		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.11)		TTGAATGATATATAACAAACC	0.303													9	54	---	---	---	---	PASS
COQ3	51805	broad.mit.edu	37	6	99817466	99817466	+	3'UTR	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99817466C>T	uc003ppk.2	-	7						NM_017421	NP_059117	Q9NZJ6	COQ3_HUMAN	hexaprenyldihydroxybenzoate methyltransferase						glycerol metabolic process|ubiquinone biosynthetic process	mitochondrial matrix	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity|3-demethylubiquinone-9 3-O-methyltransferase activity|hexaprenyldihydroxybenzoate methyltransferase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)		CTATAGTTCTCAGAAACAATT	0.353													19	149	---	---	---	---	PASS
ROS1	6098	broad.mit.edu	37	6	117710590	117710590	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117710590G>A	uc003pxp.1	-	12	1881	c.1682C>T	c.(1681-1683)CCG>CTG	p.P561L	ROS1_uc011ebi.1_Intron|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	561	Fibronectin type-III 3.|Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AAGCTCCTGCGGGCGGCCTGG	0.557			T	GOPC|ROS1	glioblastoma|NSCLC								18	145	---	---	---	---	PASS
RNF217	154214	broad.mit.edu	37	6	125366487	125366487	+	Missense_Mutation	SNP	G	A	A	rs150679432		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125366487G>A	uc003pzs.2	+	4	475	c.137G>A	c.(136-138)CGT>CAT	p.R46H	RNF217_uc003pzr.2_Missense_Mutation_p.R103H|RNF217_uc003pzt.2_RNA	NM_152553	NP_689766	Q8TC41	RN217_HUMAN	ring finger protein 217	46	IBR-type.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0162)		GAACTTGGCCGTATTGATTCC	0.413													4	96	---	---	---	---	PASS
THEMIS	387357	broad.mit.edu	37	6	128150707	128150707	+	Missense_Mutation	SNP	T	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128150707T>G	uc003qbi.2	-	4	942	c.623A>C	c.(622-624)AAG>ACG	p.K208T	THEMIS_uc010kfa.2_Missense_Mutation_p.K111T|THEMIS_uc011ebt.1_Missense_Mutation_p.K208T|THEMIS_uc010kfb.2_Missense_Mutation_p.K173T	NM_001010923	NP_001010923	Q8N1K5	THMS1_HUMAN	thymocyte selection pathway associated isoform	208	CABIT 1.				negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)|skin(2)	4						TGAGTCCCACTTATTTGAAAA	0.363													28	107	---	---	---	---	PASS
FUCA2	2519	broad.mit.edu	37	6	143825240	143825240	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143825240G>A	uc003qjm.2	-	3	654	c.562C>T	c.(562-564)CAT>TAT	p.H188Y	FUCA2_uc003qjn.2_5'Flank	NM_032020	NP_114409	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma precursor	188					fucose metabolic process	extracellular region	alpha-L-fucosidase activity|cation binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		AAGAGCGGATGAAACCATTCA	0.443													22	87	---	---	---	---	PASS
PLEKHG1	57480	broad.mit.edu	37	6	151116991	151116991	+	Splice_Site	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151116991G>C	uc003qny.1	+	6	895	c.583_splice	c.e6-1	p.S195_splice	PLEKHG1_uc011eel.1_Splice_Site_p.S235_splice|PLEKHG1_uc011eem.1_Splice_Site_p.S254_splice|PLEKHG1_uc003qnz.2_Splice_Site_p.S195_splice	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		TTTCCTTGCAGAGTGAAGAGT	0.343													14	133	---	---	---	---	PASS
PLEKHG1	57480	broad.mit.edu	37	6	151116998	151116998	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151116998G>A	uc003qny.1	+	6	901	c.589G>A	c.(589-591)GAG>AAG	p.E197K	PLEKHG1_uc011eel.1_Missense_Mutation_p.E237K|PLEKHG1_uc011eem.1_Missense_Mutation_p.E256K|PLEKHG1_uc003qnz.2_Missense_Mutation_p.E197K	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G	197	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		GCAGAGTGAAGAGTTCCACAT	0.358													15	138	---	---	---	---	PASS
SYNE1	23345	broad.mit.edu	37	6	152651857	152651857	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152651857T>C	uc010kiw.2	-	78	14565	c.13963A>G	c.(13963-13965)ATT>GTT	p.I4655V	SYNE1_uc003qot.3_Missense_Mutation_p.I4584V|SYNE1_uc003qou.3_Missense_Mutation_p.I4655V|SYNE1_uc010kiz.2_Missense_Mutation_p.I410V	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4655	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AAGGCAACAATTACATTAAAT	0.428										HNSCC(10;0.0054)			17	117	---	---	---	---	PASS
SUN1	23353	broad.mit.edu	37	7	897568	897568	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:897568G>A	uc011jvp.1	+	14	1577	c.1498G>A	c.(1498-1500)GAG>AAG	p.E500K	GET4_uc003sjj.1_RNA|SUN1_uc003sjf.2_Missense_Mutation_p.E417K|SUN1_uc011jvq.1_Missense_Mutation_p.E397K|SUN1_uc003sjg.2_Missense_Mutation_p.E405K|SUN1_uc011jvr.1_Missense_Mutation_p.E298K|SUN1_uc003sji.2_Missense_Mutation_p.E338K|SUN1_uc003sjk.2_Missense_Mutation_p.E139K	NM_001130965	NP_001124437	O94901	SUN1_HUMAN	unc-84 homolog A isoform a	527	Perinuclear space.				cytoskeletal anchoring at nuclear membrane|nuclear matrix anchoring at nuclear membrane	integral to membrane|nuclear inner membrane|SUN-KASH complex	protein binding				0						GACCGGCTGTGAGACAGTGGA	0.468													91	218	---	---	---	---	PASS
TYW1B	441250	broad.mit.edu	37	7	72300234	72300234	+	5'Flank	SNP	G	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72300234G>T	uc011kej.1	-						TYW1B_uc011keh.1_5'Flank|TYW1B_uc011kek.1_5'Flank|SBDSP1_uc003twf.2_RNA|SBDSP1_uc011kel.1_RNA|SBDSP1_uc003twg.2_RNA|SBDSP1_uc003twh.2_RNA|SBDSP1_uc003twe.2_RNA	NM_001145440	NP_001138912	Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0						GAACAGCCGCGATGTCGATCT	0.642													18	50	---	---	---	---	PASS
ACHE	43	broad.mit.edu	37	7	100489998	100489998	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100489998C>T	uc003uxd.2	-	2	1666	c.1510G>A	c.(1510-1512)GCC>ACC	p.A504T	UFSP1_uc003uxc.3_5'Flank|ACHE_uc003uxe.2_Missense_Mutation_p.A504T|ACHE_uc003uxf.2_Missense_Mutation_p.A504T|ACHE_uc003uxg.2_Missense_Mutation_p.A504T|ACHE_uc003uxh.2_Missense_Mutation_p.A416T|ACHE_uc003uxi.2_Missense_Mutation_p.A504T	NM_000665	NP_000656	P22303	ACES_HUMAN	acetylcholinesterase isoform E4-E6 precursor	504					acetylcholine catabolic process in synaptic cleft|amyloid precursor protein metabolic process|cell adhesion|cell proliferation|choline metabolic process|DNA replication|muscle organ development|neurotransmitter biosynthetic process|osteoblast development|positive regulation of protein secretion|regulation of axonogenesis|regulation of dendrite morphogenesis|response to wounding|synapse assembly	anchored to membrane|axon|basal lamina|cell junction|cell surface|dendrite|endoplasmic reticulum lumen|extracellular space|Golgi apparatus|neuromuscular junction|nucleus|perinuclear region of cytoplasm|postsynaptic membrane|presynaptic membrane|synaptic cleft	acetylcholine binding|acetylcholinesterase activity|beta-amyloid binding|carboxylesterase activity|cholinesterase activity|collagen binding|laminin-1 binding|protein homodimerization activity|serine hydrolase activity			skin(2)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Atropine(DB00572)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium bromide(DB00944)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tacrine(DB00382)|Tubocurarine(DB01199)	AGTCGCTGGGCGAAGATTTTC	0.627													13	80	---	---	---	---	PASS
TAS2R16	50833	broad.mit.edu	37	7	122635518	122635518	+	Silent	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122635518G>A	uc003vkl.1	-	1	237	c.171C>T	c.(169-171)TTC>TTT	p.F57F		NM_016945	NP_058641	Q9NYV7	T2R16_HUMAN	taste receptor T2R16	57	Helical; Name=2; (Potential).				detection of chemical stimulus involved in sensory perception of bitter taste	endoplasmic reticulum|external side of plasma membrane|trans-Golgi network	bitter taste receptor activity|protein binding			ovary(1)|skin(1)	2						ACTGTAGACAGAAGCGAGAGA	0.428													25	73	---	---	---	---	PASS
GRM8	2918	broad.mit.edu	37	7	126544080	126544080	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126544080C>G	uc003vlr.2	-	4	1275	c.964G>C	c.(964-966)GAG>CAG	p.E322Q	GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Missense_Mutation_p.E322Q|GRM8_uc010lkz.1_RNA|GRM8_uc003vlu.1_Missense_Mutation_p.E43Q	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a	322	Extracellular (Potential).				negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)	GCAATCTCCTCTTGCTGATAG	0.418										HNSCC(24;0.065)			3	148	---	---	---	---	PASS
CUL1	8454	broad.mit.edu	37	7	148484186	148484186	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148484186G>A	uc010lpg.2	+	13	1979	c.1453G>A	c.(1453-1455)GAA>AAA	p.E485K	CUL1_uc003wey.2_Missense_Mutation_p.E485K|CUL1_uc003wez.2_Missense_Mutation_p.E375K|CUL1_uc003wfa.2_Missense_Mutation_p.E146K	NM_003592	NP_003583	Q13616	CUL1_HUMAN	cullin 1	485					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			TGACGATGCCGAAGCCAGCAT	0.398													30	72	---	---	---	---	PASS
MTMR9	66036	broad.mit.edu	37	8	11172556	11172556	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11172556G>T	uc003wtm.2	+	7	1494	c.1096G>T	c.(1096-1098)GAA>TAA	p.E366*	MTMR9_uc010lrx.2_Nonsense_Mutation_p.E259*|MTMR9_uc011kxa.1_Nonsense_Mutation_p.E281*	NM_015458	NP_056273	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	366	Myotubularin phosphatase.					cytoplasm	phosphatase activity|protein binding				0			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		GGCCCTGATTGAAAGAGAGTG	0.488													25	125	---	---	---	---	PASS
INTS9	55756	broad.mit.edu	37	8	28651378	28651378	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28651378A>G	uc003xha.2	-	10	1282	c.983T>C	c.(982-984)TTC>TCC	p.F328S	INTS9_uc011lav.1_Missense_Mutation_p.F304S|INTS9_uc011law.1_Missense_Mutation_p.F307S|INTS9_uc011lax.1_Missense_Mutation_p.F221S|INTS9_uc010lvc.2_RNA|INTS9_uc003xhb.2_Missense_Mutation_p.F328S	NM_018250	NP_060720	Q9NV88	INT9_HUMAN	integrator complex subunit 9 isoform 1	328					snRNA processing	integrator complex	protein binding			central_nervous_system(1)|pancreas(1)	2		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)		AGGGGAGATGAAGTAGAGGGG	0.468													7	110	---	---	---	---	PASS
GSR	2936	broad.mit.edu	37	8	30537169	30537169	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30537169C>T	uc003xih.1	-	13	1528	c.1437G>A	c.(1435-1437)ATG>ATA	p.M479I		NM_000637	NP_000628	P00390	GSHR_HUMAN	glutathione reductase precursor	479					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)	CAAGTCCCTGCATATGGATCC	0.343													8	89	---	---	---	---	PASS
ANK1	286	broad.mit.edu	37	8	41581117	41581117	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41581117C>T	uc003xok.2	-	8	830	c.746G>A	c.(745-747)AGG>AAG	p.R249K	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoi.2_Missense_Mutation_p.R249K|ANK1_uc003xoj.2_Missense_Mutation_p.R249K|ANK1_uc003xol.2_Missense_Mutation_p.R249K|ANK1_uc003xom.2_Missense_Mutation_p.R282K	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	249	ANK 7.|89 kDa domain.				axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CACGTTGCCCCTGCGGGAGGC	0.637													4	107	---	---	---	---	PASS
DNM1	1759	broad.mit.edu	37	9	130986561	130986561	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130986561G>C	uc011mau.1	+	10	1315	c.1228G>C	c.(1228-1230)GAG>CAG	p.E410Q	DNM1_uc010mxr.2_Intron|DNM1_uc011mat.1_Missense_Mutation_p.E410Q	NM_004408	NP_004399	Q05193	DYN1_HUMAN	dynamin 1 isoform 1	410					receptor-mediated endocytosis	microtubule	GTP binding|GTPase activity			ovary(2)	2						CATGGCCTTTGAGACCATTGT	0.408													9	115	---	---	---	---	PASS
COL5A1	1289	broad.mit.edu	37	9	137664657	137664657	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137664657C>T	uc004cfe.2	+	26	2690	c.2308C>T	c.(2308-2310)CCT>TCT	p.P770S		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	770	Triple-helical region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CAAAGAAGGCCCTCCAGGAGA	0.607													11	131	---	---	---	---	PASS
ITGA8	8516	broad.mit.edu	37	10	15614236	15614236	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15614236G>A	uc001ioc.1	-	25	2611	c.2611C>T	c.(2611-2613)CCT>TCT	p.P871S	ITGA8_uc010qcb.1_Missense_Mutation_p.P856S	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor	871	Extracellular (Potential).				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6						TTGATATTAGGATTTGGTTGG	0.413													20	85	---	---	---	---	PASS
OR13A1	79290	broad.mit.edu	37	10	45799078	45799078	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45799078C>T	uc001jcc.1	-	4	1102	c.793G>A	c.(793-795)GTG>ATG	p.V265M	OR13A1_uc001jcd.1_Missense_Mutation_p.V261M	NM_001004297	NP_001004297	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A,	265	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						ATGCACACCACGGTGAGGTGG	0.572													39	96	---	---	---	---	PASS
ARHGAP22	58504	broad.mit.edu	37	10	49667753	49667753	+	Silent	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49667753G>A	uc001jgt.2	-	5	930	c.633C>T	c.(631-633)GAC>GAT	p.D211D	ARHGAP22_uc001jgs.2_Silent_p.D121D|ARHGAP22_uc001jgu.2_Silent_p.D227D|ARHGAP22_uc010qgl.1_Silent_p.D168D|ARHGAP22_uc010qgm.1_Silent_p.D217D|ARHGAP22_uc001jgv.2_5'UTR	NM_021226	NP_067049	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 2	211	Rho-GAP.				angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	GTPase activator activity			ovary(1)	1						TCTCCCCACAGTCGAAGGAAT	0.617													17	171	---	---	---	---	PASS
TTC18	118491	broad.mit.edu	37	10	75013653	75013653	+	3'UTR	SNP	C	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75013653C>G	uc009xrc.2	-	28					TTC18_uc001jty.2_3'UTR|MRPS16_uc010qkh.1_5'Flank|MRPS16_uc001jts.1_5'Flank|MRPS16_uc001jtt.1_5'Flank|uc001jtu.1_RNA|TTC18_uc001jtv.3_3'UTR|TTC18_uc001jtw.3_3'UTR|TTC18_uc001jtx.2_3'UTR	NM_145170	NP_660153	Q5T0N1	TTC18_HUMAN	tetratricopeptide repeat domain 18								binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)					TTCTCCAGCTCCAGGCTTCAT	0.428													3	37	---	---	---	---	PASS
MGEA5	10724	broad.mit.edu	37	10	103547231	103547231	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103547231A>G	uc001ktv.2	-	15	2947	c.2504T>C	c.(2503-2505)TTC>TCC	p.F835S	MGEA5_uc001ktu.2_RNA|MGEA5_uc010qqe.1_Missense_Mutation_p.F782S|MGEA5_uc009xws.2_Missense_Mutation_p.F768S	NM_012215	NP_036347	O60502	NCOAT_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	835	Histone acetyltransferase activity (By similarity).				glycoprotein catabolic process	cytoplasm|nucleus	histone acetyltransferase activity|hyalurononglucosaminidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		ATTAGCAAGGAAAGTTTCTGG	0.383													8	101	---	---	---	---	PASS
CCKBR	887	broad.mit.edu	37	11	6291461	6291461	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6291461G>A	uc001mcp.2	+	3	740	c.547G>A	c.(547-549)GGA>AGA	p.G183R	CCKBR_uc001mcq.2_Missense_Mutation_p.G111R|CCKBR_uc001mcr.2_Missense_Mutation_p.G183R|CCKBR_uc001mcs.2_Missense_Mutation_p.G183R|CCKBR_uc001mct.1_5'Flank	NM_176875	NP_795344	P32239	GASR_HUMAN	cholecystokinin B receptor	183	Helical; Name=4; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception		1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding			lung(5)|ovary(2)|breast(1)	8		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	GCTGCTGTCCGGACTACTCAT	0.667													14	70	---	---	---	---	PASS
USH1C	10083	broad.mit.edu	37	11	17553040	17553040	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17553040C>T	uc001mnf.2	-	3	263	c.154G>A	c.(154-156)GAA>AAA	p.E52K	USH1C_uc001mne.2_Missense_Mutation_p.E52K|USH1C_uc009yhb.2_Missense_Mutation_p.E52K|USH1C_uc001mng.2_RNA|USH1C_uc001mnd.2_Missense_Mutation_p.E16K	NM_005709	NP_005700	Q9Y6N9	USH1C_HUMAN	harmonin isoform a	52					equilibrioception|G2/M transition of mitotic cell cycle|photoreceptor cell maintenance|sensory perception of sound	apical part of cell|cytoplasm|stereocilium	protein binding			ovary(1)	1						CGGCTGGGTTCATTGATGACC	0.617													9	46	---	---	---	---	PASS
RAB3IL1	5866	broad.mit.edu	37	11	61675662	61675662	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61675662G>C	uc001nso.2	-	2	286	c.128C>G	c.(127-129)TCT>TGT	p.S43C	RAB3IL1_uc001nsp.2_Missense_Mutation_p.S90C	NM_013401	NP_037533	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	43							protein binding			skin(2)|central_nervous_system(1)	3						CTCCCCTGCAGAGGTCTCCAC	0.711													3	11	---	---	---	---	PASS
MAP4K2	5871	broad.mit.edu	37	11	64557669	64557669	+	Missense_Mutation	SNP	C	G	G	rs148398112		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64557669C>G	uc001obh.2	-	29	2331	c.2239G>C	c.(2239-2241)GAG>CAG	p.E747Q	MAP4K2_uc001obg.2_RNA|MAP4K2_uc001obi.2_Missense_Mutation_p.E739Q	NM_004579	NP_004570	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase	747	CNH.				activation of JUN kinase activity|immune response|positive regulation of JNK cascade|vesicle targeting	basolateral plasma membrane|Golgi membrane|soluble fraction	ATP binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(1)|pancreas(1)	2						CCCACAGTCTCGATGGGGAAA	0.617													12	79	---	---	---	---	PASS
ATG2A	23130	broad.mit.edu	37	11	64662776	64662776	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64662776C>T	uc001obx.2	-	40	5681	c.5566G>A	c.(5566-5568)GAC>AAC	p.D1856N	uc009ypx.2_5'Flank|ATG2A_uc001obw.2_Missense_Mutation_p.D621N	NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1856							protein binding			ovary(1)|central_nervous_system(1)	2						CGCACTGTGTCGTAGGCCTTG	0.706													4	98	---	---	---	---	PASS
INPPL1	3636	broad.mit.edu	37	11	71949087	71949087	+	Missense_Mutation	SNP	C	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71949087C>A	uc001osf.2	+	27	3701	c.3554C>A	c.(3553-3555)GCT>GAT	p.A1185D	INPPL1_uc001osg.2_Missense_Mutation_p.A943D	NM_001567	NP_001558	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1185					actin filament organization|cell adhesion|endocytosis	actin cortical patch|cytosol	actin binding|SH2 domain binding|SH3 domain binding			skin(2)|ovary(1)|breast(1)	4						TTTCCTTAGGCTCCGTGCCTG	0.657											OREG0021191	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	22	---	---	---	---	PASS
SLC35F2	54733	broad.mit.edu	37	11	107677535	107677535	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107677535C>T	uc001pjq.2	-	4	903	c.482G>A	c.(481-483)AGA>AAA	p.R161K	SLC35F2_uc010rvu.1_Missense_Mutation_p.R13K|SLC35F2_uc001pjs.2_Missense_Mutation_p.R161K	NM_017515	NP_059985	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2	161					transport	integral to membrane				central_nervous_system(1)	1		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		GTGGATCACTCTGTATCTTGC	0.458													16	90	---	---	---	---	PASS
SDHD	6392	broad.mit.edu	37	11	111959637	111959637	+	Silent	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111959637C>T	uc001pmz.2	+	3	277	c.216C>T	c.(214-216)GTC>GTT	p.V72V	TIMM8B_uc001pmx.2_5'Flank|TIMM8B_uc001pmy.2_5'Flank	NM_003002	NP_002993	O14521	DHSD_HUMAN	succinate dehydrogenase complex, subunit D	72	Helical; (By similarity).				respiratory electron transport chain|transport|tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain complex II	electron carrier activity|heme binding|succinate dehydrogenase activity|ubiquinone binding				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.13e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;1.05e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0515)	Succinic acid(DB00139)	AGAGGGTTGTCAGTGTTTTGC	0.498			Mis|N|F|S			paraganglioma|pheochromocytoma			Familial_Paragangliomas|Carney-Stratakis_syndrome|Cowden_syndrome				22	63	---	---	---	---	PASS
APOA4	337	broad.mit.edu	37	11	116692360	116692360	+	Nonsense_Mutation	SNP	G	T	T	rs145317065		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116692360G>T	uc001pps.1	-	3	518	c.414C>A	c.(412-414)TAC>TAA	p.Y138*		NM_000482	NP_000473			apolipoprotein A-IV precursor												0	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		GCTGGTCCGCGTagggctcca	0.358													11	42	---	---	---	---	PASS
MLL	4297	broad.mit.edu	37	11	118375024	118375024	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118375024C>T	uc001pta.2	+	27	8431	c.8408C>T	c.(8407-8409)TCA>TTA	p.S2803L	MLL_uc001ptb.2_Missense_Mutation_p.S2806L	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	2803					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)		CAGCTCAGCTCATTGGAGTCA	0.443			T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								5	165	---	---	---	---	PASS
ROBO4	54538	broad.mit.edu	37	11	124755027	124755027	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124755027G>A	uc001qbg.2	-	17	3051	c.2911C>T	c.(2911-2913)CGG>TGG	p.R971W	ROBO4_uc010sas.1_Missense_Mutation_p.R826W	NM_019055	NP_061928	Q8WZ75	ROBO4_HUMAN	roundabout homolog 4, magic roundabout	971					angiogenesis|cell differentiation	integral to membrane	receptor activity			ovary(1)|skin(1)	2	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		CTTCCCAGCCGCTGGGTGTGG	0.622													17	81	---	---	---	---	PASS
GALNT8	26290	broad.mit.edu	37	12	4835834	4835834	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4835834G>C	uc001qne.1	+	2	440	c.348G>C	c.(346-348)ATG>ATC	p.M116I		NM_017417	NP_059113	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	116	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(1)|skin(1)	4						AAACCCAAATGAAACTCTTCC	0.498													3	36	---	---	---	---	PASS
C12orf11	55726	broad.mit.edu	37	12	27077408	27077408	+	Silent	SNP	C	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27077408C>A	uc001rhk.3	-	7	1221	c.684G>T	c.(682-684)CCG>CCT	p.P228P	C12orf11_uc010sjk.1_Silent_p.P127P	NM_018164	NP_060634	Q9NVM9	M89BB_HUMAN	hypothetical protein LOC55726	228					cell division|mitosis|regulation of mitotic cell cycle		protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	Colorectal(261;0.0847)					TGGTTAAAACCGGGGACAACT	0.318													28	104	---	---	---	---	PASS
TMPRSS12	283471	broad.mit.edu	37	12	51279250	51279250	+	Intron	SNP	C	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51279250C>G	uc001rwx.3	+						TMPRSS12_uc001rwy.2_Missense_Mutation_p.L292V	NM_182559	NP_872365	Q86WS5	TMPSC_HUMAN	transmembrane protease, serine 12 precursor						proteolysis	integral to membrane	serine-type endopeptidase activity				0						TGATAACTTTCTGGTGGTCTT	0.333													29	79	---	---	---	---	PASS
CYP27B1	1594	broad.mit.edu	37	12	58157882	58157882	+	Missense_Mutation	SNP	T	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58157882T>G	uc001spz.1	-	7	1366	c.1214A>C	c.(1213-1215)AAT>ACT	p.N405T	CYP27B1_uc001sqa.1_Missense_Mutation_p.N170T	NM_000785	NP_000776	O15528	CP27B_HUMAN	cytochrome P450, family 27, subfamily B,	405					bone mineralization|calcium ion homeostasis|calcium ion transport|decidualization|G1 to G0 transition|hormone biosynthetic process|negative regulation of calcidiol 1-monooxygenase activity|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of keratinocyte differentiation|positive regulation of vitamin D 24-hydroxylase activity|positive regulation of vitamin D receptor signaling pathway|regulation of bone mineralization|response to estrogen stimulus|response to interferon-gamma|response to lipopolysaccharide|response to tumor necrosis factor|response to vitamin D|vitamin D biosynthetic process|xenobiotic metabolic process	mitochondrial outer membrane	calcidiol 1-monooxygenase activity|electron carrier activity|heme binding			central_nervous_system(3)	3	all_cancers(7;8.09e-80)|Lung NSC(6;2.26e-27)|all_lung(6;1.99e-25)|all_epithelial(6;3.62e-18)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;1.97e-113)|all cancers(5;1.54e-78)|BRCA - Breast invasive adenocarcinoma(9;0.0294)		Calcidiol(DB00146)|Calcitriol(DB00136)|Ergocalciferol(DB00153)	TTTACTCACATTTTTGGGGAT	0.458													17	44	---	---	---	---	PASS
KNTC1	9735	broad.mit.edu	37	12	123057784	123057784	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123057784G>C	uc001ucv.2	+	26	2398	c.2235G>C	c.(2233-2235)ATG>ATC	p.M745I	KNTC1_uc010taf.1_Missense_Mutation_p.M708I	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore	745					cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		GAGTTTACATGAGAGAACATG	0.398													33	157	---	---	---	---	PASS
KNTC1	9735	broad.mit.edu	37	12	123057806	123057806	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123057806G>A	uc001ucv.2	+	26	2420	c.2257G>A	c.(2257-2259)GAG>AAG	p.E753K	KNTC1_uc010taf.1_Missense_Mutation_p.E716K	NM_014708	NP_055523	P50748	KNTC1_HUMAN	Rough Deal homolog, centromere/kinetochore	753					cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		CTTGCAAGAGGAGGAACTTCT	0.378													28	153	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19426166	19426166	+	RNA	SNP	T	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19426166T>C	uc010tcj.1	-	1		c.19944A>G				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						CAACCATTCATGCAGTGTTAC	0.388													34	143	---	---	---	---	PASS
DCLK1	9201	broad.mit.edu	37	13	36401843	36401843	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36401843G>C	uc001uvf.2	-	10	1569	c.1336C>G	c.(1336-1338)CCC>GCC	p.P446A	DCLK1_uc001uve.3_Missense_Mutation_p.P139A|DCLK1_uc010teh.1_Missense_Mutation_p.P139A|DCLK1_uc010abk.2_Intron	NM_004734	NP_004725	O15075	DCLK1_HUMAN	doublecortin-like kinase 1	446	Protein kinase.				cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		ACGATATTGGGATGCTTCACT	0.388													15	105	---	---	---	---	PASS
LPAR6	10161	broad.mit.edu	37	13	48985928	48985928	+	Nonsense_Mutation	SNP	A	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48985928A>C	uc010acu.2	-	1	1726	c.632T>G	c.(631-633)TTA>TGA	p.L211*	RB1_uc001vcb.2_Intron|LPAR6_uc001vcc.1_Intron|LPAR6_uc001vce.2_Nonsense_Mutation_p.L211*|LPAR6_uc001vcf.2_Nonsense_Mutation_p.L211*	NM_001162498	NP_001155970	P43657	LPAR6_HUMAN	G-protein coupled purinergic receptor P2Y5	211	Cytoplasmic (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled	p.?(4)		ovary(4)	4						AGGTTTGGTTAAAGTTTTTAG	0.264													10	61	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	13	64321208	64321208	+	RNA	SNP	T	A	A	rs141510771	by1000genomes	TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64321208T>A	uc010thk.1	+	1		c.249T>A								Homo sapiens hypothetical LOC647264, mRNA (cDNA clone MGC:189721 IMAGE:9057045), complete cds.																		ggaactggcttcggctgtggg	0.085													3	14	---	---	---	---	PASS
CIDEB	27141	broad.mit.edu	37	14	24776597	24776597	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24776597G>A	uc001won.2	-	2	290	c.166C>T	c.(166-168)CGC>TGC	p.R56C	CIDEB_uc001woo.2_Missense_Mutation_p.R56C|CIDEB_uc001wop.2_Missense_Mutation_p.R56C|LTB4R2_uc001woq.1_5'Flank|LTB4R2_uc010alo.2_5'Flank|LTB4R2_uc001wor.2_5'Flank	NM_014430	NP_055245	Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	56	CIDE-N.				apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis	cytosol					0				GBM - Glioblastoma multiforme(265;0.0181)		AGCTCCTGGCGGGTGGCAGCT	0.587													15	114	---	---	---	---	PASS
PTGDR	5729	broad.mit.edu	37	14	52735281	52735281	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52735281G>A	uc001wzq.2	+	1	851	c.749G>A	c.(748-750)GGG>GAG	p.G250E		NM_000953	NP_000944	Q13258	PD2R_HUMAN	prostaglandin D2 receptor	250	Cytoplasmic (Potential).					integral to membrane|plasma membrane	prostaglandin D receptor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)	CGCGCGGACGGGAGGGAAGCG	0.667													36	148	---	---	---	---	PASS
GPHB5	122876	broad.mit.edu	37	14	63784372	63784372	+	Silent	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63784372C>T	uc010apu.2	-	1	192	c.192G>A	c.(190-192)GTG>GTA	p.V64V	GPHB5_uc001xgc.2_Silent_p.V54V	NM_145171	NP_660154	Q86YW7	GPHB5_HUMAN	glycoprotein beta 5	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						extracellular region	hormone activity			breast(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00372)|all cancers(60;0.0226)|BRCA - Breast invasive adenocarcinoma(234;0.0978)		TCCCAGGTCTCACAGCGACCC	0.532													6	50	---	---	---	---	PASS
ACTN1	87	broad.mit.edu	37	14	69371375	69371375	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69371375C>T	uc001xkl.2	-	7	983	c.673G>A	c.(673-675)GAA>AAA	p.E225K	ACTN1_uc010ttb.1_Missense_Mutation_p.E160K|ACTN1_uc001xkm.2_Missense_Mutation_p.E225K|ACTN1_uc001xkn.2_Missense_Mutation_p.E225K|ACTN1_uc001xko.1_Missense_Mutation_p.E160K|ACTN1_uc010ttd.1_Missense_Mutation_p.E204K	NM_001102	NP_001093	P12814	ACTN1_HUMAN	actinin, alpha 1 isoform b	225	CH 2.|Actin-binding.				focal adhesion assembly|negative regulation of cellular component movement|platelet activation|platelet degranulation|regulation of apoptosis	actin cytoskeleton|cytosol|extracellular region|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|sarcomere	actin binding|calcium ion binding|integrin binding|vinculin binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		CTTTCACCTTCGGCATCCAGC	0.567													6	114	---	---	---	---	PASS
C14orf177	283598	broad.mit.edu	37	14	99182494	99182494	+	5'UTR	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99182494G>C	uc001yfz.1	+	3						NM_182560	NP_872366	Q52M58	CN177_HUMAN	hypothetical protein LOC283598												0		Melanoma(154;0.128)				TCAGCCGTGGGAGCCACGGGA	0.592													3	28	---	---	---	---	PASS
MIR323	442897	broad.mit.edu	37	14	101492118	101492118	+	RNA	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101492118G>A	hsa-mir-323|MI0000807	+			c.50G>A			uc001yjy.1_RNA|MIR758_hsa-mir-758|MI0003757_5'Flank|MIR329-1_hsa-mir-329-1|MI0001725_5'Flank|MIR329-2_hsa-mir-329-2|MI0001726_5'Flank																	0						TATTTATGGCGCACATTACAC	0.557													13	192	---	---	---	---	PASS
INO80	54617	broad.mit.edu	37	15	41372084	41372084	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41372084T>A	uc001zni.2	-	9	1159	c.946A>T	c.(946-948)AAG>TAG	p.K316*	INO80_uc010ucu.1_RNA	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1	316	Assembles INO80 complex module consisting of conserved components ACTR8, ACTL6A and YY1.|DBINO.				cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4						CGCACCTCCTTCATGCACTGG	0.527													30	200	---	---	---	---	PASS
SPG11	80208	broad.mit.edu	37	15	44876169	44876169	+	Missense_Mutation	SNP	A	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44876169A>C	uc001ztx.2	-	30	5740	c.5709T>G	c.(5707-5709)TTT>TTG	p.F1903L	SPG11_uc010bdw.2_Missense_Mutation_p.F192L|SPG11_uc010ueh.1_Missense_Mutation_p.F1903L|SPG11_uc010uei.1_Missense_Mutation_p.F1903L|SPG11_uc001zty.1_Missense_Mutation_p.F632L	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	1903	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		CTGGATTATAAAAATGAAAAT	0.473													16	65	---	---	---	---	PASS
SPG11	80208	broad.mit.edu	37	15	44876180	44876180	+	Missense_Mutation	SNP	A	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44876180A>C	uc001ztx.2	-	30	5729	c.5698T>G	c.(5698-5700)TAT>GAT	p.Y1900D	SPG11_uc010bdw.2_Missense_Mutation_p.Y189D|SPG11_uc010ueh.1_Missense_Mutation_p.Y1900D|SPG11_uc010uei.1_Missense_Mutation_p.Y1900D|SPG11_uc001zty.1_Missense_Mutation_p.Y629D	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	1900	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		AAATGAAAATACCGGCATACT	0.473													17	73	---	---	---	---	PASS
CSNK1G1	53944	broad.mit.edu	37	15	64496768	64496768	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64496768G>A	uc002anf.2	-	9	1351	c.871C>T	c.(871-873)CGA>TGA	p.R291*	CSNK1G1_uc002ane.2_RNA|CSNK1G1_uc002ang.1_Nonsense_Mutation_p.R291*|CSNK1G1_uc002anh.1_Nonsense_Mutation_p.R291*|CSNK1G1_uc002anj.2_Nonsense_Mutation_p.R273*	NM_022048	NP_071331	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1	291	Protein kinase.				Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0						CTGACATATCGAAGGTAGGTT	0.448													4	148	---	---	---	---	PASS
CD276	80381	broad.mit.edu	37	15	73994784	73994784	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73994784G>A	uc002avv.1	+	3	502	c.268G>A	c.(268-270)GCC>ACC	p.A90T	CD276_uc010bjd.1_5'UTR|CD276_uc002avu.1_Missense_Mutation_p.A90T|CD276_uc002avw.1_Missense_Mutation_p.A90T|CD276_uc010ulb.1_Missense_Mutation_p.A36T|CD276_uc002avx.2_5'Flank	NM_001024736	NP_001019907	Q5ZPR3	CD276_HUMAN	CD276 antigen isoform a	90	Ig-like V-type 1.|Extracellular (Potential).				cell proliferation|immune response|positive regulation of interferon-gamma biosynthetic process|positive regulation of T cell proliferation|regulation of immune response|T cell activation	external side of plasma membrane|integral to membrane	receptor binding			skin(1)	1						CAGCGCCTATGCCAACCGCAC	0.642													5	60	---	---	---	---	PASS
SGK269	79834	broad.mit.edu	37	15	77426021	77426021	+	Missense_Mutation	SNP	C	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77426021C>A	uc002bcm.2	-	5	3711	c.3403G>T	c.(3403-3405)GCC>TCC	p.A1135S		NM_024776	NP_079052	Q9H792	PEAK1_HUMAN	NKF3 kinase family member	1135					cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading	actin cytoskeleton|cytoplasm|focal adhesion	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding				0				STAD - Stomach adenocarcinoma(199;0.124)		CCTCCAAAGGCGATGGCATCG	0.488													3	126	---	---	---	---	PASS
AGBL1	123624	broad.mit.edu	37	15	87217600	87217600	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87217600C>T	uc002blz.1	+	22	3096	c.3016C>T	c.(3016-3018)CAG>TAG	p.Q1006*		NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	1006					C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0						CTGCAGCCATCAGCTCCTGGC	0.562													7	24	---	---	---	---	PASS
MSLNL	401827	broad.mit.edu	37	16	823284	823284	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:823284C>T	uc002cjz.1	-	10	1984	c.1984G>A	c.(1984-1986)GCC>ACC	p.A662T		NM_001025190	NP_001020361	Q96KJ4	MSLNL_HUMAN	mesothelin-like	311	Extracellular (Potential).				cell adhesion	integral to membrane				breast(3)|ovary(1)	4						CGCAGCGTGGCGGCCGTGATG	0.652													17	80	---	---	---	---	PASS
ZNF597	146434	broad.mit.edu	37	16	3486866	3486866	+	Missense_Mutation	SNP	T	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3486866T>G	uc002cvd.2	-	4	1017	c.833A>C	c.(832-834)AAT>ACT	p.N278T		NM_152457	NP_689670	Q96LX8	ZN597_HUMAN	zinc finger protein 597	278					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TGGTTTCTCATTAAAATGTTT	0.443													36	204	---	---	---	---	PASS
C16orf89	146556	broad.mit.edu	37	16	5110356	5110356	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5110356G>A	uc010bud.2	-	3	642	c.554C>T	c.(553-555)ACG>ATG	p.T185M	ALG1_uc002cyj.2_Intron|C16orf89_uc002cyk.3_Missense_Mutation_p.T185M	NM_152459	NP_689672	Q6UX73	CP089_HUMAN	hypothetical protein LOC146556 isoform 1	147						extracellular region				ovary(1)|skin(1)	2						GGGCCCGAACGTGGGGTACAC	0.597													14	69	---	---	---	---	PASS
UMOD	7369	broad.mit.edu	37	16	20352631	20352631	+	Silent	SNP	G	A	A	rs144461487		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20352631G>A	uc002dgz.2	-	7	1488	c.1359C>T	c.(1357-1359)ACC>ACT	p.T453T	UMOD_uc002dha.2_Silent_p.T453T|UMOD_uc002dhb.2_Silent_p.T486T	NM_003361	NP_003352	P07911	UROM_HUMAN	uromodulin precursor	453	ZP.				cellular defense response|negative regulation of cell proliferation	anchored to membrane|apical plasma membrane|basolateral plasma membrane|cilium membrane|extrinsic to membrane|primary cilium|spindle pole	calcium ion binding			ovary(1)|skin(1)	2						TGAACATGCCGGTCCCGCCCA	0.587													17	79	---	---	---	---	PASS
CDH8	1006	broad.mit.edu	37	16	61891104	61891104	+	Missense_Mutation	SNP	C	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61891104C>A	uc002eog.1	-	4	838	c.586G>T	c.(586-588)GAC>TAC	p.D196Y	CDH8_uc002eoh.2_5'UTR	NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	196	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		TAAACTGGGTCATCAGCGTCG	0.388													14	55	---	---	---	---	PASS
SF3B3	23450	broad.mit.edu	37	16	70575582	70575582	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70575582C>T	uc002ezf.2	+	9	1289	c.1078C>T	c.(1078-1080)CAA>TAA	p.Q360*		NM_012426	NP_036558	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3	360					protein complex assembly	catalytic step 2 spliceosome|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(1)	1		Ovarian(137;0.0694)				TTACTTATATCAAATTGCACA	0.413													36	214	---	---	---	---	PASS
HYDIN	54768	broad.mit.edu	37	16	70884498	70884498	+	Silent	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70884498G>A	uc002ezr.2	-	74	12629	c.12501C>T	c.(12499-12501)ATC>ATT	p.I4167I	HYDIN_uc010cfy.2_RNA	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	4168										ovary(1)|skin(1)	2		Ovarian(137;0.0654)				CCACATTGCAGATCAAATTAA	0.448													10	65	---	---	---	---	PASS
ARHGEF15	22899	broad.mit.edu	37	17	8216353	8216353	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8216353C>T	uc002glc.2	+	3	836	c.715C>T	c.(715-717)CGT>TGT	p.R239C	ARHGEF15_uc002glb.1_3'UTR|ARHGEF15_uc002gld.2_Missense_Mutation_p.R239C|ARHGEF15_uc010vuw.1_Intron	NM_173728	NP_776089	O94989	ARHGF_HUMAN	Rho guanine exchange factor 15	239					negative regulation of synapse maturation|regulation of Rho protein signal transduction	dendrite|intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3						CAGGGTCCCCCGTCGGGCCTC	0.706													10	170	---	---	---	---	PASS
MYH2	4620	broad.mit.edu	37	17	10448678	10448678	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10448678G>A	uc010coi.2	-	5	618	c.490C>T	c.(490-492)CAG>TAG	p.Q164*	uc002gml.1_Intron|MYH2_uc002gmp.3_Nonsense_Mutation_p.Q164*|MYH2_uc010coj.2_Nonsense_Mutation_p.Q164*	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	164	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						AGCATGAACTGATAGGCGTTG	0.532													43	283	---	---	---	---	PASS
MPRIP	23164	broad.mit.edu	37	17	17080692	17080692	+	Silent	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17080692G>A	uc002gqu.1	+	21	2981	c.2925G>A	c.(2923-2925)GAG>GAA	p.E975E	MPRIP_uc002gqv.1_Silent_p.E975E|MPRIP_uc002gqw.1_Silent_p.E730E|MPRIP_uc002gqx.1_Silent_p.E1204E|MPRIP_uc002gqy.1_Silent_p.E1204E|MPRIP_uc010cpl.1_Silent_p.E161E|MPRIP_uc010cpm.1_Silent_p.E161E	NM_201274	NP_958431	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase-Rho interacting protein	975	Potential.					cytoplasm|cytoskeleton	actin binding				0						CACTGGGGGAGAAGTCCCCTG	0.577													6	90	---	---	---	---	PASS
MPRIP	23164	broad.mit.edu	37	17	17080713	17080713	+	Silent	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17080713G>A	uc002gqu.1	+	21	3002	c.2946G>A	c.(2944-2946)ACG>ACA	p.T982T	MPRIP_uc002gqv.1_Silent_p.T982T|MPRIP_uc002gqw.1_Silent_p.T737T|MPRIP_uc002gqx.1_Silent_p.T1211T|MPRIP_uc002gqy.1_Silent_p.T1211T|MPRIP_uc010cpl.1_Silent_p.T168T|MPRIP_uc010cpm.1_Silent_p.T168T	NM_201274	NP_958431	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase-Rho interacting protein	982						cytoplasm|cytoskeleton	actin binding				0						ACAGTGCCACGGTGTCCGGAT	0.587													6	72	---	---	---	---	PASS
KIAA0100	9703	broad.mit.edu	37	17	26942017	26942017	+	3'UTR	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26942017C>T	uc002hbu.2	-	39					SGK494_uc010waq.1_5'Flank|SGK494_uc010war.1_5'Flank|SGK494_uc002hbr.1_5'Flank|uc002hbs.1_Intron|KIAA0100_uc002hbt.2_3'UTR	NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor							extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)					GCCCCTCCCACCCCACAAGTC	0.572													21	223	---	---	---	---	PASS
MYO19	80179	broad.mit.edu	37	17	34857010	34857010	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34857010G>A	uc010wcy.1	-	23	3138	c.2146C>T	c.(2146-2148)CCG>TCG	p.P716S	MYO19_uc002hmw.2_Missense_Mutation_p.P516S|MYO19_uc010cuu.2_RNA	NM_001163735	NP_001157207	Q96H55	MYO19_HUMAN	myosin XIX isoform 2	716						mitochondrial outer membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)	1		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GTTAGGACCGGCAGAGTGTGG	0.582													4	147	---	---	---	---	PASS
ACE	1636	broad.mit.edu	37	17	61568636	61568636	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61568636G>A	uc002jau.1	+	19	2828	c.2806G>A	c.(2806-2808)GTG>ATG	p.V936M	ACE_uc002jav.1_Missense_Mutation_p.V362M|ACE_uc010ddv.1_Missense_Mutation_p.V163M|ACE_uc010wpj.1_Missense_Mutation_p.V362M|ACE_uc002jaw.1_RNA|ACE_uc010wpk.1_Missense_Mutation_p.V182M	NM_000789	NP_000780	P12821	ACE_HUMAN	angiotensin I converting enzyme 1 isoform 1	936	Extracellular (Potential).|Peptidase M2 2.				arachidonic acid secretion|hormone catabolic process|kidney development|peptide catabolic process|regulation of smooth muscle cell migration	endosome|external side of plasma membrane|extracellular space|integral to membrane|membrane fraction|plasma membrane	actin binding|bradykinin receptor binding|carboxypeptidase activity|chloride ion binding|drug binding|metallopeptidase activity|peptidyl-dipeptidase activity|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4					Benazepril(DB00542)|Captopril(DB01197)|Deserpidine(DB01089)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	GCTGCTGCCCGTGCCTCCTGA	0.617													13	101	---	---	---	---	PASS
CCDC40	55036	broad.mit.edu	37	17	78022498	78022498	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78022498G>A	uc010dht.2	+	5	820	c.793G>A	c.(793-795)GAG>AAG	p.E265K	CCDC40_uc010wub.1_Missense_Mutation_p.E265K|CCDC40_uc002jxm.3_Missense_Mutation_p.E48K	NM_017950	NP_060420	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	265					axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium|cytoplasm				ovary(3)	3	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			AGTGGAGTCCGAGGGGAGTGA	0.612													8	52	---	---	---	---	PASS
RNF213	57674	broad.mit.edu	37	17	78326609	78326609	+	Intron	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78326609G>A	uc002jyh.1	+						uc002jyi.1_RNA|RNF213_uc010dhw.1_5'Flank	NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213											ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CCAGGGTTTCGGCTTCAGGGT	0.537													8	82	---	---	---	---	PASS
RPTOR	57521	broad.mit.edu	37	17	78704398	78704398	+	Silent	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78704398G>A	uc002jyt.1	+	5	1351	c.546G>A	c.(544-546)CTG>CTA	p.L182L	RPTOR_uc002jys.2_Silent_p.L182L|RPTOR_uc010wuf.1_5'UTR|RPTOR_uc010wug.1_Silent_p.L182L	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1	182					cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6						TATATGACCTGCAGACGTGGA	0.532													13	94	---	---	---	---	PASS
C18orf8	29919	broad.mit.edu	37	18	21109562	21109562	+	Intron	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21109562C>T	uc010xax.1	+						C18orf8_uc002kul.2_Intron|C18orf8_uc010xay.1_Intron|NPC1_uc010dlu.1_RNA	NM_013326	NP_037458	Q96DM3	MIC1_HUMAN	colon cancer-associated protein Mic1											ovary(1)	1	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TTTTGCACCTCGTTGGTATTT	0.423													18	101	---	---	---	---	PASS
C18orf8	29919	broad.mit.edu	37	18	21110070	21110070	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21110070C>T	uc010xax.1	+	18	1694	c.1573C>T	c.(1573-1575)CAC>TAC	p.H525Y	C18orf8_uc002kul.2_RNA|C18orf8_uc010xay.1_Missense_Mutation_p.H149Y|NPC1_uc010dlu.1_Intron	NM_013326	NP_037458	Q96DM3	MIC1_HUMAN	colon cancer-associated protein Mic1	525	Mic1.									ovary(1)	1	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CCTGCAGTACCACGTCCTCAG	0.393													46	421	---	---	---	---	PASS
HRH4	59340	broad.mit.edu	37	18	22048844	22048844	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22048844C>G	uc002kvi.2	+	2	386	c.286C>G	c.(286-288)CTG>GTG	p.L96V	HRH4_uc010xbd.1_Intron|HRH4_uc010dlx.2_Intron	NM_021624	NP_067637	Q9H3N8	HRH4_HUMAN	histamine H4 receptor isoform 1	96	Helical; Name=3; (Potential).					integral to membrane|plasma membrane	histamine receptor activity			ovary(2)	2	all_cancers(21;0.000545)|all_epithelial(16;6.56e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)				Clozapine(DB00363)	TACTGACTATCTGTTATGTAC	0.408													20	71	---	---	---	---	PASS
ZNF521	25925	broad.mit.edu	37	18	22805418	22805418	+	Missense_Mutation	SNP	T	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22805418T>C	uc002kvk.2	-	4	2711	c.2464A>G	c.(2464-2466)ATT>GTT	p.I822V	ZNF521_uc010xbe.1_RNA|ZNF521_uc010dly.2_Missense_Mutation_p.I822V|ZNF521_uc002kvl.2_Missense_Mutation_p.I602V	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521	822	C2H2-type 20.				cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					TCTAACAAAATGATCGCATGG	0.468			T	PAX5	ALL								18	200	---	---	---	---	PASS
PALM	5064	broad.mit.edu	37	19	746578	746578	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:746578G>A	uc002lpm.1	+	9	1122	c.928G>A	c.(928-930)GAT>AAT	p.D310N	PALM_uc002lpn.1_Missense_Mutation_p.D266N|PALM_uc010xfu.1_Missense_Mutation_p.D175N	NM_002579	NP_002570	O75781	PALM_HUMAN	paralemmin isoform 1	310					cellular component movement|negative regulation of adenylate cyclase activity|negative regulation of dopamine receptor signaling pathway|positive regulation of filopodium assembly|regulation of cell shape	cytoplasmic membrane-bounded vesicle|filopodium membrane|integral to plasma membrane					0		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)		GAACGTGGAGGATGAGGCCGA	0.657													9	40	---	---	---	---	PASS
SYCE2	256126	broad.mit.edu	37	19	13029049	13029049	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13029049C>T	uc002mvr.2	-	2	133	c.118G>A	c.(118-120)GGA>AGA	p.G40R		NM_001105578	NP_001099048	Q6PIF2	SYCE2_HUMAN	synaptonemal complex central element protein 2	40					cell division	central element					0						GCTGGCCCTCCACCAGCTTCC	0.597													11	69	---	---	---	---	PASS
MLL4	9757	broad.mit.edu	37	19	36211795	36211795	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36211795A>G	uc010eei.2	+	3	1546	c.1546A>G	c.(1546-1548)AAA>GAA	p.K516E		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	516	Pro-rich.				chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CGTGGCCCCCAAAAGCACCAC	0.622													5	16	---	---	---	---	PASS
PAF1	54623	broad.mit.edu	37	19	39876761	39876761	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39876761C>G	uc002old.2	-	14	1641	c.1466G>C	c.(1465-1467)GGT>GCT	p.G489A	PAF1_uc002ole.1_Missense_Mutation_p.V418L	NM_019088	NP_061961	Q8N7H5	PAF1_HUMAN	Paf1, RNA polymerase II associated factor,	489					histone H2B ubiquitination|histone monoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			pancreas(1)	1	all_cancers(60;9.14e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.88e-06)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			CCGCTGGCCACCCCCATTGCT	0.617													7	85	---	---	---	---	PASS
KLK1	3816	broad.mit.edu	37	19	51323464	51323464	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51323464C>G	uc002ptk.1	-	3	481	c.442G>C	c.(442-444)GAA>CAA	p.E148Q	KLK1_uc010ycg.1_RNA	NM_002257	NP_002248	P06870	KLK1_HUMAN	kallikrein 1 preproprotein	148	Peptidase S1.				proteolysis	nucleus	serine-type endopeptidase activity				0		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00399)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CTCCCCACTTCGGGTTCCTCG	0.607													14	106	---	---	---	---	PASS
FLRT3	23767	broad.mit.edu	37	20	14307451	14307451	+	Silent	SNP	C	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14307451C>G	uc002wov.1	-	3	1169	c.702G>C	c.(700-702)CGG>CGC	p.R234R	MACROD2_uc002wot.2_Intron|MACROD2_uc002wou.2_Intron|FLRT3_uc002wow.1_Silent_p.R234R	NM_198391	NP_938205	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	234	Extracellular (Potential).|LRR 8.				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			kidney(1)	1		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)		TCAGGGAATTCCGCACCAGGG	0.443													12	99	---	---	---	---	PASS
GINS1	9837	broad.mit.edu	37	20	25405846	25405846	+	Splice_Site	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25405846G>A	uc002wuv.1	+	5	465	c.331_splice	c.e5-1	p.M111_splice	GINS1_uc010zte.1_Splice_Site	NM_021067	NP_066545	Q14691	PSF1_HUMAN	GINS complex subunit 1						DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle	cytoplasm|nucleoplasm				ovary(1)|central_nervous_system(1)	2						TATGTTTGCAGATGGAGTGGT	0.363													24	89	---	---	---	---	PASS
ZNF337	26152	broad.mit.edu	37	20	25666702	25666702	+	Silent	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25666702C>T	uc002wva.2	-	2	606	c.84G>A	c.(82-84)CTG>CTA	p.L28L	ZNF337_uc010ztg.1_Silent_p.L28L|ZNF337_uc002wvb.2_Silent_p.L28L|ZNF337_uc002wvc.2_Silent_p.L28L	NM_015655	NP_056470	Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	28	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CAGGGCTCAGCAGCCTCCATT	0.547													40	268	---	---	---	---	PASS
TTLL9	164395	broad.mit.edu	37	20	30513763	30513763	+	Intron	SNP	T	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30513763T>C	uc010gdx.1	+						TTLL9_uc002wwy.1_Intron|TTLL9_uc002wwz.1_RNA|TTLL9_uc002wxa.1_Intron|TTLL9_uc002wxb.1_RNA|TTLL9_uc010zto.1_Intron|TTLL9_uc002wxc.2_Missense_Mutation_p.Y152H|TTLL9_uc010ztp.1_RNA|TTLL9_uc010ztq.1_RNA	NM_001008409	NP_001008409	Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9						protein modification process	cilium|microtubule|microtubule basal body	ATP binding|tubulin-tyrosine ligase activity			ovary(2)	2			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			TGATGACCAGTGTATCCTGGG	0.502													7	16	---	---	---	---	PASS
BPIL1	80341	broad.mit.edu	37	20	31606901	31606901	+	Missense_Mutation	SNP	C	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31606901C>G	uc002wyj.2	+	10	1083	c.889C>G	c.(889-891)CTG>GTG	p.L297V		NM_025227	NP_079503	Q8N4F0	BPIL1_HUMAN	bactericidal/permeability-increasing	297						extracellular region	lipid binding			skin(2)|large_intestine(1)|ovary(1)	4						CACCTCTGCTCTGGGCCGGCT	0.567													27	203	---	---	---	---	PASS
SEMG1	6406	broad.mit.edu	37	20	43836572	43836572	+	Missense_Mutation	SNP	A	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43836572A>G	uc002xni.2	+	2	691	c.634A>G	c.(634-636)AAT>GAT	p.N212D	SEMG1_uc002xnj.2_Missense_Mutation_p.N212D|SEMG2_uc010ggz.2_Intron|SEMG1_uc002xnh.2_Missense_Mutation_p.N212D	NM_003007	NP_002998	P04279	SEMG1_HUMAN	semenogelin I preproprotein	212	42 AA repeat 1.				insemination|sexual reproduction	extracellular space|stored secretory granule	structural molecule activity			skin(2)	2		Myeloproliferative disorder(115;0.0122)				TGAGACTAAAAATTCTCATCA	0.408													12	137	---	---	---	---	PASS
CDH22	64405	broad.mit.edu	37	20	44879792	44879792	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44879792C>T	uc002xrm.2	-	1	543	c.142G>A	c.(142-144)GGA>AGA	p.G48R	CDH22_uc010ghk.1_Missense_Mutation_p.G48R	NM_021248	NP_067071	Q9UJ99	CAD22_HUMAN	cadherin 22 precursor	48	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)				TGCCGAGCTCCGGGCGCCGAC	0.587													14	15	---	---	---	---	PASS
PDXK	8566	broad.mit.edu	37	21	45173597	45173597	+	Silent	SNP	C	T	T	rs138572525		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45173597C>T	uc002zdm.3	+	9	954	c.756C>T	c.(754-756)CTC>CTT	p.L252L	PDXK_uc010gpj.2_Silent_p.L252L|PDXK_uc002zdn.3_Silent_p.L224L|PDXK_uc002zdq.3_Silent_p.L179L	NM_003681	NP_003672	O00764	PDXK_HUMAN	pyridoxal kinase	252					cell proliferation|pyridoxal 5'-phosphate salvage	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)	CCAATAACCTCAAGGTCAGCC	0.622													14	116	---	---	---	---	PASS
LSS	4047	broad.mit.edu	37	21	47627356	47627356	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47627356C>T	uc002zij.2	-	15	1532	c.1453G>A	c.(1453-1455)GAT>AAT	p.D485N	LSS_uc011afv.1_Missense_Mutation_p.D474N|LSS_uc002zil.2_Missense_Mutation_p.D485N|LSS_uc002zik.2_Missense_Mutation_p.D405N	NM_001001438	NP_001001438	P48449	ERG7_HUMAN	lanosterol synthase isoform 1	485	PFTB 2.				cholesterol biosynthetic process	endoplasmic reticulum membrane	lanosterol synthase activity				0	Breast(49;0.214)					GCCACAGCATCGCAGAGCCGT	0.612													10	17	---	---	---	---	PASS
C22orf29	79680	broad.mit.edu	37	22	19839452	19839452	+	Silent	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19839452C>T	uc002zqg.2	-	2	932	c.333G>A	c.(331-333)CCG>CCA	p.P111P	GNB1L_uc002zqd.1_Intron|GNB1L_uc002zqe.1_Intron|GNB1L_uc002zqf.1_Intron|C22orf29_uc002zqh.2_Silent_p.P111P|C22orf29_uc002zqi.2_Silent_p.P111P|C22orf29_uc010grt.1_Intron	NM_024627	NP_078903	Q7L3V2	CV029_HUMAN	hypothetical protein LOC79680	111											0	Colorectal(54;0.0993)					CCAGTAGCCACGGGGAGCCAT	0.607													18	133	---	---	---	---	PASS
ASPHD2	57168	broad.mit.edu	37	22	26839131	26839131	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26839131G>A	uc003acg.2	+	4	1466	c.1069G>A	c.(1069-1071)GAA>AAA	p.E357K		NM_020437	NP_065170	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2	357	Lumenal (Potential).				peptidyl-amino acid modification	integral to endoplasmic reticulum membrane	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity			ovary(1)	1						CGCAGCGGCCGAACGGCAGGC	0.607													64	303	---	---	---	---	PASS
C22orf30	253143	broad.mit.edu	37	22	32097734	32097734	+	Silent	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32097734C>T	uc003alp.3	-	7	6208	c.6015G>A	c.(6013-6015)AAG>AAA	p.K2005K	C22orf30_uc003alo.1_Silent_p.K1804K|C22orf30_uc010gwj.1_Intron	NM_173566	NP_775837	Q5THK1	PR14L_HUMAN	hypothetical protein LOC253143	2005											0						TCTTTGGCCTCTTCTCTGGCT	0.373													17	71	---	---	---	---	PASS
C22orf30	253143	broad.mit.edu	37	22	32099658	32099658	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32099658C>A	uc003alp.3	-	6	6071	c.5878G>T	c.(5878-5880)GAA>TAA	p.E1960*	C22orf30_uc003alo.1_Nonsense_Mutation_p.E1759*|C22orf30_uc010gwj.1_Nonsense_Mutation_p.E1759*	NM_173566	NP_775837	Q5THK1	PR14L_HUMAN	hypothetical protein LOC253143	1960											0						ACAGCTGATTCTGCTACCAAG	0.527											OREG0003534	type=REGULATORY REGION|Gene=AK123082|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	26	86	---	---	---	---	PASS
LARGE	9215	broad.mit.edu	37	22	34157439	34157439	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34157439G>A	uc003and.3	-	3	604	c.25C>T	c.(25-27)CGG>TGG	p.R9W	LARGE_uc003ane.3_Missense_Mutation_p.R9W|LARGE_uc010gwp.2_Missense_Mutation_p.R9W|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Missense_Mutation_p.R9W	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase	9	Cytoplasmic (Potential).				glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				AAGAATTTCCGTCTCCCCCTG	0.532													7	163	---	---	---	---	PASS
MICALL1	85377	broad.mit.edu	37	22	38329085	38329085	+	Silent	SNP	C	G	G			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38329085C>G	uc003aui.2	+	13	2358	c.2274C>G	c.(2272-2274)GTC>GTG	p.V758V		NM_033386	NP_203744	Q8N3F8	MILK1_HUMAN	molecule interacting with Rab13	758						cytoplasm|cytoskeleton	protein binding|zinc ion binding			breast(1)	1	Melanoma(58;0.045)					AGGCTGATGTCGAGTATGAGC	0.632													12	91	---	---	---	---	PASS
KLHDC7B	113730	broad.mit.edu	37	22	50987674	50987674	+	Missense_Mutation	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50987674G>A	uc003bmi.2	+	1	1213	c.1079G>A	c.(1078-1080)GGG>GAG	p.G360E		NM_138433	NP_612442	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	360	Kelch 2.									central_nervous_system(1)	1		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TTTCTGGCGGGGGGCATCCGT	0.667													27	123	---	---	---	---	PASS
CPT1B	1375	broad.mit.edu	37	22	51009598	51009598	+	Missense_Mutation	SNP	C	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51009598C>T	uc003bmk.3	-	14	2026	c.1864G>A	c.(1864-1866)GGG>AGG	p.G622R	CPT1B_uc003bml.2_Missense_Mutation_p.G622R|CPT1B_uc003bmm.2_Missense_Mutation_p.G622R|CPT1B_uc003bmo.2_Missense_Mutation_p.G622R|CPT1B_uc011asa.1_Missense_Mutation_p.G588R|CPT1B_uc003bmn.2_Missense_Mutation_p.G622R|CPT1B_uc011asb.1_Missense_Mutation_p.G541R|CHKB-CPT1B_uc003bmp.2_Missense_Mutation_p.G417R|uc003bmr.1_RNA	NM_001145137	NP_001138609	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B isoform a	622	Cytoplasmic (Potential).				carnitine shuttle|fatty acid beta-oxidation|regulation of fatty acid oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			ovary(1)|central_nervous_system(1)	2		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		GTGTGGGACCCCTCCATCATG	0.612													19	109	---	---	---	---	PASS
DDX53	168400	broad.mit.edu	37	X	23019072	23019072	+	Missense_Mutation	SNP	C	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23019072C>A	uc004daj.2	+	1	986	c.898C>A	c.(898-900)CTA>ATA	p.L300I		NM_182699	NP_874358	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	300	Helicase ATP-binding.					nucleus	ATP binding|ATP-dependent helicase activity|RNA binding			large_intestine(1)|ovary(1)|kidney(1)	3						GCCTGGGATGCTAGTCCTTAC	0.418													4	64	---	---	---	---	PASS
DDX53	168400	broad.mit.edu	37	X	23019219	23019219	+	Missense_Mutation	SNP	A	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23019219A>T	uc004daj.2	+	1	1133	c.1045A>T	c.(1045-1047)ATT>TTT	p.I349F		NM_182699	NP_874358	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	349	Helicase ATP-binding.					nucleus	ATP binding|ATP-dependent helicase activity|RNA binding			large_intestine(1)|ovary(1)|kidney(1)	3						TGTAGATATCATTATTGCAAC	0.353													4	84	---	---	---	---	PASS
MED12	9968	broad.mit.edu	37	X	70339981	70339981	+	Missense_Mutation	SNP	G	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70339981G>C	uc004dyy.2	+	4	713	c.514G>C	c.(514-516)GAG>CAG	p.E172Q	MED12_uc011mpq.1_Missense_Mutation_p.E172Q|MED12_uc004dyz.2_Missense_Mutation_p.E172Q|MED12_uc004dza.2_Missense_Mutation_p.E19Q	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	172					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)					AGCAATCTCTGAGACCAAGGT	0.488													27	53	---	---	---	---	PASS
PHF6	84295	broad.mit.edu	37	X	133512098	133512098	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133512098G>T	uc004exj.2	+	3	404	c.202G>T	c.(202-204)GAA>TAA	p.E68*	PHF6_uc004exk.2_Nonsense_Mutation_p.E68*|PHF6_uc011mvk.1_Intron|PHF6_uc004exh.2_Nonsense_Mutation_p.E68*|PHF6_uc010nrr.2_Nonsense_Mutation_p.E68*|PHF6_uc004exi.2_Nonsense_Mutation_p.E68*	NM_001015877	NP_001015877	Q8IWS0	PHF6_HUMAN	PHD finger protein 6 isoform 1	68					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					ATTTTCTATTGAAGATGTCCA	0.299													17	48	---	---	---	---	PASS
MAGEA1	4100	broad.mit.edu	37	X	152482885	152482885	+	Silent	SNP	G	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152482885G>A	uc004fhf.2	-	3	346	c.126C>T	c.(124-126)ACC>ACT	p.T42T		NM_004988	NP_004979	P43355	MAGA1_HUMAN	melanoma antigen family A, 1	42						cytoplasm|plasma membrane				central_nervous_system(7)|ovary(1)|lung(1)|breast(1)	10	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCTCCTCCAGGGTGCCCAGGA	0.627													39	109	---	---	---	---	PASS
KIF1B	23095	broad.mit.edu	37	1	10408017	10408017	+	Intron	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10408017delT	uc001aqx.3	+						KIF1B_uc001aqw.3_Intron|KIF1B_uc001aqy.2_Intron|KIF1B_uc001aqz.2_Intron|KIF1B_uc001ara.2_Intron|KIF1B_uc001arb.2_Intron	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CCTGTTGTCATTTTTTTTTTT	0.338													6	3	---	---	---	---	
MASP2	10747	broad.mit.edu	37	1	11094757	11094758	+	Intron	INS	-	A	A	rs113585596		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11094757_11094758insA	uc001aru.2	-							NM_006610	NP_006601	O00187	MASP2_HUMAN	mannan-binding lectin serine protease 2 isoform						complement activation, classical pathway|complement activation, lectin pathway|proteolysis	extracellular region	calcium ion binding|calcium-dependent protein binding|serine-type endopeptidase activity			ovary(2)|pancreas(1)|skin(1)	4	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)		ccctgtctcagaaaaaaaaaaa	0.173													8	5	---	---	---	---	
PTCHD2	57540	broad.mit.edu	37	1	11587001	11587002	+	Intron	INS	-	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11587001_11587002insT	uc001ash.3	+							NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2						cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GGCCCCCTCACttttttttttt	0.292													4	2	---	---	---	---	
SRRM1	10250	broad.mit.edu	37	1	24973014	24973014	+	Intron	DEL	A	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24973014delA	uc001bjm.2	+						SRRM1_uc010oel.1_Intron|SRRM1_uc009vrh.1_Intron|SRRM1_uc009vri.1_5'Flank|SRRM1_uc010oem.1_5'Flank	NM_005839	NP_005830	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1						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)		actctgtctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	27307015	27307015	+	IGR	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27307015delT								C1orf172 (20118 upstream) : TRNP1 (13180 downstream)																							AGCACCAAtcttttttttttt	0.169													4	2	---	---	---	---	
NOTCH2	4853	broad.mit.edu	37	1	120612003	120612004	+	Frame_Shift_Del	DEL	GG	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120612003_120612004delGG	uc001eik.2	-	1	273_274	c.17_18delCC	c.(16-18)CCCfs	p.P6fs	NOTCH2_uc001eil.2_Frame_Shift_Del_p.P6fs|NOTCH2_uc001eim.3_5'UTR	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	6					anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAGCAGAGCGGGGCGCAGGGC	0.663			N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	165589170	165589171	+	IGR	INS	-	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165589170_165589171insC								LOC400794 (37829 upstream) : MGST3 (11279 downstream)																							tccttccctctttccctctctc	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	223352880	223352881	+	IGR	INS	-	CTTCCTTT	CTTCCTTT	rs61837571	by1000genomes	TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223352880_223352881insCTTCCTTT								TLR5 (36256 upstream) : SUSD4 (41282 downstream)																							ttccttccttccttcctttctt	0.045													4	3	---	---	---	---	
TRIM67	440730	broad.mit.edu	37	1	231349602	231349603	+	Frame_Shift_Ins	INS	-	CCAC	CCAC			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231349602_231349603insCCAC	uc009xfn.1	+	9	2207_2208	c.2165_2166insCCAC	c.(2164-2166)CTGfs	p.L722fs		NM_001004342	NP_001004342	Q6ZTA4	TRI67_HUMAN	tripartite motif-containing 67	722	B30.2/SPRY.					cytoplasm|cytoskeleton	zinc ion binding			ovary(2)|breast(1)|kidney(1)	4	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				GTGGGCGTGCTGCTGGACCTGA	0.614													200	9	---	---	---	---	
ZNF512	84450	broad.mit.edu	37	2	27824511	27824512	+	Intron	INS	-	TTTTG	TTTTG	rs143396334	by1000genomes	TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27824511_27824512insTTTTG	uc002rla.2	+						ZNF512_uc010ylv.1_Intron|ZNF512_uc010ylw.1_Intron|ZNF512_uc002rlb.2_Intron|ZNF512_uc010ylx.1_Intron|ZNF512_uc002rlc.2_Intron|ZNF512_uc010yly.1_Intron|ZNF512_uc010ylz.1_Intron	NM_032434	NP_115810	Q96ME7	ZN512_HUMAN	zinc finger protein 512						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					tggctaattttttttgttttgt	0.000													4	3	---	---	---	---	
FEZ2	9637	broad.mit.edu	37	2	36805997	36805998	+	Frame_Shift_Del	DEL	GC	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36805997_36805998delGC	uc002rph.2	-	5	692_693	c.645_646delGC	c.(643-648)AGGCTCfs	p.R215fs	FEZ2_uc002rpe.2_Frame_Shift_Del_p.R44fs|FEZ2_uc002rpf.2_Frame_Shift_Del_p.R44fs|FEZ2_uc002rpg.2_Frame_Shift_Del_p.R215fs|FEZ2_uc002rpi.2_Frame_Shift_Del_p.R70fs|FEZ2_uc002rpj.2_Frame_Shift_Del_p.R215fs	NM_005102	NP_005093	Q9UHY8	FEZ2_HUMAN	zygin 2 isoform 1	215_216	Potential.				axon guidance|signal transduction		protein binding			ovary(1)	1		all_hematologic(82;0.21)				GACACTGAGAGCCTTTTCACTC	0.396													80	14	---	---	---	---	
EDAR	10913	broad.mit.edu	37	2	109522865	109522865	+	Intron	DEL	C	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109522865delC	uc002teq.3	-						EDAR_uc010fjn.2_Intron|EDAR_uc010yws.1_Intron	NM_022336	NP_071731	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor precursor						apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1						CAGAAAGGGGCAACAGTAGAA	0.537													28	16	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	113104288	113104290	+	IGR	DEL	CAC	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113104288_113104290delCAC								ZC3H6 (6648 upstream) : RGPD8 (21676 downstream)																							tcaccaccatcaccaccaccatc	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	131378846	131378846	+	IGR	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131378846delT								LOC150527 (71375 upstream) : C2orf14 (58777 downstream)																							GATAAGAGGGTTTTTTTTGGT	0.373													3	3	---	---	---	---	
GALNT5	11227	broad.mit.edu	37	2	158165415	158165416	+	Intron	INS	-	T	T	rs140945706	by1000genomes	TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158165415_158165416insT	uc002tzg.2	+						GALNT5_uc010zci.1_Intron	NM_014568	NP_055383	Q7Z7M9	GALT5_HUMAN	N-acetylgalactosaminyltransferase 5						glycosaminoglycan biosynthetic process	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(3)|skin(1)	4						TTGACAAGTCCtttttttttta	0.307													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	166308917	166308918	+	IGR	INS	-	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166308917_166308918insT								SCN2A (60099 upstream) : CSRNP3 (17239 downstream)																							tccttccttccttccttccttc	0.168													4	3	---	---	---	---	
LRP2	4036	broad.mit.edu	37	2	170038236	170038260	+	Intron	DEL	AGACTGCATTCTGAATTCTTTTCTG	-	-	rs61106961		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170038236_170038260delAGACTGCATTCTGAATTCTTTTCTG	uc002ues.2	-							NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	TCTGTAGAGCAGACTGCATTCTGAATTCTTTTCTGCATTCAGAAA	0.378													8	4	---	---	---	---	
PRKAR2A	5576	broad.mit.edu	37	3	48831587	48831588	+	Intron	INS	-	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48831587_48831588insT	uc010hki.1	-						PRKAR2A_uc003cux.1_Intron|PRKAR2A_uc003cuy.1_Intron	NM_004157	NP_004148	P13861	KAP2_HUMAN	cAMP-dependent protein kinase, regulatory						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|transmembrane transport|water transport	centrosome|cytosol|membrane fraction	cAMP binding|cAMP-dependent protein kinase regulator activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000176)|Kidney(197;0.00246)|KIRC - Kidney renal clear cell carcinoma(197;0.00261)		Gttttcttttcttttttttttt	0.129													4	2	---	---	---	---	
EEFSEC	60678	broad.mit.edu	37	3	127926410	127926411	+	Intron	DEL	AC	-	-	rs144896524		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127926410_127926411delAC	uc003eki.2	+						EEFSEC_uc003ekj.2_Intron	NM_021937	NP_068756	P57772	SELB_HUMAN	eukaryotic elongation factor,							cytoplasm|nucleus	GTP binding|GTPase activity|translation elongation factor activity			ovary(1)	1						CACATTGcatacacacacacac	0.312													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	128139677	128139677	+	IGR	DEL	C	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128139677delC								EEFSEC (12189 upstream) : DNAJB8 (41605 downstream)																							GTGCTCCCCTCCAGCCCAGGC	0.647													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	139607786	139607786	+	IGR	DEL	C	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139607786delC								NMNAT3 (210946 upstream) : CLSTN2 (46241 downstream)																							ttccttccttccttccttcct	0.085													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	149701114	149701114	+	IGR	DEL	G	-	-	rs34404328		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149701114delG								PFN2 (12373 upstream) : TSC22D2 (425674 downstream)																							CCAGAGAGCCGGCCCCGGTAG	0.577													9	4	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195494375	195494376	+	Intron	INS	-	CACCAT	CACCAT	rs111784679		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195494375_195494376insCACCAT	uc011bto.1	-						MUC4_uc003fuz.2_Intron|MUC4_uc003fva.2_Intron|MUC4_uc003fvb.2_Intron|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Intron|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a						cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		accatcaccaccaccatcacca	0.000													4	2	---	---	---	---	
NFXL1	152518	broad.mit.edu	37	4	47856958	47856958	+	Intron	DEL	A	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47856958delA	uc010igh.2	-						NFXL1_uc003gxo.2_Intron|NFXL1_uc003gxp.2_Intron|NFXL1_uc003gxq.3_Intron|NFXL1_uc010igi.2_Intron	NM_152995	NP_694540	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like							integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3						attaaaaggcaaaaaaaaaaa	0.129													5	3	---	---	---	---	
GUSBP1	728411	broad.mit.edu	37	5	21344732	21344732	+	Intron	DEL	C	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21344732delC	uc011cnn.1	+											Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0						ttccttccttcctttccttcc	0.000													4	2	---	---	---	---	
SRP19	6728	broad.mit.edu	37	5	112197174	112197175	+	Intron	INS	-	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112197174_112197175insA	uc003kqc.2	+						SRP19_uc003kqb.1_Intron|SRP19_uc011cvu.1_Intron|SRP19_uc011cvv.1_Intron	NM_003135	NP_003126	P09132	SRP19_HUMAN	signal recognition particle 19kDa						response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|mitochondrion|nucleolus|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding				0		all_cancers(142;0.00328)|all_epithelial(76;6.39e-05)|Prostate(80;0.00174)|Colorectal(10;0.00372)|Ovarian(225;0.156)		Epithelial(69;1.7e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.17e-08)|all cancers(49;3.96e-07)|Colorectal(14;0.0056)|COAD - Colon adenocarcinoma(37;0.0104)		GCTGCAGGTGCTACACCGCGCT	0.663													128	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	19692281	19692282	+	IGR	DEL	GT	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19692281_19692282delGT								None (None upstream) : ID4 (145335 downstream)																							ggtgtgtgtggtgtgtgtgtgt	0.470													5	3	---	---	---	---	
LRRC16A	55604	broad.mit.edu	37	6	25452223	25452224	+	Intron	INS	-	C	C	rs55733029		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25452223_25452224insC	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron|LRRC16A_uc003nez.1_Intron	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						TGCCCCCCCCTCCCCCCCCCAG	0.480													4	2	---	---	---	---	
HLA-A	3105	broad.mit.edu	37	6	29910346	29910346	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29910346delC	uc003nol.2	+	1	16	c.16delC	c.(16-18)CCCfs	p.P6fs	HLA-G_uc011dmb.1_Intron|HCG4P6_uc003nog.1_Intron|HLA-A_uc010jrq.2_5'UTR|HLA-A_uc003nok.2_5'UTR|HLA-A_uc003non.2_Frame_Shift_Del_p.P6fs|HLA-A_uc003noo.2_Frame_Shift_Del_p.P6fs|HLA-A_uc010jrr.2_Frame_Shift_Del_p.P6fs|HLA-A_uc003nom.2_5'UTR|HLA-A_uc010klp.2_5'Flank|HLA-A_uc011dmc.1_5'Flank|HLA-A_uc011dmd.1_5'Flank	NM_002116	NP_002107	P30443	1A01_HUMAN	major histocompatibility complex, class I, A	6					antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity			upper_aerodigestive_tract(1)|ovary(1)	2						CGTCATGGCGCCCCGAACCCT	0.677									Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of|Osteosarcoma_Familial_Clustering_of|Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of	Multiple Myeloma(9;0.094)			115	12	---	---	---	---	
KHDRBS2	202559	broad.mit.edu	37	6	62604848	62604849	+	Intron	INS	-	TC	TC			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62604848_62604849insTC	uc003peg.2	-							NM_152688	NP_689901	Q5VWX1	KHDR2_HUMAN	KH domain-containing, RNA-binding, signal						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			skin(7)|ovary(3)|liver(1)	11				BRCA - Breast invasive adenocarcinoma(397;0.149)		AAATACAAATTTCTCTCTCTCT	0.322													2	5	---	---	---	---	
WBSCR17	64409	broad.mit.edu	37	7	70786853	70786853	+	Intron	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70786853delT	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				ccttccttcctttccttcctt	0.000													3	3	---	---	---	---	
GIGYF1	64599	broad.mit.edu	37	7	100280314	100280315	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100280314_100280315insC	uc003uwg.1	-	20	3507_3508	c.2498_2499insG	c.(2497-2499)GGCfs	p.G833fs		NM_022574	NP_072096	O75420	PERQ1_HUMAN	PERQ amino acid rich, with GYF domain 1	833										large_intestine(1)|central_nervous_system(1)	2	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					CGCTGCTGCCGCCCCCACTCTT	0.693													45	7	---	---	---	---	
RASA4	10156	broad.mit.edu	37	7	102246649	102246649	+	Intron	DEL	C	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102246649delC	uc003vae.2	-						UPK3BL_uc003uzy.2_Intron|RASA4_uc011kla.1_Intron|RASA4_uc010lig.2_Intron|RASA4_uc003vaf.2_Intron|RASA4_uc011klb.1_Intron|RASA4_uc010lih.2_Intron|RASA4_uc011kld.1_Intron	NM_006989	NP_008920	O43374	RASL2_HUMAN	RAS p21 protein activator 4 isoform 1						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytosol|intrinsic to internal side of plasma membrane	metal ion binding|Ras GTPase activator activity				0						aagtcagtgacctggggcctg	0.090													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	44084401	44084402	+	IGR	INS	-	ATCTT	ATCTT			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44084401_44084402insATCTT								FAM75A6 (453671 upstream) : FAM27C (905834 downstream)																							TAAAGACTATATATAAAAATAA	0.277													10	6	---	---	---	---	
FAM22D	728130	broad.mit.edu	37	10	89117852	89117854	+	5'UTR	DEL	AGA	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89117852_89117854delAGA	uc001kes.2	+	1					FAM22D_uc009xte.1_5'UTR	NM_001009610	NP_001009610	Q5VT03	FA22D_HUMAN	hypothetical protein LOC728130												0						GCTGTGAGTCAGAAGGACAATTT	0.483													8	4	---	---	---	---	
FKBP4	2288	broad.mit.edu	37	12	2906174	2906174	+	Intron	DEL	G	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2906174delG	uc001qkz.2	+							NM_002014	NP_002005	Q02790	FKBP4_HUMAN	FK506 binding protein 52						negative regulation of microtubule polymerization or depolymerization|negative regulation of neuron projection development|protein folding	axonal growth cone|cytosol|membrane|microtubule|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity|protein binding, bridging				0			OV - Ovarian serous cystadenocarcinoma(31;0.00105)		Dimethyl sulfoxide(DB01093)	TGAATCTGGAGGGACAAGTAG	0.498													12	6	---	---	---	---	
ANO2	57101	broad.mit.edu	37	12	5693297	5693297	+	Intron	DEL	A	-	-	rs148573998	by1000genomes	TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5693297delA	uc001qnm.2	-							NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7						TTTAATGAACACCCCCCCCCC	0.458													4	4	---	---	---	---	
PRB4	5545	broad.mit.edu	37	12	11289902	11289902	+	Intron	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11289902delT	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1						TACTTACAAGTTTATCAAACA	0.294										HNSCC(22;0.051)			4	2	---	---	---	---	
ZFC3H1	196441	broad.mit.edu	37	12	72008918	72008919	+	Intron	DEL	GT	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72008918_72008919delGT	uc001swo.2	-							NM_144982	NP_659419	O60293	ZC3H1_HUMAN	proline/serine-rich coiled-coil 2						RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5						AACAAACACAGTGTAATTCAGT	0.351													37	13	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	80729949	80729949	+	IGR	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80729949delT								PPP1R12A (400714 upstream) : PTPRQ (108177 downstream)																							AGCGGTGATCTTTTTTTTTTT	0.373													23	7	---	---	---	---	
HSP90B1	7184	broad.mit.edu	37	12	104340286	104340286	+	Intron	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104340286delT	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)	TACATTTTGATTTTTTTTTTT	0.313													4	5	---	---	---	---	
ATP11A	23250	broad.mit.edu	37	13	113528139	113528157	+	Intron	DEL	CCTGGGATACAGTCGGGGG	-	-	rs67506160		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113528139_113528157delCCTGGGATACAGTCGGGGG	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron|ATP11A_uc010ago.2_Intron	NM_015205	NP_056020	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform a						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				gtcgtggggtcctgggatacagtcgggggcaagacaccg	0.114													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	22631320	22631322	+	Intron	DEL	AAT	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22631320_22631322delAAT	uc001wbw.2	+						uc010aiv.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdh.2_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																		GGGAGGTTTGAATATAGTAAGAA	0.463											OREG0022575	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	53	9	---	---	---	---	
FBLN5	10516	broad.mit.edu	37	14	92347465	92347466	+	Intron	INS	-	CACC	CACC	rs140834248	by1000genomes	TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92347465_92347466insCACC	uc001xzx.3	-						FBLN5_uc010aud.2_Intron|FBLN5_uc010aue.2_Intron	NM_006329	NP_006320	Q9UBX5	FBLN5_HUMAN	fibulin 5 precursor						cell-matrix adhesion|elastic fiber assembly|protein localization at cell surface|regulation of removal of superoxide radicals	extracellular space|proteinaceous extracellular matrix|soluble fraction	calcium ion binding|integrin binding|protein C-terminus binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		all_cancers(154;0.0722)				GTTCTATTCTacacacacacac	0.193													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	28927411	28927415	+	Intron	DEL	AGGGA	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28927411_28927415delAGGGA	uc010azc.2	+											Homo sapiens I.M.A.G.E. clone 321824, mRNA sequence.																		GTTTAAAAATagggaagggaaggga	0.376													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	29060833	29060833	+	IGR	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29060833delT								WHAMML2 (36548 upstream) : APBA2 (70335 downstream)																							AAAAATGACATTGGAGAATAT	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	79475225	79475225	+	IGR	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79475225delT								RASGRF1 (92010 upstream) : MIR184 (26905 downstream)																							cctcccttcctccctcttcct	0.035													4	2	---	---	---	---	
DNAH3	55567	broad.mit.edu	37	16	20970933	20970936	+	Intron	DEL	ACAC	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20970933_20970936delACAC	uc010vbe.1	-						DNAH3_uc010vbd.1_Intron	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		ctctaTTTAAacacacacacacac	0.113													4	3	---	---	---	---	
TEPP	374739	broad.mit.edu	37	16	58011490	58011491	+	Intron	DEL	TA	-	-	rs66913328		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58011490_58011491delTA	uc002emw.3	+						TEPP_uc002emv.3_Intron	NM_199456	NP_955535	Q6URK8	TEPP_HUMAN	testis/prostate/placenta-expressed protein							extracellular region				kidney(1)|central_nervous_system(1)|skin(1)	3						tgtgtgtgtgtatgtgtgtgtT	0.277													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	66388046	66388048	+	IGR	DEL	CTG	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66388046_66388048delCTG								LOC283867 (777843 upstream) : CDH5 (12477 downstream)																							ACTGGAATCTctgctgctgctgc	0.517													4	2	---	---	---	---	
ESRP2	80004	broad.mit.edu	37	16	68267099	68267100	+	Intron	INS	-	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68267099_68267100insA	uc010cfa.1	-						ESRP2_uc002evp.1_5'Flank|ESRP2_uc002evq.1_Intron	NM_024939	NP_079215	Q9H6T0	ESRP2_HUMAN	RNA binding motif protein 35B						mRNA processing|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding|nucleotide binding			ovary(1)	1						gagactgtctcaaaaaaaaaaa	0.198													5	3	---	---	---	---	
SREBF1	6720	broad.mit.edu	37	17	17722610	17722611	+	Intron	INS	-	TA	TA			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17722610_17722611insTA	uc002gru.1	-						SREBF1_uc002grp.1_5'Flank|SREBF1_uc002grq.1_Intron|SREBF1_uc002grr.1_Intron|SREBF1_uc002grs.1_Intron|SREBF1_uc002grt.1_Intron|SREBF1_uc010cpp.1_Intron|SREBF1_uc010cpq.1_Intron	NM_004176	NP_004167	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription						cellular response to starvation|cholesterol metabolic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleus	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|sterol response element binding			skin(1)	1						CCCCACTCCCTTATGCCCTGCC	0.619													106	16	---	---	---	---	
KIAA0100	9703	broad.mit.edu	37	17	26971195	26971201	+	Frame_Shift_Del	DEL	CCACAAG	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26971195_26971201delCCACAAG	uc002hbu.2	-	2	172_178	c.73_79delCTTGTGG	c.(73-81)CTTGTGGTCfs	p.L25fs	KIAA0100_uc002hbv.2_Frame_Shift_Del_p.L25fs|KIAA0100_uc010crr.1_5'UTR	NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor	25_27						extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)					GCCAACCGGACCACAAGCCACCTGCAG	0.483											OREG0024280	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	116	7	---	---	---	---	
UBTF	7343	broad.mit.edu	37	17	42284469	42284469	+	3'UTR	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42284469delT	uc002igb.2	-	20					UBTF_uc002igc.2_3'UTR|UBTF_uc010czs.2_3'UTR|UBTF_uc002igd.2_3'UTR|UBTF_uc010czt.2_3'UTR	NM_014233	NP_055048	P17480	UBF1_HUMAN	upstream binding transcription factor, RNA						positive regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm	DNA binding|protein binding				0		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CCCCACCGTATTTTTTTTTTT	0.562													3	3	---	---	---	---	
NPEPPS	9520	broad.mit.edu	37	17	45646982	45646982	+	Intron	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45646982delT	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010dba.1_Intron	NM_006310	NP_006301	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0						TATTAAGAGCttttttttttt	0.169													4	2	---	---	---	---	
KIAA1328	57536	broad.mit.edu	37	18	34465500	34465500	+	Intron	DEL	T	-	-	rs33942453		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34465500delT	uc002kzz.2	+							NM_020776	NP_065827	Q86T90	K1328_HUMAN	hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)		ATGTTAAAGGTTTTTTTTTTT	0.373													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	64559977	64559978	+	IGR	INS	-	AAGGAAGGAAGGAAGA	AAGGAAGGAAGGAAGA	rs151112863	by1000genomes	TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64559977_64559978insAAGGAAGGAAGGAAGA								CDH19 (288761 upstream) : DSEL (613841 downstream)																							aaggaaagaggaaggaaggaag	0.000													4	2	---	---	---	---	
TMPRSS9	360200	broad.mit.edu	37	19	2418290	2418290	+	Intron	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2418290delT	uc010xgx.1	+							NM_182973	NP_892018	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9						proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		cctttcctcctttccttccct	0.085													6	3	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7153066	7153066	+	Intron	DEL	A	-	-	rs113402674		TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7153066delA	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	acacccccccacacacacaca	0.050													4	4	---	---	---	---	
RPS16	6217	broad.mit.edu	37	19	39926120	39926121	+	Intron	INS	-	T	T			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39926120_39926121insT	uc002olk.2	-						RPS16_uc002oll.2_Intron|RPS16_uc002olm.2_Intron	NM_001020	NP_001011	P62249	RS16_HUMAN	ribosomal protein S16						endocrine pancreas development|ribosomal small subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome			skin(1)	1	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;4.14e-26)|all cancers(26;2.68e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			ATACCCCACTGTTCTACACCCA	0.485													3	3	---	---	---	---	
PLCB1	23236	broad.mit.edu	37	20	8731631	8731632	+	Intron	INS	-	GAGTGCA	GAGTGCA			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8731631_8731632insGAGTGCA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc002wna.2_Intron|PLCB1_uc002wnc.1_Intron|PLCB1_uc002wnd.1_Intron	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						tgcccaggctggagtgcagagg	0.114													4	3	---	---	---	---	
SFRS6	6431	broad.mit.edu	37	20	42087894	42087895	+	Intron	INS	-	A	A			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42087894_42087895insA	uc010zwg.1	+						SFRS6_uc002xki.2_5'UTR|SFRS6_uc002xkk.2_Intron	NM_006275	NP_006266	Q13247	SRSF6_HUMAN	arginine/serine-rich splicing factor 6						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding				0		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			CCCTATGACCCTTTGGCTGACC	0.515													162	10	---	---	---	---	
KCNQ2	3785	broad.mit.edu	37	20	62074688	62074690	+	Intron	DEL	CAC	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62074688_62074690delCAC	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_Intron	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	ccatcaccatcaccaccatcacc	0.000													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25627899	25627900	+	IGR	DEL	GA	-	-	rs33917499	by1000genomes	TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25627899_25627900delGA								CRYBB2 (63 upstream) : IGLL3 (85988 downstream)																							gtgtgtgtgtgagagagagaga	0.302													5	3	---	---	---	---	
SGSM3	27352	broad.mit.edu	37	22	40801548	40801549	+	Intron	INS	-	C	C			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40801548_40801549insC	uc003ayu.1	+						SGSM3_uc010gyc.1_Intron|SGSM3_uc011aos.1_Intron|SGSM3_uc011aot.1_Intron|SGSM3_uc010gyd.1_Intron	NM_015705	NP_056520	Q96HU1	SGSM3_HUMAN	small G protein signaling modulator 3						cell cycle arrest|Rap protein signal transduction	cytoplasm	Rab GTPase activator activity|Rab GTPase binding			ovary(2)	2						CAGCATGCGTGCCCCCCAAGAG	0.480													167	8	---	---	---	---	
PHEX	5251	broad.mit.edu	37	X	22129815	22129816	+	Intron	DEL	TG	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22129815_22129816delTG	uc004dah.2	+						PHEX_uc011mjr.1_Intron|PHEX_uc011mjs.1_Intron	NM_000444	NP_000435	P78562	PHEX_HUMAN	phosphate-regulating neutral endopeptidase						biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3						CTATTGTTTTTGTGTGTGTGTG	0.317													4	2	---	---	---	---	
TAF7L	54457	broad.mit.edu	37	X	100536874	100536874	+	Intron	DEL	T	-	-			TCGA-CU-A0YO-01	TCGA-CU-A0YO-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100536874delT	uc004ehb.2	-						TAF7L_uc004eha.2_Intron|TAF7L_uc004ehc.1_Intron	NM_024885	NP_079161	Q5H9L4	TAF7L_HUMAN	TATA box binding protein-associated factor, RNA						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription initiation from RNA polymerase II promoter	cytoplasm|transcription factor TFIID complex	binding			breast(1)	1						ACATCACTCCttttttttttt	0.184													9	5	---	---	---	---	
