Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
MTOR	2475	broad.mit.edu	37	1	11217322	11217322	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11217322T>A	uc001asd.2	-	30	4477	c.4356A>T	c.(4354-4356)AAA>AAT	p.K1452N		NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	1452	FAT.				cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						ACTCGTGCAGTTTCTCATACC	0.517													39	89	---	---	---	---	PASS
PLA2G2A	5320	broad.mit.edu	37	1	20302020	20302020	+	3'UTR	SNP	C	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20302020C>T	uc001bcu.2	-	5					PLA2G2A_uc001bcv.2_3'UTR|PLA2G2A_uc010oda.1_3'UTR|PLA2G2A_uc010odb.1_3'UTR	NM_001161729	NP_001155201	P14555	PA2GA_HUMAN	phospholipase A2, group IIA precursor						defense response to Gram-positive bacterium|lipid catabolic process|low-density lipoprotein particle remodeling|phosphatidic acid metabolic process|positive regulation of inflammatory response|positive regulation of macrophage derived foam cell differentiation	endoplasmic reticulum|extracellular space|membrane	calcium ion binding|calcium-dependent phospholipase A2 activity|phospholipid binding				0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000138)|Kidney(64;0.000171)|GBM - Glioblastoma multiforme(114;0.00032)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CAGTAGAAGGCTGGAAATCTG	0.502													3	7	---	---	---	---	PASS
USP48	84196	broad.mit.edu	37	1	22079531	22079531	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22079531G>T	uc001bfb.2	-	4	732	c.494C>A	c.(493-495)CCA>CAA	p.P165Q	USP48_uc010odq.1_Missense_Mutation_p.P165Q|USP48_uc009vqc.2_Missense_Mutation_p.P165Q|USP48_uc001bfc.2_Missense_Mutation_p.P165Q|USP48_uc001bfe.1_Missense_Mutation_p.P165Q|USP48_uc001bff.2_Missense_Mutation_p.P165Q	NM_032236	NP_115612	Q86UV5	UBP48_HUMAN	ubiquitin specific protease 48 isoform a	165					ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		AAATCCTGATGGATCAATGTA	0.353													40	70	---	---	---	---	PASS
ADORA3	140	broad.mit.edu	37	1	112031563	112031563	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112031563T>C	uc001ebf.2	-	3	1308	c.541A>G	c.(541-543)AAG>GAG	p.K181E	ADORA3_uc001ebg.3_Missense_Mutation_p.K100E	NM_020683	NP_065734	P33765	AA3R_HUMAN	adenosine A3 receptor isoform 1	Error:Variant_position_missing_in_P33765_after_alignment					activation of adenylate cyclase activity|inflammatory response|regulation of heart contraction	integral to plasma membrane	adenosine receptor activity, G-protein coupled			ovary(2)|large_intestine(1)|skin(1)	4		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)	GGGTGATTCTTGTAGTGGGCA	0.483													3	89	---	---	---	---	PASS
CA14	23632	broad.mit.edu	37	1	150234002	150234002	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150234002C>A	uc001etx.2	+	3	530	c.221C>A	c.(220-222)ACC>AAC	p.T74N		NM_012113	NP_036245	Q9ULX7	CAH14_HUMAN	carbonic anhydrase XIV precursor	74	Extracellular (Potential).					integral to membrane	carbonate dehydratase activity|metal ion binding			ovary(1)	1	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAGCCTGGCACCGAGCCTTTG	0.507													5	47	---	---	---	---	PASS
CADM3	57863	broad.mit.edu	37	1	159163732	159163732	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159163732T>G	uc001ftl.2	+	5	735	c.593T>G	c.(592-594)GTT>GGT	p.V198G	CADM3_uc009wsy.1_Intron|CADM3_uc001ftk.2_Missense_Mutation_p.V232G	NM_001127173	NP_001120645	Q8N126	CADM3_HUMAN	cell adhesion molecule 3 isoform 2	198	Ig-like C2-type 1.|Extracellular (Potential).				adherens junction organization|cell junction assembly|heterophilic cell-cell adhesion|homophilic cell adhesion	cell-cell junction|integral to membrane	protein homodimerization activity			ovary(2)	2	all_hematologic(112;0.0429)					ACATTCCAGGTTACCCGGGAG	0.502													20	36	---	---	---	---	PASS
ATP1A2	477	broad.mit.edu	37	1	160100072	160100072	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160100072C>T	uc001fvc.2	+	12	1774	c.1642C>T	c.(1642-1644)CGT>TGT	p.R548C	ATP1A2_uc001fvb.2_Missense_Mutation_p.R548C|ATP1A2_uc001fvd.2_Missense_Mutation_p.R284C|ATP1A2_uc009wtg.1_Missense_Mutation_p.R236C	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein	548	Cytoplasmic (Potential).				ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			ACTTGGGGAGCGTGTGCTGGG	0.622													39	69	---	---	---	---	PASS
SH2D1B	117157	broad.mit.edu	37	1	162368719	162368719	+	Silent	SNP	T	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162368719T>G	uc001gbz.1	-	3	479	c.357A>C	c.(355-357)ACA>ACC	p.T119T	SH2D1B_uc001gca.1_Intron	NM_053282	NP_444512	O14796	SH21B_HUMAN	SH2 domain containing 1B	119										pancreas(1)	1	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			TTACCACAAATGTTTCCAACT	0.398													33	75	---	---	---	---	PASS
DPT	1805	broad.mit.edu	37	1	168665781	168665781	+	3'UTR	SNP	G	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168665781G>A	uc001gfp.2	-	4						NM_001937	NP_001928	Q07507	DERM_HUMAN	dermatopontin precursor						cell adhesion	extracellular space|proteinaceous extracellular matrix				ovary(1)	1	all_hematologic(923;0.208)					TTGGTATGTGGCAAATCTAAA	0.463													3	46	---	---	---	---	PASS
FAM20B	9917	broad.mit.edu	37	1	179012867	179012867	+	5'UTR	SNP	T	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179012867T>A	uc001gmc.2	+	2						NM_014864	NP_055679	O75063	XYLK_HUMAN	hypothetical protein LOC9917 precursor							Golgi membrane|integral to membrane	ATP binding|kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(3)	3						GGAAGGTGCATCAGTGAAGAA	0.423													6	8	---	---	---	---	PASS
FAM20B	9917	broad.mit.edu	37	1	179012868	179012868	+	5'UTR	SNP	C	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179012868C>A	uc001gmc.2	+	2						NM_014864	NP_055679	O75063	XYLK_HUMAN	hypothetical protein LOC9917 precursor							Golgi membrane|integral to membrane	ATP binding|kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(3)	3						GAAGGTGCATCAGTGAAGAAA	0.428													6	8	---	---	---	---	PASS
KIAA1614	57710	broad.mit.edu	37	1	180910371	180910371	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180910371C>T	uc001gok.2	+	7	3176	c.3109C>T	c.(3109-3111)CCT>TCT	p.P1037S	KIAA1614_uc001gol.1_Missense_Mutation_p.P658S|KIAA1614_uc001gom.1_Missense_Mutation_p.P128S	NM_020950	NP_066001	Q5VZ46	K1614_HUMAN	hypothetical protein LOC57710	1037	Ser-rich.									ovary(3)|skin(1)	4						GCCCGCCCCGCCTGGCCTGAC	0.662													22	32	---	---	---	---	PASS
C1orf26	54823	broad.mit.edu	37	1	185143987	185143987	+	Silent	SNP	C	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185143987C>T	uc001grg.3	+	5	822	c.708C>T	c.(706-708)ATC>ATT	p.I236I	C1orf26_uc001grh.3_Silent_p.I236I	NM_001105518	NP_001098988	Q5T5J6	SWT1_HUMAN	hypothetical protein LOC54823	236											0						GTTTCAAAATCCCTATAAAAT	0.353													66	133	---	---	---	---	PASS
REG1A	5967	broad.mit.edu	37	2	79349111	79349111	+	Intron	SNP	C	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79349111C>G	uc002snz.2	+						REG1A_uc010ffx.1_3'UTR|REG1A_uc010ysd.1_Intron	NM_002909	NP_002900	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha precursor						positive regulation of cell proliferation	extracellular region	growth factor activity|sugar binding				0						TCTTCTGCAACAGCTCTATTG	0.517													5	124	---	---	---	---	PASS
C2orf29	55571	broad.mit.edu	37	2	101885790	101885790	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101885790G>C	uc002taw.3	+	7	1530	c.1448G>C	c.(1447-1449)AGG>ACG	p.R483T		NM_017546	NP_060016	Q9UKZ1	CB029_HUMAN	hypothetical protein LOC55571	483					cell proliferation|nuclear-transcribed mRNA poly(A) tail shortening	cytosol				ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						GAATTCAGTAGGATACGAGAA	0.393													51	76	---	---	---	---	PASS
BAZ2B	29994	broad.mit.edu	37	2	160289320	160289320	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160289320T>G	uc002uao.2	-	9	2200	c.1848A>C	c.(1846-1848)GAA>GAC	p.E616D	BAZ2B_uc002uap.2_Missense_Mutation_p.E614D|BAZ2B_uc002uas.1_Missense_Mutation_p.E553D|BAZ2B_uc002uaq.1_Missense_Mutation_p.E544D|BAZ2B_uc002uar.1_Missense_Mutation_p.E189D	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	616	Asp/Glu-rich (acidic).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						catcttcttcttcatcatctt	0.224													24	46	---	---	---	---	PASS
AGPS	8540	broad.mit.edu	37	2	178326666	178326666	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178326666G>C	uc002ull.2	+	9	963	c.916G>C	c.(916-918)GAG>CAG	p.E306Q	AGPS_uc010zfb.1_Missense_Mutation_p.E216Q	NM_003659	NP_003650	O00116	ADAS_HUMAN	alkyldihydroxyacetone phosphate synthase	306	FAD-binding PCMH-type.				ether lipid biosynthetic process	peroxisomal matrix|peroxisomal membrane|plasma membrane	alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity			ovary(2)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			AGATTCCCTGGAGTTCAGTAC	0.378													36	58	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191570	10191570	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191570T>C	uc003bvc.2	+	3	776	c.563T>C	c.(562-564)CTG>CCG	p.L188P	VHL_uc003bvd.2_Missense_Mutation_p.L147P	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	188			L -> Q (in VHLD; type I).|L -> P (in VHLD; type I-II).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.L188fs*14(2)|p.L188P(2)|p.L188Q(2)|p.D187_L188del(2)|p.L188V(1)|p.D187_N193del(1)|p.E189fs*27(1)|p.Y185fs*11(1)|p.L188R(1)|p.D187fs*14(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TACGAAGATCTGGAAGACCAC	0.502		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				18	18	---	---	---	---	PASS
PDCD6IP	10015	broad.mit.edu	37	3	33855050	33855050	+	Splice_Site	SNP	G	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33855050G>A	uc003cfx.2	+	3	420	c.265_splice	c.e3-1	p.I89_splice	PDCD6IP_uc011axv.1_Splice_Site_p.I89_splice|PDCD6IP_uc003cfy.2_Splice_Site_p.I89_splice	NM_013374	NP_037506	Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein						apoptosis|cell cycle|cell division|interspecies interaction between organisms|protein transport	cytosol|melanosome|microtubule organizing center	calcium-dependent protein binding			ovary(1)|skin(1)	2						ATTCTATCCAGATCTGCTTGA	0.323													52	34	---	---	---	---	PASS
SUCLG2	8801	broad.mit.edu	37	3	67578587	67578587	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67578587T>C	uc003dna.3	-	4	414	c.386A>G	c.(385-387)CAA>CGA	p.Q129R	SUCLG2_uc010hob.2_Missense_Mutation_p.Q10R	NM_003848	NP_003839	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming beta subunit	129	ATP-grasp.				succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity			central_nervous_system(1)|skin(1)	2		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)	TTTTGGAGTTTGTTTTGTCGC	0.348													20	20	---	---	---	---	PASS
PLXND1	23129	broad.mit.edu	37	3	129275042	129275042	+	3'UTR	SNP	G	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129275042G>A	uc003emx.2	-	36					PLXND1_uc003emw.2_3'UTR|PLXND1_uc011blb.1_3'UTR	NM_015103	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				large_intestine(1)	1						CGCCCCAGCCGTCTCTGCTCA	0.647													13	2	---	---	---	---	PASS
VPS8	23355	broad.mit.edu	37	3	184633149	184633149	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184633149G>A	uc003fpb.1	+	27	2434	c.2263G>A	c.(2263-2265)GAA>AAA	p.E755K	VPS8_uc010hyd.1_Missense_Mutation_p.E665K|VPS8_uc010hye.1_Missense_Mutation_p.E184K	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b	757							zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			GCAGGTTTTTGAATTTCTAAT	0.368													4	13	---	---	---	---	PASS
DCLK2	166614	broad.mit.edu	37	4	151169528	151169528	+	Silent	SNP	C	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151169528C>A	uc003ilm.3	+	14	2047	c.1947C>A	c.(1945-1947)CCC>CCA	p.P649P	DCLK2_uc003iln.3_Silent_p.P648P|DCLK2_uc003ilo.3_Silent_p.P666P|DCLK2_uc003ilp.3_RNA	NM_001040260	NP_001035350	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2 isoform a	649	Protein kinase.				intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)					TGAGTCACCCCTGGGTGTCAG	0.478													17	39	---	---	---	---	PASS
GPM6A	2823	broad.mit.edu	37	4	176733293	176733293	+	Intron	SNP	A	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176733293A>G	uc003iuf.2	-						GPM6A_uc003iug.2_Intron|GPM6A_uc003iuh.2_Intron|uc003iui.2_RNA	NM_201591	NP_963885	P51674	GPM6A_HUMAN	glycoprotein M6A isoform 2							cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		CAAACAAGGAAACTGCAAAAT	0.388													5	244	---	---	---	---	PASS
OSMR	9180	broad.mit.edu	37	5	38921794	38921794	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38921794A>G	uc003jln.1	+	12	2030	c.1663A>G	c.(1663-1665)ATA>GTA	p.I555V	OSMR_uc011cpj.1_5'UTR	NM_003999	NP_003990	Q99650	OSMR_HUMAN	oncostatin M receptor precursor	555	Fibronectin type-III 3.|Extracellular (Potential).				cell proliferation|positive regulation of cell proliferation	oncostatin-M receptor complex	growth factor binding|oncostatin-M receptor activity			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	all_lung(31;0.000365)					TGGAGATGTTATAGGCTATGT	0.458													46	103	---	---	---	---	PASS
BAT2	7916	broad.mit.edu	37	6	31593611	31593611	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31593611C>T	uc003nvb.3	+	8	1051	c.802C>T	c.(802-804)CAG>TAG	p.Q268*	BAT2_uc011dnv.1_RNA|BAT2_uc003nvc.3_Nonsense_Mutation_p.Q268*|BAT2_uc003nve.2_3'UTR	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	268	4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding				0						CTATGGACCCCAGGGGCCTTA	0.582													10	34	---	---	---	---	PASS
RPS18	6222	broad.mit.edu	37	6	33240437	33240437	+	Silent	SNP	T	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33240437T>C	uc003odp.1	+	2	81	c.36T>C	c.(34-36)ATT>ATC	p.I12I	VPS52_uc003odm.1_5'Flank|VPS52_uc003odn.1_5'Flank|VPS52_uc003odo.1_5'Flank|VPS52_uc011dqy.1_5'Flank|VPS52_uc011dqz.1_5'Flank|RPS18_uc010jum.1_RNA|RPS18_uc003odq.1_RNA	NM_022551	NP_072045	P62269	RS18_HUMAN	ribosomal protein S18	12					endocrine pancreas development|ribosome biogenesis|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	rRNA binding|structural constituent of ribosome				0						TCCAGCATATTTTGCGAGTAC	0.433													83	65	---	---	---	---	PASS
ABCC10	89845	broad.mit.edu	37	6	43400901	43400901	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43400901G>C	uc003ouy.1	+	3	1398	c.1183G>C	c.(1183-1185)GCT>CCT	p.A395P	ABCC10_uc003ouz.1_Missense_Mutation_p.A352P|ABCC10_uc010jyo.1_5'Flank	NM_033450	NP_258261	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C, member 10	395	ABC transmembrane type-1 1.|Helical; (Potential).					integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(6)|central_nervous_system(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			GCTTAACTTTGCTGGGAGCTT	0.607													30	24	---	---	---	---	PASS
GRM3	2913	broad.mit.edu	37	7	86468364	86468364	+	Missense_Mutation	SNP	C	A	A	rs17856664		TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86468364C>A	uc003uid.2	+	4	2633	c.1534C>A	c.(1534-1536)CCC>ACC	p.P512T	GRM3_uc010lef.2_Intron|GRM3_uc010leg.2_Missense_Mutation_p.P384T|GRM3_uc010leh.2_Missense_Mutation_p.P104T	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	512	Extracellular (Potential).			P -> A (in Ref. 3; AAH22496).	synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	GTGCAGCGACCCCTGTGCCCC	0.512													25	62	---	---	---	---	PASS
HEPACAM2	253012	broad.mit.edu	37	7	92844896	92844896	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92844896A>G	uc003umm.2	-	3	556	c.533T>C	c.(532-534)CTA>CCA	p.L178P	HEPACAM2_uc003uml.2_Missense_Mutation_p.L166P|HEPACAM2_uc010lff.2_Missense_Mutation_p.L166P|HEPACAM2_uc011khy.1_Missense_Mutation_p.L201P	NM_001039372	NP_001034461	A8MVW5	HECA2_HUMAN	HEPACAM family member 2 isoform 1	178	Ig-like C2-type 1.|Extracellular (Potential).					integral to membrane				ovary(3)|breast(1)|kidney(1)	5						TTGGTAAGCTAGCCGAGTGCC	0.522													21	47	---	---	---	---	PASS
AASS	10157	broad.mit.edu	37	7	121719654	121719654	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121719654T>G	uc003vka.2	-	20	2489	c.2393A>C	c.(2392-2394)GAA>GCA	p.E798A	AASS_uc011knu.1_RNA|AASS_uc011knv.1_RNA|AASS_uc003vkb.2_Missense_Mutation_p.E798A|AASS_uc011knw.1_Missense_Mutation_p.E286A	NM_005763	NP_005754	Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase precursor	798	Saccharopine dehydrogenase.				protein tetramerization	mitochondrial matrix	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity			upper_aerodigestive_tract(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|NADH(DB00157)	TGCCTACCATTCAGCAGCCTC	0.398													21	47	---	---	---	---	PASS
PDGFRL	5157	broad.mit.edu	37	8	17500440	17500440	+	3'UTR	SNP	A	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17500440A>C	uc003wxr.2	+	6						NM_006207	NP_006198	Q15198	PGFRL_HUMAN	platelet-derived growth factor receptor-like							extracellular region	platelet activating factor receptor activity|platelet-derived growth factor beta-receptor activity				0				Colorectal(111;0.0752)		GCGTCTCGTGAGTCCGACCCA	0.448													4	3	---	---	---	---	PASS
PRDM14	63978	broad.mit.edu	37	8	70982083	70982083	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70982083G>A	uc003xym.2	-	2	215	c.13C>T	c.(13-15)CGG>TGG	p.R5W		NM_024504	NP_078780	Q9GZV8	PRD14_HUMAN	PR domain containing 14	5					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			TCACTTGGCCGGGGTAGAGCC	0.701													3	10	---	---	---	---	PASS
LRRCC1	85444	broad.mit.edu	37	8	86048083	86048083	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86048083A>G	uc003ycw.2	+	14	2368	c.2214A>G	c.(2212-2214)ATA>ATG	p.I738M	LRRCC1_uc010maa.1_Missense_Mutation_p.I439M|LRRCC1_uc003ycx.2_Missense_Mutation_p.I645M|LRRCC1_uc003ycy.2_Missense_Mutation_p.I718M	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a	738					cell division|mitosis	centriole|nucleus					0						GTATTCAAATAGAACTTCTCA	0.308													40	54	---	---	---	---	PASS
TLE1	7088	broad.mit.edu	37	9	84199110	84199110	+	3'UTR	SNP	T	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84199110T>C	uc004aly.2	-	20					TLE1_uc004alz.2_3'UTR|TLE1_uc011lsr.1_3'UTR	NM_005077	NP_005068	Q04724	TLE1_HUMAN	transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2						CCACATAATGTTTTCAGTAGA	0.358													42	38	---	---	---	---	PASS
DAPK1	1612	broad.mit.edu	37	9	90311963	90311963	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90311963G>T	uc004apc.2	+	22	2593	c.2455G>T	c.(2455-2457)GTG>TTG	p.V819L	DAPK1_uc004apd.2_Missense_Mutation_p.V819L|DAPK1_uc011ltg.1_Intron|DAPK1_uc011lth.1_Missense_Mutation_p.V556L	NM_004938	NP_004929	P53355	DAPK1_HUMAN	death-associated protein kinase 1	819					apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2						TGGAAATCCTGTGTATTTCTG	0.398									Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				88	75	---	---	---	---	PASS
DENND1A	57706	broad.mit.edu	37	9	126143757	126143757	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126143757G>T	uc004bnz.1	-	22	3217	c.2984C>A	c.(2983-2985)CCA>CAA	p.P995Q	DENND1A_uc011lzl.1_Missense_Mutation_p.P813Q|DENND1A_uc004bny.1_Missense_Mutation_p.P777Q|DENND1A_uc011lzm.1_Missense_Mutation_p.P1006Q|DENND1A_uc010mwh.1_Missense_Mutation_p.P416Q	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1	995	Pro-rich.					cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2						CACCGAGTCTGGGGCCGGGGC	0.652													29	40	---	---	---	---	PASS
TUBAL3	79861	broad.mit.edu	37	10	5435755	5435755	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5435755T>C	uc001ihy.2	-	4	1106	c.1066A>G	c.(1066-1068)ACT>GCT	p.T356A	TUBAL3_uc001ihz.2_Missense_Mutation_p.T316A	NM_024803	NP_079079	A6NHL2	TBAL3_HUMAN	tubulin, alpha-like 3	356					microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			skin(1)	1						TTGAAACCAGTTGGACACCAA	0.567													12	22	---	---	---	---	PASS
CDNF	441549	broad.mit.edu	37	10	14880465	14880465	+	5'Flank	SNP	G	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14880465G>A	uc001inb.1	-						CDNF_uc010qbv.1_5'Flank|CDNF_uc001inc.1_5'UTR|HSPA14_uc001ind.2_Intron|HSPA14_uc001ine.2_Intron|HSPA14_uc010qbw.1_Intron|HSPA14_uc001inf.2_Intron	NM_001029954	NP_001025125	Q49AH0	CDNF_HUMAN	arginine-rich, mutated in early stage							extracellular region	growth factor activity				0						TAAGGTGAGGGGCTGCGGAGC	0.662													5	22	---	---	---	---	PASS
UBE2D1	7321	broad.mit.edu	37	10	60128479	60128479	+	Splice_Site	SNP	G	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60128479G>T	uc001jke.1	+	7	622	c.399_splice	c.e7-1	p.K133_splice		NM_003338	NP_003329	P51668	UB2D1_HUMAN	ubiquitin-conjugating enzyme E2D 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|BMP signaling pathway|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K48-linked ubiquitination|transforming growth factor beta receptor signaling pathway	cytosol|nucleoplasm	ATP binding|protein binding|ubiquitin-protein ligase activity			skin(2)	2						TGTATCTACAGATACAACAGA	0.264													19	29	---	---	---	---	PASS
LOC650623	650623	broad.mit.edu	37	10	81444997	81444997	+	RNA	SNP	T	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81444997T>C	uc010qlu.1	+	1		c.2267T>C				NR_027512				Homo sapiens BEN domain containing 3 pseudogene (LOC650623), non-coding RNA.												0						ACAACAATTTTCGGGCTTGCA	0.612													2	10	---	---	---	---	PASS
FGFR2	2263	broad.mit.edu	37	10	123353230	123353230	+	Silent	SNP	C	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123353230C>T	uc010qtk.1	-	2	749	c.102G>A	c.(100-102)GAG>GAA	p.E34E	FGFR2_uc010qtg.1_Silent_p.E34E|FGFR2_uc010qth.1_Silent_p.E34E|FGFR2_uc010qti.1_Silent_p.E34E|FGFR2_uc010qtj.1_Silent_p.E34E|FGFR2_uc010qtl.1_Silent_p.E34E|FGFR2_uc010qtm.1_Silent_p.E34E|FGFR2_uc001lfl.3_Silent_p.E34E|FGFR2_uc001lfm.2_Silent_p.E34E|FGFR2_uc001lfn.3_RNA|FGFR2_uc010qtn.1_Silent_p.E53E|FGFR2_uc010qto.1_Silent_p.E53E|FGFR2_uc001lfo.1_Silent_p.E53E|FGFR2_uc010qtp.1_Silent_p.E53E|FGFR2_uc010qtq.1_Silent_p.E53E	NM_000141	NP_000132	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2 isoform 1	34	Ig-like C2-type 1.|Extracellular (Potential).				angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)	TACCTTCTGGCTCTAATGTGG	0.483		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				16	48	---	---	---	---	PASS
CATSPER1	117144	broad.mit.edu	37	11	65793079	65793079	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65793079G>T	uc001ogt.2	-	1	910	c.772C>A	c.(772-774)CGT>AGT	p.R258S		NM_053054	NP_444282	Q8NEC5	CTSR1_HUMAN	sperm-associated cation channel 1	258	His-rich.|Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	protein binding			ovary(2)	2						GATATCCCACGCTGGTAGGAC	0.318													11	8	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	12	92133	92133	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92133G>T	uc010sdi.1	-	2	205	c.177C>A	c.(175-177)GAC>GAA	p.D59E	uc010sdj.1_RNA					SubName: Full=DEAD/H box polypeptide 11 like 11;																		GCAGCTGCCTGTCAGGAAGAG	0.592													9	39	---	---	---	---	PASS
ACSM4	341392	broad.mit.edu	37	12	7469736	7469736	+	Silent	SNP	C	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7469736C>T	uc001qsx.1	+	4	624	c.624C>T	c.(622-624)TTC>TTT	p.F208F		NM_001080454	NP_001073923	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	208					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0						TTTGCAGATTCGCCTCTGAAG	0.483													14	31	---	---	---	---	PASS
PZP	5858	broad.mit.edu	37	12	9322148	9322148	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9322148G>A	uc001qvl.2	-	16	1908	c.1879C>T	c.(1879-1881)CCT>TCT	p.P627S	PZP_uc009zgl.2_Missense_Mutation_p.P496S|PZP_uc010sgo.1_5'Flank|PZP_uc009zgm.1_5'UTR	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5						ACATTGTCAGGAAAATTGGTG	0.418													40	35	---	---	---	---	PASS
C12orf10	60314	broad.mit.edu	37	12	53693593	53693593	+	Silent	SNP	C	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53693593C>T	uc001scp.3	+	1	124	c.72C>T	c.(70-72)CGC>CGT	p.R24R	C12orf10_uc010sof.1_Silent_p.R24R|C12orf10_uc009zmx.2_Silent_p.R24R|C12orf10_uc001scq.3_5'Flank	NM_021640	NP_067653	Q86UA3	Q86UA3_HUMAN	MYG1 protein precursor	24										ovary(2)	2						CCCGGCACCGCATGCTCGGTC	0.657											OREG0021864	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	21	42	---	---	---	---	PASS
ACACB	32	broad.mit.edu	37	12	109577276	109577276	+	Silent	SNP	C	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109577276C>A	uc001tob.2	+	2	185	c.66C>A	c.(64-66)ATC>ATA	p.I22I	ACACB_uc001toc.2_Silent_p.I22I	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	22					acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	GGTTAAAAATCTGGGGGAAAA	0.453													30	91	---	---	---	---	PASS
OLFM4	10562	broad.mit.edu	37	13	53602982	53602982	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53602982G>A	uc001vhl.2	+	1	11	c.11G>A	c.(10-12)GGC>GAC	p.G4D	OLFM4_uc001vhk.1_Missense_Mutation_p.G4D	NM_006418	NP_006409	Q6UX06	OLFM4_HUMAN	olfactomedin 4 precursor	4					cell adhesion	extracellular space				skin(1)	1		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		ATGAGGCCCGGCCTCTCATTT	0.582													5	151	---	---	---	---	PASS
CGRRF1	10668	broad.mit.edu	37	14	54997070	54997070	+	Intron	SNP	T	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54997070T>C	uc001xay.2	+						CGRRF1_uc010tra.1_Intron|CGRRF1_uc001xaz.2_RNA	NM_006568	NP_006559	Q99675	CGRF1_HUMAN	cell growth regulator with ring finger domain 1						cell cycle arrest|negative regulation of cell proliferation|response to stress		zinc ion binding			ovary(1)	1						TAAGCACTCCTCAAGCATTAG	0.343													3	34	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34129174	34129174	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34129174T>C	uc001zhi.2	+	88	11706	c.11636T>C	c.(11635-11637)CTG>CCG	p.L3879P	RYR3_uc010bar.2_Missense_Mutation_p.L3874P	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3879	Helical; Name=M2; (Potential).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GTGATGCTTCTGTCCCTCCTG	0.473													9	15	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34130917	34130917	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34130917G>A	uc001zhi.2	+	89	12806	c.12736G>A	c.(12736-12738)GAC>AAC	p.D4246N	RYR3_uc010bar.2_Missense_Mutation_p.D4241N	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	4246					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TATCCATGATGACACTATGGA	0.507													16	32	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	76074470	76074470	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76074470A>G	uc010umm.1	+	8	649	c.572A>G	c.(571-573)CAG>CGG	p.Q191R	uc002bba.1_5'Flank					SubName: Full=cDNA FLJ59077, highly similar to Golgin subfamily A member 6;																		CGGTTACAGCAGACCATAAAG	0.577													3	35	---	---	---	---	PASS
IRX5	10265	broad.mit.edu	37	16	54966436	54966436	+	Silent	SNP	C	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54966436C>A	uc002ehv.2	+	2	276	c.276C>A	c.(274-276)GGC>GGA	p.G92G	IRX5_uc010cca.1_Silent_p.G144G|IRX5_uc002ehw.2_Silent_p.G26G	NM_005853	NP_005844	P78411	IRX5_HUMAN	iroquois homeobox protein 5	92					response to stimulus|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|vitamin D binding				0						ACACACCCGGCATGGCGGGCT	0.652													17	53	---	---	---	---	PASS
ALOX15	246	broad.mit.edu	37	17	4534860	4534860	+	3'UTR	SNP	T	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4534860T>G	uc002fyh.2	-	14					ALOX15_uc010vsd.1_3'UTR|ALOX15_uc010vse.1_3'UTR	NM_001140	NP_001131	P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase						inflammatory response|leukotriene biosynthetic process	nucleus	arachidonate 15-lipoxygenase activity|iron ion binding|lipoxygenase activity			skin(3)|ovary(1)|lung(1)	5				READ - Rectum adenocarcinoma(115;0.0327)	Ciclopirox(DB01188)|Masoprocol(DB00179)|Zileuton(DB00744)	GTGGCTTGGGTGATGGGGGCT	0.592													10	23	---	---	---	---	PASS
DNAH2	146754	broad.mit.edu	37	17	7721647	7721647	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7721647C>T	uc002giu.1	+	68	10419	c.10405C>T	c.(10405-10407)CGC>TGC	p.R3469C	DNAH2_uc010cnm.1_Missense_Mutation_p.R407C	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	3469	AAA 5 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)				GCTGTTGATGCGCATTGGCGA	0.567													63	124	---	---	---	---	PASS
KIAA0100	9703	broad.mit.edu	37	17	26943335	26943335	+	Intron	SNP	G	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26943335G>C	uc002hbu.2	-						SGK494_uc010waq.1_5'Flank|SGK494_uc010war.1_5'Flank|SGK494_uc002hbr.1_5'Flank|uc002hbs.1_RNA|KIAA0100_uc002hbt.2_Intron	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)					GAAATCCCAAGCCACACCAAA	0.473													5	68	---	---	---	---	PASS
SSH2	85464	broad.mit.edu	37	17	27959837	27959837	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27959837T>C	uc002heo.1	-	15	2294	c.2294A>G	c.(2293-2295)CAG>CGG	p.Q765R	SSH2_uc010wbh.1_Missense_Mutation_p.Q792R	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	765					actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2						CAGTTGAATCTGCCCAACTCC	0.473													9	48	---	---	---	---	PASS
RAPGEFL1	51195	broad.mit.edu	37	17	38340547	38340547	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38340547G>C	uc010cwu.1	+	3	553	c.63G>C	c.(61-63)TTG>TTC	p.L21F		NM_016339	NP_057423	Q9UHV5	RPGFL_HUMAN	Rap guanine nucleotide exchange factor	227					G-protein coupled receptor protein signaling pathway|nervous system development|small GTPase mediated signal transduction	intracellular|membrane fraction	guanyl-nucleotide exchange factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3						TCCATTTCTTGGACACCTACC	0.572													64	151	---	---	---	---	PASS
KRTAP4-8	728224	broad.mit.edu	37	17	39254054	39254054	+	Missense_Mutation	SNP	A	T	T	rs76270529	by1000genomes	TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39254054A>T	uc010wfo.1	-	1	322	c.283T>A	c.(283-285)TGC>AGC	p.C95S		NM_031960	NP_114166	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4.8	95	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].|15.					keratin filament					0						ctggagatgcagcagcTAGGG	0.318													5	50	---	---	---	---	PASS
KRT37	8688	broad.mit.edu	37	17	39579096	39579096	+	Silent	SNP	G	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39579096G>A	uc002hwp.1	-	3	713	c.666C>T	c.(664-666)GCC>GCT	p.A222A	uc002hwo.1_Intron	NM_003770	NP_003761	O76014	KRT37_HUMAN	keratin 37	222	Rod.|Coil 1B.					intermediate filament	structural molecule activity			skin(1)	1		Breast(137;0.000496)				CCTCCAGGTCGGCCTTGGCCA	0.662													36	50	---	---	---	---	PASS
PRKCA	5578	broad.mit.edu	37	17	64731699	64731699	+	Silent	SNP	C	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64731699C>T	uc002jfp.1	+	10	1193	c.1149C>T	c.(1147-1149)TGC>TGT	p.C383C	PRKCA_uc002jfo.1_Silent_p.C254C	NM_002737	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	383	Protein kinase.				activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)	ACGTGGAGTGCACCATGGTAG	0.522													40	75	---	---	---	---	PASS
KIF19	124602	broad.mit.edu	37	17	72350319	72350319	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72350319C>A	uc002jkm.3	+	18	2465	c.2327C>A	c.(2326-2328)ACT>AAT	p.T776N		NM_153209	NP_694941	Q2TAC6	KIF19_HUMAN	kinesin family member 19	776					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0						GAGATCCTGACTGGCACCAAG	0.657													43	112	---	---	---	---	PASS
CDH7	1005	broad.mit.edu	37	18	63477170	63477170	+	Silent	SNP	C	T	T	rs143932384		TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63477170C>T	uc002ljz.2	+	3	766	c.441C>T	c.(439-441)AAC>AAT	p.N147N	CDH7_uc002lka.2_Silent_p.N147N|CDH7_uc002lkb.2_Silent_p.N147N	NM_033646	NP_387450	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2 preproprotein	147	Extracellular (Potential).|Cadherin 1.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4		Esophageal squamous(42;0.129)				AGGATATCAACGACAATGAAC	0.507													33	92	---	---	---	---	PASS
BCKDHA	593	broad.mit.edu	37	19	41928179	41928179	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41928179G>T	uc002oqq.2	+	6	786	c.757G>T	c.(757-759)GCT>TCT	p.A253S	CYP2F1_uc010xvw.1_Intron|BCKDHA_uc002oqm.3_Missense_Mutation_p.A287S|BCKDHA_uc002oqp.1_Missense_Mutation_p.A145S|BCKDHA_uc002oqr.2_Missense_Mutation_p.A253S|BCKDHA_uc010xvz.1_Missense_Mutation_p.A231S	NM_000709	NP_000700	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha	253			A -> T (in MSUD1A).		branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|alpha-ketoacid dehydrogenase activity|carboxy-lyase activity|metal ion binding|protein binding				0						CTTCAACTTCGCTGCCACACT	0.612													4	84	---	---	---	---	PASS
ZNF233	353355	broad.mit.edu	37	19	44777290	44777290	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44777290A>G	uc002oyz.1	+	5	604	c.477A>G	c.(475-477)ATA>ATG	p.I159M	ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_Intron|ZNF233_uc002oyy.1_Translation_Start_Site	NM_181756	NP_861421	A6NK53	ZN233_HUMAN	zinc finger protein 233	159					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2		Prostate(69;0.0435)|all_neural(266;0.226)				ACTATGTAATAAAGCTACAAG	0.433													34	65	---	---	---	---	PASS
TRAPPC6A	79090	broad.mit.edu	37	19	45666460	45666460	+	Missense_Mutation	SNP	G	A	A	rs146982912		TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45666460G>A	uc002paw.2	-	6	489	c.470C>T	c.(469-471)CCG>CTG	p.P157L	TRAPPC6A_uc002pav.2_Missense_Mutation_p.P171L			O75865	TPC6A_HUMAN	SubName: Full=TRAPPC6Adelta29-42; SubName: Full=Trafficking protein particle complex 6A, isoform CRA_a;	157					vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	guanylate cyclase activity|heme binding				0		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00872)|GBM - Glioblastoma multiforme(486;0.233)		TTAGGATTTCGGAATCACCAC	0.637													16	35	---	---	---	---	PASS
ZNF525	170958	broad.mit.edu	37	19	53886962	53886962	+	3'UTR	SNP	G	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53886962G>A	uc010eqn.2	+	4					ZNF525_uc002qbl.2_Intron|ZNF765_uc010ydx.1_Intron	NR_003699				Homo sapiens cDNA FLJ39718 fis, clone SMINT2013695.												0						AATCACTGGAGAAGCCATAAT	0.393													4	17	---	---	---	---	PASS
ZNF814	730051	broad.mit.edu	37	19	58385762	58385762	+	Silent	SNP	C	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58385762C>G	uc002qqo.2	-	3	1268	c.996G>C	c.(994-996)TCG>TCC	p.S332S	ZNF814_uc002qqk.2_Intron|ZNF814_uc010yhl.1_Intron	NM_001144989	NP_001138461	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	332	C2H2-type 5.				regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0						ATTTGCTAAACGATTTCCCAC	0.358													2	3	---	---	---	---	PASS
ESF1	51575	broad.mit.edu	37	20	13695697	13695697	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13695697C>T	uc002woj.2	-	14	2488	c.2380G>A	c.(2380-2382)GCC>ACC	p.A794T		NM_016649	NP_057733	Q9H501	ESF1_HUMAN	ABT1-associated protein	794	Lys-rich.|Potential.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm				ovary(1)	1						CTTTGCCGGGCCTTCTCCTCA	0.413													62	142	---	---	---	---	PASS
CDH22	64405	broad.mit.edu	37	20	44806600	44806600	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44806600C>T	uc002xrm.2	-	10	2301	c.1900G>A	c.(1900-1902)GTT>ATT	p.V634I	CDH22_uc010ghk.1_Missense_Mutation_p.V634I	NM_021248	NP_067071	Q9UJ99	CAD22_HUMAN	cadherin 22 precursor	634	Helical; (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)				AGGATGAGAACGCAGACCAAG	0.652													7	61	---	---	---	---	PASS
ARFGEF2	10564	broad.mit.edu	37	20	47569395	47569395	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47569395A>T	uc002xtx.3	+	5	729	c.577A>T	c.(577-579)ATT>TTT	p.I193F		NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine	193					exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			GCTGAACGTCATTTTCACCCG	0.463													32	63	---	---	---	---	PASS
PRIC285	85441	broad.mit.edu	37	20	62192519	62192519	+	Silent	SNP	C	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62192519C>A	uc002yfm.2	-	15	7954	c.7062G>T	c.(7060-7062)GTG>GTT	p.V2354V	PRIC285_uc002yfl.1_Silent_p.V1785V	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285	2354					cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)			GGATCTGCCTCACGTCCAGGA	0.622													4	81	---	---	---	---	PASS
PNPLA5	150379	broad.mit.edu	37	22	44276752	44276752	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44276752G>T	uc003beg.2	-	9	1310	c.1213C>A	c.(1213-1215)CGC>AGC	p.R405S	PNPLA5_uc011aqc.1_Missense_Mutation_p.R265S|PNPLA5_uc003beh.2_Missense_Mutation_p.R291S	NM_138814	NP_620169	Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	405					lipid catabolic process		hydrolase activity				0		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				TCCAGGACGCGAGTGGCCGGA	0.667													3	39	---	---	---	---	PASS
SBF1	6305	broad.mit.edu	37	22	50905855	50905855	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50905855G>A	uc003blh.2	-	5	656	c.461C>T	c.(460-462)GCC>GTC	p.A154V	SBF1_uc011arx.1_5'Flank|SBF1_uc003bli.2_Missense_Mutation_p.A155V	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1	154	DENN.				protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		CACGTGGATGGCATAGATGAG	0.642													4	110	---	---	---	---	PASS
TEX11	56159	broad.mit.edu	37	X	69871299	69871299	+	Splice_Site	SNP	C	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69871299C>A	uc004dyl.2	-	18	1690	c.1528_splice	c.e18+1	p.A510_splice	TEX11_uc004dyk.2_Splice_Site_p.A185_splice|TEX11_uc004dym.2_Splice_Site_p.A495_splice	NM_001003811	NP_001003811	Q8IYF3	TEX11_HUMAN	testis expressed sequence 11 isoform 1								protein binding			ovary(3)|breast(1)|skin(1)	5	Renal(35;0.156)					AAAATTTATACCTCTTTCAGA	0.333													3	18	---	---	---	---	PASS
HCFC1	3054	broad.mit.edu	37	X	153228831	153228831	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153228831G>C	uc004fjp.2	-	4	1085	c.557C>G	c.(556-558)GCC>GGC	p.A186G		NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1	186	Kelch 3.				cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AATGTCCCAGGCTACCACTCC	0.527													4	57	---	---	---	---	PASS
C1orf174	339448	broad.mit.edu	37	1	3806286	3806286	+	3'UTR	DEL	G	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3806286delG	uc001alf.2	-	4					C1orf174_uc009vls.2_RNA	NM_207356	NP_997239	Q8IYL3	CA174_HUMAN	hypothetical protein LOC339448												0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)		aaaaaaaaaagaaAGGACATT	0.224													4	2	---	---	---	---	
PRAMEF5	343068	broad.mit.edu	37	1	13012832	13012832	+	Intron	DEL	A	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13012832delA	uc001aur.2	-							NM_001013407	NP_001013425	Q5TYX0	PRAM5_HUMAN	PRAME family member 5												0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;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)		agactccatcaaaaaaaaaaa	0.234													6	3	---	---	---	---	
PHACTR4	65979	broad.mit.edu	37	1	28817970	28817970	+	Intron	DEL	A	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28817970delA	uc001bpw.2	+						PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron|PHACTR4_uc001bpz.2_5'Flank	NM_001048183	NP_001041648	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4 isoform 1								actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		accctgtctcaaaaaaaaaaa	0.025													3	3	---	---	---	---	
ZCCHC11	23318	broad.mit.edu	37	1	52959475	52959475	+	Intron	DEL	T	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52959475delT	uc001ctx.2	-						ZCCHC11_uc001cty.2_Intron|ZCCHC11_uc001ctz.2_Intron|ZCCHC11_uc009vze.1_Intron|ZCCHC11_uc009vzf.1_Intron|ZCCHC11_uc001cub.2_Intron|ZCCHC11_uc001cuc.2_Intron	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform						miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3						CAGAATCGTGttttttttttg	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89399858	89399859	+	Intron	INS	-	AA	AA			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89399858_89399859insAA	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		GATTCCTGCACAGTCTGACCAG	0.569													4	2	---	---	---	---	
ANKRD57	65124	broad.mit.edu	37	2	110373676	110373677	+	3'UTR	INS	-	T	T			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110373676_110373677insT	uc002tfb.2	+	1					SEPT10_uc010ywu.1_5'Flank|SEPT10_uc002tew.2_5'Flank|SEPT10_uc002tex.2_5'Flank|SEPT10_uc002tey.2_5'Flank|SEPT10_uc010ywv.1_5'Flank	NM_023016	NP_075392	Q53LP3	ANR57_HUMAN	ankyrin repeat domain 57												0						GCAAAGGTTTATTTGTCTTAAT	0.406													5	6	---	---	---	---	
GRB14	2888	broad.mit.edu	37	2	165351047	165351047	+	Intron	DEL	A	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165351047delA	uc002ucl.2	-						GRB14_uc010zcv.1_Intron|GRB14_uc002ucm.2_Intron	NM_004490	NP_004481	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14						blood coagulation|leukocyte migration	cytosol|endosome membrane|Golgi membrane|microsome|plasma membrane	SH3/SH2 adaptor activity			ovary(5)|upper_aerodigestive_tract(1)|lung(1)	7						AAAGAGAGAGAAGGAATTTCA	0.338													63	33	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	233282753	233282753	+	IGR	DEL	T	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233282753delT								ALPPL2 (7331 upstream) : ALPI (38080 downstream)																							GGGGGGGGGGTGATCTTCTGC	0.577													6	3	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52713599	52713600	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52713599_52713600insG	uc003des.2	-	1	140_141	c.128_129insC	c.(127-129)ACTfs	p.T43fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Ins_p.T43fs|PBRM1_uc003der.2_Frame_Shift_Ins_p.T43fs|PBRM1_uc003det.2_Frame_Shift_Ins_p.T43fs|PBRM1_uc003deu.2_Frame_Shift_Ins_p.T43fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Ins_p.T43fs|PBRM1_uc010hmk.1_Frame_Shift_Ins_p.T43fs|PBRM1_uc003dey.2_Frame_Shift_Ins_p.T43fs|PBRM1_uc003dez.1_Frame_Shift_Ins_p.T43fs|PBRM1_uc003dfb.1_5'Flank	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	43					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CAGGATCTACAGTTGGAAGATT	0.475			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								27	27	---	---	---	---	
ZPLD1	131368	broad.mit.edu	37	3	102175390	102175393	+	Intron	DEL	TATC	-	-	rs10557928		TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102175390_102175393delTATC	uc003dvs.1	+						ZPLD1_uc003dvt.1_Intron|ZPLD1_uc011bhg.1_Intron	NM_175056	NP_778226	Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1							integral to membrane				ovary(2)|skin(2)|central_nervous_system(1)	5						ttatctattatatctatctatcta	0.196													4	2	---	---	---	---	
CCDC39	339829	broad.mit.edu	37	3	180372434	180372434	+	Intron	DEL	A	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180372434delA	uc010hxe.2	-						CCDC39_uc003fkn.2_Intron	NM_181426	NP_852091	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39						axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium axoneme|cytoplasm|cytoskeleton				ovary(4)	4	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			aagaaaaaggaaaaaaaaaaa	0.303													4	2	---	---	---	---	
PROM1	8842	broad.mit.edu	37	4	16034810	16034810	+	Intron	DEL	T	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16034810delT	uc003goo.2	-						PROM1_uc003gor.2_Intron|PROM1_uc003gos.2_Intron|PROM1_uc003got.2_Intron|PROM1_uc003gou.2_Intron|PROM1_uc003gop.2_Intron|PROM1_uc003goq.3_Intron|PROM1_uc010iec.1_Intron	NM_006017	NP_006008	O43490	PROM1_HUMAN	prominin 1 isoform 1						camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	7						GTTTGGTGGGTTTTTTTTTCA	0.373													4	2	---	---	---	---	
GPR125	166647	broad.mit.edu	37	4	22437978	22437979	+	Intron	INS	-	A	A	rs74420770		TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22437978_22437979insA	uc003gqm.1	-						GPR125_uc010ieo.1_Intron|GPR125_uc003gqn.1_Intron|GPR125_uc003gqo.2_Intron	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor						neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)				TGCCTAGTATTAAAAAAAAAAA	0.307													4	2	---	---	---	---	
PRDM9	56979	broad.mit.edu	37	5	23509045	23509045	+	Intron	DEL	T	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23509045delT	uc003jgo.2	+							NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9						meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6						TCTCAGCACCTTCTCCTTCCA	0.577										HNSCC(3;0.000094)			6	3	---	---	---	---	
ROS1	6098	broad.mit.edu	37	6	117704314	117704315	+	Intron	DEL	GC	-	-	rs112993324		TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117704314_117704315delGC	uc003pxp.1	-						ROS1_uc011ebi.1_Intron|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor						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)		ATCAAATAAGGCGCTTTTTTTT	0.312			T	GOPC|ROS1	glioblastoma|NSCLC								3	3	---	---	---	---	
SPDYE2	441273	broad.mit.edu	37	7	102197800	102197800	+	Intron	DEL	G	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102197800delG	uc011kkx.1	+						UPK3BL_uc003uzy.2_Intron|POLR2J3_uc003uzw.2_Intron|POLR2J3_uc011kkw.1_Intron|SPDYE2_uc003vaa.1_Intron	NM_001031618	NP_001026789	Q495Y8	SPDE2_HUMAN	speedy homolog E2												0						ttttttttttgtgtgtgtgtg	0.254													6	3	---	---	---	---	
FPGS	2356	broad.mit.edu	37	9	130567169	130567170	+	Intron	INS	-	T	T	rs72030539		TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130567169_130567170insT	uc004bsg.1	+						FPGS_uc004bsh.1_Intron|FPGS_uc011mal.1_Intron|FPGS_uc004bsi.1_Intron	NM_004957	NP_004948	Q05932	FOLC_HUMAN	folylpolyglutamate synthase isoform a precursor						folic acid metabolic process|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|one-carbon metabolic process	cytosol|mitochondrial matrix	ATP binding|tetrahydrofolylpolyglutamate synthase activity				0					L-Glutamic Acid(DB00142)	GCAACCTTTAAttttttttttt	0.213													4	2	---	---	---	---	
NACC2	138151	broad.mit.edu	37	9	138907999	138907999	+	Intron	DEL	T	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138907999delT	uc004cgw.2	-						NACC2_uc010nbh.2_Intron	NM_144653	NP_653254	Q96BF6	NACC2_HUMAN	BTB (POZ) domain containing 14A						negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization	nuclear body					0						AAATTTAAGATTTTTTTTTTG	0.303													4	2	---	---	---	---	
PLCE1	51196	broad.mit.edu	37	10	96058297	96058298	+	Frame_Shift_Ins	INS	-	C	C	rs3765524	by1000genomes	TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96058297_96058298insC	uc001kjk.2	+	24	5963_5964	c.5329_5330insC	c.(5329-5331)ACCfs	p.T1777fs	PLCE1_uc010qnx.1_Frame_Shift_Ins_p.T1761fs|PLCE1_uc001kjm.2_Frame_Shift_Ins_p.T1469fs|PLCE1_uc001kjp.2_Frame_Shift_Ins_p.T135fs	NM_016341	NP_057425	Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1 isoform 1	1777	PI-PLC Y-box.				activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)				TCAGAAACTGACCCAGCACACC	0.525													66	42	---	---	---	---	
TAF5	6877	broad.mit.edu	37	10	105132952	105132953	+	Intron	INS	-	A	A			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105132952_105132953insA	uc001kwv.2	+						TAF5_uc010qqq.1_Intron	NM_006951	NP_008882	Q15542	TAF5_HUMAN	TBP-associated factor 5						histone acetylation|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	actin cytoskeleton|transcription factor TFIID complex|transcription factor TFTC complex	protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)	2		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		gactccctctcaaaaaaaaaaa	0.173													5	3	---	---	---	---	
TRIM21	6737	broad.mit.edu	37	11	4409908	4409909	+	Intron	DEL	CA	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4409908_4409909delCA	uc001lyy.1	-							NM_003141	NP_003132	P19474	RO52_HUMAN	tripartite motif protein 21						cell cycle|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein deubiquitination|positive regulation of cell cycle|protein autoubiquitination|protein destabilization|protein monoubiquitination|protein polyubiquitination|protein trimerization	cytoplasmic mRNA processing body|nucleus	DNA binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|lung(1)	4		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;2.08e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0851)|LUSC - Lung squamous cell carcinoma(625;0.194)		cacacgcgcgcacacacacaca	0.391													6	3	---	---	---	---	
PAMR1	25891	broad.mit.edu	37	11	35462851	35462851	+	Intron	DEL	A	-	-	rs79736526		TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35462851delA	uc001mwg.2	-						PAMR1_uc001mwf.2_Intron|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Intron	NM_001001991	NP_001001991	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2						TCTTGAGGTCAAAAAAAAAAA	0.393													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	77054709	77054709	+	IGR	DEL	T	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77054709delT								OSBPL8 (101120 upstream) : ZDHHC17 (103145 downstream)																							CTCTGGGCTATaaaaaaaaaa	0.303													4	2	---	---	---	---	
RFX4	5992	broad.mit.edu	37	12	107080945	107080946	+	Intron	INS	-	TC	TC	rs57545359		TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107080945_107080946insTC	uc001tlr.2	+						RFX4_uc010swv.1_Intron|RFX4_uc001tls.2_Intron|RFX4_uc001tlt.2_Intron|RFX4_uc001tlv.2_Intron|uc001tlu.3_5'Flank	NM_213594	NP_998759	Q33E94	RFX4_HUMAN	regulatory factor X4 isoform c						transcription, DNA-dependent	nucleus	DNA binding			upper_aerodigestive_tract(1)	1						ctctgtctctatctctctctct	0.218													13	8	---	---	---	---	
C12orf51	283450	broad.mit.edu	37	12	112694331	112694331	+	Intron	DEL	A	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112694331delA	uc009zwc.2	-						C12orf51_uc010syk.1_Intron|C12orf51_uc001tts.2_Intron|C12orf51_uc001ttt.3_Intron	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						TTCTAAACAGAAAAAGAGAAA	0.398													13	8	---	---	---	---	
FAM48A	55578	broad.mit.edu	37	13	37593524	37593524	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37593524delA	uc001uwg.2	-	22	2075	c.1827delT	c.(1825-1827)TTTfs	p.F609fs	FAM48A_uc010abt.2_Frame_Shift_Del_p.F610fs|FAM48A_uc001uwh.2_Frame_Shift_Del_p.F610fs|FAM48A_uc001uwi.2_Frame_Shift_Del_p.F609fs|FAM48A_uc001uwj.2_Frame_Shift_Del_p.F610fs|FAM48A_uc001uwk.2_Frame_Shift_Del_p.F688fs|FAM48A_uc001uwd.2_Frame_Shift_Del_p.F96fs|FAM48A_uc001uwe.2_Frame_Shift_Del_p.F93fs|FAM48A_uc001uwf.2_Frame_Shift_Del_p.F187fs	NM_001014286	NP_001014308	Q8NEM7	FA48A_HUMAN	family with sequence similarity 48, member A	609					autophagy|gastrulation	SAGA-type complex	protein binding				0		Lung NSC(96;2.09e-06)|Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.0959)		all cancers(112;6.06e-07)|Epithelial(112;1.87e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00794)|BRCA - Breast invasive adenocarcinoma(63;0.0128)|GBM - Glioblastoma multiforme(144;0.0477)		TTTTTAAACCAAATGGAACAC	0.254													127	64	---	---	---	---	
THSD1P1	374500	broad.mit.edu	37	13	52803642	52803643	+	Intron	DEL	TT	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52803642_52803643delTT	uc001vgm.1	-						uc001vgn.2_Intron					Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						CAGTTTTCCCTTTTTTTTTTTT	0.332													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	56038833	56038833	+	IGR	DEL	G	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56038833delG								PRTG (3656 upstream) : NEDD4 (80298 downstream)																							aaaaaaaaaagaaGCTCCTGG	0.279													4	3	---	---	---	---	
CPNE7	27132	broad.mit.edu	37	16	89657660	89657660	+	Frame_Shift_Del	DEL	A	-	-	rs35731090	byFrequency	TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89657660delA	uc002fnp.2	+	15	1649	c.1519delA	c.(1519-1521)AAAfs	p.K507fs	CPNE7_uc002fnq.2_Frame_Shift_Del_p.K432fs	NM_014427	NP_055242	Q9UBL6	CPNE7_HUMAN	copine 7 isoform b	507	VWFA.				lipid metabolic process		transporter activity				0		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		GAGCACCGGGAAAGCCTCTGT	0.642													6	5	---	---	---	---	
ANKFN1	162282	broad.mit.edu	37	17	54305178	54305178	+	Intron	DEL	T	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54305178delT	uc002iun.1	+						uc002iuo.2_5'Flank	NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2						CTTCTCTCTCTTTTTTTTTTC	0.333													4	2	---	---	---	---	
LLGL2	3993	broad.mit.edu	37	17	73568906	73568906	+	Intron	DEL	A	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73568906delA	uc002joh.2	+						LLGL2_uc002joi.2_Intron|LLGL2_uc010dgg.1_Intron|LLGL2_uc002joj.2_Intron|LLGL2_uc010wsd.1_Intron	NM_001031803	NP_001026973	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 isoform c						cell cycle|cell division|exocytosis|regulation of establishment or maintenance of cell polarity	cytoplasm|intracellular membrane-bounded organelle	PDZ domain binding			ovary(2)	2	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			atctcggaggaaaaaaaaaaa	0.264													3	3	---	---	---	---	
C19orf6	91304	broad.mit.edu	37	19	1014538	1014547	+	Intron	DEL	CGTGATGGGG	-	-	rs143052245		TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1014538_1014547delCGTGATGGGG	uc002lqr.1	-						C19orf6_uc002lqq.1_5'Flank|C19orf6_uc002lqs.1_Intron	NM_001033026	NP_001028198	Q4ZIN3	MBRL_HUMAN	membralin isoform 1							cytoplasm|integral to membrane				pancreas(2)|breast(1)	3		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		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)|GBM - Glioblastoma multiforme(1328;0.0252)|STAD - Stomach adenocarcinoma(1328;0.18)		CAAGGGCCTACGTGATGGGGCGTGATGGGG	0.681													6	5	---	---	---	---	
ALDH16A1	126133	broad.mit.edu	37	19	49964584	49964584	+	Intron	DEL	A	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49964584delA	uc002pnt.2	+						ALDH16A1_uc010yar.1_Intron|ALDH16A1_uc010yas.1_Intron|ALDH16A1_uc010yat.1_Intron	NM_153329	NP_699160	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1								oxidoreductase activity|protein binding			skin(1)	1		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		aggggctgggacctggactcc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	19176245	19176246	+	IGR	INS	-	TTTA	TTTA	rs148687767	by1000genomes	TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19176245_19176246insTTTA								C20orf79 (381212 upstream) : SLC24A3 (17044 downstream)																							TCACATGGGATtttatttattt	0.213													6	3	---	---	---	---	
SLA2	84174	broad.mit.edu	37	20	35261962	35261962	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35261962delC	uc002xfv.2	-	4	624	c.262delG	c.(262-264)GCCfs	p.A88fs	SLA2_uc002xfu.2_Frame_Shift_Del_p.A88fs	NM_032214	NP_115590	Q9H6Q3	SLAP2_HUMAN	Src-like-adaptor 2 isoform a	88	SH3.				antigen receptor-mediated signaling pathway|B cell mediated immunity|intracellular receptor mediated signaling pathway|negative regulation of B cell activation|negative regulation of calcium-mediated signaling|negative regulation of transcription from RNA polymerase II promoter|T cell activation	cytoplasmic membrane-bounded vesicle|endosome membrane|plasma membrane	protein N-terminus binding|SH3/SH2 adaptor activity				0	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				GAGACTTTGGCCACGTGGACG	0.597													130	59	---	---	---	---	
CBS	875	broad.mit.edu	37	21	44473883	44473887	+	3'UTR	DEL	GCCAG	-	-	rs71872941		TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44473883_44473887delGCCAG	uc002zcu.2	-	17					CBS_uc002zcs.1_3'UTR|CBS_uc002zct.2_3'UTR|CBS_uc002zcw.3_Intron|CBS_uc002zcv.2_3'UTR	NM_000071	NP_000062	P35520	CBS_HUMAN	cystathionine-beta-synthase						cysteine biosynthetic process from serine|cysteine biosynthetic process via cystathionine|homocysteine catabolic process|hydrogen sulfide biosynthetic process|L-cysteine catabolic process|L-serine catabolic process	cytosol|nucleolus	cystathionine beta-synthase activity|heme binding|protein homodimerization activity|pyridoxal phosphate binding|ubiquitin protein ligase binding				0					L-Cysteine(DB00151)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|S-Adenosylmethionine(DB00118)	GGATAACGGTGCCAGGCCAGGCAGT	0.585													6	4	---	---	---	---	
GGT1	2678	broad.mit.edu	37	22	25016169	25016170	+	Intron	INS	-	T	T	rs28418841	by1000genomes	TCGA-CZ-5987-01A-11D-1669-08	TCGA-CZ-5987-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25016169_25016170insT	uc003aan.1	+						GGT1_uc003aas.1_Intron|GGT1_uc003aat.1_Intron|GGT1_uc003aau.1_Intron|GGT1_uc003aav.1_Intron|GGT1_uc003aaw.1_Intron|GGT1_uc003aax.1_Intron	NM_013430	NP_038347	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1 precursor						glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding				0					Glutathione(DB00143)	aaaaaaaaaaaaTCTTTCCTCC	0.277													3	4	---	---	---	---	
