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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	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	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
PRAMEF11	440560	broad.mit.edu	37	1	12887546	12887546	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:12887546C>T	uc001auk.2	-	3	507	c.311G>A	c.(310-312)CGG>CAG	p.R104Q		NM_001146344	NP_001139816	O60813	PRA11_HUMAN	PRAME family member 11	104											0						CAAGGGCTGCCGTTCTCTCAT	0.493													5	420					0	0	0.001984	0	0
EIF4G3	8672	broad.mit.edu	37	1	21276537	21276538	+	Missense_Mutation	DNP	GC	AA	AA			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:21276537_21276538GC>AA	uc001bec.2	-	8	869_870	c.613_614GC>TT	c.(613-615)GCT>TTT	p.A205F	EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Missense_Mutation_p.A204F|EIF4G3_uc009vpz.2_Missense_Mutation_p.A205F|EIF4G3_uc001bed.2_Missense_Mutation_p.A205F|EIF4G3_uc001bef.2_Missense_Mutation_p.A204F|EIF4G3_uc001bee.2_Missense_Mutation_p.A211F|EIF4G3_uc001beg.2_Missense_Mutation_p.A204F|EIF4G3_uc010odk.1_Missense_Mutation_p.A205F|EIF4G3_uc001beh.2_Missense_Mutation_p.A216F	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4	205					interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		GGTGCTGGCAGCAAGATGAGCG	0.48													7	32					0	0	0.004672	0	0
GRHL3	57822	broad.mit.edu	37	1	24663626	24663626	+	Missense_Mutation	SNP	A	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:24663626A>C	uc001biy.2	+	5	732	c.686A>C	c.(685-687)TAC>TCC	p.Y229S	GRHL3_uc001bix.2_Missense_Mutation_p.Y224S|GRHL3_uc001biz.2_Missense_Mutation_p.Y131S	NM_021180	NP_067003	Q8TE85	GRHL3_HUMAN	sister-of-mammalian grainyhead protein isoform	224					regulation of actin cytoskeleton organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		CCAGAGGACTACCCCAGCCTC	0.562													7	53					0	0	0.005443	0	0
TRIM33	51592	broad.mit.edu	37	1	114964258	114964258	+	Missense_Mutation	SNP	G	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:114964258G>T	uc001eew.2	-	11	1945	c.1861C>A	c.(1861-1863)CAC>AAC	p.H621N	TRIM33_uc010owr.1_Missense_Mutation_p.H211N|TRIM33_uc010ows.1_Missense_Mutation_p.H229N|TRIM33_uc001eex.2_Missense_Mutation_p.H621N	NM_015906	NP_056990	Q9UPN9	TRI33_HUMAN	tripartite motif-containing 33 protein isoform	621					negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	11	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGGTTTGAGTGCTAATAAGAA	0.398			T	RET	papillary thyroid								33	45					2.42023e-17	2.71066e-17	0.003271	1	0
ADAM15	8751	broad.mit.edu	37	1	155032387	155032387	+	Missense_Mutation	SNP	A	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:155032387A>T	uc001fgr.1	+	17	2106	c.2005A>T	c.(2005-2007)AGC>TGC	p.S669C	ADAM15_uc001fgq.1_Missense_Mutation_p.S354C|ADAM15_uc010peu.1_Missense_Mutation_p.S686C|ADAM15_uc001fgt.1_Missense_Mutation_p.S669C|ADAM15_uc010pev.1_Missense_Mutation_p.S679C|ADAM15_uc001fgs.1_Missense_Mutation_p.S669C|ADAM15_uc001fgu.1_Missense_Mutation_p.S669C|ADAM15_uc001fgw.1_Missense_Mutation_p.S669C|ADAM15_uc001fgv.1_Missense_Mutation_p.S669C|ADAM15_uc001fgx.1_Missense_Mutation_p.S669C|ADAM15_uc001fgz.1_RNA|ADAM15_uc001fgy.1_RNA|ADAM15_uc001fha.1_RNA|ADAM15_uc001fhb.1_5'UTR	NM_207197	NP_997080	Q13444	ADA15_HUMAN	a disintegrin and metalloproteinase domain 15	669	EGF-like.|Extracellular (Potential).				angiogenesis|cell-matrix adhesion|collagen catabolic process|proteolysis	acrosomal vesicle|adherens junction|endomembrane system|flagellum|integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			central_nervous_system(3)|skin(2)|ovary(1)	6	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			GGTCTGTGACAGCAACAGGCA	0.557													150	216					0	0	0.014410	0	0
ASH1L	55870	broad.mit.edu	37	1	155408153	155408153	+	Silent	SNP	T	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:155408153T>A	uc009wqq.2	-	5	6273	c.5793A>T	c.(5791-5793)CCA>CCT	p.P1931P	ASH1L_uc001fkt.2_Silent_p.P1931P	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	1931					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			CCTCTGGTAATGGCTTCTGCT	0.363													65	113					0	0	0.014410	0	0
MSTO2P	100129405	broad.mit.edu	37	1	155719118	155719118	+	RNA	SNP	C	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:155719118C>G	uc010pgp.1	+	11		c.1204C>G				NR_024117				Homo sapiens SLTP005 (LST005) mRNA, complete cds.												0						GTTATGGCAGCCAGCTCACCC	0.398													4	16					0	0	0.004007	0	0
ISG20L2	81875	broad.mit.edu	37	1	156693972	156693972	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:156693972G>A	uc001fps.1	-	2	1177	c.916C>T	c.(916-918)CTC>TTC	p.L306F	ISG20L2_uc001fpt.1_Missense_Mutation_p.L306F	NM_030980	NP_112242	Q9H9L3	I20L2_HUMAN	interferon stimulated exonuclease gene	306	Exonuclease.				ribosome biogenesis	nucleolus	exonuclease activity|nucleic acid binding|protein binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTCTTGGTGAGATGCTTCAGA	0.587													16	178					0	0	0.004990	0	0
FCRL4	83417	broad.mit.edu	37	1	157557285	157557285	+	Silent	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:157557285G>A	uc001fqw.2	-	5	764	c.628C>T	c.(628-630)CTG>TTG	p.L210L	FCRL4_uc010phy.1_RNA	NM_031282	NP_112572	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4 precursor	210	Ig-like C2-type 3.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(2)|kidney(1)|skin(1)	4	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				TCACAGCTCAGGTTTACAGAA	0.493													6	334					0	0	0.001168	0	0
IGSF9	57549	broad.mit.edu	37	1	159898194	159898194	+	Missense_Mutation	SNP	G	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:159898194G>T	uc001fur.2	-	19	3182	c.2984C>A	c.(2983-2985)CCT>CAT	p.P995H	IGSF9_uc001fuq.2_Missense_Mutation_p.P979H|CCDC19_uc001ful.2_5'Flank|TAGLN2_uc001fun.1_5'Flank|TAGLN2_uc001fuo.1_5'Flank|TAGLN2_uc010piy.1_5'Flank|IGSF9_uc001fup.2_Missense_Mutation_p.P141H	NM_001135050	NP_001128522	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9 isoform a	995	Cytoplasmic (Potential).					cell junction|integral to membrane|synapse				ovary(2)|central_nervous_system(2)|large_intestine(1)	5	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			GGCTGTGTAAGGGGGCTCTGC	0.647													6	4					0.00198382	0.00210405	0.001984	1	0
PROX1	5629	broad.mit.edu	37	1	214178606	214178606	+	Silent	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:214178606C>T	uc001hkh.2	+	3	2096	c.1824C>T	c.(1822-1824)TCC>TCT	p.S608S		NM_002763	NP_002754	Q92786	PROX1_HUMAN	prospero homeobox 1	608	Prospero-type homeobox.				aorta smooth muscle tissue morphogenesis|atrial cardiac muscle tissue morphogenesis|brain development|dorsal spinal cord development|embryonic retina morphogenesis in camera-type eye|endocardium formation|hepatocyte differentiation|kidney development|lens fiber cell morphogenesis|lung development|lymphangiogenesis|negative regulation of bile acid biosynthetic process|negative regulation of cell proliferation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of viral genome replication|neural tube development|olfactory placode formation|optic placode formation involved in camera-type eye formation|otic placode formation|pancreas development|positive regulation of cyclin-dependent protein kinase activity|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of heart growth|positive regulation of S phase of mitotic cell cycle|positive regulation of sarcomere organization|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment|skeletal muscle thin filament assembly|venous blood vessel morphogenesis|ventricular cardiac muscle tissue morphogenesis|ventricular cardiac myofibril development|ventricular septum morphogenesis	cytoplasm|nucleus	DBD domain binding|LBD domain binding|ligand-dependent nuclear receptor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding			ovary(3)|lung(1)|central_nervous_system(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		CCTACTTCTCCGACGTAAAGG	0.378													28	51					0	0	0.004656	0	0
BPNT1	10380	broad.mit.edu	37	1	220232235	220232235	+	Missense_Mutation	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:220232235T>C	uc001hma.2	-	9	1050	c.878A>G	c.(877-879)TAC>TGC	p.Y293C	BPNT1_uc010pug.1_Missense_Mutation_p.Y238C|BPNT1_uc010puh.1_Missense_Mutation_p.Y257C|BPNT1_uc001hmb.3_Intron	NM_006085	NP_006076	O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1	293					3'-phosphoadenosine 5'-phosphosulfate metabolic process|nervous system development|xenobiotic metabolic process	cytosol	3'(2'),5'-bisphosphate nucleotidase activity			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0558)		GCTTGCATAGTAGTCATAATT	0.338													48	145					0	0	0.014410	0	0
LBR	3930	broad.mit.edu	37	1	225611758	225611758	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:225611758G>A	uc001hoy.2	-	2	163	c.20C>T	c.(19-21)GCC>GTC	p.A7V	LBR_uc001hoz.2_Missense_Mutation_p.A7V|LBR_uc001hpa.1_Missense_Mutation_p.A7V	NM_002296	NP_002287	Q14739	LBR_HUMAN	lamin B receptor	7	Nucleoplasmic (Potential).				cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		TTCACCATCGGCAAATTTCCT	0.373													6	556					0	0	0.003080	0	0
ZNF503	84858	broad.mit.edu	37	10	77159027	77159027	+	Missense_Mutation	SNP	G	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr10:77159027G>T	uc001jxg.2	-	2	1757	c.1421C>A	c.(1420-1422)CCG>CAG	p.P474Q	C10orf41_uc010qlf.1_5'Flank	NM_032772	NP_116161	Q96F45	ZN503_HUMAN	zinc finger protein 503	474	Ala-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1	all_cancers(46;0.105)|all_epithelial(25;0.00449)|Prostate(51;0.0112)|Ovarian(15;0.088)					ACCGTGCAGCGGGTGCGTGGG	0.721													22	7					4.7796e-09	5.18717e-09	0.004656	1	0
KIF20B	9585	broad.mit.edu	37	10	91470809	91470809	+	Silent	SNP	A	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr10:91470809A>G	uc001kgs.1	+	6	654	c.582A>G	c.(580-582)AAA>AAG	p.K194K	KIF20B_uc001kgr.1_Silent_p.K194K	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1	194	Kinesin-motor.				cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3						TGAACCTTAAACCACATAGAT	0.353													3	98					0	0	0.004672	0	0
ADD3	120	broad.mit.edu	37	10	111860425	111860425	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr10:111860425C>T	uc001kyt.3	+	3	328	c.14C>T	c.(13-15)GCC>GTC	p.A5V	ADD3_uc001kys.3_Missense_Mutation_p.A5V|ADD3_uc001kyu.2_Missense_Mutation_p.A5V|ADD3_uc001kyv.2_Missense_Mutation_p.A5V|ADD3_uc001kyw.2_Missense_Mutation_p.A5V	NM_016824	NP_058432	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma) isoform a	5						cytoskeleton	actin binding|calmodulin binding|metal ion binding|structural constituent of cytoskeleton			ovary(2)|skin(2)|large_intestine(1)	5		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		AGCTCAGATGCCAGCCAAGGC	0.388													3	51					0	0	0.009096	0	0
KNDC1	85442	broad.mit.edu	37	10	135009191	135009191	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr10:135009191G>A	uc001llz.1	+	10	1601	c.1600G>A	c.(1600-1602)GTT>ATT	p.V534I	KNDC1_uc001lma.1_Missense_Mutation_p.V469I|KNDC1_uc001lmb.1_5'Flank	NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)	534	KIND 2.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		TGTGGCCGCCGTTCTGTGGAC	0.667													12	21					0	0	0.008871	0	0
FRG2B	441581	broad.mit.edu	37	10	135440204	135440205	+	Missense_Mutation	DNP	TG	CA	CA			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr10:135440204_135440205TG>CA	uc010qvg.1	-	1	95_96	c.42_43CA>TG	c.(40-45)TCCATC>TCTGTC	p.I15V		NM_001080998	NP_001074467	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	15						nucleus					0		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		GAGCACTGGATGGAGGAGCAGT	0.505													94	333					0	0	0.004672	0	0
OR10A5	144124	broad.mit.edu	37	11	6867579	6867579	+	Missense_Mutation	SNP	T	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr11:6867579T>G	uc001met.1	+	1	666	c.666T>G	c.(664-666)ATT>ATG	p.I222M		NM_178168	NP_835462	Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A,	222	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		ATACTCGCATTGCTGCTGCTA	0.473													6	226					0	0	0.001984	0	0
OR5P2	120065	broad.mit.edu	37	11	7817940	7817940	+	Missense_Mutation	SNP	A	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr11:7817940A>T	uc001mfp.1	-	1	550	c.550T>A	c.(550-552)TCC>ACC	p.S184T		NM_153444	NP_703145	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P,	184	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TCAGAACAGGAGAGTTCAAGT	0.398													30	48					0	0	0.007291	0	0
CCDC67	159989	broad.mit.edu	37	11	93090210	93090210	+	Splice_Site	SNP	G	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr11:93090210G>T	uc001pdq.2	+	4	397	c.297_splice	c.e4+1	p.Q99_splice	CCDC67_uc001pdo.1_Splice_Site_p.Q99_splice|CCDC67_uc001pdp.2_Splice_Site_p.Q99_splice	NM_181645	NP_857596	Q05D60	CCD67_HUMAN	coiled-coil domain containing 67											ovary(1)	1		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				AAAGGCTCAAGTAAGAAAACT	0.299													2	4					6.4e-05	6.83969e-05	0.004672	1	0
GLB1L3	112937	broad.mit.edu	37	11	134147793	134147793	+	Missense_Mutation	SNP	A	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr11:134147793A>C	uc009zdf.2	+	3	709	c.349A>C	c.(349-351)AAT>CAT	p.N117H	GLB1L3_uc010scs.1_Missense_Mutation_p.N117H|GLB1L3_uc010sct.1_5'UTR	NM_001080407	NP_001073876	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1 like 3	117					carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		CTGTGGCTTCAATACTGTCAC	0.612													15	22					0	0	0.012319	0	0
Unknown	0	broad.mit.edu	37	12	92000	92000	+	Missense_Mutation	SNP	A	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:92000A>T	uc010sdi.1	-	2	338	c.310T>A	c.(310-312)TTG>ATG	p.L104M	uc010sdj.1_RNA					SubName: Full=DEAD/H box polypeptide 11 like 11;																		GGTCCTGGCAACACTCTGGAC	0.572													7	7					0	0	0.001984	0	0
LTBR	4055	broad.mit.edu	37	12	6494285	6494285	+	Silent	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:6494285C>T	uc001qny.1	+	3	459	c.291C>T	c.(289-291)ATC>ATT	p.I97I	LTBR_uc010sfc.1_Silent_p.I78I|LTBR_uc001qnz.1_Silent_p.I92I	NM_002342	NP_002333	P36941	TNR3_HUMAN	lymphotoxin beta receptor precursor	97	Extracellular (Potential).|TNFR-Cys 2.				apoptosis|cellular response to mechanical stimulus|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	protein binding|receptor activity			lung(2)	2						ACCTGACCATCTGCCAGCTGT	0.617													209	139					0	0	0.014410	0	0
TAS2R10	50839	broad.mit.edu	37	12	10978002	10978002	+	Silent	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:10978002C>T	uc001qyy.1	-	1	867	c.867G>A	c.(865-867)TTG>TTA	p.L289L		NM_023921	NP_076410	Q9NYW0	T2R10_HUMAN	taste receptor, type 2, member 10	289	Cytoplasmic (Potential).				sensory perception of taste	integral to membrane	taste receptor activity				0						GCAGTACCCTCAAAGAGGCTT	0.438													3	35					0	0	0.004672	0	0
TM7SF3	51768	broad.mit.edu	37	12	27156249	27156249	+	Missense_Mutation	SNP	G	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:27156249G>T	uc010sjl.1	-	2	404	c.166C>A	c.(166-168)CAT>AAT	p.H56N		NM_016551	NP_057635	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3 precursor	56						integral to membrane|plasma membrane				upper_aerodigestive_tract(2)	2	Colorectal(261;0.0847)					GAAATATCATGCAAAATAGCT	0.343													21	39					7.45023e-12	8.21285e-12	0.010504	1	0
DENND5B	160518	broad.mit.edu	37	12	31633182	31633182	+	Missense_Mutation	SNP	A	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:31633182A>G	uc001rki.1	-	3	431	c.245T>C	c.(244-246)ATG>ACG	p.M82T	DENND5B_uc001rkh.1_Missense_Mutation_p.M117T|DENND5B_uc009zjq.1_Missense_Mutation_p.M1T|DENND5B_uc001rkj.2_Missense_Mutation_p.M104T|DENND5B_uc001rkk.1_Missense_Mutation_p.M4T	NM_144973	NP_659410	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	82	UDENN.					integral to membrane				ovary(1)|central_nervous_system(1)	2						CCCTTTAGGCATGCACAACTG	0.353													2	4					0	0	0.004672	0	0
TIMELESS	8914	broad.mit.edu	37	12	56822670	56822670	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:56822670C>T	uc001slf.2	-	11	1469	c.1301G>A	c.(1300-1302)CGC>CAC	p.R434H	TIMELESS_uc001slg.2_Missense_Mutation_p.R433H	NM_003920	NP_003911	Q9UNS1	TIM_HUMAN	timeless homolog	434					cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin				ovary(5)|breast(2)|pancreas(1)	8						CACTCACCGGCGTGCCCAGGA	0.517													29	71					0	0	0.007291	0	0
GRIP1	23426	broad.mit.edu	37	12	66765685	66765685	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:66765685G>A	uc001stk.2	-	22	2886	c.2645C>T	c.(2644-2646)ACG>ATG	p.T882M	GRIP1_uc010sta.1_Missense_Mutation_p.T826M|GRIP1_uc001stj.2_Missense_Mutation_p.T649M|GRIP1_uc001stl.1_Missense_Mutation_p.T759M|GRIP1_uc001stm.2_Missense_Mutation_p.T867M	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	934					androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		CAAACTCATCGTGCTCCCCGA	0.512													45	118					0	0	0.011902	0	0
POLR3B	55703	broad.mit.edu	37	12	106820975	106820975	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:106820975C>T	uc001tlp.2	+	13	1324	c.1102C>T	c.(1102-1104)CTT>TTT	p.L368F	POLR3B_uc001tlq.2_Missense_Mutation_p.L310F	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	DNA-directed RNA polymerase III B isoform 1	368					innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2						TTTTTTTTAGCTTTTATCTCT	0.274													4	9					0	0	0.001168	0	0
SSH1	54434	broad.mit.edu	37	12	109182194	109182194	+	Missense_Mutation	SNP	T	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr12:109182194T>A	uc001tnm.2	-	15	2807	c.2720A>T	c.(2719-2721)CAC>CTC	p.H907L	SSH1_uc001tnl.2_Missense_Mutation_p.H595L	NM_018984	NP_061857	Q8WYL5	SSH1_HUMAN	slingshot 1 isoform 1	907	Interaction with YWHAG.				actin cytoskeleton organization|cell morphogenesis|cellular response to ATP|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of cellular protein metabolic process|regulation of lamellipodium assembly	cleavage furrow|cytoplasm|cytoskeleton|lamellipodium|midbody|plasma membrane	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(4)	4						ACTACTGGTGTGGTCCAGGCG	0.587													121	57					0	0	0.014410	0	0
KIAA0586	9786	broad.mit.edu	37	14	58949256	58949256	+	Silent	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr14:58949256C>T	uc001xdv.3	+	20	3015	c.2742C>T	c.(2740-2742)CTC>CTT	p.L914L	KIAA0586_uc010trr.1_Silent_p.L1031L|KIAA0586_uc001xdt.3_Silent_p.L946L|KIAA0586_uc001xdu.3_Silent_p.L975L|KIAA0586_uc010trs.1_Silent_p.L905L|KIAA0586_uc010trt.1_Silent_p.L850L|KIAA0586_uc010tru.1_Silent_p.L850L	NM_014749	NP_055564	E9PGW8	E9PGW8_HUMAN	talpid3 protein	914										ovary(1)	1						GTGGCGCCCTCCAGCTTTTTG	0.378													25	26					0	0	0.003330	0	0
ZFP36L1	677	broad.mit.edu	37	14	69256762	69256762	+	Missense_Mutation	SNP	A	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr14:69256762A>G	uc001xkh.1	-	2	635	c.505T>C	c.(505-507)TAC>CAC	p.Y169H	ZFP36L1_uc001xki.1_Missense_Mutation_p.Y169H	NM_004926	NP_004917	Q07352	TISB_HUMAN	butyrate response factor 1	169	C3H1-type 2.				regulation of mRNA stability	cytosol|nucleus	DNA binding|mRNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		CGGGGCCCGTAGGGGCAAAAG	0.677											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	17	29					0	0	0.003271	0	0
TRIP11	9321	broad.mit.edu	37	14	92491671	92491671	+	Missense_Mutation	SNP	G	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr14:92491671G>C	uc001xzy.2	-	3	1083	c.295C>G	c.(295-297)CAA>GAA	p.Q99E		NM_004239	NP_004230	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	99	Potential.				transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)		TGTTGAAGTTGATTTCGGTAA	0.308			T	PDGFRB	AML								25	24					0	0	0.003330	0	0
USP3	9960	broad.mit.edu	37	15	63882867	63882867	+	Missense_Mutation	SNP	T	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr15:63882867T>G	uc002amf.2	+	15	1534	c.1405T>G	c.(1405-1407)TCT>GCT	p.S469A	USP3_uc002amg.2_Missense_Mutation_p.S384A|USP3_uc002amh.2_Missense_Mutation_p.S447A|USP3_uc010uij.1_Missense_Mutation_p.S425A|USP3_uc010uik.1_Missense_Mutation_p.S220A|USP3_uc010bgs.2_Missense_Mutation_p.S452A|USP3_uc002ami.2_Missense_Mutation_p.S300A|uc002amj.2_Intron|uc002amk.2_Intron|uc002aml.2_Intron	NM_006537	NP_006528	Q9Y6I4	UBP3_HUMAN	ubiquitin thiolesterase 3	469					DNA repair|histone deubiquitination|mitotic cell cycle|regulation of protein stability|ubiquitin-dependent protein catabolic process	nuclear chromatin	histone binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(80;0.0187)		CAGGGTTGGTTCTGGACATTA	0.403													70	111					0	0	0.014410	0	0
DENND4A	10260	broad.mit.edu	37	15	66021476	66021476	+	Missense_Mutation	SNP	T	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr15:66021476T>G	uc002aph.2	-	11	1799	c.1421A>C	c.(1420-1422)TAC>TCC	p.Y474S	DENND4A_uc002api.2_Missense_Mutation_p.Y474S|DENND4A_uc002apj.3_Missense_Mutation_p.Y474S|DENND4A_uc010ujj.1_Missense_Mutation_p.Y474S	NM_005848	NP_005839	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A isoform 2	474	DENN.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						GAGATCAAAGTATCTTGAATC	0.413													2	6					0	0	0.004672	0	0
CRTC3	64784	broad.mit.edu	37	15	91161146	91161146	+	Missense_Mutation	SNP	G	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr15:91161146G>C	uc002bpp.2	+	8	751	c.645G>C	c.(643-645)GAG>GAC	p.E215D	CRTC3_uc002bpo.2_Missense_Mutation_p.E215D	NM_022769	NP_073606	Q6UUV7	CRTC3_HUMAN	transducer of regulated CREB protein 3 isoform	215					interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus			CRTC3/MAML2(26)	salivary_gland(26)|ovary(1)	27	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)			TGAAAGAAGAGAATCTGTTAA	0.403			T	MAML2	salivary gland mucoepidermoid								36	52					0	0	0.005524	0	0
CACNA1H	8912	broad.mit.edu	37	16	1263882	1263882	+	Missense_Mutation	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr16:1263882T>C	uc002cks.2	+	27	5128	c.4880T>C	c.(4879-4881)ATC>ACC	p.I1627T	CACNA1H_uc002ckt.2_Missense_Mutation_p.I1621T|CACNA1H_uc002cku.2_Missense_Mutation_p.I333T|CACNA1H_uc010brj.2_Missense_Mutation_p.I338T|CACNA1H_uc002ckv.2_Missense_Mutation_p.I327T	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	1627	Helical; Name=S1 of repeat IV; (Potential).|IV.				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)	ACCTTCATCATCTGTGTCAAC	0.637													19	11					0	0	0.008871	0	0
SRCAP	10847	broad.mit.edu	37	16	30736125	30736125	+	Missense_Mutation	SNP	C	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr16:30736125C>G	uc002dze.1	+	25	5765	c.5380C>G	c.(5380-5382)CCA>GCA	p.P1794A	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Missense_Mutation_p.P1589A|SRCAP_uc010bzz.1_Missense_Mutation_p.P1364A	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	1794	Pro-rich.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)			gagccctgccccagttcctac	0.1													26	55					0	0	0.007291	0	0
COQ9	57017	broad.mit.edu	37	16	57494525	57494525	+	Nonsense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr16:57494525C>T	uc002elq.2	+	9	962	c.946C>T	c.(946-948)CAG>TAG	p.Q316*	COQ9_uc002elr.2_Nonsense_Mutation_p.Q281*|COQ9_uc002els.2_Nonsense_Mutation_p.Q109*|POLR2C_uc010vhq.1_5'Flank|POLR2C_uc002elt.1_5'Flank	NM_020312	NP_064708	O75208	COQ9_HUMAN	coenzyme Q9 homolog precursor	316					ubiquinone biosynthetic process	mitochondrion				breast(1)	1						AGGTCTAAACCAGCGTCGGTG	0.438													16	87					0	0	0.007413	0	0
MMP15	4324	broad.mit.edu	37	16	58073792	58073792	+	Missense_Mutation	SNP	A	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr16:58073792A>G	uc002ena.2	+	4	1427	c.454A>G	c.(454-456)ACG>GCG	p.T152A		NM_002428	NP_002419	P51511	MMP15_HUMAN	matrix metalloproteinase 15 preproprotein	152	Extracellular (Potential).				protein modification process|proteolysis	extracellular matrix|integral to plasma membrane	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|protein binding|zinc ion binding			central_nervous_system(2)|breast(1)	3						CCAGAACTACACGGAGAAGTT	0.632													3	111					0	0	0.009096	0	0
NEK8	284086	broad.mit.edu	37	17	27067537	27067537	+	Missense_Mutation	SNP	C	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:27067537C>G	uc002hcp.2	+	11	1474	c.1474C>G	c.(1474-1476)CCC>GCC	p.P492A		NM_178170	NP_835464	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	492	RCC1 3.					cytoplasm|primary cilium	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|pancreas(1)|liver(1)|skin(1)	6	Lung NSC(42;0.0158)					GGTGCCCATGCCCCCAGGACA	0.567													74	198					0	0	0.014410	0	0
CACNB1	782	broad.mit.edu	37	17	37331566	37331566	+	Silent	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:37331566C>T	uc002hrm.1	-	14	1830	c.1677G>A	c.(1675-1677)CTG>CTA	p.L559L	CACNB1_uc002hrl.1_Silent_p.L331L	NM_000723	NP_000714	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1	559				L -> M (in Ref. 3; AAA36167).	axon guidance	voltage-gated calcium channel complex				large_intestine(1)|ovary(1)	2					Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Verapamil(DB00661)	GGTTGTCGGTCAGCTCTTCCT	0.662											OREG0024371	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	227	492					0	0	0.014410	0	0
CDC6	990	broad.mit.edu	37	17	38447499	38447499	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:38447499C>T	uc002huj.1	+	3	578	c.368C>T	c.(367-369)TCA>TTA	p.S123L		NM_001254	NP_001245	Q99741	CDC6_HUMAN	cell division cycle 6 protein	123					cell division|DNA replication|DNA replication checkpoint|M/G1 transition of mitotic cell cycle|mitosis|negative regulation of cell proliferation|negative regulation of DNA replication|positive regulation of cell cycle cytokinesis|positive regulation of chromosome segregation|regulation of cyclin-dependent protein kinase activity|regulation of mitotic anaphase|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm|spindle midzone|spindle pole	ATP binding|kinase binding|nucleoside-triphosphatase activity			ovary(2)|breast(1)	3						ATACTTTCTTCAGTTAGAAAA	0.373													102	71					0	0	0.014410	0	0
KCNJ2	3759	broad.mit.edu	37	17	68171425	68171425	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:68171425G>A	uc010dfg.2	+	2	646	c.245G>A	c.(244-246)CGG>CAG	p.R82Q	KCNJ2_uc002jir.2_Missense_Mutation_p.R82Q	NM_000891	NP_000882	P63252	IRK2_HUMAN	potassium inwardly-rectifying channel J2	82	Helical; Name=M1; (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity|protein binding				0	Breast(10;1.64e-08)					ATTCGCTGGCGGTGGATGCTG	0.512													73	144					0	0	0.014410	0	0
RAB37	326624	broad.mit.edu	37	17	72736931	72736931	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:72736931G>A	uc002jlk.2	+	2	174	c.118G>A	c.(118-120)GTC>ATC	p.V40I	RAB37_uc002jlc.2_Intron|RAB37_uc010dfu.2_Intron|RAB37_uc002jld.2_Intron|RAB37_uc010wrb.1_Missense_Mutation_p.V8I|RAB37_uc010wrc.1_Missense_Mutation_p.V45I|RAB37_uc010wrd.1_Intron|RAB37_uc010wre.1_Intron|RAB37_uc002jll.3_RNA	NM_001006638	NP_001006639	Q96AX2	RAB37_HUMAN	RAB37, member RAS oncogene family isoform 2	40	GTP (By similarity).				protein transport|small GTPase mediated signal transduction	ER-Golgi intermediate compartment	GTP binding			ovary(1)	1						AGACACAGGCGTCGGCAAAAC	0.567													25	384					0	0	0.008361	0	0
ACOX1	51	broad.mit.edu	37	17	73945931	73945931	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:73945931C>T	uc002jqf.2	-	10	1636	c.1346G>A	c.(1345-1347)TGT>TAT	p.C449Y	ACOX1_uc010wsq.1_Missense_Mutation_p.C411Y|ACOX1_uc002jqe.2_Missense_Mutation_p.C449Y|ACOX1_uc010wsr.1_Missense_Mutation_p.C381Y	NM_007292	NP_009223	Q15067	ACOX1_HUMAN	acyl-Coenzyme A oxidase 1 isoform b	449				C -> R (in Ref. 2; AAA18595).	fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|prostaglandin metabolic process|very long-chain fatty acid metabolic process	peroxisomal matrix	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity|flavin adenine dinucleotide binding|protein N-terminus binding			ovary(1)	1						CACCATGCCACACACCAACTT	0.453													90	71					0	0	0.014410	0	0
FAM59A	64762	broad.mit.edu	37	18	29867890	29867890	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr18:29867890G>A	uc002kxl.2	-	4	726	c.670C>T	c.(670-672)CCC>TCC	p.P224S	FAM59A_uc002kxk.1_Missense_Mutation_p.P224S	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A	224	CABIT.									ovary(1)|skin(1)	2						AGTTCCAGGGGACTTCGGGTG	0.522													49	78					0	0	0.014410	0	0
HMSD	284293	broad.mit.edu	37	18	61621714	61621714	+	Missense_Mutation	SNP	A	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr18:61621714A>G	uc010dqj.2	+	3	294	c.145A>G	c.(145-147)ATT>GTT	p.I49V		NM_001123366	NP_001116838	A8MTL9	HMSD_HUMAN	histocompatibility (minor) serpin domain	49						extracellular region	serine-type endopeptidase inhibitor activity				0						TCTTGTTGCAATTAACAGAAC	0.348													13	123					0	0	0.013537	0	0
COL5A3	50509	broad.mit.edu	37	19	10096525	10096525	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:10096525C>T	uc002mmq.1	-	31	2485	c.2399G>A	c.(2398-2400)GGA>GAA	p.G800E		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	800	Triple-helical region.				collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)			TACCTTAGGTCCAGGGCGTCC	0.582													205	183					0	0	0.014410	0	0
SMARCA4	6597	broad.mit.edu	37	19	11141551	11141551	+	Missense_Mutation	SNP	C	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:11141551C>G	uc002mqf.3	+	25	3812	c.3528C>G	c.(3526-3528)AGC>AGG	p.S1176R	SMARCA4_uc010dxp.2_Missense_Mutation_p.S1176R|SMARCA4_uc010dxo.2_Missense_Mutation_p.S1176R|SMARCA4_uc002mqg.1_Missense_Mutation_p.S1176R|SMARCA4_uc010dxq.2_Missense_Mutation_p.S1176R|SMARCA4_uc010dxr.2_Missense_Mutation_p.S1176R|SMARCA4_uc002mqj.3_Missense_Mutation_p.S1176R|SMARCA4_uc010dxs.2_Missense_Mutation_p.S1176R|SMARCA4_uc010dxt.1_Missense_Mutation_p.S396R|SMARCA4_uc002mqh.3_Missense_Mutation_p.S299R|SMARCA4_uc002mqi.1_Missense_Mutation_p.S379R	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	1176	Helicase C-terminal.				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.S1176C(1)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TTTTTGACAGCGACTGGAATC	0.622			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				15	11					0	0	0.004990	0	0
ZNF99	7652	broad.mit.edu	37	19	22940093	22940093	+	Silent	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:22940093G>A	uc010xrh.1	-	6	2238	c.2238C>T	c.(2236-2238)TAC>TAT	p.Y746Y		NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				CTTCACATTTGTAGGGTTTCT	0.353													3	31					0	0	0.004672	0	0
LOC100101266	100101266	broad.mit.edu	37	19	24345885	24345885	+	RNA	SNP	T	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:24345885T>A	uc010edb.1	-	1		c.365A>T				NR_003603				Homo sapiens hepatitis A virus cellular receptor 1 pseudogene (LOC100101266), non-coding RNA.												0						GATAGAGTGATTTTCATGTCA	0.453													22	32					0	0	0.014323	0	0
PLEKHG2	64857	broad.mit.edu	37	19	39915323	39915323	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:39915323C>T	uc010xuz.1	+	19	3875	c.3550C>T	c.(3550-3552)CCA>TCA	p.P1184S	PLEKHG2_uc010xuy.1_Missense_Mutation_p.P1125S|PLEKHG2_uc002olj.2_Intron|PLEKHG2_uc010xva.1_Missense_Mutation_p.P962S	NM_022835	NP_073746	Q9H7P9	PKHG2_HUMAN	common-site lymphoma/leukemia guanine nucleotide	1184	Pro-rich.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			skin(2)|pancreas(1)|breast(1)	4	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;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			ACTTCCGGAGCCAAGCCTTAC	0.562													107	142					0	0	0.014410	0	0
MEGF8	1954	broad.mit.edu	37	19	42872696	42872696	+	Silent	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:42872696T>C	uc002otl.3	+	35	6797	c.6162T>C	c.(6160-6162)TGT>TGC	p.C2054C	MEGF8_uc002otm.3_Silent_p.C1662C|MEGF8_uc002otn.3_5'Flank	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2121	Extracellular (Potential).|PSI 7.					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)				CCCTGGGCTGTGCTCAGGCAA	0.697													10	13					0	0	0.010729	0	0
KCNC3	3748	broad.mit.edu	37	19	50832052	50832052	+	Silent	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:50832052G>A	uc002pru.1	-	1	583	c.288C>T	c.(286-288)GGC>GGT	p.G96G	NR1H2_uc002prv.3_5'Flank	NM_004977	NP_004968	Q14003	KCNC3_HUMAN	Shaw-related voltage-gated potassium channel	96	Cytoplasmic (Potential).				cell death	voltage-gated potassium channel complex	voltage-gated potassium channel activity			pancreas(1)	1		all_neural(266;0.057)|Ovarian(192;0.208)		OV - Ovarian serous cystadenocarcinoma(262;0.00283)|GBM - Glioblastoma multiforme(134;0.0181)		CATGGCGCACGCCGCCCACGT	0.512													4	6					0	0	0.009096	0	0
LENG8	114823	broad.mit.edu	37	19	54963393	54963393	+	Silent	SNP	T	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:54963393T>G	uc002qfv.1	+	3	306	c.162T>G	c.(160-162)GCT>GCG	p.A54A	LENG8_uc002qfw.2_Silent_p.A54A			Q96PV6	LENG8_HUMAN	RecName: Full=Leukocyte receptor cluster member 8;	54							protein binding			central_nervous_system(1)|pancreas(1)	2	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		AGTCAGGAGCTGCCGGCGGCT	0.657													35	40					0	0	0.007835	0	0
PPP1R12C	54776	broad.mit.edu	37	19	55603617	55603617	+	Silent	SNP	G	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:55603617G>C	uc002qix.2	-	19	2149	c.2133C>G	c.(2131-2133)CTC>CTG	p.L711L	PPP1R12C_uc010yfs.1_Silent_p.L636L|PPP1R12C_uc002qiy.2_Silent_p.L709L	NM_017607	NP_060077	Q9BZL4	PP12C_HUMAN	protein phosphatase 1, regulatory subunit 12C	711	Potential.					cytoplasm				ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		GCTCCACCTTGAGCTGCGCCA	0.692													4	12					0	0	0.000602	0	0
NLRP5	126206	broad.mit.edu	37	19	56544099	56544099	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:56544099C>T	uc002qmj.2	+	8	2399	c.2399C>T	c.(2398-2400)ACC>ATC	p.T800I	NLRP5_uc002qmi.2_Missense_Mutation_p.T781I	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	800	LRR 3.					mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		GCCATGAAGACCCTGTGTGCC	0.607													49	81					0	0	0.014410	0	0
PRKCE	5581	broad.mit.edu	37	2	46372319	46372319	+	Silent	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:46372319T>C	uc002rut.2	+	12	1877	c.1680T>C	c.(1678-1680)AAT>AAC	p.N560N		NM_005400	NP_005391	Q02156	KPCE_HUMAN	protein kinase C, epsilon	560	Protein kinase.				activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)			GGATTCTGAATGGTGTGACGA	0.537													103	137					0	0	0.014410	0	0
DCTN1	1639	broad.mit.edu	37	2	74589259	74589259	+	Missense_Mutation	SNP	G	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:74589259G>C	uc002skx.2	-	31	3930	c.3619C>G	c.(3619-3621)CTC>GTC	p.L1207V	SLC4A5_uc002skl.2_RNA|DCTN1_uc002skt.1_Missense_Mutation_p.L141V|DCTN1_uc002skv.2_Missense_Mutation_p.L1073V|DCTN1_uc002sku.2_Missense_Mutation_p.L1068V|DCTN1_uc002skw.1_Missense_Mutation_p.L1183V|DCTN1_uc010ffd.2_Missense_Mutation_p.L1182V|DCTN1_uc002sky.2_Missense_Mutation_p.L1165V	NM_004082	NP_004073	Q14203	DCTN1_HUMAN	dynactin 1 isoform 1	1207	Potential.				cell death|G2/M transition of mitotic cell cycle|mitosis|nervous system development	centrosome|cytosol|kinetochore|microtubule|spindle pole	motor activity|protein binding			ovary(3)|skin(2)	5						GTCTCCTTGAGGACCTCATCC	0.557													39	39					0	0	0.004878	0	0
RGPD3	653489	broad.mit.edu	37	2	107049613	107049613	+	Silent	SNP	A	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:107049613A>G	uc010ywi.1	-	16	2391	c.2334T>C	c.(2332-2334)CAT>CAC	p.H778H		NM_001144013	NP_001137485	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	778					intracellular transport		binding			ovary(1)	1						ATGGTGTAGAATGTTTTATTT	0.353													60	131					0	0	0.014410	0	0
DPP10	57628	broad.mit.edu	37	2	116598392	116598392	+	Missense_Mutation	SNP	C	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:116598392C>A	uc002tla.1	+	25	2706	c.2249C>A	c.(2248-2250)ACT>AAT	p.T750N	DPP10_uc002tlb.1_Missense_Mutation_p.T700N|DPP10_uc002tlc.1_Missense_Mutation_p.T746N|DPP10_uc002tle.2_Missense_Mutation_p.T754N|DPP10_uc002tlf.1_Missense_Mutation_p.T743N	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	750	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						GTGAATTATACTATGCAGGTA	0.358													31	35					3.80469e-20	4.29562e-20	0.009535	1	0
SMPD4	55627	broad.mit.edu	37	2	130932501	130932501	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:130932501C>T	uc002tqq.1	-	3	749	c.229G>A	c.(229-231)GAC>AAC	p.D77N	SMPD4_uc002tqp.1_5'Flank|SMPD4_uc010yzy.1_Missense_Mutation_p.D77N|SMPD4_uc010yzz.1_Intron|SMPD4_uc002tqr.1_Missense_Mutation_p.D77N|SMPD4_uc002tqs.1_5'UTR|SMPD4_uc002tqt.1_5'UTR|SMPD4_uc010zaa.1_5'UTR|SMPD4_uc010zab.1_Missense_Mutation_p.D77N|SMPD4_uc010zac.1_Intron|SMPD4_uc010zad.1_Intron	NM_017951	NP_060421	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4 isoform 2	38					sphingomyelin catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|trans-Golgi network	metal ion binding|protein binding|sphingomyelin phosphodiesterase activity|sphingomyelin phosphodiesterase D activity				0	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	GCTGGAAAGTCCTCAATGACT	0.418													16	213					0	0	0.003163	0	0
ITGB6	3694	broad.mit.edu	37	2	160982928	160982928	+	Silent	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:160982928T>C	uc002ubh.2	-	11	1861	c.1845A>G	c.(1843-1845)GAA>GAG	p.E615E	ITGB6_uc010fou.2_Silent_p.E615E|ITGB6_uc010zcq.1_Silent_p.E573E|ITGB6_uc010fov.1_Silent_p.E615E	NM_000888	NP_000879	P18564	ITB6_HUMAN	integrin, beta 6 precursor	615	Extracellular (Potential).|IV.|Cysteine-rich tandem repeats.				cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|multicellular organismal development	integrin complex	receptor activity			ovary(1)|lung(1)|skin(1)	3						TAGGACATCGTTCACAGGTTG	0.502													14	104					0	0	0.002450	0	0
HSPD1	3329	broad.mit.edu	37	2	198358118	198358118	+	Missense_Mutation	SNP	G	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:198358118G>T	uc002uui.2	-	7	936	c.799C>A	c.(799-801)CAC>AAC	p.H267N	HSPD1_uc002uuj.2_Missense_Mutation_p.H265N|HSPD1_uc010zgx.1_Missense_Mutation_p.H258N|HSPD1_uc010fsm.2_Missense_Mutation_p.H78N|HSPD1_uc002uuk.2_Missense_Mutation_p.H267N	NM_002156	NP_002147	P10809	CH60_HUMAN	chaperonin	267					'de novo' protein folding|activation of caspase activity|B cell cytokine production|B cell proliferation|chaperone-mediated protein complex assembly|interspecies interaction between organisms|isotype switching to IgG isotypes|MyD88-dependent toll-like receptor signaling pathway|negative regulation of apoptosis|positive regulation of apoptosis|positive regulation of interferon-alpha production|positive regulation of interferon-gamma production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of macrophage activation|positive regulation of T cell activation|positive regulation of T cell mediated immune response to tumor cell|protein maturation|protein refolding|protein stabilization|response to unfolded protein|T cell activation	cell surface|coated pit|coated vesicle|cytosol|early endosome|extracellular space|lipopolysaccharide receptor complex|mitochondrial inner membrane|mitochondrial matrix|stored secretory granule	ATP binding|ATPase activity|cell surface binding|chaperone binding|DNA replication origin binding|lipopolysaccharide binding|p53 binding|single-stranded DNA binding				0			Epithelial(96;0.225)			GGCTTACGGTGAGCATTGGCA	0.388													73	95					2.32582e-20	2.64727e-20	0.014410	1	0
ACADL	33	broad.mit.edu	37	2	211081149	211081149	+	Missense_Mutation	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:211081149T>C	uc002vdz.3	-	4	686	c.458A>G	c.(457-459)CAG>CGG	p.Q153R		NM_001608	NP_001599	P28330	ACADL_HUMAN	long-chain acyl-CoA dehydrogenase precursor	153					carnitine catabolic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|negative regulation of fatty acid biosynthetic process|negative regulation of fatty acid oxidation|regulation of cholesterol metabolic process|temperature homeostasis	mitochondrial matrix	long-chain-acyl-CoA dehydrogenase activity|palmitoyl-CoA oxidase activity				0		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		GTGCTTAATCTGTTCTTCTGA	0.383													19	40					0	0	0.008871	0	0
BARD1	580	broad.mit.edu	37	2	215593624	215593624	+	Missense_Mutation	SNP	T	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:215593624T>G	uc002veu.2	-	11	2245	c.2110A>C	c.(2110-2112)AGT>CGT	p.S704R	BARD1_uc010zjm.1_Silent_p.S558S	NM_000465	NP_000456	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	704	BRCT 2.				cell cycle arrest|DNA repair|negative regulation of apoptosis|negative regulation of mRNA 3'-end processing|negative regulation of protein export from nucleus|positive regulation of apoptosis|positive regulation of protein catabolic process|protein K6-linked ubiquitination|regulation of phosphorylation|tissue homeostasis	BRCA1-A complex|BRCA1-BARD1 complex|cytoplasm	kinase binding|protein heterodimerization activity|protein homodimerization activity|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GGCTTTCTACTGAGGATCTGG	0.493									Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				34	23					0	0	0.013726	0	0
STK25	10494	broad.mit.edu	37	2	242437690	242437690	+	Missense_Mutation	SNP	C	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:242437690C>A	uc002wbm.2	-	8	1263	c.992G>T	c.(991-993)AGC>ATC	p.S331I	STK25_uc002wbk.2_Missense_Mutation_p.S150I|STK25_uc002wbl.2_3'UTR|STK25_uc002wbn.2_Missense_Mutation_p.S331I|STK25_uc002wbo.2_Missense_Mutation_p.S254I|STK25_uc010zos.1_Missense_Mutation_p.S237I|STK25_uc010zot.1_Missense_Mutation_p.S257I|STK25_uc002wbp.2_Missense_Mutation_p.S331I|STK25_uc010fzo.2_Missense_Mutation_p.S254I|STK25_uc010zou.1_Missense_Mutation_p.S237I|STK25_uc010zov.1_Missense_Mutation_p.S237I	NM_006374	NP_006365	O00506	STK25_HUMAN	serine/threonine kinase 25	331					response to oxidative stress|signal transduction	Golgi apparatus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity				0		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		GTGAAGCTTGCTGTGTGGACT	0.652													9	170					1.76689e-08	1.90281e-08	0.006214	1	0
FASTKD5	60493	broad.mit.edu	37	20	3128940	3128940	+	Silent	SNP	A	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr20:3128940A>G	uc002whz.2	-	2	1088	c.777T>C	c.(775-777)CCT>CCC	p.P259P	uc002whv.1_Intron|UBOX5_uc002whw.2_Intron|UBOX5_uc002whx.2_Intron|UBOX5_uc002why.1_Intron	NM_021826	NP_068598	Q7L8L6	FAKD5_HUMAN	FAST kinase domains 5	259					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity				0						TTAAAAACCTAGGTACTTTGC	0.393													31	81					0	0	0.013726	0	0
ZHX3	23051	broad.mit.edu	37	20	39831715	39831715	+	Silent	SNP	G	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr20:39831715G>T	uc002xjs.1	-	3	2220	c.1842C>A	c.(1840-1842)ACC>ACA	p.T614T	ZHX3_uc002xjq.1_Intron|ZHX3_uc002xjr.1_Silent_p.T614T|ZHX3_uc002xjt.1_Silent_p.T614T|ZHX3_uc002xju.1_Silent_p.T614T|ZHX3_uc002xjv.1_Silent_p.T614T|ZHX3_uc002xjw.1_Silent_p.T614T|ZHX3_uc010ggg.1_Silent_p.T614T	NM_015035	NP_055850	Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	614	Homeobox 3.				negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Myeloproliferative disorder(115;0.00425)				CCTTGTATTTGGTTGGTGTGA	0.537													159	96					4.3967e-48	5.12948e-48	0.014410	1	0
DSCAM	1826	broad.mit.edu	37	21	41710196	41710196	+	Missense_Mutation	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr21:41710196T>C	uc002yyq.1	-	8	2067	c.1615A>G	c.(1615-1617)AAG>GAG	p.K539E	DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	539	Extracellular (Potential).|Ig-like C2-type 6.				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TTAGAGTTCTTGTACCATTTA	0.438													68	21					0	0	0.014410	0	0
Unknown	0	broad.mit.edu	37	22	18844766	18844766	+	RNA	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:18844766G>A	uc002zoe.2	+	4		c.2020G>A			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		CAGCCTCTGAGGGCAGCAGTG	0.557													3	14					0	0	0.004672	0	0
AIFM3	150209	broad.mit.edu	37	22	21330826	21330826	+	Silent	SNP	G	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:21330826G>C	uc002ztj.2	+	11	1247	c.1029G>C	c.(1027-1029)CTG>CTC	p.L343L	AIFM3_uc002ztk.2_Silent_p.L343L|AIFM3_uc002ztl.2_Silent_p.L349L|AIFM3_uc011ahx.1_Silent_p.L331L|AIFM3_uc002ztm.1_Silent_p.L155L|LZTR1_uc002ztn.2_5'Flank	NM_144704	NP_653305	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor,	343					activation of caspase activity by cytochrome c|cell redox homeostasis|electron transport chain|induction of apoptosis|mitochondrial depolarization|transport	endoplasmic reticulum|mitochondrial inner membrane	2 iron, 2 sulfur cluster binding|caspase activator activity|flavin adenine dinucleotide binding|metal ion binding|oxidoreductase activity|protein binding			ovary(2)|lung(2)	4	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			CCGGCTTCCTGGGTGAGAGGT	0.642													26	36					0	0	0.012213	0	0
LOC96610	96610	broad.mit.edu	37	22	23237695	23237695	+	RNA	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:23237695C>T	uc011aim.1	+	363		c.15098C>T			uc011aiw.1_Missense_Mutation_p.P156S|uc010gtu.1_RNA|uc002zws.2_Intron					Parts of antibodies, mostly variable regions.												0						AGATGGCAGCCCCGTCAAGGC	0.597													15	26					0	0	0.004990	0	0
LOC644165	644165	broad.mit.edu	37	22	25043021	25043021	+	Missense_Mutation	SNP	C	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:25043021C>G	uc011ajv.1	+	4	751	c.394C>G	c.(394-396)CGA>GGA	p.R132G	POM121L10P_uc003aaz.3_RNA|POM121L10P_uc003abc.2_RNA	NR_024494				Homo sapiens cDNA FLJ57042 complete cds, moderately similar to Breakpoint cluster region protein (EC 2.7.11.1).												0						TGGAGGAGATCGAGCGCCGAG	0.632													13	18					0	0	0.002450	0	0
EIF4ENIF1	56478	broad.mit.edu	37	22	31837941	31837941	+	Silent	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:31837941T>C	uc003akz.1	-	17	2534	c.2370A>G	c.(2368-2370)AGA>AGG	p.R790R	EIF4ENIF1_uc003akx.1_Silent_p.R445R|EIF4ENIF1_uc003aky.1_Silent_p.R470R|EIF4ENIF1_uc003ala.1_Silent_p.R790R|EIF4ENIF1_uc003alb.1_Silent_p.R616R|EIF4ENIF1_uc003akw.1_Silent_p.R280R	NM_019843	NP_062817	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E	790						nucleus	protein binding|protein transporter activity			ovary(1)	1						TGGGTGTTTTTCTCCCAGTTG	0.527													16	147					0	0	0.004990	0	0
DEPDC5	9681	broad.mit.edu	37	22	32198798	32198798	+	Missense_Mutation	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:32198798T>C	uc003als.2	+	15	1197	c.1055T>C	c.(1054-1056)CTG>CCG	p.L352P	DEPDC5_uc011als.1_Missense_Mutation_p.L352P|DEPDC5_uc011alu.1_Missense_Mutation_p.L352P|DEPDC5_uc011alv.1_RNA|DEPDC5_uc003alt.2_Missense_Mutation_p.L352P|DEPDC5_uc003alr.1_Missense_Mutation_p.L352P|DEPDC5_uc011alt.1_Missense_Mutation_p.L324P	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1	352					intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8						CTCATGATCCTGACCAAGCAG	0.512													5	184					0	0	0.000602	0	0
CELSR1	9620	broad.mit.edu	37	22	46931045	46931045	+	Missense_Mutation	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:46931045T>C	uc003bhw.1	-	1	2023	c.2023A>G	c.(2023-2025)ATC>GTC	p.I675V		NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	675	Extracellular (Potential).|Cadherin 4.				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		AGCACCGTGATGGACACGCTG	0.657													11	22					0	0	0.013537	0	0
LMF2	91289	broad.mit.edu	37	22	50941823	50941823	+	Silent	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:50941823C>T	uc003blp.2	-	14	2152	c.2121G>A	c.(2119-2121)AAG>AAA	p.K707K	LMF2_uc010hba.2_Silent_p.K529K|LMF2_uc003blo.2_Silent_p.K682K	NM_033200	NP_149977	Q9BU23	LMF2_HUMAN	lipase maturation factor 2	707						endoplasmic reticulum membrane|integral to membrane				breast(1)	1		all_cancers(38;1.31e-09)|all_epithelial(38;1.81e-08)|all_lung(38;0.000817)|Breast(42;0.00387)|Lung NSC(38;0.0124)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		AACACAGCTACTTCTTTCGCC	0.662													3	30					0	0	0.000602	0	0
BHLHE40	8553	broad.mit.edu	37	3	5024904	5024904	+	Missense_Mutation	SNP	A	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:5024904A>T	uc003bqf.2	+	5	1073	c.766A>T	c.(766-768)AGT>TGT	p.S256C	BHLHE40_uc011asw.1_Missense_Mutation_p.S116C	NM_003670	NP_003661	O14503	BHE40_HUMAN	basic helix-loop-helix family, member e40	256						Golgi apparatus|nucleolus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						CGACTTGCGCAGTGAGCAGCC	0.572													78	45					0	0	0.014410	0	0
SLC6A6	6533	broad.mit.edu	37	3	14508150	14508150	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:14508150G>A	uc010heg.2	+	14	1150	c.859G>A	c.(859-861)GAC>AAC	p.D287N	SLC6A6_uc003byq.2_Missense_Mutation_p.D287N|SLC6A6_uc003byr.2_RNA	NM_001134367	NP_001127839	P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter	287					cellular amino acid metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity|taurine:sodium symporter activity			ovary(1)	1						CCGCCTTGAGGACCCACAGGT	0.642													92	64					0	0	0.014410	0	0
BAP1	8314	broad.mit.edu	37	3	52441417	52441417	+	Silent	SNP	G	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:52441417G>C	uc003ddx.2	-	6	550	c.435C>G	c.(433-435)GCC>GCG	p.A145A	BAP1_uc010hmh.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	145					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CCACACACCTGGCATGGCTAT	0.547			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								56	137					0	0	0.014410	0	0
PDZRN3	23024	broad.mit.edu	37	3	73432828	73432828	+	Silent	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:73432828C>T	uc003dpl.1	-	10	2985	c.2889G>A	c.(2887-2889)GCG>GCA	p.A963A	PDZRN3_uc011bgh.1_Silent_p.A620A|PDZRN3_uc010hoe.1_Silent_p.A661A|PDZRN3_uc011bgf.1_Silent_p.A680A|PDZRN3_uc011bgg.1_Silent_p.A683A	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	963							ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		TCTCGCTCACCGCGTCGTCGT	0.672													64	168					0	0	0.014410	0	0
SLC2A2	6514	broad.mit.edu	37	3	170732492	170732492	+	Missense_Mutation	SNP	A	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:170732492A>G	uc003fhe.1	-	3	446	c.137T>C	c.(136-138)TTG>TCG	p.L46S	SLC2A2_uc003fhf.1_5'UTR|SLC2A2_uc011bpu.1_Intron	NM_000340	NP_000331	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose	46	Extracellular (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)			TGGAACACCCAAAACATGTCT	0.333													50	135					0	0	0.014410	0	0
EIF2B5	8893	broad.mit.edu	37	3	183861938	183861938	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:183861938G>A	uc003fmp.2	+	14	2285	c.1921G>A	c.(1921-1923)GAC>AAC	p.D641N	EIF2B5_uc003fmq.2_Missense_Mutation_p.D362N|EIF2B5_uc003fmr.2_Missense_Mutation_p.D49N	NM_003907	NP_003898	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B,	641	W2.				astrocyte development|myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|positive regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus|RNA metabolic process	cytosol|eukaryotic translation initiation factor 2B complex|nucleus	guanyl-nucleotide exchange factor activity|transferase activity|translation initiation factor activity|translation initiation factor binding			ovary(5)	5	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			GCGCGCAGCCGACCATTTGGA	0.473													115	331					0	0	0.014410	0	0
MUC4	4585	broad.mit.edu	37	3	195505813	195505814	+	Missense_Mutation	DNP	TC	CT	CT			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr3:195505813_195505814TC>CT	uc011bto.1	-	3	12713_12714	c.12253_12254GA>AG	c.(12253-12255)GAC>AGC	p.D4085S	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGTGTCGGTGACAGGA	0.594													4	17					0	0	0.004672	0	0
CD180	4064	broad.mit.edu	37	5	66479676	66479676	+	Missense_Mutation	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr5:66479676T>C	uc003juy.2	-	3	1143	c.995A>G	c.(994-996)CAT>CGT	p.H332R		NM_005582	NP_005573	Q99467	CD180_HUMAN	CD180 molecule precursor	332	Extracellular (Potential).|LRR 10.				inflammatory response|innate immune response	integral to membrane|plasma membrane	receptor activity			ovary(1)	1		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		TTGATCGAAATGATTTACACT	0.448													75	106					0	0	0.014410	0	0
PCDHB1	29930	broad.mit.edu	37	5	140433403	140433403	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr5:140433403C>T	uc003lik.1	+	1	2425	c.2348C>T	c.(2347-2349)GCC>GTC	p.A783V		NM_013340	NP_037472	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1 precursor	783	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTCCCTCATGCCACTGGGGAG	0.473													4	131					0	0	0.009096	0	0
SLC6A7	6534	broad.mit.edu	37	5	149580661	149580661	+	Missense_Mutation	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr5:149580661T>C	uc003lrr.2	+	6	1104	c.733T>C	c.(733-735)TTC>CTC	p.F245L		NM_014228	NP_055043	Q99884	SC6A7_HUMAN	solute carrier family 6, member 7	245	Helical; Name=5; (Potential).					integral to plasma membrane|membrane fraction	neurotransmitter:sodium symporter activity|proline:sodium symporter activity				0		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)	GGTGGTGTATTTCACGGCCAC	0.498													44	50					0	0	0.009718	0	0
WWC1	23286	broad.mit.edu	37	5	167836950	167836950	+	Silent	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr5:167836950G>A	uc003lzu.2	+	8	984	c.891G>A	c.(889-891)CAG>CAA	p.Q297Q	WWC1_uc003lzv.2_Silent_p.Q297Q|WWC1_uc011den.1_Silent_p.Q297Q|WWC1_uc003lzw.2_Silent_p.Q96Q	NM_015238	NP_056053	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1 isoform 3	297	Potential.				cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		GCAACAATCAGTTGGCAGAGA	0.483													69	75					0	0	0.014410	0	0
PRELID1	27166	broad.mit.edu	37	5	176733459	176733459	+	Missense_Mutation	SNP	A	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr5:176733459A>C	uc003mfx.2	+	5	700	c.548A>C	c.(547-549)AAG>ACG	p.K183T	RAB24_uc003mfu.2_5'Flank|RAB24_uc003mfv.2_5'Flank|RAB24_uc003mfw.2_5'Flank|PRELID1_uc003mfy.2_Missense_Mutation_p.K181T|MXD3_uc010jkk.2_3'UTR	NM_013237	NP_037369	Q9Y255	PRLD1_HUMAN	PRELI domain containing 1 precursor	183					immune response|multicellular organismal development	mitochondrion|nucleus					0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGACAGCCAAGGAAGCCAAG	0.577													8	14					0	0	0.004482	0	0
RPP40	10799	broad.mit.edu	37	6	4998958	4998958	+	Missense_Mutation	SNP	T	C	C	rs146507302	byFrequency	TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr6:4998958T>C	uc003mwl.2	-	5	586	c.551A>G	c.(550-552)CAT>CGT	p.H184R	RPP40_uc003mwm.2_Missense_Mutation_p.H161R	NM_006638	NP_006629	O75818	RPP40_HUMAN	ribonuclease P 40kDa subunit	184					tRNA processing	nucleolar ribonuclease P complex	protein binding|ribonuclease P activity				0	Ovarian(93;0.11)	all_hematologic(90;0.0895)				ACCTGTTTTATGCCAAGCCAA	0.299													20	1					0	0	0.008871	0	0
MSH5	4439	broad.mit.edu	37	6	31712029	31712029	+	Silent	SNP	A	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr6:31712029A>G	uc003nwv.1	+	7	679	c.600A>G	c.(598-600)GAA>GAG	p.E200E	MSH5_uc003nwt.1_Silent_p.E217E|MSH5_uc003nwu.1_Silent_p.E200E|MSH5_uc003nww.1_Silent_p.E200E|MSH5_uc003nwx.1_Silent_p.E217E|MSH5_uc011dof.1_5'Flank	NM_172166	NP_751898	O43196	MSH5_HUMAN	mutS homolog 5 isoform c	200					chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			ovary(2)|breast(1)	3						TTGAACTGGAAGACTATAATG	0.502								Direct_reversal_of_damage|MMR					48	113					0	0	0.014410	0	0
LRRC1	55227	broad.mit.edu	37	6	53787458	53787458	+	Missense_Mutation	SNP	C	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr6:53787458C>A	uc003pcd.1	+	14	1719	c.1442C>A	c.(1441-1443)CCA>CAA	p.P481Q		NM_018214	NP_060684	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	481						cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		CGAGCCACTCCACACCCAGGG	0.408													169	23					2.30628e-61	2.73626e-61	0.014410	1	0
SDK1	221935	broad.mit.edu	37	7	4153049	4153049	+	Missense_Mutation	SNP	C	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:4153049C>G	uc003smx.2	+	24	3702	c.3563C>G	c.(3562-3564)ACC>AGC	p.T1188S	SDK1_uc010kso.2_Missense_Mutation_p.T464S	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	1188	Fibronectin type-III 6.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GCCAGTGAGACCAGCCTGCGG	0.667													23	335					0	0	0.009535	0	0
ARL4A	10124	broad.mit.edu	37	7	12728407	12728407	+	Missense_Mutation	SNP	G	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:12728407G>C	uc003ssp.2	+	2	805	c.528G>C	c.(526-528)AAG>AAC	p.K176N	ARL4A_uc003ssq.2_Missense_Mutation_p.K176N|ARL4A_uc003ssr.2_Missense_Mutation_p.K176N|ARL4A_uc003sss.2_Missense_Mutation_p.K176N	NM_001037164	NP_001032241	P40617	ARL4A_HUMAN	ADP-ribosylation factor-like 4A	176					small GTPase mediated signal transduction	cytoplasm|nucleolus|plasma membrane	GTP binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (126;0.176)		ATGGCCTAAAGGAAGGACTTG	0.368													61	74					0	0	0.014410	0	0
CAMK2B	816	broad.mit.edu	37	7	44259810	44259810	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:44259810C>T	uc003tkq.2	-	23	2062	c.1852G>A	c.(1852-1854)GCT>ACT	p.A618T	CAMK2B_uc003tkp.2_Missense_Mutation_p.A494T|CAMK2B_uc003tkx.2_Missense_Mutation_p.A454T|CAMK2B_uc010kyd.2_RNA|CAMK2B_uc003tkr.2_Missense_Mutation_p.A470T|CAMK2B_uc003tks.2_Missense_Mutation_p.A469T|CAMK2B_uc003tku.2_Missense_Mutation_p.A455T|CAMK2B_uc003tkv.2_Missense_Mutation_p.A431T|CAMK2B_uc003tkt.2_Missense_Mutation_p.A444T|CAMK2B_uc003tkw.2_Missense_Mutation_p.A401T|CAMK2B_uc010kyc.2_Missense_Mutation_p.A494T|CAMK2B_uc003tkn.2_Missense_Mutation_p.A251T	NM_001220	NP_001211	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II	618					interferon-gamma-mediated signaling pathway|synaptic transmission	cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)|ovary(1)	2						CGGATGTAAGCGATGCAGGCG	0.652													6	47					0	0	0.001984	0	0
LANCL2	55915	broad.mit.edu	37	7	55459595	55459595	+	Missense_Mutation	SNP	G	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:55459595G>C	uc003tqp.2	+	2	892	c.314G>C	c.(313-315)GGC>GCC	p.G105A		NM_018697	NP_061167	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2	105					negative regulation of transcription, DNA-dependent|positive regulation of abscisic acid mediated signaling pathway	cortical actin cytoskeleton|cytosol|nucleus|plasma membrane	ATP binding|catalytic activity|GTP binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding			ovary(1)|skin(1)	2	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			GCTTATACTGGCTGGACAGGT	0.393													26	117					0	0	0.008361	0	0
GTF2IRD2	84163	broad.mit.edu	37	7	74212378	74212378	+	Silent	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:74212378T>C	uc003ubd.1	-	16	1657	c.1473A>G	c.(1471-1473)AAA>AAG	p.K491K	GTF2IRD2_uc010lbt.1_Silent_p.K38K	NM_173537	NP_775808	Q86UP8	GTD2A_HUMAN	GTF2I repeat domain containing 2	491					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						tcctgagcccttttttcagct	0													4	529					0	0	0.009096	0	0
ABCB1	5243	broad.mit.edu	37	7	87148688	87148688	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:87148688C>T	uc003uiz.1	-	24	3299	c.2881G>A	c.(2881-2883)GCC>ACC	p.A961T	ABCB1_uc011khc.1_Missense_Mutation_p.A897T	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	961	ABC transmembrane type-1 2.				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)	ACCAAGTAGGCTCCAAACCGG	0.308													37	58					0	0	0.004289	0	0
ASB4	51666	broad.mit.edu	37	7	95157443	95157443	+	Missense_Mutation	SNP	A	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:95157443A>T	uc011kij.1	+	3	806	c.806A>T	c.(805-807)CAC>CTC	p.H269L	ASB4_uc003unx.2_Missense_Mutation_p.H269L	NM_016116	NP_057200	Q9Y574	ASB4_HUMAN	ankyrin repeat and SOCS box-containing protein 4	269	ANK 6.				intracellular signal transduction					central_nervous_system(1)	1	all_cancers(62;2.27e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.218)|all_lung(186;0.246)		STAD - Stomach adenocarcinoma(171;0.0151)			GTGCTCATGCACATGATGCTG	0.567											OREG0018172	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	108					0	0	0.000602	0	0
PILRB	29990	broad.mit.edu	37	7	99950090	99950090	+	Translation_Start_Site	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:99950090G>A	uc003uuk.2	+	7	1084	c.-1412G>A	c.(-1414--1410)GCGTG>GCATG		PILRB_uc003uul.2_Translation_Start_Site|PILRB_uc003uum.1_RNA	NM_013440	NP_038468	Q9UKJ0	PILRB_HUMAN	paired immunoglobulin-like type 2 receptor beta						activation of transmembrane receptor protein tyrosine kinase activity	integral to plasma membrane	protein binding|receptor activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTGACCCTGCGTGTCACTGCA	0.701													6	5					0	0	0.004482	0	0
SLC12A9	56996	broad.mit.edu	37	7	100463708	100463708	+	Silent	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr7:100463708T>C	uc003uwp.2	+	14	2368	c.2226T>C	c.(2224-2226)GAT>GAC	p.D742D	SLC12A9_uc011kki.1_Silent_p.D273D|SLC12A9_uc003uwr.2_Silent_p.D478D|SLC12A9_uc003uws.2_Silent_p.D273D|SLC12A9_uc003uwt.2_Silent_p.D478D|SLC12A9_uc003uwv.2_Silent_p.D273D|TRIP6_uc010lhk.1_5'Flank|TRIP6_uc003uww.2_5'Flank	NM_020246	NP_064631	Q9BXP2	S12A9_HUMAN	solute carrier family 12 (potassium/chloride	742	Helical; (Potential).					integral to membrane|plasma membrane	cation:chloride symporter activity				0	Lung NSC(181;0.041)|all_lung(186;0.0581)					GCTATGTGGATGTCTGCGGCC	0.692													300	340					0	0	0.014410	0	0
PRSS55	203074	broad.mit.edu	37	8	10396268	10396268	+	Missense_Mutation	SNP	C	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr8:10396268C>A	uc003wta.2	+	5	1039	c.1024C>A	c.(1024-1026)CTG>ATG	p.L342M	uc010lru.2_Intron|PRSS55_uc003wtb.2_Intron	NM_198464	NP_940866	Q6UWB4	PRS55_HUMAN	hypothetical protein LOC203074 precursor	342	Helical; (Potential).				proteolysis	integral to membrane	serine-type endopeptidase activity			ovary(1)	1						GCTCTGTCCCCTGTCCCATGT	0.527													138	235					6.41558e-43	7.42299e-43	0.014410	1	0
TMEM67	91147	broad.mit.edu	37	8	94792858	94792858	+	Missense_Mutation	SNP	A	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr8:94792858A>C	uc011lgk.1	+	8	823	c.752A>C	c.(751-753)AAT>ACT	p.N251T	TMEM67_uc010mat.1_Missense_Mutation_p.N166T|TMEM67_uc010maw.2_Intron|TMEM67_uc003yga.3_Missense_Mutation_p.N170T	NM_153704	NP_714915	Q5HYA8	MKS3_HUMAN	meckelin isoform 1	251					cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			GCTCTTGGAAATATGTGTGTG	0.363													116	137					0	0	0.014410	0	0
ZNF658	26149	broad.mit.edu	37	9	40774146	40774146	+	Nonsense_Mutation	SNP	C	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr9:40774146C>A	uc004abs.2	-	5	1281	c.1129G>T	c.(1129-1131)GAA>TAA	p.E377*	ZNF658_uc010mmm.1_Nonsense_Mutation_p.E377*|ZNF658_uc010mmn.1_Nonsense_Mutation_p.E377*	NM_033160	NP_149350	Q5TYW1	ZN658_HUMAN	zinc finger protein 658	377					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		AATTTATCTTCTGTGTGAATT	0.403													98	136					4.66267e-56	5.4855e-56	0.014410	1	0
Unknown	0	broad.mit.edu	37	MT	3890	3890	+	RNA	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chrM:3890G>A	uc004cos.3	+	2		c.2183G>A			uc011mfh.1_5'Flank					Homo sapiens mRNA expressed only in placental villi, clone SMAP47.																		AGAGACCAACCGAACCCCCTT	0.512													84	6					0	0	0.014410	0	0
Unknown	0	broad.mit.edu	37	MT	9612	9612	+	RNA	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chrM:9612G>A	uc011mfi.1	+	1		c.950G>A			uc004cov.3_5'Flank|uc004cow.1_5'Flank|uc004cox.3_5'Flank					Homo sapiens mRNA for OK/SW-CL.16, complete cds.																		TAAACACATCCGTATTACTCG	0.483													7	63					0	0	0.001984	0	0
Unknown	0	broad.mit.edu	37	MT	12640	12640	+	RNA	SNP	G	A	A			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chrM:12640G>A	uc004cox.3	+	1		c.304G>A			uc004coy.2_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		GGTCCATCATAGAATTCTCAC	0.373													5	46					0	0	0.001168	0	0
Unknown	0	broad.mit.edu	37	MT	14348	14348	+	RNA	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chrM:14348T>C	uc004cox.3	+	1		c.2012T>C			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CCACCCCATCATACTCTTTCA	0.498													6	70					0	0	0.001168	0	0
YY2	404281	broad.mit.edu	37	X	21857904	21857904	+	Missense_Mutation	SNP	T	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chrX:21857904T>C	uc010nfq.2	+	1	249	c.52T>C	c.(52-54)TAC>CAC	p.Y18H	MBTPS2_uc004dae.2_Missense_Mutation_p.Y18H|MBTPS2_uc004dab.2_Missense_Mutation_p.Y18H	NM_206923	NP_996806	O15391	TYY2_HUMAN	YY2 transcription factor	Error:Variant_position_missing_in_O15391_after_alignment					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	DNA binding|zinc ion binding			breast(1)|skin(1)	2						GACTGTCGTCTACCTGACCGA	0.672													4	0					0	0	0.000602	0	0
SPIN3	169981	broad.mit.edu	37	X	57021007	57021007	+	Missense_Mutation	SNP	G	C	C			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chrX:57021007G>C	uc010nkj.2	-	2	660	c.374C>G	c.(373-375)GCA>GGA	p.A125G	SPIN3_uc004duu.3_Intron|SPIN3_uc004duw.3_Intron|SPIN3_uc004duv.3_Intron|SPIN3_uc004dux.1_Missense_Mutation_p.A125G	NM_001010862	NP_001010862	Q5JUX0	SPIN3_HUMAN	spindlin family, member 3	125					gamete generation					ovary(1)|central_nervous_system(1)	2						CATTATTTCTGCCAAGTGTGT	0.418													8	181					0	0	0.006214	0	0
TAF9B	51616	broad.mit.edu	37	X	77387232	77387232	+	Missense_Mutation	SNP	G	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chrX:77387232G>T	uc004eda.2	-	7	702	c.631C>A	c.(631-633)CCT>ACT	p.P211T		NM_015975	NP_057059	Q9HBM6	TAF9B_HUMAN	transcription associated factor 9B	211					negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell growth|transcription initiation, DNA-dependent	transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding				0						ATCATTGAAGGATTAATCAGA	0.398													26	61					3.1745e-13	3.52722e-13	0.008361	1	0
BPNT1	10380	broad.mit.edu	37	1	220232228	220232229	+	Frame_Shift_Ins	INS	-	GCATA	GCATA			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:220232228_220232229insGCATA	uc001hma.2	-	9	1056_1057	c.884_885insTATGC	c.(883-885)GCAfs	p.A295fs	BPNT1_uc010pug.1_Frame_Shift_Ins_p.A240fs|BPNT1_uc010puh.1_Frame_Shift_Ins_p.A259fs|BPNT1_uc001hmb.3_Intron	NM_006085	NP_006076	O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1	295					3'-phosphoadenosine 5'-phosphosulfate metabolic process|nervous system development|xenobiotic metabolic process	cytosol	3'(2'),5'-bisphosphate nucleotidase activity			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0558)		GAACTCGGCTTGCATAGTAGTC	0.317													28	278	---	---	---	---					
FMN2	56776	broad.mit.edu	37	1	240255569	240255571	+	In_Frame_Del	DEL	GGC	-	-	rs35817759		TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr1:240255569_240255571delGGC	uc010pyd.1	+	1	385_387	c.160_162delGGC	c.(160-162)GGCdel	p.G59del	FMN2_uc010pye.1_In_Frame_Del_p.G59del	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	59					actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			GGGGGGAgggggcggcggcggcg	0.557													4	9	---	---	---	---					
NXF1	10482	broad.mit.edu	37	11	62567920	62567921	+	Frame_Shift_Ins	INS	-	G	G			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr11:62567920_62567921insG	uc001nvf.1	-	10	1080_1081	c.944_945insC	c.(943-945)CTGfs	p.L315fs	NXF1_uc001nvg.1_Frame_Shift_Ins_p.L315fs|NXF1_uc009yog.1_Frame_Shift_Ins_p.L358fs|NXF1_uc010rmh.1_Frame_Shift_Ins_p.L178fs	NM_006362	NP_006353	Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1 isoform 1	315	LRR 2.|Interaction with THOC4.				gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding			skin(3)	3						CTTCTAGCTTCAGCCCCTTTAT	0.550													23	57	---	---	---	---					
CD248	57124	broad.mit.edu	37	11	66082566	66082566	+	Frame_Shift_Del	DEL	T	-	-			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr11:66082566delT	uc001ohm.1	-	1	1950	c.1933delA	c.(1933-1935)ATCfs	p.I645fs		NM_020404	NP_065137	Q9HCU0	CD248_HUMAN	tumor endothelial marker 1 precursor	645	Pro-rich.|Extracellular (Potential).					integral to membrane|proteinaceous extracellular matrix	calcium ion binding|sugar binding			large_intestine(3)	3					Cefalotin(DB00456)	TCCCTTGGGATTTGGGGGGCT	0.657													64	86	---	---	---	---					
ATP7B	540	broad.mit.edu	37	13	52548120	52548120	+	Frame_Shift_Del	DEL	T	-	-			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr13:52548120delT	uc001vfw.2	-	2	1393	c.1236delA	c.(1234-1236)GAAfs	p.E412fs	ATP7B_uc010adv.2_Frame_Shift_Del_p.E412fs|ATP7B_uc001vfx.2_Frame_Shift_Del_p.E412fs|ATP7B_uc001vfy.2_Frame_Shift_Del_p.E301fs|ATP7B_uc010tgt.1_Frame_Shift_Del_p.E412fs|ATP7B_uc010tgu.1_Frame_Shift_Del_p.E412fs|ATP7B_uc010tgv.1_Frame_Shift_Del_p.E412fs|ATP7B_uc010tgw.1_Frame_Shift_Del_p.E380fs	NM_000053	NP_000044	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	412	HMA 4.|Cytoplasmic (Potential).				ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)		CAGCTCTGAGTTCTTCTGGGC	0.468									Wilson_disease				59	89	---	---	---	---					
EIF5	1983	broad.mit.edu	37	14	103807312	103807312	+	Frame_Shift_Del	DEL	A	-	-			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr14:103807312delA	uc001ymq.2	+	12	1741	c.1219delA	c.(1219-1221)AAGfs	p.K407fs	EIF5_uc001ymr.2_Frame_Shift_Del_p.K407fs|EIF5_uc001yms.2_Frame_Shift_Del_p.K407fs|EIF5_uc001ymt.2_Frame_Shift_Del_p.K407fs|EIF5_uc001ymu.2_Frame_Shift_Del_p.K407fs	NM_001969	NP_001960	P55010	IF5_HUMAN	eukaryotic translation initiation factor 5	407					regulation of translational initiation|RNA metabolic process	cytosol	GTP binding|GTPase activity|translation initiation factor activity			pancreas(1)|breast(1)|skin(1)	3		Melanoma(154;0.155)	Epithelial(46;0.182)			GGTGTATTCGAAGGCTGCCAG	0.378													16	38	---	---	---	---					
NR2F2	7026	broad.mit.edu	37	15	96875754	96875755	+	Frame_Shift_Ins	INS	-	T	T			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr15:96875754_96875755insT	uc010uri.1	+	1	1644_1645	c.420_421insT	c.(418-423)CTCAAAfs	p.L140fs	NR2F2_uc002btp.2_Intron|NR2F2_uc010urj.1_5'Flank|MIR1469_hsa-mir-1469|MI0007074_5'Flank|NR2F2_uc010urk.1_5'Flank	NM_021005	NP_066285	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	140_141	Interaction with ZFPM2 (By similarity).|Nuclear receptor.				lipid metabolic process|negative regulation of cyclin-dependent protein kinase activity|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment	nucleus	ligand-regulated transcription factor activity|protein homodimerization activity|retinoic acid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(1)	3	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			AAAAGTGCCTCAAAGTGGGCAT	0.604													23	64	---	---	---	---					
RNF43	54894	broad.mit.edu	37	17	56435501	56435502	+	Frame_Shift_Ins	INS	-	G	G	rs144487242	by1000genomes	TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:56435501_56435502insG	uc002iwf.2	-	8	3591_3592	c.1635_1636insC	c.(1633-1638)TCCAGCfs	p.S545fs	RNF43_uc010wnv.1_Frame_Shift_Ins_p.S504fs|RNF43_uc002iwh.3_Frame_Shift_Ins_p.S545fs|RNF43_uc002iwg.3_Frame_Shift_Ins_p.S545fs|RNF43_uc010dcw.2_Frame_Shift_Ins_p.S418fs	NM_017763	NP_060233	Q68DV7	RNF43_HUMAN	ring finger protein 43 precursor	545_546	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding			ovary(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGGACATGGCTGGAAACCTGGG	0.624													9	256	---	---	---	---					
DDX5	1655	broad.mit.edu	37	17	62500099	62500102	+	Splice_Site	DEL	ACAG	-	-			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr17:62500099_62500102delACAG	uc002jek.2	-	4	688	c.441_splice	c.e4+1	p.S147_splice	DDX5_uc010deh.2_Splice_Site_p.S147_splice|DDX5_uc002jej.2_Splice_Site_p.S42_splice|DDX5_uc010wqa.1_Intron|DDX5_uc002jel.1_5'Flank	NM_004396	NP_004387	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5						cell growth|regulation of alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA helicase activity|transcription cofactor activity			ovary(2)|lung(1)	3	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			TCCCAAACTTACAGACAATGTTTT	0.397			T	ETV4	prostate								45	134	---	---	---	---					
ZNF17	7565	broad.mit.edu	37	19	57931956	57931959	+	Frame_Shift_Del	DEL	TTCT	-	-			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr19:57931956_57931959delTTCT	uc002qoo.1	+	3	1327_1330	c.1096_1099delTTCT	c.(1096-1101)TTCTTTfs	p.F366fs	ZNF547_uc002qpm.3_Intron|ZNF17_uc002qop.1_Frame_Shift_Del_p.F368fs	NM_006959	NP_008890	P17021	ZNF17_HUMAN	zinc finger protein 17	366_367	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		ATGTGGGAAATTCTTTATGGACAG	0.387													15	130	---	---	---	---					
RGPD1	400966	broad.mit.edu	37	2	87141020	87141020	+	Frame_Shift_Del	DEL	G	-	-			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr2:87141020delG	uc010fgv.2	+	1	115	c.48delG	c.(46-48)CAGfs	p.Q16fs	RMND5A_uc002srs.3_Intron	NM_001024457	NP_001019628	Q68DN6	RGPD1_HUMAN	RANBP2-like and GRIP domain containing 1	Error:Variant_position_missing_in_Q68DN6_after_alignment					intracellular transport		binding				0						CCTCGGTGCAGGGCTCCGCCC	0.667													3	3	---	---	---	---					
PCSK2	5126	broad.mit.edu	37	20	17207956	17207957	+	In_Frame_Ins	INS	-	GGT	GGT			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr20:17207956_17207957insGGT	uc002wpm.2	+	1	326_327	c.6_7insGGT	c.(4-9)insGGT	p.4_5insG	PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_In_Frame_Ins_p.4_5insG	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	4_5					enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	GAAGGATGAAGGGTGGTTGTGT	0.530													92	129	---	---	---	---					
POLDIP3	84271	broad.mit.edu	37	22	42998037	42998037	+	Frame_Shift_Del	DEL	G	-	-			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr22:42998037delG	uc003bcu.2	-	3	575	c.476delC	c.(475-477)CCAfs	p.P159fs	POLDIP3_uc011app.1_Frame_Shift_Del_p.P80fs|POLDIP3_uc003bcv.2_Intron|POLDIP3_uc011apq.1_Frame_Shift_Del_p.P176fs|POLDIP3_uc010gza.2_RNA|POLDIP3_uc011apr.1_Intron|POLDIP3_uc010gzb.1_Intron	NM_032311	NP_115687	Q9BY77	PDIP3_HUMAN	DNA polymerase delta interacting protein 3	159					positive regulation of translation	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding				0						GGGATGAAGTGGTGCCATGGC	0.498													80	123	---	---	---	---					
OR2J3	442186	broad.mit.edu	37	6	29080474	29080475	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr6:29080474_29080475delTT	uc011dll.1	+	1	807_808	c.807_808delTT	c.(805-810)AATTCTfs	p.N269fs		NM_001005216	NP_001005216	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J,	269_270	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						CATCAGGAAATTCTCAAGATCA	0.441													79	10	---	---	---	---					
KCNS2	3788	broad.mit.edu	37	8	99441466	99441466	+	Frame_Shift_Del	DEL	A	-	-			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr8:99441466delA	uc003yin.2	+	2	1609	c.1259delA	c.(1258-1260)CAAfs	p.Q420fs		NM_020697	NP_065748	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel,	420	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			TACCGGCGCCAAAAGCAACTT	0.498													114	159	---	---	---	---					
FLJ46321	389763	broad.mit.edu	37	9	84609703	84609703	+	Frame_Shift_Del	DEL	A	-	-			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr9:84609703delA	uc004amn.2	+	4	4365	c.4318delA	c.(4318-4320)AAAfs	p.K1440fs		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	1440						integral to membrane					0						GGGGCTTGGGAAAGCTCAGCA	0.552													29	57	---	---	---	---					
SVEP1	79987	broad.mit.edu	37	9	113234604	113234615	+	Splice_Site	DEL	CTGGATAGTCGG	-	-			TCGA-AL-3468-01A-01D-1252-08	TCGA-AL-3468-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	3ace8906-6fda-48fe-8e46-4140e9ed7fce	e04284b9-b5a9-481b-b1bb-0377a566a154	g.chr9:113234604_113234615delCTGGATAGTCGG	uc010mtz.2	-	15	2937	c.2600_splice	c.e15-1	p.G867_splice	SVEP1_uc010mua.1_Splice_Site_p.G867_splice	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7						CCACCTGGTCCTGGATAGTCGGGGCAGAGACA	0.481													18	31	---	---	---	---					
