Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
PLEKHN1	84069	broad.mit.edu	37	1	909251	909251	+	Silent	SNP	C	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:909251C>A	uc001ace.2	+	13	1664	c.1629C>A	c.(1627-1629)CCC>CCA	p.P543P	PLEKHN1_uc001acd.2_Silent_p.P491P|PLEKHN1_uc001acf.2_Silent_p.P456P	NM_032129	NP_115505	Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N	543											0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		GACCCACGCCCTCGAGCCCAC	0.687													3	47	---	---	---	---	PASS
MMEL1	79258	broad.mit.edu	37	1	2541226	2541226	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2541226C>T	uc001ajy.2	-	5	551	c.337G>A	c.(337-339)GAC>AAC	p.D113N	MMEL1_uc009vlg.1_RNA	NM_033467	NP_258428	Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	113	Lumenal (Potential).				proteolysis	extracellular region|integral to membrane|intracellular membrane-bounded organelle	metal ion binding|metalloendopeptidase activity				0	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		TAGAAGTCGTCACACGGTTCC	0.602													19	46	---	---	---	---	PASS
PRAMEF11	440560	broad.mit.edu	37	1	12887579	12887579	+	Missense_Mutation	SNP	G	T	T	rs2486717	by1000genomes	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12887579G>T	uc001auk.2	-	3	474	c.278C>A	c.(277-279)ACA>AAA	p.T93K		NM_001146344	NP_001139816	O60813	PRA11_HUMAN	PRAME family member 11	93											0						CTGCACTGGTGTTTTGTTCCT	0.493													6	233	---	---	---	---	PASS
UBXN11	91544	broad.mit.edu	37	1	26623424	26623424	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26623424C>G	uc001blw.2	-	8	691	c.418G>C	c.(418-420)GTC>CTC	p.V140L	UBXN11_uc001blz.1_Missense_Mutation_p.V107L|UBXN11_uc001blv.2_Missense_Mutation_p.V102L|UBXN11_uc001bly.2_Intron|UBXN11_uc001blx.2_5'UTR|UBXN11_uc001bma.2_Missense_Mutation_p.V107L|UBXN11_uc001bmb.1_Missense_Mutation_p.V140L|UBXN11_uc010ofb.1_Missense_Mutation_p.V65L|UBXN11_uc010ofc.1_Intron	NM_183008	NP_892120	Q5T124	UBX11_HUMAN	socius isoform 2	140	Potential.					cytoplasm|cytoskeleton				ovary(1)	1						ATCTCCCTGACCTGCCGCTGC	0.662													5	10	---	---	---	---	PASS
ZC3H12A	80149	broad.mit.edu	37	1	37941073	37941073	+	5'UTR	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37941073G>A	uc001cbb.3	+	2						NM_025079	NP_079355	Q5D1E8	ZC12A_HUMAN	zinc finger CCCH-type containing 12A						angiogenesis|apoptosis|cell differentiation	cytoplasm|nucleus|plasma membrane	endonuclease activity|metal ion binding			ovary(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GAGCTGTGGCGCGGGGCCTTC	0.582													32	90	---	---	---	---	PASS
LEPR	3953	broad.mit.edu	37	1	66067338	66067338	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66067338C>T	uc001dci.2	+	9	1460	c.1258C>T	c.(1258-1260)CAT>TAT	p.H420Y	LEPR_uc001dcg.2_Missense_Mutation_p.H420Y|LEPR_uc001dch.2_Missense_Mutation_p.H420Y|LEPR_uc009waq.2_Intron|LEPR_uc001dcj.2_Missense_Mutation_p.H420Y|LEPR_uc001dck.2_Missense_Mutation_p.H420Y	NM_002303	NP_002294	P48357	LEPR_HUMAN	leptin receptor isoform 1	420	Extracellular (Potential).|Ig-like.				energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		TGAATGCCATCATCGCTATGC	0.353													32	84	---	---	---	---	PASS
GIPC2	54810	broad.mit.edu	37	1	78601512	78601512	+	3'UTR	SNP	A	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78601512A>G	uc001dik.2	+	6						NM_017655	NP_060125	Q8TF65	GIPC2_HUMAN	PDZ domain protein GIPC2							cytoplasm				ovary(1)	1						GTTTTTGGACACCTTTACTAA	0.308													7	24	---	---	---	---	PASS
CAPZA1	829	broad.mit.edu	37	1	113212821	113212821	+	3'UTR	SNP	A	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113212821A>G	uc001ecj.1	+	10						NM_006135	NP_006126	P52907	CAZA1_HUMAN	F-actin capping protein alpha-1 subunit						actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex|WASH complex	actin binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TATGATAAATAAGTGATTTAT	0.363													11	18	---	---	---	---	PASS
RPRD2	23248	broad.mit.edu	37	1	150432593	150432593	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150432593C>T	uc009wlr.2	+	9	1412	c.1211C>T	c.(1210-1212)ACA>ATA	p.T404I	RPRD2_uc010pcc.1_Missense_Mutation_p.T378I|RPRD2_uc001eup.3_Missense_Mutation_p.T378I	NM_015203	NP_056018	Q5VT52	RPRD2_HUMAN	Regulation of nuclear pre-mRNA domain containing	404							protein binding			ovary(1)	1						TCTGTACCTACAAAGCCAACA	0.438													16	26	---	---	---	---	PASS
SLC39A1	27173	broad.mit.edu	37	1	153932643	153932643	+	Silent	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153932643C>T	uc001fdh.2	-	4	1075	c.906G>A	c.(904-906)AGG>AGA	p.R302R	CRTC2_uc010ped.1_5'Flank|SLC39A1_uc001fdi.2_Silent_p.R302R|SLC39A1_uc001fdj.2_Silent_p.R302R|SLC39A1_uc001fdk.2_Silent_p.R302R|SLC39A1_uc010pee.1_Silent_p.R200R|SLC39A1_uc001fdl.2_Silent_p.R302R	NM_014437	NP_055252	Q9NY26	S39A1_HUMAN	solute carrier family 39 (zinc transporter),	302	Cytoplasmic (Potential).			R -> G (in Ref. 4; BAC11502).		endoplasmic reticulum membrane|integral to membrane|membrane fraction|plasma membrane	zinc ion transmembrane transporter activity				0	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)	Colorectal(1306;0.019)		CCTTGAGGATCCTTTGCTCAG	0.557													42	85	---	---	---	---	PASS
SLC25A44	9673	broad.mit.edu	37	1	156169881	156169881	+	Silent	SNP	C	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156169881C>A	uc001fnp.2	+	2	565	c.243C>A	c.(241-243)ACC>ACA	p.T81T	SLC25A44_uc010phc.1_Intron|SLC25A44_uc009wrr.2_Silent_p.T81T|SLC25A44_uc010phd.1_Intron|SLC25A44_uc010phe.1_Intron	NM_014655	NP_055470	Q96H78	S2544_HUMAN	solute carrier family 25, member 44	81	Solcar 1.|Helical; Name=2; (Potential).				transmembrane transport	integral to membrane|mitochondrial inner membrane	binding			ovary(1)	1	Hepatocellular(266;0.158)					TGGTCAATACCTTCACCCTCA	0.517													21	52	---	---	---	---	PASS
SLAMF7	57823	broad.mit.edu	37	1	160718025	160718025	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160718025G>A	uc001fwq.2	+	2	112	c.97G>A	c.(97-99)GTT>ATT	p.V33I	SLAMF7_uc010pjn.1_Intron|SLAMF7_uc001fws.2_Intron|SLAMF7_uc001fwr.2_Missense_Mutation_p.V33I|SLAMF7_uc010pjo.1_Missense_Mutation_p.V33I|SLAMF7_uc010pjp.1_Intron|SLAMF7_uc010pjq.1_Missense_Mutation_p.V33I|SLAMF7_uc010pjr.1_Intron	NM_021181	NP_067004	Q9NQ25	SLAF7_HUMAN	SLAM family member 7	33	Extracellular (Potential).				cell adhesion|natural killer cell activation|natural killer cell mediated cytotoxicity	integral to membrane	receptor activity			skin(2)|ovary(1)	3	all_cancers(52;2.63e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GGTCGGTTCCGTTGGTGGGGC	0.498													23	71	---	---	---	---	PASS
MPZL1	9019	broad.mit.edu	37	1	167734877	167734877	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167734877A>C	uc001geo.2	+	2	351	c.149A>C	c.(148-150)AAT>ACT	p.N50T	MPZL1_uc001gen.3_Missense_Mutation_p.N50T|MPZL1_uc001gep.2_Missense_Mutation_p.N50T|MPZL1_uc001geq.2_Missense_Mutation_p.N50T|MPZL1_uc009wvh.2_RNA	NM_003953	NP_003944	O95297	MPZL1_HUMAN	myelin protein zero-like 1 isoform a	50	Extracellular (Potential).|Ig-like V-type.				cell-cell signaling|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	protein binding|structural molecule activity			ovary(2)	2	all_hematologic(923;0.215)					TTCGTGGCAAATGGTACACAA	0.488													32	67	---	---	---	---	PASS
FMO2	2327	broad.mit.edu	37	1	171178243	171178243	+	3'UTR	SNP	G	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171178243G>C	uc001ghk.1	+	9					FMO2_uc010pmd.1_3'UTR	NM_001460	NP_001451	Q99518	FMO2_HUMAN	flavin containing monooxygenase 2						drug metabolic process|NADPH oxidation|organic acid metabolic process|toxin metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|host cell microsome|integral to membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GGGCCTTCTTGCTGTTGTTGT	0.408													5	18	---	---	---	---	PASS
IVNS1ABP	10625	broad.mit.edu	37	1	185267160	185267160	+	3'UTR	SNP	A	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185267160A>G	uc001grl.2	-	15					IVNS1ABP_uc001gri.2_3'UTR|IVNS1ABP_uc001grj.2_3'UTR|IVNS1ABP_uc009wyj.2_3'UTR|IVNS1ABP_uc009wyk.2_RNA	NM_006469	NP_006460	Q9Y6Y0	NS1BP_HUMAN	influenza virus NS1A binding protein						interspecies interaction between organisms|response to virus|RNA splicing|transcription from RNA polymerase III promoter	cytoplasm|cytoskeleton|spliceosomal complex|transcription factor complex				ovary(4)|central_nervous_system(1)	5						AGAGGGTCTTAAATTTGTTAA	0.383													49	135	---	---	---	---	PASS
PRG4	10216	broad.mit.edu	37	1	186276051	186276051	+	Silent	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186276051C>T	uc001gru.3	+	7	1251	c.1200C>T	c.(1198-1200)ACC>ACT	p.T400T	PRG4_uc001grt.3_Silent_p.T359T|PRG4_uc009wyl.2_Silent_p.T307T|PRG4_uc009wym.2_Silent_p.T266T|PRG4_uc010poo.1_RNA	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	400	59 X 8 AA repeats of K-X-P-X-P-T-T-X.|7.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						CACCCACCACCACCAAGGAGC	0.647													5	43	---	---	---	---	PASS
PRG4	10216	broad.mit.edu	37	1	186276052	186276052	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186276052A>C	uc001gru.3	+	7	1252	c.1201A>C	c.(1201-1203)ACC>CCC	p.T401P	PRG4_uc001grt.3_Missense_Mutation_p.T360P|PRG4_uc009wyl.2_Missense_Mutation_p.T308P|PRG4_uc009wym.2_Missense_Mutation_p.T267P|PRG4_uc010poo.1_RNA	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	401	59 X 8 AA repeats of K-X-P-X-P-T-T-X.|7.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						ACCCACCACCACCAAGGAGCC	0.642													8	41	---	---	---	---	PASS
CFH	3075	broad.mit.edu	37	1	196709894	196709894	+	Silent	SNP	A	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196709894A>G	uc001gtj.3	+	18	3168	c.2928A>G	c.(2926-2928)GAA>GAG	p.E976E		NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	976	Sushi 16.				complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6						GCTTAGGAGAAAAATGGTCTC	0.348													9	214	---	---	---	---	PASS
OR2M2	391194	broad.mit.edu	37	1	248343390	248343390	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248343390T>A	uc010pzf.1	+	1	103	c.103T>A	c.(103-105)TTT>ATT	p.F35I		NM_001004688	NP_001004688	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M,	35	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			CCTGGGCATCTTTTTAGTGGC	0.522													14	533	---	---	---	---	PASS
ALLC	55821	broad.mit.edu	37	2	3727474	3727474	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3727474T>C	uc010ewt.2	+	5	349	c.188T>C	c.(187-189)GTC>GCC	p.V63A		NM_018436	NP_060906	Q8N6M5	ALLC_HUMAN	allantoicase isoform a	82							allantoicase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		GACTGGTGTGTCCTCAGGCTG	0.572										HNSCC(21;0.051)			34	124	---	---	---	---	PASS
MAPRE3	22924	broad.mit.edu	37	2	27245101	27245101	+	Silent	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27245101G>A	uc002rhw.2	+	2	168	c.15G>A	c.(13-15)GTG>GTA	p.V5V	MAPRE3_uc002rhx.2_Silent_p.V5V|MAPRE3_uc010yld.1_Silent_p.V5V	NM_012326	NP_036458	Q9UPY8	MARE3_HUMAN	microtubule-associated protein, RP/EB family,	5					cell division|mitosis|positive regulation of transcription, DNA-dependent	cytoplasm|cytoplasmic microtubule|microtubule|midbody|perinuclear region of cytoplasm	microtubule binding|protein binding|small GTPase regulator activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCGTCAATGTGTACTCCACAT	0.502													66	219	---	---	---	---	PASS
SMEK2	57223	broad.mit.edu	37	2	55825590	55825590	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55825590T>A	uc002rzc.2	-	4	1258	c.883A>T	c.(883-885)ATT>TTT	p.I295F	SMEK2_uc002rzb.2_Missense_Mutation_p.I295F|SMEK2_uc002rzd.2_Missense_Mutation_p.I295F|SMEK2_uc002rza.2_Missense_Mutation_p.I171F	NM_001122964	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 isoform 1	295						microtubule organizing center|nucleus	protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TTGAAGAAAATAAAAGACGTA	0.333													28	68	---	---	---	---	PASS
USP34	9736	broad.mit.edu	37	2	61566797	61566797	+	Silent	SNP	A	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61566797A>G	uc002sbe.2	-	17	2542	c.2520T>C	c.(2518-2520)CAT>CAC	p.H840H		NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	840					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			TGTTGAATTGATGTTTATGAA	0.328													27	68	---	---	---	---	PASS
GLI2	2736	broad.mit.edu	37	2	121747767	121747767	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121747767C>T	uc010flp.2	+	13	4307	c.4277C>T	c.(4276-4278)TCG>TTG	p.S1426L	GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Missense_Mutation_p.S1098L|GLI2_uc002tmu.3_Missense_Mutation_p.S1081L	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	1426					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				AACATGGGGTCGGTGCCTCCC	0.657													10	37	---	---	---	---	PASS
MARS2	92935	broad.mit.edu	37	2	198571443	198571443	+	Silent	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198571443G>A	uc002uuq.2	+	1	1357	c.1314G>A	c.(1312-1314)CCG>CCA	p.P438P	uc002uup.2_Intron	NM_138395	NP_612404	Q96GW9	SYMM_HUMAN	methionine-tRNA synthetase 2 precursor	438					methionyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|methionine-tRNA ligase activity			ovary(1)|central_nervous_system(1)|skin(1)	3					L-Methionine(DB00134)	TGGTGGGGCCGTCAGTTCGTG	0.517													49	115	---	---	---	---	PASS
IKZF2	22807	broad.mit.edu	37	2	213878698	213878698	+	Intron	SNP	T	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213878698T>A	uc002vem.2	-						IKZF2_uc010fuu.2_Intron|IKZF2_uc002vej.2_Intron|IKZF2_uc002vek.2_Intron|IKZF2_uc010fuv.2_Intron|IKZF2_uc002vel.2_Intron|IKZF2_uc010fuw.2_Intron|IKZF2_uc010fux.2_Intron|IKZF2_uc010fuy.2_Intron|IKZF2_uc002ven.2_Intron|IKZF2_uc002vei.2_Nonsense_Mutation_p.K3*	NM_016260	NP_057344	Q9UKS7	IKZF2_HUMAN	helios isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Esophageal squamous(248;0.0559)|Renal(323;0.218)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792)		GATAATTTCTTCAACATTTTG	0.348													8	86	---	---	---	---	PASS
SMARCAL1	50485	broad.mit.edu	37	2	217280065	217280065	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217280065G>C	uc002vgc.3	+	3	968	c.638G>C	c.(637-639)AGT>ACT	p.S213T	SMARCAL1_uc010fvf.2_RNA|SMARCAL1_uc002vgd.3_Missense_Mutation_p.S213T|SMARCAL1_uc010fvg.2_Missense_Mutation_p.S213T	NM_014140	NP_054859	Q9NZC9	SMAL1_HUMAN	SWI/SNF-related matrix-associated	213					chromatin modification|DNA metabolic process|regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity			ovary(3)|breast(3)|skin(1)	7		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		AGCTCAGAGAGTGTAACGCCC	0.522									Schimke_Immuno-Osseous_Dysplasia				35	84	---	---	---	---	PASS
CUL3	8452	broad.mit.edu	37	2	225368421	225368421	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225368421G>C	uc002vny.2	-	9	1709	c.1325C>G	c.(1324-1326)ACA>AGA	p.T442R	CUL3_uc010zls.1_Missense_Mutation_p.T376R|CUL3_uc010fwy.1_Missense_Mutation_p.T448R	NM_003590	NP_003581	Q13618	CUL3_HUMAN	cullin 3	442					cell cycle arrest|cell migration|cyclin catabolic process|cytokinesis|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|mitotic anaphase|negative regulation of Rho protein signal transduction|positive regulation of cell proliferation|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|Golgi apparatus|nucleus|polar microtubule	ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|kidney(1)	4		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		ACTTTTATTTGTGAGAAGTCT	0.313													16	42	---	---	---	---	PASS
COL4A4	1286	broad.mit.edu	37	2	227886850	227886850	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227886850C>T	uc010zlt.1	-	43	4784	c.4130G>A	c.(4129-4131)CGA>CAA	p.R1377Q		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	1377	Triple-helical region.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GCCTGGGATTCGGGGACAGTC	0.582													15	347	---	---	---	---	PASS
SETD2	29072	broad.mit.edu	37	3	47125664	47125664	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47125664T>A	uc003cqs.2	-	12	5659	c.5606A>T	c.(5605-5607)GAC>GTC	p.D1869V	SETD2_uc003cqv.2_Missense_Mutation_p.D1936V|SETD2_uc003cqt.1_RNA	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1869					regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AGTGTCTGTGTCAGCTTCTGT	0.458			N|F|S|Mis		clear cell renal carcinoma								55	102	---	---	---	---	PASS
ZXDC	79364	broad.mit.edu	37	3	126160625	126160625	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126160625G>A	uc003eiv.2	-	8	2431	c.2377C>T	c.(2377-2379)CAG>TAG	p.Q793*	ZXDC_uc010hsh.2_RNA	NM_025112	NP_079388	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C isoform 1	793	Interaction with CIITA.				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.155)		AGCTGGACCTGGACGCCCTGC	0.672													16	42	---	---	---	---	PASS
EPHB1	2047	broad.mit.edu	37	3	134967305	134967305	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134967305A>T	uc003eqt.2	+	14	2864	c.2644A>T	c.(2644-2646)ATC>TTC	p.I882F	EPHB1_uc003equ.2_Missense_Mutation_p.I443F	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	882	Cytoplasmic (Potential).|Protein kinase.					integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30						AGATAAGATGATCCGGAACCC	0.557													9	25	---	---	---	---	PASS
TP63	8626	broad.mit.edu	37	3	189604291	189604291	+	Silent	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189604291G>A	uc003fry.2	+	11	1547	c.1458G>A	c.(1456-1458)CAG>CAA	p.Q486Q	TP63_uc003frz.2_Silent_p.Q486Q|TP63_uc010hzc.1_Silent_p.Q486Q|TP63_uc003fsc.2_Silent_p.Q392Q|TP63_uc003fsd.2_Silent_p.Q392Q|TP63_uc010hzd.1_Silent_p.Q307Q	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1	486					anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		ACCCTCAGCAGCGCAACGCCC	0.498									Hay-Wells_syndrome	HNSCC(45;0.13)			34	74	---	---	---	---	PASS
RBPJ	3516	broad.mit.edu	37	4	26322655	26322655	+	Intron	SNP	C	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26322655C>A	uc003grx.1	+						RBPJ_uc003gry.1_Intron|RBPJ_uc003grz.1_Intron|RBPJ_uc011bxt.1_Intron|RBPJ_uc003gsa.1_5'UTR|RBPJ_uc003gsb.1_Missense_Mutation_p.A2E	NM_005349	NP_005340	Q06330	SUH_HUMAN	recombining binding protein suppressor of						DNA recombination|negative regulation of transcription, DNA-dependent|positive regulation of transcription of Notch receptor target	cytoplasm|nucleolus|nucleoplasm	DNA binding|protein binding|recombinase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|central_nervous_system(1)	3		Breast(46;0.0503)				TGGAAGATGGCGCCTGTTGTG	0.652													3	33	---	---	---	---	PASS
RPL9	6133	broad.mit.edu	37	4	39459154	39459154	+	Intron	SNP	G	A	A	rs2608830	byFrequency	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39459154G>A	uc003gub.2	-						RPL9_uc003guc.2_Intron|RPL9_uc011byk.1_Intron|RPL9_uc011byl.1_Intron|RPL9_uc003gud.1_3'UTR|LIAS_uc003gue.3_5'Flank|LIAS_uc011bym.1_5'Flank|LIAS_uc003guf.2_5'Flank|LIAS_uc003gug.2_5'Flank|LIAS_uc003guh.2_5'Flank	NM_001024921	NP_001020092	P32969	RL9_HUMAN	ribosomal protein L9						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|nucleolus|ribosome	rRNA binding|structural constituent of ribosome			skin(1)	1						ATAAAGCACAGGTTTGAGAAA	0.403													3	79	---	---	---	---	PASS
PKD2	5311	broad.mit.edu	37	4	88986968	88986968	+	Missense_Mutation	SNP	T	G	G	rs138982773	by1000genomes	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88986968T>G	uc003hre.2	+	12	2361	c.2295T>G	c.(2293-2295)GAT>GAG	p.D765E	PKD2_uc011cdf.1_Missense_Mutation_p.D183E|PKD2_uc011cdg.1_Missense_Mutation_p.D91E|PKD2_uc011cdh.1_5'UTR	NM_000297	NP_000288	Q13563	PKD2_HUMAN	polycystin 2	765	|EF-hand.|EF-hand domain.|Cytoplasmic (Potential).					basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body	calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity			skin(1)	1		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		ACGACCAAGATGGAGACCAAG	0.438													5	134	---	---	---	---	PASS
ADH5	128	broad.mit.edu	37	4	100009871	100009871	+	5'UTR	SNP	C	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100009871C>G	uc003hui.2	-	1					ADH5_uc003huk.1_5'UTR|uc003hum.1_5'Flank|uc003hul.1_5'Flank	NM_000671	NP_000662	P11766	ADHX_HUMAN	class III alcohol dehydrogenase, chi subunit						ethanol oxidation|response to redox state		alcohol dehydrogenase (NAD) activity|electron carrier activity|fatty acid binding|formaldehyde dehydrogenase activity|S-(hydroxymethyl)glutathione dehydrogenase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;2.5e-07)	NADH(DB00157)	TTCTGGTCGGCGCGGGGGGCT	0.706													8	55	---	---	---	---	PASS
SPZ1	84654	broad.mit.edu	37	5	79616823	79616823	+	Silent	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79616823G>A	uc003kgn.2	+	1	1034	c.789G>A	c.(787-789)GAG>GAA	p.E263E	uc011ctk.1_RNA	NM_032567	NP_115956	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	263	Potential.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(1)	1		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		AACATACTGAGCTCAGTAAAC	0.358													24	73	---	---	---	---	PASS
ALDH7A1	501	broad.mit.edu	37	5	125896835	125896835	+	Intron	SNP	T	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125896835T>C	uc003ktx.2	-						ALDH7A1_uc003ktv.2_Translation_Start_Site|ALDH7A1_uc003kty.2_Intron|ALDH7A1_uc011cxa.1_Intron	NM_001182	NP_001173	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1						cellular aldehyde metabolic process|lysine catabolic process|sensory perception of sound	cytosol|mitochondrial matrix|nucleus	aldehyde dehydrogenase (NAD) activity|betaine-aldehyde dehydrogenase activity|L-aminoadipate-semialdehyde dehydrogenase activity			kidney(2)|ovary(1)	3		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)	NADH(DB00157)|Pyridoxine(DB00165)	aaaaaaattatatataaaaat	0.313													18	35	---	---	---	---	PASS
DDX46	9879	broad.mit.edu	37	5	134126242	134126242	+	Silent	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134126242G>A	uc003kzw.2	+	13	1794	c.1626G>A	c.(1624-1626)CAG>CAA	p.Q542Q	DDX46_uc003kzv.1_RNA	NM_014829	NP_055644	Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	542	Helicase ATP-binding.				mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTGAACCCCAGGTAATCATTA	0.323													27	121	---	---	---	---	PASS
MIR886	100126299	broad.mit.edu	37	5	135416288	135416288	+	RNA	SNP	G	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135416288G>C	hsa-mir-886|MI0005527	-			c.10G>C																				0						CTCCGACCCGGGTAGGAGTGT	0.587													14	41	---	---	---	---	PASS
PCDH12	51294	broad.mit.edu	37	5	141337417	141337417	+	5'UTR	SNP	G	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141337417G>T	uc003llx.2	-	1						NM_016580	NP_057664	Q9NPG4	PCD12_HUMAN	protocadherin 12 precursor						neuron recognition	integral to plasma membrane	calcium ion binding			ovary(3)	3		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTTGCATCATGCTTACCGCCA	0.512													19	103	---	---	---	---	PASS
C5orf40	408263	broad.mit.edu	37	5	156769986	156769986	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156769986T>C	uc003lwu.2	-	2	747	c.559A>G	c.(559-561)AAC>GAC	p.N187D	CYFIP2_uc003lwq.2_Intron|CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron	NM_001001343	NP_001001343	Q8TBE3	FNDC9_HUMAN	hypothetical protein LOC408263	187						integral to membrane					0	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TCTCTGGAGTTCTTGCGTGGC	0.627											OREG0016977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	218	---	---	---	---	PASS
MBOAT1	154141	broad.mit.edu	37	6	20144501	20144501	+	Silent	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20144501G>A	uc003ncx.1	-	4	574	c.369C>T	c.(367-369)ATC>ATT	p.I123I	MBOAT1_uc011dji.1_5'UTR	NM_001080480	NP_001073949	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain	123					phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			ATATTCGGCTGATGTGGCATA	0.358													43	141	---	---	---	---	PASS
B3GAT2	135152	broad.mit.edu	37	6	71571408	71571408	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71571408G>C	uc003pfv.2	-	4	1586	c.930C>G	c.(928-930)AAC>AAG	p.N310K	SMAP1_uc003pfr.2_3'UTR|SMAP1_uc003pfs.2_3'UTR|SMAP1_uc010kao.2_3'UTR|SMAP1_uc010kap.2_3'UTR|B3GAT2_uc011dxz.1_RNA|B3GAT2_uc003pfw.2_3'UTR	NM_080742	NP_542780	Q9NPZ5	B3GA2_HUMAN	beta-1,3-glucuronyltransferase 2	310	Lumenal (Potential).				carbohydrate biosynthetic process	Golgi membrane|integral to membrane	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity|metal ion binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3						ACTTTGGCTCGTTGGCTAGAT	0.493													27	42	---	---	---	---	PASS
RBM16	22828	broad.mit.edu	37	6	155154022	155154022	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155154022G>T	uc003qqa.2	+	21	3541	c.3309G>T	c.(3307-3309)GAG>GAT	p.E1103D	TIAM2_uc003qqb.2_5'UTR|RBM16_uc011efj.1_Missense_Mutation_p.E1169D|RBM16_uc011efk.1_Missense_Mutation_p.E1148D|RBM16_uc003qpz.2_Missense_Mutation_p.E1103D|RBM16_uc010kji.2_Intron	NM_014892	NP_055707	Q9UPN6	SCAF8_HUMAN	RNA-binding motif protein 16	1103					mRNA processing|RNA splicing	nuclear matrix|spliceosomal complex	nucleotide binding|RNA binding|RNA polymerase core enzyme binding				0		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;2.33e-15)|BRCA - Breast invasive adenocarcinoma(81;0.00524)		ATGAGAGAGAGCATCGGGTTC	0.463													30	52	---	---	---	---	PASS
HEATR2	54919	broad.mit.edu	37	7	780466	780466	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:780466C>T	uc010krz.1	+	3	811	c.791C>T	c.(790-792)GCG>GTG	p.A264V	HEATR2_uc003siz.2_Missense_Mutation_p.A132V	NM_017802	NP_060272	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	264	HEAT 3.						protein binding			skin(1)	1		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		GTCCGGCGGGCGGTGGCCTCC	0.637													47	205	---	---	---	---	PASS
MACC1	346389	broad.mit.edu	37	7	20180451	20180451	+	3'UTR	SNP	C	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20180451C>G	uc003sus.3	-	7					MACC1_uc010kug.2_3'UTR	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3						cacacacagacacacacacac	0.159													3	55	---	---	---	---	PASS
MYL7	58498	broad.mit.edu	37	7	44179950	44179950	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44179950G>C	uc003tkg.2	-	4	282	c.270C>G	c.(268-270)TTC>TTG	p.F90L		NM_021223	NP_067046	Q01449	MLRA_HUMAN	myosin light chain 2a	90					actin filament-based movement|smooth muscle contraction	A band|myosin complex	ATPase activity, coupled|calcium ion binding|microfilament motor activity				0						AGAGCGTGAGGAAGACGGTGA	0.542													30	145	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82583794	82583794	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82583794G>A	uc003uhx.2	-	5	6764	c.6475C>T	c.(6475-6477)CAT>TAT	p.H2159Y	PCLO_uc003uhv.2_Missense_Mutation_p.H2159Y|PCLO_uc010lec.2_5'Flank	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2090					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						AGCGATTCATGGGCAATTATC	0.403													28	118	---	---	---	---	PASS
DNAJC2	27000	broad.mit.edu	37	7	102982243	102982243	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102982243T>C	uc003vbo.2	-	2	474	c.223A>G	c.(223-225)ATG>GTG	p.M75V	DNAJC2_uc003vbn.2_5'UTR|DNAJC2_uc010lix.2_Missense_Mutation_p.M75V|DNAJC2_uc003vbp.2_5'UTR|DNAJC2_uc003vbq.1_RNA|DNAJC2_uc003vbr.1_Missense_Mutation_p.M75V	NM_014377	NP_055192	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	75					'de novo' cotranslational protein folding|chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane	chromatin binding|DNA binding|histone binding|Hsp70 protein binding|ubiquitin binding			kidney(1)	1						GTTTTCAGCATGGGAAACTCT	0.368													110	159	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131895713	131895713	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131895713G>T	uc003vra.3	-	10	2516	c.2287C>A	c.(2287-2289)CAG>AAG	p.Q763K		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	763	Extracellular (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1						GAGGTGTTCTGGCACTGTACG	0.617													8	54	---	---	---	---	PASS
CNTNAP2	26047	broad.mit.edu	37	7	146829512	146829512	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146829512G>A	uc003weu.1	+	8	1775	c.1259G>A	c.(1258-1260)GGC>GAC	p.G420D		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	420	Extracellular (Potential).|Laminin G-like 2.				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			GATAATTTGGGCAATGTGGAG	0.478										HNSCC(39;0.1)			46	96	---	---	---	---	PASS
SGK223	157285	broad.mit.edu	37	8	8185726	8185726	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8185726C>T	uc003wsh.3	-	4	2566	c.2566G>A	c.(2566-2568)GAC>AAC	p.D856N		NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin	856							ATP binding|non-membrane spanning protein tyrosine kinase activity				0						TGAGATTCGTCGTGGACGTTG	0.567													83	280	---	---	---	---	PASS
MFHAS1	9258	broad.mit.edu	37	8	8748228	8748228	+	Silent	SNP	G	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8748228G>T	uc003wsj.1	-	1	2904	c.2341C>A	c.(2341-2343)CGG>AGG	p.R781R		NM_004225	NP_004216	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified	781											0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		TGGGTGGCCCGGAGCAGTTCC	0.627													22	43	---	---	---	---	PASS
EXTL3	2137	broad.mit.edu	37	8	28575522	28575522	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28575522A>C	uc003xgz.1	+	3	2539	c.1946A>C	c.(1945-1947)GAA>GCA	p.E649A		NM_001440	NP_001431	O43909	EXTL3_HUMAN	exostoses-like 3	649	Lumenal (Potential).					integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding|protein binding			skin(2)	2		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		TCTGGCAAGGAATTTCAGGCA	0.547													20	64	---	---	---	---	PASS
WHSC1L1	54904	broad.mit.edu	37	8	38135924	38135924	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38135924T>G	uc003xli.2	-	22	4285	c.3767A>C	c.(3766-3768)GAG>GCG	p.E1256A	WHSC1L1_uc011lbm.1_Missense_Mutation_p.E1245A|WHSC1L1_uc010lwe.2_Missense_Mutation_p.E1207A|WHSC1L1_uc003xlh.2_Missense_Mutation_p.E35A	NM_023034	NP_075447	Q9BZ95	NSD3_HUMAN	WHSC1L1 protein isoform long	1256	SET.				cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			AAATGTTAACTCCATCCCTGA	0.443			T	NUP98	AML								8	29	---	---	---	---	PASS
CHD7	55636	broad.mit.edu	37	8	61769234	61769234	+	Silent	SNP	T	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61769234T>C	uc003xue.2	+	34	7872	c.7395T>C	c.(7393-7395)TTT>TTC	p.F2465F		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2465					central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CTTCAAAGTTTATCTTGCCTA	0.423													43	154	---	---	---	---	PASS
EEF1D	1936	broad.mit.edu	37	8	144671911	144671911	+	Intron	SNP	T	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144671911T>A	uc011lki.1	-						EEF1D_uc003yyp.1_Missense_Mutation_p.D114V|EEF1D_uc003yyq.1_Missense_Mutation_p.D164V|EEF1D_uc011lkj.1_Missense_Mutation_p.D114V|EEF1D_uc003yyr.2_Missense_Mutation_p.D114V|EEF1D_uc003yyt.2_Missense_Mutation_p.D114V|EEF1D_uc011lkk.1_Intron|EEF1D_uc003yys.2_Intron|EEF1D_uc003yyv.2_Intron|EEF1D_uc003yyu.2_Intron|EEF1D_uc011lkl.1_Intron	NM_001130057	NP_001123529	P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			AAGTGACTTGTCCAGCCACAC	0.672													3	10	---	---	---	---	PASS
EEF1D	1936	broad.mit.edu	37	8	144671912	144671912	+	Intron	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144671912C>T	uc011lki.1	-						EEF1D_uc003yyp.1_Missense_Mutation_p.D114N|EEF1D_uc003yyq.1_Missense_Mutation_p.D164N|EEF1D_uc011lkj.1_Missense_Mutation_p.D114N|EEF1D_uc003yyr.2_Missense_Mutation_p.D114N|EEF1D_uc003yyt.2_Missense_Mutation_p.D114N|EEF1D_uc011lkk.1_Intron|EEF1D_uc003yys.2_Intron|EEF1D_uc003yyv.2_Intron|EEF1D_uc003yyu.2_Intron|EEF1D_uc011lkl.1_Intron	NM_001130057	NP_001123529	P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			AGTGACTTGTCCAGCCACACG	0.672													3	11	---	---	---	---	PASS
DOCK8	81704	broad.mit.edu	37	9	340260	340260	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:340260C>A	uc003zgf.2	+	14	1730	c.1618C>A	c.(1618-1620)CCG>ACG	p.P540T	DOCK8_uc011lls.1_Missense_Mutation_p.P540T|DOCK8_uc010mgu.2_5'UTR|DOCK8_uc010mgv.2_Missense_Mutation_p.P472T|DOCK8_uc003zgg.2_Missense_Mutation_p.P472T|DOCK8_uc003zgh.2_RNA	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	540	DHR-1.				blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CCGGACACGCCCGCACAAAGA	0.423													19	56	---	---	---	---	PASS
DOCK8	81704	broad.mit.edu	37	9	340261	340261	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:340261C>A	uc003zgf.2	+	14	1731	c.1619C>A	c.(1618-1620)CCG>CAG	p.P540Q	DOCK8_uc011lls.1_Missense_Mutation_p.P540Q|DOCK8_uc010mgu.2_5'UTR|DOCK8_uc010mgv.2_Missense_Mutation_p.P472Q|DOCK8_uc003zgg.2_Missense_Mutation_p.P472Q|DOCK8_uc003zgh.2_RNA	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	540	DHR-1.				blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CGGACACGCCCGCACAAAGAG	0.418													19	56	---	---	---	---	PASS
MLLT3	4300	broad.mit.edu	37	9	20346394	20346394	+	3'UTR	SNP	A	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20346394A>C	uc003zoe.2	-	11					MLLT3_uc011lne.1_3'UTR|MLLT3_uc011lnf.1_3'UTR	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		aaaaaaaaccaaaaaaaaaaa	0.299			T	MLL	ALL								4	20	---	---	---	---	PASS
TLE4	7091	broad.mit.edu	37	9	82333685	82333685	+	Silent	SNP	T	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82333685T>C	uc004ald.2	+	16	2313	c.1464T>C	c.(1462-1464)CCT>CCC	p.P488P	TLE4_uc004alc.2_Silent_p.P463P|TLE4_uc010mpr.2_Silent_p.P342P|TLE4_uc004ale.2_Silent_p.P100P|TLE4_uc011lsq.1_Silent_p.P431P|TLE4_uc010mps.2_Silent_p.P387P|TLE4_uc004alf.2_Silent_p.P402P	NM_007005	NP_008936	O60756	BCE1_HUMAN	transducin-like enhancer protein 4	Error:Variant_position_missing_in_O60756_after_alignment										lung(2)|ovary(1)|breast(1)|skin(1)	5						AGCCTGTCCCTTTTCCACCCG	0.542													3	78	---	---	---	---	PASS
DIRAS2	54769	broad.mit.edu	37	9	93375806	93375806	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93375806C>T	uc004aqx.1	-	2	415	c.304G>A	c.(304-306)GAA>AAA	p.E102K		NM_017594	NP_060064	Q96HU8	DIRA2_HUMAN	Di-Ras2	102					small GTPase mediated signal transduction	intracellular|plasma membrane	GTP binding|GTPase activity				0						CAGATTTGTTCGTAGATGGGC	0.592													5	103	---	---	---	---	PASS
PIP4K2A	5305	broad.mit.edu	37	10	22896899	22896899	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22896899C>T	uc001irl.3	-	3	544	c.296G>A	c.(295-297)CGT>CAT	p.R99H		NM_005028	NP_005019	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	99	PIPK.						1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding			ovary(1)|skin(1)	2						CCGCAGGTTACGGAAGACCAT	0.438													22	35	---	---	---	---	PASS
OR4C6	219432	broad.mit.edu	37	11	55433591	55433591	+	3'UTR	SNP	C	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55433591C>A	uc001nht.3	+	3						NM_001004704	NP_001004704	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2						CTGAGAACATCATGTATTTCC	0.398													9	34	---	---	---	---	PASS
MS4A12	54860	broad.mit.edu	37	11	60265040	60265040	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60265040C>A	uc001npr.2	+	2	306	c.249C>A	c.(247-249)AAC>AAA	p.N83K	MS4A12_uc009ynb.2_Missense_Mutation_p.N83K	NM_017716	NP_060186	Q9NXJ0	M4A12_HUMAN	membrane-spanning 4-domains, subfamily A, member	83	Cytoplasmic (Potential).					integral to membrane	receptor activity				0						CAGTAATGAACTTTAAAGAAG	0.388													20	71	---	---	---	---	PASS
PRPF19	27339	broad.mit.edu	37	11	60658695	60658695	+	Silent	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60658695G>A	uc001nqf.2	-	16	1665	c.1458C>T	c.(1456-1458)CAC>CAT	p.H486H		NM_014502	NP_055317	Q9UMS4	PRP19_HUMAN	PRP19/PSO4 pre-mRNA processing factor 19	486	WD 7.				DNA repair|protein polyubiquitination|spliceosome assembly	catalytic step 2 spliceosome|nuclear speck|spindle|ubiquitin ligase complex	DNA binding|identical protein binding|ubiquitin-ubiquitin ligase activity			ovary(1)	1						TGAACTTGGCGTGATGCCCGA	0.542													12	42	---	---	---	---	PASS
SNHG1	23642	broad.mit.edu	37	11	62620742	62620742	+	Intron	SNP	T	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62620742T>G	uc001nvp.2	-						SLC3A2_uc001nwb.2_5'Flank|SLC3A2_uc001nwc.2_5'Flank|SLC3A2_uc001nwd.2_5'Flank|SLC3A2_uc001nwe.2_5'Flank|SLC3A2_uc001nwf.2_5'Flank|SNHG1_uc001nvo.2_Intron|SNHG1_uc001nvq.2_Intron|SNHG1_uc001nvs.2_Intron|SNHG1_uc001nvr.2_Intron|SNHG1_uc001nvt.2_RNA|SNHG1_uc001nvu.2_Intron|SNORD22_uc001nvv.2_5'Flank					Homo sapiens cDNA FLJ38530 fis, clone HCHON2001039.												0						CTATTGGCTGTAAAGCCTCCT	0.398													9	27	---	---	---	---	PASS
CLSTN3	9746	broad.mit.edu	37	12	7301668	7301668	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7301668C>A	uc001qsr.2	+	13	2226	c.1948C>A	c.(1948-1950)CAT>AAT	p.H650N	CLSTN3_uc001qss.2_Missense_Mutation_p.H662N	NM_014718	NP_055533	Q9BQT9	CSTN3_HUMAN	calsyntenin 3 precursor	650	Extracellular (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(1)	1						TGGCACTGCTCATTTTGCCCG	0.582													16	68	---	---	---	---	PASS
STYK1	55359	broad.mit.edu	37	12	10772767	10772767	+	Silent	SNP	G	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10772767G>C	uc001qys.2	-	11	1766	c.1245C>G	c.(1243-1245)CTC>CTG	p.L415L		NM_018423	NP_060893	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	415						integral to membrane|plasma membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8						AGTTGTAGAAGAGGCTCTCCA	0.453										HNSCC(73;0.22)			132	215	---	---	---	---	PASS
ALG10	84920	broad.mit.edu	37	12	34178892	34178892	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34178892G>A	uc001rlm.2	+	3	783	c.464G>A	c.(463-465)GGA>GAA	p.G155E		NM_032834	NP_116223	Q5BKT4	AG10A_HUMAN	asparagine-linked glycosylation 10 homolog	155	Helical; (Potential).				dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			skin(1)	1	Lung NSC(5;3.82e-05)|Acute lymphoblastic leukemia(23;0.0142)|all_hematologic(23;0.0429)	Lung NSC(34;0.204)|all_lung(34;0.235)				ACAGAAGCAGGATCTATGTTT	0.353													78	308	---	---	---	---	PASS
FBXW8	26259	broad.mit.edu	37	12	117448166	117448166	+	Silent	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117448166G>A	uc001twg.1	+	8	1360	c.1278G>A	c.(1276-1278)TTG>TTA	p.L426L	FBXW8_uc001twf.1_Silent_p.L360L|FBXW8_uc009zwp.1_RNA	NM_153348	NP_699179	Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8 isoform	426							protein binding			ovary(2)|pancreas(1)	3	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)		GCCGCCTCTTGAAGCTGGGTA	0.547													11	127	---	---	---	---	PASS
FBXW8	26259	broad.mit.edu	37	12	117448167	117448167	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117448167A>C	uc001twg.1	+	8	1361	c.1279A>C	c.(1279-1281)AAG>CAG	p.K427Q	FBXW8_uc001twf.1_Missense_Mutation_p.K361Q|FBXW8_uc009zwp.1_RNA	NM_153348	NP_699179	Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8 isoform	427							protein binding			ovary(2)|pancreas(1)	3	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)		CCGCCTCTTGAAGCTGGGTAA	0.552													10	128	---	---	---	---	PASS
BRCA2	675	broad.mit.edu	37	13	32911477	32911477	+	Silent	SNP	A	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32911477A>T	uc001uub.1	+	11	3212	c.2985A>T	c.(2983-2985)GGA>GGT	p.G995G		NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	995	Interaction with NPM1.				cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AATGGGCAGGACTCTTAGGTC	0.323			D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			29	89	---	---	---	---	PASS
ATP7B	540	broad.mit.edu	37	13	52539139	52539139	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52539139G>T	uc001vfw.2	-	5	1895	c.1738C>A	c.(1738-1740)CAC>AAC	p.H580N	ATP7B_uc010adv.2_Intron|ATP7B_uc001vfx.2_Missense_Mutation_p.H580N|ATP7B_uc001vfy.2_Missense_Mutation_p.H469N|ATP7B_uc010tgt.1_Missense_Mutation_p.H580N|ATP7B_uc010tgu.1_Missense_Mutation_p.H580N|ATP7B_uc010tgv.1_Missense_Mutation_p.H580N|ATP7B_uc010tgw.1_Intron	NM_000053	NP_000044	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	580	HMA 6.|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)		TCTATGTTGTGGACACAGGAC	0.517									Wilson_disease				20	95	---	---	---	---	PASS
PCDH8	5100	broad.mit.edu	37	13	53422672	53422672	+	5'UTR	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53422672C>T	uc001vhi.2	-	1					PCDH8_uc001vhj.2_5'UTR	NM_002590	NP_002581	O95206	PCDH8_HUMAN	protocadherin 8 isoform 1 precursor						cell-cell signaling|homophilic cell adhesion	cell junction|dendrite|integral to plasma membrane|postsynaptic membrane|presynaptic membrane	calcium ion binding			breast(1)	1		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		CTTTGCGAGCCCTGTGCGGGA	0.627													6	7	---	---	---	---	PASS
EDDM3B	64184	broad.mit.edu	37	14	21238699	21238699	+	Silent	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21238699C>T	uc001vyd.2	+	2	488	c.390C>T	c.(388-390)GAC>GAT	p.D130D		NM_022360	NP_071755	P56851	EP3B_HUMAN	human epididymis-specific 3 beta precursor	130					spermatid development	extracellular region				ovary(1)	1						GTAGCATGGACGGGTATGTTG	0.413													14	61	---	---	---	---	PASS
NUMB	8650	broad.mit.edu	37	14	73746101	73746101	+	Silent	SNP	A	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73746101A>G	uc001xny.1	-	12	1448	c.1128T>C	c.(1126-1128)CTT>CTC	p.L376L	NUMB_uc010aro.1_Intron|NUMB_uc010arp.1_Intron|NUMB_uc010arq.1_Intron|NUMB_uc010arr.1_Intron|NUMB_uc001xoa.1_Intron|NUMB_uc001xnz.1_Silent_p.L365L|NUMB_uc001xob.1_Intron|NUMB_uc001xod.1_Intron|NUMB_uc001xoc.1_Silent_p.L376L|NUMB_uc010ars.1_Silent_p.L365L|NUMB_uc010ttz.1_Intron|NUMB_uc001xoe.2_5'Flank	NM_001005743	NP_001005743	P49757	NUMB_HUMAN	numb homolog isoform 1	376					axon guidance|lateral ventricle development|neuroblast division in subventricular zone|positive regulation of neurogenesis	integral to plasma membrane				ovary(2)|central_nervous_system(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		CTGGCTTAGCAAGCACATGGA	0.527													16	61	---	---	---	---	PASS
GPR65	8477	broad.mit.edu	37	14	88477438	88477438	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88477438T>G	uc001xvv.2	+	2	777	c.247T>G	c.(247-249)TCT>GCT	p.S83A		NM_003608	NP_003599	Q8IYL9	PSYR_HUMAN	G protein-coupled receptor 65	83	Extracellular (Potential).				actin cytoskeleton reorganization|activation of Rho GTPase activity|apoptosis|immune response|multicellular organismal development|positive regulation of cAMP biosynthetic process|positive regulation of stress fiber assembly|response to acidity	integral to plasma membrane	G-protein coupled receptor activity				0						CTGGACTTTCTCTCCTGCCTT	0.408													80	305	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106090903	106090903	+	RNA	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106090903C>T	uc010tyt.1	-	3648		c.62508G>A			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron					Parts of antibodies, mostly variable regions.												0						CATTCCCCTCCTGCCACCTGC	0.587													47	203	---	---	---	---	PASS
DUOX1	53905	broad.mit.edu	37	15	45454451	45454451	+	Missense_Mutation	SNP	A	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45454451A>T	uc001zus.1	+	32	4470	c.4124A>T	c.(4123-4125)CAG>CTG	p.Q1375L	DUOX1_uc001zut.1_Missense_Mutation_p.Q1375L|DUOX1_uc010bee.1_Missense_Mutation_p.Q755L	NM_017434	NP_059130	Q9NRD9	DUOX1_HUMAN	dual oxidase 1 precursor	1375	Cytoplasmic (Potential).|FAD-binding FR-type.				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity			ovary(5)|skin(2)|breast(1)	8		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GAGGGCCACCAGGAGTGGCAT	0.542													24	66	---	---	---	---	PASS
FBN1	2200	broad.mit.edu	37	15	48779393	48779393	+	Silent	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48779393G>A	uc001zwx.1	-	29	3796	c.3468C>T	c.(3466-3468)ATC>ATT	p.I1156I		NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	1156	EGF-like 18; calcium-binding.				heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CACATTCATTGATGTCTGTCG	0.458													20	62	---	---	---	---	PASS
UNC13C	440279	broad.mit.edu	37	15	54626051	54626051	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54626051G>A	uc002ack.2	+	14	4581	c.4581G>A	c.(4579-4581)ATG>ATA	p.M1527I	UNC13C_uc002acl.2_Missense_Mutation_p.M357I	NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	1527					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TTTTTAGGATGAAGGTATCTC	0.373													8	16	---	---	---	---	PASS
CELF6	60677	broad.mit.edu	37	15	72579580	72579580	+	3'UTR	SNP	T	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72579580T>A	uc002auh.2	-	12					uc002aug.2_Intron|CELF6_uc002auk.3_RNA|CELF6_uc010biv.1_RNA|CELF6_uc010biw.2_3'UTR|CELF6_uc010ukl.1_3'UTR|CELF6_uc010ukm.1_3'UTR|CELF6_uc002aui.2_3'UTR|CELF6_uc002auj.2_3'UTR	NM_052840	NP_443072	Q96J87	CELF6_HUMAN	bruno-like 6, RNA binding protein						mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	nucleotide binding|RNA binding			large_intestine(1)|central_nervous_system(1)|skin(1)	3						GGACTCACCTTTCTGTGGCTG	0.557													13	33	---	---	---	---	PASS
LRRK1	79705	broad.mit.edu	37	15	101597210	101597210	+	Silent	SNP	A	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101597210A>T	uc002bwr.2	+	28	4801	c.4482A>T	c.(4480-4482)CGA>CGT	p.R1494R	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA|LRRK1_uc002bws.2_RNA	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	1494	Protein kinase.				small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AGTTCCGGCGACTGCAGGCGC	0.637													27	82	---	---	---	---	PASS
PIGQ	9091	broad.mit.edu	37	16	633428	633428	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:633428G>T	uc002cho.2	+	10	2179	c.2077G>T	c.(2077-2079)GGC>TGC	p.G693C	PIGQ_uc010bqw.2_3'UTR|PIGQ_uc002chn.2_3'UTR|PIGQ_uc010uui.1_3'UTR|PIGQ_uc002chp.2_Missense_Mutation_p.G263C|uc010uuj.1_Missense_Mutation_p.H120N	NM_148920	NP_683721	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	693					C-terminal protein lipidation|carbohydrate metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			central_nervous_system(1)	1		Hepatocellular(780;0.00335)				GCTCCCCAGTGGCTCTGCCCT	0.682													17	61	---	---	---	---	PASS
RTN4RL1	146760	broad.mit.edu	37	17	1840903	1840903	+	Silent	SNP	G	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1840903G>T	uc002ftp.2	-	2	232	c.213C>A	c.(211-213)CCC>CCA	p.P71P		NM_178568	NP_848663	Q86UN2	R4RL1_HUMAN	reticulon 4 receptor-like 1 precursor	71	LRR 1.				axon regeneration	anchored to plasma membrane	receptor activity				0						TGAAGTGGCCGGGCTGGAGGA	0.637													6	26	---	---	---	---	PASS
FAM83G	644815	broad.mit.edu	37	17	18874656	18874656	+	3'UTR	SNP	A	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18874656A>C	uc002guw.2	-	6					SLC5A10_uc002gur.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815											ovary(1)|central_nervous_system(1)	2						GTGTGGCTCCAGGCTGGGACA	0.667													3	62	---	---	---	---	PASS
EPN2	22905	broad.mit.edu	37	17	19186717	19186717	+	Silent	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19186717G>A	uc002gvd.3	+	3	733	c.285G>A	c.(283-285)CAG>CAA	p.Q95Q	EPN2_uc002gvc.2_Silent_p.Q95Q|EPN2_uc010vyn.1_Silent_p.Q95Q|EPN2_uc010cql.1_Intron|EPN2_uc002gve.3_Silent_p.Q95Q|EPN2_uc002gvf.3_Intron|EPN2_uc010vyo.1_Intron|EPN2_uc002gvg.1_Silent_p.Q95Q|EPN2_uc010vyp.1_Silent_p.Q95Q|EPN2_uc010vyq.1_Silent_p.Q95Q|EPN2_uc002gvh.1_Silent_p.Q95Q	NM_014964	NP_055779	O95208	EPN2_HUMAN	epsin 2 isoform b	95	ENTH.				endocytosis		lipid binding			skin(1)	1	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)					TGGCCCAGCAGTGCCGGGAGA	0.567													13	37	---	---	---	---	PASS
NLK	51701	broad.mit.edu	37	17	26449740	26449740	+	Silent	SNP	T	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26449740T>C	uc010crj.2	+	2	782	c.570T>C	c.(568-570)TGT>TGC	p.C190C	NLK_uc010cri.1_RNA	NM_016231	NP_057315	Q9UBE8	NLK_HUMAN	nemo like kinase	190	Protein kinase.				intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		AGATGTTGTGTTTTTTTAAGC	0.388													43	110	---	---	---	---	PASS
KRT36	8689	broad.mit.edu	37	17	39643672	39643672	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39643672C>A	uc002hwt.2	-	5	918	c.918G>T	c.(916-918)CAG>CAT	p.Q306H		NM_003771	NP_003762	O76013	KRT36_HUMAN	keratin 36	306	Rod.|Coil 2.					intermediate filament	protein binding|structural constituent of epidermis				0		Breast(137;0.000286)				TGATCTCCGTCTGGCAGCACT	0.607													3	26	---	---	---	---	PASS
GPATCH8	23131	broad.mit.edu	37	17	42477630	42477630	+	Silent	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42477630G>A	uc002igw.1	-	8	1879	c.1815C>T	c.(1813-1815)GGC>GGT	p.G605G	GPATCH8_uc002igv.1_Silent_p.G527G|GPATCH8_uc010wiz.1_Silent_p.G527G	NM_001002909	NP_001002909	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	605						intracellular	nucleic acid binding|zinc ion binding			ovary(2)|kidney(1)|skin(1)	4		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		CAGGATCTAGGCCTTGGAGAT	0.448											OREG0024461	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	39	74	---	---	---	---	PASS
CCDC47	57003	broad.mit.edu	37	17	61841511	61841511	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61841511G>C	uc002jbs.3	-	4	748	c.412C>G	c.(412-414)CTA>GTA	p.L138V	CCDC47_uc010ddx.2_Missense_Mutation_p.L138V|CCDC47_uc002jbt.2_Missense_Mutation_p.L138V	NM_020198	NP_064583	Q96A33	CCD47_HUMAN	coiled-coil domain containing 47 precursor	138	Helical; (Potential).					integral to membrane	protein binding				0						AAAATTTCTAGATAATAACTC	0.393													52	127	---	---	---	---	PASS
TNRC6C	57690	broad.mit.edu	37	17	76046332	76046332	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76046332G>A	uc002jud.2	+	4	1789	c.1189G>A	c.(1189-1191)GAA>AAA	p.E397K	TNRC6C_uc002juf.2_Missense_Mutation_p.E397K|TNRC6C_uc002jue.2_Missense_Mutation_p.E397K	NM_018996	NP_061869	Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C isoform 2	397	Sufficient for interaction with argonaute family proteins.|Gly-rich.				gene silencing by RNA|regulation of translation		nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			TACAGCAAGTGAAGGAAGTAG	0.532													33	70	---	---	---	---	PASS
ASPSCR1	79058	broad.mit.edu	37	17	79954308	79954308	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79954308G>T	uc002kcx.2	+	7	616	c.519G>T	c.(517-519)AAG>AAT	p.K173N	ASPSCR1_uc002kcw.1_Missense_Mutation_p.K173N|ASPSCR1_uc002kcy.2_Missense_Mutation_p.K173N|ASPSCR1_uc002kcz.2_Intron|ASPSCR1_uc002kda.2_Missense_Mutation_p.K96N|ASPSCR1_uc002kdb.1_Missense_Mutation_p.K96N	NM_024083	NP_076988	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region,	173							protein binding		ASPSCR1/TFE3(161)	soft_tissue(118)|kidney(43)|breast(1)	162	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			TTGTCATGAAGTGCTACGACC	0.532			T	TFE3	alveolar soft part sarcoma								10	49	---	---	---	---	PASS
C18orf19	125228	broad.mit.edu	37	18	13681730	13681730	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13681730T>C	uc010dlh.2	-	3	779	c.347A>G	c.(346-348)CAA>CGA	p.Q116R	C18orf19_uc010dlg.2_Missense_Mutation_p.Q116R|C18orf19_uc010dli.2_Missense_Mutation_p.Q116R|C18orf19_uc002ksj.3_Missense_Mutation_p.Q116R|C18orf19_uc010dlj.2_Intron	NM_001098801	NP_001092271	Q96ND0	CR019_HUMAN	hypothetical protein LOC125228	116						integral to membrane				breast(2)	2						AGATTTGTCTTGCAAAGGATC	0.398													47	161	---	---	---	---	PASS
MKNK2	2872	broad.mit.edu	37	19	2037842	2037842	+	3'UTR	SNP	A	C	C	rs78772412	byFrequency	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2037842A>C	uc002lus.2	-	14					MKNK2_uc002luq.1_Intron|MKNK2_uc010xgu.1_3'UTR|MKNK2_uc010xgv.1_3'UTR|MKNK2_uc002lur.2_Intron|MKNK2_uc002lut.1_3'UTR	NM_199054	NP_951009	Q9HBH9	MKNK2_HUMAN	MAP kinase-interacting serine/threonine kinase 2						cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation		ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(1)|breast(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGAAAAAAAAAAAAAAACAA	0.527													8	19	---	---	---	---	PASS
AP3D1	8943	broad.mit.edu	37	19	2115366	2115366	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2115366C>T	uc002luz.2	-	20	2424	c.2201G>A	c.(2200-2202)CGG>CAG	p.R734Q	AP3D1_uc002luy.2_Missense_Mutation_p.R643Q|AP3D1_uc002lva.2_Missense_Mutation_p.R734Q	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	734	Potential.				eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCTTCTGCCGGTGCCGCCG	0.542													10	42	---	---	---	---	PASS
VAV1	7409	broad.mit.edu	37	19	6853050	6853050	+	Silent	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6853050C>T	uc002mfu.1	+	25	2389	c.2292C>T	c.(2290-2292)CCC>CCT	p.P764P	VAV1_uc010xjh.1_Silent_p.P732P|VAV1_uc010dva.1_Silent_p.P742P|VAV1_uc002mfv.1_Silent_p.P709P	NM_005428	NP_005419	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	764	SH2.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1)	16						TGCAGTTCCCCTTCAAGGAGC	0.542													17	77	---	---	---	---	PASS
SMARCA4	6597	broad.mit.edu	37	19	11129632	11129632	+	Splice_Site	SNP	G	A	A	rs113895708		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11129632G>A	uc002mqf.3	+	17	2723	c.2439_splice	c.e17-1	p.S813_splice	SMARCA4_uc010dxp.2_Splice_Site_p.S813_splice|SMARCA4_uc010dxo.2_Splice_Site_p.S813_splice|SMARCA4_uc002mqg.1_Splice_Site_p.S813_splice|SMARCA4_uc010dxq.2_Splice_Site_p.S813_splice|SMARCA4_uc010dxr.2_Splice_Site_p.S813_splice|SMARCA4_uc002mqj.3_Splice_Site_p.S813_splice|SMARCA4_uc010dxs.2_Splice_Site_p.S813_splice|SMARCA4_uc010dxt.1_Splice_Site_p.S33_splice|SMARCA4_uc002mqh.3_5'Flank|SMARCA4_uc002mqi.1_5'Flank	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated						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.?(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)				TGTTCCATCAGAACGCTGTCC	0.557			F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				41	91	---	---	---	---	PASS
PKN1	5585	broad.mit.edu	37	19	14578458	14578458	+	Intron	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14578458C>T	uc002myp.2	+						PKN1_uc002myq.2_Intron|PKN1_uc002myr.2_5'UTR	NM_002741	NP_002732	Q16512	PKN1_HUMAN	protein kinase N1 isoform 2						activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	endosome|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding			ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8						GTGCAGGTGACACCACTCCCT	0.667													12	52	---	---	---	---	PASS
EMR3	84658	broad.mit.edu	37	19	14740973	14740973	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14740973T>A	uc002mzi.3	-	14	1838	c.1690A>T	c.(1690-1692)ACA>TCA	p.T564S	EMR3_uc010dzp.2_Missense_Mutation_p.T512S|EMR3_uc010xnv.1_Missense_Mutation_p.T438S	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor	564	Helical; Name=6; (Potential).				neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6						AGACACCATGTGCAGCCCAGG	0.502													14	59	---	---	---	---	PASS
RYR1	6261	broad.mit.edu	37	19	39026031	39026031	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39026031A>G	uc002oit.2	+	81	11645	c.11515A>G	c.(11515-11517)AGC>GGC	p.S3839G	RYR1_uc002oiu.2_Missense_Mutation_p.S3834G|RYR1_uc002oiv.1_Missense_Mutation_p.S754G	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	3839					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	GCAAACATGCAGGTAGGTTCG	0.448													46	119	---	---	---	---	PASS
SHKBP1	92799	broad.mit.edu	37	19	41094660	41094660	+	Silent	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41094660C>T	uc002oob.2	+	14	1516	c.1467C>T	c.(1465-1467)GGC>GGT	p.G489G	SHKBP1_uc002ooc.2_Silent_p.G464G|SHKBP1_uc002ood.2_Silent_p.G489G|SHKBP1_uc010xvl.1_Silent_p.G412G|SHKBP1_uc002ooe.2_Silent_p.G326G|SHKBP1_uc002oof.2_Silent_p.G326G|SHKBP1_uc010xvm.1_Silent_p.G269G|SHKBP1_uc010xvn.1_Silent_p.G367G	NM_138392	NP_612401	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	489						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|pancreas(1)	2			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			ATGGGCATGGCGGCTGCAGTG	0.622													3	60	---	---	---	---	PASS
CEACAM5	1048	broad.mit.edu	37	19	42224890	42224890	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42224890C>T	uc002ork.2	+	8	1941	c.1820C>T	c.(1819-1821)TCG>TTG	p.S607L	CEACAM5_uc002orj.1_Missense_Mutation_p.S606L|CEACAM5_uc002orl.2_Missense_Mutation_p.S607L	NM_004363	NP_004354	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion	607	Ig-like 7.					anchored to membrane|basolateral plasma membrane|integral to plasma membrane				skin(2)	2				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		TCTTACCTTTCGGGAGCGAAC	0.547													5	152	---	---	---	---	PASS
SNAP25	6616	broad.mit.edu	37	20	10273881	10273881	+	Missense_Mutation	SNP	C	T	T	rs1051276		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10273881C>T	uc002wnq.1	+	5	448	c.236C>T	c.(235-237)ACG>ATG	p.T79M	SNAP25_uc002wnr.1_Intron|SNAP25_uc002wns.1_Missense_Mutation_p.T16M|SNAP25_uc010gca.1_Intron|SNAP25_uc010gcb.1_Missense_Mutation_p.T16M|SNAP25_uc010gcc.1_Intron	NM_130811	NP_570824	P60880	SNP25_HUMAN	synaptosomal-associated protein 25 isoform	79	t-SNARE coiled-coil homology 1.				energy reserve metabolic process|glutamate secretion|neurotransmitter uptake|synaptic vesicle docking involved in exocytosis	cell junction|growth cone|perinuclear region of cytoplasm|synapse|synaptosome				skin(2)	2					Botulinum Toxin Type A(DB00083)	AAGAATTTGACGGACCTAGGA	0.458													5	139	---	---	---	---	PASS
DONSON	29980	broad.mit.edu	37	21	34956957	34956957	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34956957C>T	uc002ysk.2	-	4	791	c.724G>A	c.(724-726)GCT>ACT	p.A242T	DONSON_uc002ysn.1_Missense_Mutation_p.A125T|DONSON_uc002ysi.1_Missense_Mutation_p.A2T|DONSON_uc002ysj.2_5'UTR|DONSON_uc002ysl.2_5'UTR|DONSON_uc010gme.2_Missense_Mutation_p.A215T|DONSON_uc002ysm.2_Missense_Mutation_p.A242T	NM_017613	NP_060083	Q9NYP3	DONS_HUMAN	downstream neighbor of SON	242					multicellular organismal development	nucleus				ovary(1)|central_nervous_system(1)	2						GTCTTTCCAGCCATTTTTCTA	0.433													33	94	---	---	---	---	PASS
SIM2	6493	broad.mit.edu	37	21	38084845	38084845	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38084845T>A	uc002yvr.2	+	3	327	c.271T>A	c.(271-273)TTT>ATT	p.F91I	SIM2_uc002yvq.2_Missense_Mutation_p.F91I	NM_005069	NP_005060	Q14190	SIM2_HUMAN	single-minded homolog 2 long isoform	91	PAS 1.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1						TTTGGATGGATTTGTTTTTGT	0.378													25	100	---	---	---	---	PASS
TRPM2	7226	broad.mit.edu	37	21	45859019	45859019	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45859019T>A	uc002zet.1	+	31	4450	c.4237T>A	c.(4237-4239)TCT>ACT	p.S1413T	TRPM2_uc002zeu.1_Missense_Mutation_p.S1413T|TRPM2_uc002zew.1_Missense_Mutation_p.S1413T|TRPM2_uc010gpt.1_Missense_Mutation_p.S1463T|TRPM2_uc002zex.1_Missense_Mutation_p.S1199T|TRPM2_uc002zey.1_Missense_Mutation_p.S892T|TRPM2_uc011aff.1_Missense_Mutation_p.S94T	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	1413	Nudix hydrolase.|Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3						GCACTGGCCGTCTTTTGAAAA	0.592													11	44	---	---	---	---	PASS
CLCN5	1184	broad.mit.edu	37	X	49775291	49775291	+	Intron	SNP	A	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49775291A>C	uc004dor.1	+						CLCN5_uc004doq.1_Intron|hsa-mir-500b|MI0015903_RNA|MIR660_hsa-mir-660|MI0003684_5'Flank	NM_001127899	NP_001121371	P51795	CLCN5_HUMAN	chloride channel 5 isoform a						excretion	apical part of cell|endosome membrane|Golgi membrane|integral to plasma membrane	antiporter activity|ATP binding			ovary(2)|lung(1)|central_nervous_system(1)	4	Ovarian(276;0.236)					CCCCTCTCTAATCCTTGCTAC	0.507													7	3	---	---	---	---	PASS
FAM120C	54954	broad.mit.edu	37	X	54114286	54114286	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54114286A>G	uc004dsz.3	-	12	2622	c.2539T>C	c.(2539-2541)TGC>CGC	p.C847R	FAM120C_uc011moh.1_Intron	NM_017848	NP_060318	Q9NX05	F120C_HUMAN	hypothetical protein LOC54954	847										ovary(1)|central_nervous_system(1)	2						CATGGACAGCAATGCTCCCAA	0.537													3	49	---	---	---	---	PASS
BHLHB9	80823	broad.mit.edu	37	X	102004677	102004677	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102004677G>T	uc010nog.2	+	4	1325	c.754G>T	c.(754-756)GCT>TCT	p.A252S	BHLHB9_uc011mrq.1_Missense_Mutation_p.A252S|BHLHB9_uc011mrr.1_Missense_Mutation_p.A252S|BHLHB9_uc011mrs.1_Missense_Mutation_p.A252S|BHLHB9_uc011mrt.1_Missense_Mutation_p.A252S|BHLHB9_uc004ejo.2_Missense_Mutation_p.A252S|BHLHB9_uc011mru.1_Missense_Mutation_p.A252S|BHLHB9_uc011mrv.1_Missense_Mutation_p.A252S	NM_001142526	NP_001135998	Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class	252						cytoplasm|nucleus	binding			ovary(2)	2						TCTGGCCTCCGCTGAAGAAAA	0.517													48	42	---	---	---	---	PASS
PLS3	5358	broad.mit.edu	37	X	114880823	114880823	+	Silent	SNP	G	C	C			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114880823G>C	uc004eqd.2	+	13	1869	c.1479G>C	c.(1477-1479)CTG>CTC	p.L493L	PLS3_uc010nqg.2_Silent_p.L275L|PLS3_uc011mtf.1_Silent_p.L480L|PLS3_uc004eqe.2_Silent_p.L493L|PLS3_uc011mtg.1_Silent_p.L466L|PLS3_uc011mth.1_Silent_p.L448L|PLS3_uc011mti.1_Silent_p.L169L|PLS3_uc011mtj.1_Silent_p.L87L|PLS3_uc011mtk.1_Silent_p.L154L|PLS3_uc011mtl.1_RNA	NM_005032	NP_005023	P13797	PLST_HUMAN	plastin 3	493	Actin-binding 2.|CH 3.					cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2						ACCAAACCCTGACTTTAGCTT	0.418													41	50	---	---	---	---	PASS
FUCA1	2517	broad.mit.edu	37	1	24175455	24175456	+	Intron	INS	-	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24175455_24175456insT	uc001bie.2	-							NM_000147	NP_000138	P04066	FUCO_HUMAN	fucosidase, alpha-L-1, tissue precursor						fucose metabolic process|glycosaminoglycan catabolic process	lysosome	alpha-L-fucosidase activity|cation binding			breast(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		TGCTGTTTTAAttttttttttt	0.183													4	2	---	---	---	---	
CATSPER4	378807	broad.mit.edu	37	1	26527208	26527214	+	Intron	DEL	GGCCTTA	-	-	rs71697047		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26527208_26527214delGGCCTTA	uc010oez.1	+						CATSPER4_uc010oey.1_Intron|CATSPER4_uc009vsf.2_Intron	NM_198137	NP_937770	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4						cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|voltage-gated ion channel activity			ovary(1)	1		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		CTGAAATGAGGGCCTTAGAACCCTGGG	0.565													6	7	---	---	---	---	
MACF1	23499	broad.mit.edu	37	1	39833676	39833676	+	Intron	DEL	T	-	-	rs111840698		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39833676delT	uc010oiu.1	+						MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TGTTTGTTTGTTTTTTTTAAA	0.159													4	2	---	---	---	---	
C1orf173	127254	broad.mit.edu	37	1	75059958	75059959	+	Intron	DEL	GT	-	-	rs35732328		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75059958_75059959delGT	uc001dgg.2	-						uc001dgh.2_Intron|C1orf173_uc001dgi.3_Intron	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254											ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5						AAAATGGGGCgtgtgtgtgtgt	0.312													4	2	---	---	---	---	
SLC30A10	55532	broad.mit.edu	37	1	220115031	220115032	+	Intron	DEL	TC	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220115031_220115032delTC	uc001hlu.1	-									Q6XR72	ZNT10_HUMAN	Synthetic construct DNA, clone: pF1KB7405, Homo sapiens SLC30A10 gene for solute carrier family 30, member 10, without stop codon, in Flexi system.						zinc ion transport	integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)		tttctccctttctctctctctc	0.099													6	3	---	---	---	---	
CMPK2	129607	broad.mit.edu	37	2	6995442	6995447	+	Intron	DEL	GCCTCT	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6995442_6995447delGCCTCT	uc002qyo.2	-						CMPK2_uc010yis.1_Intron|CMPK2_uc010ewv.2_Intron	NM_207315	NP_997198	Q5EBM0	CMPK2_HUMAN	UMP-CMP kinase 2 precursor						dTDP biosynthetic process	mitochondrion	ATP binding|cytidylate kinase activity|thymidylate kinase activity|UMP kinase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ctgctctctcgcctctgcctctgccc	0.000													5	3	---	---	---	---	
MTA3	57504	broad.mit.edu	37	2	42752764	42752771	+	Intron	DEL	TACTTTCT	-	-	rs59291067		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42752764_42752771delTACTTTCT	uc002rso.1	+							NM_020744	NP_065795	Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2						ccttccttcctactttctttctttcttt	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	54278851	54278851	+	IGR	DEL	A	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54278851delA								PSME4 (80874 upstream) : ACYP2 (63559 downstream)																							CTGATGCAGCAAAAAAAGGAA	0.294													5	3	---	---	---	---	
HK2	3099	broad.mit.edu	37	2	75095103	75095104	+	Intron	INS	-	TA	TA	rs142180635	by1000genomes	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75095103_75095104insTA	uc002snd.2	+							NM_000189	NP_000180	P52789	HXK2_HUMAN	hexokinase 2						apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2						TACCCAACATGTACTCAGTATT	0.490													4	6	---	---	---	---	
C2orf3	6936	broad.mit.edu	37	2	75918986	75918987	+	Intron	INS	-	AA	AA	rs144955620	by1000genomes	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75918986_75918987insAA	uc002sno.2	-						C2orf3_uc010ffs.2_Intron|C2orf3_uc002snn.2_Intron|C2orf3_uc010fft.2_Intron	NM_003203	NP_003194	P16383	GCF_HUMAN	hypothetical protein LOC6936						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						AGTTGGTGGGTAAAGGGTTTGT	0.248													3	6	---	---	---	---	
GPAT2	150763	broad.mit.edu	37	2	96689661	96689661	+	Intron	DEL	C	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96689661delC	uc002svf.2	-						GPAT2_uc002svd.2_Intron|GPAT2_uc002sve.2_Intron|GPAT2_uc002svg.2_Intron|GPAT2_uc010yuh.1_Intron|GPAT2_uc002svh.2_Intron	NM_207328	NP_997211	Q6NUI2	GPAT2_HUMAN	glycerol-3-phosphate acyltransferase 2,						glycerol-3-phosphate metabolic process|phospholipid biosynthetic process|triglyceride biosynthetic process	integral to membrane|mitochondrial outer membrane	glycerol-3-phosphate O-acyltransferase activity				0						TCTCCAACTGCCCTGCCTACC	0.632													7	5	---	---	---	---	
ANKRD36	375248	broad.mit.edu	37	2	97864367	97864367	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97864367delA	uc010yva.1	+	44	2971	c.2727delA	c.(2725-2727)GGAfs	p.G909fs	ANKRD36_uc002sxo.2_Frame_Shift_Del_p.G325fs|ANKRD36_uc002sxp.3_Intron|ANKRD36_uc002sxq.1_RNA	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	909											0						TAGCCAGAGGAAAAAAGGATG	0.303													4	2	---	---	---	---	
MFSD9	84804	broad.mit.edu	37	2	103343084	103343085	+	Intron	DEL	CA	-	-	rs112803412		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103343084_103343085delCA	uc002tcb.2	-						MFSD9_uc010fja.2_Intron	NM_032718	NP_116107	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing						transmembrane transport	integral to membrane|plasma membrane	transporter activity			ovary(2)|breast(2)	4						ctcgcgcacgcacacacacaca	0.361													3	3	---	---	---	---	
MRPS9	64965	broad.mit.edu	37	2	105706585	105706589	+	Intron	DEL	AAAAC	-	-	rs67433632		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105706585_105706589delAAAAC	uc002tcn.3	+							NM_182640	NP_872578	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9 precursor						DNA damage response, detection of DNA damage|translation	mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome				0						TCTTTCTTTAaaaacaaaacaaaac	0.341													6	3	---	---	---	---	
PAX8	7849	broad.mit.edu	37	2	114004578	114004579	+	Intron	DEL	GT	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114004578_114004579delGT	uc010yxt.1	-						PAX8_uc010yxu.1_Intron|PAX8_uc010yxv.1_Intron|PAX8_uc002tjm.2_Intron|PAX8_uc002tjn.2_Intron|PAX8_uc010fku.1_Intron|LOC654433_uc002tjq.3_Intron|LOC654433_uc010fks.2_Intron|LOC654433_uc010fkt.2_Intron|LOC654433_uc002tjr.3_Intron	NM_003466	NP_003457	Q06710	PAX8_HUMAN	paired box 8 isoform PAX8A						branching involved in ureteric bud morphogenesis|cellular response to gonadotropin stimulus|central nervous system development|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|metanephric collecting duct development|metanephric comma-shaped body morphogenesis|metanephric distal convoluted tubule development|metanephric nephron tubule formation|metanephric S-shaped body morphogenesis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|otic vesicle development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric field specification|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of thyroid-stimulating hormone secretion|thyroid gland development|transcription, DNA-dependent	nucleoplasm	protein binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid-stimulating hormone receptor activity			ovary(1)|lung(1)	2						ACAGGTGCTGGTGTGTGTGTGT	0.569			T	PPARG	follicular thyroid		Thyroid dysgenesis 						4	2	---	---	---	---	
PLEKHB2	55041	broad.mit.edu	37	2	132109442	132109446	+	Intron	DEL	TTTTG	-	-	rs70994755		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132109442_132109446delTTTTG	uc002tsh.2	+									Q96CS7	PKHB2_HUMAN	SubName: Full=Putative uncharacterized protein PLEKHB2;							membrane	protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0828)		attttcttTCTTTTGTTTTGTTTTA	0.234													6	3	---	---	---	---	
CYP20A1	57404	broad.mit.edu	37	2	204137273	204137274	+	Intron	INS	-	A	A	rs72103565		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204137273_204137274insA	uc002uzv.3	+						CYP20A1_uc002uzx.3_Intron|CYP20A1_uc010zif.1_Intron|CYP20A1_uc002uzy.3_Intron|CYP20A1_uc002uzw.3_Intron|CYP20A1_uc010ftw.2_Intron	NM_177538	NP_803882	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A,							integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0						aaccctgactcaaaaaaaaaaa	0.104													5	3	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191507	10191507	+	Frame_Shift_Del	DEL	G	-	-	rs5030821		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191507delG	uc003bvc.2	+	3	713	c.500delG	c.(499-501)CGGfs	p.R167fs	VHL_uc003bvd.2_Frame_Shift_Del_p.R126fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	167			R -> G (in VHLD; type I-II).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.R167W(6)|p.R167Q(4)|p.R167fs*3(2)|p.R167G(1)|p.S168fs*2(1)|p.R167fs*1(1)|p.V166fs*6(1)|p.R167fs*6(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CAGGTTGTCCGGAGCCTAGTC	0.512		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				32	18	---	---	---	---	
NT5DC2	64943	broad.mit.edu	37	3	52559178	52559181	+	Intron	DEL	GGGT	-	-	rs61419666		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52559178_52559181delGGGT	uc003deo.2	-						NT5DC2_uc003dem.2_Intron|NT5DC2_uc003den.2_Intron|NT5DC2_uc010hmi.2_Intron|NT5DC2_uc010hmj.2_Intron	NM_022908	NP_075059	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2 isoform 2								hydrolase activity|metal ion binding				0				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)		GGGGGGGGGGGGGTTTCCTGGCCC	0.701													5	4	---	---	---	---	
IFT122	55764	broad.mit.edu	37	3	129178453	129178456	+	Intron	DEL	TTCC	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129178453_129178456delTTCC	uc003emm.2	+						IFT122_uc003eml.2_Intron|IFT122_uc003emn.2_Intron|IFT122_uc003emo.2_Intron|IFT122_uc003emp.2_Intron|IFT122_uc010htc.2_Intron|IFT122_uc011bky.1_Intron|IFT122_uc003emq.2_Intron|IFT122_uc011bkx.1_Intron|IFT122_uc011bkz.1_5'Flank	NM_052989	NP_443715	Q9HBG6	IF122_HUMAN	WD repeat domain 10 isoform 2						camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2						ccttccttctttccttccttcctt	0.010													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	31961719	31961722	+	IGR	DEL	CTCT	-	-	rs77033972		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31961719_31961722delCTCT								PCDH7 (813298 upstream) : None (None downstream)																							tcctccctccctctttctttcctt	0.064													5	3	---	---	---	---	
NUP54	53371	broad.mit.edu	37	4	77054013	77054014	+	Intron	INS	-	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77054013_77054014insT	uc003hjs.2	-						NUP54_uc010ije.2_Intron|NUP54_uc011cbs.1_Intron|NUP54_uc011cbt.1_Intron|NUP54_uc003hjt.2_Intron	NM_017426	NP_059122	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa						carbohydrate metabolic process|glucose transport|mRNA transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleoplasm				ovary(1)|lung(1)	2						AAAATGtttccttttttttttt	0.168													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	88802886	88802889	+	IGR	DEL	AAAG	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88802886_88802889delAAAG								MEPE (34944 upstream) : SPP1 (93913 downstream)																							gaagaaagaaaaagaaagagagag	0.049													4	3	---	---	---	---	
SDHA	6389	broad.mit.edu	37	5	225328	225329	+	Intron	INS	-	G	G	rs34815560		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:225328_225329insG	uc003jao.3	+						SDHA_uc003jan.2_Intron|SDHA_uc011clv.1_Intron|SDHA_uc011clw.1_Intron|SDHA_uc003jap.3_Intron|SDHA_uc003jaq.3_5'Flank	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,						nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	actgaggctaagGATGGAATCA	0.297									Familial_Paragangliomas				3	3	---	---	---	---	
MTRR	4552	broad.mit.edu	37	5	7885675	7885676	+	Intron	INS	-	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7885675_7885676insT	uc003jed.2	+						MTRR_uc010itn.1_Intron|MTRR_uc003jee.3_Intron|MTRR_uc003jef.3_Intron|MTRR_uc003jeg.3_Intron|MTRR_uc010ito.2_Intron	NM_024010	NP_076915	Q9UBK8	MTRR_HUMAN	methionine synthase reductase isoform 2						methionine biosynthetic process	cytosol	[methionine synthase] reductase activity|flavin adenine dinucleotide binding|FMN binding|iron ion binding|NADP binding			ovary(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	ACAATTGTGTGTTTTTTTTTTT	0.252													4	3	---	---	---	---	
FLJ37543	285668	broad.mit.edu	37	5	60979878	60979879	+	Intron	INS	-	CCTCTCTCCCCACCTCCCTCT	CCTCTCTCCCCACCTCCCTCT	rs146756502	by1000genomes	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60979878_60979879insCCTCTCTCCCCACCTCCCTCT	uc003jst.1	+						uc003jsu.1_Intron|uc010iwo.1_Intron|uc003jsv.2_Intron	NM_173667	NP_775938	Q2M2E5	CE064_HUMAN	hypothetical protein LOC285668 precursor							extracellular region					0		Lung NSC(810;0.000468)|Prostate(74;0.0283)|Breast(144;0.237)				ttccttccttcctcccttcctt	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	166327307	166327308	+	IGR	INS	-	AAGG	AAGG	rs145009687	by1000genomes	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166327307_166327308insAAGG								None (None upstream) : ODZ2 (384535 downstream)																							cctgaaaaaaaaaggaaggaag	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	173545096	173545096	+	IGR	DEL	T	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173545096delT								HMP19 (8915 upstream) : MSX2 (606479 downstream)																							cttccttccctccttccttcc	0.000													4	2	---	---	---	---	
NOP16	51491	broad.mit.edu	37	5	175814066	175814069	+	Intron	DEL	TCTC	-	-	rs145796794		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175814066_175814069delTCTC	uc011dfl.1	-						NOP16_uc003med.2_Intron|NOP16_uc003mee.2_Intron|NOP16_uc011dfm.1_Intron|HIGD2A_uc003meg.2_5'Flank	NM_016391	NP_057475	Q9Y3C1	NOP16_HUMAN	NOP16 nucleolar protein homolog							nucleolus				ovary(1)|central_nervous_system(1)	2						GGAGGCTTTTTCTCTCTCtctctc	0.245													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	41391768	41391769	+	IGR	DEL	AC	-	-	rs71698304		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41391768_41391769delAC								NCR2 (73143 upstream) : FOXP4 (122395 downstream)																							Aacaccacatacacacacacac	0.267													3	3	---	---	---	---	
MDN1	23195	broad.mit.edu	37	6	90409615	90409616	+	Intron	INS	-	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90409615_90409616insA	uc003pnn.1	-							NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCAAAACTAGTAAAAAAAAAAC	0.337													5	6	---	---	---	---	
HDAC9	9734	broad.mit.edu	37	7	18826440	18826443	+	Intron	DEL	TTCA	-	-	rs148795227	by1000genomes	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18826440_18826443delTTCA	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc011jyd.1_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc003sua.1_Intron	NM_058176	NP_478056	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 1						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)	ccttccttccttcattccttcctt	0.211													5	3	---	---	---	---	
NDUFB2	4708	broad.mit.edu	37	7	140404902	140404902	+	Intron	DEL	T	-	-	rs72099907		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140404902delT	uc003vwa.2	+						NDUFB2_uc010lnl.2_Intron	NM_004546	NP_004537	O95178	NDUB2_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.00956)				NADH(DB00157)	CTGTATCTGCttttttttttt	0.164													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	99947747	99947747	+	IGR	DEL	T	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99947747delT								LOC340508 (103520 upstream) : ZNF322B (9886 downstream)																							TTTTCACTTCTTTCAAGCCTT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	112295225	112295238	+	IGR	DEL	TTTTTTTTTTTTTT	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112295225_112295238delTTTTTTTTTTTTTT								PTPN3 (34632 upstream) : PALM2 (107834 downstream)																							CTTTTCTGGGtttttttttttttttttttttttt	0.229													5	4	---	---	---	---	
EHMT1	79813	broad.mit.edu	37	9	140682104	140682104	+	Intron	DEL	T	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140682104delT	uc011mfc.1	+						EHMT1_uc004cob.1_Intron	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		AGGAGGGGCCTGTCTTAAGAG	0.657													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42600053	42600053	+	IGR	DEL	T	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42600053delT								None (None upstream) : LOC441666 (227262 downstream)																							ttgaacggaattgaatggaat	0.000													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	65402008	65402008	+	IGR	DEL	T	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65402008delT								REEP3 (20037 upstream) : None (None downstream)																							ccttccttccttttttttttt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	10392080	10392081	+	IGR	INS	-	CTT	CTT	rs143361134		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10392080_10392081insCTT								GABARAPL1 (16358 upstream) : KLRD1 (64969 downstream)																							ttccttccttccttcttccttc	0.045													4	2	---	---	---	---	
COPZ1	22818	broad.mit.edu	37	12	54730828	54730829	+	Intron	DEL	AG	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54730828_54730829delAG	uc001sfs.1	+						COPZ1_uc001sft.2_Intron|COPZ1_uc009znm.1_Intron|COPZ1_uc010sot.1_Intron|uc010sou.1_5'Flank|MIR148B_hsa-mir-148b|MI0000811_5'Flank	NM_016057	NP_057141	P61923	COPZ1_HUMAN	coatomer protein complex, subunit zeta 1						COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol					0						aaaaaaaaaaagaaGCCCCTGA	0.203													9	5	---	---	---	---	
SLC25A3	5250	broad.mit.edu	37	12	98991896	98991896	+	Intron	DEL	T	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98991896delT	uc001tfo.2	+						SLC25A3_uc001tfm.2_Intron|SLC25A3_uc001tfn.2_Intron|SLC25A3_uc001tfp.2_Intron|SLC25A3_uc001tfq.2_Intron|SLC25A3_uc001tfr.2_Intron|SLC25A3_uc001tfs.2_Intron|SLC25A3_uc009ztn.2_Intron|SLC25A3_uc001tft.2_Intron|SNORA53_uc001tfu.1_5'Flank	NM_005888	NP_005879	Q00325	MPCP_HUMAN	solute carrier family 25 member 3 isoform a						generation of precursor metabolites and energy	integral to plasma membrane|mitochondrial inner membrane	phosphate carrier activity|symporter activity				0		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)		TCTTGCCTTATTTTAGCACTG	0.338													17	13	---	---	---	---	
SLC17A8	246213	broad.mit.edu	37	12	100774908	100774915	+	Intron	DEL	CATCTCAG	-	-	rs68046331		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100774908_100774915delCATCTCAG	uc010svi.1	+						SLC17A8_uc009ztx.2_Intron	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3						TAGCTCCTCCcatctcagcatctcagca	0.221													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	108972445	108972447	+	IGR	DEL	CCT	-	-	rs140801524	by1000genomes	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108972445_108972447delCCT								ISCU (9287 upstream) : TMEM119 (11177 downstream)																							atcaccaccacctccatcaccac	0.000													4	2	---	---	---	---	
KSR2	283455	broad.mit.edu	37	12	117965094	117965107	+	Intron	DEL	ACACACACACACAG	-	-	rs59836858		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117965094_117965107delACACACACACACAG	uc001two.2	-							NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGacacacacacacacacacacagacacacacac	0.234													7	4	---	---	---	---	
GCN1L1	10985	broad.mit.edu	37	12	120602669	120602670	+	Intron	INS	-	T	T			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120602669_120602670insT	uc001txo.2	-							NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis						regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					attacagcttgttttttttttt	0.000													4	2	---	---	---	---	
STARD13	90627	broad.mit.edu	37	13	33751958	33751959	+	Intron	INS	-	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33751958_33751959insA	uc001uuw.2	-						STARD13_uc001uuu.2_Intron|STARD13_uc001uuv.2_Intron|STARD13_uc001uux.2_Intron|STARD13_uc010tec.1_Intron|STARD13_uc010abh.1_Intron	NM_178006	NP_821074	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		aggaaggaaggaaggaaggaag	0.000													4	2	---	---	---	---	
LECT1	11061	broad.mit.edu	37	13	53283015	53283015	+	Intron	DEL	A	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53283015delA	uc001vhf.2	-						LECT1_uc001vhg.2_Intron|LECT1_uc001vhh.2_Intron	NM_007015	NP_008946	O75829	LECT1_HUMAN	leukocyte cell derived chemotaxin 1 isoform 1						cartilage development|proteoglycan metabolic process	endomembrane system|extracellular region|integral to membrane				ovary(2)	2		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.38e-08)		TTGGGCTAATAGTTAAACATA	0.328													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	78093839	78093842	+	IGR	DEL	TTCC	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78093839_78093842delTTCC								MYCBP2 (192662 upstream) : SCEL (15967 downstream)																							tttctttcttttccttccttcctt	0.020													4	2	---	---	---	---	
NALCN	259232	broad.mit.edu	37	13	102028868	102028872	+	Intron	DEL	AAAAT	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102028868_102028872delAAAAT	uc001vox.1	-						NALCN_uc001voy.2_Intron|NALCN_uc001voz.2_Intron|NALCN_uc001vpa.2_Intron	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ctccatctcaaaaataaaataaaat	0.141													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	23211221	23211222	+	IGR	INS	-	AG	AG	rs72167420		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23211221_23211222insAG								ABHD4 (129964 upstream) : OXA1L (24509 downstream)																							gaaagaaagaaagagagagaga	0.020													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	54361815	54361818	+	IGR	DEL	CTTC	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54361815_54361818delCTTC								DDHD1 (741769 upstream) : BMP4 (54639 downstream)																							ccctccctctcttccttccttcct	0.000													5	4	---	---	---	---	
C14orf37	145407	broad.mit.edu	37	14	58727897	58727898	+	Intron	INS	-	T	T	rs11402145		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58727897_58727898insT	uc010tro.1	-						PSMA3_uc001xdj.1_Intron|PSMA3_uc001xdk.1_Intron	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor							integral to membrane	binding				0						GTCCAACAGAAttttttttttt	0.109													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	95193580	95193580	+	IGR	DEL	A	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95193580delA								SERPINA13 (80250 upstream) : GSC (40981 downstream)																							TCAGTTTCTTAAaaaaaaaaa	0.363													5	3	---	---	---	---	
FAM82A2	55177	broad.mit.edu	37	15	41037611	41037611	+	Intron	DEL	T	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41037611delT	uc001zmo.1	-						FAM82A2_uc001zmp.1_Intron|FAM82A2_uc001zmq.1_Intron	NM_018145	NP_060615	Q96TC7	RMD3_HUMAN	family with sequence similarity 82, member A2						apoptosis|cell differentiation	integral to membrane|microtubule|mitochondrial membrane|nucleus|spindle pole	protein binding				0						ACTTTTTTtcttttttttttt	0.219													9	4	---	---	---	---	
GATM	2628	broad.mit.edu	37	15	45668604	45668615	+	Intron	DEL	CTTCAGGAAGCT	-	-	rs138059319		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45668604_45668615delCTTCAGGAAGCT	uc001zvc.2	-						GATM_uc001zvb.2_Intron|GATM_uc010uev.1_Intron	NM_001482	NP_001473	P50440	GATM_HUMAN	L-arginine:glycine amidinotransferase precursor						creatine biosynthetic process	mitochondrial inner membrane|mitochondrial intermembrane space	glycine amidinotransferase activity|protein binding				0		all_cancers(109;1.25e-09)|all_epithelial(112;5.56e-08)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.87e-16)|GBM - Glioblastoma multiforme(94;1.97e-06)	Creatine(DB00148)|Glycine(DB00145)|L-Ornithine(DB00129)	aagggaagagcttcaggaagctcttcaggaag	0.198													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84063040	84063041	+	IGR	INS	-	AGGG	AGGG			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84063040_84063041insAGGG								BNC1 (109572 upstream) : SH3GL3 (53050 downstream)																							gggagggagggaggaaggatgg	0.203													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	87757789	87757796	+	IGR	DEL	GGAAGGAA	-	-	rs146367126		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87757789_87757796delGGAAGGAA								AGBL1 (185506 upstream) : NCRNA00052 (362364 downstream)																							ggggaaggacggaaggaaggaaggaagg	0.226													4	3	---	---	---	---	
CCDC64B	146439	broad.mit.edu	37	16	3078617	3078619	+	Intron	DEL	ATT	-	-	rs150643417		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3078617_3078619delATT	uc002ctf.3	-						CCDC64B_uc002cte.3_Intron	NM_001103175	NP_001096645	A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B												0						AGTGGGGATCATTATAACCCGTA	0.645													3	3	---	---	---	---	
IQCK	124152	broad.mit.edu	37	16	19830814	19830814	+	Intron	DEL	A	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19830814delA	uc002dgr.2	+						IQCK_uc002dgs.2_Intron|IQCK_uc010vat.1_Intron|IQCK_uc010bwc.2_Intron|IQCK_uc010vau.1_Intron	NM_153208	NP_694940	Q8N0W5	IQCK_HUMAN	IQ motif containing K											skin(1)	1						gactccatctaaaaaaaaaaa	0.154													7	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	32490382	32490382	+	IGR	DEL	A	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32490382delA								HERC2P4 (326508 upstream) : TP53TG3B (194459 downstream)																							ACAAGAGACCAGGGGGATAAG	0.393													5	4	---	---	---	---	
CCDC47	57003	broad.mit.edu	37	17	61841925	61841925	+	Intron	DEL	T	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61841925delT	uc002jbs.3	-						CCDC47_uc010ddx.2_Intron|CCDC47_uc002jbt.2_Intron	NM_020198	NP_064583	Q96A33	CCD47_HUMAN	coiled-coil domain containing 47 precursor							integral to membrane	protein binding				0						TAGGTGTTGATTTTTTTTTTT	0.353													4	2	---	---	---	---	
FTSJ3	117246	broad.mit.edu	37	17	61900955	61900955	+	Intron	DEL	A	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61900955delA	uc002jbz.2	-						FTSJ3_uc002jca.2_Intron	NM_017647	NP_060117	Q8IY81	RRMJ3_HUMAN	FtsJ homolog 3						RNA methylation|rRNA processing	nucleolus	methyltransferase activity|nucleic acid binding			ovary(1)	1						actccgtctcaaaaaaaaaaa	0.169													6	6	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3581662	3581663	+	Intron	INS	-	A	A			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3581662_3581663insA	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				TTCTCACCATGaaaaaaaaaaa	0.381													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	41181708	41181709	+	IGR	INS	-	GGCAGGCT	GGCAGGCT	rs140205752	by1000genomes	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41181708_41181709insGGCAGGCT								SYT4 (324093 upstream) : None (None downstream)																							gaaggaaggaaggctggcttac	0.000													6	5	---	---	---	---	
LMAN1	3998	broad.mit.edu	37	18	57026573	57026574	+	5'Flank	INS	-	C	C	rs140141851	by1000genomes	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57026573_57026574insC	uc002lhz.2	-						LMAN1_uc010xek.1_5'Flank	NM_005570	NP_005561	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1 precursor						blood coagulation|ER to Golgi vesicle-mediated transport|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	mannose binding|metal ion binding|unfolded protein binding			skin(1)	1		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	AGCCCGGGGGACCCCCAAGGGC	0.752													8	4	---	---	---	---	
MUC16	94025	broad.mit.edu	37	19	8969553	8969554	+	Intron	INS	-	TT	TT	rs36058947		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8969553_8969554insTT	uc002mkp.2	-						MUC16_uc010dwi.2_Intron|MUC16_uc010dwj.2_Intron|MUC16_uc010xki.1_Intron	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						tttttcttttcttttttttttt	0.178													5	4	---	---	---	---	
SAE1	10055	broad.mit.edu	37	19	47653332	47653332	+	Intron	DEL	A	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47653332delA	uc002pgc.2	+						SAE1_uc002pgd.2_Intron|SAE1_uc010ekx.2_Intron|SAE1_uc010ekw.2_Intron|SAE1_uc010xyk.1_Intron|SAE1_uc002pge.2_Intron	NM_016402	NP_057486	Q9UBE0	SAE1_HUMAN	SubName: Full=SUMO-1 activating enzyme subunit 1, isoform CRA_b; SubName: Full=cDNA, FLJ96708, Homo sapiens SUMO-1 activating enzyme subunit 1 (SAE1), mRNA;						protein sumoylation|protein ubiquitination	nucleus	ATP-dependent protein binding|enzyme activator activity|ligase activity|protein C-terminus binding|protein heterodimerization activity|ubiquitin activating enzyme activity			ovary(1)	1		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		agactgtctcaaaaaaaaaaa	0.095													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	14665295	14665296	+	Intron	DEL	CC	-	-	rs11470618		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14665295_14665296delCC	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002wox.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				CATAACCTCAcccccccccccc	0.243													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	42043560	42043563	+	IGR	DEL	GAAG	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42043560_42043563delGAAG								PTPRT (225003 upstream) : SFRS6 (42941 downstream)																							aaaaaaaaaagaaggaaggaagga	0.005													3	3	---	---	---	---	
COL6A2	1292	broad.mit.edu	37	21	47536840	47536841	+	Intron	INS	-	ACAC	ACAC	rs147352816	by1000genomes	TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47536840_47536841insACAC	uc002zia.1	+						COL6A2_uc002zhy.1_Intron|COL6A2_uc002zhz.1_Intron|COL6A2_uc002zib.1_Intron	NM_001849	NP_001840	P12110	CO6A2_HUMAN	alpha 2 type VI collagen isoform 2C2 precursor						axon guidance|cell-cell adhesion|extracellular matrix organization|protein heterotrimerization	collagen|extracellular space|protein complex	extracellular matrix structural constituent|protein binding, bridging			central_nervous_system(7)|ovary(1)	8	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		Tacacacgcatacacacacaca	0.480													5	3	---	---	---	---	
MPST	4357	broad.mit.edu	37	22	37420445	37420445	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37420445delC	uc003aqj.2	+	3	601	c.189delC	c.(187-189)GACfs	p.D63fs	MPST_uc003aqi.1_Frame_Shift_Del_p.D63fs|MPST_uc003aqm.2_Frame_Shift_Del_p.D63fs|MPST_uc011amu.1_Frame_Shift_Del_p.D83fs|MPST_uc003aql.2_Frame_Shift_Del_p.D63fs|MPST_uc003aqn.2_Frame_Shift_Del_p.D63fs|MPST_uc003aqo.2_Frame_Shift_Del_p.D63fs	NM_001130517	NP_001123989	P25325	THTM_HUMAN	mercaptopyruvate sulfurtransferase isoform 2	63	Rhodanese 1.				cyanate catabolic process|response to toxin		3-mercaptopyruvate sulfurtransferase activity|thiosulfate sulfurtransferase activity				0						TCGACATCGACCAGTGCAGCG	0.716													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	25042267	25042270	+	IGR	DEL	CTTC	-	-	rs111892426		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25042267_25042270delCTTC								ARX (8202 upstream) : None (None downstream)																							tccttgcttgcttccttccttcct	0.230													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	52613556	52613557	+	IGR	DEL	AC	-	-			TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:52613556_52613557delAC								XAGE1D (369605 upstream) : SSX8 (38428 downstream)																							acacacacagacacacacacac	0.361													2	4	---	---	---	---	
OPHN1	4983	broad.mit.edu	37	X	67331929	67331934	+	Intron	DEL	ACAGAG	-	-	rs59924749		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67331929_67331934delACAGAG	uc004dww.3	-						OPHN1_uc011mpg.1_Intron	NM_002547	NP_002538	O60890	OPHN1_HUMAN	oligophrenin 1						axon guidance|endocytosis|filopodium assembly|small GTPase mediated signal transduction|substrate-dependent cell migration, cell extension	axon|cell junction|cytosol|dendritic spine|synapse	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(2)	2						acacacacacacagagagagattcgg	0.078													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13601466	13601467	+	IGR	INS	-	T	T	rs112972965		TCGA-BP-4963-01A-01D-1462-08	TCGA-BP-4963-11A-01D-1462-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13601466_13601467insT								None (None upstream) : None (None downstream)																							AGAGCAGGCTCTTGCCCACATC	0.490													3	3	---	---	---	---	
