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
PRDM2	7799	broad.mit.edu	37	1	14107286	14107286	+	Missense_Mutation	SNP	C	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14107286C>A	uc001avi.2	+	8	3852	c.2996C>A	c.(2995-2997)TCT>TAT	p.S999Y	PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Missense_Mutation_p.S999Y|PRDM2_uc001avj.2_Intron|PRDM2_uc001avk.2_Missense_Mutation_p.S798Y|PRDM2_uc009voe.2_Intron|PRDM2_uc009vof.2_Intron	NM_012231	NP_036363	Q13029	PRDM2_HUMAN	retinoblastoma protein-binding zinc finger	999	Pro-rich.					Golgi apparatus|nucleus	DNA binding|histone-lysine N-methyltransferase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		CCAGCCCCCTCTTCCAGTGCA	0.607													94	67	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16935231	16935231	+	5'UTR	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16935231G>A	uc009vos.1	-	2					NBPF1_uc001aza.3_RNA|NBPF1_uc001azb.1_RNA|NBPF1_uc001azc.1_RNA	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CCGGGTCACCGGGAACCTTCG	0.378													13	59	---	---	---	---	PASS
MST1P2	11209	broad.mit.edu	37	1	16974542	16974542	+	RNA	SNP	C	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974542C>A	uc009vow.2	+	5		c.1352C>A			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_RNA|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						CGGGCTAGGGCTGAGTGCAGC	0.692													7	74	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19475090	19475090	+	Missense_Mutation	SNP	T	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19475090T>A	uc001bbi.2	-	50	7465	c.7461A>T	c.(7459-7461)GAA>GAT	p.E2487D	UBR4_uc001bbk.1_Missense_Mutation_p.E141D	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	2487					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		CAAAGCAGCTTTCCAGGGCTT	0.512													134	119	---	---	---	---	PASS
CSMD2	114784	broad.mit.edu	37	1	34076828	34076828	+	Missense_Mutation	SNP	G	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34076828G>C	uc001bxn.1	-	41	6065	c.6036C>G	c.(6034-6036)AAC>AAG	p.N2012K	CSMD2_uc001bxm.1_Missense_Mutation_p.N2052K|CSMD2_uc001bxo.1_Missense_Mutation_p.N925K	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2012	CUB 12.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CGGTGGAGAAGTTCAGGAACT	0.547													15	30	---	---	---	---	PASS
RIMS3	9783	broad.mit.edu	37	1	41101622	41101622	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41101622C>T	uc001cfu.1	-	4	794	c.325G>A	c.(325-327)GAT>AAT	p.D109N	RIMS3_uc001cfv.1_Missense_Mutation_p.D109N	NM_014747	NP_055562	Q9UJD0	RIMS3_HUMAN	regulating synaptic membrane exocytosis 3	109					neurotransmitter transport	cell junction|synapse					0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)			GTGCTCCCATCGGTGGACTCC	0.682													81	44	---	---	---	---	PASS
SPATA6	54558	broad.mit.edu	37	1	48764299	48764299	+	3'UTR	SNP	A	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48764299A>T	uc001crr.1	-	13					SPATA6_uc001crs.1_3'UTR|SPATA6_uc010omv.1_3'UTR	NM_019073	NP_061946	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6 precursor						cell differentiation|multicellular organismal development|spermatogenesis	extracellular region				ovary(1)	1						CATTTTTTTTAAAAAAAGGAA	0.284													5	23	---	---	---	---	PASS
GLIS1	148979	broad.mit.edu	37	1	53986418	53986418	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53986418C>T	uc001cvr.1	-	6	1657	c.1090G>A	c.(1090-1092)GAG>AAG	p.E364K		NM_147193	NP_671726	Q8NBF1	GLIS1_HUMAN	GLIS family zinc finger 1	364					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1						ACGTCGGCCTCGGTGTCAGGG	0.662													13	21	---	---	---	---	PASS
TGFBR3	7049	broad.mit.edu	37	1	92185658	92185658	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92185658G>A	uc001doh.2	-	9	1671	c.1205C>T	c.(1204-1206)CCG>CTG	p.P402L	TGFBR3_uc009wde.2_Missense_Mutation_p.P179L|TGFBR3_uc010osy.1_Missense_Mutation_p.P360L|TGFBR3_uc001doi.2_Missense_Mutation_p.P401L|TGFBR3_uc001doj.2_Missense_Mutation_p.P401L	NM_003243	NP_003234	Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	402	Extracellular (Potential).				BMP signaling pathway|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cell growth|cell migration|definitive erythrocyte differentiation|heart trabecula formation|immune response|intracellular protein kinase cascade|liver development|negative regulation of cellular component movement|negative regulation of epithelial cell proliferation|palate development|pathway-restricted SMAD protein phosphorylation|response to follicle-stimulating hormone stimulus|response to luteinizing hormone stimulus|response to prostaglandin E stimulus|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis	external side of plasma membrane|extracellular space|inhibin-betaglycan-ActRII complex|integral to plasma membrane|intracellular membrane-bounded organelle	coreceptor activity|heparin binding|PDZ domain binding|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type III|type II transforming growth factor beta receptor binding			ovary(3)	3		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		GAAAGGAAACGGAAGGCCTCC	0.572													67	56	---	---	---	---	PASS
NBPF14	25832	broad.mit.edu	37	1	148009487	148009487	+	Missense_Mutation	SNP	T	C	C	rs150588308	by1000genomes	TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148009487T>C	uc001eqq.2	-	16	1837	c.1820A>G	c.(1819-1821)GAG>GGG	p.E607G	LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqf.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Missense_Mutation_p.E180G|NBPF14_uc001eqx.2_Intron|NBPF14_uc010pad.1_Intron|NBPF14_uc001eqs.1_Intron	NM_015383	NP_056198	Q5TI25	NBPFE_HUMAN	hypothetical protein LOC25832	607	NBPF 7.					cytoplasm				ovary(1)	1	all_hematologic(923;0.032)					GACTTCAGGCTCTTTCTCATC	0.478													5	224	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152279046	152279046	+	Missense_Mutation	SNP	G	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152279046G>T	uc001ezu.1	-	3	8352	c.8316C>A	c.(8314-8316)GAC>GAA	p.D2772E		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2772	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCTGGAGCTGTCTTGTGCCT	0.597									Ichthyosis				168	560	---	---	---	---	PASS
SLC39A1	27173	broad.mit.edu	37	1	153932939	153932939	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153932939G>A	uc001fdh.2	-	4	779	c.610C>T	c.(610-612)CGG>TGG	p.R204W	CRTC2_uc010ped.1_5'Flank|SLC39A1_uc001fdi.2_Missense_Mutation_p.R204W|SLC39A1_uc001fdj.2_Missense_Mutation_p.R204W|SLC39A1_uc001fdk.2_Missense_Mutation_p.R204W|SLC39A1_uc010pee.1_Missense_Mutation_p.R102W|SLC39A1_uc001fdl.2_Missense_Mutation_p.R204W	NM_014437	NP_055252	Q9NY26	S39A1_HUMAN	solute carrier family 39 (zinc transporter),	204	Extracellular (Potential).					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)		GCCCGAGCCCGGTCTCGCTGC	0.662													41	35	---	---	---	---	PASS
RXRG	6258	broad.mit.edu	37	1	165370612	165370612	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165370612C>T	uc001gda.2	-	10	1580	c.1280G>A	c.(1279-1281)CGT>CAT	p.R427H		NM_006917	NP_008848	P48443	RXRG_HUMAN	retinoid X receptor, gamma isoform a	427	Ligand-binding (By similarity).				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tretinoin(DB00755)	GCCAATGGAACGCAGAGCTGG	0.602													23	94	---	---	---	---	PASS
DNM3	26052	broad.mit.edu	37	1	172017754	172017754	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172017754C>T	uc001gie.2	+	10	1375	c.1199C>T	c.(1198-1200)ACA>ATA	p.T400I	DNM3_uc001gid.3_Missense_Mutation_p.T400I|DNM3_uc009wwb.2_Missense_Mutation_p.T400I|DNM3_uc001gif.2_Missense_Mutation_p.T400I	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a	400					endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1						ACCTTCAGGACAGGGTTGTTT	0.333													5	25	---	---	---	---	PASS
TNR	7143	broad.mit.edu	37	1	175355398	175355398	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175355398G>A	uc001gkp.1	-	6	1628	c.1547C>T	c.(1546-1548)TCG>TTG	p.S516L	TNR_uc009wwu.1_Missense_Mutation_p.S516L	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	516	Fibronectin type-III 3.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					CACAGTGTCCGAGACATCGCG	0.512													12	57	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176525340	176525340	+	5'UTR	SNP	A	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176525340A>C	uc001gkz.2	+	2					PAPPA2_uc001gky.1_5'UTR|PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						GTCTGTGAACAAAACAGTTTC	0.517													15	48	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176525345	176525345	+	5'UTR	SNP	A	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176525345A>T	uc001gkz.2	+	2					PAPPA2_uc001gky.1_5'UTR|PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						TGAACAAAACAGTTTCCCTGG	0.512													16	56	---	---	---	---	PASS
CACNA1E	777	broad.mit.edu	37	1	181745478	181745478	+	Intron	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181745478G>A	uc001gow.2	+						CACNA1E_uc009wxs.2_Intron|CACNA1E_uc001gox.1_Missense_Mutation_p.G1020E|CACNA1E_uc009wxt.2_Intron	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						AGAAGGAAAGGAGATTCCTCT	0.552													9	21	---	---	---	---	PASS
KIF21B	23046	broad.mit.edu	37	1	200968596	200968596	+	Splice_Site	SNP	T	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200968596T>C	uc001gvs.1	-	13	2085	c.1768_splice	c.e13-1	p.E590_splice	KIF21B_uc001gvr.1_Splice_Site_p.E590_splice|KIF21B_uc009wzl.1_Splice_Site_p.E590_splice|KIF21B_uc010ppn.1_Splice_Site_p.E590_splice	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6						TTCCTCCTCCTGGGCACCAGG	0.632													95	35	---	---	---	---	PASS
ACBD3	64746	broad.mit.edu	37	1	226340215	226340215	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226340215C>T	uc001hpy.2	-	7	1243	c.1196G>A	c.(1195-1197)CGA>CAA	p.R399Q		NM_022735	NP_073572	Q9H3P7	GCP60_HUMAN	acyl-Coenzyme A binding domain containing 3	399	GOLD.				steroid biosynthetic process|transport	Golgi membrane|integral to membrane|mitochondrion	fatty-acyl-CoA binding|protein binding				0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.121)		CACTTCTCCTCGGCCCACTGT	0.463													135	225	---	---	---	---	PASS
ACBD3	64746	broad.mit.edu	37	1	226340229	226340229	+	Silent	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226340229C>T	uc001hpy.2	-	7	1229	c.1182G>A	c.(1180-1182)GTG>GTA	p.V394V		NM_022735	NP_073572	Q9H3P7	GCP60_HUMAN	acyl-Coenzyme A binding domain containing 3	394	GOLD.			KEKIQQDADSVITV -> QREDSAGCRFRDYS (in Ref. 2).	steroid biosynthetic process|transport	Golgi membrane|integral to membrane|mitochondrion	fatty-acyl-CoA binding|protein binding				0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.121)		CCACTGTAATCACGGAATCTG	0.453													141	249	---	---	---	---	PASS
MYT1L	23040	broad.mit.edu	37	2	1983502	1983502	+	Silent	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1983502C>T	uc002qxe.2	-	6	875	c.48G>A	c.(46-48)GGG>GGA	p.G16G	MYT1L_uc002qxd.2_Silent_p.G16G|MYT1L_uc002qxf.1_RNA	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	16					cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		TACCTCGAACCCCTTTGGACC	0.597													9	65	---	---	---	---	PASS
ID2	3398	broad.mit.edu	37	2	8822191	8822191	+	5'UTR	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8822191G>A	uc010yiu.1	+	3					ID2_uc002qza.2_5'UTR	NM_002166	NP_002157	Q02363	ID2_HUMAN	inhibitor of DNA binding 2						cellular senescence|embryonic digestive tract morphogenesis|endodermal digestive tract morphogenesis|epithelial cell differentiation involved in mammary gland alveolus development|mammary gland epithelial cell proliferation|negative regulation of neural precursor cell proliferation|negative regulation of neuron differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|neuron fate commitment|positive regulation of blood pressure|positive regulation of cell cycle arrest|positive regulation of smooth muscle cell proliferation|positive regulation of transcription, DNA-dependent	protein complex	protein binding				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GCTTCATTCTGAGCCGAGCCC	0.701													11	6	---	---	---	---	PASS
NAGK	55577	broad.mit.edu	37	2	71297621	71297621	+	Intron	SNP	G	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71297621G>T	uc002shp.3	+						NAGK_uc010fea.2_Intron|NAGK_uc002shq.3_Intron|NAGK_uc002shr.2_5'UTR	NM_017567	NP_060037	Q9UJ70	NAGK_HUMAN	N-Acetylglucosamine kinase						N-acetylglucosamine metabolic process|N-acetylmannosamine metabolic process		ATP binding|N-acetylglucosamine kinase activity|protein binding				0					N-Acetyl-D-glucosamine(DB00141)	GTGCCCTCTTGTGTTCTGTAG	0.527											OREG0014689	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	31	40	---	---	---	---	PASS
CTNNA2	1496	broad.mit.edu	37	2	79971689	79971689	+	Silent	SNP	A	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79971689A>T	uc010ysh.1	+	2	284	c.279A>T	c.(277-279)GTA>GTT	p.V93V	CTNNA2_uc010yse.1_Silent_p.V93V|CTNNA2_uc010ysf.1_Silent_p.V93V|CTNNA2_uc010ysg.1_Silent_p.V93V	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1	93					axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9						TGGCTGCTGTAGAGGATGTGC	0.428													22	16	---	---	---	---	PASS
FAHD2A	51011	broad.mit.edu	37	2	96078765	96078765	+	3'UTR	SNP	C	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96078765C>G	uc002sur.2	+	8					FAHD2A_uc002sus.2_3'UTR|uc002sut.1_5'Flank	NM_016044	NP_057128	Q96GK7	FAH2A_HUMAN	fumarylacetoacetate hydrolase domain containing								hydrolase activity|metal ion binding			ovary(1)	1						CAGCCTAGCCCAGGGAAAGGC	0.552													9	5	---	---	---	---	PASS
SCN9A	6335	broad.mit.edu	37	2	167162315	167162315	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167162315C>T	uc010fpl.2	-	5	924	c.583G>A	c.(583-585)GTC>ATC	p.V195I	SCN9A_uc002udr.1_Missense_Mutation_p.V66I|SCN9A_uc002uds.1_Missense_Mutation_p.V66I|SCN9A_uc002udt.1_Missense_Mutation_p.V66I	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	195	Helical; Name=S3 of repeat I; (Potential).|I.					voltage-gated sodium channel complex	voltage-gated sodium channel activity	p.V195I(1)		ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)	AAAACAATGACGACAAAATCC	0.398													27	69	---	---	---	---	PASS
DNAH7	56171	broad.mit.edu	37	2	196865506	196865506	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196865506G>A	uc002utj.3	-	12	1376	c.1275C>T	c.(1273-1275)ATC>ATT	p.I425I		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	425	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12						CATTTAGAAAGATATCTATAT	0.343													158	150	---	---	---	---	PASS
IKZF2	22807	broad.mit.edu	37	2	213872344	213872344	+	Missense_Mutation	SNP	C	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213872344C>A	uc002vem.2	-	8	1490	c.1321G>T	c.(1321-1323)GTC>TTC	p.V441F	IKZF2_uc010fuu.2_Missense_Mutation_p.V296F|IKZF2_uc002vej.2_Missense_Mutation_p.V388F|IKZF2_uc002vek.2_RNA|IKZF2_uc010fuv.2_Missense_Mutation_p.V367F|IKZF2_uc002vel.2_Missense_Mutation_p.V362F|IKZF2_uc010fuw.2_Missense_Mutation_p.V215F|IKZF2_uc010fux.2_Missense_Mutation_p.V215F|IKZF2_uc010fuy.2_Missense_Mutation_p.V369F|IKZF2_uc002ven.2_Missense_Mutation_p.V415F|IKZF2_uc002vei.2_Missense_Mutation_p.V219F	NM_016260	NP_057344	Q9UKS7	IKZF2_HUMAN	helios isoform 1	441					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)		AAAGCTTTGACATCCTCCTTC	0.483													9	63	---	---	---	---	PASS
HRH1	3269	broad.mit.edu	37	3	11301151	11301151	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11301151G>A	uc010hdr.2	+	2	770	c.428G>A	c.(427-429)CGA>CAA	p.R143Q	HRH1_uc010hds.2_Missense_Mutation_p.R143Q|HRH1_uc010hdt.2_Missense_Mutation_p.R143Q|HRH1_uc003bwb.3_Missense_Mutation_p.R143Q	NM_001098213	NP_001091683	P35367	HRH1_HUMAN	histamine receptor H1	143	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|inflammatory response	cytoplasm|integral to plasma membrane|nucleus	histamine receptor activity			large_intestine(1)|ovary(1)	2					Aceprometazine(DB01615)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzquinamide(DB00767)|Bepotastine(DB04890)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlophedianol(DB04837)|Chlorpheniramine(DB01114)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clemastine(DB00283)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Maprotiline(DB00934)|Meclizine(DB00737)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nedocromil(DB00716)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Pemirolast(DB00885)|Phenindamine(DB01619)|Pheniramine(DB01620)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Terfenadine(DB00342)|Thiethylperazine(DB00372)|Trazodone(DB00656)|Trimeprazine(DB01246)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	ACCAAGACCCGAGCCTCGGCC	0.552													51	187	---	---	---	---	PASS
PRKCD	5580	broad.mit.edu	37	3	53213624	53213624	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53213624G>A	uc003dgl.2	+	4	500	c.147G>A	c.(145-147)CCG>CCA	p.P49P	PRKCD_uc003dgm.2_Silent_p.P49P|PRKCD_uc003dgn.2_Silent_p.P49P	NM_006254	NP_006245	Q05655	KPCD_HUMAN	protein kinase C, delta	49	C2.				activation of phospholipase C activity|cellular component disassembly involved in apoptosis|cellular senescence|interferon-gamma-mediated signaling pathway|intracellular signal transduction|mRNA metabolic process|negative regulation of insulin receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein binding|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of ceramide biosynthetic process|positive regulation of glucosylceramide catabolic process|positive regulation of protein dephosphorylation|positive regulation of sphingomyelin catabolic process|protein stabilization|regulation of receptor activity|termination of signal transduction	cytosol|endoplasmic reticulum|nucleoplasm	ATP binding|calcium-independent protein kinase C activity|enzyme activator activity|enzyme binding|insulin receptor substrate binding|metal ion binding|protein C-terminus binding			central_nervous_system(4)|lung(3)|stomach(1)|skin(1)	9		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)		AGAAGAAGCCGACCATGTATC	0.592													20	43	---	---	---	---	PASS
ERC2	26059	broad.mit.edu	37	3	55984554	55984554	+	Missense_Mutation	SNP	G	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55984554G>C	uc003dhr.1	-	13	2558	c.2302C>G	c.(2302-2304)CTC>GTC	p.L768V	ERC2_uc003dhq.1_RNA|ERC2_uc003dht.1_Missense_Mutation_p.L247V	NM_015576	NP_056391	O15083	ERC2_HUMAN	cytomatrix protein p110	768	Potential.					cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		TTGTGCTTGAGGTTGGCCACC	0.413													3	81	---	---	---	---	PASS
ATXN7	6314	broad.mit.edu	37	3	63985136	63985136	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63985136G>A	uc003dlw.3	+	13	3225	c.2672G>A	c.(2671-2673)CGT>CAT	p.R891H	ATXN7_uc010hnv.2_Silent_p.T913T|ATXN7_uc011bfn.1_Missense_Mutation_p.R746H	NM_000333	NP_000324	O15265	ATX7_HUMAN	ataxin 7 isoform a	891				PKARP -> VGNGL (in Ref. 2; AAC39765/ AAC19163).	cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		CCAAAGGCACGTCCCTGACAG	0.448													16	26	---	---	---	---	PASS
CD200	4345	broad.mit.edu	37	3	112054803	112054803	+	Missense_Mutation	SNP	C	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112054803C>A	uc003dyw.2	+	2	170	c.26C>A	c.(25-27)ACA>AAA	p.T9K	CD200_uc010hqd.1_Intron|CD200_uc003dyx.2_Intron|CD200_uc003dyy.2_Intron|CD200_uc003dyz.2_Intron	NM_001004196	NP_001004196	P41217	OX2G_HUMAN	CD200 antigen isoform b	Error:Variant_position_missing_in_P41217_after_alignment					regulation of immune response	integral to plasma membrane					0		Acute lymphoblastic leukemia(4;1.7e-08)|all_hematologic(4;8.82e-05)				CTGACCAGGACAATTGGGGGC	0.274													27	116	---	---	---	---	PASS
C3orf30	152405	broad.mit.edu	37	3	118865565	118865565	+	Missense_Mutation	SNP	C	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118865565C>G	uc003ecb.1	+	1	569	c.529C>G	c.(529-531)CAG>GAG	p.Q177E	IGSF11_uc003eby.2_5'Flank|IGSF11_uc003ebz.2_5'Flank|IGSF11_uc010hqs.2_5'Flank|C3orf30_uc011biw.1_Missense_Mutation_p.Q177E	NM_152539	NP_689752	Q96M34	CC030_HUMAN	hypothetical protein LOC152405	177										ovary(2)	2				GBM - Glioblastoma multiforme(114;0.222)		AGGTTCCAGACAGACCGACCA	0.527													38	79	---	---	---	---	PASS
SI	6476	broad.mit.edu	37	3	164786928	164786928	+	Missense_Mutation	SNP	G	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164786928G>C	uc003fei.2	-	4	373	c.311C>G	c.(310-312)CCT>CGT	p.P104R		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	104	Lumenal.|P-type 1.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	GAAGCACCAAGGAATAAGAGA	0.343										HNSCC(35;0.089)			34	71	---	---	---	---	PASS
EIF4A2	1974	broad.mit.edu	37	3	186501413	186501413	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186501413C>T	uc003fqs.2	+	1	53	c.14C>T	c.(13-15)TCC>TTC	p.S5F	EIF4A2_uc003fqt.2_RNA|EIF4A2_uc003fqu.2_Missense_Mutation_p.S5F|EIF4A2_uc003fqv.2_5'UTR|EIF4A2_uc003fqw.2_5'UTR|SNORD2_uc010hyu.1_5'Flank|EIF4A2_uc011bsb.1_5'Flank	NM_001967	NP_001958	Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	5					interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	ATP binding|ATP-dependent helicase activity|protein binding|translation initiation factor activity			ovary(2)|breast(2)	4	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		TCTGGTGGCTCCGCGGATTAT	0.562			T	BCL6	NHL								81	184	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195505836	195505836	+	Missense_Mutation	SNP	G	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195505836G>C	uc011bto.1	-	3	12691	c.12231C>G	c.(12229-12231)CAC>CAG	p.H4077Q	MUC4_uc003fva.2_5'Flank|MUC4_uc003fvb.2_5'Flank|MUC4_uc003fvc.2_5'Flank|MUC4_uc003fvd.2_5'Flank|MUC4_uc003fve.2_5'Flank|MUC4_uc010hzr.2_5'Flank|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCTGTGG	0.597													9	7	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511815	195511815	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511815G>A	uc011bto.1	-	2	7096	c.6636C>T	c.(6634-6636)ACC>ACT	p.T2212T	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGGGCTGGTGACAGGAA	0.602													3	5	---	---	---	---	PASS
RGS12	6002	broad.mit.edu	37	4	3317854	3317854	+	5'UTR	SNP	A	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3317854A>C	uc003ggw.2	+	2					RGS12_uc003ggu.2_5'UTR|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_RNA|RGS12_uc003ggv.2_5'UTR|RGS12_uc003ggx.1_5'UTR	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1							condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ATATGGCTCCAAGGGAACAAT	0.488													21	255	---	---	---	---	PASS
RGS12	6002	broad.mit.edu	37	4	3425321	3425321	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3425321G>A	uc003ggw.2	+	13	4091	c.3187G>A	c.(3187-3189)GTG>ATG	p.V1063M	RGS12_uc003ggv.2_Missense_Mutation_p.V1063M|RGS12_uc003ggy.1_Missense_Mutation_p.V461M|RGS12_uc003ggz.2_Missense_Mutation_p.V415M|RGS12_uc010icu.1_Missense_Mutation_p.V262M|RGS12_uc011bvs.1_Missense_Mutation_p.V405M|RGS12_uc003gha.2_Missense_Mutation_p.V405M|RGS12_uc010icv.2_Missense_Mutation_p.V262M|RGS12_uc003ghb.2_Missense_Mutation_p.V262M	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1	1063	RBD 2.					condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GCTGCGGCCCGTGGTGGCCAG	0.632													35	93	---	---	---	---	PASS
TMPRSS11F	389208	broad.mit.edu	37	4	68964665	68964665	+	Silent	SNP	A	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68964665A>G	uc003hdt.1	-	2	152	c.103T>C	c.(103-105)TTA>CTA	p.L35L		NM_207407	NP_997290	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	35	Helical; Signal-anchor for type II membrane protein; (Potential).				proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1						ACAATTGCTAATGTGAAAAGA	0.388													3	14	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79429990	79429990	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79429990C>T	uc003hlb.2	+	63	10050	c.9610C>T	c.(9610-9612)CCT>TCT	p.P3204S	FRAS1_uc003hlc.1_Missense_Mutation_p.P206S	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	3199	Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						CCCCTGCGACCCTCATTTCCC	0.567													11	15	---	---	---	---	PASS
RG9MTD2	93587	broad.mit.edu	37	4	100479211	100479211	+	Silent	SNP	A	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100479211A>G	uc003huy.2	-	3	656	c.343T>C	c.(343-345)TTA>CTA	p.L115L	RG9MTD2_uc003huz.3_Silent_p.L115L|RG9MTD2_uc003hva.3_Silent_p.L115L	NM_152292	NP_689505	Q8TBZ6	RG9D2_HUMAN	RNA (guanine-9-) methyltransferase domain	115							methyltransferase activity			ovary(2)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;1.7e-08)		GATACCTTTAATACCATCAAG	0.328													10	18	---	---	---	---	PASS
UGT8	7368	broad.mit.edu	37	4	115597250	115597250	+	Missense_Mutation	SNP	G	T	T	rs77695673		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115597250G>T	uc003ibs.2	+	6	1954	c.1432G>T	c.(1432-1434)GCC>TCC	p.A478S	UGT8_uc003ibt.2_Missense_Mutation_p.A478S|UGT8_uc011cge.1_RNA	NM_001128174	NP_001121646	Q16880	CGT_HUMAN	UDP-galactose-ceramide galactosyltransferase 8	478	Helical; (Potential).				central nervous system development|peripheral nervous system development	integral to membrane	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity			ovary(1)|skin(1)	2		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)		ACTGGATATTGCCTTTGTGCT	0.373													50	83	---	---	---	---	PASS
SRD5A1	6715	broad.mit.edu	37	5	6633926	6633926	+	Silent	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6633926C>T	uc003jdw.2	+	1	427	c.237C>T	c.(235-237)CTC>CTT	p.L79L	NSUN2_uc003jdu.2_5'Flank|NSUN2_uc011cmk.1_5'Flank|NSUN2_uc003jdv.2_5'Flank|SRD5A1_uc011cml.1_RNA|SRD5A1_uc011cmm.1_Missense_Mutation_p.S88F	NM_001047	NP_001038	P18405	S5A1_HUMAN	steroid-5-alpha-reductase 1	79					androgen biosynthetic process|cell differentiation|sex determination|sex differentiation	endoplasmic reticulum membrane|integral to membrane|microsome	3-oxo-5-alpha-steroid 4-dehydrogenase activity|electron carrier activity				0					Dutasteride(DB01126)|Finasteride(DB01216)	CCCCGCGTCTCCGCAGCGCGC	0.736													16	157	---	---	---	---	PASS
MARVELD2	153562	broad.mit.edu	37	5	68737477	68737477	+	Missense_Mutation	SNP	C	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68737477C>G	uc003jwq.2	+	7	1732	c.1673C>G	c.(1672-1674)TCT>TGT	p.S558C	MARVELD2_uc010ixf.2_Missense_Mutation_p.S546C|MARVELD2_uc003jwr.1_Intron|MARVELD2_uc003jws.1_RNA	NM_001038603	NP_001033692	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2 isoform 1	558	Cytoplasmic (Potential).				sensory perception of sound	integral to membrane|tight junction					0		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)		CAAGGTTATTCTTAACGCTTA	0.179													24	34	---	---	---	---	PASS
PDGFRB	5159	broad.mit.edu	37	5	149515232	149515232	+	Missense_Mutation	SNP	C	T	T	rs80162387	by1000genomes	TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149515232C>T	uc003lro.2	-	3	719	c.250G>A	c.(250-252)GTG>ATG	p.V84M	PDGFRB_uc010jhd.2_Translation_Start_Site|PDGFRB_uc011dcg.1_Missense_Mutation_p.V84M	NM_002609	NP_002600	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor beta	84	Extracellular (Potential).|Ig-like C2-type 1.				aorta morphogenesis|cardiac myofibril assembly|hemopoiesis|metanephric glomerular capillary formation|metanephric glomerular mesangial cell proliferation involved in metanephros development|peptidyl-tyrosine phosphorylation|positive regulation of calcium ion import|positive regulation of chemotaxis|positive regulation of DNA biosynthetic process|positive regulation of ERK1 and ERK2 cascade|positive regulation of MAP kinase activity|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of mitosis|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|protein autophosphorylation|regulation of actin cytoskeleton organization|retina vasculature development in camera-type eye|smooth muscle cell chemotaxis	apical plasma membrane|cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet activating factor receptor activity|platelet-derived growth factor beta-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|vascular endothelial growth factor receptor activity			central_nervous_system(4)|lung(4)|breast(3)|stomach(2)|prostate(2)|large_intestine(1)|ovary(1)	17		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGTGTGAGCACGCTGGAGAAG	0.597			T	ETV6|TRIP11|HIP1|RAB5EP|H4|NIN|HCMOGT-1|PDE4DIP	MPD|AML|CMML|CML								8	102	---	---	---	---	PASS
FAM136B	387071	broad.mit.edu	37	6	3045879	3045879	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3045879G>A	uc011dhr.1	+	1	262	c.262G>A	c.(262-264)GAC>AAC	p.D88N		NM_001012983	NP_001013001			hypothetical protein LOC387071												0	Ovarian(93;0.0386)	all_hematologic(90;0.108)				GCATTGCAATGACAAAGCCAA	0.547													41	106	---	---	---	---	PASS
KIF13A	63971	broad.mit.edu	37	6	17777555	17777555	+	Missense_Mutation	SNP	T	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17777555T>C	uc003ncg.3	-	34	4228	c.4123A>G	c.(4123-4125)AAA>GAA	p.K1375E	KIF13A_uc003ncf.2_Missense_Mutation_p.K1362E|KIF13A_uc003nch.3_Missense_Mutation_p.K1375E|KIF13A_uc003nci.3_Missense_Mutation_p.K1362E|KIF13A_uc003nce.1_5'UTR	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	1375					cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			TGCCGGGCTTTGGTGGAAAGT	0.368													10	33	---	---	---	---	PASS
HIST1H2AC	8334	broad.mit.edu	37	6	26124400	26124400	+	5'UTR	SNP	G	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26124400G>C	uc003ngm.2	+	1					HIST1H2BC_uc003ngk.3_5'Flank|HIST1H2BC_uc003ngl.2_5'Flank|HIST1H2AC_uc003ngn.2_5'Flank|HIST1H2AC_uc003ngo.2_5'Flank|HIST1H2AC_uc003ngp.2_5'Flank	NM_003512	NP_003503	Q93077	H2A1C_HUMAN	histone cluster 1, H2ac						nucleosome assembly	nucleosome|nucleus	DNA binding				0						CATATTTCTTGATTTTGTTTG	0.438													7	28	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	6	26322343	26322343	+	RNA	SNP	G	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26322343G>C	uc003nhn.2	-	1		c.291C>G								full-length cDNA clone CS0DF024YI14 of Fetal brain of Homo sapiens (human).																		GCGGACTTCTGATAACGTCTA	0.498													12	25	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	6	26322388	26322388	+	RNA	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26322388G>A	uc003nhn.2	-	1		c.246C>T								full-length cDNA clone CS0DF024YI14 of Fetal brain of Homo sapiens (human).																		GGCCTGTAACGATGAGGTTTC	0.483													14	27	---	---	---	---	PASS
CUL9	23113	broad.mit.edu	37	6	43156294	43156294	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43156294G>A	uc003ouk.2	+	8	2096	c.2021G>A	c.(2020-2022)CGC>CAC	p.R674H	CUL9_uc003ouj.1_3'UTR|CUL9_uc003oul.2_Missense_Mutation_p.R674H|CUL9_uc010jyk.2_5'UTR|CUL9_uc003oum.1_3'UTR	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	674					ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|lung(3)|skin(2)|breast(1)|central_nervous_system(1)	12						CCCGGTCCTCGCAGCTCCCTG	0.542													53	43	---	---	---	---	PASS
TJAP1	93643	broad.mit.edu	37	6	43472738	43472738	+	Silent	SNP	T	C	C	rs145858223		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43472738T>C	uc003ovd.2	+	11	1195	c.819T>C	c.(817-819)GAT>GAC	p.D273D	TJAP1_uc003ovf.2_Silent_p.D263D|TJAP1_uc003ove.2_Silent_p.D263D|TJAP1_uc003ovc.2_Silent_p.D263D|TJAP1_uc010jyp.2_Silent_p.D232D|TJAP1_uc011dvh.1_Silent_p.D263D|TJAP1_uc003ovg.2_Silent_p.D139D|TJAP1_uc011dvi.1_Silent_p.D273D|TJAP1_uc011dvj.1_Silent_p.D73D|TJAP1_uc003ovi.2_Silent_p.D139D	NM_001146016	NP_001139488	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 isoform a	273	Pro-rich.					Golgi apparatus|tight junction	protein binding				0	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			TCCCAGGTGATCCAGCCAGTC	0.652													5	80	---	---	---	---	PASS
HSP90AB1	3326	broad.mit.edu	37	6	44216418	44216418	+	Nonsense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44216418C>T	uc003oxa.1	+	2	136	c.52C>T	c.(52-54)CAG>TAG	p.Q18*	HSP90AB1_uc011dvr.1_Nonsense_Mutation_p.Q18*|HSP90AB1_uc003oxb.1_Nonsense_Mutation_p.Q18*|HSP90AB1_uc011dvs.1_5'UTR|HSP90AB1_uc003oxc.1_5'Flank	NM_007355	NP_031381	P08238	HS90B_HUMAN	heat shock 90kDa protein 1, beta	18					axon guidance|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of nitric oxide biosynthetic process|protein folding|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to unfolded protein	cytosol|melanosome	ATP binding|nitric-oxide synthase regulator activity|TPR domain binding|unfolded protein binding	p.Q18*(1)		lung(3)|breast(1)	4	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TTTTGCCTTTCAGGCAGAAAT	0.423													91	209	---	---	---	---	PASS
ME1	4199	broad.mit.edu	37	6	83963391	83963391	+	Missense_Mutation	SNP	G	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83963391G>T	uc003pjy.2	-	7	877	c.771C>A	c.(769-771)AAC>AAA	p.N257K	ME1_uc011dzb.1_Missense_Mutation_p.N182K|ME1_uc011dzc.1_Missense_Mutation_p.N91K	NM_002395	NP_002386	P48163	MAOX_HUMAN	cytosolic malic enzyme 1	257					carbohydrate metabolic process|cellular lipid metabolic process|malate metabolic process|NADP biosynthetic process|response to carbohydrate stimulus|response to hormone stimulus	cytosol	ADP binding|electron carrier activity|malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|manganese ion binding|NAD binding|NADP binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)	NADH(DB00157)	TTCGATACTTGTTCAGGAGAC	0.328													21	89	---	---	---	---	PASS
AKD1	221264	broad.mit.edu	37	6	109980580	109980580	+	Nonsense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109980580G>A	uc003ptn.2	-	7	558	c.481C>T	c.(481-483)CAA>TAA	p.Q161*	AKD1_uc003ptr.3_Nonsense_Mutation_p.Q161*|AKD1_uc003pts.1_RNA	NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	adenylate kinase domain containing 1 isoform 1	161					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1						TGCTGTCTTTGCCCAGAAATT	0.303													35	39	---	---	---	---	PASS
GPR126	57211	broad.mit.edu	37	6	142691909	142691909	+	Missense_Mutation	SNP	G	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142691909G>C	uc010khc.2	+	4	1459	c.1048G>C	c.(1048-1050)GCT>CCT	p.A350P	GPR126_uc010khd.2_Missense_Mutation_p.A350P|GPR126_uc010khe.2_Missense_Mutation_p.A350P|GPR126_uc010khf.2_Missense_Mutation_p.A350P|GPR126_uc003qix.2_Missense_Mutation_p.A350P	NM_020455	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126 alpha 1	350	Pentaxin.|Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		AGCTCTGAAAGCTGAAAGCAA	0.358													3	48	---	---	---	---	PASS
TAB2	23118	broad.mit.edu	37	6	149700178	149700178	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149700178C>T	uc003qmj.2	+	3	1305	c.1127C>T	c.(1126-1128)ACG>ATG	p.T376M	TAB2_uc011eec.1_Missense_Mutation_p.T344M|TAB2_uc010kia.1_Missense_Mutation_p.T376M|TAB2_uc010kib.1_Missense_Mutation_p.T376M|TAB2_uc003qmk.3_RNA	NM_015093	NP_055908	Q9NYJ8	TAB2_HUMAN	mitogen-activated protein kinase kinase kinase 7	376					activation of MAPK activity|heart development|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	K63-linked polyubiquitin binding|zinc ion binding				0						CCCCCAAATACGGATGAGCTG	0.493													26	60	---	---	---	---	PASS
FOXK1	221937	broad.mit.edu	37	7	4794201	4794201	+	Silent	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4794201C>T	uc003snc.1	+	3	868	c.858C>T	c.(856-858)GCC>GCT	p.A286A	FOXK1_uc003sna.1_Silent_p.A123A|FOXK1_uc003snb.1_Silent_p.A286A	NM_001037165	NP_001032242	P85037	FOXK1_HUMAN	forkhead box K1	286					cell differentiation|embryo development|muscle organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			upper_aerodigestive_tract(1)|skin(1)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		CAGCAAAGGCCGCGTCGGAGC	0.657													11	59	---	---	---	---	PASS
PRPS1L1	221823	broad.mit.edu	37	7	18067430	18067430	+	5'UTR	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18067430C>T	uc003stz.2	-	1						NM_175886	NP_787082	P21108	PRPS3_HUMAN	phosphoribosyl pyrophosphate synthetase 1-like						nucleoside metabolic process|ribonucleoside monophosphate biosynthetic process		ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			ovary(1)	1	Lung NSC(10;0.0385)|all_lung(11;0.0736)					AGAGGCACTCCGTCGAGCGAT	0.572													10	32	---	---	---	---	PASS
DNAH11	8701	broad.mit.edu	37	7	21826264	21826264	+	Missense_Mutation	SNP	C	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21826264C>G	uc003svc.2	+	60	9672	c.9641C>G	c.(9640-9642)GCC>GGC	p.A3214G		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3214	Stalk (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						GAGCTGAAAGCCTTTCCCAAC	0.512									Kartagener_syndrome				9	96	---	---	---	---	PASS
HECW1	23072	broad.mit.edu	37	7	43484652	43484652	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43484652G>A	uc003tid.1	+	11	2486	c.1881G>A	c.(1879-1881)ACG>ACA	p.T627T	HECW1_uc011kbi.1_Silent_p.T627T	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	627					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23						CTCCAGGCACGGCGCACCCTG	0.706													11	20	---	---	---	---	PASS
GPC2	221914	broad.mit.edu	37	7	99774879	99774879	+	5'UTR	SNP	C	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99774879C>G	uc003utv.2	-	1					GPC2_uc010lgr.2_RNA|GPC2_uc003utw.1_5'UTR|STAG3_uc010lgs.1_5'Flank|STAG3_uc003utx.1_5'Flank|STAG3_uc011kjk.1_5'Flank	NM_152742	NP_689955	Q8N158	GPC2_HUMAN	glypican 2 precursor							anchored to membrane|endoplasmic reticulum|extracellular space|plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)|pancreas(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CAGAGCCTCCCAAACTCGGGA	0.627													21	9	---	---	---	---	PASS
FBXO24	26261	broad.mit.edu	37	7	100187841	100187841	+	Silent	SNP	C	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100187841C>G	uc003uvm.1	+	3	476	c.183C>G	c.(181-183)GCC>GCG	p.A61A	FBXO24_uc010lha.1_RNA|FBXO24_uc003uvl.1_Silent_p.A61A|FBXO24_uc003uvn.1_Intron|uc011kjy.1_Intron|FBXO24_uc011kjz.1_Silent_p.A99A|FBXO24_uc011kka.1_Silent_p.A49A	NM_033506	NP_277041	O75426	FBX24_HUMAN	F-box only protein 24 isoform 1	61	F-box.					ubiquitin ligase complex	ubiquitin-protein ligase activity			ovary(3)|skin(1)	4	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					ACCTTGTTGCCCTCGGCCAGA	0.607													64	31	---	---	---	---	PASS
PCOLCE	5118	broad.mit.edu	37	7	100200011	100200011	+	5'UTR	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100200011C>T	uc003uvo.2	+	1					uc011kjy.1_RNA|PCOLCE_uc011kkb.1_5'UTR|PCOLCE_uc010lhb.1_RNA	NM_002593	NP_002584	Q15113	PCOC1_HUMAN	procollagen C-endopeptidase enhancer						multicellular organismal development	extracellular space	collagen binding|heparin binding|peptidase activator activity				0	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					gccgccaccgctgctgctgct	0.557													6	73	---	---	---	---	PASS
ACHE	43	broad.mit.edu	37	7	100491616	100491616	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100491616G>A	uc003uxd.2	-	1	394	c.238C>T	c.(238-240)CCA>TCA	p.P80S	ACHE_uc003uxe.2_Missense_Mutation_p.P80S|ACHE_uc003uxf.2_Missense_Mutation_p.P80S|ACHE_uc003uxg.2_Missense_Mutation_p.P80S|ACHE_uc003uxh.2_Missense_Mutation_p.P80S|ACHE_uc003uxi.2_Missense_Mutation_p.P80S|ACHE_uc003uxj.1_Missense_Mutation_p.P199S	NM_000665	NP_000656	P22303	ACES_HUMAN	acetylcholinesterase isoform E4-E6 precursor	80					acetylcholine catabolic process in synaptic cleft|amyloid precursor protein metabolic process|cell adhesion|cell proliferation|choline metabolic process|DNA replication|muscle organ development|neurotransmitter biosynthetic process|osteoblast development|positive regulation of protein secretion|regulation of axonogenesis|regulation of dendrite morphogenesis|response to wounding|synapse assembly	anchored to membrane|axon|basal lamina|cell junction|cell surface|dendrite|endoplasmic reticulum lumen|extracellular space|Golgi apparatus|neuromuscular junction|nucleus|perinuclear region of cytoplasm|postsynaptic membrane|presynaptic membrane|synaptic cleft	acetylcholine binding|acetylcholinesterase activity|beta-amyloid binding|carboxylesterase activity|cholinesterase activity|collagen binding|laminin-1 binding|protein homodimerization activity|serine hydrolase activity			skin(2)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Atropine(DB00572)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium bromide(DB00944)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tacrine(DB00382)|Tubocurarine(DB01199)	GGCTCCGGTGGCAGAAAGCGA	0.627													28	146	---	---	---	---	PASS
ORAI2	80228	broad.mit.edu	37	7	102087006	102087006	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102087006G>A	uc010lhz.1	+	4	507	c.272G>A	c.(271-273)CGG>CAG	p.R91Q	ORAI2_uc003uzj.2_Missense_Mutation_p.R91Q|ORAI2_uc003uzk.2_Missense_Mutation_p.R91Q|ORAI2_uc011kks.1_Missense_Mutation_p.R14Q	NM_001126340	NP_001119812	Q96SN7	ORAI2_HUMAN	ORAI calcium release-activated calcium modulator	91						integral to membrane	protein binding			ovary(1)|kidney(1)	2						CAGTACCCGCGGCCGCTGCTG	0.662													17	72	---	---	---	---	PASS
MLL5	55904	broad.mit.edu	37	7	104681357	104681357	+	5'UTR	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104681357G>A	uc003vcm.2	+	3					MLL5_uc010lja.1_5'UTR|MLL5_uc010ljb.1_5'UTR|MLL5_uc003vcl.2_5'UTR|MLL5_uc010ljc.2_5'UTR	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5						cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3						GGATACCAATGCATAGGACTC	0.448													18	66	---	---	---	---	PASS
DDHD2	23259	broad.mit.edu	37	8	38095117	38095117	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38095117G>A	uc003xlb.2	+	4	850	c.473G>A	c.(472-474)AGA>AAA	p.R158K	DDHD2_uc003xla.2_Missense_Mutation_p.R158K|DDHD2_uc003xlc.2_Missense_Mutation_p.R158K|DDHD2_uc011lbl.1_Silent_p.Q10Q	NM_015214	NP_056029	O94830	DDHD2_HUMAN	DDHD domain containing 2 isoform 1	158					lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			TCTCCCAACAGAGAAATTATT	0.333													16	57	---	---	---	---	PASS
KCNB2	9312	broad.mit.edu	37	8	73480335	73480335	+	Silent	SNP	A	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73480335A>G	uc003xzb.2	+	2	954	c.366A>G	c.(364-366)GAA>GAG	p.E122E		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	122	Cytoplasmic (Potential).				regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)			TTGGCCAAGAACTTGATTACT	0.448													37	120	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77776411	77776411	+	Silent	SNP	T	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77776411T>C	uc003yav.2	+	11	10713	c.10326T>C	c.(10324-10326)GTT>GTC	p.V3442V		NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	3438						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			AAGAGCATGTTAGATTATTAC	0.433										HNSCC(33;0.089)			6	24	---	---	---	---	PASS
POU5F1B	5462	broad.mit.edu	37	8	128429170	128429170	+	Silent	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128429170C>T	uc003ysf.2	+	1	1314	c.1059C>T	c.(1057-1059)GGC>GGT	p.G353G	uc003ysc.1_Intron|uc003ysd.1_Intron|LOC727677_uc003yse.1_Intron|uc011liu.1_5'Flank	NM_001159542	NP_001153014	Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	353						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						TCACTCTGGGCTCTCCCATGC	0.577													12	14	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139734291	139734291	+	Silent	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139734291C>T	uc003yvd.2	-	26	2736	c.2289G>A	c.(2287-2289)CCG>CCA	p.P763P	COL22A1_uc011ljo.1_Silent_p.P63P	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	763	Collagen-like 5.|Pro-rich.|Gly-rich.			GKDGPNGPPGPPGTK -> CILAAKTAPGLKQLN (in Ref. 2; AAH42075).	cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TGGTTCCTGGCGGACCTGGTG	0.478										HNSCC(7;0.00092)			7	17	---	---	---	---	PASS
BOP1	23246	broad.mit.edu	37	8	145512927	145512927	+	Missense_Mutation	SNP	G	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145512927G>C	uc003zbr.1	-	2	226	c.158C>G	c.(157-159)TCC>TGC	p.S53C	HSF1_uc003zbt.3_5'Flank|HSF1_uc003zbu.3_5'Flank	NM_015201	NP_056016	Q14137	BOP1_HUMAN	block of proliferation 1	53					cell proliferation|maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|regulation of cell cycle	nucleoplasm|PeBoW complex	protein binding				0	all_cancers(97;4.06e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;2.61e-39)|all cancers(56;1.37e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.087)			CTCGCTGTCGGAGACGCCAGA	0.622													72	41	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68414113	68414113	+	RNA	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68414113C>T	uc004aex.2	+	1		c.668C>T								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		TCCTGGCTCACGAAAGCCCCC	0.657													3	11	---	---	---	---	PASS
C9orf78	51759	broad.mit.edu	37	9	132590413	132590413	+	3'UTR	SNP	C	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132590413C>A	uc004byp.2	-	9					C9orf78_uc004byo.2_3'UTR	NM_016520	NP_057604	Q9NZ63	CI078_HUMAN	chromosome 9 open reading frame 78												0		Ovarian(14;0.00556)				GAGAGGAAGGCGATATTTACA	0.313													4	124	---	---	---	---	PASS
SETX	23064	broad.mit.edu	37	9	135205856	135205856	+	Missense_Mutation	SNP	C	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135205856C>A	uc004cbk.2	-	10	1312	c.1129G>T	c.(1129-1131)GAT>TAT	p.D377Y	SETX_uc004cbj.2_5'UTR|SETX_uc010mzt.2_5'UTR	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	377					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		GGACAATAATCTGGGCAAATG	0.388													29	14	---	---	---	---	PASS
AGAP6	414189	broad.mit.edu	37	10	51748381	51748381	+	5'UTR	SNP	T	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51748381T>C	uc001jix.3	+	1						NM_001077665	NP_001071133	Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			skin(1)	1						AGACCATCTCTGCAAGTGCAG	0.706													5	21	---	---	---	---	PASS
ZNF518A	9849	broad.mit.edu	37	10	97920043	97920043	+	Missense_Mutation	SNP	G	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97920043G>T	uc001klp.2	+	6	4821	c.3964G>T	c.(3964-3966)GAT>TAT	p.D1322Y	ZNF518A_uc001klo.1_Missense_Mutation_p.D792Y|ZNF518A_uc001klq.2_Missense_Mutation_p.D1322Y|ZNF518A_uc001klr.2_Missense_Mutation_p.D1322Y	NM_014803	NP_055618	Q6AHZ1	Z518A_HUMAN	zinc finger protein 518	1322					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		GCTTTCAAAAGATTCCATCAG	0.388													4	49	---	---	---	---	PASS
PHRF1	57661	broad.mit.edu	37	11	607297	607297	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:607297G>A	uc001lqe.2	+	14	1972	c.1841G>A	c.(1840-1842)CGG>CAG	p.R614Q	PHRF1_uc010qwc.1_Missense_Mutation_p.R613Q|PHRF1_uc010qwd.1_Missense_Mutation_p.R612Q|PHRF1_uc010qwe.1_Missense_Mutation_p.R610Q|PHRF1_uc009ybz.1_Missense_Mutation_p.R404Q|PHRF1_uc009yca.1_RNA	NM_020901	NP_065952	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	614							RNA polymerase binding|zinc ion binding				0						GTTCAGGCTCGGAACTTGTCA	0.667													44	137	---	---	---	---	PASS
C11orf48	79081	broad.mit.edu	37	11	62439154	62439154	+	5'Flank	SNP	G	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62439154G>T	uc001nue.2	-						C11orf48_uc001nuf.2_5'UTR|C11orf48_uc010rmd.1_5'UTR|C11orf83_uc001nui.3_5'UTR	NM_024099	NP_077004	Q9BQE6	CK048_HUMAN	hypothetical protein LOC79081												0						TAGTGAGACCGCGCGGCAACA	0.617													3	45	---	---	---	---	PASS
PLCB3	5331	broad.mit.edu	37	11	64035013	64035013	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64035013G>A	uc001nzb.2	+	31	3690	c.3690G>A	c.(3688-3690)GAG>GAA	p.E1230E	PLCB3_uc009ypg.1_Silent_p.E1230E|PLCB3_uc009yph.1_Silent_p.E1163E|PLCB3_uc009ypi.2_Silent_p.E1230E|GPR137_uc009ypj.1_5'Flank	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3	1230					intracellular signal transduction|lipid catabolic process|synaptic transmission	cytosol	calcium ion binding|calmodulin binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|pancreas(1)	2						GCCAGGAGGAGAACACGCAGC	0.652													8	3	---	---	---	---	PASS
PYGM	5837	broad.mit.edu	37	11	64525784	64525784	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64525784G>A	uc001oax.3	-	4	1279	c.462C>T	c.(460-462)GCC>GCT	p.A154A	PYGM_uc001oay.3_Intron	NM_005609	NP_005600	P11217	PYGM_HUMAN	muscle glycogen phosphorylase isoform 1	154					glucose metabolic process|glycogen catabolic process	cytosol	glycogen phosphorylase activity|protein binding			ovary(2)	2					Pyridoxal Phosphate(DB00114)	AGCCATAGGCGGCCAGGCCCA	0.602													122	42	---	---	---	---	PASS
SYTL2	54843	broad.mit.edu	37	11	85444894	85444894	+	Intron	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85444894G>A	uc010rth.1	-						SYTL2_uc010rtg.1_Intron|SYTL2_uc010rti.1_Intron|SYTL2_uc010rtj.1_Intron|SYTL2_uc001pbf.3_3'UTR|SYTL2_uc010rtf.1_Intron	NM_001162951	NP_001156423	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform g						intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		cacccgcctcggcctcccaaa	0.109													12	24	---	---	---	---	PASS
ANKRD49	54851	broad.mit.edu	37	11	94231644	94231644	+	Silent	SNP	T	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94231644T>C	uc001pew.2	+	3	805	c.666T>C	c.(664-666)TAT>TAC	p.Y222Y	ANKRD49_uc001pex.2_3'UTR|ANKRD49_uc001pey.2_RNA	NM_017704	NP_060174	Q8WVL7	ANR49_HUMAN	fetal globin inducing factor	222					positive regulation of transcription, DNA-dependent					central_nervous_system(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CAAGTATCTATCACTACCTCT	0.398													41	64	---	---	---	---	PASS
PPP2R1B	5519	broad.mit.edu	37	11	111614171	111614171	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111614171C>T	uc001plx.1	-	12	1567	c.1483G>A	c.(1483-1485)GTT>ATT	p.V495I	PPP2R1B_uc001plw.1_Missense_Mutation_p.V495I|PPP2R1B_uc010rwi.1_Missense_Mutation_p.V431I|PPP2R1B_uc010rwj.1_Missense_Mutation_p.V334I|PPP2R1B_uc010rwk.1_Missense_Mutation_p.V450I|PPP2R1B_uc010rwl.1_Missense_Mutation_p.V368I	NM_002716	NP_002707	P30154	2AAB_HUMAN	beta isoform of regulatory subunit A, protein	495	HEAT 13.						protein binding				0		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		ACTTTGGGAACAATAGTATTT	0.383													13	168	---	---	---	---	PASS
TECTA	7007	broad.mit.edu	37	11	121039497	121039497	+	Silent	SNP	G	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121039497G>C	uc010rzo.1	+	19	5862	c.5862G>C	c.(5860-5862)ACG>ACC	p.T1954T		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	1954	ZP.				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TAGTGTTGACGACTCGAGATG	0.483													25	63	---	---	---	---	PASS
A2ML1	144568	broad.mit.edu	37	12	9006743	9006743	+	Silent	SNP	T	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9006743T>A	uc001quz.3	+	21	2708	c.2610T>A	c.(2608-2610)ATT>ATA	p.I870I	A2ML1_uc001qva.1_Silent_p.I450I|A2ML1_uc010sgm.1_Silent_p.I370I	NM_144670	NP_653271	A8K2U0	A2ML1_HUMAN	alpha-2-macroglobulin-like 1 precursor	714						extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3						ACTTTACTATTAGTACAAAGA	0.458													13	39	---	---	---	---	PASS
LIMA1	51474	broad.mit.edu	37	12	50616335	50616335	+	Intron	SNP	T	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50616335T>C	uc001rwj.3	-						LIMA1_uc001rwh.3_5'Flank|LIMA1_uc001rwi.3_5'UTR|LIMA1_uc001rwk.3_Intron|LIMA1_uc010smr.1_Intron|LIMA1_uc010sms.1_Intron	NM_016357	NP_057441	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1 isoform b						actin filament bundle assembly|negative regulation of actin filament depolymerization|ruffle organization	cytoplasm|focal adhesion|stress fiber	actin filament binding|actin monomer binding|zinc ion binding			ovary(1)	1						TGTTGTTCTTTGTAAAATGAA	0.433													25	29	---	---	---	---	PASS
KRT74	121391	broad.mit.edu	37	12	52962081	52962081	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52962081G>A	uc001sap.1	-	7	1275	c.1227C>T	c.(1225-1227)GGC>GGT	p.G409G		NM_175053	NP_778223	Q7RTS7	K2C74_HUMAN	keratin 6 irs4	409	Rod.|Coil 2.					keratin filament	structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.191)		GGTGCAGGGCGCCCTCCAGCT	0.652													35	113	---	---	---	---	PASS
ARHGAP9	64333	broad.mit.edu	37	12	57870622	57870622	+	Intron	SNP	T	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57870622T>C	uc001sod.2	-						ARHGAP9_uc001sny.2_5'Flank|ARHGAP9_uc001snz.2_Intron|ARHGAP9_uc001soa.2_5'UTR|ARHGAP9_uc001sob.2_Intron|ARHGAP9_uc001soc.2_Intron|ARHGAP9_uc001soe.1_Intron|ARHGAP9_uc010sro.1_3'UTR	NM_032496	NP_115885	Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9 isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			lung(1)	1			GBM - Glioblastoma multiforme(3;3.37e-34)			GCAGGGAGGATCTTGGCCTTC	0.582													28	117	---	---	---	---	PASS
HSP90B1	7184	broad.mit.edu	37	12	104326676	104326676	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104326676G>A	uc001tkb.1	+	4	472	c.367G>A	c.(367-369)GAA>AAA	p.E123K	HSP90B1_uc010swg.1_Intron|HSP90B1_uc009zui.1_Missense_Mutation_p.E123K|LOC253724_uc010swf.1_5'Flank|LOC253724_uc009zuh.2_5'Flank	NM_003299	NP_003290	P14625	ENPL_HUMAN	heat shock protein 90kDa beta, member 1	123					actin rod assembly|anti-apoptosis|cellular response to ATP|ER-associated protein catabolic process|protein folding|protein transport|regulation of phosphoprotein phosphatase activity|response to hypoxia|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|melanosome|microsome|midbody|perinuclear region of cytoplasm	ATP binding|calcium ion binding|low-density lipoprotein particle receptor binding|protein phosphatase binding|RNA binding|unfolded protein binding|virion binding			ovary(2)|skin(1)	3					Rifabutin(DB00615)	ACTGACTGATGAAAATGCTCT	0.343													87	110	---	---	---	---	PASS
RCBTB1	55213	broad.mit.edu	37	13	50129739	50129739	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50129739C>T	uc001vde.1	-	6	776	c.515G>A	c.(514-516)CGA>CAA	p.R172Q		NM_018191	NP_060661	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and	172	RCC1 3.				cell cycle|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(1)	1		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		TGTAACTTTTCGAGGAGTTGG	0.443													16	35	---	---	---	---	PASS
SNW1	22938	broad.mit.edu	37	14	78184464	78184464	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78184464G>A	uc001xuf.2	-	14	1605	c.1578C>T	c.(1576-1578)CAC>CAT	p.H526H	SNW1_uc010tvm.1_Silent_p.H451H|SNW1_uc010asu.2_Silent_p.H364H|SNW1_uc010tvn.1_Missense_Mutation_p.T553M	NM_012245	NP_036377	Q13573	SNW1_HUMAN	SKI-interacting protein	526					negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|regulation of transcription from RNA polymerase II promoter	catalytic step 2 spliceosome|nucleoplasm	Notch binding			ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CTTCATGCTCGTGTTCCTTGG	0.468													100	182	---	---	---	---	PASS
TMEM62	80021	broad.mit.edu	37	15	43461795	43461795	+	Missense_Mutation	SNP	G	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43461795G>T	uc001zqr.2	+	11	1580	c.1301G>T	c.(1300-1302)CGG>CTG	p.R434L	TMEM62_uc010bda.2_Missense_Mutation_p.R304L|TMEM62_uc001zqt.2_Missense_Mutation_p.R3L	NM_024956	NP_079232	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	434	Helical; (Potential).					integral to membrane				ovary(1)|breast(1)	2		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)		CTGCAGGCCCGGGTCCTTTTT	0.378													3	72	---	---	---	---	PASS
HBA1	3039	broad.mit.edu	37	16	226701	226701	+	5'UTR	SNP	C	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:226701C>G	uc002cfx.1	+	1					HBA2_uc002cfw.2_Intron|HBA1_uc002cfy.1_5'Flank	NM_000558	NP_000549	P69905	HBA_HUMAN	alpha 1 globin						hydrogen peroxide catabolic process|positive regulation of cell death|protein heterooligomerization	cytosolic small ribosomal subunit|haptoglobin-hemoglobin complex|hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity|protein binding				0		all_cancers(16;2.03e-06)|all_epithelial(16;5.16e-06)|Hepatocellular(16;0.000325)|Lung NSC(18;0.0138)|all_lung(18;0.0306)			Amodiaquine(DB00613)|Chloroquine(DB00608)|Iron Dextran(DB00893)|Mefloquine(DB00358)|Primaquine(DB01087)|Quinine(DB00468)	CCCACAGACTCAGAGAGAACC	0.547													7	11	---	---	---	---	PASS
SULT1A1	6817	broad.mit.edu	37	16	28620355	28620355	+	5'UTR	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28620355C>T	uc002dqi.2	-	1					uc010vct.1_Intron|SULT1A1_uc002dqj.2_Intron|SULT1A1_uc002dqk.2_Intron|SULT1A1_uc002dql.2_Intron|SULT1A1_uc002dqm.2_Intron|SULT1A1_uc002dqn.2_Intron|SULT1A1_uc002dqo.2_Intron|SULT1A1_uc002dqp.2_Intron	NM_177534	NP_803878	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A,						3'-phosphoadenosine 5'-phosphosulfate metabolic process|catecholamine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|xenobiotic metabolic process	cytosol	aryl sulfotransferase activity|flavonol 3-sulfotransferase activity				0						GGCTCTAATGcggtggttccc	0.030													3	26	---	---	---	---	PASS
ATP2A1	487	broad.mit.edu	37	16	28913653	28913653	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28913653C>T	uc002dro.1	+	17	2654	c.2470C>T	c.(2470-2472)CCC>TCC	p.P824S	uc010vct.1_Intron|ATP2A1_uc002drn.1_Missense_Mutation_p.P824S|ATP2A1_uc002drp.1_Missense_Mutation_p.P699S	NM_173201	NP_775293	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, fast twitch 1 isoform	824	Cytoplasmic (By similarity).				apoptosis in response to endoplasmic reticulum stress|apoptotic mitochondrial changes|ATP biosynthetic process|calcium ion import|elevation of endoplasmic reticulum calcium ion concentration|elevation of mitochondrial calcium ion concentration|maintenance of mitochondrion location|negative regulation of striated muscle contraction|platelet activation|positive regulation of fast-twitch skeletal muscle fiber contraction|reduction of endoplasmic reticulum calcium ion concentration|relaxation of skeletal muscle|response to endoplasmic reticulum stress	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|H zone|I band|microsome|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum|sarcoplasmic reticulum membrane	ATP binding|ATP binding|calcium ion binding|calcium ion binding|calcium-transporting ATPase activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						CCCCCGGAGCCCCAAGGAGCC	0.647													51	631	---	---	---	---	PASS
SEPT1	1731	broad.mit.edu	37	16	30391429	30391429	+	Intron	SNP	A	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30391429A>G	uc002dxy.2	-						SEPT1_uc002dxw.2_5'Flank|SEPT1_uc002dxx.2_Intron|SEPT1_uc010veq.1_3'UTR	NM_052838	NP_443070	Q8WYJ6	SEPT1_HUMAN	septin 1						cell cycle|cell division	microtubule organizing center|septin complex	GTP binding|protein binding			ovary(1)	1			Colorectal(24;0.193)			agacagtgagacacagagata	0.204													13	98	---	---	---	---	PASS
RPGRIP1L	23322	broad.mit.edu	37	16	53679568	53679568	+	Silent	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53679568C>T	uc002ehp.2	-	17	2716	c.2652G>A	c.(2650-2652)CTG>CTA	p.L884L	RPGRIP1L_uc002eho.3_Silent_p.L884L|RPGRIP1L_uc010vgy.1_Silent_p.L884L|RPGRIP1L_uc010cbx.2_Silent_p.L884L|RPGRIP1L_uc010vgz.1_Silent_p.L884L	NM_015272	NP_056087	Q68CZ1	FTM_HUMAN	RPGRIP1-like isoform a	884					negative regulation of G-protein coupled receptor protein signaling pathway	cell-cell junction|centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)				CCAACGAAATCAGAGGCACAT	0.333													34	70	---	---	---	---	PASS
MYO1C	4641	broad.mit.edu	37	17	1375225	1375225	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1375225C>T	uc002fsp.2	-	19	2217	c.1997G>A	c.(1996-1998)CGC>CAC	p.R666H	MYO1C_uc002fsn.2_Missense_Mutation_p.R647H|MYO1C_uc002fso.2_Missense_Mutation_p.R631H|MYO1C_uc010vqj.1_Missense_Mutation_p.R631H|MYO1C_uc010vqk.1_Missense_Mutation_p.R642H	NM_001080779	NP_001074248	O00159	MYO1C_HUMAN	myosin IC isoform a	666	Myosin head-like.				mRNA transport|protein transport|transmembrane transport	basal plasma membrane|cytoplasm|filamentous actin|lateral plasma membrane|nuclear pore|nucleolus|nucleoplasm|stereocilium membrane	actin binding|ATP binding|calmodulin binding|motor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TTCGTATTTGCGGCGATAGGC	0.637													6	221	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577568	7577568	+	Missense_Mutation	SNP	C	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577568C>A	uc002gim.2	-	7	907	c.713G>T	c.(712-714)TGT>TTT	p.C238F	TP53_uc002gig.1_Missense_Mutation_p.C238F|TP53_uc002gih.2_Missense_Mutation_p.C238F|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.C106F|TP53_uc010cng.1_Missense_Mutation_p.C106F|TP53_uc002gii.1_Missense_Mutation_p.C106F|TP53_uc010cnh.1_Missense_Mutation_p.C238F|TP53_uc010cni.1_Missense_Mutation_p.C238F|TP53_uc002gij.2_Missense_Mutation_p.C238F|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.C145F|TP53_uc002gio.2_Missense_Mutation_p.C106F	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	238	|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).	Zinc.	C -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> F (in sporadic cancers; somatic mutation).|C -> S (in LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> Y (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|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|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.C238Y(47)|p.C238F(34)|p.C238S(18)|p.C238R(14)|p.0?(7)|p.C238*(4)|p.C238W(2)|p.Y236_M243delYMCNSSCM(1)|p.C238fs*2(1)|p.V225fs*23(1)|p.C238_N239insX(1)|p.C238_M246delCNSSCMGGM(1)|p.C238fs*9(1)|p.M237_N239delMCN(1)|p.C238fs*21(1)|p.C238del(1)|p.C238G(1)|p.C238C(1)|p.M237fs*1(1)|p.C145F(1)|p.H233fs*6(1)|p.H233_C242del10(1)|p.N239_C242del(1)|p.M237_C238insX(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GGAACTGTTACACATGTAGTT	0.572		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			60	8	---	---	---	---	PASS
TP53I13	90313	broad.mit.edu	37	17	27899299	27899299	+	Nonsense_Mutation	SNP	C	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27899299C>G	uc002hee.2	+	6	691	c.653C>G	c.(652-654)TCA>TGA	p.S218*		NM_138349	NP_612358	Q8NBR0	P5I13_HUMAN	tumor protein p53 inducible protein 13	218	Extracellular (Potential).					cytoplasm|integral to membrane|plasma membrane					0				READ - Rectum adenocarcinoma(3;0.236)		CCCACTCGCTCAGCCCTGAGG	0.637													55	13	---	---	---	---	PASS
CASKIN2	57513	broad.mit.edu	37	17	73498739	73498739	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73498739G>A	uc002joc.2	-	18	2966	c.2416C>T	c.(2416-2418)CCC>TCC	p.P806S	CASKIN2_uc010wsc.1_Missense_Mutation_p.P724S	NM_020753	NP_065804	Q8WXE0	CSKI2_HUMAN	cask-interacting protein 2 isoform a	806	Pro-rich.					cytoplasm				pancreas(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCCTCTGTGGGGCCAGGGCGG	0.701													4	44	---	---	---	---	PASS
CCDC57	284001	broad.mit.edu	37	17	80059594	80059594	+	Missense_Mutation	SNP	C	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80059594C>G	uc002kdx.1	-	17	2749	c.2712G>C	c.(2710-2712)AGG>AGC	p.R904S		NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	905										ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			TCTTGGGGGGCCTCTGGCAGC	0.612													210	45	---	---	---	---	PASS
SETBP1	26040	broad.mit.edu	37	18	42530725	42530725	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42530725G>A	uc010dni.2	+	4	1716	c.1420G>A	c.(1420-1422)GAG>AAG	p.E474K		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	474						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		GATAGAGAATGAGTCCCCCTC	0.483									Schinzel-Giedion_syndrome				66	27	---	---	---	---	PASS
HDGFRP2	84717	broad.mit.edu	37	19	4499523	4499523	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4499523G>A	uc002mao.2	+	14	1704	c.1611G>A	c.(1609-1611)GAG>GAA	p.E537E	HDGFRP2_uc002map.2_Silent_p.E537E|HDGFRP2_uc010dtz.1_RNA|HDGFRP2_uc010dua.2_Silent_p.E2E|HDGFRP2_uc002maq.1_Silent_p.E2E	NM_001001520	NP_001001520	Q7Z4V5	HDGR2_HUMAN	hepatoma-derived growth factor-related protein 2	537	Potential.				transcription, DNA-dependent	nucleus	DNA binding|protein binding				0						ACGTAATGGAGAAGGCAGCAG	0.463													9	47	---	---	---	---	PASS
PRR22	163154	broad.mit.edu	37	19	5783026	5783026	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5783026G>A	uc002mdb.1	-	1	1585	c.1226C>T	c.(1225-1227)CCG>CTG	p.P409L	PRR22_uc010xiv.1_Missense_Mutation_p.P411L	NM_153359	NP_699190	Q8IZ63	PRR22_HUMAN	proline rich 22 isoform 2	409											0						CCTGGGCCCCGGGGGAGTGGC	0.667													6	11	---	---	---	---	PASS
EMR4P	326342	broad.mit.edu	37	19	6981182	6981182	+	5'UTR	SNP	C	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6981182C>A	uc010xjk.1	-	6					EMR4P_uc010dve.1_Intron	NR_024075				RecName: Full=Putative EGF-like module-containing mucin-like hormone receptor-like 4; AltName: Full=G-protein coupled receptor 127; AltName: Full=G-protein coupled receptor PGR16; Flags: Precursor;												0						GTTGAGTAGCCCTTCTTGCAA	0.378													4	25	---	---	---	---	PASS
C19orf39	126074	broad.mit.edu	37	19	11486191	11486191	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11486191G>A	uc002mrg.1	+	2	226	c.189G>A	c.(187-189)AAG>AAA	p.K63K		NM_175871	NP_787067	Q6NVH7	CS039_HUMAN	hypothetical protein LOC126074	63											0						CCTTCTAGAAGATCCGCTTCC	0.582													99	308	---	---	---	---	PASS
MAST1	22983	broad.mit.edu	37	19	12958899	12958899	+	Intron	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12958899C>T	uc002mvm.2	+						MAST1_uc002mvk.2_Intron|MAST1_uc002mvl.2_3'UTR	NM_014975	NP_055790	Q9Y2H9	MAST1_HUMAN	microtubule associated serine/threonine kinase						cytoskeleton organization|intracellular protein kinase cascade	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7						CCGGGCTGATCTCAGGCTCAG	0.413													17	7	---	---	---	---	PASS
ANO8	57719	broad.mit.edu	37	19	17440975	17440975	+	Missense_Mutation	SNP	G	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17440975G>T	uc002ngf.2	-	10	1391	c.1232C>A	c.(1231-1233)GCC>GAC	p.A411D	ANO8_uc010eap.2_RNA	NM_020959	NP_066010	Q9HCE9	ANO8_HUMAN	anoctamin 8	411	Helical; (Potential).|Leu-rich.					chloride channel complex	chloride channel activity			ovary(3)	3						GTAGCCCTCGGCACTCACACT	0.627													26	78	---	---	---	---	PASS
USF2	7392	broad.mit.edu	37	19	35770065	35770065	+	Intron	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35770065G>A	uc002nyq.1	+						USF2_uc010xss.1_Missense_Mutation_p.A347T|USF2_uc002nyr.1_Intron|USF2_uc002nys.1_Intron|USF2_uc002nyt.1_Intron|USF2_uc002nyu.1_Intron|USF2_uc002nyv.1_Intron	NM_003367	NP_003358	Q15853	USF2_HUMAN	upstream stimulatory factor 2 isoform 1						lipid homeostasis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter by glucose	nucleus	bHLH transcription factor binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity				0	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CGTCGTGTCCGCCAGATCGAG	0.687													7	20	---	---	---	---	PASS
ZNF461	92283	broad.mit.edu	37	19	37147421	37147421	+	Missense_Mutation	SNP	A	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37147421A>G	uc002oem.2	-	4	389	c.161T>C	c.(160-162)GTA>GCA	p.V54A	ZNF461_uc002oen.2_Missense_Mutation_p.V23A|ZNF461_uc010xtj.1_Missense_Mutation_p.V54A	NM_153257	NP_694989	Q8TAF7	ZN461_HUMAN	gonadotropin inducible transcription repressor	54	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TGAGGAGATTACGGCTGGCTT	0.433													3	67	---	---	---	---	PASS
ZNF567	163081	broad.mit.edu	37	19	37210842	37210842	+	Missense_Mutation	SNP	G	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37210842G>T	uc010xtl.1	+	6	1438	c.1216G>T	c.(1216-1218)GCA>TCA	p.A406S	ZNF567_uc002oeo.1_Missense_Mutation_p.A406S|ZNF567_uc010xtk.1_Missense_Mutation_p.A406S|ZNF567_uc002oep.3_Missense_Mutation_p.A375S|ZNF567_uc002oeq.1_Missense_Mutation_p.A375S	NM_152603	NP_689816	Q8N184	ZN567_HUMAN	zinc finger protein 567	406	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TCACCAGAAGGCAAATCTTAC	0.433													17	56	---	---	---	---	PASS
SULT2B1	6820	broad.mit.edu	37	19	49055556	49055556	+	Missense_Mutation	SNP	A	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49055556A>T	uc002pjl.2	+	1	128	c.47A>T	c.(46-48)TAT>TTT	p.Y16F		NM_177973	NP_814444	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	16				Missing: Increases the cholesterol sulfotransferase activity.|Missing: Loss of the cholesterol sulfotransferase activity.	3'-phosphoadenosine 5'-phosphosulfate metabolic process|steroid metabolic process|xenobiotic metabolic process	cytosol	alcohol sulfotransferase activity|protein binding|steroid sulfotransferase activity			skin(1)	1		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		TGGGACACCTATGAAGATGAC	0.672													18	34	---	---	---	---	PASS
KLK5	25818	broad.mit.edu	37	19	51453127	51453127	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51453127C>T	uc002pue.2	-	4	537	c.319G>A	c.(319-321)GCC>ACC	p.A107T	KLK5_uc002puf.2_Missense_Mutation_p.A107T|KLK5_uc002pug.2_Missense_Mutation_p.A107T	NM_001077491	NP_001070959	Q9Y337	KLK5_HUMAN	kallikrein-related peptidase 5 preproprotein	107	Peptidase S1.				epidermis development|positive regulation of G-protein coupled receptor protein signaling pathway|proteolysis	extracellular space	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00379)|GBM - Glioblastoma multiforme(134;0.00888)		CTGCAGTGGGCGGCCGTGAGC	0.512													40	11	---	---	---	---	PASS
SAPS1	22870	broad.mit.edu	37	19	55758320	55758320	+	Missense_Mutation	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55758320G>A	uc002qjw.3	-	2	394	c.152C>T	c.(151-153)CCA>CTA	p.P51L	SAPS1_uc002qjv.2_Missense_Mutation_p.P113L	NM_014931	NP_055746	Q9UPN7	PP6R1_HUMAN	SAPS domain family, member 1	51	Interaction with PPP6C.				regulation of phosphoprotein phosphatase activity	cytoplasm	protein phosphatase binding				0		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		CAGGTGGGGTGGCTGCAGCAG	0.657													19	30	---	---	---	---	PASS
C20orf117	140710	broad.mit.edu	37	20	35443917	35443917	+	Missense_Mutation	SNP	C	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35443917C>A	uc002xgd.1	-	5	1541	c.1214G>T	c.(1213-1215)CGA>CTA	p.R405L	C20orf117_uc002xge.1_RNA	NM_199181	NP_954650	O94964	K0889_HUMAN	hypothetical protein LOC140710 isoform 2	405											0		Myeloproliferative disorder(115;0.00874)				TCTGCAGAGTCGGACCGCATG	0.677													4	9	---	---	---	---	PASS
IFNGR2	3460	broad.mit.edu	37	21	34805103	34805103	+	Missense_Mutation	SNP	C	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34805103C>A	uc002yrp.3	+	6	1452	c.804C>A	c.(802-804)TTC>TTA	p.F268L	IFNGR2_uc002yrq.3_Missense_Mutation_p.F287L|IFNGR2_uc010gma.2_Missense_Mutation_p.F189L|IFNGR2_uc002yrr.3_Missense_Mutation_p.F189L|TMEM50B_uc002yrs.1_RNA	NM_005534	NP_005525	P38484	INGR2_HUMAN	interferon gamma receptor 2 precursor	268	Helical; (Potential).				regulation of interferon-gamma-mediated signaling pathway|response to virus	endoplasmic reticulum|integral to plasma membrane	interferon-gamma receptor activity				0					Interferon gamma-1b(DB00033)	CCTGTTTCTTCCTGGTCCTGA	0.468													45	85	---	---	---	---	PASS
SLC19A1	6573	broad.mit.edu	37	21	46951334	46951334	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46951334G>A	uc002zhl.1	-	3	1037	c.918C>T	c.(916-918)AAC>AAT	p.N306N	SLC19A1_uc010gpy.1_Silent_p.N306N|SLC19A1_uc011aft.1_Silent_p.N266N|SLC19A1_uc002zhm.1_Silent_p.N306N|SLC19A1_uc010gpz.1_Silent_p.N185N	NM_194255	NP_919231	P41440	S19A1_HUMAN	solute carrier family 19 member 1	306	Extracellular (Probable).				folic acid metabolic process	integral to plasma membrane|membrane fraction	folic acid binding|folic acid transporter activity|methotrexate transporter activity|reduced folate carrier activity				0				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)		CTGCCGCGCCGTTGTAGACCC	0.662													34	103	---	---	---	---	PASS
C22orf24	25775	broad.mit.edu	37	22	32334024	32334024	+	Missense_Mutation	SNP	A	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32334024A>G	uc003aly.2	-	2	196	c.29T>C	c.(28-30)CTG>CCG	p.L10P	C22orf24_uc003alx.2_RNA	NM_015372	NP_056187	Q9Y442	CV024_HUMAN	hypothetical protein LOC25775	10						integral to membrane				central_nervous_system(1)	1						CTTTTGATGCAGCCCTGTTGT	0.378													124	348	---	---	---	---	PASS
TST	7263	broad.mit.edu	37	22	37414345	37414345	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37414345G>A	uc003aqg.2	-	1	1129	c.429C>T	c.(427-429)TCC>TCT	p.S143S	TST_uc003aqh.2_Silent_p.S143S|MPST_uc003aqi.1_5'Flank|MPST_uc003aqj.2_5'Flank|MPST_uc003aqm.2_5'Flank|MPST_uc011amu.1_5'Flank|MPST_uc003aql.2_5'Flank	NM_003312	NP_003303	Q16762	THTR_HUMAN	thiosulfate sulfurtransferase	143	Rhodanese 1.				cyanate catabolic process|rRNA transport	mitochondrial matrix|plasma membrane	5S rRNA binding|thiosulfate sulfurtransferase activity				0						GTGAGGGCTCGGATGTCACCG	0.607													25	71	---	---	---	---	PASS
SMCR7L	54471	broad.mit.edu	37	22	39910417	39910417	+	3'UTR	SNP	T	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39910417T>A	uc003axx.2	+	6					SMCR7L_uc003axw.2_Intron|SMCR7L_uc003axy.2_3'UTR	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471							integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)					CCTCACAGGGTTCCTGCTGCC	0.512											OREG0026577	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	21	---	---	---	---	PASS
RRP7B	91695	broad.mit.edu	37	22	42972584	42972584	+	RNA	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42972584G>A	uc003bcs.2	-	5		c.495C>T			RRP7B_uc003bct.2_RNA					Homo sapiens cDNA FLJ90011 fis, clone HEMBA1000443, highly similar to Gastric cancer antigen Zg14.												0						CCTCAGGGTCGGGCACAGAGT	0.642													5	14	---	---	---	---	PASS
ZNF645	158506	broad.mit.edu	37	X	22291957	22291957	+	Silent	SNP	G	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22291957G>A	uc004dai.1	+	1	898	c.849G>A	c.(847-849)GCG>GCA	p.A283A		NM_152577	NP_689790	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	283	Pro-rich.					intracellular	zinc ion binding			lung(1)|pancreas(1)	2						AGCATTATGCGCCACCTCCAT	0.473													69	20	---	---	---	---	PASS
HMGB3	3149	broad.mit.edu	37	X	150156179	150156179	+	Intron	SNP	G	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150156179G>T	uc004fep.2	+						HMGB3_uc004feq.2_3'UTR|HMGB3_uc004fer.2_Intron	NM_005342	NP_005333	O15347	HMGB3_HUMAN	high-mobility group box 3						DNA recombination|multicellular organismal development	chromosome|nucleus	DNA bending activity|double-stranded DNA binding				0	Acute lymphoblastic leukemia(192;6.56e-05)					TACCTGAGATGAGGACTGCAT	0.388													3	23	---	---	---	---	PASS
FLNA	2316	broad.mit.edu	37	X	153592464	153592464	+	Missense_Mutation	SNP	C	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153592464C>T	uc004fkk.2	-	15	2455	c.2206G>A	c.(2206-2208)GTG>ATG	p.V736M	FLNA_uc010nuu.1_Missense_Mutation_p.V736M	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	736	Filamin 5.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TTCCTGGGCACGTAGGAGCAG	0.612													73	18	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	5761932	5761933	+	IGR	INS	-	AGGAAGGA	AGGAAGGA	rs76080214	by1000genomes	TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5761932_5761933insAGGAAGGA								AJAP1 (918082 upstream) : NPHP4 (160937 downstream)																							agaagggagggaggaaggaagg	0.000													3	6	---	---	---	---	
MTOR	2475	broad.mit.edu	37	1	11188748	11188749	+	Intron	INS	-	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11188748_11188749insA	uc001asd.2	-						MTOR_uc001asc.2_Intron	NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated						cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29						GTTTCTAAAAGAAAATAAAGAA	0.386													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	162386108	162386109	+	IGR	DEL	AG	-	-	rs66942414		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162386108_162386109delAG								SH2D1B (4180 upstream) : UHMK1 (80855 downstream)																							gaaggaagaaagagaaagaaag	0.089													6	3	---	---	---	---	
HMCN1	83872	broad.mit.edu	37	1	186057700	186057700	+	Intron	DEL	T	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186057700delT	uc001grq.1	+							NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						AGTTTAAAGGTTTTTTTATGT	0.303													3	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	242995203	242995204	+	IGR	INS	-	GAAA	GAAA	rs10926878	by1000genomes	TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242995203_242995204insGAAA								PLD5 (307205 upstream) : CEP170 (292527 downstream)																							aaggaaggaaggaaggaaggag	0.000													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	247621623	247621624	+	IGR	DEL	TG	-	-	rs113974544		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247621623_247621624delTG								OR2B11 (6339 upstream) : OR2W5 (32806 downstream)																							ATAAGAACTCtgtgtgtgtgtg	0.356													3	5	---	---	---	---	
CDKL4	344387	broad.mit.edu	37	2	39417450	39417453	+	Frame_Shift_Del	DEL	TGTT	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39417450_39417453delTGTT	uc002rrm.2	-	5	645_648	c.645_648delAACA	c.(643-648)AGAACAfs	p.R215fs	CDKL4_uc010fal.1_Frame_Shift_Del_p.R215fs	NM_001009565	NP_001009565	Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4	215_216	Protein kinase.					cytoplasm	ATP binding|cyclin-dependent protein kinase activity			ovary(1)	1		all_hematologic(82;0.248)				TCATACCTAGTGTTCTGATTATCA	0.343													96	25	---	---	---	---	
GGCX	2677	broad.mit.edu	37	2	85787730	85787730	+	Intron	DEL	A	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85787730delA	uc002sps.2	-						GGCX_uc010yss.1_5'Flank|GGCX_uc010yst.1_Intron	NM_000821	NP_000812	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase isoform 1						blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification	endoplasmic reticulum membrane|integral to membrane|membrane fraction	gamma-glutamyl carboxylase activity			ovary(1)	1					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|L-Glutamic Acid(DB00142)|Menadione(DB00170)|Phytonadione(DB01022)	ccgtctaaggaaaaaaaaaaa	0.174													4	2	---	---	---	---	
RNF181	51255	broad.mit.edu	37	2	85823477	85823477	+	Intron	DEL	A	-	-	rs71390085		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85823477delA	uc002spv.1	+							NM_016494	NP_057578	Q9P0P0	RN181_HUMAN	ring finger protein 181								ligase activity|zinc ion binding				0						tagcagttgtaaactatttcc	0.085													0	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	193866302	193866321	+	IGR	DEL	GAAAGAAAGAAAGAAAGAAA	-	-	rs7355353	by1000genomes	TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193866302_193866321delGAAAGAAAGAAAGAAAGAAA								PCGEM1 (224681 upstream) : None (None downstream)																							aggaaggaaggaaagaaagaaagaaagaaagaaagaaaga	0.059													7	7	---	---	---	---	
STK17B	9262	broad.mit.edu	37	2	197028246	197028246	+	Intron	DEL	A	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197028246delA	uc002utk.2	-						STK17B_uc010fsh.2_Intron	NM_004226	NP_004217	O94768	ST17B_HUMAN	serine/threonine kinase 17B						apoptosis|induction of apoptosis|intracellular protein kinase cascade	nucleus	ATP binding|protein serine/threonine kinase activity			lung(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.141)			AAATACAACTAAAAAAAAAAA	0.308													6	3	---	---	---	---	
SLC4A3	6508	broad.mit.edu	37	2	220504959	220504959	+	Intron	DEL	G	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220504959delG	uc002vmp.3	+						SLC4A3_uc002vmo.3_Intron|SLC4A3_uc010fwm.2_Intron	NM_005070	NP_005061	P48751	B3A3_HUMAN	solute carrier family 4, anion exchanger, member						bicarbonate transport	integral to plasma membrane|membrane fraction	inorganic anion exchanger activity			ovary(2)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	5		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCCCCCCCCCGCCCCTCCTTC	0.383													4	2	---	---	---	---	
KLHL30	377007	broad.mit.edu	37	2	239053011	239053012	+	Intron	INS	-	GAAGGAAA	GAAGGAAA	rs72336409		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239053011_239053012insGAAGGAAA	uc002vxr.1	+							NM_198582	NP_940984	Q0D2K2	KLH30_HUMAN	kelch-like 30												0		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GAGGGTGCTCggaaggaaggaa	0.069													5	6	---	---	---	---	
SLC35A5	55032	broad.mit.edu	37	3	112282152	112282152	+	Intron	DEL	T	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112282152delT	uc003dze.2	+						ATG3_uc003dzd.2_5'Flank|ATG3_uc003dzc.2_5'Flank|ATG3_uc010hqe.2_5'Flank	NM_017945	NP_060415	Q9BS91	S35A5_HUMAN	solute carrier family 35, member A5							Golgi membrane|integral to membrane	nucleotide-sugar transmembrane transporter activity|sugar:hydrogen symporter activity			ovary(1)	1						TAAAAATTCCTTTTTTGTCCT	0.338													29	17	---	---	---	---	
NMD3	51068	broad.mit.edu	37	3	160953120	160953121	+	Intron	INS	-	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160953120_160953121insA	uc003feb.1	+						NMD3_uc003fec.2_Intron|NMD3_uc003fed.1_Intron|NMD3_uc010hwh.2_Intron	NM_015938	NP_057022	Q96D46	NMD3_HUMAN	NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			tttctgttaggaaaaaaaaaaa	0.079													3	3	---	---	---	---	
LSG1	55341	broad.mit.edu	37	3	194373326	194373327	+	Intron	INS	-	AGTG	AGTG			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194373326_194373327insAGTG	uc003fui.2	-							NM_018385	NP_060855	Q9H089	LSG1_HUMAN	large subunit GTPase 1						nuclear export|protein transport	Cajal body|endoplasmic reticulum	GTP binding|hydrolase activity				0	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		cccgtgatgccagtgggcaaca	0.104													42	13	---	---	---	---	
WDR19	57728	broad.mit.edu	37	4	39257615	39257616	+	Intron	INS	-	CAGGAATAATTGTAGGAAATATACGTAAATGC	CAGGAATAATTGTAGGAAATATACGTAAATGC	rs150257136	by1000genomes	TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39257615_39257616insCAGGAATAATTGTAGGAAATATACGTAAATGC	uc003gtv.2	+						WDR19_uc011byi.1_Intron|WDR19_uc003gtw.1_Intron	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1						CACTGACTCCGCAGGAATAATT	0.317													4	2	---	---	---	---	
IGJ	3512	broad.mit.edu	37	4	71522909	71522909	+	Intron	DEL	G	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71522909delG	uc003hfn.3	-						IGJ_uc010ihz.2_Intron	NM_144646	NP_653247	P01591	IGJ_HUMAN	immunoglobulin J chain						immune response	extracellular region	antigen binding				0			Lung(101;0.235)			ATATTACTATGGAAAAAAATA	0.308													27	15	---	---	---	---	
BMP2K	55589	broad.mit.edu	37	4	79697893	79697897	+	Intron	DEL	GGCTC	-	-	rs67018255		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79697893_79697897delGGCTC	uc003hlk.2	+						BMP2K_uc010ijl.1_Intron|BMP2K_uc003hlj.2_Intron	NM_198892	NP_942595	Q9NSY1	BMP2K_HUMAN	BMP-2 inducible kinase isoform a							nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1						CGCCCGGGGAGGCTCGGACAGGCAG	0.659													3	6	---	---	---	---	
HPSE	10855	broad.mit.edu	37	4	84234175	84234175	+	Intron	DEL	A	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84234175delA	uc003hoj.3	-						HPSE_uc010ika.2_Intron|HPSE_uc011ccq.1_Intron|HPSE_uc011ccr.1_Intron|HPSE_uc011ccs.1_Intron|HPSE_uc011cct.1_Intron|HPSE_uc003hok.3_Intron	NM_001098540	NP_001092010	Q9Y251	HPSE_HUMAN	heparanase precursor						carbohydrate metabolic process|cell adhesion|proteoglycan metabolic process	extracellular region|lysosomal membrane|nucleus	beta-glucuronidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Heparin(DB01109)	actctgtctcaaaaaaaaaaa	0.139													4	4	---	---	---	---	
IRX4	50805	broad.mit.edu	37	5	1879669	1879671	+	In_Frame_Del	DEL	CCT	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1879669_1879671delCCT	uc003jcz.2	-	4	802_804	c.683_685delAGG	c.(682-687)GAGGGG>GGG	p.E228del	IRX4_uc011cmf.1_In_Frame_Del_p.E89del	NM_016358	NP_057442	P78413	IRX4_HUMAN	iroquois homeobox 4	228	Poly-Glu.				heart development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				GBM - Glioblastoma multiforme(108;0.242)		tcctcgcccccctcctcctcctc	0.507													141	7	---	---	---	---	
CDH18	1016	broad.mit.edu	37	5	19747499	19747499	+	Intron	DEL	T	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19747499delT	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TTTTCTGCAGTTTTTTTTTTT	0.289													4	3	---	---	---	---	
C6orf134	79969	broad.mit.edu	37	6	30608890	30608893	+	Intron	DEL	ACAT	-	-	rs3130038		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30608890_30608893delACAT	uc003nqu.2	+						C6orf134_uc003nqr.3_Intron|C6orf134_uc003rdc.2_Intron|C6orf134_uc003nqs.3_Intron|C6orf134_uc003rdd.2_Intron|C6orf134_uc003nqt.2_Intron|C6orf134_uc011dmm.1_Intron|C6orf134_uc003nqv.2_Intron	NM_024909	NP_079185	Q5SQI0	ATAT_HUMAN	hypothetical protein LOC79969 isoform 2								tubulin N-acetyltransferase activity				0						Ccatatacacacatacacacacac	0.363													5	3	---	---	---	---	
AMPH	273	broad.mit.edu	37	7	38543103	38543103	+	Intron	DEL	T	-	-	rs10225047		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38543103delT	uc003tgu.2	-						AMPH_uc003tgv.2_Intron	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5						GGCGGGGGGGTGGGTGGTGGA	0.423													3	4	---	---	---	---	
C7orf10	79783	broad.mit.edu	37	7	40192302	40192303	+	Intron	INS	-	T	T			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40192302_40192303insT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13								transferase activity			ovary(2)	2						AAATTAAGGTGttttttttttt	0.158													4	2	---	---	---	---	
GLI3	2737	broad.mit.edu	37	7	42069787	42069789	+	Intron	DEL	CCT	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42069787_42069789delCCT	uc011kbh.1	-						GLI3_uc011kbg.1_Intron	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3						negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19						atcactcaggcctcctcctcctc	0.000									Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67206114	67206117	+	IGR	DEL	TTCT	-	-	rs56895053		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67206114_67206117delTTCT								STAG3L4 (419602 upstream) : None (None downstream)																							ccttccttccttctttccttcctt	0.113													7	4	---	---	---	---	
PEX1	5189	broad.mit.edu	37	7	92146721	92146721	+	Frame_Shift_Del	DEL	T	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92146721delT	uc003uly.2	-	5	1204	c.1108delA	c.(1108-1110)ATTfs	p.I370fs	PEX1_uc011khr.1_Frame_Shift_Del_p.I162fs|PEX1_uc010ley.2_Frame_Shift_Del_p.I370fs|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_RNA	NM_000466	NP_000457	O43933	PEX1_HUMAN	peroxin1	370					microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TCTGACCTAATTTTTTTTTGA	0.353													418	7	---	---	---	---	
BET1	10282	broad.mit.edu	37	7	93633654	93633655	+	5'UTR	INS	-	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93633654_93633655insC	uc003unf.1	-	1					BET1_uc003une.3_RNA	NM_005868	NP_005859	O15155	BET1_HUMAN	blocked early in transport 1						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	protein binding				0	all_cancers(62;2.22e-10)|all_epithelial(64;1.38e-09)|Lung NSC(181;0.218)	Breast(660;0.000162)|Ovarian(593;0.000626)	STAD - Stomach adenocarcinoma(171;0.000967)			CCCCTAAAGCGCCACGACATCA	0.594													52	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98409190	98409190	+	IGR	DEL	T	-	-	rs112577704		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98409190delT								NPTX2 (150009 upstream) : TMEM130 (34922 downstream)																							gtggtgatggttggtggtggt	0.085													4	6	---	---	---	---	
GNB2	2783	broad.mit.edu	37	7	100274859	100274863	+	Intron	DEL	CACTG	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100274859_100274863delCACTG	uc003uwb.2	+						GNB2_uc003uwc.2_Intron|GNB2_uc010lhd.2_Intron|GNB2_uc010lhe.2_Intron|GNB2_uc003uwd.2_Intron|GNB2_uc010lhf.2_Intron|GNB2_uc003uwe.2_Intron|GNB2_uc003uwf.2_5'UTR	NM_005273	NP_005264	P62879	GBB2_HUMAN	guanine nucleotide-binding protein, beta-2						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|synaptic transmission	perinuclear region of cytoplasm|plasma membrane	GTPase activity|GTPase binding|signal transducer activity			ovary(2)	2	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)	Ovarian(593;0.238)				gtgatggtgccactgcactccagcc	0.185													12	24	---	---	---	---	
CSMD1	64478	broad.mit.edu	37	8	3216949	3216949	+	Intron	DEL	A	-	-	rs34858861		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3216949delA	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc003wqe.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TGCTATTACTAAAAAAAAAAA	0.308													5	4	---	---	---	---	
ASAH1	427	broad.mit.edu	37	8	17924607	17924608	+	Intron	INS	-	A	A	rs111579639		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17924607_17924608insA	uc003wyl.2	-						ASAH1_uc010ltb.1_Intron|ASAH1_uc003wym.2_Intron|ASAH1_uc003wyn.2_Intron|ASAH1_uc003wyo.2_Intron	NM_177924	NP_808592	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase 1 isoform a						ceramide metabolic process	lysosome	ceramidase activity				0				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		atctaagacctgtgcacctgtg	0.119													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	80796048	80796049	+	IGR	INS	-	TG	TG			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80796048_80796049insTG								HEY1 (115950 upstream) : MRPS28 (35047 downstream)																							ttctgtctttctctctctctct	0.000													4	2	---	---	---	---	
TAF5	6877	broad.mit.edu	37	10	105133276	105133277	+	Frame_Shift_Ins	INS	-	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105133276_105133277insA	uc001kwv.2	+	2	744_745	c.721_722insA	c.(721-723)TATfs	p.Y241fs	TAF5_uc010qqq.1_Frame_Shift_Ins_p.Y241fs	NM_006951	NP_008882	Q15542	TAF5_HUMAN	TBP-associated factor 5	241					histone acetylation|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	actin cytoskeleton|transcription factor TFIID complex|transcription factor TFTC complex	protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)	2		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		CCAACTTTTTTATCCTCTGTTT	0.371													165	105	---	---	---	---	
VAX1	11023	broad.mit.edu	37	10	118897631	118897632	+	5'UTR	DEL	GC	-	-	rs71677026		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118897631_118897632delGC	uc009xyx.2	-	1					VAX1_uc001ldb.1_5'UTR	NM_001112704	NP_001106175	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1 isoform a							nucleus	sequence-specific DNA binding			ovary(2)	2				all cancers(201;0.0108)		AGGGGGGGGGGCGGAGAAGGAA	0.441													10	5	---	---	---	---	
KDM2A	22992	broad.mit.edu	37	11	66983146	66983146	+	Intron	DEL	A	-	-	rs113780245	by1000genomes	TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66983146delA	uc001ojw.2	+						KDM2A_uc001ojx.2_Intron|KDM2A_uc001ojy.2_Intron	NM_012308	NP_036440	Q9Y2K7	KDM2A_HUMAN	F-box and leucine-rich repeat protein 11						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			ovary(4)|lung(3)|breast(1)|skin(1)	9						AATACGGTAGAAAAAAAAAAA	0.328													4	2	---	---	---	---	
RPS3	6188	broad.mit.edu	37	11	75113378	75113379	+	Intron	INS	-	CCTTGCTT	CCTTGCTT			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75113378_75113379insCCTTGCTT	uc001owh.2	+						RPS3_uc001owg.2_Intron|RPS3_uc001owi.2_Intron|RPS3_uc001owk.1_Intron|SNORD15B_uc001owl.1_5'Flank	NM_001005	NP_000996	P23396	RS3_HUMAN	ribosomal protein S3						activation of caspase activity|endocrine pancreas development|induction of apoptosis|negative regulation of DNA repair|negative regulation of NF-kappaB transcription factor activity|response to DNA damage stimulus|translational elongation|translational initiation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleus|ruffle membrane	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|endonuclease activity|iron-sulfur cluster binding|mRNA binding|NF-kappaB binding|protein kinase binding|structural constituent of ribosome				0						AACAGGATATCCCTTGCTTCCT	0.391													94	56	---	---	---	---	
ANKRD42	338699	broad.mit.edu	37	11	82923946	82923946	+	Intron	DEL	T	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82923946delT	uc001ozz.1	+						ANKRD42_uc009yvi.1_3'UTR|ANKRD42_uc010rsv.1_Intron|ANKRD42_uc001paa.2_Intron|ANKRD42_uc001pab.1_Intron	NM_182603	NP_872409	Q8N9B4	ANR42_HUMAN	ankyrin repeat domain 42											skin(1)	1						ATTTTGTAAGttttttttttt	0.224													4	2	---	---	---	---	
MLL2	8085	broad.mit.edu	37	12	49425220	49425220	+	Frame_Shift_Del	DEL	G	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49425220delG	uc001rta.3	-	39	13268	c.13268delC	c.(13267-13269)CCAfs	p.P4423fs		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	4423					chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						CAGGGCACATGGCTCTTCCCG	0.622			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			57	30	---	---	---	---	
MLL2	8085	broad.mit.edu	37	12	49434781	49434785	+	Frame_Shift_Del	DEL	GCACA	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49434781_49434785delGCACA	uc001rta.3	-	31	6768_6772	c.6768_6772delTGTGC	c.(6766-6774)GCTGTGCCTfs	p.A2256fs		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	2256_2258	Pro-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						GGGCTCTCAGGCACAGCCAAGTTAT	0.634			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			95	46	---	---	---	---	
MYO1H	283446	broad.mit.edu	37	12	109826796	109826798	+	Intron	DEL	CTT	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109826796_109826798delCTT	uc010sxn.1	+							NM_001101421	NP_001094891	Q8N1T3	MYO1H_HUMAN	myosin 1H							myosin complex	motor activity				0						CACTTCGATCCTTTGTGCTaaga	0.227													39	36	---	---	---	---	
KDM2B	84678	broad.mit.edu	37	12	122018158	122018158	+	Intron	DEL	G	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122018158delG	uc001uat.2	-						KDM2B_uc001uas.2_5'UTR|KDM2B_uc001uau.2_Intron|KDM2B_uc001uav.3_Intron	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2						CAGCAGTTGTGGGGGGGGGGA	0.552													6	3	---	---	---	---	
HECTD1	25831	broad.mit.edu	37	14	31647112	31647112	+	Intron	DEL	T	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31647112delT	uc001wrc.1	-							NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		tttttagaaattttttttttt	0.318													4	2	---	---	---	---	
AK7	122481	broad.mit.edu	37	14	96953557	96953557	+	Intron	DEL	A	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96953557delA	uc001yfn.2	+							NM_152327	NP_689540	Q96M32	KAD7_HUMAN	adenylate kinase 7						cell projection organization	cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity			ovary(1)	1		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		ctaaaaatacaaaaaaaaaaa	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	98311208	98311211	+	IGR	DEL	GAAG	-	-	rs111619571	by1000genomes	TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98311208_98311211delGAAG								VRK1 (963258 upstream) : C14orf64 (80736 downstream)																							aggaaggaaagaaggaaggaagga	0.123													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	23265335	23265336	+	IGR	INS	-	G	G			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23265335_23265336insG								GOLGA9P (2592 upstream) : HERC2P2 (16929 downstream)																							AGGCAGGAAGAGGGGGCTCCCA	0.639													10	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	27848010	27848011	+	IGR	DEL	TG	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27848010_27848011delTG								GABRG3 (69876 upstream) : OCA2 (152014 downstream)																							TCCCTCTTTCtgtgtgtgtgtg	0.337													4	4	---	---	---	---	
EIF3J	8669	broad.mit.edu	37	15	44852434	44852434	+	Intron	DEL	T	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44852434delT	uc001ztv.2	+						EIF3J_uc010ueg.1_Intron|EIF3J_uc001ztw.2_Intron	NM_003758	NP_003749	O75822	EIF3J_HUMAN	eukaryotic translation initiation factor 3,							cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity				0		all_cancers(109;2.81e-14)|all_epithelial(112;2.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;3.13e-20)|GBM - Glioblastoma multiforme(94;9.81e-07)|COAD - Colon adenocarcinoma(120;0.0754)|Colorectal(105;0.0758)		TGGTATGCCCTTTTTTTTTTA	0.294													26	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	60200406	60200406	+	IGR	DEL	G	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60200406delG								MED13 (57763 upstream) : TBC1D3P2 (141663 downstream)																							aagaaagaaaggaaggaagga	0.000													4	2	---	---	---	---	
ABCA9	10350	broad.mit.edu	37	17	66985397	66985398	+	Intron	INS	-	CTCTCA	CTCTCA	rs138281321	by1000genomes	TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66985397_66985398insCTCTCA	uc002jhu.2	-						ABCA9_uc010dez.2_Intron	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9						transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)					tctctctctctcacacacacac	0.015													4	4	---	---	---	---	
TXNL1	9352	broad.mit.edu	37	18	54283363	54283363	+	Intron	DEL	A	-	-	rs35834292		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54283363delA	uc002lgg.2	-						TXNL1_uc010xdz.1_Intron|TXNL1_uc002lgh.2_Intron|TXNL1_uc002lgi.2_Intron|TXNL1_uc002lgj.1_Intron	NM_004786	NP_004777	O43396	TXNL1_HUMAN	thioredoxin-like 1						cell redox homeostasis|electron transport chain|glycerol ether metabolic process|transport	cytoplasm	electron carrier activity|protein disulfide oxidoreductase activity				0				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)		actctgtctcaaaaaaaaaaa	0.100													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	3131446	3131446	+	IGR	DEL	C	-	-	rs66993077		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3131446delC								GNA11 (9994 upstream) : GNA15 (4745 downstream)																							aaaaaaaaaacaaaaaaaaaa	0.348													5	4	---	---	---	---	
DENND1C	79958	broad.mit.edu	37	19	6477590	6477590	+	Intron	DEL	T	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6477590delT	uc002mfe.2	-						DENND1C_uc002mfb.2_5'Flank|DENND1C_uc002mfc.2_5'Flank|DENND1C_uc002mfd.2_Intron|DENND1C_uc010xje.1_Intron	NM_024898	NP_079174	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity			large_intestine(1)	1						GTCCTGGGAGTTTtttttttt	0.308													4	2	---	---	---	---	
ARHGEF18	23370	broad.mit.edu	37	19	7515569	7515569	+	Intron	DEL	G	-	-	rs12974506		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7515569delG	uc002mgi.2	+						ARHGEF18_uc010xjm.1_Intron|ARHGEF18_uc002mgh.2_Intron|ARHGEF18_uc002mgj.1_Intron	NM_001130955	NP_001124427	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)				ATGTTAATGCGGGATCTTGCT	0.433													4	2	---	---	---	---	
FBN3	84467	broad.mit.edu	37	19	8191887	8191900	+	Intron	DEL	TGAGCTGTGTGTGT	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8191887_8191900delTGAGCTGTGTGTGT	uc002mjf.2	-							NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11						ATGTGTGTGCTGAGCTGTGTGTGTACATGCTGTA	0.383													2	5	---	---	---	---	
NFIX	4784	broad.mit.edu	37	19	13105127	13105128	+	5'Flank	DEL	GT	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13105127_13105128delGT	uc002mwd.2	+							NM_002501	NP_002492	Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			GGGCAACCCAgtgtgtgtgtgt	0.431													2	4	---	---	---	---	
ANKRD27	84079	broad.mit.edu	37	19	33132673	33132673	+	Intron	DEL	C	-	-	rs149712420		TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33132673delC	uc002ntn.1	-						ANKRD27_uc002nto.1_Intron	NM_032139	NP_115515	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)						early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)	5	Esophageal squamous(110;0.137)					TTTACTTCTtctttttttttt	0.169													4	2	---	---	---	---	
KCNQ2	3785	broad.mit.edu	37	20	62074087	62074089	+	Intron	DEL	CCT	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62074087_62074089delCCT	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_Intron	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	atcatcaccacctccaccatcac	0.000													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	62604561	62604562	+	IGR	DEL	GT	-	-			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62604561_62604562delGT								ZNF512B (3343 upstream) : SAMD10 (904 downstream)																							tgtgtgtgtggtgtgtgtgtgt	0.208													3	3	---	---	---	---	
BAGE2	85319	broad.mit.edu	37	21	11085863	11085864	+	Intron	INS	-	C	C			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11085863_11085864insC	uc002yit.1	-						BAGE_uc002yix.2_Intron	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		catcaccaccaccaccatcacc	0.000													6	6	---	---	---	---	
C2CD2	25966	broad.mit.edu	37	21	43329661	43329662	+	Intron	INS	-	A	A			TCGA-C4-A0F7-01	TCGA-C4-A0F7-01									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43329661_43329662insA	uc002yzw.2	-						C2CD2_uc002yzt.2_5'Flank|C2CD2_uc002yzu.2_Intron|C2CD2_uc002yzv.2_Intron|C2CD2_uc002yzx.1_Intron	NM_015500	NP_056315	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2 isoform							cytosol|extracellular region|nucleus				ovary(1)	1						TTATGAGTCCTAAAAAATGCAA	0.292													86	15	---	---	---	---	
