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
MRPS15	64960	broad.mit.edu	37	1	36926350	36926350	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36926350G>A	uc001cas.2	-	5	492	c.328C>T	c.(328-330)CAG>TAG	p.Q110*		NM_031280	NP_112570	P82914	RT15_HUMAN	mitochondrial ribosomal protein S15 precursor	110					translation	mitochondrial small ribosomal subunit|nuclear membrane	structural constituent of ribosome			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TTCATAAACTGTTCTTGCTTG	0.522													24	61	---	---	---	---	PASS
C1orf123	54987	broad.mit.edu	37	1	53686011	53686011	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53686011G>C	uc001cvd.2	-	2	54	c.12C>G	c.(10-12)ATC>ATG	p.I4M	C1orf123_uc001cvc.2_5'Flank|C1orf123_uc001cve.2_Missense_Mutation_p.I4M	NM_017887	NP_060357	Q9NWV4	CA123_HUMAN	hypothetical protein LOC54987	4										pancreas(2)	2						GTTGCAGCGCGATTTTCTGAG	0.607													11	26	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62330119	62330119	+	Silent	SNP	A	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62330119A>G	uc001dab.2	+	20	2763	c.2649A>G	c.(2647-2649)TCA>TCG	p.S883S	INADL_uc009waf.1_Silent_p.S883S|INADL_uc001daa.2_Silent_p.S883S|INADL_uc001dad.3_Silent_p.S580S|INADL_uc001dac.2_RNA	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	883					intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						AAGATCCCTCACCATCCATGG	0.428													26	65	---	---	---	---	PASS
LRRC40	55631	broad.mit.edu	37	1	70671195	70671195	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70671195T>C	uc001der.1	-	1	81	c.29A>G	c.(28-30)CAG>CGG	p.Q10R	SFRS11_uc009wbi.2_5'Flank|SFRS11_uc009wbj.1_5'Flank|SFRS11_uc010oqo.1_5'Flank|SFRS11_uc001des.2_5'Flank|SFRS11_uc001det.2_5'Flank	NM_017768	NP_060238	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	10										ovary(1)	1						GCGGAGATCCTGCCCCGCTAT	0.612													9	23	---	---	---	---	PASS
SYDE2	84144	broad.mit.edu	37	1	85648206	85648206	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85648206G>C	uc009wcm.2	-	3	2168	c.2119C>G	c.(2119-2121)CAG>GAG	p.Q707E	SYDE2_uc001dku.3_Missense_Mutation_p.Q707E	NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	707	C2.				activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)		GAATCTACCTGAATTGCACAA	0.383													3	76	---	---	---	---	PASS
RHOC	389	broad.mit.edu	37	1	113244079	113244079	+	3'UTR	SNP	G	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113244079G>T	uc001ecp.1	-	6					RHOC_uc001ecq.1_3'UTR|RHOC_uc001ecr.1_3'UTR|RHOC_uc009wgk.1_3'UTR	NM_001042679	NP_001036144	P08134	RHOC_HUMAN	ras homolog gene family, member C precursor						axon guidance|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity|signal transducer activity			ovary(1)	1	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCAGCATGGAGCCCTCAGGAG	0.602													10	12	---	---	---	---	PASS
THEM5	284486	broad.mit.edu	37	1	151820729	151820729	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151820729C>G	uc009wnd.2	-	4	636	c.504G>C	c.(502-504)GAG>GAC	p.E168D		NM_182578	NP_872384	Q8N1Q8	THEM5_HUMAN	thioesterase superfamily member 5	168							hydrolase activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			TAGAAAAGGTCTCGTCCATCA	0.592													17	45	---	---	---	---	PASS
HRNR	388697	broad.mit.edu	37	1	152191194	152191194	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152191194C>T	uc001ezt.1	-	3	2987	c.2911G>A	c.(2911-2913)GAA>AAA	p.E971K		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	971	11.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCATGTTGTTCGCTCCTAGAT	0.562													5	295	---	---	---	---	PASS
GPATCH4	54865	broad.mit.edu	37	1	156568885	156568885	+	Intron	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156568885G>C	uc001fpm.2	-						GPATCH4_uc001fpl.2_5'UTR	NM_015590	NP_056405	Q5T3I0	GPTC4_HUMAN	G patch domain containing 4 isoform 1							intracellular	nucleic acid binding			ovary(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GAGAAGAAGAGGTGATATCAT	0.413													6	21	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176738772	176738772	+	Silent	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176738772G>C	uc001gkz.2	+	16	5517	c.4353G>C	c.(4351-4353)GGG>GGC	p.G1451G	PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	1451	Sushi 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						GTTCTTCTGGGCACTGGGACC	0.473													41	93	---	---	---	---	PASS
ZNF281	23528	broad.mit.edu	37	1	200377519	200377519	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200377519C>T	uc001gve.2	-	2	1422	c.1315G>A	c.(1315-1317)GTA>ATA	p.V439I	ZNF281_uc001gvf.1_Missense_Mutation_p.V439I|ZNF281_uc001gvg.1_Missense_Mutation_p.V403I	NM_012482	NP_036614	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	439					negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|breast(1)	2						GGCATTTCTACTGAGTAACTC	0.373													8	119	---	---	---	---	PASS
ZFP36L2	678	broad.mit.edu	37	2	43452470	43452470	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43452470A>G	uc002rsv.3	-	2	764	c.473T>C	c.(472-474)CTG>CCG	p.L158P	LOC100129726_uc010ynx.1_5'Flank	NM_006887	NP_008818	P47974	TISD_HUMAN	zinc finger protein 36, C3H type-like 2	158	C3H1-type 1.|RNA-binding.				cell proliferation	nucleus	DNA binding|RNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				GGGCCGGCACAGCTCGGTCTT	0.657													6	34	---	---	---	---	PASS
CCDC88A	55704	broad.mit.edu	37	2	55562094	55562094	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55562094T>G	uc002ryv.2	-	15	2705	c.1863A>C	c.(1861-1863)AAA>AAC	p.K621N	CCDC88A_uc010yoz.1_Missense_Mutation_p.K621N|CCDC88A_uc010ypa.1_Missense_Mutation_p.K621N|CCDC88A_uc010ypb.1_Missense_Mutation_p.K523N|CCDC88A_uc002ryu.2_5'UTR|CCDC88A_uc002ryw.2_5'UTR	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1	621	Potential.				activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4						CTCCTTTTTCTTTATAATGTT	0.239													15	41	---	---	---	---	PASS
ATP6V1B1	525	broad.mit.edu	37	2	71190718	71190718	+	Silent	SNP	C	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71190718C>A	uc002shj.2	+	11	1164	c.1077C>A	c.(1075-1077)ATC>ATA	p.I359I	ATP6V1B1_uc010fdv.2_Silent_p.I342I|ATP6V1B1_uc010fdw.2_RNA|ATP6V1B1_uc010fdx.2_Silent_p.I317I	NM_001692	NP_001683	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1	359					ATP hydrolysis coupled proton transport|calcium ion homeostasis|cellular iron ion homeostasis|excretion|inner ear morphogenesis|insulin receptor signaling pathway|ossification|pH reduction|sensory perception of sound|transferrin transport	apical plasma membrane|basolateral plasma membrane|cytosol|endomembrane system|lateral plasma membrane|microvillus|proton-transporting V-type ATPase, V1 domain|vacuolar proton-transporting V-type ATPase complex	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			skin(1)	1						CCCACCCTATCCCAGACTTGA	0.562													25	83	---	---	---	---	PASS
ZNF638	27332	broad.mit.edu	37	2	71658543	71658543	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71658543T>C	uc002shx.2	+	26	6056	c.5737T>C	c.(5737-5739)TCT>CCT	p.S1913P	ZNF638_uc002shy.2_Missense_Mutation_p.S1913P|ZNF638_uc002shz.2_Missense_Mutation_p.S1913P|ZNF638_uc002sia.2_Missense_Mutation_p.S1913P|ZNF638_uc010fed.2_RNA|ZNF638_uc002sic.2_Missense_Mutation_p.S1010P|ZNF638_uc002sid.2_Missense_Mutation_p.S282P	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638	1913					RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4						ATCAGTGGCGTCTGATGTCCC	0.303													22	70	---	---	---	---	PASS
TMEM131	23505	broad.mit.edu	37	2	98375417	98375417	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98375417G>T	uc002syh.3	-	40	5535	c.5306C>A	c.(5305-5307)CCA>CAA	p.P1769Q	TMEM131_uc002syg.2_Missense_Mutation_p.P149Q	NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein	1769	Ser-rich.					integral to membrane				ovary(4)|central_nervous_system(2)	6						ATCTGTCGCTGGCGACTCCCA	0.587													14	30	---	---	---	---	PASS
DCAF17	80067	broad.mit.edu	37	2	172337514	172337514	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172337514G>T	uc002ugx.2	+	14	1682	c.1453G>T	c.(1453-1455)GAC>TAC	p.D485Y	DCAF17_uc010zdq.1_RNA|DCAF17_uc010zdr.1_RNA|DCAF17_uc010fqg.2_Missense_Mutation_p.D205Y	NM_025000	NP_079276	Q5H9S7	DCA17_HUMAN	DDB1 and CUL4 associated factor 17 isoform 1	485						CUL4 RING ubiquitin ligase complex|integral to membrane|nucleolus					0						CTTTGACAGAGACTTGGTGCT	0.398													5	203	---	---	---	---	PASS
ZDBF2	57683	broad.mit.edu	37	2	207174466	207174466	+	Missense_Mutation	SNP	A	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207174466A>T	uc002vbp.2	+	5	5464	c.5214A>T	c.(5212-5214)GAA>GAT	p.E1738D		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1738							nucleic acid binding|zinc ion binding			ovary(3)	3						GAGATCTAGAAGTGAGCTGTG	0.443													22	59	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10191536	10191536	+	Nonsense_Mutation	SNP	A	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191536A>T	uc003bvc.2	+	3	742	c.529A>T	c.(529-531)AGA>TGA	p.R177*	VHL_uc003bvd.2_Nonsense_Mutation_p.R136*	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	177			R -> RLRVKPE (in VHLD; type I).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.R177*(3)|p.R177fs*25(2)|p.R177fs*37(1)|p.Y175fs*1(1)|p.R176fs*24(1)|p.R176fs*36(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GAATTACAGGAGACTGGACAT	0.527		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				21	15	---	---	---	---	PASS
TRIM71	131405	broad.mit.edu	37	3	32932071	32932071	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32932071G>C	uc003cff.2	+	4	1438	c.1375G>C	c.(1375-1377)GTC>CTC	p.V459L		NM_001039111	NP_001034200	Q2Q1W2	LIN41_HUMAN	tripartite motif-containing 71	459					multicellular organismal development	cytoplasm	zinc ion binding			ovary(2)|large_intestine(1)	3						AGACGACCGAGTCATGTTCAC	0.612													26	24	---	---	---	---	PASS
UBP1	7342	broad.mit.edu	37	3	33481335	33481335	+	Silent	SNP	G	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33481335G>T	uc003cfq.3	-	1	536	c.6C>A	c.(4-6)GCC>GCA	p.A2A	UBP1_uc003cfr.3_Silent_p.A2A|UBP1_uc010hga.2_Silent_p.A2A	NM_014517	NP_055332	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a) isoform a	2					negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			kidney(2)	2						TGAGCACCCAGGCCATCTTCC	0.726													16	14	---	---	---	---	PASS
LRIG1	26018	broad.mit.edu	37	3	66431991	66431991	+	Silent	SNP	C	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66431991C>T	uc003dmx.2	-	17	2696	c.2682G>A	c.(2680-2682)CAG>CAA	p.Q894Q	SLC25A26_uc011bft.1_Intron|LRIG1_uc011bfu.1_Silent_p.Q514Q|LRIG1_uc003dmw.2_Silent_p.Q560Q|LRIG1_uc010hnz.2_Silent_p.Q610Q|LRIG1_uc010hoa.2_Silent_p.Q871Q	NM_015541	NP_056356	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like	894	Cytoplasmic (Potential).					integral to membrane				skin(3)|ovary(2)	5		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		AGAGCTTTGGCTGCCTGCAGG	0.537													3	85	---	---	---	---	PASS
PIK3CA	5290	broad.mit.edu	37	3	178921334	178921334	+	Nonsense_Mutation	SNP	T	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178921334T>A	uc003fjk.2	+	5	973	c.816T>A	c.(814-816)TAT>TAA	p.Y272*		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	272	PI3K-RBD.				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			TCTTACAGTATATAAGAAGCT	0.368		57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			23	34	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62812747	62812747	+	Silent	SNP	C	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62812747C>T	uc010ihh.2	+	13	2504	c.2331C>T	c.(2329-2331)GTC>GTT	p.V777V	LPHN3_uc003hcq.3_Silent_p.V777V|LPHN3_uc003hct.2_Silent_p.V170V	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	764	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						CTGTTATTGTCAATTCCCCTG	0.383													82	168	---	---	---	---	PASS
ETFDH	2110	broad.mit.edu	37	4	159627355	159627355	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159627355G>C	uc003iqb.2	+	11	1632	c.1300G>C	c.(1300-1302)GAA>CAA	p.E434Q	ETFDH_uc011cjg.1_Missense_Mutation_p.E387Q|ETFDH_uc010iqr.2_Missense_Mutation_p.E31Q|ETFDH_uc011cjh.1_Missense_Mutation_p.E373Q|ETFDH_uc010iqs.2_Missense_Mutation_p.E356Q	NM_004453	NP_004444	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	434					fatty acid beta-oxidation using acyl-CoA dehydrogenase|respiratory electron transport chain|response to oxidative stress|transport	integral to mitochondrial inner membrane|mitochondrial matrix	4 iron, 4 sulfur cluster binding|electron carrier activity|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding|metal ion binding|oxidoreductase activity, oxidizing metal ions with flavin as acceptor|ubiquinone binding			large_intestine(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)		CCATGTAACTGAATATGAGGA	0.373													32	64	---	---	---	---	PASS
ASB5	140458	broad.mit.edu	37	4	177190090	177190090	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177190090T>C	uc003iuq.1	-	1	186	c.170A>G	c.(169-171)GAA>GGA	p.E57G		NM_080874	NP_543150	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box-containing protein	57					intracellular signal transduction					skin(2)	2		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		TCCATAAAATTCAGCTGCTAT	0.388													3	98	---	---	---	---	PASS
CTNND2	1501	broad.mit.edu	37	5	10988319	10988319	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10988319G>T	uc003jfa.1	-	20	3392	c.3247C>A	c.(3247-3249)CTC>ATC	p.L1083I	CTNND2_uc010itt.2_Missense_Mutation_p.L992I|CTNND2_uc011cmy.1_Missense_Mutation_p.L746I|CTNND2_uc011cmz.1_Missense_Mutation_p.L650I|CTNND2_uc010itu.1_RNA|CTNND2_uc011cmx.1_Missense_Mutation_p.L675I	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	1083					multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8						CTTTCTTTGAGGCTGATCATT	0.512											OREG0016517	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	26	90	---	---	---	---	PASS
CCDC125	202243	broad.mit.edu	37	5	68581285	68581285	+	Nonsense_Mutation	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68581285G>C	uc003jvv.1	-	10	1152	c.1109C>G	c.(1108-1110)TCA>TGA	p.S370*	CCDC125_uc003jvx.1_Missense_Mutation_p.H311D|CCDC125_uc003jvy.1_RNA|CCDC125_uc003jvw.2_Nonsense_Mutation_p.S245*	NM_176816	NP_789786	Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	370						cytoplasm					0		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)		ACTCCTTGGTGATGGAAATCC	0.433													44	129	---	---	---	---	PASS
GPR98	84059	broad.mit.edu	37	5	90086882	90086882	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90086882G>C	uc003kju.2	+	70	14332	c.14236G>C	c.(14236-14238)GAG>CAG	p.E4746Q	GPR98_uc003kjt.2_Missense_Mutation_p.E2452Q|GPR98_uc003kjw.2_Missense_Mutation_p.E407Q	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	4746	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ACTGGATCTGGAGAAGAGTAT	0.443													19	50	---	---	---	---	PASS
PHF15	23338	broad.mit.edu	37	5	133914214	133914214	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133914214G>C	uc003kzo.1	+	11	1759	c.1580G>C	c.(1579-1581)GGC>GCC	p.G527A	PHF15_uc011cxt.1_Missense_Mutation_p.G571A|PHF15_uc003kzk.2_Missense_Mutation_p.G587A|PHF15_uc003kzl.2_3'UTR|PHF15_uc003kzm.2_Missense_Mutation_p.G528A|PHF15_uc003kzn.2_3'UTR	NM_015288	NP_056103	Q9NQC1	JADE2_HUMAN	PHD finger protein 15	527					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCCATCGATGGCACCTTCTTC	0.602													95	105	---	---	---	---	PASS
CATSPER3	347732	broad.mit.edu	37	5	134344575	134344575	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134344575A>C	uc003lag.2	+	5	788	c.720A>C	c.(718-720)GAA>GAC	p.E240D		NM_178019	NP_821138	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	240	Extracellular (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	calcium channel activity|voltage-gated ion channel activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACAATCGGGAATTTGCTTTGA	0.537													57	55	---	---	---	---	PASS
LAMA4	3910	broad.mit.edu	37	6	112575349	112575349	+	Missense_Mutation	SNP	C	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112575349C>G	uc003pvu.2	-	2	313	c.4G>C	c.(4-6)GCT>CCT	p.A2P	LAMA4_uc003pvv.2_Missense_Mutation_p.A2P|LAMA4_uc003pvt.2_Missense_Mutation_p.A2P|LAMA4_uc003pvw.2_Missense_Mutation_p.A2P|LAMA4_uc010kdz.1_Missense_Mutation_p.A2P|LAMA4_uc010kea.1_Missense_Mutation_p.A2P	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	2					cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		GAGCTCAAAGCCATTTCTCCG	0.642													10	11	---	---	---	---	PASS
MAP3K4	4216	broad.mit.edu	37	6	161537951	161537951	+	3'UTR	SNP	G	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161537951G>T	uc003qtn.2	+	27					MAP3K4_uc003qto.2_3'UTR|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_3'UTR|MAP3K4_uc003qtp.2_3'UTR|MAP3K4_uc003qtq.2_3'UTR	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4						activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		ACTACTGTATGTAATATTTAC	0.418													44	58	---	---	---	---	PASS
ASZ1	136991	broad.mit.edu	37	7	117003505	117003505	+	3'UTR	SNP	A	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117003505A>T	uc003vjb.2	-	13					ASZ1_uc011kno.1_3'UTR|ASZ1_uc011knp.1_3'UTR	NM_130768	NP_570124	Q8WWH4	ASZ1_HUMAN	ankyrin repeat, SAM and basic leucine zipper						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(10;0.00156)|all_lung(10;0.00175)		STAD - Stomach adenocarcinoma(10;0.000512)			ACCACTTTTTAAAAAAAAACT	0.254													6	6	---	---	---	---	PASS
NDUFA5	4698	broad.mit.edu	37	7	123196626	123196626	+	Intron	SNP	A	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123196626A>G	uc003vks.2	-						NDUFA5_uc003vkr.2_Intron|NDUFA5_uc003vkt.1_3'UTR	NM_005000	NP_004991	Q16718	NDUA5_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0					NADH(DB00157)	aagcccagtaaagaaagcgca	0.000													2	5	---	---	---	---	PASS
TSGA14	95681	broad.mit.edu	37	7	130044447	130044447	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130044447T>C	uc003vpz.2	-	6	427	c.380A>G	c.(379-381)AAC>AGC	p.N127S	TSGA14_uc010lmf.2_Intron|TSGA14_uc003vqa.2_Missense_Mutation_p.N127S|TSGA14_uc011kpg.1_Missense_Mutation_p.N111S	NM_018718	NP_061188	Q9BYV8	CEP41_HUMAN	testis specific, 14	127					G2/M transition of mitotic cell cycle	centrosome|cytosol					0	Melanoma(18;0.0435)					TCCTGCGTTGTTTATGAACTG	0.493													51	84	---	---	---	---	PASS
C7orf49	78996	broad.mit.edu	37	7	134853498	134853498	+	Intron	SNP	T	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134853498T>C	uc003vsl.2	-						C7orf49_uc003vsh.2_Intron|C7orf49_uc003vsj.2_5'Flank|C7orf49_uc003vsk.2_Intron|C7orf49_uc003vsm.2_Intron|C7orf49_uc003vsn.2_Missense_Mutation_p.K45E|C7orf49_uc003vso.2_Intron	NM_024033	NP_076938	Q9BWK5	MRI_HUMAN	modulator of retrovirus infection							cytoplasm				large_intestine(1)|ovary(1)	2						CTGCTCCACTTGCCAGATTCG	0.572													3	151	---	---	---	---	PASS
CLN8	2055	broad.mit.edu	37	8	1728748	1728748	+	3'UTR	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1728748G>C	uc003wpo.3	+	3						NM_018941	NP_061764	Q9UBY8	CLN8_HUMAN	ceroid-lipofuscinosis, neuronal 8						cell death|ceramide biosynthetic process|cholesterol metabolic process|lipid transport|negative regulation of proteolysis|phospholipid metabolic process	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.67e-05)|READ - Rectum adenocarcinoma(644;0.0913)		TCCAGCCGGGGCTCCGGGGCG	0.572													6	23	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	8	12428040	12428040	+	Intron	SNP	C	A	A	rs4115597	by1000genomes	TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12428040C>A	uc003wvy.3	-						uc003wvz.1_RNA|uc003wwa.2_RNA					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		GATAAATTGGCAAACCTTTTC	0.398													5	18	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55533660	55533660	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55533660A>C	uc003xsd.1	+	2	282	c.134A>C	c.(133-135)GAC>GCC	p.D45A	RP1_uc011ldy.1_Missense_Mutation_p.D45A	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	45	Doublecortin 1.				axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AAGAGCGGAGACCCCCAATTC	0.537													32	79	---	---	---	---	PASS
ZFAT	57623	broad.mit.edu	37	8	135524782	135524782	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135524782T>G	uc003yup.2	-	14	3472	c.3297A>C	c.(3295-3297)GAA>GAC	p.E1099D	ZFAT_uc011ljj.1_Missense_Mutation_p.E218D|ZFAT_uc003yun.2_Missense_Mutation_p.E1087D|ZFAT_uc003yuo.2_Missense_Mutation_p.E1087D|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_RNA|ZFAT_uc003yuq.2_Missense_Mutation_p.E1087D|ZFAT_uc010mej.2_Missense_Mutation_p.E1037D	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1	1099					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			CTTGAACGTCTTCTTCGGCCT	0.527													52	122	---	---	---	---	PASS
ZBTB5	9925	broad.mit.edu	37	9	37441467	37441467	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37441467A>C	uc003zzx.2	-	2	1282	c.1082T>G	c.(1081-1083)GTT>GGT	p.V361G		NM_014872	NP_055687	O15062	ZBTB5_HUMAN	zinc finger and BTB domain containing 5	361					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(29;0.00733)|Lung(182;0.226)		ACTGACCACAACTCCTTCCAC	0.517													25	53	---	---	---	---	PASS
CELF2	10659	broad.mit.edu	37	10	11047307	11047307	+	5'UTR	SNP	C	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11047307C>A	uc001iki.3	+	1					CELF2_uc010qbi.1_5'UTR|CELF2_uc010qbj.1_5'UTR	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						GATGTTTGAGCATACTTCTGA	0.313													13	166	---	---	---	---	PASS
KIAA0913	23053	broad.mit.edu	37	10	75553698	75553698	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75553698T>G	uc009xrl.2	+	12	2553	c.2521T>G	c.(2521-2523)TTG>GTG	p.L841V	KIAA0913_uc001jve.2_Missense_Mutation_p.L841V|KIAA0913_uc001jvf.2_Missense_Mutation_p.L841V|KIAA0913_uc001jvh.2_RNA|KIAA0913_uc001jvi.2_Missense_Mutation_p.L264V|KIAA0913_uc010qkr.1_Missense_Mutation_p.L264V|KIAA0913_uc001jvj.2_Missense_Mutation_p.L264V	NM_015037	NP_055852	A7E2V4	K0913_HUMAN	hypothetical protein LOC23053	841							zinc ion binding			breast(1)	1	Prostate(51;0.0112)					GGCCTTCCTGTTGACAGTGCT	0.557													7	13	---	---	---	---	PASS
SMC3	9126	broad.mit.edu	37	10	112341762	112341762	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112341762T>C	uc001kze.2	+	9	755	c.629T>C	c.(628-630)CTA>CCA	p.L210P		NM_005445	NP_005436	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	210	Potential.				cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		AAGGAAGAACTAGCTCAGTAT	0.378													70	146	---	---	---	---	PASS
MICALCL	84953	broad.mit.edu	37	11	12315780	12315780	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12315780T>A	uc001mkg.1	+	3	1093	c.802T>A	c.(802-804)TCC>ACC	p.S268T		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	268					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding			skin(1)	1				Epithelial(150;0.00177)		TCCACCCAAGTCCCCACTGCG	0.617													16	18	---	---	---	---	PASS
MRGPRX4	117196	broad.mit.edu	37	11	18194921	18194921	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18194921G>T	uc001mnv.1	+	1	538	c.118G>T	c.(118-120)GTC>TTC	p.V40F		NM_054032	NP_473373	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	40	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1						CATTTCCCTTGTCGGACTGAC	0.552													55	112	---	---	---	---	PASS
OR4C11	219429	broad.mit.edu	37	11	55371310	55371310	+	Silent	SNP	C	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55371310C>T	uc010rii.1	-	1	540	c.540G>A	c.(538-540)CAG>CAA	p.Q180Q		NM_001004700	NP_001004700	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C,	180	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						TCAACAAGGGCTGCAAATCAC	0.413													3	105	---	---	---	---	PASS
CPT1A	1374	broad.mit.edu	37	11	68522400	68522400	+	3'UTR	SNP	C	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68522400C>T	uc001oog.3	-	19					CPT1A_uc001oof.3_Intron|CPT1A_uc009ysj.2_3'UTR	NM_001876	NP_001867	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A liver isoform						carnitine shuttle|fatty acid beta-oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			skin(2)	2	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		L-Carnitine(DB00583)|Perhexiline(DB01074)	TACATTCACACTGCATTTCTA	0.358													5	24	---	---	---	---	PASS
DHCR7	1717	broad.mit.edu	37	11	71153366	71153366	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71153366G>C	uc001oqk.2	-	5	605	c.355C>G	c.(355-357)CAT>GAT	p.H119D	DHCR7_uc001oql.2_Missense_Mutation_p.H119D	NM_001163817	NP_001157289	Q9UBM7	DHCR7_HUMAN	7-dehydrocholesterol reductase	119					cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|nuclear outer membrane	7-dehydrocholesterol reductase activity|protein binding			ovary(1)|liver(1)	2					NADH(DB00157)	AGAAACTTATGGCAGAAGTCA	0.612									Smith-Lemli-Opitz_syndrome				7	12	---	---	---	---	PASS
MLL	4297	broad.mit.edu	37	11	118374160	118374160	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118374160C>A	uc001pta.2	+	27	7567	c.7544C>A	c.(7543-7545)CCA>CAA	p.P2515Q	MLL_uc001ptb.2_Missense_Mutation_p.P2518Q	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	2515					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)		TTACAGGCACCACGGAAACGC	0.453			T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								3	47	---	---	---	---	PASS
CLECL1	160365	broad.mit.edu	37	12	9885824	9885824	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9885824C>A	uc001qwj.2	-	1	37	c.37G>T	c.(37-39)GAG>TAG	p.E13*		NM_172004	NP_742001	Q8IZS7	CLCL1_HUMAN	type II transmembrane protein DCAL1	13	Cytoplasmic (Potential).					integral to membrane|plasma membrane	sugar binding				0						GCAGATTTCTCGAATACTTGT	0.363													3	142	---	---	---	---	PASS
PPFIBP1	8496	broad.mit.edu	37	12	27835400	27835400	+	Silent	SNP	T	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27835400T>C	uc001ric.1	+	22	2522	c.2145T>C	c.(2143-2145)AAT>AAC	p.N715N	PPFIBP1_uc010sjr.1_Silent_p.N546N|PPFIBP1_uc001rib.1_Silent_p.N709N|PPFIBP1_uc001ria.2_Silent_p.N684N|PPFIBP1_uc001rid.1_Silent_p.N562N|PPFIBP1_uc001rif.1_Silent_p.N222N	NM_003622	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein binding protein 1	715					cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)					AAGAAACCAATCATGGGAAGC	0.353													43	117	---	---	---	---	PASS
NACA	4666	broad.mit.edu	37	12	57110097	57110097	+	Intron	SNP	G	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57110097G>A	uc001slz.2	-						NACA_uc001sly.2_Intron|NACA_uc009zoy.1_Silent_p.L1739L|NACA_uc001smc.2_Intron|NACA_uc001sma.2_Intron|NACA_uc001smb.2_Intron|NACA_uc010squ.1_Intron	NM_001113201	NP_001106672	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha						interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1						TCTGAACAGGGAGTAGAGGGG	0.517			T	BCL6	NHL								85	116	---	---	---	---	PASS
NEDD1	121441	broad.mit.edu	37	12	97303613	97303613	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97303613G>C	uc001teu.3	+	3	415	c.76G>C	c.(76-78)GAT>CAT	p.D26H	NEDD1_uc001tev.3_Missense_Mutation_p.D26H|NEDD1_uc010svc.1_Intron|NEDD1_uc001tew.2_Missense_Mutation_p.D33H|NEDD1_uc001tex.2_5'Flank	NM_152905	NP_690869	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally	26	WD 1.				cell division|G2/M transition of mitotic cell cycle|mitosis	cytosol					0						GACATTGGTGGATAAATTCAA	0.368													25	56	---	---	---	---	PASS
CAMKK2	10645	broad.mit.edu	37	12	121712085	121712085	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121712085G>C	uc001tzu.2	-	2	369	c.245C>G	c.(244-246)CCC>CGC	p.P82R	CAMKK2_uc001tzt.2_Missense_Mutation_p.P82R|CAMKK2_uc001tzv.2_Missense_Mutation_p.P82R|CAMKK2_uc001tzw.2_Missense_Mutation_p.P82R|CAMKK2_uc001tzx.2_Missense_Mutation_p.P82R|CAMKK2_uc001tzy.2_Missense_Mutation_p.P82R|CAMKK2_uc001uaa.1_Missense_Mutation_p.P82R|CAMKK2_uc001uab.2_Missense_Mutation_p.P82R|CAMKK2_uc001uac.2_Missense_Mutation_p.P82R|CAMKK2_uc001uad.1_Missense_Mutation_p.P82R	NM_006549	NP_006540	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase	82					calcium-mediated signaling|MAPKKK cascade|positive regulation of transcription, DNA-dependent|protein autophosphorylation|regulation of protein kinase activity	cytoplasm	ATP binding|calcium ion binding|calmodulin binding|calmodulin-dependent protein kinase activity|protein tyrosine kinase activity			lung(1)|large_intestine(1)|stomach(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GGTGTCAAGGGGGACCTCTTG	0.697													7	8	---	---	---	---	PASS
ZCCHC8	55596	broad.mit.edu	37	12	122962402	122962402	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122962402A>G	uc001ucn.2	-	13	1462	c.1331T>C	c.(1330-1332)ATG>ACG	p.M444T	ZCCHC8_uc001ucl.2_Missense_Mutation_p.M55T|ZCCHC8_uc001ucm.2_Missense_Mutation_p.M206T|ZCCHC8_uc009zxp.2_Missense_Mutation_p.M206T|ZCCHC8_uc009zxq.2_Missense_Mutation_p.M206T	NM_017612	NP_060082	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	444						catalytic step 2 spliceosome	nucleic acid binding|protein binding|zinc ion binding				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		ATCGAGCTCCATGTCGGCGGG	0.353													14	40	---	---	---	---	PASS
TMEM132B	114795	broad.mit.edu	37	12	126135244	126135244	+	Silent	SNP	C	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126135244C>T	uc001uhe.1	+	7	1652	c.1644C>T	c.(1642-1644)AGC>AGT	p.S548S	TMEM132B_uc001uhf.1_Silent_p.S60S	NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	548	Extracellular (Potential).					integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CCCGGGAAAGCGATGACGAGG	0.537													15	29	---	---	---	---	PASS
ELF1	1997	broad.mit.edu	37	13	41525466	41525466	+	Silent	SNP	T	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41525466T>A	uc001uxs.2	-	4	733	c.360A>T	c.(358-360)ATA>ATT	p.I120I	ELF1_uc010tfc.1_Silent_p.I120I|ELF1_uc010acd.2_Silent_p.I13I	NM_172373	NP_758961	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription	120					positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		ATCACTCACTTATTCGTTTTT	0.353													35	41	---	---	---	---	PASS
DCAF11	80344	broad.mit.edu	37	14	24588354	24588354	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24588354G>C	uc001wlv.2	+	9	1060	c.780G>C	c.(778-780)AGG>AGC	p.R260S	DCAF11_uc001wlw.2_Missense_Mutation_p.R260S|DCAF11_uc001wlz.2_Missense_Mutation_p.R160S|DCAF11_uc001wly.2_Missense_Mutation_p.R216S|DCAF11_uc001wme.2_Missense_Mutation_p.R220S|DCAF11_uc010tny.1_Missense_Mutation_p.R127S|DCAF11_uc001wmd.2_Missense_Mutation_p.R260S|DCAF11_uc001wmc.2_Missense_Mutation_p.R160S|DCAF11_uc001wmb.3_Missense_Mutation_p.R234S|DCAF11_uc001wma.3_Missense_Mutation_p.R260S	NM_001163484	NP_001156956	Q8TEB1	DCA11_HUMAN	DDB1 and CUL4 associated factor 11 isoform 1	260						CUL4 RING ubiquitin ligase complex	protein binding				0						TTGCTTTTAGGCCAGATGAGC	0.463													86	173	---	---	---	---	PASS
GABRA5	2558	broad.mit.edu	37	15	27128585	27128585	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27128585C>A	uc001zbd.1	+	7	717	c.378C>A	c.(376-378)AGC>AGA	p.S126R	GABRB3_uc001zbb.2_Intron	NM_000810	NP_000801	P31644	GBRA5_HUMAN	gamma-aminobutyric acid A receptor, alpha 5	126	Extracellular (Potential).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(1)	1		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	TCCTTGCCAGCAAGATCTGGA	0.552													29	71	---	---	---	---	PASS
APBA2	321	broad.mit.edu	37	15	29346371	29346371	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29346371A>G	uc001zck.2	+	3	491	c.284A>G	c.(283-285)GAG>GGG	p.E95G	APBA2_uc010azj.2_Missense_Mutation_p.E95G|APBA2_uc010uat.1_Missense_Mutation_p.E95G|APBA2_uc001zcl.2_Missense_Mutation_p.E95G|APBA2_uc010uas.1_Missense_Mutation_p.E95G	NM_005503	NP_005494	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,	95	Poly-Glu.				nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		GAGGAGGAGGAGGGCATCACC	0.607													3	122	---	---	---	---	PASS
WDR72	256764	broad.mit.edu	37	15	53957926	53957926	+	Missense_Mutation	SNP	A	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53957926A>T	uc002acj.2	-	14	1847	c.1805T>A	c.(1804-1806)ATT>AAT	p.I602N	WDR72_uc010bfi.1_Missense_Mutation_p.I602N	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	602										lung(1)|skin(1)	2				all cancers(107;0.0511)		ATTAAGAATAATTCGTGCTCT	0.388													26	53	---	---	---	---	PASS
CNOT1	23019	broad.mit.edu	37	16	58555184	58555184	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58555184G>A	uc002env.2	-	48	7248	c.6955C>T	c.(6955-6957)CCT>TCT	p.P2319S	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Missense_Mutation_p.P2314S|CNOT1_uc002ent.2_Missense_Mutation_p.P257S|CNOT1_uc010vik.1_Missense_Mutation_p.P1276S	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	2319					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		AGACCCCAAGGATGTGGCCTA	0.388													44	94	---	---	---	---	PASS
CMTM4	146223	broad.mit.edu	37	16	66670397	66670397	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66670397A>G	uc002epz.2	-	2	456	c.274T>C	c.(274-276)TGC>CGC	p.C92R	CMTM4_uc002eqa.2_Missense_Mutation_p.C92R	NM_178818	NP_848933	Q8IZR5	CKLF4_HUMAN	chemokine-like factor superfamily 4 isoform 1	92	MARVEL.|Helical; (Potential).				chemotaxis	extracellular space|integral to membrane	cytokine activity			pancreas(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)		AACGCACTGCAGCTCACAAAC	0.478													33	54	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	90161902	90161902	+	3'UTR	SNP	A	G	G	rs6500471	by1000genomes	TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90161902A>G	uc002fqp.2	+	3					uc002fqq.2_3'UTR					Homo sapiens, Similar to tubulin, beta, 2, clone IMAGE:4873024, mRNA.																		ATATGTTCCAAGACCCTAAAA	0.537													3	37	---	---	---	---	PASS
MAPK7	5598	broad.mit.edu	37	17	19284305	19284305	+	Silent	SNP	C	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19284305C>G	uc002gvn.2	+	4	1169	c.783C>G	c.(781-783)CTC>CTG	p.L261L	B9D1_uc010cqm.1_5'Flank|B9D1_uc002gvl.3_5'Flank|MAPK7_uc002gvo.2_Silent_p.L122L|MAPK7_uc002gvq.2_Silent_p.L261L|MAPK7_uc002gvp.2_Silent_p.L261L	NM_139033	NP_620602	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7 isoform 1	261	Necessary for oligomerization (By similarity).|Protein kinase.				cell cycle|cell differentiation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|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|nucleoplasm	ATP binding|MAP kinase activity|protein binding			central_nervous_system(4)|lung(3)|stomach(1)|skin(1)	9	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					GGCGCCAGCTCTTCCCAGGCA	0.572													30	31	---	---	---	---	PASS
KRT36	8689	broad.mit.edu	37	17	39643651	39643651	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39643651T>A	uc002hwt.2	-	5	939	c.939A>T	c.(937-939)AGA>AGT	p.R313S		NM_003771	NP_003762	O76013	KRT36_HUMAN	keratin 36	313	Rod.|Coil 2.					intermediate filament	protein binding|structural constituent of epidermis				0		Breast(137;0.000286)				TGACCGTACGTCTCAGCTCGA	0.637													14	18	---	---	---	---	PASS
CSH1	1442	broad.mit.edu	37	17	61973929	61973929	+	5'UTR	SNP	A	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61973929A>T	uc002jcs.1	-	1					CSH2_uc002jck.2_5'UTR|CSH1_uc002jcp.1_5'Flank|CSH1_uc002jcq.1_5'Flank|CSH1_uc002jcr.1_5'UTR|CSH1_uc002jct.1_5'UTR|CSH1_uc002jcu.1_5'UTR|CSH1_uc002jcv.1_5'UTR|CSH1_uc002jcw.2_5'UTR|CSH1_uc002jcy.2_5'UTR	NM_001317	NP_001308	P01243	CSH_HUMAN	chorionic somatomammotropin hormone 1 isoform 1						female pregnancy|signal transduction	extracellular region	hormone activity|metal ion binding			skin(1)	1						GGGCCTTGGGATCCTAGAGCC	0.567									Russell-Silver_syndrome				17	36	---	---	---	---	PASS
HDGFRP2	84717	broad.mit.edu	37	19	4501245	4501245	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4501245G>A	uc002mao.2	+	16	1925	c.1832G>A	c.(1831-1833)GGG>GAG	p.G611E	HDGFRP2_uc002map.2_Missense_Mutation_p.G611E|HDGFRP2_uc010dua.2_Intron|HDGFRP2_uc002maq.1_Missense_Mutation_p.G81E	NM_001001520	NP_001001520	Q7Z4V5	HDGR2_HUMAN	hepatoma-derived growth factor-related protein 2	611					transcription, DNA-dependent	nucleus	DNA binding|protein binding				0						TCACAGAAGGGGGAGAGCGCA	0.652													3	61	---	---	---	---	PASS
ILF3	3609	broad.mit.edu	37	19	10799989	10799989	+	3'UTR	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10799989G>C	uc002mpn.2	+	20					ILF3_uc002mpo.2_3'UTR|ILF3_uc002mpq.2_3'UTR	NM_012218	NP_036350	Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3 isoform a						M phase|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleolus|ribonucleoprotein complex	DNA binding|double-stranded RNA binding|protein binding|protein binding			ovary(3)	3			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)			GTACAGATAAGCCCCCGCGGG	0.562													29	71	---	---	---	---	PASS
NPHS1	4868	broad.mit.edu	37	19	36340202	36340202	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36340202T>C	uc002oby.2	-	7	776	c.776A>G	c.(775-777)CAG>CGG	p.Q259R		NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	259	Ig-like C2-type 3.|Extracellular (Potential).				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)|skin(1)	5	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTCCAAGCTCTGTCCTGCCCG	0.652													8	14	---	---	---	---	PASS
LIPE	3991	broad.mit.edu	37	19	42930843	42930843	+	Silent	SNP	A	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42930843A>G	uc002otr.2	-	1	736	c.459T>C	c.(457-459)GCT>GCC	p.A153A	uc010eif.1_Intron|uc002ott.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron|LIPE_uc002ots.1_5'Flank	NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase	153					cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)				GTGTTGATTCAGCTTCTTGTT	0.542													3	136	---	---	---	---	PASS
CTSA	5476	broad.mit.edu	37	20	44523539	44523539	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44523539A>G	uc002xqj.3	+	10	1421	c.947A>G	c.(946-948)CAG>CGG	p.Q316R	CTSA_uc002xqh.2_Missense_Mutation_p.Q334R|CTSA_uc002xqi.2_RNA|CTSA_uc010zxi.1_Missense_Mutation_p.Q317R|CTSA_uc002xqk.3_Missense_Mutation_p.Q316R	NM_001127695	NP_001121167	P10619	PPGB_HUMAN	cathepsin A isoform b precursor	316					intracellular protein transport|proteolysis	endoplasmic reticulum|lysosome|nucleus	enzyme activator activity|protein binding|serine-type carboxypeptidase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				ATGTGGCATCAGGTGTGCGAG	0.617													3	69	---	---	---	---	PASS
PDXK	8566	broad.mit.edu	37	21	45152325	45152325	+	Intron	SNP	T	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45152325T>G	uc002zdm.3	+						PDXK_uc010gpj.2_Intron|PDXK_uc002zdn.3_Intron|PDXK_uc002zdo.2_Splice_Site|PDXK_uc002zdp.2_Missense_Mutation_p.C23G	NM_003681	NP_003672	O00764	PDXK_HUMAN	pyridoxal kinase						cell proliferation|pyridoxal 5'-phosphate salvage	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)	TTTGATGGGGTGTGTGAAACG	0.507													26	74	---	---	---	---	PASS
RIBC2	26150	broad.mit.edu	37	22	45818209	45818209	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45818209C>T	uc011aqs.1	+	5	790	c.581C>T	c.(580-582)ACA>ATA	p.T194I		NM_015653	NP_056468	Q9H4K1	RIBC2_HUMAN	RIB43A domain with coiled-coils 2	126											0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TTTGACGAGACAGCCAAGCAC	0.542													5	175	---	---	---	---	PASS
AMELX	265	broad.mit.edu	37	X	11316724	11316724	+	Silent	SNP	C	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11316724C>A	uc004cut.2	+	5	269	c.201C>A	c.(199-201)CCC>CCA	p.P67P	ARHGAP6_uc004cup.1_Intron|ARHGAP6_uc004cuo.1_Intron|ARHGAP6_uc004cur.1_Intron|ARHGAP6_uc004cun.1_Intron|ARHGAP6_uc011mif.1_Intron|AMELX_uc004cus.2_Silent_p.P81P|AMELX_uc004cuu.2_Silent_p.P51P	NM_001142	NP_001133	Q99217	AMELX_HUMAN	amelogenin (X chromosome) isoform 1 precursor	67					cell adhesion|cell proliferation|chondrocyte differentiation|enamel mineralization|epithelial to mesenchymal transition|ion homeostasis|odontogenesis of dentine-containing tooth|osteoblast differentiation|positive regulation of collagen biosynthetic process|positive regulation of tooth mineralization|signal transduction	proteinaceous extracellular matrix	cell surface binding|growth factor activity|hydroxyapatite binding|identical protein binding|structural constituent of tooth enamel				0						AAATCATCCCCGTGCTGTCCC	0.587													3	106	---	---	---	---	PASS
AR	367	broad.mit.edu	37	X	66765719	66765719	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66765719C>T	uc004dwu.1	+	1	1846	c.731C>T	c.(730-732)TCG>TTG	p.S244L	AR_uc011mpd.1_Missense_Mutation_p.S244L|AR_uc011mpe.1_RNA|AR_uc011mpf.1_Missense_Mutation_p.S244L	NM_000044	NP_000035	P10275	ANDR_HUMAN	androgen receptor isoform 1	242	Modulating.				cell death|cell growth|cell proliferation|cell-cell signaling|negative regulation of apoptosis|negative regulation of integrin biosynthetic process|positive regulation of cell proliferation|positive regulation of integrin biosynthetic process|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|regulation of establishment of protein localization in plasma membrane|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transport	cytoplasm|nuclear chromatin|nucleoplasm	androgen binding|androgen receptor activity|beta-catenin binding|enzyme binding|ligand-regulated transcription factor activity|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(3)|lung(2)|breast(2)|central_nervous_system(1)	8	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone(DB04839)|Dromostanolone(DB00858)|Finasteride(DB01216)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Nandrolone(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Testosterone(DB00624)	AAGGCAGTGTCGGTGTCCATG	0.597									Androgen_Insensitivity_Syndrome				21	51	---	---	---	---	PASS
FOXO4	4303	broad.mit.edu	37	X	70320778	70320778	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70320778G>A	uc004dys.1	+	2	1051	c.698G>A	c.(697-699)GGC>GAC	p.G233D	FOXO4_uc010nkz.2_Missense_Mutation_p.G233D|FOXO4_uc004dyt.1_Missense_Mutation_p.G178D	NM_005938	NP_005929	P98177	FOXO4_HUMAN	forkhead box O4	233					cell cycle arrest|cell differentiation|embryo development|G1 phase of mitotic cell cycle|insulin receptor signaling pathway|mitotic cell cycle G2/M transition DNA damage checkpoint|muscle organ development|negative regulation of angiogenesis|negative regulation of cell proliferation|negative regulation of smooth muscle cell differentiation|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase 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			central_nervous_system(2)|prostate(1)	3	Renal(35;0.156)					AGCCCTGTCGGCCACTTTGCC	0.592											OREG0019856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	15	---	---	---	---	PASS
MIR384	494333	broad.mit.edu	37	X	76139785	76139785	+	RNA	SNP	A	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76139785A>G	hsa-mir-384|MI0001145	-			c.1A>G			uc010nlv.1_Intron|uc010nlw.1_RNA																	0						CTGATTTAACATTCTGCCTAT	0.149													2	9	---	---	---	---	PASS
NXF2B	728343	broad.mit.edu	37	X	101615563	101615563	+	Nonsense_Mutation	SNP	C	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101615563C>A	uc004ejb.3	-	34	3712	c.1840G>T	c.(1840-1842)GAG>TAG	p.E614*	NXF2B_uc004eiz.3_3'UTR|NXF2B_uc004eja.3_Nonsense_Mutation_p.E614*|NXF2_uc004eiy.3_Nonsense_Mutation_p.E614*	NM_001099686	NP_001093156	Q9GZY0	NXF2_HUMAN	nuclear RNA export factor 2B	614	TAP-C.				mRNA export from nucleus|multicellular organismal development	actin cytoskeleton|cytoplasm|nuclear RNA export factor complex	nucleocytoplasmic transporter activity|nucleotide binding|RNA binding			ovary(1)	1						ATCTTGCCCTCGGTCTAGAGA	0.507													30	57	---	---	---	---	PASS
BHLHB9	80823	broad.mit.edu	37	X	102005705	102005705	+	3'UTR	SNP	G	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102005705G>A	uc010nog.2	+	4					BHLHB9_uc011mrq.1_3'UTR|BHLHB9_uc011mrr.1_3'UTR|BHLHB9_uc011mrs.1_3'UTR|BHLHB9_uc011mrt.1_3'UTR|BHLHB9_uc004ejo.2_3'UTR|BHLHB9_uc011mru.1_3'UTR|BHLHB9_uc011mrv.1_3'UTR	NM_001142526	NP_001135998	Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class							cytoplasm|nucleus	binding			ovary(2)	2						CTATTTTGGGGGTATCAAATG	0.358													2	2	---	---	---	---	PASS
BCORL1	63035	broad.mit.edu	37	X	129171471	129171471	+	Missense_Mutation	SNP	G	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129171471G>T	uc004evb.1	+	9	4549	c.4435G>T	c.(4435-4437)GGG>TGG	p.G1479W	BCORL1_uc004evc.1_Missense_Mutation_p.G315W	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	1479	ANK 1.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7						GCTGGAGCACGGGGCCAACGT	0.612													4	135	---	---	---	---	PASS
PHF6	84295	broad.mit.edu	37	X	133511646	133511646	+	5'UTR	SNP	T	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133511646T>C	uc004exj.2	+	2					PHF6_uc004exk.2_5'UTR|PHF6_uc011mvk.1_5'UTR|PHF6_uc004exh.2_5'UTR|PHF6_uc010nrr.2_5'UTR|PHF6_uc004exi.2_5'UTR	NM_001015877	NP_001015877	Q8IWS0	PHF6_HUMAN	PHD finger protein 6 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					AATTTAAAAATCATGTCAAGC	0.338													103	89	---	---	---	---	PASS
ZNF185	7739	broad.mit.edu	37	X	152128271	152128271	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152128271G>C	uc010ntv.1	+	17	1472	c.1435G>C	c.(1435-1437)GTG>CTG	p.V479L	ZNF185_uc011myg.1_Missense_Mutation_p.V511L|ZNF185_uc011myh.1_Missense_Mutation_p.V482L|ZNF185_uc011myi.1_Missense_Mutation_p.V450L|ZNF185_uc011myj.1_Missense_Mutation_p.V420L|ZNF185_uc011myk.1_Missense_Mutation_p.V480L|ZNF185_uc004fgw.3_Missense_Mutation_p.V258L|ZNF185_uc004fgu.2_Missense_Mutation_p.V108L|ZNF185_uc004fgv.2_Missense_Mutation_p.V176L|ZNF185_uc004fgx.2_Missense_Mutation_p.V117L	NM_007150	NP_009081	O15231	ZN185_HUMAN	zinc finger protein 185	479						cytoplasm|cytoskeleton|focal adhesion	zinc ion binding			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)					GGGGAAGGATGTGGCCACCAA	0.567													4	31	---	---	---	---	PASS
RERE	473	broad.mit.edu	37	1	8420358	8420358	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8420358delC	uc001ape.2	-	19	4019	c.3209delG	c.(3208-3210)TGCfs	p.C1070fs	RERE_uc001apf.2_Frame_Shift_Del_p.C1070fs|RERE_uc010nzx.1_Frame_Shift_Del_p.C802fs|RERE_uc001apd.2_Frame_Shift_Del_p.C516fs	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	1070	Pro-rich.				multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		CGCACCAGAGCAGGGTGGCTG	0.701													4	2	---	---	---	---	
PBX1	5087	broad.mit.edu	37	1	164839428	164839429	+	Intron	INS	-	CTTT	CTTT	rs77254277	byFrequency	TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164839428_164839429insCTTT	uc010pkw.1	+							NM_002585	NP_002576	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5						ttctctattgactttctttctt	0.000			T	TCF3|EWSR1	pre B-ALL|myoepithelioma								3	3	---	---	---	---	
ALDH9A1	223	broad.mit.edu	37	1	165664747	165664748	+	Intron	DEL	TC	-	-	rs7512672		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165664747_165664748delTC	uc001gdh.1	-						ALDH9A1_uc010pky.1_Intron|ALDH9A1_uc010pkz.1_Intron|ALDH9A1_uc010pla.1_Intron	NM_000696	NP_000687	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9A1						carnitine biosynthetic process|cellular aldehyde metabolic process|hormone metabolic process|neurotransmitter biosynthetic process	cytosol|plasma membrane	3-chloroallyl aldehyde dehydrogenase activity|4-trimethylammoniobutyraldehyde dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|aminobutyraldehyde dehydrogenase activity				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				NADH(DB00157)	tttttttttttcttgagatgga	0.094													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	199130171	199130172	+	IGR	INS	-	G	G	rs145131094	by1000genomes	TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199130171_199130172insG								MIR181A1 (301889 upstream) : NR5A2 (866598 downstream)																							gaaggaaggaagaaggaaggaa	0.084													3	3	---	---	---	---	
TARBP1	6894	broad.mit.edu	37	1	234608725	234608726	+	Intron	INS	-	T	T	rs141043621	by1000genomes	TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234608725_234608726insT	uc001hwd.2	-							NM_005646	NP_005637	Q13395	TARB1_HUMAN	TAR RNA binding protein 1						regulation of transcription from RNA polymerase II promoter|RNA processing	nucleus	RNA binding|RNA methyltransferase activity			ovary(2)|skin(1)	3	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			TCAGAGGGAGATTTTTTTTTGC	0.257													5	3	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61483709	61483709	+	Intron	DEL	A	-	-	rs34025877		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61483709delA	uc002sbe.2	-						USP34_uc002sbf.2_Intron	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			AATGCTCAGCaaaaaaatttt	0.244													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	86133367	86133368	+	IGR	INS	-	CTTCC	CTTCC	rs138359602	by1000genomes	TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86133367_86133368insCTTCC								ST3GAL5 (17210 upstream) : LOC90784 (113971 downstream)																							cttctttccttcttcccttccc	0.050													5	3	---	---	---	---	
LOC541471	541471	broad.mit.edu	37	2	112009160	112009161	+	Intron	INS	-	GACTGC	GACTGC			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112009160_112009161insGACTGC	uc002the.2	-											Homo sapiens hypothetical LOC541471, mRNA (cDNA clone IMAGE:3459303).												0						accatcaccattaccaccacca	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	133018713	133018714	+	IGR	DEL	GG	-	-	rs144729406		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133018713_133018714delGG								NCRNA00164 (3171 upstream) : GPR39 (155433 downstream)																							TGGGCGGGGTGGTGGGGGGTGC	0.530													4	2	---	---	---	---	
ABCB6	10058	broad.mit.edu	37	2	220082643	220082643	+	Intron	DEL	A	-	-	rs75859701		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220082643delA	uc002vkc.1	-						ABCB6_uc010fwe.1_Intron|ABCB6_uc010zku.1_Intron	NM_005689	NP_005680	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B, member 6						cadmium ion transmembrane transport|cellular iron ion homeostasis|detoxification of cadmium ion|porphyrin biosynthetic process	ATP-binding cassette (ABC) transporter complex|Golgi apparatus|integral to mitochondrial outer membrane|plasma membrane|vacuolar membrane	ATP binding|efflux transmembrane transporter activity|heme binding|heme-transporting ATPase activity			breast(1)|central_nervous_system(1)	2		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TTACAGGCTTAAAAAAAAAAA	0.443													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	231033634	231033634	+	IGR	DEL	T	-	-	rs33940219		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231033634delT								FBXO36 (85618 upstream) : SP110 (11 downstream)																							gaagtattaatttttttTTTT	0.159													4	2	---	---	---	---	
AGPAT9	84803	broad.mit.edu	37	4	84502563	84502564	+	Intron	INS	-	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84502563_84502564insA	uc003how.2	+						AGPAT9_uc003hox.2_Intron|AGPAT9_uc003hoy.2_Intron	NM_032717	NP_116106	Q53EU6	GPAT3_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 9						phospholipid biosynthetic process|regulation of TOR signaling cascade|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	glycerol-3-phosphate O-acyltransferase activity			skin(1)	1		Hepatocellular(203;0.114)				CCCACTGCAATTGTTTGTCTCT	0.376													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	21319616	21319617	+	IGR	DEL	GT	-	-	rs71615676		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21319616_21319617delGT								None (None upstream) : GUSBP1 (22325 downstream)																							GTAAGGgtgcgtgtgtgtgtgt	0.282													4	3	---	---	---	---	
NDUFS4	4724	broad.mit.edu	37	5	52942409	52942410	+	Intron	DEL	AA	-	-	rs10571887		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52942409_52942410delAA	uc003jpe.2	+							NM_002495	NP_002486	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4						brain development|cAMP-mediated signaling|mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|positive regulation of fibroblast proliferation|reactive oxygen species metabolic process|regulation of protein phosphorylation|response to cAMP|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			central_nervous_system(1)	1		Lung NSC(810;8.27e-05)|Breast(144;0.0848)			NADH(DB00157)	ATATTCAGATAAGTGTGGCTTA	0.327													1	7	---	---	---	---	
SV2C	22987	broad.mit.edu	37	5	75507289	75507292	+	Intron	DEL	GTGT	-	-	rs34055477		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75507289_75507292delGTGT	uc003kei.1	+							NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		TTCTGGTtgcgtgtgtgtgtgtgt	0.314													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	102177111	102177114	+	IGR	DEL	ACAC	-	-	rs142181984		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102177111_102177114delACAC								SLCO6A1 (342391 upstream) : PAM (24413 downstream)																							ACCTACAAATacacacacacacac	0.294													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	144588487	144588490	+	IGR	DEL	AGAA	-	-	rs144645373		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144588487_144588490delAGAA								KCTD16 (731543 upstream) : PRELID2 (550092 downstream)																							agagagaaagagaaagaaagaagg	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	145743981	145743982	+	IGR	INS	-	TT	TT			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145743981_145743982insTT								POU4F3 (23898 upstream) : TCERG1 (82891 downstream)																							tccttccttccttccttccttc	0.040													4	2	---	---	---	---	
FAM153B	202134	broad.mit.edu	37	5	175530031	175530031	+	Intron	DEL	G	-	-			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175530031delG	uc003mdk.2	+							NM_001079529	NP_001072997	P0C7A2	F153B_HUMAN	hypothetical protein LOC202134											ovary(1)	1	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		CCTGCACTGCGTGGTGTGCAC	0.507													4	2	---	---	---	---	
ATG5	9474	broad.mit.edu	37	6	106727356	106727357	+	Intron	INS	-	G	G	rs146277372	by1000genomes	TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106727356_106727357insG	uc003prf.2	-						ATG5_uc010kdb.2_Intron|ATG5_uc003prg.2_Intron|ATG5_uc010kdc.2_Intron	NM_004849	NP_004840	Q9H1Y0	ATG5_HUMAN	APG5 autophagy 5-like						apoptosis|autophagic vacuole assembly|negative regulation of type I interferon production|post-translational protein modification	autophagic vacuole|pre-autophagosomal structure membrane	protein binding			large_intestine(1)	1	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		CCATGAACAGAGGACACCAAAA	0.396													4	4	---	---	---	---	
CCM2	83605	broad.mit.edu	37	7	45036479	45036482	+	5'Flank	DEL	GTGA	-	-	rs2331203		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45036479_45036482delGTGA	uc003tmn.2	+									Q9BSQ5	CCM2_HUMAN	Homo sapiens PP10187 mRNA, complete cds.						endothelial tube morphogenesis|integrin-mediated signaling pathway|stress-activated MAPK cascade|vasculogenesis	cytoplasm	protein binding				0						gtgtgtgtgtgtgagacagatctg	0.000									Familial_Cerebral_Cavernous_Angioma				3	3	---	---	---	---	
COL22A1	169044	broad.mit.edu	37	8	139601386	139601386	+	3'UTR	DEL	A	-	-	rs72284088		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139601386delA	uc003yvd.2	-	65					COL22A1_uc011ljo.1_3'UTR	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1						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)			taaaagaaagaaaaaaaaaag	0.328										HNSCC(7;0.00092)			4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	99649569	99649588	+	IGR	DEL	AAGGAAGGAAGGAAGGAAGG	-	-	rs12237068	by1000genomes	TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99649569_99649588delAAGGAAGGAAGGAAGGAAGG								ZNF782 (11713 upstream) : LOC441454 (21769 downstream)																							gcaaaaaagaaaggaaggaaggaaggaaggaaggaaggaa	0.005													2	4	---	---	---	---	
XPA	7507	broad.mit.edu	37	9	100461277	100461278	+	5'Flank	DEL	GT	-	-			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100461277_100461278delGT	uc004axr.3	-						XPA_uc004axs.3_5'Flank	NM_000380	NP_000371	P23025	XPA_HUMAN	xeroderma pigmentosum, complementation group A						nucleotide-excision repair, DNA damage removal	nucleoplasm	damaged DNA binding|metal ion binding|nucleotide binding|protein domain specific binding|protein homodimerization activity			breast(1)	1		Acute lymphoblastic leukemia(62;0.158)				CCCAGCTACGGTGTCCGGCTGG	0.624			Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		NER	Xeroderma_Pigmentosum				26	12	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42400410	42400410	+	IGR	DEL	C	-	-	rs74186261		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42400410delC								None (None upstream) : LOC441666 (426905 downstream)																							aacgggatttcttcacataat	0.000													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	59302920	59302921	+	IGR	INS	-	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59302920_59302921insG								None (None upstream) : IPMK (652697 downstream)																							gaaggaaggaaggaaggaagga	0.000													4	2	---	---	---	---	
NAV2	89797	broad.mit.edu	37	11	19966252	19966255	+	Intron	DEL	TTCC	-	-			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19966252_19966255delTTCC	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6						tcttccttctttccttccttcctt	0.000													4	2	---	---	---	---	
PDE2A	5138	broad.mit.edu	37	11	72307501	72307508	+	Intron	DEL	ATCTCTCT	-	-	rs145397044		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72307501_72307508delATCTCTCT	uc010rrc.1	-						PDE2A_uc001oso.2_Intron|PDE2A_uc010rra.1_Intron|PDE2A_uc001osn.2_Intron|PDE2A_uc010rrb.1_Intron|PDE2A_uc010rrd.1_Intron	NM_002599	NP_002590	O00408	PDE2A_HUMAN	phosphodiesterase 2A isoform 1						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)	TATGGCTCCCAtctctctctctctctct	0.447													4	2	---	---	---	---	
TYR	7299	broad.mit.edu	37	11	88911150	88911151	+	Frame_Shift_Ins	INS	-	A	A			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88911150_88911151insA	uc001pcs.2	+	1	111_112	c.29_30insA	c.(28-30)CTGfs	p.L10fs		NM_000372	NP_000363	P14679	TYRO_HUMAN	tyrosinase precursor	10					eye pigment biosynthetic process|melanin biosynthetic process from tyrosine|visual perception	Golgi-associated vesicle|integral to membrane|lysosome|melanosome membrane|perinuclear region of cytoplasm	copper ion binding|monophenol monooxygenase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|NADH(DB00157)	TACTGCCTGCTGTGGAGTTTCC	0.525									Oculocutaneous_Albinism				50	31	---	---	---	---	
YLPM1	56252	broad.mit.edu	37	14	75230551	75230551	+	Frame_Shift_Del	DEL	A	-	-			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75230551delA	uc001xqj.3	+	1	483	c.359delA	c.(358-360)CAGfs	p.Q120fs		NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	120	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		TATCAGAAGCAGCAGCAGTAC	0.682													14	11	---	---	---	---	
KIAA0430	9665	broad.mit.edu	37	16	15724209	15724210	+	Frame_Shift_Ins	INS	-	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15724209_15724210insG	uc002ddr.2	-	7	1696_1697	c.1503_1504insC	c.(1501-1506)CCCAGGfs	p.P501fs	KIAA0430_uc002ddq.2_Frame_Shift_Ins_p.P500fs|KIAA0430_uc010uzv.1_Frame_Shift_Ins_p.P497fs|KIAA0430_uc010uzw.1_Frame_Shift_Ins_p.P500fs	NM_014647	NP_055462	Q9Y4F3	LKAP_HUMAN	limkain b1	500_501						peroxisome	nucleotide binding|RNA binding				0						AGTGGTAACCTGGGGGGCAAGT	0.436													71	31	---	---	---	---	
TEPP	374739	broad.mit.edu	37	16	58019066	58019066	+	Intron	DEL	G	-	-	rs35768173		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58019066delG	uc002emw.3	+						TEPP_uc002emv.3_Intron	NM_199456	NP_955535	Q6URK8	TEPP_HUMAN	testis/prostate/placenta-expressed protein							extracellular region				kidney(1)|central_nervous_system(1)|skin(1)	3						GGCTTGTCCTGGGGGGGGGCG	0.677													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	60214732	60214735	+	IGR	DEL	TCTT	-	-			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60214732_60214735delTCTT								None (None upstream) : None (None downstream)																							ttcttctttctctttctttctttc	0.000													4	4	---	---	---	---	
USP6	9098	broad.mit.edu	37	17	5047791	5047792	+	Intron	INS	-	T	T			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5047791_5047792insT	uc002gau.1	+						USP6_uc002gav.1_Intron|USP6_uc010ckz.1_Intron	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6						protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5						AAATACTTCTCTTTTTTTTTTT	0.297			T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								4	2	---	---	---	---	
TMEM220	388335	broad.mit.edu	37	17	10619317	10619318	+	Intron	INS	-	GATA	GATA	rs146093202	by1000genomes	TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10619317_10619318insGATA	uc002gmx.2	-						TMEM220_uc002gmy.2_Intron	NM_001004313	NP_001004313	Q6QAJ8	TM220_HUMAN	transmembrane protein 220							integral to membrane					0						tataCTGCCCTGACACAAAATG	0.203													4	2	---	---	---	---	
ZNF519	162655	broad.mit.edu	37	18	14124193	14124193	+	Intron	DEL	G	-	-			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14124193delG	uc002kst.1	-						ZNF519_uc002ksq.1_Intron|ZNF519_uc002ksr.1_Intron|ZNF519_uc010dlm.1_Intron	NM_145287	NP_660330	Q8TB69	ZN519_HUMAN	zinc finger protein 519						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						aaaaaaaaaaGATTTTCTTTT	0.164													4	2	---	---	---	---	
KATNAL2	83473	broad.mit.edu	37	18	44626462	44626469	+	Intron	DEL	TCTCTTCC	-	-	rs3217429		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44626462_44626469delTCTCTTCC	uc002lco.2	+						KATNAL2_uc002lcp.3_Intron	NM_031303	NP_112593	Q8IYT4	KATL2_HUMAN	katanin p60 subunit A-like 2							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4						GCTAGCAGGGTCTCTTCCTCAAGCACTG	0.457											OREG0024959	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	3	---	---	---	---	
GNG7	2788	broad.mit.edu	37	19	2618341	2618342	+	Intron	DEL	GT	-	-	rs67734337		TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2618341_2618342delGT	uc002lwd.2	-							NM_052847	NP_443079	O60262	GBG7_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		tatgtgtgtggtgtgtgtgtgt	0.233													4	3	---	---	---	---	
MUC16	94025	broad.mit.edu	37	19	9080282	9080283	+	Intron	DEL	AG	-	-			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9080282_9080283delAG	uc002mkp.2	-							NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						aaagaaagaaagagaaagaaag	0.015													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25723837	25723838	+	IGR	INS	-	G	G			TCGA-B8-5159-01A-01D-1421-08	TCGA-B8-5159-10A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25723837_25723838insG								IGLL3 (7646 upstream) : LRP5L (23548 downstream)																							TTCCCAGGTCTGGGCATGGGGG	0.540													4	2	---	---	---	---	
