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
MST1P2	11209	broad.mit.edu	37	1	16974758	16974758	+	RNA	SNP	G	A	A	rs28484638	by1000genomes	TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16974758G>A	uc010och.1	+	7		c.1218G>A			MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						GGCCGGGGCGGGGTCTCGGCC	0.716													4	16	---	---	---	---	PASS
RPS6KA1	6195	broad.mit.edu	37	1	26897964	26897964	+	Missense_Mutation	SNP	A	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26897964A>T	uc001bmr.1	+	18	1778	c.1615A>T	c.(1615-1617)AGC>TGC	p.S539C	RPS6KA1_uc010ofe.1_Missense_Mutation_p.S447C|RPS6KA1_uc010off.1_Missense_Mutation_p.S523C|RPS6KA1_uc001bms.1_Missense_Mutation_p.S548C|RPS6KA1_uc009vsl.1_Missense_Mutation_p.S382C	NM_002953	NP_002944	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	539	Protein kinase 2.				axon guidance|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|synaptic transmission|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|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		CCTGAAGCCCAGCAACATCCT	0.597													6	28	---	---	---	---	PASS
DIO1	1733	broad.mit.edu	37	1	54370442	54370442	+	Silent	SNP	A	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54370442A>G	uc010onx.1	+	3	464	c.441A>G	c.(439-441)GCA>GCG	p.A147A	DIO1_uc010onw.1_Silent_p.A83A|DIO1_uc009vzl.2_Intron|DIO1_uc001cwb.2_Intron|DIO1_uc010ony.1_Silent_p.A147A|DIO1_uc001cwd.2_RNA|DIO1_uc001cwe.2_Intron|DIO1_uc001cwf.2_RNA|DIO1_uc001cwg.2_RNA	NM_000792	NP_000783	P49895	IOD1_HUMAN	deiodinase, iodothyronine, type I isoform a	147					hormone biosynthetic process|thyroid hormone generation	endoplasmic reticulum membrane|integral to membrane|plasma membrane	selenium binding|thyroxine 5'-deiodinase activity				0						GTTCCATAGCAGATTTTCTTG	0.398													34	127	---	---	---	---	PASS
RABGGTB	5876	broad.mit.edu	37	1	76255648	76255648	+	Silent	SNP	G	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76255648G>A	uc001dgy.1	+	4	392	c.321G>A	c.(319-321)CTG>CTA	p.L107L	RABGGTB_uc009wbt.1_RNA|RABGGTB_uc001dha.1_Silent_p.L61L	NM_004582	NP_004573	P53611	PGTB2_HUMAN	RAB geranylgeranyltransferase, beta subunit	107	PFTB 2.				protein modification process|visual perception		metal ion binding|protein binding|Rab geranylgeranyltransferase activity			ovary(1)	1						TTCTTACGCTGTATGACAGTA	0.328													33	87	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142713773	142713773	+	Intron	SNP	C	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142713773C>G	uc001eiw.1	+						uc001eix.1_RNA					Homo sapiens PNAS-130 mRNA, complete cds.																		TCTTTTTCCACATTGTCATTT	0.284													7	70	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	142713774	142713774	+	Intron	SNP	A	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142713774A>G	uc001eiw.1	+						uc001eix.1_RNA					Homo sapiens PNAS-130 mRNA, complete cds.																		CTTTTTCCACATTGTCATTTT	0.284													8	71	---	---	---	---	PASS
NUP210L	91181	broad.mit.edu	37	1	154112289	154112289	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154112289G>A	uc001fdw.2	-	5	778	c.706C>T	c.(706-708)CCA>TCA	p.P236S	NUP210L_uc010peh.1_Missense_Mutation_p.P236S	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like isoform 1	236						integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			TTATAGAATGGTTCATGAATT	0.353													87	247	---	---	---	---	PASS
FAM129A	116496	broad.mit.edu	37	1	184777143	184777143	+	Intron	SNP	G	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184777143G>T	uc001gra.2	-						FAM129A_uc001grb.1_Intron|FAM129A_uc009wyh.1_Intron|FAM129A_uc009wyi.1_Missense_Mutation_p.A265D	NM_052966	NP_443198	Q9BZQ8	NIBAN_HUMAN	niban protein isoform 2						negative regulation of protein phosphorylation|positive regulation of protein phosphorylation|positive regulation of translation|response to endoplasmic reticulum stress	cytoplasm|nucleus|plasma membrane				ovary(3)|skin(1)	4						GGTCTCACTGGCCAGCACCCA	0.557													25	93	---	---	---	---	PASS
PIK3C2B	5287	broad.mit.edu	37	1	204423683	204423683	+	Intron	SNP	C	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204423683C>T	uc001haw.2	-						PIK3C2B_uc010pqv.1_Intron|PIK3C2B_uc001hax.1_3'UTR	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta						cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TTAGGGTTAACAAGGAGCCTG	0.289													29	54	---	---	---	---	PASS
LPIN1	23175	broad.mit.edu	37	2	11911638	11911638	+	Missense_Mutation	SNP	C	A	A	rs145629147	byFrequency	TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11911638C>A	uc010yjn.1	+	5	703	c.429C>A	c.(427-429)AGC>AGA	p.S143R	LPIN1_uc010yjm.1_Missense_Mutation_p.S192R|LPIN1_uc002rbt.2_Missense_Mutation_p.S143R|LPIN1_uc002rbs.2_Missense_Mutation_p.S143R	NM_145693	NP_663731	Q14693	LPIN1_HUMAN	lipin 1	143					fatty acid catabolic process|transcription, DNA-dependent|triglyceride biosynthetic process|triglyceride mobilization	cytosol|endoplasmic reticulum membrane	phosphatidate phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TCGCTCCCAGCGAGACGCCGT	0.537													12	49	---	---	---	---	PASS
SLC5A7	60482	broad.mit.edu	37	2	108627273	108627273	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108627273G>A	uc002tdv.2	+	9	1975	c.1699G>A	c.(1699-1701)GAT>AAT	p.D567N	SLC5A7_uc010ywm.1_Missense_Mutation_p.D320N|SLC5A7_uc010fjj.2_Missense_Mutation_p.D567N|SLC5A7_uc010ywn.1_Missense_Mutation_p.D454N	NM_021815	NP_068587	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (choline transporter),	567	Cytoplasmic (Potential).				acetylcholine biosynthetic process|neurotransmitter secretion	integral to membrane|plasma membrane	choline:sodium symporter activity			ovary(2)|central_nervous_system(1)|skin(1)	4					Choline(DB00122)	CCTTGATGTTGATTCCAGTCC	0.393													17	48	---	---	---	---	PASS
TBR1	10716	broad.mit.edu	37	2	162276727	162276727	+	Silent	SNP	T	C	C			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162276727T>C	uc002ubw.1	+	5	1451	c.1149T>C	c.(1147-1149)GAT>GAC	p.D383D	TBR1_uc010foy.2_Silent_p.D96D	NM_006593	NP_006584	Q16650	TBR1_HUMAN	T-box, brain, 1	383	T-box.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						TGAAAATAGATCACAACCCTT	0.353													4	121	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179603926	179603926	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179603926C>A	uc010zfh.1	-	46	13745	c.13521G>T	c.(13519-13521)GAG>GAT	p.E4507D	TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Missense_Mutation_p.E4440D|TTN_uc010zfj.1_Missense_Mutation_p.E4315D|TTN_uc002umz.1_Intron	NM_133437	NP_597681	Q8WZ42	TITIN_HUMAN	titin isoform novex-2	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CATTCAAGGCCTCACAGACAT	0.368													3	45	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179605552	179605552	+	Silent	SNP	G	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179605552G>A	uc010zfh.1	-	46	12119	c.11895C>T	c.(11893-11895)GGC>GGT	p.G3965G	TTN_uc010zfg.1_Intron|TTN_uc010zfi.1_Silent_p.G3898G|TTN_uc010zfj.1_Silent_p.G3773G|TTN_uc002umz.1_Intron	NM_133437	NP_597681	Q8WZ42	TITIN_HUMAN	titin isoform novex-2	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGTGAATACTGCCATTGATGC	0.463													44	138	---	---	---	---	PASS
CRBN	51185	broad.mit.edu	37	3	3214484	3214484	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3214484A>G	uc003bpq.2	-	4	522	c.503T>C	c.(502-504)CTT>CCT	p.L168P	CRBN_uc003bpr.2_Missense_Mutation_p.L167P|CRBN_uc010hbw.2_Missense_Mutation_p.L168P|CRBN_uc011aso.1_Missense_Mutation_p.L105P	NM_016302	NP_057386	Q96SW2	CRBN_HUMAN	cereblon	168	Lon.				proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination	Cul4A-RING ubiquitin ligase complex|cytoplasm|membrane|nucleus	ATP-dependent peptidase activity|protein binding			ovary(1)	1				Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079)		TCTTAGCTCAAGGACTTTGAA	0.343													5	114	---	---	---	---	PASS
CD96	10225	broad.mit.edu	37	3	111343188	111343188	+	Missense_Mutation	SNP	T	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111343188T>A	uc003dxw.2	+	11	1476	c.1306T>A	c.(1306-1308)TCC>ACC	p.S436T	CD96_uc003dxx.2_Missense_Mutation_p.S420T|CD96_uc010hpy.1_Missense_Mutation_p.S420T	NM_198196	NP_937839	P40200	TACT_HUMAN	CD96 antigen isoform 1 precursor	436	Extracellular (Potential).|Pro/Ser/Thr-rich.				cell adhesion|immune response|regulation of immune response	integral to plasma membrane				skin(2)|central_nervous_system(1)	3						AGCCAGCAATTCCAGTATGAC	0.398									Opitz_Trigonocephaly_syndrome				31	103	---	---	---	---	PASS
ACAP2	23527	broad.mit.edu	37	3	195066024	195066024	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195066024C>A	uc003fun.3	-	5	549	c.308G>T	c.(307-309)AGA>ATA	p.R103I	ACAP2_uc003fuo.2_Missense_Mutation_p.R103I	NM_012287	NP_036419	Q15057	ACAP2_HUMAN	centaurin, beta 2	103	BAR.				regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2						CTTAATTGATCTCTGAGTTTG	0.294													22	38	---	---	---	---	PASS
NDST4	64579	broad.mit.edu	37	4	115858626	115858626	+	Missense_Mutation	SNP	C	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115858626C>G	uc003ibu.2	-	5	1934	c.1255G>C	c.(1255-1257)GTG>CTG	p.V419L	NDST4_uc010imw.2_RNA	NM_022569	NP_072091	Q9H3R1	NDST4_HUMAN	heparan sulfate N-deacetylase/N-sulfotransferase	419	Lumenal (Potential).|Heparan sulfate N-deacetylase 4.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			skin(3)|ovary(1)	4		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		TGTGGGGCCACAGCATAGCCC	0.443													3	60	---	---	---	---	PASS
INPP4B	8821	broad.mit.edu	37	4	143044502	143044502	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143044502G>C	uc003iix.3	-	21	2555	c.1960C>G	c.(1960-1962)CAG>GAG	p.Q654E	INPP4B_uc003iiw.3_Missense_Mutation_p.Q654E|INPP4B_uc011chm.1_RNA|INPP4B_uc011chn.1_Missense_Mutation_p.Q469E|INPP4B_uc011cho.1_RNA|INPP4B_uc011chp.1_Missense_Mutation_p.Q525E	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,	654					signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)					TGAAGCTGCTGTAGGAAGCCT	0.363													4	125	---	---	---	---	PASS
GUSBP1	728411	broad.mit.edu	37	5	21497244	21497244	+	3'UTR	SNP	G	C	C			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21497244G>C	uc010iub.2	+	6					GUSBP1_uc011cnn.1_RNA|GUSBP1_uc003jgh.3_Intron	NR_027028				SubName: Full=Putative uncharacterized protein GUSBL2;												0						ACTGGTGTAAGACATCACAAT	0.483													3	68	---	---	---	---	PASS
AQPEP	206338	broad.mit.edu	37	5	115336812	115336812	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115336812A>C	uc003kro.2	+	10	1860	c.1696A>C	c.(1696-1698)ATA>CTA	p.I566L	AQPEP_uc003krp.2_RNA|AQPEP_uc003krq.2_RNA|AQPEP_uc003krr.2_RNA|AQPEP_uc003krs.2_RNA	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin	566	Lumenal (Potential).				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0						AATAAAAAACATAATGGACAG	0.373													4	165	---	---	---	---	PASS
EBF1	1879	broad.mit.edu	37	5	158526512	158526512	+	5'UTR	SNP	T	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158526512T>A	uc010jip.2	-	1					EBF1_uc011ddw.1_5'Flank|EBF1_uc011ddx.1_5'UTR|EBF1_uc003lxl.3_5'UTR|uc003lxm.1_5'Flank	NM_024007	NP_076870	Q9UH73	COE1_HUMAN	early B-cell factor						multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTGTGGAAAATCTCCTCCCCC	0.343			T	HMGA2	lipoma								9	202	---	---	---	---	PASS
CCNJL	79616	broad.mit.edu	37	5	159682576	159682576	+	Silent	SNP	C	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159682576C>T	uc003lyb.1	-	6	1119	c.867G>A	c.(865-867)ACG>ACA	p.T289T	CCNJL_uc011dee.1_Silent_p.T241T|CCNJL_uc003lyc.1_RNA|CCNJL_uc011def.1_Silent_p.T241T	NM_024565	NP_078841	Q8IV13	CCNJL_HUMAN	cyclin J-like	289						nucleus					0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTTCAATACACGTGCTGAGGT	0.552													8	305	---	---	---	---	PASS
RAB24	53917	broad.mit.edu	37	5	176728945	176728945	+	Silent	SNP	A	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176728945A>G	uc003mfv.2	-	8	897	c.528T>C	c.(526-528)GCT>GCC	p.A176A	RAB24_uc003mfu.2_Silent_p.A147A|RAB24_uc003mfw.2_Silent_p.A176A|PRELID1_uc003mfx.2_5'Flank|PRELID1_uc003mfy.2_5'Flank	NM_130781	NP_570137	Q969Q5	RAB24_HUMAN	RAB24 gene product	176					autophagy|protein transport|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|protein binding				0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCTGGAAGGCAGCCACACTGA	0.547													31	120	---	---	---	---	PASS
SERINC1	57515	broad.mit.edu	37	6	122768141	122768141	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122768141G>C	uc003pyy.1	-	9	1074	c.1004C>G	c.(1003-1005)ACT>AGT	p.T335S	SERINC1_uc003pyx.1_RNA	NM_020755	NP_065806	Q9NRX5	SERC1_HUMAN	serine incorporator 1	335	Cytoplasmic (Potential).				phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	L-serine transmembrane transporter activity|protein binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.126)		ATTGTTTGAAGTACGGATGCT	0.338													16	59	---	---	---	---	PASS
LATS1	9113	broad.mit.edu	37	6	150023180	150023180	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150023180C>T	uc003qmu.1	-	2	631	c.83G>A	c.(82-84)CGG>CAG	p.R28Q	LATS1_uc010kif.1_5'UTR|LATS1_uc003qmv.1_Missense_Mutation_p.R28Q|LATS1_uc003qmw.2_Missense_Mutation_p.R28Q|LATS1_uc010kig.1_5'UTR	NM_004690	NP_004681	O95835	LATS1_HUMAN	LATS homolog 1	28					cell division|cytoplasmic sequestering of protein|G2/M transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|positive regulation of peptidyl-serine phosphorylation|regulation of actin filament polymerization|sister chromatid segregation	microtubule organizing center|spindle pole	ATP binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		TAACATTTGCCGGCTACTGAC	0.393													41	117	---	---	---	---	PASS
BAZ1B	9031	broad.mit.edu	37	7	72892210	72892210	+	Silent	SNP	T	C	C			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72892210T>C	uc003tyc.2	-	7	1926	c.1581A>G	c.(1579-1581)GAA>GAG	p.E527E		NM_032408	NP_115784	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	527	Lys-rich.				ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)				GCTCTAGAAGTTCATAGCGTT	0.418													12	198	---	---	---	---	PASS
CLDN4	1364	broad.mit.edu	37	7	73245666	73245666	+	Silent	SNP	C	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73245666C>T	uc003tzi.3	+	1	474	c.135C>T	c.(133-135)ACC>ACT	p.T45T	RFC2_uc011kfa.1_Intron|CLDN4_uc003tzh.1_RNA	NM_001305	NP_001296	O14493	CLD4_HUMAN	claudin 4	45	Extracellular (Potential).				calcium-independent cell-cell adhesion	integral to plasma membrane|tight junction	identical protein binding|structural molecule activity|transmembrane receptor activity				0		Lung NSC(55;0.159)				CCTCGCAGACCATCTGGGAGG	0.657													15	37	---	---	---	---	PASS
RELN	5649	broad.mit.edu	37	7	103141225	103141225	+	Silent	SNP	T	C	C			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103141225T>C	uc003vca.2	-	53	8794	c.8634A>G	c.(8632-8634)TCA>TCG	p.S2878S	RELN_uc010liz.2_Silent_p.S2878S	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2878	EGF-like 7.				axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		AGTTTGGCCCTGAGTATCCCG	0.512													3	159	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	8	12435889	12435889	+	Intron	SNP	C	A	A	rs617055	by1000genomes	TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12435889C>A	uc003wvy.3	-						uc003wwb.1_RNA					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																		TAACTTCAGACTCAGCTTAGA	0.483													8	34	---	---	---	---	PASS
MYST3	7994	broad.mit.edu	37	8	41804117	41804117	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41804117A>G	uc010lxb.2	-	13	2532	c.1988T>C	c.(1987-1989)ATC>ACC	p.I663T	MYST3_uc010lxc.2_Missense_Mutation_p.I663T|MYST3_uc003xon.3_Missense_Mutation_p.I663T|MYST3_uc010lxd.2_Missense_Mutation_p.I663T	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic	663	Mediates interaction with BRPF1, required for histone H3 acetyltransferase activity.|Catalytic.|Interaction with RUNX1-1.				histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)			ACTGAAATCGATGAGAAACCT	0.313													14	30	---	---	---	---	PASS
PRUNE2	158471	broad.mit.edu	37	9	79461509	79461509	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79461509A>G	uc010mpk.2	-	4	554	c.430T>C	c.(430-432)TCC>CCC	p.S144P	PRUNE2_uc004akn.2_Missense_Mutation_p.S144P	NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	144					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0						AGAGAAGAGGAAGACTCTCGG	0.478													23	50	---	---	---	---	PASS
MYO3A	53904	broad.mit.edu	37	10	26313006	26313006	+	Missense_Mutation	SNP	T	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26313006T>G	uc001isn.2	+	9	1147	c.787T>G	c.(787-789)TTC>GTC	p.F263V	MYO3A_uc009xko.1_Missense_Mutation_p.F263V|MYO3A_uc009xkp.1_RNA|MYO3A_uc009xkq.1_Missense_Mutation_p.F263V	NM_017433	NP_059129	Q8NEV4	MYO3A_HUMAN	myosin IIIA	263	Protein kinase.				protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18						ATTCAATGACTTCATAAGCAA	0.368													53	125	---	---	---	---	PASS
ADAMTS14	140766	broad.mit.edu	37	10	72462194	72462194	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72462194G>A	uc001jrh.2	+	3	649	c.649G>A	c.(649-651)GCA>ACA	p.A217T	ADAMTS14_uc001jrg.2_Missense_Mutation_p.A217T	NM_080722	NP_542453	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1	217					collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6						GCAGGAGTGGGCAGAACCTGA	0.617													5	75	---	---	---	---	PASS
ANKRD22	118932	broad.mit.edu	37	10	90591656	90591656	+	Missense_Mutation	SNP	C	A	A	rs143516492		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90591656C>A	uc001kfj.3	-	2	517	c.149G>T	c.(148-150)CGA>CTA	p.R50L		NM_144590	NP_653191	Q5VYY1	ANR22_HUMAN	ankyrin repeat domain 22	50	ANK 1.										0		Colorectal(252;0.0163)		Colorectal(12;6.29e-05)|COAD - Colon adenocarcinoma(12;7.69e-05)		CACATGCCCTCGCCTGCAAGC	0.468													111	228	---	---	---	---	PASS
UBQLN3	50613	broad.mit.edu	37	11	5528857	5528857	+	Silent	SNP	G	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5528857G>A	uc001may.1	-	2	2018	c.1932C>T	c.(1930-1932)GAC>GAT	p.D644D	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_5'Flank|OR51B5_uc001maq.1_5'Flank	NM_017481	NP_059509	Q9H347	UBQL3_HUMAN	ubiquilin 3	644	UBA.									ovary(3)	3		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAGCATCCACGTCGCCCCCCG	0.527													23	70	---	---	---	---	PASS
DAGLA	747	broad.mit.edu	37	11	61511889	61511889	+	Silent	SNP	C	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61511889C>T	uc001nsa.2	+	20	3168	c.3057C>T	c.(3055-3057)ATC>ATT	p.I1019I		NM_006133	NP_006124	Q9Y4D2	DGLA_HUMAN	neural stem cell-derived dendrite regulator	1019	Cytoplasmic (Potential).				cell death|lipid catabolic process|platelet activation	integral to membrane|plasma membrane	acylglycerol lipase activity|metal ion binding|triglyceride lipase activity			ovary(2)|central_nervous_system(1)	3				READ - Rectum adenocarcinoma(4;0.219)		CTGACAAGATCCGGACTTCTA	0.662													18	46	---	---	---	---	PASS
C11orf9	745	broad.mit.edu	37	11	61543864	61543864	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61543864A>G	uc001nsc.1	+	10	1555	c.1459A>G	c.(1459-1461)AAC>GAC	p.N487D	C11orf9_uc001nse.1_Missense_Mutation_p.N478D|C11orf9_uc010rll.1_5'Flank	NM_001127392	NP_001120864	Q9Y2G1	MRF_HUMAN	myelin gene regulatory factor isoform 2	487	NDT80.				central nervous system myelination|positive regulation of myelination|positive regulation of transcription, DNA-dependent	integral to membrane|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1						GACCACCGCTAACAACATGCG	0.647											OREG0021012	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	25	---	---	---	---	PASS
SLC22A25	387601	broad.mit.edu	37	11	62933648	62933648	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62933648A>G	uc001nwr.1	-	7	1153	c.1153T>C	c.(1153-1155)TTT>CTT	p.F385L	SLC22A10_uc010rmo.1_Intron|SLC22A25_uc009yoq.1_RNA|SLC22A25_uc001nws.1_RNA|SLC22A25_uc001nwt.1_3'UTR	NM_199352	NP_955384	Q6T423	S22AP_HUMAN	putative UST1-like organic anion transporter	385	Helical; Name=8; (Potential).				transmembrane transport	integral to membrane				ovary(3)|skin(1)	4						ACTGCACCAAAGAGAGTCTGC	0.498													5	78	---	---	---	---	PASS
NCAPD2	9918	broad.mit.edu	37	12	6619242	6619242	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6619242C>A	uc001qoo.2	+	4	251	c.205C>A	c.(205-207)CAC>AAC	p.H69N	NCAPD2_uc009zen.1_Intron|NCAPD2_uc010sfd.1_Intron|SCARNA10_uc009zeo.1_5'Flank	NM_014865	NP_055680	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	69	Interactions with SMC2 and SMC4.				cell division|mitotic chromosome condensation	condensin core heterodimer|cytoplasm	histone binding			ovary(2)|lung(1)|breast(1)|kidney(1)	5						CCCTCATAGTCACTTTCGAAG	0.438													11	23	---	---	---	---	PASS
RASSF3	283349	broad.mit.edu	37	12	65088573	65088573	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65088573A>G	uc001ssd.2	+	5	718	c.598A>G	c.(598-600)AAT>GAT	p.N200D	RASSF3_uc009zqn.2_RNA|RASSF3_uc001sse.2_Missense_Mutation_p.N130D	NM_178169	NP_835463	Q86WH2	RASF3_HUMAN	Ras association (RalGDS/AF-6) domain family	200	SARAH.				signal transduction	cytoplasm|microtubule	identical protein binding				0			Lung(2;0.00133)|LUAD - Lung adenocarcinoma(6;0.0665)|LUSC - Lung squamous cell carcinoma(43;0.132)	GBM - Glioblastoma multiforme(28;0.0611)		AGAACTACAGAATTTCTTGCG	0.478													3	156	---	---	---	---	PASS
DNAH10	196385	broad.mit.edu	37	12	124383326	124383326	+	Missense_Mutation	SNP	C	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124383326C>A	uc001uft.3	+	55	9276	c.9251C>A	c.(9250-9252)GCC>GAC	p.A3084D		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3084	Potential.|Stalk (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GCCTGCGAGGCCTTGCTGGAG	0.642													6	21	---	---	---	---	PASS
GTF2F2	2963	broad.mit.edu	37	13	45841372	45841372	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45841372A>C	uc001uzw.2	+	7	651	c.491A>C	c.(490-492)GAA>GCA	p.E164A	GTF2F2_uc001uzv.2_Missense_Mutation_p.E164A	NM_004128	NP_004119	P13984	T2FB_HUMAN	general transcription factor IIF, polypeptide 2,	164					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	microtubule cytoskeleton|transcription factor TFIIF complex	ATP binding|ATP-dependent helicase activity|DNA binding|protein binding				0		Lung NSC(96;0.00115)|Prostate(109;0.00578)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000647)		ATATAGATCGAATATGAAAGG	0.299													17	69	---	---	---	---	PASS
TEP1	7011	broad.mit.edu	37	14	20850092	20850092	+	Silent	SNP	G	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20850092G>A	uc001vxe.2	-	30	4444	c.4404C>T	c.(4402-4404)TGC>TGT	p.C1468C	TEP1_uc010ahk.2_Silent_p.C811C|TEP1_uc010tlf.1_RNA|TEP1_uc010tlg.1_Silent_p.C1360C|TEP1_uc010tlh.1_5'UTR	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1468	NACHT.				telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		TCTGGACGAGGCAGGCAAACG	0.607													5	68	---	---	---	---	PASS
SMEK1	55671	broad.mit.edu	37	14	91975891	91975891	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91975891C>T	uc001xzn.2	-	1	923	c.101G>A	c.(100-102)CGG>CAG	p.R34Q	SMEK1_uc001xzm.2_Missense_Mutation_p.R34Q|SMEK1_uc001xzo.2_Missense_Mutation_p.R34Q|SMEK1_uc010atz.2_Missense_Mutation_p.R34Q|SMEK1_uc001xzp.1_RNA	NM_032560	NP_115949	Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1	34	WH1.					microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		GCCCTTCAGCCGCTCCACGTA	0.706													7	5	---	---	---	---	PASS
FBLN5	10516	broad.mit.edu	37	14	92413647	92413647	+	5'UTR	SNP	C	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92413647C>G	uc001xzx.3	-	1					FBLN5_uc010aud.2_5'Flank|FBLN5_uc010aue.2_5'UTR	NM_006329	NP_006320	Q9UBX5	FBLN5_HUMAN	fibulin 5 precursor						cell-matrix adhesion|elastic fiber assembly|protein localization at cell surface|regulation of removal of superoxide radicals	extracellular space|proteinaceous extracellular matrix|soluble fraction	calcium ion binding|integrin binding|protein C-terminus binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		all_cancers(154;0.0722)				GGAGCTCGGGCACGTCGGCCT	0.672													4	9	---	---	---	---	PASS
RTL1	388015	broad.mit.edu	37	14	101351021	101351021	+	Silent	SNP	C	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101351021C>T	uc010txj.1	-	1	164	c.105G>A	c.(103-105)GCG>GCA	p.A35A	uc010txk.1_5'Flank|MIR136_hsa-mir-136|MI0000475_5'Flank	NM_001134888	NP_001128360	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	35										pancreas(1)	1						TGCCCGACGTCGCCTCGGTGG	0.582													10	9	---	---	---	---	PASS
ZSCAN29	146050	broad.mit.edu	37	15	43653099	43653099	+	3'UTR	SNP	G	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43653099G>A	uc001zrk.1	-	5					ZSCAN29_uc001zrj.1_3'UTR|ZSCAN29_uc010bdf.1_3'UTR|ZSCAN29_uc001zrl.1_RNA|ZSCAN29_uc010bdg.1_3'UTR	NM_152455	NP_689668	Q8IWY8	ZSC29_HUMAN	zinc finger protein 690						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		TCTTTAGACTGCCTTGGGGAT	0.403													3	18	---	---	---	---	PASS
ZSCAN29	146050	broad.mit.edu	37	15	43653100	43653100	+	3'UTR	SNP	C	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43653100C>A	uc001zrk.1	-	5					ZSCAN29_uc001zrj.1_3'UTR|ZSCAN29_uc010bdf.1_3'UTR|ZSCAN29_uc001zrl.1_RNA|ZSCAN29_uc010bdg.1_3'UTR	NM_152455	NP_689668	Q8IWY8	ZSC29_HUMAN	zinc finger protein 690						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		CTTTAGACTGCCTTGGGGATT	0.403													3	18	---	---	---	---	PASS
ZSCAN29	146050	broad.mit.edu	37	15	43653101	43653101	+	3'UTR	SNP	C	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43653101C>T	uc001zrk.1	-	5					ZSCAN29_uc001zrj.1_3'UTR|ZSCAN29_uc010bdf.1_3'UTR|ZSCAN29_uc001zrl.1_RNA|ZSCAN29_uc010bdg.1_3'UTR	NM_152455	NP_689668	Q8IWY8	ZSC29_HUMAN	zinc finger protein 690						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		TTTAGACTGCCTTGGGGATTT	0.403													3	21	---	---	---	---	PASS
BLM	641	broad.mit.edu	37	15	91304206	91304206	+	Missense_Mutation	SNP	A	C	C			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91304206A>C	uc002bpr.2	+	7	1700	c.1603A>C	c.(1603-1605)AAA>CAA	p.K535Q	BLM_uc010uqh.1_Missense_Mutation_p.K535Q|BLM_uc010uqi.1_Missense_Mutation_p.K160Q|BLM_uc010bnx.2_Missense_Mutation_p.K535Q|BLM_uc002bps.1_Missense_Mutation_p.K97Q	NM_000057	NP_000048	P54132	BLM_HUMAN	Bloom syndrome protein	535					double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			AGATCAGAATAAACATACTGC	0.358			Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				25	66	---	---	---	---	PASS
N4BP1	9683	broad.mit.edu	37	16	48596011	48596011	+	Silent	SNP	G	C	C			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48596011G>C	uc002efp.2	-	2	780	c.543C>G	c.(541-543)TCC>TCG	p.S181S		NM_153029	NP_694574	O75113	N4BP1_HUMAN	Nedd4 binding protein 1	181					negative regulation of proteasomal ubiquitin-dependent protein catabolic process|negative regulation of protein ubiquitination	nucleolus|PML body					0		all_cancers(37;0.179)|all_lung(18;0.11)				CTTTTTTCAAGGAAGTGGGCA	0.378													3	57	---	---	---	---	PASS
E2F4	1874	broad.mit.edu	37	16	67229832	67229832	+	Missense_Mutation	SNP	G	A	A	rs3830472		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67229832G>A	uc002erz.2	+	7	1019	c.956G>A	c.(955-957)AGC>AAC	p.S319N		NM_001950	NP_001941	Q16254	E2F4_HUMAN	E2F transcription factor 4	319	Poly-Ser.		S -> SSSS.		G1 phase of mitotic cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			central_nervous_system(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		agcagcagcagcaacagtaac	0.453													4	74	---	---	---	---	PASS
SF3B3	23450	broad.mit.edu	37	16	70594436	70594436	+	Missense_Mutation	SNP	G	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70594436G>A	uc002ezf.2	+	16	2286	c.2075G>A	c.(2074-2076)CGG>CAG	p.R692Q		NM_012426	NP_036558	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3	692					protein complex assembly	catalytic step 2 spliceosome|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(1)	1		Ovarian(137;0.0694)				ACTCGCACTCGGTACCTGGGG	0.537													31	54	---	---	---	---	PASS
NF1	4763	broad.mit.edu	37	17	29687577	29687577	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29687577G>T	uc002hgg.2	+	57	8566	c.8233G>T	c.(8233-8235)GGA>TGA	p.G2745*	NF1_uc002hgh.2_Nonsense_Mutation_p.G2724*|NF1_uc010cso.2_Nonsense_Mutation_p.G933*|NF1_uc010wbt.1_Nonsense_Mutation_p.G223*|NF1_uc010wbu.1_RNA	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2745			G -> R (in a breast cancer sample; somatic mutation).		actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.G2745R(1)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GTACCTGCCTGGAATTGATGA	0.423			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			51	150	---	---	---	---	PASS
GRN	2896	broad.mit.edu	37	17	42426617	42426617	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42426617G>T	uc002igp.1	+	2	304	c.85G>T	c.(85-87)GCC>TCC	p.A29S	GRN_uc002igq.1_Missense_Mutation_p.A29S|GRN_uc002igr.1_5'Flank	NM_002087	NP_002078	P28799	GRN_HUMAN	granulin precursor	29					signal transduction	extracellular space	cytokine activity|growth factor activity			ovary(2)|central_nervous_system(2)|skin(1)	5		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		CTGCCCTGTGGCCTGCTGCCT	0.647													9	22	---	---	---	---	PASS
IGF2BP1	10642	broad.mit.edu	37	17	47103846	47103846	+	Missense_Mutation	SNP	G	C	C			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47103846G>C	uc002iom.2	+	4	638	c.304G>C	c.(304-306)GCT>CCT	p.A102P	IGF2BP1_uc010dbj.2_Missense_Mutation_p.A102P	NM_006546	NP_006537	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding	102	RRM 2.				CRD-mediated mRNA stabilization|negative regulation of translation|regulation of mRNA stability involved in response to stress	CRD-mediated mRNA stability complex|cytosol|dendritic spine|lamellipodium|nucleus|plasma membrane|stress granule	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			kidney(1)	1						CAGCCTGCTGGCTCAGTATGG	0.547													4	55	---	---	---	---	PASS
SMURF2	64750	broad.mit.edu	37	17	62576936	62576936	+	Missense_Mutation	SNP	T	C	C			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62576936T>C	uc002jep.1	-	8	1131	c.743A>G	c.(742-744)CAT>CGT	p.H248R	SMURF2_uc002jeq.1_Missense_Mutation_p.H7R|SMURF2_uc002jer.1_Missense_Mutation_p.H7R	NM_022739	NP_073576	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	248					BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			TGGAGGAGTATGTAAATGTGT	0.413													45	131	---	---	---	---	PASS
L3MBTL4	91133	broad.mit.edu	37	18	6264037	6264037	+	Missense_Mutation	SNP	A	G	G			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6264037A>G	uc002kmz.3	-	5	288	c.128T>C	c.(127-129)GTC>GCC	p.V43A	L3MBTL4_uc010dkt.2_Missense_Mutation_p.V43A	NM_173464	NP_775735	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4	43					chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)				CGCTGAAGGGACTGGAAGAGA	0.428													4	75	---	---	---	---	PASS
STXBP2	6813	broad.mit.edu	37	19	7703632	7703632	+	Missense_Mutation	SNP	C	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7703632C>T	uc002mha.3	+	2	103	c.58C>T	c.(58-60)CGG>TGG	p.R20W	STXBP2_uc002mhb.3_Missense_Mutation_p.R20W|STXBP2_uc010dvj.2_RNA|STXBP2_uc010xjr.1_Missense_Mutation_p.R20W|STXBP2_uc010dvk.2_Intron|STXBP2_uc002mhc.3_5'UTR|STXBP2_uc010dvl.1_5'Flank	NM_006949	NP_008880	Q15833	STXB2_HUMAN	syntaxin binding protein 2 isoform a	20					leukocyte mediated cytotoxicity|neutrophil degranulation|protein transport|regulation of mast cell degranulation|vesicle docking involved in exocytosis	azurophil granule|cytolytic granule|cytosol|specific granule|tertiary granule	syntaxin-3 binding			central_nervous_system(1)	1						CGGAGTTATTCGGAGTGTCAA	0.582													23	70	---	---	---	---	PASS
APLP1	333	broad.mit.edu	37	19	36362618	36362618	+	Silent	SNP	G	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36362618G>A	uc002oce.2	+	5	780	c.642G>A	c.(640-642)GGG>GGA	p.G214G	APLP1_uc010xsz.1_Silent_p.G175G|APLP1_uc002ocf.2_Silent_p.G214G|APLP1_uc002ocg.2_Silent_p.G117G|APLP1_uc010xta.1_Silent_p.G208G	NM_005166	NP_005157	P51693	APLP1_HUMAN	amyloid precursor-like protein 1 isoform 2	214	Extracellular (Potential).				apoptosis|cell adhesion|cellular response to norepinephrine stimulus|endocytosis|negative regulation of cAMP biosynthetic process|nervous system development|organ morphogenesis	basement membrane|integral to membrane|perinuclear region of cytoplasm|plasma membrane	alpha-2A adrenergic receptor binding|alpha-2B adrenergic receptor binding|alpha-2C adrenergic receptor binding|heparin binding|identical protein binding|metal ion binding			ovary(2)	2	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)			CCCCTCCAGGGACCCCCGACC	0.647													12	25	---	---	---	---	PASS
HIF3A	64344	broad.mit.edu	37	19	46815932	46815932	+	Intron	SNP	G	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46815932G>A	uc002peh.2	+						HIF3A_uc002pef.1_3'UTR|HIF3A_uc002peg.3_Intron|HIF3A_uc010xxx.1_Intron|HIF3A_uc002pei.3_Intron|HIF3A_uc002pej.1_Intron|HIF3A_uc002pek.2_Intron|HIF3A_uc010xxy.1_Intron|HIF3A_uc002pel.2_Intron|HIF3A_uc010xxz.1_Intron	NM_152795	NP_690008	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		GAGGGGCTGGGGTGGCTGTGT	0.478													34	72	---	---	---	---	PASS
NCAPH2	29781	broad.mit.edu	37	22	50960439	50960439	+	Missense_Mutation	SNP	G	A	A	rs117383090	by1000genomes	TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50960439G>A	uc003blr.3	+	13	1255	c.1133G>A	c.(1132-1134)CGG>CAG	p.R378Q	NCAPH2_uc003blv.2_Missense_Mutation_p.R378Q|NCAPH2_uc010hbb.2_Missense_Mutation_p.R229Q|NCAPH2_uc003blu.3_RNA|NCAPH2_uc003bls.3_RNA|NCAPH2_uc003blt.3_RNA|NCAPH2_uc003blw.3_RNA|NCAPH2_uc003blx.3_Missense_Mutation_p.R378Q|NCAPH2_uc003bly.3_RNA	NM_152299	NP_689512	Q6IBW4	CNDH2_HUMAN	kleisin beta isoform 2	378					chromosome condensation	chromosome|nucleus				ovary(1)|skin(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.212)		GACAGCAGGCGGCTTCGGCGA	0.587													21	81	---	---	---	---	PASS
VCX	26609	broad.mit.edu	37	X	7811214	7811214	+	5'UTR	SNP	C	T	T	rs150595614	by1000genomes	TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7811214C>T	uc004crz.2	+	2						NM_013452	NP_038480	Q9H320	VCX1_HUMAN	variable charge, X chromosome						chromatin organization|ribosome assembly|spermatogenesis	nucleolus	chromatin binding				0		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				CTGGAGTTAGCCGACCGTTGC	0.607													5	40	---	---	---	---	PASS
KIAA2022	340533	broad.mit.edu	37	X	73962035	73962035	+	Missense_Mutation	SNP	G	T	T			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73962035G>T	uc004eby.2	-	3	2974	c.2357C>A	c.(2356-2358)ACT>AAT	p.T786N		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	786					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15						TGGTAGAAAAGTGGAACTCTT	0.403													35	39	---	---	---	---	PASS
PRAMEF9	343070	broad.mit.edu	37	1	13645585	13645586	+	Intron	INS	-	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13645585_13645586insA	uc001ava.1	+							NM_001010890	NP_001010890	Q5VWM5	PRAM9_HUMAN	PRAME family member 9												0	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		gacttggtctcaaaaaaaaaaa	0.208													3	3	---	---	---	---	
AHCTF1	25909	broad.mit.edu	37	1	247067140	247067140	+	Intron	DEL	A	-	-	rs34620854		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247067140delA	uc001ibu.1	-						AHCTF1_uc001ibv.1_Intron	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS						cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			actctgtctcaaaaaaaaaaa	0.095													4	3	---	---	---	---	
ZNF638	27332	broad.mit.edu	37	2	71590192	71590192	+	Intron	DEL	A	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71590192delA	uc002shx.2	+						ZNF638_uc010fec.2_Intron|ZNF638_uc010yqw.1_Intron|ZNF638_uc002shw.2_Intron|ZNF638_uc002shy.2_Intron|ZNF638_uc002shz.2_Intron|ZNF638_uc002sia.2_Intron|ZNF638_uc002sib.1_Intron|ZNF638_uc010fed.2_5'Flank	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638						RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4						AAAAGTTGTGAAAAGTCCTTT	0.274													21	14	---	---	---	---	
REV1	51455	broad.mit.edu	37	2	100017906	100017907	+	Intron	INS	-	A	A	rs113809724		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100017906_100017907insA	uc002tad.2	-						REV1_uc002tac.2_Intron	NM_016316	NP_057400	Q9UBZ9	REV1_HUMAN	REV1-like isoform 1						DNA replication|error-prone translesion synthesis|response to UV	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding			ovary(2)	2						TTGACTTTGGCAAAAAAAAAAA	0.188								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					5	3	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52643654	52643654	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52643654delC	uc003des.2	-	16	2254	c.2242delG	c.(2242-2244)GATfs	p.D748fs	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Frame_Shift_Del_p.D748fs|PBRM1_uc003der.2_Frame_Shift_Del_p.D716fs|PBRM1_uc003det.2_Frame_Shift_Del_p.D763fs|PBRM1_uc003deu.2_Frame_Shift_Del_p.D763fs|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Frame_Shift_Del_p.D748fs|PBRM1_uc010hmk.1_Frame_Shift_Del_p.D748fs|PBRM1_uc003dey.2_Frame_Shift_Del_p.D748fs|PBRM1_uc003dez.1_Frame_Shift_Del_p.D748fs|PBRM1_uc003dfb.1_Frame_Shift_Del_p.D661fs|PBRM1_uc003dfa.1_Frame_Shift_Del_p.D94fs|PBRM1_uc003dfc.2_Frame_Shift_Del_p.D115fs	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	748					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		ACAAGAGCATCTTTGTAGATC	0.433			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								87	49	---	---	---	---	
FRAS1	80144	broad.mit.edu	37	4	79430319	79430319	+	Intron	DEL	G	-	-	rs34380083		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79430319delG	uc003hlb.2	+						FRAS1_uc003hlc.1_Intron	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						CATAAGAAAaggttatatgct	0.159													2	5	---	---	---	---	
GFM2	84340	broad.mit.edu	37	5	74037263	74037263	+	Intron	DEL	A	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74037263delA	uc003kdh.1	-						GFM2_uc003kdi.1_Intron|GFM2_uc010izj.1_Intron|GFM2_uc010izk.1_Intron|GFM2_uc003kdj.1_Intron|GFM2_uc010izl.1_Intron	NM_032380	NP_115756	Q969S9	RRF2M_HUMAN	mitochondrial elongation factor G2 isoform 1						mitochondrial translation|ribosome disassembly	mitochondrion	GTP binding|GTPase activity				0		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		TGCAAAGTTTAAAAAAAAAAT	0.269													4	2	---	---	---	---	
TCERG1	10915	broad.mit.edu	37	5	145889882	145889883	+	Intron	DEL	AA	-	-	rs67804115		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145889882_145889883delAA	uc003lob.2	+						TCERG1_uc003loc.2_Intron	NM_006706	NP_006697	O14776	TCRG1_HUMAN	transcription elongation regulator 1 isoform 1						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			ovary(1)|skin(1)	2		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			aatttttcttaaaaaaaaaaaa	0.015													6	3	---	---	---	---	
SLC17A5	26503	broad.mit.edu	37	6	74320415	74320415	+	Intron	DEL	A	-	-	rs10707321		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74320415delA	uc003phn.3	-						SLC17A5_uc010kax.2_Intron|SLC17A5_uc010kay.2_Intron|SLC17A5_uc011dyo.1_Intron	NM_012434	NP_036566	Q9NRA2	S17A5_HUMAN	sialin						anion transport	integral to plasma membrane|lysosomal membrane|membrane fraction	sialic acid:hydrogen symporter activity			skin(5)|central_nervous_system(1)	6						ATTTCATGAGAAAAAAAAAAT	0.308													4	4	---	---	---	---	
TULP4	56995	broad.mit.edu	37	6	158882455	158882456	+	Intron	INS	-	AAG	AAG	rs113168644		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158882455_158882456insAAG	uc003qrf.2	+						TULP4_uc011efo.1_Intron|TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1						intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		aaaaaaaaaaaaaaggaaaaaa	0.168													7	4	---	---	---	---	
C7orf10	79783	broad.mit.edu	37	7	40228055	40228055	+	Intron	DEL	C	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40228055delC	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004	Q9HAC7	CG010_HUMAN	dermal papilla derived protein 13								transferase activity			ovary(2)	2						aaaaaaaaaacaaaCCCCAAA	0.194													13	6	---	---	---	---	
MSR1	4481	broad.mit.edu	37	8	16035613	16035613	+	Intron	DEL	T	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16035613delT	uc003wwz.2	-						MSR1_uc010lsu.2_Intron|MSR1_uc003wxa.2_Intron|MSR1_uc003wxb.2_Intron|MSR1_uc011kxz.1_Intron	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1						cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		TCAGTTTTTCttttttttttt	0.139													4	2	---	---	---	---	
LETM2	137994	broad.mit.edu	37	8	38249933	38249933	+	Intron	DEL	A	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38249933delA	uc003xlm.1	+						LETM2_uc003xlk.2_Intron|LETM2_uc011lbn.1_Intron|LETM2_uc003xll.1_Intron|LETM2_uc003xln.1_Intron|LETM2_uc003xlo.1_Intron	NM_144652	NP_653253	Q2VYF4	LETM2_HUMAN	leucine zipper-EF-hand containing transmembrane							integral to membrane|mitochondrial inner membrane					0	all_cancers(2;6.77e-47)|all_epithelial(2;1.01e-50)|all_lung(3;1.25e-23)|Lung NSC(2;2.76e-23)|Colorectal(12;0.000442)|Esophageal squamous(3;0.00202)	all_lung(54;0.0657)|Hepatocellular(245;0.152)|Lung NSC(58;0.175)	Epithelial(3;1.17e-42)|all cancers(3;5.44e-38)|BRCA - Breast invasive adenocarcinoma(5;5.44e-27)|LUSC - Lung squamous cell carcinoma(2;7.12e-25)|Lung(2;4.49e-22)|COAD - Colon adenocarcinoma(9;0.114)			aTGGGAGTGGAAAAAAAAAAA	0.154													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	78808344	78808345	+	IGR	INS	-	A	A			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78808344_78808345insA								PCSK5 (6 upstream) : RFK (192088 downstream)																							aagccaaaaagaaaaaaaaaaa	0.233													4	2	---	---	---	---	
CACNB2	783	broad.mit.edu	37	10	18825202	18825203	+	Intron	INS	-	GG	GG	rs150214686	by1000genomes	TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18825202_18825203insGG	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron|CACNB2_uc001ipw.2_Intron|CACNB2_uc001ipx.2_Intron|CACNB2_uc001ipz.2_Intron|CACNB2_uc001ipy.2_Intron|CACNB2_uc010qco.1_Intron|CACNB2_uc001iqa.2_Intron|NSUN6_uc001iqb.2_Intron	NM_201596	NP_963890	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2						axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)	tttttttttttgggggacaagg	0.144													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	134206019	134206020	+	IGR	INS	-	G	G	rs142843997		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134206019_134206020insG								LRRC27 (11009 upstream) : PWWP2B (4682 downstream)																							atgatggtgatgtgataatggt	0.000													3	7	---	---	---	---	
HEPHL1	341208	broad.mit.edu	37	11	93839460	93839460	+	Intron	DEL	T	-	-	rs144455207		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93839460delT	uc001pep.2	+						uc001pen.1_Intron	NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor						copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				Atttcttttcttttttttttt	0.179													4	2	---	---	---	---	
EI24	9538	broad.mit.edu	37	11	125452221	125452222	+	Intron	INS	-	T	T	rs115034429	by1000genomes	TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125452221_125452222insT	uc001qca.2	+						EI24_uc001qcb.2_Intron|EI24_uc010sbd.1_Intron|EI24_uc009zbl.2_Intron|EI24_uc001qcc.2_Intron|EI24_uc010sbe.1_Intron|EI24_uc010sbf.1_Intron	NM_004879	NP_004870	O14681	EI24_HUMAN	etoposide induced 2.4 isoform 1						apoptosis|autophagy|induction of apoptosis|negative regulation of cell growth	endoplasmic reticulum membrane|integral to membrane|nuclear membrane				ovary(1)	1	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)		CTAATTATTTCTTTTTTTTTTT	0.351													4	2	---	---	---	---	
SLCO1B3	28234	broad.mit.edu	37	12	21008017	21008017	+	Frame_Shift_Del	DEL	T	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21008017delT	uc001rek.2	+	3	266	c.140delT	c.(139-141)ATTfs	p.I47fs	SLCO1B3_uc001rel.2_Frame_Shift_Del_p.I47fs|SLCO1B3_uc010sil.1_Frame_Shift_Del_p.I47fs|LST-3TM12_uc010sim.1_Frame_Shift_Del_p.I47fs	NM_019844	NP_062818	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family,	47	Helical; Name=1; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)					GGTGGAATCATTATGAAAATT	0.318													39	20	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	24737258	24737263	+	5'Flank	DEL	CCCCCA	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24737258_24737263delCCCCCA	uc001rgb.1	-											Homo sapiens cDNA FLJ32894 fis, clone TESTI2004994.																		CTTCGATTAGcccccacccccacccc	0.432													4	2	---	---	---	---	
PKP2	5318	broad.mit.edu	37	12	32994260	32994261	+	Intron	INS	-	G	G	rs143525894	by1000genomes	TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32994260_32994261insG	uc001rlj.3	-						PKP2_uc001rlk.3_Intron|PKP2_uc010skj.1_Intron	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b						cell-cell adhesion	desmosome|integral to membrane|nucleus	binding			ovary(1)|pancreas(1)	2	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					TTTGGGGGGTTGGGGGGCCAGC	0.465													4	4	---	---	---	---	
GLI1	2735	broad.mit.edu	37	12	57859127	57859127	+	Intron	DEL	G	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57859127delG	uc001snx.2	+						GLI1_uc009zpq.2_Intron	NM_005269	NP_005260	P08151	GLI1_HUMAN	GLI family zinc finger 1 isoform 1						epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	transcription regulatory region DNA binding|zinc ion binding			skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1)	15			GBM - Glioblastoma multiforme(3;3.99e-32)			GGAAGGACAAGGGATATAAGT	0.498													8	4	---	---	---	---	
LOC283392	283392	broad.mit.edu	37	12	72666481	72666483	+	Intron	DEL	AAG	-	-	rs111457826		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72666481_72666483delAAG	uc010stv.1	-						TRHDE_uc001sxa.2_5'Flank	NR_026836				Homo sapiens thyrotropin-releasing hormone degrading enzyme, mRNA (cDNA clone IMAGE:4992272).												0						gaagaagaaaaagaagaggaaga	0.488													6	3	---	---	---	---	
LCP1	3936	broad.mit.edu	37	13	46704724	46704724	+	Intron	DEL	T	-	-	rs35095925		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46704724delT	uc001vaz.3	-						LCP1_uc010ack.2_Intron|LCP1_uc001vay.3_Intron|LCP1_uc001vba.3_Intron	NM_002298	NP_002289	P13796	PLSL_HUMAN	L-plastin						regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)		TATTGGGTTGTTTTTTTTTTT	0.338			T	BCL6	NHL 								4	3	---	---	---	---	
HEATR5A	25938	broad.mit.edu	37	14	31819967	31819970	+	Intron	DEL	TTTG	-	-	rs72055697		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31819967_31819970delTTTG	uc001wrf.3	-						HEATR5A_uc010ami.2_Intron|HEATR5A_uc001wrg.1_Intron|HEATR5A_uc010tpk.1_Intron	NM_015473	NP_056288	Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A								binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		TAGGTAAGTTtttgtttgtttgtt	0.176													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	32635922	32635922	+	5'Flank	DEL	T	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32635922delT	uc001zfv.1	-						uc001zfw.1_5'Flank					Homo sapiens cDNA FLJ43588 fis, clone SKNSH2009991.																		CATAACGCTCTTTTTTTTTTT	0.413													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	7987448	7987449	+	IGR	INS	-	CTTC	CTTC	rs138580127	by1000genomes	TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7987448_7987449insCTTC								A2BP1 (224108 upstream) : TMEM114 (632054 downstream)																							ttccttcttttcttccttcctt	0.173													4	3	---	---	---	---	
RPL27	6155	broad.mit.edu	37	17	41154524	41154524	+	Intron	DEL	A	-	-	rs76067241		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41154524delA	uc002icj.2	+						RPL27_uc002ick.2_Intron	NM_000988	NP_000979	P61353	RL27_HUMAN	ribosomal protein L27						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	structural constituent of ribosome				0		Breast(137;0.000717)|Ovarian(249;0.0776)		BRCA - Breast invasive adenocarcinoma(366;0.157)		actccgtctcaaaaaaaaaaa	0.204													4	2	---	---	---	---	
TBCB	1155	broad.mit.edu	37	19	36606379	36606380	+	5'UTR	INS	-	CAG	CAG			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36606379_36606380insCAG	uc002odg.1	+	1					POLR2I_uc002ode.2_5'Flank|POLR2I_uc002odf.2_5'Flank|TBCB_uc002odh.1_5'Flank	NM_001281	NP_001272	Q99426	TBCB_HUMAN	cytoskeleton associated protein 1						'de novo' posttranslational protein folding|cell differentiation|nervous system development	cytoplasm|microtubule	protein binding				0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GGCTGATAGCCCAGCAGCAGCA	0.733													5	3	---	---	---	---	
SNRPD2	6633	broad.mit.edu	37	19	46191995	46191995	+	Intron	DEL	T	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46191995delT	uc002pcw.2	-						SNRPD2_uc002pcv.2_Intron	NM_004597	NP_004588	P62316	SMD2_HUMAN	small nuclear ribonucleoprotein D2 isoform 1						ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	catalytic step 2 spliceosome|cytosol|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	protein binding				0		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00546)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.194)		ctaacagacattttttttttt	0.174													5	4	---	---	---	---	
PLK1S1	55857	broad.mit.edu	37	20	21146788	21146789	+	Intron	INS	-	T	T	rs145883029		TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21146788_21146789insT	uc002wsb.2	+						PLK1S1_uc010zsh.1_Intron|PLK1S1_uc010zsi.1_Intron|PLK1S1_uc010zsj.1_Intron|uc002wsc.2_Intron|PLK1S1_uc002wsd.2_Intron	NM_018474	NP_060944	Q2M2Z5	KIZ_HUMAN	polo-like kinase 1 substrate 1 isoform 1						spindle organization	centrosome	protein kinase binding				0						tgtattttGTATTTTTTTTTTT	0.153													8	5	---	---	---	---	
TYMP	1890	broad.mit.edu	37	22	50968827	50968828	+	5'Flank	DEL	AG	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50968827_50968828delAG	uc003bmb.3	-						TYMP_uc003bmc.3_5'Flank|TYMP_uc003bmd.3_5'Flank|TYMP_uc010hbd.2_5'Flank|TYMP_uc003bme.3_5'Flank|TYMP_uc003bmf.3_5'Flank|TYMP_uc011arz.1_5'Flank	NM_001113756	NP_001107228	P19971	TYPH_HUMAN	endothelial cell growth factor 1						angiogenesis|cell differentiation|chemotaxis|DNA replication|mitochondrial genome maintenance|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol	growth factor activity|platelet-derived growth factor receptor binding|pyrimidine-nucleoside phosphorylase activity|thymidine phosphorylase activity			ovary(1)	1		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Docetaxel(DB01248)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Sulfasalazine(DB00795)|Tamoxifen(DB00675)	CAGGACGCGCAGAGAGAGAGAG	0.708													4	2	---	---	---	---	
DHRSX	207063	broad.mit.edu	37	X	2209751	2209751	+	Intron	DEL	T	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2209751delT	uc004cqf.3	-							NM_145177	NP_660160	Q8N5I4	DHRSX_HUMAN	dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				GAAGTAACACttttttttttt	0.164													11	14	---	---	---	---	
REPS2	9185	broad.mit.edu	37	X	17086437	17086437	+	Intron	DEL	A	-	-			TCGA-B0-5710-01A-11D-1669-08	TCGA-B0-5710-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17086437delA	uc004cxv.1	+						REPS2_uc004cxw.1_Intron|REPS2_uc011miw.1_Intron	NM_004726	NP_004717	Q8NFH8	REPS2_HUMAN	RALBP1 associated Eps domain containing 2						epidermal growth factor receptor signaling pathway|protein complex assembly	cytoplasm	calcium ion binding|protein binding			skin(2)|central_nervous_system(1)	3	Hepatocellular(33;0.183)					actctgtctcaaaaaaaaaaa	0.124													4	2	---	---	---	---	
