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
SPEN	23013	broad.mit.edu	37	1	16258202	16258202	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16258202C>A	uc001axk.1	+	11	5671	c.5467C>A	c.(5467-5469)CGT>AGT	p.R1823S	SPEN_uc010obp.1_Missense_Mutation_p.R1782S	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1823					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CAAAAGCAAGCGTTCAAAGAC	0.507													3	81	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19455493	19455493	+	Silent	SNP	G	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19455493G>C	uc001bbi.2	-	61	8986	c.8982C>G	c.(8980-8982)GTC>GTG	p.V2994V	UBR4_uc001bbk.1_Silent_p.V641V	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	2994					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GGATGGCCCGGACACCGCCAA	0.512													4	97	---	---	---	---	PASS
PLA2G2F	64600	broad.mit.edu	37	1	20470069	20470069	+	Silent	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20470069G>A	uc009vpp.1	+	3	398	c.300G>A	c.(298-300)AAG>AAA	p.K100K		NM_022819	NP_073730	Q9BZM2	PA2GF_HUMAN	phospholipase A2, group IIF	57					lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|phospholipase A2 activity			ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.000524)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)		GCCAGCCCAAGGATGAGGTGG	0.637													8	73	---	---	---	---	PASS
EIF4G3	8672	broad.mit.edu	37	1	21268372	21268372	+	Silent	SNP	C	T	T	rs150884106	byFrequency	TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21268372C>T	uc001bec.2	-	9	1363	c.1107G>A	c.(1105-1107)ACG>ACA	p.T369T	EIF4G3_uc010odi.1_5'UTR|EIF4G3_uc010odj.1_Silent_p.T368T|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Silent_p.T369T|EIF4G3_uc001bef.2_Silent_p.T368T|EIF4G3_uc001bee.2_Silent_p.T375T|EIF4G3_uc001beg.2_Silent_p.T368T|EIF4G3_uc010odk.1_Silent_p.T369T|EIF4G3_uc001beh.2_Silent_p.T380T	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4	369					interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		CAATGCTCTCCGTGGCTGATA	0.383													21	174	---	---	---	---	PASS
MYOM3	127294	broad.mit.edu	37	1	24410862	24410862	+	Intron	SNP	T	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24410862T>A	uc001bin.3	-						MYOM3_uc001bim.3_Intron|MYOM3_uc001bio.2_Intron|MYOM3_uc001bip.1_Missense_Mutation_p.Q346L	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3											skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		aactgtgagctgattaaacct	0.070													3	12	---	---	---	---	PASS
IL28RA	163702	broad.mit.edu	37	1	24484205	24484205	+	Silent	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24484205T>C	uc001bis.2	-	7	991	c.978A>G	c.(976-978)GAA>GAG	p.E326E	IL28RA_uc001bir.2_Silent_p.E297E|IL28RA_uc001bit.2_3'UTR|IL28RA_uc001biu.2_Silent_p.E242E	NM_170743	NP_734464	Q8IU57	I28RA_HUMAN	interleukin 28 receptor, alpha isoform 1	326	Cytoplasmic (Potential).				cytokine-mediated signaling pathway|negative regulation of cell proliferation|regulation of defense response to virus by host	interleukin-28 receptor complex	protein binding|receptor activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00117)|all_lung(284;0.00151)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.21e-24)|Colorectal(126;6.61e-08)|COAD - Colon adenocarcinoma(152;3.56e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00918)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.185)		CCTCCTCCTCTTCGTCCTCTG	0.592													39	223	---	---	---	---	PASS
EXTL1	2134	broad.mit.edu	37	1	26355761	26355761	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26355761T>A	uc001blf.2	+	2	1724	c.857T>A	c.(856-858)TTC>TAC	p.F286Y		NM_004455	NP_004446	Q92935	EXTL1_HUMAN	exostoses-like 1	286	Lumenal (Potential).				skeletal system development	integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|protein binding			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		GCCTCGCGCTTCCTCCAAGCC	0.622													12	83	---	---	---	---	PASS
FOXJ3	22887	broad.mit.edu	37	1	42730816	42730816	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42730816T>A	uc001che.2	-	6	726	c.414A>T	c.(412-414)AAA>AAT	p.K138N	FOXJ3_uc001chf.2_Missense_Mutation_p.K138N|FOXJ3_uc001chg.2_Missense_Mutation_p.K138N|FOXJ3_uc001chh.1_Missense_Mutation_p.K138N	NM_014947	NP_055762	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	138	Fork-head.				embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ATCGAGGCACTTTAAGGAAAC	0.333													16	166	---	---	---	---	PASS
INADL	10207	broad.mit.edu	37	1	62341007	62341007	+	Silent	SNP	T	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62341007T>A	uc001dab.2	+	21	3042	c.2928T>A	c.(2926-2928)CTT>CTA	p.L976L	INADL_uc009waf.1_Silent_p.L976L|INADL_uc001daa.2_Silent_p.L976L|INADL_uc001dad.3_Silent_p.L673L|INADL_uc001dac.2_RNA	NM_176877	NP_795352	Q8NI35	INADL_HUMAN	InaD-like	976					intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4						TGGAAAATCTTAATTCATTAG	0.338													11	115	---	---	---	---	PASS
CLCA4	22802	broad.mit.edu	37	1	87025997	87025997	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87025997C>T	uc009wcs.2	+	3	448	c.404C>T	c.(403-405)CCT>CTT	p.P135L	CLCA4_uc009wct.2_5'UTR|CLCA4_uc009wcu.2_Intron	NM_012128	NP_036260	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	135						apical plasma membrane|extracellular region|integral to plasma membrane	chloride channel activity			ovary(2)	2		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		CACTTCACCCCTGACCTTCTA	0.383													12	90	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	145039633	145039633	+	5'UTR	SNP	C	T	T	rs2762750		TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145039633C>T	uc001elx.3	-	1					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_5'UTR|PDE4DIP_uc001eln.3_5'UTR|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TCCTTAGTCTCAGGACGCTCC	0.597			T	PDGFRB	MPD								6	43	---	---	---	---	PASS
LCE3E	353145	broad.mit.edu	37	1	152538366	152538366	+	3'UTR	SNP	T	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152538366T>G	uc001faa.2	-	2						NM_178435	NP_848522	Q5T5B0	LCE3E_HUMAN	late cornified envelope 3E						keratinization					ovary(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		Lung(1;0.000294)|LUAD - Lung adenocarcinoma(1;0.00527)|LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)		GGGATTCTTGTTTCCTCCAAA	0.577													14	114	---	---	---	---	PASS
TMEM79	84283	broad.mit.edu	37	1	156255181	156255181	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156255181C>T	uc010phi.1	+	2	360	c.164C>T	c.(163-165)TCT>TTT	p.S55F	SMG5_uc001foc.3_5'Flank|TMEM79_uc001fod.2_Intron|TMEM79_uc009wrw.2_Missense_Mutation_p.S55F	NM_032323	NP_115699	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	55						integral to membrane				central_nervous_system(1)	1	Hepatocellular(266;0.158)					TCAGCTGGATCTCCCACAGCC	0.642													6	72	---	---	---	---	PASS
COPA	1314	broad.mit.edu	37	1	160262375	160262375	+	Silent	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160262375G>A	uc009wti.2	-	28	3253	c.2859C>T	c.(2857-2859)GGC>GGT	p.G953G	COPA_uc001fvv.3_Silent_p.G962G	NM_004371	NP_004362	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha isoform	953					COPI coating of Golgi vesicle|intracellular protein transport|pancreatic juice secretion|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|extracellular space|microsome|soluble fraction	hormone activity|structural molecule activity			ovary(1)|skin(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GCTTGTAGGGGCCAAACTGGA	0.408													4	124	---	---	---	---	PASS
CACNA1E	777	broad.mit.edu	37	1	181732642	181732642	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181732642T>C	uc001gow.2	+	34	4955	c.4790T>C	c.(4789-4791)CTG>CCG	p.L1597P	CACNA1E_uc009wxs.2_Missense_Mutation_p.L1485P|CACNA1E_uc001gox.1_Missense_Mutation_p.L823P|CACNA1E_uc009wxt.2_Missense_Mutation_p.L823P	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	1597	Cytoplasmic (Potential).|IV.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6						CGCATTTTGCTGTGGACCTTT	0.498													3	43	---	---	---	---	PASS
NCOA1	8648	broad.mit.edu	37	2	24896299	24896299	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24896299A>G	uc002rfk.2	+	5	579	c.321A>G	c.(319-321)ATA>ATG	p.I107M	NCOA1_uc010eye.2_Missense_Mutation_p.I107M|NCOA1_uc002rfi.2_Translation_Start_Site|NCOA1_uc002rfj.2_Missense_Mutation_p.I107M|NCOA1_uc002rfl.2_Missense_Mutation_p.I107M	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1	107									PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAGGAGTGATAGAAAAGGAAT	0.338			T	PAX3	alveolar rhadomyosarcoma								3	123	---	---	---	---	PASS
C2orf39	92749	broad.mit.edu	37	2	26654795	26654795	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26654795A>T	uc002rhg.2	+	7	883	c.809A>T	c.(808-810)GAG>GTG	p.E270V	C2orf39_uc010eym.1_RNA	NM_145038	NP_659475	Q96MC2	CC164_HUMAN	hypothetical protein LOC92749	270	Potential.										0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAGGACTATGAGAAGCAGCTG	0.488													8	113	---	---	---	---	PASS
VWA3B	200403	broad.mit.edu	37	2	98828414	98828414	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98828414C>G	uc002syo.2	+	13	2023	c.1759C>G	c.(1759-1761)CTG>GTG	p.L587V	VWA3B_uc010yvh.1_Missense_Mutation_p.L437V|VWA3B_uc002syj.2_RNA|VWA3B_uc002syk.1_RNA|VWA3B_uc002syl.1_Missense_Mutation_p.L106V|VWA3B_uc002sym.2_Missense_Mutation_p.L587V|VWA3B_uc002syn.1_RNA|VWA3B_uc010yvi.1_Missense_Mutation_p.L244V|VWA3B_uc002syp.1_5'UTR|VWA3B_uc002syq.1_5'UTR|VWA3B_uc002syr.1_5'UTR	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	587	VWFA.									ovary(3)|large_intestine(2)|skin(1)	6						CACAAACACCCTGAGTGCCCT	0.428													9	86	---	---	---	---	PASS
RGPD5	84220	broad.mit.edu	37	2	113127775	113127775	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113127775G>C	uc002ths.1	-	23	5355	c.5278C>G	c.(5278-5280)CCT>GCT	p.P1760A	RGPD8_uc010fkk.1_Missense_Mutation_p.P1620A	NM_005054	NP_005045	Q99666	RGPD5_HUMAN	RANBP2-like and GRIP domain containing 5 isoform	1760					intracellular transport	cytoplasm	binding				0						GAACGGGAAGGATTTTCTTCC	0.308													3	52	---	---	---	---	PASS
LRP1B	53353	broad.mit.edu	37	2	141122269	141122269	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141122269C>T	uc002tvj.1	-	72	12064	c.11092G>A	c.(11092-11094)GAC>AAC	p.D3698N		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3698	Extracellular (Potential).|LDL-receptor class A 30.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TCTCCACAGTCGTCCTCTCCA	0.408										TSP Lung(27;0.18)			14	112	---	---	---	---	PASS
IGFBP2	3485	broad.mit.edu	37	2	217526552	217526552	+	Intron	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217526552C>T	uc010zjt.1	+						IGFBP2_uc010zju.1_3'UTR	NM_000597	NP_000588	P18065	IBP2_HUMAN	insulin-like growth factor binding protein 2,						positive regulation of activated T cell proliferation|regulation of cell growth|regulation of insulin-like growth factor receptor signaling pathway	extracellular space	insulin-like growth factor I binding|insulin-like growth factor II binding				0		Renal(323;0.0458)		Epithelial(149;2.9e-06)|all cancers(144;0.000223)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00968)		GTCCTCACTCCGGGCGTCCCC	0.502													4	23	---	---	---	---	PASS
PASK	23178	broad.mit.edu	37	2	242079960	242079960	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242079960G>T	uc002wao.1	-	3	497	c.405C>A	c.(403-405)TTC>TTA	p.F135L	PASK_uc010zol.1_Intron|PASK_uc010zom.1_Missense_Mutation_p.F135L|PASK_uc010fzl.1_Missense_Mutation_p.F135L|PASK_uc010zon.1_Intron|PASK_uc002waq.2_Missense_Mutation_p.F135L	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	135	PAS 1.				regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		CATCCACCGTGAAGATGGCCT	0.547													3	43	---	---	---	---	PASS
NKIRAS1	28512	broad.mit.edu	37	3	23942431	23942431	+	Silent	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23942431G>A	uc003ccj.2	-	4	606	c.204C>T	c.(202-204)GGC>GGT	p.G68G	NKIRAS1_uc003cck.2_Silent_p.G68G|NKIRAS1_uc003ccl.2_Silent_p.G68G|NKIRAS1_uc003ccm.2_Silent_p.G68G	NM_020345	NP_065078	Q9NYS0	KBRS1_HUMAN	kappa B-ras 1	68	Interactions with NFKBIA and NFKBIB.				I-kappaB kinase/NF-kappaB cascade|small GTPase mediated signal transduction	cytoplasm	GTP binding|GTPase activity				0						GCAGCTCCACGCCTTCCTGTA	0.413													4	134	---	---	---	---	PASS
SCN10A	6336	broad.mit.edu	37	3	38783881	38783881	+	Silent	SNP	G	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38783881G>T	uc003ciq.2	-	13	2007	c.2007C>A	c.(2005-2007)CTC>CTA	p.L669L		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	669	Helical; Name=S1 of repeat II; (Potential).|II.				sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)	AGGTGATGGTGAGCTCTGCAA	0.527													10	68	---	---	---	---	PASS
ACOX2	8309	broad.mit.edu	37	3	58490979	58490979	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58490979A>G	uc003dkl.2	-	15	2193	c.2018T>C	c.(2017-2019)CTT>CCT	p.L673P		NM_003500	NP_003491	Q99424	ACOX2_HUMAN	acyl-Coenzyme A oxidase 2	673					bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity|acyl-CoA dehydrogenase activity|pristanoyl-CoA oxidase activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		ACTTTGTAAAAGTGGTCTTAT	0.363													28	167	---	---	---	---	PASS
MYLK	4638	broad.mit.edu	37	3	123471302	123471302	+	Silent	SNP	G	A	A	rs149179973	byFrequency	TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123471302G>A	uc003ego.2	-	5	531	c.249C>T	c.(247-249)TGC>TGT	p.C83C	MYLK_uc011bjw.1_Silent_p.C83C|MYLK_uc003egp.2_Silent_p.C83C|MYLK_uc003egq.2_Silent_p.C83C|MYLK_uc003egr.2_Silent_p.C83C|MYLK_uc003egs.2_Intron|MYLK_uc010hrs.1_Silent_p.C83C|MYLK_uc003egu.1_Silent_p.C93C	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	83	Ig-like C2-type 1.				aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CCCGGATGCCGCAATCCAGCA	0.582													4	53	---	---	---	---	PASS
RFC4	5984	broad.mit.edu	37	3	186508173	186508173	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186508173T>C	uc003fqz.2	-	9	1047	c.824A>G	c.(823-825)GAT>GGT	p.D275G	RFC4_uc011bsc.1_Missense_Mutation_p.D275G	NM_002916	NP_002907	P35249	RFC4_HUMAN	replication factor C 4	275					cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|phosphatidylinositol-mediated signaling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|large_intestine(1)	5	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		AAATACTCCATCAATTTTCTC	0.428													6	68	---	---	---	---	PASS
TNK2	10188	broad.mit.edu	37	3	195594610	195594610	+	Silent	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195594610C>T	uc003fvu.1	-	12	3057	c.2514G>A	c.(2512-2514)CCG>CCA	p.P838P	TNK2_uc003fvq.1_Silent_p.P245P|TNK2_uc003fvr.1_Silent_p.P363P|TNK2_uc003fvs.1_Silent_p.P870P|TNK2_uc003fvt.1_Silent_p.P916P|TNK2_uc010hzw.1_RNA	NM_005781	NP_005772	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2 isoform 1	838	Pro-rich.|EBD domain (By similarity).			Missing (in Ref. 4; AAH08884).|PRA -> AG (in Ref. 1; AAA53570).	positive regulation of peptidyl-tyrosine phosphorylation|protein ubiquitination|small GTPase mediated signal transduction	adherens junction|cytoplasmic vesicle membrane|endosome|nucleus	ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1)	10	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	GACCAGCCCGCGGGCCAGGGG	0.652													4	38	---	---	---	---	PASS
UGT2B10	7365	broad.mit.edu	37	4	69692199	69692199	+	Silent	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69692199C>T	uc003hee.2	+	4	1096	c.1071C>T	c.(1069-1071)CCC>CCT	p.P357P	UGT2B10_uc011cam.1_Silent_p.P273P	NM_001075	NP_001066	P36537	UDB10_HUMAN	UDP glucuronosyltransferase 2B10 isoform 1	357					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(3)|ovary(2)	5						AGTGGATACCCCAGAATGACC	0.378													12	100	---	---	---	---	PASS
SMR3A	26952	broad.mit.edu	37	4	71232724	71232724	+	3'UTR	SNP	G	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71232724G>T	uc003hfg.1	+	3					SMR3B_uc011cas.1_Intron	NM_012390	NP_036522	Q99954	SMR3A_HUMAN	submaxillary gland androgen regulated protein 3							extracellular region					0		all_hematologic(202;0.196)				ACAGACAACTGCAACAGGTGC	0.453													7	52	---	---	---	---	PASS
TRIM2	23321	broad.mit.edu	37	4	154191516	154191516	+	5'UTR	SNP	C	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154191516C>A	uc003ing.2	+	2					TRIM2_uc003inh.2_Silent_p.G20G|TRIM2_uc003ini.1_Silent_p.G11G	NM_001130067	NP_001123539	Q9C040	TRIM2_HUMAN	tripartite motif-containing 2 isoform 2							cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		AGACAGCCGGCCCCCCATGTC	0.488													8	165	---	---	---	---	PASS
HMGCS1	3157	broad.mit.edu	37	5	43295906	43295906	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43295906T>A	uc003jnr.3	-	6	1060	c.853A>T	c.(853-855)AAT>TAT	p.N285Y	HMGCS1_uc003jnp.3_5'Flank|HMGCS1_uc003jnq.3_Missense_Mutation_p.N285Y	NM_001098272	NP_001091742	Q01581	HMCS1_HUMAN	hydroxymethylglutaryl-CoA synthase 1	285					cholesterol biosynthetic process|isoprenoid biosynthetic process	cytosol|soluble fraction	hydroxymethylglutaryl-CoA synthase activity				0						TTCTGGTCATTAAGGAAGTCA	0.353													16	106	---	---	---	---	PASS
NDUFAF2	91942	broad.mit.edu	37	5	60394842	60394842	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60394842A>G	uc003jsp.3	+	3	368	c.241A>G	c.(241-243)ACT>GCT	p.T81A	NDUFAF2_uc003jso.3_RNA	NM_174889	NP_777549	Q8N183	MIMIT_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha	81						membrane|mitochondrion	electron carrier activity|NADH dehydrogenase (ubiquinone) activity				0		Lung NSC(810;3.36e-05)|Prostate(74;0.0225)|Ovarian(174;0.17)|Breast(144;0.237)				AACAAGAAAGACTCCACCTAC	0.279													4	87	---	---	---	---	PASS
VCAN	1462	broad.mit.edu	37	5	82834030	82834030	+	Silent	SNP	T	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82834030T>A	uc003kii.3	+	8	5564	c.5208T>A	c.(5206-5208)TCT>TCA	p.S1736S	VCAN_uc003kij.3_Silent_p.S749S|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Silent_p.S400S	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	1736	GAG-beta.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)		GTACGGCTTCTACATTTGAGG	0.398													12	117	---	---	---	---	PASS
FTMT	94033	broad.mit.edu	37	5	121187839	121187839	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121187839C>T	uc003kss.2	+	1	190	c.181C>T	c.(181-183)CCC>TCC	p.P61S		NM_177478	NP_803431	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial precursor	61					cellular iron ion homeostasis|iron ion transport|positive regulation of cell proliferation|positive regulation of lyase activity|positive regulation of oxidoreductase activity|positive regulation of transferase activity	mitochondrion	ferric iron binding|ferroxidase activity			ovary(1)	1		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		CCCTACCGGGCCCGCCGCCGG	0.741													7	23	---	---	---	---	PASS
ZNF608	57507	broad.mit.edu	37	5	124079840	124079840	+	Silent	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124079840C>T	uc003ktq.1	-	1	966	c.843G>A	c.(841-843)TTG>TTA	p.L281L	ZNF608_uc003ktr.1_RNA|ZNF608_uc003kts.1_Silent_p.L281L|ZNF608_uc003ktt.1_Silent_p.L281L	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	281	Potential.					intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		CCTTCTTTACCAACATAGAGT	0.552													27	295	---	---	---	---	PASS
SRA1	10011	broad.mit.edu	37	5	139930679	139930679	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139930679G>T	uc003lga.2	-	4	1072	c.466C>A	c.(466-468)CCT>ACT	p.P156T	SRA1_uc003lfz.2_Missense_Mutation_p.P82T|SRA1_uc010jfm.2_Missense_Mutation_p.P82T	NM_001035235	NP_001030312	Q9HD15	SRA1_HUMAN	steroid receptor RNA activator 1	156					apoptosis|cell differentiation|cell proliferation|transcription, DNA-dependent	cytoplasm|ribonucleoprotein complex	receptor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCTTTACAGGTATTGACAAC	0.517													16	112	---	---	---	---	PASS
PCDHA6	56142	broad.mit.edu	37	5	140209579	140209579	+	Missense_Mutation	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140209579C>T	uc003lho.2	+	1	1930	c.1903C>T	c.(1903-1905)CGT>TGT	p.R635C	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc011dab.1_Missense_Mutation_p.R635C	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	635	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCACCACTCGTGTCCTGGA	0.662													5	78	---	---	---	---	PASS
PCDHA8	56140	broad.mit.edu	37	5	140221216	140221216	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140221216A>C	uc003lhs.2	+	1	310	c.310A>C	c.(310-312)ATC>CTC	p.I104L	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhr.1_Missense_Mutation_p.I104L	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	104	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGTGCAGCATCCACCTGGA	0.567													7	204	---	---	---	---	PASS
PCDHA12	56137	broad.mit.edu	37	5	140255242	140255242	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140255242G>A	uc003lic.2	+	1	312	c.185G>A	c.(184-186)CGC>CAC	p.R62H	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc011daf.1_Missense_Mutation_p.R62H	NM_018903	NP_061726	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12 isoform 1 precursor	62	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGTGCCGCGCCTGTTCCGG	0.612													4	134	---	---	---	---	PASS
PCDHB9	56127	broad.mit.edu	37	5	140568303	140568303	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140568303G>A	uc003liw.1	+	3	1412	c.1412G>A	c.(1411-1413)GGC>GAC	p.G471D		NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	471	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGCACATCGGCAGTGTCAGC	0.657													28	202	---	---	---	---	PASS
CCNJL	79616	broad.mit.edu	37	5	159680734	159680734	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159680734G>A	uc003lyb.1	-	7	1211	c.959C>T	c.(958-960)CCC>CTC	p.P320L	CCNJL_uc011dee.1_Missense_Mutation_p.P272L|CCNJL_uc003lyc.1_RNA	NM_024565	NP_078841	Q8IV13	CCNJL_HUMAN	cyclin J-like	320						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)			GGGGGTGGGGGGTGTGCCGGG	0.632													4	60	---	---	---	---	PASS
SLC17A1	6568	broad.mit.edu	37	6	25830810	25830810	+	5'UTR	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25830810T>C	uc003nfh.3	-	2					SLC17A1_uc011djy.1_RNA|SLC17A1_uc010jqb.1_5'UTR|SLC17A1_uc010jqc.1_5'UTR	NM_005074	NP_005065	Q14916	NPT1_HUMAN	solute carrier family 17 (sodium phosphate),						sodium ion transport|urate metabolic process	integral to plasma membrane|membrane fraction	sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(3)|pancreas(1)	4						GCTTCTCTTCTTGCTGAAGGG	0.448													14	112	---	---	---	---	PASS
HIST1H2AM	8336	broad.mit.edu	37	6	27860940	27860940	+	5'UTR	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27860940T>C	uc003nkb.1	-	1					HIST1H3J_uc003nka.2_5'Flank|HIST1H2BO_uc003nkc.1_5'Flank	NM_003514	NP_003505	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am						nucleosome assembly	nucleosome|nucleus	DNA binding|enzyme binding			ovary(2)	2						TAAAACGACCTGTGGCCTAAG	0.557													5	37	---	---	---	---	PASS
MEP1A	4224	broad.mit.edu	37	6	46800830	46800830	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46800830G>A	uc010jzh.1	+	11	1206	c.1164G>A	c.(1162-1164)TGG>TGA	p.W388*	MEP1A_uc011dwg.1_Nonsense_Mutation_p.W110*|MEP1A_uc011dwh.1_Nonsense_Mutation_p.W416*|MEP1A_uc011dwi.1_Nonsense_Mutation_p.W288*	NM_005588	NP_005579	Q16819	MEP1A_HUMAN	meprin A alpha precursor	388	Extracellular (Potential).|MAM.				digestion|proteolysis	extracellular space|integral to plasma membrane|soluble fraction	metalloendopeptidase activity|zinc ion binding			pancreas(2)|ovary(1)	3			Lung(136;0.192)			ACCACAATTGGAAAATTGCCC	0.368													8	126	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51618022	51618022	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51618022T>C	uc003pah.1	-	57	9203	c.8927A>G	c.(8926-8928)AAG>AGG	p.K2976R	PKHD1_uc010jzn.1_Missense_Mutation_p.K959R|PKHD1_uc003pai.2_Missense_Mutation_p.K2976R	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	2976	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					TCGGCTGGACTTCCTGAAGGA	0.453													8	103	---	---	---	---	PASS
DST	667	broad.mit.edu	37	6	56501389	56501389	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56501389T>A	uc003pdf.2	-	22	2955	c.2927A>T	c.(2926-2928)GAG>GTG	p.E976V	DST_uc003pcz.3_Missense_Mutation_p.E798V|DST_uc011dxj.1_Missense_Mutation_p.E827V|DST_uc011dxk.1_Missense_Mutation_p.E838V|DST_uc003pcy.3_Missense_Mutation_p.E472V|DST_uc003pdb.2_Missense_Mutation_p.E472V|DST_uc003pdc.3_Missense_Mutation_p.E472V|DST_uc003pdd.3_Missense_Mutation_p.E472V	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	798					cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TATGTGCTGCTCCACACACTG	0.448													12	124	---	---	---	---	PASS
CASP8AP2	9994	broad.mit.edu	37	6	90573113	90573113	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90573113T>A	uc003pnr.2	+	7	1881	c.1685T>A	c.(1684-1686)TTG>TAG	p.L562*	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Nonsense_Mutation_p.L562*|CASP8AP2_uc011dzz.1_Nonsense_Mutation_p.L562*	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	562					cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		ATGAAAAAATTGAACTTAACT	0.358													3	13	---	---	---	---	PASS
AHI1	54806	broad.mit.edu	37	6	135784313	135784313	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135784313T>C	uc003qgi.2	-	8	1265	c.881A>G	c.(880-882)CAA>CGA	p.Q294R	AHI1_uc003qgh.2_Missense_Mutation_p.Q294R|AHI1_uc003qgj.2_Missense_Mutation_p.Q294R|AHI1_uc003qgk.3_RNA|AHI1_uc003qgl.3_Missense_Mutation_p.Q294R	NM_001134831	NP_001128303	Q8N157	AHI1_HUMAN	Abelson helper integration site 1 isoform a	294						adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)		TGTATCATCTTGCATGCTGTC	0.313													4	88	---	---	---	---	PASS
MIOS	54468	broad.mit.edu	37	7	7613096	7613096	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7613096G>A	uc003srf.2	+	4	1298	c.990G>A	c.(988-990)TGG>TGA	p.W330*	MIOS_uc010ktp.1_Nonsense_Mutation_p.W330*	NM_019005	NP_061878	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog	330											0						CCTTTGCGTGGCATCCAACAA	0.418													6	201	---	---	---	---	PASS
POM121L12	285877	broad.mit.edu	37	7	53103958	53103958	+	Silent	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53103958C>T	uc003tpz.2	+	1	610	c.594C>T	c.(592-594)TTC>TTT	p.F198F		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	POM121 membrane glycoprotein-like 12	198											0						CGTTGTGGTTCGAGGTCTCAG	0.637													12	112	---	---	---	---	PASS
CUX1	1523	broad.mit.edu	37	7	101925178	101925178	+	Missense_Mutation	SNP	T	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101925178T>G	uc003uyt.2	+	21	1887	c.1868T>G	c.(1867-1869)TTC>TGC	p.F623C	CUX1_uc011kkn.1_Missense_Mutation_p.F584C|CUX1_uc003uyw.2_Missense_Mutation_p.F577C|CUX1_uc003uyv.2_Missense_Mutation_p.F607C|CUX1_uc003uyu.2_Missense_Mutation_p.F621C|CUX1_uc003uyz.2_RNA	NM_001913	NP_001904	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform b	Error:Variant_position_missing_in_P39880_after_alignment					negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8						ATCGGCTTCTTCTACACACTG	0.647													19	39	---	---	---	---	PASS
MET	4233	broad.mit.edu	37	7	116371932	116371932	+	Intron	SNP	T	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116371932T>A	uc003vij.2	+						MET_uc010lkh.2_Intron|MET_uc011knc.1_Intron|MET_uc011knd.1_Intron|MET_uc011kne.1_Intron|MET_uc011knf.1_Intron|MET_uc011kng.1_Intron|MET_uc011knh.1_Intron|MET_uc011kni.1_Intron|MET_uc011knj.1_Intron|MET_uc010lkg.2_3'UTR|MET_uc011kna.1_Intron|MET_uc011knb.1_Intron	NM_000245	NP_000236	P08581	MET_HUMAN	met proto-oncogene isoform b precursor						axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding			upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			TTTCTGAGAGTAGCTGTGTCT	0.388			Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)				4	64	---	---	---	---	PASS
MET	4233	broad.mit.edu	37	7	116415115	116415115	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116415115T>A	uc003vij.2	+	15	3396	c.3209T>A	c.(3208-3210)GTG>GAG	p.V1070E	MET_uc010lkh.2_Missense_Mutation_p.V1088E|MET_uc011knj.1_Missense_Mutation_p.V640E	NM_000245	NP_000236	P08581	MET_HUMAN	met proto-oncogene isoform b precursor	1070	Cytoplasmic (Potential).				axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding	p.Q1029_G1105del(1)		upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			CAGCATGTAGTGATTGGGCCC	0.433			Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)				57	145	---	---	---	---	PASS
GALNT11	63917	broad.mit.edu	37	7	151807716	151807716	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151807716G>C	uc010lqg.1	+	7	1296	c.1066G>C	c.(1066-1068)GAA>CAA	p.E356Q	GALNT11_uc011kvm.1_Missense_Mutation_p.E275Q|GALNT11_uc003wku.2_Missense_Mutation_p.E356Q|GALNT11_uc003wkw.1_Missense_Mutation_p.E104Q	NM_022087	NP_071370	Q8NCW6	GLT11_HUMAN	N-acetylgalactosaminyltransferase 11	356	Catalytic subdomain B.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)		AGAAAATTTGGAAATATCATT	0.353													76	171	---	---	---	---	PASS
MSR1	4481	broad.mit.edu	37	8	16032735	16032735	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16032735C>G	uc003wwz.2	-	3	376	c.178G>C	c.(178-180)GTG>CTG	p.V60L	MSR1_uc010lsu.2_Missense_Mutation_p.V78L|MSR1_uc003wxa.2_Missense_Mutation_p.V60L|MSR1_uc003wxb.2_Missense_Mutation_p.V60L|MSR1_uc011kxz.1_Intron	NM_138715	NP_619729	P21757	MSRE_HUMAN	macrophage scavenger receptor 1 isoform type 1	60	Helical; Signal-anchor for type II membrane protein; (Potential).				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)		ACTGCAAACACGAGGAGGTAA	0.423													9	74	---	---	---	---	PASS
PHYHIP	9796	broad.mit.edu	37	8	22084409	22084409	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22084409A>G	uc003xbk.3	-	4	989	c.295T>C	c.(295-297)TAC>CAC	p.Y99H	PHYHIP_uc003xbj.3_Missense_Mutation_p.Y99H	NM_001099335	NP_001092805	Q92561	PHYIP_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein	99	Fibronectin type-III.										0				Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0629)		GACACCAGGTACTCCCCATCG	0.652													7	63	---	---	---	---	PASS
SGK3	23678	broad.mit.edu	37	8	67748020	67748020	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67748020T>C	uc003xwr.2	+	9	847	c.548T>C	c.(547-549)CTG>CCG	p.L183P	SGK3_uc003xwp.2_Missense_Mutation_p.L177P|SGK3_uc003xwt.2_Missense_Mutation_p.L183P|SGK3_uc003xwu.2_Missense_Mutation_p.L183P	NM_001033578	NP_001028750	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase 3 isoform	183	Protein kinase.				cell communication|response to stress	cytoplasmic membrane-bounded vesicle|early endosome	ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity			ovary(1)|large_intestine(1)|lung(1)|breast(1)	4	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)			AAACGGAAACTGGATGGAAAA	0.289													18	120	---	---	---	---	PASS
PABPC1	26986	broad.mit.edu	37	8	101724674	101724674	+	Silent	SNP	A	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101724674A>G	uc003yjs.1	-	7	1392	c.888T>C	c.(886-888)CTT>CTC	p.L296L	PABPC1_uc011lhc.1_Silent_p.L264L|PABPC1_uc011lhd.1_Silent_p.L251L|PABPC1_uc003yjt.1_Silent_p.L293L|PABPC1_uc003yju.2_RNA	NM_002568	NP_002559	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	296	RRM 4.				mRNA polyadenylation|mRNA stabilization|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|translation	catalytic step 2 spliceosome|cytosol	nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity				0	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TTTTCACATAAAGATTAACAC	0.338													40	229	---	---	---	---	PASS
ADCY8	114	broad.mit.edu	37	8	131880119	131880119	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131880119G>T	uc003ytd.3	-	9	2439	c.2183C>A	c.(2182-2184)GCA>GAA	p.A728E	ADCY8_uc010mds.2_Intron	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	728	Helical; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			ACTTTGTATTGCCGTGATAAA	0.358										HNSCC(32;0.087)			11	71	---	---	---	---	PASS
CDKN2A	1029	broad.mit.edu	37	9	21974753	21974753	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21974753A>C	uc003zpk.2	-	1	286	c.74T>G	c.(73-75)GTA>GGA	p.V25G	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_Missense_Mutation_p.V25G|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Intron	NM_000077	NP_000068	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 1	25	ANK 1.				cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(1112)|p.?(23)|p.V25fs*1(2)|p.R22fs*14(1)		haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3678		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CACCTCCTCTACCCGACCCCG	0.736		17							Uveal_Melanoma_Familial|Familial_Malignant_Melanoma_and_Tumors_of_the_Nervous_System|Hereditary_Melanoma	HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)			7	18	---	---	---	---	PASS
PRKACG	5568	broad.mit.edu	37	9	71628711	71628711	+	Missense_Mutation	SNP	C	T	T	rs138606760		TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71628711C>T	uc004agy.2	-	1	329	c.298G>A	c.(298-300)GAC>AAC	p.D100N		NM_002732	NP_002723	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic,	100	Protein kinase.				activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|gluconeogenesis|intracellular protein kinase cascade|male gonad development|nerve growth factor receptor signaling pathway|regulation of insulin secretion|spermatogenesis|transmembrane transport|triglyceride catabolic process|water transport	cytosol|nucleoplasm	ATP binding|cAMP-dependent protein kinase activity			ovary(1)|pancreas(1)|skin(1)	3						AACGGAAAGTCGATCGCCTGC	0.557													16	114	---	---	---	---	PASS
AGTPBP1	23287	broad.mit.edu	37	9	88193989	88193989	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88193989T>C	uc011ltd.1	-	23	3221	c.3188A>G	c.(3187-3189)CAT>CGT	p.H1063R	AGTPBP1_uc004aod.3_Missense_Mutation_p.H689R|AGTPBP1_uc011ltc.1_Intron|AGTPBP1_uc010mqc.2_Missense_Mutation_p.H1023R|AGTPBP1_uc011lte.1_Missense_Mutation_p.H1075R	NM_015239	NP_056054	Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	1063					C-terminal protein deglutamylation|cerebellar Purkinje cell differentiation|eye photoreceptor cell differentiation|mitochondrion organization|neuromuscular process|olfactory bulb development|protein side chain deglutamylation|proteolysis	cytosol|mitochondrion|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(4)|large_intestine(2)|skin(1)	7						TGGGGCGATATGGCTCAGTAT	0.328													15	73	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	88464491	88464491	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88464491T>A	uc004aoh.1	+	10	1781	c.678T>A	c.(676-678)AAT>AAA	p.N226K						RecName: Full=Kinesin-like protein KIF27;																		CTAAGTATAATATGAAATGTT	0.373													10	55	---	---	---	---	PASS
TDRD7	23424	broad.mit.edu	37	9	100235850	100235850	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100235850A>G	uc004axj.2	+	11	2246	c.2021A>G	c.(2020-2022)AAG>AGG	p.K674R	TDRD7_uc011lux.1_Missense_Mutation_p.K600R|TDRD7_uc010msp.1_5'UTR|TDRD7_uc011luy.1_Missense_Mutation_p.K23R	NM_014290	NP_055105	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	674					lens fiber cell differentiation|lens morphogenesis in camera-type eye|posttranscriptional regulation of gene expression|spermatogenesis	chromatoid body	mRNA binding			ovary(2)|pancreas(1)	3		Acute lymphoblastic leukemia(62;0.158)				GTGCCTTGTAAGGGTCTGAAC	0.423													3	160	---	---	---	---	PASS
CRAT	1384	broad.mit.edu	37	9	131864768	131864768	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131864768G>A	uc004bxh.2	-	5	823	c.541C>T	c.(541-543)CGA>TGA	p.R181*	CRAT_uc004bxg.2_Nonsense_Mutation_p.R160*|CRAT_uc004bxk.3_Nonsense_Mutation_p.R160*	NM_000755	NP_000746	P43155	CACP_HUMAN	carnitine acetyltransferase precursor	181					energy derivation by oxidation of organic compounds|fatty acid beta-oxidation using acyl-CoA oxidase|transport	endoplasmic reticulum|mitochondrial inner membrane|peroxisomal matrix	carnitine O-acetyltransferase activity			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	CCCGGCACTCGGCAGGAGGAC	0.607													44	362	---	---	---	---	PASS
ANKRD30A	91074	broad.mit.edu	37	10	37508065	37508065	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37508065A>T	uc001iza.1	+	34	3356	c.3257A>T	c.(3256-3258)AAG>ATG	p.K1086M		NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1142	Potential.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(7)|breast(1)|skin(1)	9						TTAAAAGAAAAGAATGCTGAA	0.353													22	240	---	---	---	---	PASS
RBP3	5949	broad.mit.edu	37	10	48388693	48388693	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48388693G>T	uc001jez.2	-	1	2299	c.2185C>A	c.(2185-2187)CTT>ATT	p.L729I		NM_002900	NP_002891	P10745	RET3_HUMAN	retinol-binding protein 3 precursor	729	4 X approximate tandem repeats.|3.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			large_intestine(1)|central_nervous_system(1)	2					Vitamin A(DB00162)	GCCTCAATAAGGTAGGTGAGC	0.632													6	81	---	---	---	---	PASS
EIF5AL1	143244	broad.mit.edu	37	10	81272911	81272911	+	3'UTR	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81272911G>A	uc009xrx.2	+	1					uc010qls.1_5'Flank	NM_001099692	NP_001093162	Q6IS14	IF5AL_HUMAN	eukaryotic translation initiation factor 5A-like						mRNA transport|peptidyl-lysine modification to hypusine|positive regulation of translational elongation|positive regulation of translational termination|protein transport|translational frameshifting|transmembrane transport	endoplasmic reticulum membrane|nuclear pore	ribosome binding|translation elongation factor activity				0	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)			GTGATCCTCCGAACCTGCAGA	0.557													5	29	---	---	---	---	PASS
RGR	5995	broad.mit.edu	37	10	86007363	86007363	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86007363C>A	uc001kdc.1	+	2	134	c.96C>A	c.(94-96)AGC>AGA	p.S32R	RGR_uc001kdb.1_Intron|RGR_uc001kdd.1_Missense_Mutation_p.S32R|RGR_uc001kde.1_Missense_Mutation_p.S32R	NM_001012720	NP_001012738	P47804	RGR_HUMAN	retinal G-protein coupled receptor isoform 2	32	Helical; Name=1; (Potential).				phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity|protein binding			ovary(1)	1						CCGGTCTCAGCCTCAATACCC	0.602													10	258	---	---	---	---	PASS
POLL	27343	broad.mit.edu	37	10	103345853	103345853	+	Missense_Mutation	SNP	T	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103345853T>A	uc001ktg.1	-	2	942	c.176A>T	c.(175-177)GAA>GTA	p.E59V	DPCD_uc010qpz.1_Intron|POLL_uc001ktd.1_5'Flank|POLL_uc001kte.1_5'Flank|POLL_uc001kth.1_Intron|POLL_uc001kti.1_Missense_Mutation_p.E59V|POLL_uc001ktj.1_Missense_Mutation_p.E59V|POLL_uc001ktf.2_Missense_Mutation_p.E59V|POLL_uc001ktk.1_Intron|POLL_uc010qqa.1_Intron|POLL_uc010qqb.1_Intron|POLL_uc001ktm.2_Missense_Mutation_p.E59V|POLL_uc001ktl.2_5'UTR|POLL_uc010qqc.1_5'UTR|POLL_uc010qqd.1_5'UTR|DPCD_uc001ktn.2_5'Flank	NM_013274	NP_037406	Q9UGP5	DPOLL_HUMAN	DNA-directed DNA polymerase lambda	59	BRCT.				DNA replication|nucleotide-excision repair|somatic hypermutation of immunoglobulin genes	nucleus	DNA binding|DNA-directed DNA polymerase activity|lyase activity|metal ion binding				0		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)		CTCAAAGAGTTCTGCCCGGGC	0.552								DNA_polymerases_(catalytic_subunits)					8	55	---	---	---	---	PASS
SORCS3	22986	broad.mit.edu	37	10	107005305	107005305	+	Silent	SNP	C	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107005305C>A	uc001kyi.1	+	21	3101	c.2874C>A	c.(2872-2874)CTC>CTA	p.L958L	SORCS3_uc010qqz.1_RNA	NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	958	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TGTAGCCTCTCATCACTTTGG	0.453													15	175	---	---	---	---	PASS
SORCS3	22986	broad.mit.edu	37	10	107005306	107005306	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107005306A>T	uc001kyi.1	+	21	3102	c.2875A>T	c.(2875-2877)ATC>TTC	p.I959F	SORCS3_uc010qqz.1_RNA	NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	959	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		GTAGCCTCTCATCACTTTGGA	0.453													15	173	---	---	---	---	PASS
OR4C16	219428	broad.mit.edu	37	11	55340433	55340433	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55340433C>A	uc010rih.1	+	1	830	c.830C>A	c.(829-831)ACA>AAA	p.T277K		NM_001004701	NP_001004701	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C,	277	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		all_epithelial(135;0.0748)				ACAGTTGGAACATCTTTTCTC	0.393													7	84	---	---	---	---	PASS
ESRRA	2101	broad.mit.edu	37	11	64082235	64082235	+	Silent	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64082235G>A	uc001nzq.1	+	5	771	c.594G>A	c.(592-594)GTG>GTA	p.V198V	ESRRA_uc001nzr.1_Silent_p.V197V|ESRRA_uc001nzs.1_Silent_p.V198V|ESRRA_uc009ypn.1_Intron	NM_004451	NP_004442	P11474	ERR1_HUMAN	estrogen-related receptor alpha	198					positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein domain specific binding|sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding				0						ATGCACTGGTGTCTCATCTGC	0.418													7	67	---	---	---	---	PASS
FAU	2197	broad.mit.edu	37	11	64888968	64888968	+	Intron	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64888968T>C	uc001ocx.2	-						FAU_uc001ocy.1_Missense_Mutation_p.E75G|MRPL49_uc001ocz.1_5'Flank|MRPL49_uc001oda.1_5'Flank	NM_001997	NP_001988	P35544	UBIM_HUMAN	ubiquitin-like protein fubi and ribosomal												0						CCTCTCTCACTCACCTCCAAG	0.577													9	65	---	---	---	---	PASS
CPT1A	1374	broad.mit.edu	37	11	68575043	68575043	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68575043C>T	uc001oog.3	-	4	515	c.345G>A	c.(343-345)TGG>TGA	p.W115*	CPT1A_uc001oof.3_Nonsense_Mutation_p.W115*|CPT1A_uc009ysj.2_Nonsense_Mutation_p.W115*	NM_001876	NP_001867	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A liver isoform	115	Helical; (Potential).				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)	TGAGGGCCACCCACAGGCCGG	0.602													7	48	---	---	---	---	PASS
NARS2	79731	broad.mit.edu	37	11	78176959	78176959	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78176959A>C	uc001ozi.2	-	11	1503	c.1127T>G	c.(1126-1128)TTC>TGC	p.F376C	NARS2_uc010rsq.1_Missense_Mutation_p.F149C	NM_024678	NP_078954	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial	376					asparaginyl-tRNA aminoacylation	mitochondrial matrix	asparagine-tRNA ligase activity|ATP binding|nucleic acid binding			ovary(2)	2	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	CCTCATGTAGAAAGGCTTGAG	0.423													11	67	---	---	---	---	PASS
PUS7L	83448	broad.mit.edu	37	12	44124418	44124418	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44124418G>C	uc001rnq.3	-	9	2356	c.1867C>G	c.(1867-1869)CTA>GTA	p.L623V	PUS7L_uc001rnr.3_Missense_Mutation_p.L623V|PUS7L_uc001rns.3_Missense_Mutation_p.L623V|PUS7L_uc009zkb.2_Missense_Mutation_p.L310V	NM_001098615	NP_001092085	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S.	623	TRUD.				pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			pancreas(1)	1	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		CATGTCTGTAGTCCATCTCTG	0.388													3	131	---	---	---	---	PASS
BEST3	144453	broad.mit.edu	37	12	70049005	70049005	+	Missense_Mutation	SNP	A	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70049005A>C	uc001svg.2	-	10	1916	c.1689T>G	c.(1687-1689)AGT>AGG	p.S563R	BEST3_uc001svd.1_Intron|BEST3_uc001sve.1_Intron|BEST3_uc001svf.2_Missense_Mutation_p.S350R|BEST3_uc010stm.1_Missense_Mutation_p.S457R	NM_032735	NP_116124	Q8N1M1	BEST3_HUMAN	vitelliform macular dystrophy 2-like 3 isoform	563	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	chloride channel activity				0	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			CTGTCTGGGGACTGGGGCCTC	0.537													5	81	---	---	---	---	PASS
RSRC2	65117	broad.mit.edu	37	12	123005091	123005091	+	Intron	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123005091G>A	uc001ucr.2	-						RSRC2_uc001uco.2_Intron|RSRC2_uc001ucp.2_5'UTR|RSRC2_uc001ucq.2_5'UTR|RSRC2_uc001ucs.2_5'UTR|RSRC2_uc001uct.2_Intron|RSRC2_uc001ucu.2_Intron	NM_023012	NP_075388	Q7L4I2	RSRC2_HUMAN	arginine/serine-rich coiled-coil 2 isoform a											ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)		ATCTGAGTCTGCAGCGTCTTC	0.333													6	141	---	---	---	---	PASS
FARP1	10160	broad.mit.edu	37	13	99083408	99083408	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99083408G>T	uc001vnj.2	+	18	2353	c.2017G>T	c.(2017-2019)GTG>TTG	p.V673L	FARP1_uc001vnh.2_Missense_Mutation_p.V673L	NM_005766	NP_005757	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF, and pleckstrin domain protein 1	673	DH.				regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			GCTGCAGAAGGTGTGTTACCT	0.602													3	31	---	---	---	---	PASS
SAV1	60485	broad.mit.edu	37	14	51131954	51131954	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51131954C>A	uc001wyg.1	-	3	639	c.478G>T	c.(478-480)GAA>TAA	p.E160*	SAV1_uc001wyh.1_Nonsense_Mutation_p.E160*	NM_021818	NP_068590	Q9H4B6	SAV1_HUMAN	WW45 protein	160					hippo signaling cascade	cytoplasm|nucleus	identical protein binding			breast(1)	1	all_epithelial(31;0.000611)|Breast(41;0.0333)					TGGTTGTATTCATAATATCTG	0.368													10	62	---	---	---	---	PASS
AHSA1	10598	broad.mit.edu	37	14	77929008	77929008	+	Silent	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77929008T>C	uc001xtw.2	+	4	538	c.378T>C	c.(376-378)GAT>GAC	p.D126D	AHSA1_uc010tvk.1_Silent_p.D126D	NM_012111	NP_036243	O95433	AHSA1_HUMAN	activator of heat shock 90kDa protein ATPase	126					protein folding|response to stress	cytosol|endoplasmic reticulum	ATPase activator activity|chaperone binding				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		TTGCCAAAGATGAGCCTGACA	0.458													19	80	---	---	---	---	PASS
ATG2B	55102	broad.mit.edu	37	14	96775900	96775900	+	Missense_Mutation	SNP	C	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96775900C>G	uc001yfi.2	-	29	4558	c.4193G>C	c.(4192-4194)GGT>GCT	p.G1398A		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	1398										ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AAGTACTGGACCACGTGAGGA	0.388													6	77	---	---	---	---	PASS
ASPG	374569	broad.mit.edu	37	14	104573557	104573557	+	Silent	SNP	C	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104573557C>A	uc001yoq.1	+	12	1368	c.1308C>A	c.(1306-1308)ACC>ACA	p.T436T	ASPG_uc001yoo.1_Silent_p.T464T|ASPG_uc001yop.1_Silent_p.T436T|ASPG_uc001yor.1_Silent_p.T436T	NM_001080464	NP_001073933	Q86U10	LPP60_HUMAN	60 kDa lysophospholipase	436	ANK 3.				lipid catabolic process		1-alkyl-2-acetylglycerophosphocholine esterase activity|asparaginase activity|lysophospholipase activity				0						ACGGCCAAACCCCACTGCACG	0.657													3	38	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105420172	105420172	+	Missense_Mutation	SNP	G	A	A	rs143515877	by1000genomes	TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105420172G>A	uc010axc.1	-	7	1736	c.1616C>T	c.(1615-1617)CCG>CTG	p.P539L	AHNAK2_uc001ypx.2_Missense_Mutation_p.P439L	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	539						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TTCCCTGCCCGGCATCCACCC	0.592													5	217	---	---	---	---	PASS
NARG2	79664	broad.mit.edu	37	15	60734524	60734524	+	Intron	SNP	A	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60734524A>C	uc002agp.2	-						NARG2_uc002ago.2_Intron|NARG2_uc002agq.3_3'UTR	NM_024611	NP_078887	Q659A1	NARG2_HUMAN	NMDA receptor regulated 2 isoform a							nucleus				ovary(1)|lung(1)	2						GAAAGTAAAAAAGGGCAGAAT	0.149													6	21	---	---	---	---	PASS
MESP1	55897	broad.mit.edu	37	15	90293454	90293454	+	Missense_Mutation	SNP	A	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90293454A>T	uc002bol.2	-	2	806	c.728T>A	c.(727-729)CTT>CAT	p.L243H		NM_018670	NP_061140	Q9BRJ9	MESP1_HUMAN	mesoderm posterior 1	243					cardiac atrium formation|cardiac cell fate determination|cardiac vascular smooth muscle cell differentiation|cardiac ventricle formation|cardioblast anterior-lateral migration|cardioblast migration to the midline involved in heart field formation|endothelial cell differentiation|gastrulation|growth involved in heart morphogenesis|heart looping|lateral mesoderm development|negative regulation of endodermal cell fate specification|negative regulation of mesodermal cell fate specification|negative regulation of transcription, DNA-dependent|neurogenesis|Notch signaling pathway|positive regulation of heart induction by negative regulation of canonical Wnt receptor signaling pathway|positive regulation of hepatocyte differentiation|positive regulation of Notch signaling pathway|positive regulation of striated muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|secondary heart field specification|sinoatrial node cell differentiation|sinus venosus morphogenesis		sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			GTCGCCCGGAAGGAGCTGTAG	0.662													10	97	---	---	---	---	PASS
UMOD	7369	broad.mit.edu	37	16	20362092	20362092	+	5'UTR	SNP	A	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20362092A>C	uc002dgz.2	-	2					UMOD_uc002dha.2_5'UTR|UMOD_uc002dhb.2_5'UTR	NM_003361	NP_003352	P07911	UROM_HUMAN	uromodulin precursor						cellular defense response|negative regulation of cell proliferation	anchored to membrane|apical plasma membrane|basolateral plasma membrane|cilium membrane|extrinsic to membrane|primary cilium|spindle pole	calcium ion binding			ovary(1)|skin(1)	2						TCAGGTCTAGATAGCACCTGC	0.512													3	40	---	---	---	---	PASS
RRN3P1	730092	broad.mit.edu	37	16	21817457	21817457	+	Silent	SNP	G	A	A	rs150520281	by1000genomes	TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21817457G>A	uc010vbl.1	-	7	603	c.106C>T	c.(106-108)CTG>TTG	p.L36L	uc002diq.3_Intron	NR_003370				SubName: Full=Putative uncharacterized protein ENSP00000219758;												0						CTTACATCCAGCTTGAGTAGT	0.254													4	30	---	---	---	---	PASS
RILP	83547	broad.mit.edu	37	17	1549693	1549693	+	3'UTR	SNP	C	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1549693C>G	uc002ftd.2	-	8					SCARF1_uc002fsy.1_5'Flank|SCARF1_uc002fsz.1_5'Flank|SCARF1_uc002fta.1_5'Flank|SCARF1_uc010cjv.1_5'Flank	NM_031430	NP_113618	Q96NA2	RILP_HUMAN	Rab interacting lysosomal protein						endosome to lysosome transport|protein transport	late endosome membrane|lysosomal membrane|phagocytic vesicle membrane	Rab GTPase binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GGAGCCCTGTCCTCATTTGAG	0.652													12	61	---	---	---	---	PASS
LLGL1	3996	broad.mit.edu	37	17	18144912	18144912	+	Silent	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18144912C>T	uc002gsp.2	+	18	2711	c.2650C>T	c.(2650-2652)CTG>TTG	p.L884L		NM_004140	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1	884	WD 13.				cortical actin cytoskeleton organization|exocytosis|protein complex assembly	cortical actin cytoskeleton	protein kinase binding|structural molecule activity			breast(2)|skin(2)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)	6	all_neural(463;0.228)					CCTCACCAACCTGGGTGACGT	0.642													5	73	---	---	---	---	PASS
CACNA1G	8913	broad.mit.edu	37	17	48683592	48683592	+	Intron	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48683592G>A	uc002irk.1	+						CACNA1G_uc002iri.1_Missense_Mutation_p.V1544I|CACNA1G_uc002irj.1_Intron|CACNA1G_uc002irl.1_Intron|CACNA1G_uc002irm.1_Intron|CACNA1G_uc002irn.1_Intron|CACNA1G_uc002iro.1_Intron|CACNA1G_uc002irp.1_Intron|CACNA1G_uc002irq.1_Intron|CACNA1G_uc002irr.1_Intron|CACNA1G_uc002irs.1_Intron|CACNA1G_uc002irt.1_Intron|CACNA1G_uc002irv.1_Intron|CACNA1G_uc002irw.1_Intron|CACNA1G_uc002iru.1_Intron|CACNA1G_uc002irx.1_Intron|CACNA1G_uc002iry.1_Intron|CACNA1G_uc002irz.1_Intron|CACNA1G_uc002isa.1_Intron|CACNA1G_uc002isb.1_Intron|CACNA1G_uc002isc.1_Intron|CACNA1G_uc002isd.1_Intron|CACNA1G_uc002ise.1_Intron|CACNA1G_uc002isf.1_Intron|CACNA1G_uc002isg.1_Intron|CACNA1G_uc002ish.1_Intron|CACNA1G_uc002isi.1_Intron|CACNA1G_uc002isj.2_Intron	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G						axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	GTCTCTAGCCGTCCttaaaga	0.308													4	5	---	---	---	---	PASS
TOB1	10140	broad.mit.edu	37	17	48940954	48940954	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48940954A>G	uc002isw.2	-	1	460	c.425T>C	c.(424-426)ATA>ACA	p.I142T	TOB1_uc010wmy.1_Missense_Mutation_p.I142T|TOB1_uc010wmz.1_Missense_Mutation_p.I142T	NM_005749	NP_005740	P50616	TOB1_HUMAN	transducer of ERBB2, 1	142					negative regulation of cell proliferation		SH3/SH2 adaptor activity			large_intestine(1)	1			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			TGGGTCACTTATGGGCATAAA	0.483											OREG0024576	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	59	---	---	---	---	PASS
RECQL5	9400	broad.mit.edu	37	17	73625306	73625306	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73625306T>C	uc010dgl.2	-	16	2353	c.2197A>G	c.(2197-2199)AAA>GAA	p.K733E	RECQL5_uc010dgk.2_Missense_Mutation_p.K706E|RECQL5_uc002jot.3_5'Flank	NM_004259	NP_004250	O94762	RECQ5_HUMAN	RecQ protein-like 5 isoform 1	733					DNA recombination|DNA repair	cytoplasm|nuclear membrane|nucleolus|nucleoplasm	ATP binding|ATP-dependent helicase activity|DNA helicase activity|nucleic acid binding			kidney(3)	3	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			GAGGAACTTTTTGCCTTCTTC	0.647								Other_identified_genes_with_known_or_suspected_DNA_repair_function					3	58	---	---	---	---	PASS
CYGB	114757	broad.mit.edu	37	17	74533652	74533652	+	5'UTR	SNP	G	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74533652G>T	uc002jru.1	-	1					CYGB_uc002jrv.1_Intron|PRCD_uc002jrw.1_Intron|PRCD_uc002jrx.2_5'Flank|PRCD_uc002jry.1_5'Flank	NM_134268	NP_599030	Q8WWM9	CYGB_HUMAN	cytoglobin						response to oxidative stress	cytoplasm	heme binding|oxygen binding|oxygen transporter activity|peroxidase activity				0						GCCCGGCTTTGCTCggcggcg	0.338													3	15	---	---	---	---	PASS
MGAT5B	146664	broad.mit.edu	37	17	74936814	74936814	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74936814G>A	uc002jti.2	+	13	1862	c.1759G>A	c.(1759-1761)GTG>ATG	p.V587M	MGAT5B_uc002jth.2_Missense_Mutation_p.V576M	NM_198955	NP_945193	Q3V5L5	MGT5B_HUMAN	N-acetylglucosaminyltranferase VB isoform 2	578	Lumenal (Potential).					Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(2)|skin(1)	3						CCCTTGCCAGGTGTTCTCCCA	0.557													17	128	---	---	---	---	PASS
WDR7	23335	broad.mit.edu	37	18	54424323	54424323	+	Silent	SNP	A	G	G	rs145083205		TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54424323A>G	uc002lgk.1	+	15	2710	c.2499A>G	c.(2497-2499)GTA>GTG	p.V833V	WDR7_uc010dpk.1_RNA|WDR7_uc002lgl.1_Silent_p.V833V	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	833										ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)		ACTGCACCGTATCGTTTGGCC	0.488													22	181	---	---	---	---	PASS
TSHZ1	10194	broad.mit.edu	37	18	72998494	72998494	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72998494G>A	uc002lly.2	+	2	1560	c.997G>A	c.(997-999)GAG>AAG	p.E333K		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	378						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		GGCCCTGAGTGAGTCAGCCAA	0.627													11	60	---	---	---	---	PASS
TCF3	6929	broad.mit.edu	37	19	1612391	1612391	+	Intron	SNP	C	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1612391C>A	uc002ltr.2	-						TCF3_uc002ltn.2_Translation_Start_Site|TCF3_uc002lto.2_Intron|TCF3_uc002ltt.3_Missense_Mutation_p.R543M|TCF3_uc002ltq.2_Intron|TCF3_uc002lts.1_Missense_Mutation_p.R458M	NM_003200	NP_003191	P15923	TFE2_HUMAN	transcription factor 3 isoform E12						B cell lineage commitment|B cell lineage commitment|G1 phase of mitotic cell cycle|immunoglobulin V(D)J recombination|muscle cell differentiation|positive regulation of B cell proliferation|positive regulation of cell cycle|positive regulation of muscle cell differentiation|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus|protein complex|transcription factor complex	bHLH transcription factor binding|DNA binding|E-box binding|identical protein binding|mitogen-activated protein kinase kinase kinase binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|vitamin D response element binding			lung(2)|breast(2)|ovary(1)|large_intestine(1)|skin(1)	7		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		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)		CTCCCGGTCCCTCAGGTCTTT	0.657			T	PBX1|HLF|TFPT	pre B-ALL								6	64	---	---	---	---	PASS
ZNF562	54811	broad.mit.edu	37	19	9763749	9763749	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9763749G>A	uc010xks.1	-	6	1320	c.1157C>T	c.(1156-1158)ACG>ATG	p.T386M	ZNF562_uc002mly.2_Missense_Mutation_p.T386M|ZNF562_uc002mlx.2_Missense_Mutation_p.T314M|ZNF562_uc010xkt.1_Missense_Mutation_p.T349M|ZNF562_uc010xku.1_Missense_Mutation_p.T317M|ZNF562_uc010xkv.1_Missense_Mutation_p.T385M|ZNF562_uc010xkw.1_Missense_Mutation_p.T270M	NM_001130032	NP_001123504	Q6V9R5	ZN562_HUMAN	zinc finger protein 562 isoform a	386	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						TTGAGTAAGCGTTGAAGATCT	0.413													4	129	---	---	---	---	PASS
CCDC130	81576	broad.mit.edu	37	19	13865150	13865150	+	Silent	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13865150T>C	uc002mxb.1	+	4	554	c.51T>C	c.(49-51)CCT>CCC	p.P17P	CCDC130_uc010xnf.1_Silent_p.P17P|CCDC130_uc002mxc.1_Silent_p.P17P|CCDC130_uc002mxd.1_5'UTR|CCDC130_uc010dzf.1_5'UTR	NM_030818	NP_110445	P13994	CC130_HUMAN	coiled-coil domain containing 130	17					response to virus		protein binding				0			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)			ACTTCAACCCTGAGAAGGTAA	0.502													4	81	---	---	---	---	PASS
UPF1	5976	broad.mit.edu	37	19	18960913	18960913	+	Missense_Mutation	SNP	A	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18960913A>G	uc002nkg.2	+	4	766	c.491A>G	c.(490-492)AAA>AGA	p.K164R	UPF1_uc002nkf.2_Missense_Mutation_p.K164R	NM_002911	NP_002902	Q92900	RENT1_HUMAN	regulator of nonsense transcripts 1	164	Sufficient for interaction with RENT2.				cell cycle|DNA repair|DNA replication|histone mRNA catabolic process|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational termination	chromatin|cytoplasmic mRNA processing body|exon-exon junction complex	ATP binding|ATP-dependent RNA helicase activity|chromatin binding|DNA binding|protein binding|protein binding|RNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2						GTGAGGGCAAAATGCAAAGAG	0.522													11	87	---	---	---	---	PASS
SF4	57794	broad.mit.edu	37	19	19427268	19427268	+	Missense_Mutation	SNP	T	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19427268T>G	uc002nmh.2	-	2	171	c.169A>C	c.(169-171)AAT>CAT	p.N57H	SF4_uc002nmi.2_5'UTR|SF4_uc002nmj.2_5'UTR|SF4_uc010xqr.1_RNA|SF4_uc010xqs.1_RNA	NM_172231	NP_757386	Q8IWZ8	SUGP1_HUMAN	splicing factor 4	57					nuclear mRNA splicing, via spliceosome	nucleoplasm|spliceosomal complex	RNA binding				0						GCCACCTGATTCTGCTTGGCT	0.527													10	91	---	---	---	---	PASS
ZNF568	374900	broad.mit.edu	37	19	37413679	37413679	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37413679T>C	uc002ofc.2	+	3	522	c.7T>C	c.(7-9)TCT>CCT	p.S3P	ZNF568_uc010efg.2_5'UTR|ZNF568_uc010xtn.1_Intron|ZNF568_uc002ofd.2_Intron|ZNF568_uc010efe.2_Intron|ZNF568_uc010eff.1_5'UTR	NM_198539	NP_940941	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	3					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTGAATGACATCTCAATCTTC	0.522													3	79	---	---	---	---	PASS
SIPA1L3	23094	broad.mit.edu	37	19	38591731	38591731	+	Missense_Mutation	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38591731G>A	uc002ohk.2	+	6	2403	c.1894G>A	c.(1894-1896)GCC>ACC	p.A632T		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	632	Rap-GAP.				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CTATTGCAAGGCCGGCCAGAG	0.617													9	32	---	---	---	---	PASS
CYP2A7	1549	broad.mit.edu	37	19	41450678	41450678	+	Intron	SNP	A	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41450678A>G	uc002opo.2	-						CYP2B7P1_uc002opq.2_RNA	NM_000764	NP_000755	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TTGAAAAACCAGACGCCTTCA	0.463													8	300	---	---	---	---	PASS
ZNF234	10780	broad.mit.edu	37	19	44660472	44660472	+	Silent	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44660472G>A	uc002oym.2	+	6	610	c.303G>A	c.(301-303)GGG>GGA	p.G101G	ZNF234_uc002oyl.3_Silent_p.G101G	NM_006630	NP_006621	Q14588	ZN234_HUMAN	zinc finger protein 234	101	KRNB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)				TTTACTGGGGGCAAATCTGGA	0.448													4	143	---	---	---	---	PASS
LILRB1	10859	broad.mit.edu	37	19	55147219	55147219	+	Intron	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55147219C>T	uc002qgj.2	+						LILRB1_uc010erp.1_Silent_p.L218L|LILRB1_uc002qgl.2_Intron|LILRB1_uc002qgk.2_Intron|LILRB1_uc002qgm.2_Intron|LILRB1_uc010erq.2_Intron|LILRB1_uc010err.2_Intron	NM_006669	NP_006660	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor,						regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity			large_intestine(1)|ovary(1)|skin(1)	3				GBM - Glioblastoma multiforme(193;0.0188)		CTCACTCTCTCCTGCTGTCCT	0.647										HNSCC(37;0.09)			3	17	---	---	---	---	PASS
PCSK2	5126	broad.mit.edu	37	20	17434533	17434533	+	Silent	SNP	C	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17434533C>T	uc002wpm.2	+	9	1352	c.1032C>T	c.(1030-1032)GAC>GAT	p.D344D	PCSK2_uc002wpl.2_Silent_p.D325D|PCSK2_uc010zrm.1_Silent_p.D309D	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	344	Catalytic.				enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	CCCTGTACGACGAGAGCTGCT	0.597													17	61	---	---	---	---	PASS
SGK2	10110	broad.mit.edu	37	20	42199332	42199332	+	Missense_Mutation	SNP	G	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42199332G>C	uc002xkv.2	+	6	835	c.616G>C	c.(616-618)GCC>CCC	p.A206P	SGK2_uc002xkt.2_RNA|SGK2_uc002xkr.2_Missense_Mutation_p.A146P|SGK2_uc010ggm.2_Missense_Mutation_p.A146P|SGK2_uc002xks.2_Missense_Mutation_p.A145P|SGK2_uc002xku.2_Missense_Mutation_p.A146P	NM_016276	NP_057360	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2 isoform	206	Protein kinase.				intracellular protein kinase cascade|response to oxidative stress		ATP binding|potassium channel regulator activity|protein serine/threonine kinase activity|sodium channel regulator activity			lung(3)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)	6		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			GGTGGCCAGCGCCATTGGCTA	0.627													19	79	---	---	---	---	PASS
PLTP	5360	broad.mit.edu	37	20	44538612	44538612	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44538612G>T	uc002xqn.1	-	4	378	c.298C>A	c.(298-300)CGC>AGC	p.R100S	PLTP_uc002xql.1_Missense_Mutation_p.R12S|PLTP_uc002xqm.1_Missense_Mutation_p.R120S|PLTP_uc002xqo.1_Missense_Mutation_p.R100S|PLTP_uc002xqp.1_Missense_Mutation_p.R100S|PLTP_uc002xqq.1_Missense_Mutation_p.R69S|PLTP_uc010zxj.1_Intron|PLTP_uc010ghj.1_Missense_Mutation_p.R100S	NM_006227	NP_006218	P55058	PLTP_HUMAN	phospholipid transfer protein isoform a	100					cellular lipid metabolic process|lipid transport	extracellular region	lipid binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)				CTCCGGAAGCGCAGCCCCAAG	0.532													13	63	---	---	---	---	PASS
PREX1	57580	broad.mit.edu	37	20	47292733	47292733	+	Missense_Mutation	SNP	G	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47292733G>T	uc002xtw.1	-	14	1686	c.1663C>A	c.(1663-1665)CAG>AAG	p.Q555K		NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	555	DEP 2.				actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GCCCTCACCTGAGCCAGCAGC	0.512													22	168	---	---	---	---	PASS
KCNJ15	3772	broad.mit.edu	37	21	39671492	39671492	+	Missense_Mutation	SNP	T	G	G			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39671492T>G	uc002ywv.2	+	4	611	c.309T>G	c.(307-309)AAT>AAG	p.N103K	KCNJ15_uc002yww.2_Missense_Mutation_p.N103K|KCNJ15_uc002ywx.2_Missense_Mutation_p.N103K	NM_002243	NP_002234	Q99712	IRK15_HUMAN	potassium inwardly-rectifying channel J15	103	Extracellular (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity			ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	6						CCATTTCAAATCATACCCCCT	0.493													12	101	---	---	---	---	PASS
GAL3ST1	9514	broad.mit.edu	37	22	30951966	30951966	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30951966C>A	uc003aig.1	-	4	386	c.246G>T	c.(244-246)AAG>AAT	p.K82N	GAL3ST1_uc003aih.1_Missense_Mutation_p.K82N|GAL3ST1_uc003aii.1_Missense_Mutation_p.K82N|GAL3ST1_uc010gvz.1_Missense_Mutation_p.K82N	NM_004861	NP_004852	Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	82	Lumenal (Potential).				protein N-linked glycosylation	Golgi membrane|integral to plasma membrane|membrane fraction	galactosylceramide sulfotransferase activity				0						TCTTGTGCGTCTTCAAGAACA	0.642													15	100	---	---	---	---	PASS
IFT27	11020	broad.mit.edu	37	22	37159081	37159081	+	Intron	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37159081T>C	uc003apv.1	-						IFT27_uc003apu.1_Intron|IFT27_uc003apw.1_3'UTR	NM_006860	NP_006851	Q9BW83	IFT27_HUMAN	RAB, member of RAS oncogene family-like 4						small GTPase mediated signal transduction	intraflagellar transport particle B|microtubule-based flagellum	GTP binding				0						ACAACCAAAATATGGCACTTC	0.542													4	44	---	---	---	---	PASS
PCDH19	57526	broad.mit.edu	37	X	99662750	99662750	+	Silent	SNP	G	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99662750G>A	uc010nmz.2	-	1	2522	c.846C>T	c.(844-846)AAC>AAT	p.N282N	PCDH19_uc004efw.3_Silent_p.N282N|PCDH19_uc004efx.3_Silent_p.N282N	NM_020766	NP_001098713	Q8TAB3	PCD19_HUMAN	protocadherin 19 isoform b	282	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7						GCGTGCGGTCGTTGACGTAGC	0.602													12	63	---	---	---	---	PASS
HAUS7	55559	broad.mit.edu	37	X	152719888	152719888	+	Missense_Mutation	SNP	T	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152719888T>C	uc004fho.1	-	9	1597	c.1039A>G	c.(1039-1041)ATC>GTC	p.I347V	HAUS7_uc004fhl.2_RNA|HAUS7_uc004fhm.2_RNA|HAUS7_uc004fhn.1_Missense_Mutation_p.I406V|HAUS7_uc004fhp.1_RNA	NM_017518	NP_059988	Q99871	HAUS7_HUMAN	HAUS augmin-like complex subunit 7	347					cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleolus|plasma membrane|spindle	thioesterase binding				0						CCCCAGCAGATCTGCTCGCCT	0.567													6	18	---	---	---	---	PASS
PNCK	139728	broad.mit.edu	37	X	152936765	152936765	+	Missense_Mutation	SNP	C	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152936765C>A	uc011myu.1	-	7	1024	c.838G>T	c.(838-840)GCC>TCC	p.A280S	PNCK_uc011myt.1_Missense_Mutation_p.A214S|PNCK_uc004fia.2_Missense_Mutation_p.A232S|PNCK_uc004fhz.3_Missense_Mutation_p.A95S|PNCK_uc010nuh.2_3'UTR|PNCK_uc011myv.1_3'UTR|PNCK_uc011myw.1_3'UTR	NM_001039582	NP_001034671	Q6P2M8	KCC1B_HUMAN	pregnancy upregulated non-ubiquitously expressed	197	Protein kinase.					cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			breast(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ACGCCCAGGGCCCACACATCT	0.642													4	28	---	---	---	---	PASS
LAPTM5	7805	broad.mit.edu	37	1	31207795	31207796	+	Intron	INS	-	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31207795_31207796insA	uc001bsc.2	-							NM_006762	NP_006753	Q13571	LAPM5_HUMAN	lysosomal protein transmembrane 5						transport	integral to plasma membrane|lysosomal membrane					0		Colorectal(325;0.0199)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0966)|Medulloblastoma(700;0.151)|Ovarian(437;0.192)		STAD - Stomach adenocarcinoma(196;0.0196)|READ - Rectum adenocarcinoma(331;0.0649)		gcgcctcctggaatcgatatga	0.010													2	5	---	---	---	---	
SF3A3	10946	broad.mit.edu	37	1	38447614	38447615	+	Intron	INS	-	T	T	rs111640788		TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38447614_38447615insT	uc001cci.2	-						SF3A3_uc010oik.1_Intron	NM_006802	NP_006793	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3						nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nuclear speck	nucleic acid binding|protein binding|zinc ion binding				0	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GGCTAATTTTGGTTTTTTTTGC	0.307													5	3	---	---	---	---	
FAF1	11124	broad.mit.edu	37	1	51425565	51425567	+	Intron	DEL	CCG	-	-			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51425565_51425567delCCG	uc009vyx.1	-						FAF1_uc009vyw.1_5'Flank|FAF1_uc001cse.1_5'UTR	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity	p.0?(3)		ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		gtcgccgccaccgccgccgccgc	0.458													8	4	---	---	---	---	
ZRANB3	84083	broad.mit.edu	37	2	136148395	136148395	+	Intron	DEL	A	-	-			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136148395delA	uc002tum.2	-						ZRANB3_uc002tuk.2_Intron|ZRANB3_uc002tul.2_Intron|ZRANB3_uc002tun.1_Intron	NM_032143	NP_115519	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3							intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)		ATACACCTGGaaaaaaaaaaa	0.204													6	3	---	---	---	---	
ATOH1	474	broad.mit.edu	37	4	94750011	94750011	+	5'Flank	DEL	T	-	-			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94750011delT	uc003hta.1	+							NM_005172	NP_005163	Q92858	ATOH1_HUMAN	atonal homolog 1						transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.57e-07)		GGAAAGGGCCTTTTTTTTGGT	0.567													4	2	---	---	---	---	
SGMS2	166929	broad.mit.edu	37	4	108824688	108824689	+	Intron	DEL	TG	-	-			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108824688_108824689delTG	uc003hyl.3	+						uc003hym.1_Intron|SGMS2_uc003hyn.2_Intron|SGMS2_uc003hyo.2_Intron	NM_001136258	NP_001129730	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2						sphingomyelin biosynthetic process	integral to Golgi membrane|integral to plasma membrane	ceramide cholinephosphotransferase activity|kinase activity|sphingomyelin synthase activity			lung(1)	1				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)	Choline(DB00122)	tgaatgtgaatgtgtgtgtgtg	0.292													4	2	---	---	---	---	
SMAD5	4090	broad.mit.edu	37	5	135496896	135496898	+	Intron	DEL	ATA	-	-	rs149475910		TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135496896_135496898delATA	uc003lbj.1	+						SMAD5_uc003lbk.1_Intron|SMAD5_uc003lbl.1_Intron	NM_001001419	NP_001001419	Q99717	SMAD5_HUMAN	SMAD family member 5						BMP signaling pathway|embryonic pattern specification|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|transcription factor complex	sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ATGCCAAGGTATAATAGCTGTTT	0.315													5	10	---	---	---	---	
HACE1	57531	broad.mit.edu	37	6	105300074	105300075	+	Intron	INS	-	TGTG	TGTG	rs2499661	by1000genomes	TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105300074_105300075insTGTG	uc003pqu.1	-						HACE1_uc010kcy.1_Intron|HACE1_uc010kcz.1_Intron	NM_020771	NP_065822	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing, E3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	endoplasmic reticulum	ubiquitin-protein ligase activity			ovary(5)|lung(2)	7		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		TCCAAACtgtctgtgtgtgtgt	0.119													5	3	---	---	---	---	
SYTL3	94120	broad.mit.edu	37	6	159166782	159166783	+	Intron	INS	-	A	A	rs11481135		TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159166782_159166783insA	uc003qrp.2	+						SYTL3_uc011efp.1_Intron|SYTL3_uc003qro.2_Intron|SYTL3_uc003qrq.2_Intron|SYTL3_uc003qrr.2_Intron|SYTL3_uc003qrs.2_Intron|SYTL3_uc011efq.1_Intron	NM_001009991	NP_001009991	Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3						intracellular protein transport	endomembrane system|membrane	Rab GTPase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		agacaattattaaaaaaaaaaa	0.054													4	4	---	---	---	---	
RPS6KA2	6196	broad.mit.edu	37	6	166952428	166952429	+	Intron	INS	-	TT	TT			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166952428_166952429insTT	uc003qvb.1	-						RPS6KA2_uc011ego.1_Intron|RPS6KA2_uc010kkl.1_Intron|RPS6KA2_uc003qvc.1_Intron|RPS6KA2_uc003qvd.1_Intron	NM_021135	NP_066958	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide						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|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		GTGtttttttcttttttttttc	0.223													4	2	---	---	---	---	
FKBP6	8468	broad.mit.edu	37	7	72754919	72754920	+	Intron	INS	-	TTT	TTT	rs68028107		TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72754919_72754920insTTT	uc003tya.2	+						FKBP6_uc003twz.2_Intron|FKBP6_uc011kew.1_Intron|FKBP6_uc010lbe.1_Intron	NM_003602	NP_003593	O75344	FKBP6_HUMAN	FK506 binding protein 6 isoform a						protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)				AAAATGCTGtcttttttttttt	0.238													4	2	---	---	---	---	
ACTR3B	57180	broad.mit.edu	37	7	152513741	152513741	+	Intron	DEL	A	-	-			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152513741delA	uc003wle.1	+						ACTR3B_uc003wlf.1_Intron|ACTR3B_uc003wlg.1_Intron|ACTR3B_uc011kvp.1_Intron	NM_020445	NP_065178	Q9P1U1	ARP3B_HUMAN	actin-related protein 3-beta isoform 1						regulation of actin filament polymerization	cell projection|cytoplasm|cytoskeleton	actin binding|ATP binding				0		all_hematologic(28;0.0592)|Prostate(32;0.191)	OV - Ovarian serous cystadenocarcinoma(82;0.0287)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0434)		GGATGGAAATAAAAAAAAAAA	0.313													6	3	---	---	---	---	
TTF1	7270	broad.mit.edu	37	9	135273373	135273373	+	Intron	DEL	A	-	-			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135273373delA	uc004cbl.2	-						TTF1_uc011mcp.1_Intron|TTF1_uc004cbm.2_Intron	NM_007344	NP_031370	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase						negative regulation of DNA replication|regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription	nucleolus|nucleoplasm	DNA binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		actccgtctcaaaaaaaaaaa	0.119													4	2	---	---	---	---	
NRIP3	56675	broad.mit.edu	37	11	9005796	9005806	+	Intron	DEL	TTATTTTTTTT	-	-			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9005796_9005806delTTATTTTTTTT	uc001mhg.2	-						NRIP3_uc010rbu.1_Intron	NM_020645	NP_065696	Q9NQ35	NRIP3_HUMAN	nuclear receptor interacting protein 3						proteolysis		aspartic-type endopeptidase activity				0				Epithelial(150;4.77e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0241)		TGAGCATGTGttattttttttttattttttt	0.175													8	6	---	---	---	---	
SLC35F2	54733	broad.mit.edu	37	11	107686319	107686320	+	Intron	INS	-	A	A			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107686319_107686320insA	uc001pjq.2	-						SLC35F2_uc010rvu.1_Intron|SLC35F2_uc001pjs.2_Intron	NM_017515	NP_059985	Q8IXU6	S35F2_HUMAN	solute carrier family 35, member F2						transport	integral to membrane				central_nervous_system(1)	1		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)		aacacacacacaaaaaaaaaaa	0.149													4	2	---	---	---	---	
RBM19	9904	broad.mit.edu	37	12	114282321	114282322	+	Intron	INS	-	G	G	rs141502612	by1000genomes	TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114282321_114282322insG	uc009zwi.2	-						RBM19_uc001tvn.3_Intron|RBM19_uc001tvm.2_Intron	NM_001146699	NP_001140171	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19						multicellular organismal development|positive regulation of embryonic development	chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|RNA binding			skin(3)|ovary(1)|liver(1)|central_nervous_system(1)	6	Medulloblastoma(191;0.163)|all_neural(191;0.178)					gcaggtctggaggggctgtggg	0.238													3	3	---	---	---	---	
MEGF11	84465	broad.mit.edu	37	15	66257236	66257237	+	Intron	INS	-	A	A	rs138144863	by1000genomes	TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66257236_66257237insA	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821	A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1						CGCCCATTCCCAGCTCATACCT	0.673													3	4	---	---	---	---	
SEC14L5	9717	broad.mit.edu	37	16	5057607	5057608	+	Intron	INS	-	T	T			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5057607_5057608insT	uc002cye.2	+							NM_014692	NP_055507	O43304	S14L5_HUMAN	SEC14-like 5							integral to membrane|intracellular	transporter activity				0						ttctttctttcttttttttttt	0.094													5	3	---	---	---	---	
ATF7IP2	80063	broad.mit.edu	37	16	10532277	10532277	+	Intron	DEL	T	-	-			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10532277delT	uc002czu.2	+						ATF7IP2_uc002czv.2_Intron|ATF7IP2_uc010uyo.1_Intron|ATF7IP2_uc010uyp.1_Intron|ATF7IP2_uc002czw.2_Intron|ATF7IP2_uc010uyq.1_Intron	NM_024997	NP_079273	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						aatttttgggttttttttttt	0.000													3	3	---	---	---	---	
LOC283922	283922	broad.mit.edu	37	16	74372915	74372915	+	Intron	DEL	T	-	-	rs67181940		TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74372915delT	uc002fcr.2	-						LOC283922_uc010vms.1_Intron					Homo sapiens cDNA FLJ39449 fis, clone PROST2008360, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA.												0						ACGTAGtttgttttttttttt	0.204													6	4	---	---	---	---	
SLC35B1	10237	broad.mit.edu	37	17	47783728	47783728	+	Intron	DEL	G	-	-	rs138147992		TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47783728delG	uc002iph.1	-						SLC35B1_uc002ipi.1_Intron|SLC35B1_uc002ipj.1_Intron|SLC35B1_uc010wly.1_Intron	NM_005827	NP_005818	P78383	S35B1_HUMAN	solute carrier family 35, member B1							endoplasmic reticulum membrane|integral to membrane|microsome	UDP-galactose transmembrane transporter activity				0						aaaaaaaaaagaaaagaaaag	0.378													5	3	---	---	---	---	
C17orf99	100141515	broad.mit.edu	37	17	76154380	76154381	+	Intron	INS	-	A	A	rs113477288		TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76154380_76154381insA	uc002jus.3	+						C17orf99_uc010wts.1_5'Flank	NM_001163075	NP_001156547	Q6UX52	CQ099_HUMAN	hypothetical protein LOC100141515 precursor							extracellular region					0						TCCTCCTACACAtttttttttt	0.342													4	2	---	---	---	---	
FOXK2	3607	broad.mit.edu	37	17	80544130	80544130	+	Intron	DEL	C	-	-	rs57940566	by1000genomes	TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80544130delC	uc002kfn.2	+						FOXK2_uc002kfm.1_Intron|FOXK2_uc010diu.2_Intron	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			gaaaggtgggccgggggggga	0.149													4	3	---	---	---	---	
NAPG	8774	broad.mit.edu	37	18	10548534	10548534	+	Intron	DEL	A	-	-			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10548534delA	uc002kon.2	+						NAPG_uc010wzr.1_Intron|NAPG_uc002koo.2_Intron|NAPG_uc002kop.2_Intron	NM_003826	NP_003817	Q99747	SNAG_HUMAN	N-ethylmaleimide-sensitive factor attachment						cellular membrane fusion|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein complex assembly|protein stabilization	membrane|membrane fraction|mitochondrion	protein binding				0						GGTGTTTTACACCTTTTTTTT	0.363													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11610673	11610674	+	IGR	INS	-	C	C			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11610673_11610674insC								FAM38B (908694 upstream) : GNAL (78462 downstream)																							AAGACTGAAGACaaaaaaaaaa	0.302													4	2	---	---	---	---	
ANKLE1	126549	broad.mit.edu	37	19	17395193	17395193	+	Intron	DEL	T	-	-	rs68029926		TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17395193delT	uc002nga.2	+						ANKLE1_uc010xpm.1_Intron|ANKLE1_uc010eao.1_Intron|ANKLE1_uc010xpn.1_Intron|ANKLE1_uc002nfy.2_Intron|ANKLE1_uc002nfz.2_Intron	NM_152363	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat domain 41							nuclear envelope					0						Cttcttcttctttttttttat	0.199													5	4	---	---	---	---	
C20orf132	140699	broad.mit.edu	37	20	35742230	35742233	+	Intron	DEL	TCTG	-	-			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35742230_35742233delTCTG	uc010zvu.1	-						C20orf132_uc002xgk.2_Intron	NM_152503	NP_689716	Q9H579	CT132_HUMAN	hypothetical protein LOC140699 isoform 1												0		Myeloproliferative disorder(115;0.00878)				TGTATAtctatctgtctgtctgtc	0.039													6	3	---	---	---	---	
SREBF2	6721	broad.mit.edu	37	22	42289406	42289413	+	Intron	DEL	GTTTGTTT	-	-			TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42289406_42289413delGTTTGTTT	uc003bbi.2	+						WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|SREBF2_uc003bbj.2_Intron	NM_004599	NP_004590	Q12772	SRBP2_HUMAN	sterol regulatory element-binding transcription						cholesterol metabolic process	ER to Golgi transport vesicle membrane|Golgi membrane|nucleus|SREBP-SCAP-Insig complex	protein C-terminus binding			breast(2)|ovary(1)|central_nervous_system(1)	4						TGTTGAGTCCgtttgtttgtttgtttgt	0.250													4	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	28582961	28582962	+	IGR	INS	-	AT	AT	rs4008413		TCGA-CW-6087-01A-11D-1669-08	TCGA-CW-6087-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28582961_28582962insAT								None (None upstream) : None (None downstream)																							AAGTATAAAACAAAAACCTAAA	0.322													4	2	---	---	---	---	
