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
PRAMEF1	65121	broad.mit.edu	37	1	12853441	12853441	+	Missense_Mutation	SNP	C	A	A	rs75270454	byFrequency	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12853441C>A	uc001auj.1	+	2	168	c.65C>A	c.(64-66)GCC>GAC	p.A22D		NM_023013	NP_075389	O95521	PRAM1_HUMAN	PRAME family member 1	22											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGAGACCAGGCCTTGTCCATC	0.562													3	15	---	---	---	---	PASS
ZNF684	127396	broad.mit.edu	37	1	41007325	41007325	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41007325G>A	uc001cft.1	+	4	432	c.181G>A	c.(181-183)GAG>AAG	p.E61K		NM_152373	NP_689586	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	61	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			CCTCAAGGTAGAGCAAGGACA	0.498													21	72	---	---	---	---	PASS
STXBP3	6814	broad.mit.edu	37	1	109289328	109289328	+	5'UTR	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109289328G>A	uc001dvy.2	+	1					STXBP3_uc001dvz.2_RNA	NM_007269	NP_009200	O00186	STXB3_HUMAN	syntaxin binding protein 3						negative regulation of calcium ion-dependent exocytosis|neutrophil degranulation|platelet aggregation|protein transport|vesicle docking involved in exocytosis	cytosol|nucleus|platelet alpha granule|specific granule|tertiary granule	syntaxin-2 binding			ovary(3)|central_nervous_system(1)	4		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		GGGAGTGGAAGGTGGTGGCTG	0.687											OREG0013625	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	19	58	---	---	---	---	PASS
GNAT2	2780	broad.mit.edu	37	1	110151406	110151406	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110151406T>C	uc001dya.2	-	4	521	c.308A>G	c.(307-309)GAC>GGC	p.D103G		NM_005272	NP_005263	P19087	GNAT2_HUMAN	guanine nucleotide binding protein, alpha	103					detection of chemical stimulus involved in sensory perception of bitter taste|G-protein signaling, coupled to cAMP nucleotide second messenger|rhodopsin mediated phototransduction	heterotrimeric G-protein complex|photoreceptor inner segment|photoreceptor outer segment membrane	G-protein beta/gamma-subunit complex binding|G-protein coupled photoreceptor activity|G-protein-coupled receptor binding|GTP binding|GTPase activity				0		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0422)|Colorectal(144;0.108)|Epithelial(280;0.125)|all cancers(265;0.129)|LUSC - Lung squamous cell carcinoma(189;0.227)		CTGTCGCCCGTCATCCTGTAA	0.493													16	30	---	---	---	---	PASS
GSTM4	2948	broad.mit.edu	37	1	110199939	110199939	+	Intron	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110199939C>T	uc001dyf.2	+						GSTM4_uc009wfi.2_3'UTR|GSTM4_uc001dyg.2_Intron|GSTM4_uc009wfj.2_Intron|GSTM4_uc001dyh.2_Intron|GSTM2_uc001dyi.2_Intron	NM_000850	NP_000841	Q03013	GSTM4_HUMAN	glutathione S-transferase mu 4 isoform 1						xenobiotic metabolic process	endoplasmic reticulum membrane	glutathione transferase activity				0		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0123)|Colorectal(144;0.0129)|Epithelial(280;0.0147)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.0471)|LUSC - Lung squamous cell carcinoma(189;0.227)	Glutathione(DB00143)	GGGGAAAGTGCGACGTGTCTC	0.537													8	41	---	---	---	---	PASS
AMPD1	270	broad.mit.edu	37	1	115221022	115221022	+	Nonsense_Mutation	SNP	T	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115221022T>A	uc001efe.1	-	8	1108	c.1024A>T	c.(1024-1026)AAG>TAG	p.K342*	AMPD1_uc001eff.1_Nonsense_Mutation_p.K338*	NM_000036	NP_000027	P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1 (isoform M)	342					purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			ovary(2)|large_intestine(1)|skin(1)	4	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	AAAAGTTCCTTTAGGGTCAGA	0.383													33	94	---	---	---	---	PASS
HIST2H2AC	8338	broad.mit.edu	37	1	149858593	149858593	+	Silent	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149858593C>T	uc001etd.2	+	1	69	c.69C>T	c.(67-69)GGC>GGT	p.G23G	HIST2H2BE_uc001etc.2_5'Flank	NM_003517	NP_003508	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	23					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)|skin(1)	2	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			CCCGCGCTGGCCTCCAGTTCC	0.657													14	136	---	---	---	---	PASS
HIST2H2AB	317772	broad.mit.edu	37	1	149859278	149859278	+	Silent	SNP	A	G	G			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149859278A>G	uc001ete.2	-	1	189	c.189T>C	c.(187-189)ATT>ATC	p.I63I	HIST2H2BE_uc001etc.2_5'Flank	NM_175065	NP_778235	Q8IUE6	H2A2B_HUMAN	histone cluster 2, H2ab	63					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)|breast(1)	2	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			CCAGCTCCAGAATTTCCGCGG	0.637													9	118	---	---	---	---	PASS
HIST2H2AB	317772	broad.mit.edu	37	1	149859398	149859398	+	Silent	SNP	A	G	G			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149859398A>G	uc001ete.2	-	1	69	c.69T>C	c.(67-69)GGT>GGC	p.G23G	HIST2H2BE_uc001etc.2_5'Flank	NM_175065	NP_778235	Q8IUE6	H2A2B_HUMAN	histone cluster 2, H2ab	23					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)|breast(1)	2	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			GGAACTGGAGACCAGCGCGGG	0.652													6	71	---	---	---	---	PASS
HIST2H2AB	317772	broad.mit.edu	37	1	149859428	149859428	+	Silent	SNP	A	G	G			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149859428A>G	uc001ete.2	-	1	39	c.39T>C	c.(37-39)GCT>GCC	p.A13A	HIST2H2BE_uc001etc.2_5'Flank	NM_175065	NP_778235	Q8IUE6	H2A2B_HUMAN	histone cluster 2, H2ab	13					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)|breast(1)	2	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			ACTTGGCCTTAGCGCGGGCCT	0.587													9	48	---	---	---	---	PASS
UFC1	51506	broad.mit.edu	37	1	161123726	161123726	+	5'UTR	SNP	G	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161123726G>T	uc001fyd.3	+	1						NM_016406	NP_057490	Q9Y3C8	UFC1_HUMAN	ubiquitin-fold modifier conjugating enzyme 1						protein ufmylation		protein binding|UFM1 conjugating enzyme activity				0	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			TAAAGATGACGGCGCCTTGAG	0.502													13	21	---	---	---	---	PASS
PXDN	7837	broad.mit.edu	37	2	1652062	1652062	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1652062C>T	uc002qxa.2	-	17	3554	c.3490G>A	c.(3490-3492)GAC>AAC	p.D1164N		NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	1164					extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		ATCCCGTGGTCCCGGCCCCGC	0.597													12	20	---	---	---	---	PASS
DYSF	8291	broad.mit.edu	37	2	71825715	71825715	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71825715T>C	uc002sie.2	+	33	3918	c.3542T>C	c.(3541-3543)TTC>TCC	p.F1181S	DYSF_uc010feg.2_Missense_Mutation_p.F1212S|DYSF_uc010feh.2_Missense_Mutation_p.F1167S|DYSF_uc002sig.3_Missense_Mutation_p.F1167S|DYSF_uc010yqx.1_RNA|DYSF_uc010fee.2_Missense_Mutation_p.F1181S|DYSF_uc010fef.2_Missense_Mutation_p.F1198S|DYSF_uc010fei.2_Missense_Mutation_p.F1198S|DYSF_uc010fek.2_Missense_Mutation_p.F1199S|DYSF_uc010fej.2_Missense_Mutation_p.F1168S|DYSF_uc010fel.2_Missense_Mutation_p.F1168S|DYSF_uc010feo.2_Missense_Mutation_p.F1213S|DYSF_uc010fem.2_Missense_Mutation_p.F1182S|DYSF_uc010fen.2_Missense_Mutation_p.F1199S|DYSF_uc002sif.2_Missense_Mutation_p.F1182S|DYSF_uc010yqy.1_Missense_Mutation_p.F62S	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	1181	Cytoplasmic (Potential).|C2 4.					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7						ATCGTCTCCTTCCTGCACCAG	0.597													4	44	---	---	---	---	PASS
LOC401010	401010	broad.mit.edu	37	2	132201085	132201085	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132201085C>A	uc002tst.2	-	1	1383	c.917G>T	c.(916-918)CGT>CTT	p.R306L		NR_002826				SubName: Full=cDNA FLJ12694 fis, clone NT2RP1000358, highly similar to Homo sapiens mRNA; cDNA DKFZp564C186 (from clone DKFZp564C186);												0						CGTCAGGGCACGGATGCAGTG	0.597													9	14	---	---	---	---	PASS
MIR663B	100302269	broad.mit.edu	37	2	133015485	133015485	+	5'Flank	SNP	C	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133015485C>A	hsa-mir-663b|MI0006336	-						NCRNA00164_uc002ttj.3_RNA																	0						AACCCACACACAACCTGTCGG	0.697													4	41	---	---	---	---	PASS
BAZ2B	29994	broad.mit.edu	37	2	160240140	160240140	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160240140C>A	uc002uao.2	-	24	4090	c.3738G>T	c.(3736-3738)TGG>TGT	p.W1246C	BAZ2B_uc002uap.2_Missense_Mutation_p.W1210C	NM_013450	NP_038478	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1246					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4						CTTCTACCACCCATTTATCTC	0.308													36	103	---	---	---	---	PASS
SLC4A10	57282	broad.mit.edu	37	2	162696378	162696378	+	Silent	SNP	A	G	G			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162696378A>G	uc002ubx.3	+	4	541	c.357A>G	c.(355-357)ACA>ACG	p.T119T	SLC4A10_uc010fpa.1_Silent_p.T131T|SLC4A10_uc010zcr.1_RNA|SLC4A10_uc002uby.3_Silent_p.T119T|SLC4A10_uc010zcs.1_Silent_p.T130T	NM_022058	NP_071341	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate	119	Cytoplasmic (Potential).				bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5						ACCTTTTCACAGAACTGGATG	0.438													30	89	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179404327	179404327	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179404327T>G	uc010zfg.1	-	301	90985	c.90761A>C	c.(90760-90762)GAT>GCT	p.D30254A	uc002umo.2_RNA|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.D23949A|TTN_uc010zfi.1_Missense_Mutation_p.D23882A|TTN_uc010zfj.1_Missense_Mutation_p.D23757A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	31181							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACCACCATCATCAGCAGGAGG	0.527													19	55	---	---	---	---	PASS
ANKRD44	91526	broad.mit.edu	37	2	197946412	197946412	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197946412C>T	uc002uua.1	-	15	1497	c.1420G>A	c.(1420-1422)GAA>AAA	p.E474K	ANKRD44_uc002utz.3_Missense_Mutation_p.E206K|ANKRD44_uc002uub.2_Missense_Mutation_p.E499K|ANKRD44_uc010zgw.1_Missense_Mutation_p.E427K	NM_153697	NP_710181	Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	499							protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CTTTCAAGTTCTTCTGAATTA	0.363													18	117	---	---	---	---	PASS
EIF4E2	9470	broad.mit.edu	37	2	233431788	233431788	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233431788G>A	uc002vta.2	+	6	607	c.529G>A	c.(529-531)GAA>AAA	p.E177K	EIF4E2_uc002vtb.1_Missense_Mutation_p.E177K|EIF4E2_uc010zmi.1_Missense_Mutation_p.E132K	NM_004846	NP_004837	O60573	IF4E2_HUMAN	eukaryotic translation initiation factor 4E	177	7-methylguanosine-containing mRNA cap binding.				regulation of translation	cytoplasm|mRNA cap binding complex	RNA cap binding|translation initiation factor activity|ubiquitin protein ligase binding				0		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;2.3e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000912)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		CCTCTGGTAGGAAGACATTAT	0.507													20	37	---	---	---	---	PASS
COL6A3	1293	broad.mit.edu	37	2	238280964	238280964	+	Silent	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238280964C>T	uc002vwl.2	-	9	3981	c.3696G>A	c.(3694-3696)AGG>AGA	p.R1232R	COL6A3_uc002vwo.2_Silent_p.R1026R|COL6A3_uc010znj.1_Silent_p.R625R|COL6A3_uc002vwq.2_Silent_p.R1026R|COL6A3_uc002vwr.2_Silent_p.R825R	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1232	Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		AGACCACGTCCCTCTTGCCAC	0.542													8	11	---	---	---	---	PASS
C2orf85	285093	broad.mit.edu	37	2	242815348	242815348	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242815348G>C	uc010fzu.1	+	2	1664	c.1641G>C	c.(1639-1641)TGG>TGC	p.W547C		NM_173821	NP_776182	Q14D33	CB085_HUMAN	hypothetical protein LOC285093	547	Helical; (Potential).					integral to membrane				ovary(1)	1						TCTGGATCTGGGTGTCCATGA	0.662													7	11	---	---	---	---	PASS
KIF15	56992	broad.mit.edu	37	3	44847461	44847461	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44847461C>T	uc003cnx.3	+	16	2103	c.1954C>T	c.(1954-1956)CAT>TAT	p.H652Y	KIF15_uc010hiq.2_Missense_Mutation_p.H555Y|KIF15_uc003cny.1_Missense_Mutation_p.H287Y	NM_020242	NP_064627	Q9NS87	KIF15_HUMAN	kinesin family member 15	652	Potential.				blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		GAATAAAATTCATGCTGAAAC	0.383													17	18	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52437163	52437163	+	Nonsense_Mutation	SNP	G	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52437163G>C	uc003ddx.2	-	14	1996	c.1881C>G	c.(1879-1881)TAC>TAG	p.Y627*	BAP1_uc003ddw.2_Intron|BAP1_uc010hmg.2_RNA|BAP1_uc010hmh.2_Intron	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	627	Interaction with BRCA1.				monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CCTTGGGTGAGTATTTCTCCC	0.582			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								17	15	---	---	---	---	PASS
UGT2A1	10941	broad.mit.edu	37	4	70460937	70460937	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70460937C>T	uc003hem.3	-	4	1090	c.1027G>A	c.(1027-1029)GCC>ACC	p.A343T	UGT2A1_uc011caq.1_Missense_Mutation_p.A509T|UGT2A1_uc010ihu.2_Missense_Mutation_p.A343T|UGT2A1_uc010iht.2_Missense_Mutation_p.A299T|UGT2A1_uc010ihs.2_Missense_Mutation_p.A344T	NM_006798	NP_006789	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family,	343	Extracellular (Potential).				detection of chemical stimulus|sensory perception of smell	integral to membrane	glucuronosyltransferase activity|glucuronosyltransferase activity			ovary(1)	1						CCTAATGTGGCTGGTTTCTTT	0.378													46	86	---	---	---	---	PASS
HNRNPD	3184	broad.mit.edu	37	4	83280713	83280713	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83280713C>T	uc003hmm.1	-	3	688	c.370G>A	c.(370-372)GTA>ATA	p.V124I	HNRNPD_uc003hml.1_RNA|HNRNPD_uc003hmn.1_Missense_Mutation_p.V105I|HNRNPD_uc003hmo.1_Missense_Mutation_p.V124I|HNRNPD_uc003hmp.1_Missense_Mutation_p.V105I|HNRNPD_uc010ijr.1_Missense_Mutation_p.V105I|HNRNPD_uc011cci.1_Intron	NM_031370	NP_112738	Q14103	HNRPD_HUMAN	heterogeneous nuclear ribonucleoprotein D	124	RRM 1.				nuclear mRNA splicing, via spliceosome|positive regulation of transcription, DNA-dependent|RNA catabolic process|transcription, DNA-dependent	cytosol|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding|telomeric DNA binding				0						GTGCAGTCTACAACTTCACCA	0.398													15	74	---	---	---	---	PASS
SORBS2	8470	broad.mit.edu	37	4	186577860	186577860	+	Intron	SNP	G	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186577860G>T	uc003iyl.2	-						SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Intron|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cky.1_Intron|SORBS2_uc003iyp.2_Intron|SORBS2_uc011cku.1_5'UTR|SORBS2_uc011ckv.1_5'UTR|SORBS2_uc003iyd.2_Intron|SORBS2_uc003iye.2_Intron|SORBS2_uc003iya.2_Intron|SORBS2_uc003iyb.2_Intron|SORBS2_uc003iyc.2_Intron|SORBS2_uc003iyg.2_Intron|SORBS2_uc003iyf.2_Intron|SORBS2_uc003iyo.1_5'UTR	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2							actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TCAGCCAGCTGCTGCCTGCCC	0.557													5	16	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	5	179078891	179078891	+	Missense_Mutation	SNP	T	C	C	rs150053447	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179078891T>C	uc003mkj.1	+	1	349	c.140T>C	c.(139-141)CTG>CCG	p.L47P						RecName: Full=Putative uncharacterized protein LOC285679;																		TCACCAAACCTGACCAGCTCC	0.587													5	53	---	---	---	---	PASS
LRRC16A	55604	broad.mit.edu	37	6	25285102	25285102	+	Nonsense_Mutation	SNP	G	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25285102G>T	uc011djw.1	+	2	479	c.103G>T	c.(103-105)GAA>TAA	p.E35*	LRRC16A_uc010jpx.2_Nonsense_Mutation_p.E35*|LRRC16A_uc010jpy.2_Nonsense_Mutation_p.E35*	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	35					actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4						AGTAAAGTTGGAAGTTAAGGG	0.264													23	131	---	---	---	---	PASS
HIST1H2BJ	8970	broad.mit.edu	37	6	27100432	27100432	+	Missense_Mutation	SNP	C	T	T	rs137867381		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27100432C>T	uc003niv.2	-	1	144	c.98G>A	c.(97-99)AGC>AAC	p.S33N	HIST1H2BJ_uc003niu.1_RNA|HIST1H2AG_uc003niw.2_5'Flank	NM_021058	NP_066402	P06899	H2B1J_HUMAN	histone cluster 1, H2bj	33				KRKRS -> SAAH (in Ref. 1; CAA24950).	defense response to bacterium|nucleosome assembly	nucleosome|nucleus	DNA binding				0						CTCCTTGCGGCTGCGCTTGCG	0.557													19	12	---	---	---	---	PASS
CRISP2	7180	broad.mit.edu	37	6	49667553	49667553	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49667553T>C	uc003ozq.2	-	6	491	c.235A>G	c.(235-237)ACT>GCT	p.T79A	CRISP2_uc003ozl.2_Missense_Mutation_p.T79A|CRISP2_uc003ozn.2_Missense_Mutation_p.T79A|CRISP2_uc003ozr.2_Missense_Mutation_p.T79A|CRISP2_uc003ozo.2_Missense_Mutation_p.T79A|CRISP2_uc003ozm.2_Missense_Mutation_p.T79A|CRISP2_uc003ozp.2_Missense_Mutation_p.T79A	NM_001142408	NP_001135880	P16562	CRIS2_HUMAN	cysteine-rich secretory protein 2 precursor	79						extracellular space				skin(1)	1	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			TGTTGTAAAGTGCACTTGTTT	0.269													27	94	---	---	---	---	PASS
DPY19L1	23333	broad.mit.edu	37	7	35029520	35029520	+	Silent	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35029520C>T	uc003tem.3	-	7	724	c.579G>A	c.(577-579)TTG>TTA	p.L193L		NM_015283	NP_056098	Q2PZI1	D19L1_HUMAN	dpy-19-like 1	193	Helical; (Potential).					integral to membrane					0						AAAAGAAGCACAACACTGTAA	0.338													26	63	---	---	---	---	PASS
MYO1G	64005	broad.mit.edu	37	7	45005737	45005737	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45005737T>A	uc003tmh.2	-	16	2236	c.2092A>T	c.(2092-2094)ACA>TCA	p.T698S	MYO1G_uc003tmf.2_Missense_Mutation_p.T141S|MYO1G_uc003tmg.2_Missense_Mutation_p.T460S|MYO1G_uc010kym.2_Missense_Mutation_p.T583S|MYO1G_uc003tmi.1_3'UTR	NM_033054	NP_149043	B0I1T2	MYO1G_HUMAN	myosin IG	698						myosin complex|plasma membrane	actin binding|ATP binding|calmodulin binding|motor activity			breast(2)|ovary(1)|pancreas(1)	4						GTGACCAGTGTCCGGGGTGAG	0.642													8	27	---	---	---	---	PASS
FGL2	10875	broad.mit.edu	37	7	76826154	76826154	+	Silent	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76826154C>T	uc003ugb.2	-	2	802	c.762G>A	c.(760-762)CTG>CTA	p.L254L	CCDC146_uc003ufz.1_Intron|CCDC146_uc003uga.2_Intron	NM_006682	NP_006673	Q14314	FGL2_HUMAN	fibrinogen-like 2 precursor	254	Fibrinogen C-terminal.				signal transduction	fibrinogen complex	receptor binding			skin(2)	2						GACGTGCCTGCAGCACTGTCC	0.493													5	33	---	---	---	---	PASS
SMO	6608	broad.mit.edu	37	7	128845209	128845209	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128845209G>A	uc003vor.2	+	3	983	c.703G>A	c.(703-705)GCG>ACG	p.A235T	SMO_uc003vos.2_5'Flank	NM_005631	NP_005622	Q99835	SMO_HUMAN	smoothened precursor	235	Helical; Name=1; (Potential).				adenohypophysis development|axon extension involved in axon guidance|canonical Wnt receptor signaling pathway|cardioblast differentiation|central nervous system neuron differentiation|cerebellar cortex morphogenesis|ciliary receptor clustering involved in smoothened signaling pathway|determination of left/right symmetry|dorsal/ventral neural tube patterning|embryonic camera-type eye development|embryonic digestive tract morphogenesis|embryonic neurocranium morphogenesis|embryonic viscerocranium morphogenesis|exocrine pancreas development|facial nerve development|floor plate formation|gonad development|heart morphogenesis|muscle cell fate commitment|negative regulation of apoptosis|neural crest cell migration|neuron fate commitment|neuron projection regeneration|odontogenesis of dentine-containing tooth|osteoblast differentiation|otolith morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of neuroblast proliferation|positive regulation of smoothened signaling pathway|semicircular canal morphogenesis|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation|smoothened signaling pathway involved in ventral spinal cord patterning|spermatogenesis|vasculogenesis	cilium|cytoplasm|integral to membrane|neuronal cell body|plasma membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			skin(19)|large_intestine(10)|central_nervous_system(3)|upper_aerodigestive_tract(2)|biliary_tract(1)|lung(1)|liver(1)	37						CAGCTACATCGCGGCCTTCGG	0.677			Mis		skin basal cell 								11	10	---	---	---	---	PASS
AHCYL2	23382	broad.mit.edu	37	7	129064971	129064971	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129064971C>A	uc011kov.1	+	15	1751	c.1697C>A	c.(1696-1698)CCC>CAC	p.P566H	AHCYL2_uc003vot.2_Missense_Mutation_p.P565H|AHCYL2_uc003vov.2_Missense_Mutation_p.P463H|AHCYL2_uc011kow.1_Missense_Mutation_p.P464H|AHCYL2_uc011kox.1_Missense_Mutation_p.P463H	NM_015328	NP_056143	Q96HN2	SAHH3_HUMAN	S-adenosylhomocysteine hydrolase-like 2 isoform	566					one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2						TACCTGTTGCCCAAGAAGATG	0.448													11	49	---	---	---	---	PASS
C8orf46	254778	broad.mit.edu	37	8	67405801	67405801	+	5'UTR	SNP	A	G	G	rs12545784	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67405801A>G	uc003xwg.2	+	1					C8orf46_uc003xwh.2_RNA|C8orf46_uc011let.1_5'UTR	NM_152765	NP_689978	Q8TAG6	CH046_HUMAN	hypothetical protein LOC254778											skin(2)	2			Epithelial(68;0.0224)|BRCA - Breast invasive adenocarcinoma(89;0.0508)|all cancers(69;0.0558)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			TCCCTGAGCCAGACTGGATTA	0.522													32	183	---	---	---	---	PASS
C8orf46	254778	broad.mit.edu	37	8	67405822	67405822	+	5'UTR	SNP	C	A	A	rs2555583		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67405822C>A	uc003xwg.2	+	1					C8orf46_uc003xwh.2_RNA|C8orf46_uc011let.1_5'UTR	NM_152765	NP_689978	Q8TAG6	CH046_HUMAN	hypothetical protein LOC254778											skin(2)	2			Epithelial(68;0.0224)|BRCA - Breast invasive adenocarcinoma(89;0.0508)|all cancers(69;0.0558)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			GGATGCCTCGCGACTAGGGGT	0.532													22	255	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139825225	139825225	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139825225C>A	uc003yvd.2	-	8	1730	c.1283G>T	c.(1282-1284)AGA>ATA	p.R428I		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	428					cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TTCTGCGTGTCTCGAGTCACA	0.517										HNSCC(7;0.00092)			8	53	---	---	---	---	PASS
SEMA4D	10507	broad.mit.edu	37	9	91977095	91977095	+	3'UTR	SNP	T	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91977095T>A	uc011ltm.1	-	21					SEMA4D_uc011ltn.1_RNA|SEMA4D_uc011lto.1_RNA|SEMA4D_uc004aql.2_RNA|SEMA4D_uc004aqm.2_RNA	NM_001142287	NP_001135759	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 2						anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2						AGCACCTAATTTTTTAAGTCT	0.522													11	4	---	---	---	---	PASS
TMOD1	7111	broad.mit.edu	37	9	100326390	100326390	+	Silent	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100326390G>A	uc004axk.1	+	6	771	c.558G>A	c.(556-558)ACG>ACA	p.T186T	TMOD1_uc004axl.1_Silent_p.T186T	NM_003275	NP_003266	P28289	TMOD1_HUMAN	tropomodulin 1	186					muscle filament sliding	cytosol	actin binding				0		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)		TAGAGGAAACGCTGGAACGGA	0.463													46	21	---	---	---	---	PASS
TRUB2	26995	broad.mit.edu	37	9	131077879	131077879	+	Silent	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131077879G>A	uc004buq.1	-	4	355	c.345C>T	c.(343-345)CTC>CTT	p.L115L		NM_015679	NP_056494	O95900	TRUB2_HUMAN	TruB pseudouridine (psi) synthase homolog 2	115					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(1)	1						TATCGGTGAGGAGCCTGCATC	0.582													19	14	---	---	---	---	PASS
CUBN	8029	broad.mit.edu	37	10	16975260	16975260	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16975260T>A	uc001ioo.2	-	40	6002	c.5950A>T	c.(5950-5952)ACG>TCG	p.T1984S		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1984	CUB 14.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GCATCTCCCGTCCTCAGGAAG	0.512													6	19	---	---	---	---	PASS
LIPN	643418	broad.mit.edu	37	10	90534901	90534901	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90534901A>C	uc010qmw.1	+	8	944	c.944A>C	c.(943-945)AAT>ACT	p.N315T		NM_001102469	NP_001095939	Q5VXI9	LIPN_HUMAN	lipase-like, ab-hydrolase domain containing 4	315					lipid catabolic process	extracellular region	hydrolase activity				0		Colorectal(252;0.0161)		Colorectal(12;4.83e-05)|COAD - Colon adenocarcinoma(12;6.5e-05)		GACGCTGATAATATGAAACAT	0.333													12	65	---	---	---	---	PASS
PKD2L1	9033	broad.mit.edu	37	10	102056953	102056953	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102056953C>A	uc001kqx.1	-	6	1352	c.969G>T	c.(967-969)GAG>GAT	p.E323D	PKD2L1_uc009xwm.1_Missense_Mutation_p.E276D	NM_016112	NP_057196	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	323	Helical; (Potential).				signal transduction	integral to membrane	calcium activated cation channel activity|calcium ion binding|cytoskeletal protein binding			ovary(4)	4		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		TAGCTGGAAACTCCACCACCA	0.597													8	21	---	---	---	---	PASS
RBM20	282996	broad.mit.edu	37	10	112540834	112540834	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112540834C>T	uc001kzf.2	+	2	525	c.467C>T	c.(466-468)GCT>GTT	p.A156V		NM_001134363	NP_001127835	Q5T481	RBM20_HUMAN	RNA binding motif protein 20	156						nucleus	nucleotide binding|RNA binding|zinc ion binding				0						CCCCAACATGCTGCAGCCATA	0.592													9	33	---	---	---	---	PASS
OR4P4	81300	broad.mit.edu	37	11	55406555	55406555	+	Missense_Mutation	SNP	A	G	G			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55406555A>G	uc010rij.1	+	1	722	c.722A>G	c.(721-723)CAT>CGT	p.H241R		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	241	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1						TGTAGTTCTCATGTAATTGTT	0.378													10	56	---	---	---	---	PASS
MS4A14	84689	broad.mit.edu	37	11	60164088	60164088	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60164088G>A	uc001npj.2	+	1	602	c.37G>A	c.(37-39)GTC>ATC	p.V13I	MS4A14_uc001npi.2_Intron|MS4A14_uc001npn.2_5'UTR|MS4A14_uc001npk.2_Missense_Mutation_p.V13I|MS4A14_uc001npl.2_5'UTR|MS4A14_uc001npm.2_5'UTR	NM_032597	NP_115986	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member	13						integral to membrane	receptor activity			breast(1)	1						GGCAACTCACGTCATCACTAT	0.458													28	54	---	---	---	---	PASS
PLCB3	5331	broad.mit.edu	37	11	64029901	64029901	+	Silent	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64029901G>A	uc001nzb.2	+	18	2061	c.2061G>A	c.(2059-2061)GCG>GCA	p.A687A	PLCB3_uc009ypg.1_Silent_p.A687A|PLCB3_uc009yph.1_Silent_p.A620A|PLCB3_uc009ypi.2_Silent_p.A687A	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3	687	PI-PLC Y-box.				intracellular signal transduction|lipid catabolic process|synaptic transmission	cytosol	calcium ion binding|calmodulin binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|pancreas(1)	2						AGCTCAACGCGGGCGTTTTTG	0.637													7	18	---	---	---	---	PASS
SYVN1	84447	broad.mit.edu	37	11	64897312	64897312	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64897312T>C	uc001odb.2	-	14	1578	c.1484A>G	c.(1483-1485)CAT>CGT	p.H495R	SYVN1_uc001odc.2_Missense_Mutation_p.H494R|SYVN1_uc009yqc.2_Missense_Mutation_p.H443R	NM_172230	NP_757385	Q86TM6	SYVN1_HUMAN	synoviolin 1 isoform b	495	Cytoplasmic (Potential).				ER-associated protein catabolic process|response to stress	endoplasmic reticulum membrane|integral to membrane|nucleus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(1)	1						CTGCCGCTCATGGCCCTCCAG	0.652													7	26	---	---	---	---	PASS
RDX	5962	broad.mit.edu	37	11	110150412	110150412	+	Silent	SNP	C	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110150412C>A	uc001pku.2	-	2	316	c.6G>T	c.(4-6)CCG>CCT	p.P2P	RDX_uc009yxx.1_RNA|RDX_uc009yxy.2_Silent_p.P2P|RDX_uc009yxz.2_5'UTR|RDX_uc009yya.2_Silent_p.P2P|RDX_uc010rwe.1_5'UTR	NM_002906	NP_002897	P35241	RADI_HUMAN	radixin	2					actin filament capping	cleavage furrow|cytoskeleton|extrinsic to membrane|Golgi apparatus|nucleolus|plasma membrane	actin binding				0		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		TTACTGGTTTCGGCATTTTCT	0.274													15	67	---	---	---	---	PASS
CRYAB	1410	broad.mit.edu	37	11	111780950	111780950	+	Intron	SNP	G	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111780950G>T	uc001pmf.1	-						CRYAB_uc010rwp.1_Missense_Mutation_p.P142Q|HSPB2_uc001pmg.2_5'Flank|HSPB2_uc009yyj.2_5'Flank|C11orf52_uc001pmh.2_5'Flank	NM_001885	NP_001876	P02511	CRYAB_HUMAN	crystallin, alpha B						anti-apoptosis|muscle contraction|negative regulation of intracellular transport|protein folding|protein homooligomerization|response to heat	cytoplasm|nucleus	protein homodimerization activity|structural constituent of eye lens|unfolded protein binding				0		all_cancers(61;1.26e-15)|all_epithelial(67;9.52e-10)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.57e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.57e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.051)		GTTATGGCTTGGGACTGGAAT	0.418													4	3	---	---	---	---	PASS
ZBTB16	7704	broad.mit.edu	37	11	113934420	113934420	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113934420C>T	uc001pop.2	+	2	662	c.398C>T	c.(397-399)ACG>ATG	p.T133M	ZBTB16_uc001poo.1_Missense_Mutation_p.T133M|ZBTB16_uc001poq.2_Missense_Mutation_p.T133M	NM_006006	NP_005997	Q05516	ZBT16_HUMAN	promyelocytic leukemia zinc finger protein	133					apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		GACAATGACACGGAGGCCACC	0.582													5	12	---	---	---	---	PASS
GRIN2B	2904	broad.mit.edu	37	12	13906356	13906356	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13906356G>A	uc001rbt.2	-	3	1084	c.905C>T	c.(904-906)ACT>ATT	p.T302I		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	302	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	AGAAGCAGCAGTGGTGATTAT	0.507													8	100	---	---	---	---	PASS
ITPR2	3709	broad.mit.edu	37	12	26553126	26553126	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26553126C>T	uc001rhg.2	-	53	7882	c.7465G>A	c.(7465-7467)GTG>ATG	p.V2489M	ITPR2_uc009zjg.1_Missense_Mutation_p.V640M	NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	2489	Extracellular (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity	p.V2489G(1)		kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)					TGGTTCAGCACGGTGACAATG	0.413													27	52	---	---	---	---	PASS
C12orf11	55726	broad.mit.edu	37	12	27066946	27066946	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27066946G>C	uc001rhk.3	-	13	2072	c.1535C>G	c.(1534-1536)CCT>CGT	p.P512R	C12orf11_uc001rhj.3_Missense_Mutation_p.P80R|C12orf11_uc010sjk.1_Missense_Mutation_p.P411R	NM_018164	NP_060634	Q9NVM9	M89BB_HUMAN	hypothetical protein LOC55726	512					cell division|mitosis|regulation of mitotic cell cycle		protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	Colorectal(261;0.0847)					TGTGGAAATAGGTAGAGGATC	0.308													33	55	---	---	---	---	PASS
KIF21A	55605	broad.mit.edu	37	12	39716607	39716607	+	Silent	SNP	T	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39716607T>C	uc001rly.2	-	27	3680	c.3534A>G	c.(3532-3534)GGA>GGG	p.G1178G	KIF21A_uc001rlv.2_Silent_p.G183G|KIF21A_uc001rlw.2_Silent_p.G495G|KIF21A_uc001rlx.2_Silent_p.G1165G|KIF21A_uc001rlz.2_Silent_p.G1142G|KIF21A_uc010skl.1_Silent_p.G1158G	NM_017641	NP_060111	Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1178					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|pancreas(1)|lung(1)|skin(1)	7		Lung NSC(34;0.179)|all_lung(34;0.213)				AGGAGGCATCTCCTGTACTAG	0.478													5	84	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49444338	49444338	+	Silent	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49444338C>T	uc001rta.3	-	11	3033	c.3033G>A	c.(3031-3033)CCG>CCA	p.P1011P		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1011	Pro-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						TGGGAGAAGCCGGCCCCACTG	0.612			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			28	97	---	---	---	---	PASS
ESPL1	9700	broad.mit.edu	37	12	53686061	53686061	+	Splice_Site	SNP	G	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53686061G>T	uc001sck.2	+	28	5888	c.5797_splice	c.e28-1	p.Y1933_splice	ESPL1_uc001scj.2_Splice_Site_p.Y1608_splice	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	separase						apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3						CTCCTCCTCAGTATGGGGCCT	0.527													9	21	---	---	---	---	PASS
PPP1R12A	4659	broad.mit.edu	37	12	80184250	80184250	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80184250G>A	uc001syz.2	-	20	2930	c.2663C>T	c.(2662-2664)TCT>TTT	p.S888F	PPP1R12A_uc010suc.1_Missense_Mutation_p.S801F|PPP1R12A_uc001sza.2_Missense_Mutation_p.S832F|PPP1R12A_uc010sud.1_Missense_Mutation_p.S888F|PPP1R12A_uc001szb.2_Missense_Mutation_p.S888F|PPP1R12A_uc001syy.2_RNA	NM_002480	NP_002471	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	888						contractile fiber	protein binding|signal transducer activity			ovary(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	7						AACATACCTAGAAATGGAATC	0.229													4	58	---	---	---	---	PASS
MED13L	23389	broad.mit.edu	37	12	116409971	116409971	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116409971C>T	uc001tvw.2	-	26	5857	c.5802G>A	c.(5800-5802)ATG>ATA	p.M1934I		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1934					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		AGATTCCACACATCCGGCACA	0.478													12	64	---	---	---	---	PASS
ATP8A2	51761	broad.mit.edu	37	13	26413708	26413708	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26413708G>A	uc001uqk.2	+	30	3044	c.2902G>A	c.(2902-2904)GCC>ACC	p.A968T	ATP8A2_uc010tdi.1_Missense_Mutation_p.A903T|ATP8A2_uc010tdj.1_RNA|ATP8A2_uc010aaj.1_Missense_Mutation_p.A518T	NM_016529	NP_057613	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter-like,	928	Helical; (Potential).				ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		CTGCATCAACGCCTTGGTCCA	0.517													37	63	---	---	---	---	PASS
NBEA	26960	broad.mit.edu	37	13	36046544	36046544	+	Silent	SNP	G	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36046544G>T	uc001uvb.2	+	41	6662	c.6456G>T	c.(6454-6456)GTG>GTT	p.V2152V	NBEA_uc010abi.2_Silent_p.V808V|NBEA_uc010tee.1_5'UTR	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	2152						cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CAGGCCCAGTGGTTCTCAGCA	0.577													8	14	---	---	---	---	PASS
RCBTB2	1102	broad.mit.edu	37	13	49084795	49084795	+	Missense_Mutation	SNP	T	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49084795T>A	uc001vch.2	-	10	1267	c.896A>T	c.(895-897)TAT>TTT	p.Y299F	RCBTB2_uc010tgg.1_Missense_Mutation_p.Y304F|RCBTB2_uc001vci.2_Missense_Mutation_p.Y275F|RCBTB2_uc010tgh.1_Intron|RCBTB2_uc001vcj.2_Intron|RCBTB2_uc010acv.1_RNA|RCBTB2_uc010tgi.1_Intron	NM_001268	NP_001259	O95199	RCBT2_HUMAN	regulator of chromosome condensation and BTB	299	RCC1 5.						Ran guanyl-nucleotide exchange factor activity			ovary(2)|lung(2)|skin(1)	5		all_cancers(8;4.86e-71)|all_epithelial(8;2.11e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;2.3e-10)|Lung NSC(96;1.07e-07)|Breast(56;1.53e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.00826)|Myeloproliferative disorder(33;0.0179)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(99;1.8e-09)|LUSC - Lung squamous cell carcinoma(3;0.116)		AGGAGTAGGATAGGACTGGTT	0.453													12	24	---	---	---	---	PASS
MIPOL1	145282	broad.mit.edu	37	14	37777677	37777677	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37777677G>A	uc001wuc.2	+	10	1284	c.781G>A	c.(781-783)GAA>AAA	p.E261K	MIPOL1_uc010amr.2_Intron|MIPOL1_uc001wub.3_Missense_Mutation_p.E230K|MIPOL1_uc001wud.2_Missense_Mutation_p.E261K|MIPOL1_uc010ams.2_Missense_Mutation_p.E261K|MIPOL1_uc001wue.2_Missense_Mutation_p.E230K|MIPOL1_uc010amt.2_Missense_Mutation_p.E80K	NM_138731	NP_620059	Q8TD10	MIPO1_HUMAN	mirror-image polydactyly 1	261	Potential.									ovary(1)|central_nervous_system(1)	2	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)		AATAACTGCAGAAGAAATGAG	0.358													27	27	---	---	---	---	PASS
CHRM5	1133	broad.mit.edu	37	15	34355731	34355731	+	Nonsense_Mutation	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34355731G>A	uc001zhk.1	+	3	1483	c.813G>A	c.(811-813)TGG>TGA	p.W271*	CHRM5_uc001zhl.1_Nonsense_Mutation_p.W271*	NM_012125	NP_036257	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5	271	Cytoplasmic (By similarity).				cell proliferation|inhibition of adenylate cyclase activity by muscarinic acetylcholine receptor signaling pathway	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)	AGGCCTCCTGGTCATCCTCCC	0.612													6	8	---	---	---	---	PASS
NDUFAF1	51103	broad.mit.edu	37	15	41689026	41689026	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41689026G>C	uc001znx.2	-	2	614	c.232C>G	c.(232-234)CCT>GCT	p.P78A	NDUFAF1_uc010bcf.2_RNA	NM_016013	NP_057097	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha	78					mitochondrial electron transport, NADH to ubiquinone|protein complex assembly	mitochondrial respiratory chain complex I	unfolded protein binding			ovary(1)	1		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		CTAACATCAGGCTTCTCCTCA	0.428													24	29	---	---	---	---	PASS
TELO2	9894	broad.mit.edu	37	16	1550655	1550655	+	Silent	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1550655C>T	uc002cly.2	+	9	1527	c.1236C>T	c.(1234-1236)GTC>GTT	p.V412V	TELO2_uc010uvg.1_Silent_p.V412V	NM_016111	NP_057195	Q9Y4R8	TELO2_HUMAN	TEL2, telomere maintenance 2, homolog	412						chromosome, telomeric region|cytoplasm|membrane|nucleus	protein binding				0		Hepatocellular(780;0.219)				TGGCAGAGGTCGTTAGTGCCC	0.697													4	6	---	---	---	---	PASS
MKL2	57496	broad.mit.edu	37	16	14328057	14328057	+	Missense_Mutation	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14328057G>A	uc010uza.1	+	9	903	c.748G>A	c.(748-750)GAT>AAT	p.D250N	MKL2_uc002dcg.2_Missense_Mutation_p.D250N|MKL2_uc002dch.2_Missense_Mutation_p.D239N|MKL2_uc010uzb.1_Missense_Mutation_p.D199N	NM_014048	NP_054767	Q9ULH7	MKL2_HUMAN	megakaryoblastic leukemia 2 protein	239					cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5						TCCAACTGCAGATCAGCCTCC	0.507													39	74	---	---	---	---	PASS
MT1G	4495	broad.mit.edu	37	16	56701251	56701251	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56701251C>T	uc002eju.1	-	2	139	c.67G>A	c.(67-69)GAG>AAG	p.E23K	MT1G_uc002ejv.1_RNA|MT1H_uc002ejw.2_5'Flank	NM_005950	NP_005941	P13640	MT1G_HUMAN	metallothionein 1G	24	Beta.						metal ion binding|protein binding				0						CATTTGCACTCTTTGCACTTG	0.567													6	93	---	---	---	---	PASS
HYDIN	54768	broad.mit.edu	37	16	70986456	70986456	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70986456C>A	uc002ezr.2	-	41	6524	c.6396G>T	c.(6394-6396)ATG>ATT	p.M2132I		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	2133										ovary(1)|skin(1)	2		Ovarian(137;0.0654)				CCACCAGAGTCATCTCGGAGG	0.552													15	50	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	16722824	16722824	+	RNA	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16722824G>A	uc002gqq.1	-	4		c.990C>T								full-length cDNA clone CS0DI013YN06 of Placenta Cot 25-normalized of Homo sapiens (human).																		GTTCTTCTCTGCCATCTTCTC	0.552													10	7	---	---	---	---	PASS
LOC284100	284100	broad.mit.edu	37	17	36214775	36214775	+	RNA	SNP	G	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36214775G>T	uc002hom.1	-	2		c.184C>A			LOC284100_uc002hon.1_RNA					Homo sapiens cDNA FLJ37577 fis, clone BRCOC2003513, moderately similar to 14-3-3 protein epsilon (14-3-3E).												0						CTTGCCAGTGGTAGCTGCTGG	0.353													23	1	---	---	---	---	PASS
GRB7	2886	broad.mit.edu	37	17	37899552	37899552	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37899552C>T	uc002hsr.2	+	5	833	c.583C>T	c.(583-585)CCA>TCA	p.P195S	GRB7_uc002hss.2_Missense_Mutation_p.P195S|GRB7_uc010cwc.2_Missense_Mutation_p.P195S|GRB7_uc002hst.2_Missense_Mutation_p.P195S	NM_005310	NP_005301	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7	195					blood coagulation|epidermal growth factor receptor signaling pathway|leukocyte migration|negative regulation of translation|positive regulation of cell migration|stress granule assembly	cytosol|focal adhesion|stress granule	phosphatidylinositol binding|protein kinase binding|SH3/SH2 adaptor activity			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CAAGAGCTCCCCAGTGAGTGC	0.607													18	28	---	---	---	---	PASS
SOX9	6662	broad.mit.edu	37	17	70120330	70120330	+	Missense_Mutation	SNP	C	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70120330C>A	uc002jiw.2	+	3	1704	c.1332C>A	c.(1330-1332)GAC>GAA	p.D444E		NM_000346	NP_000337	P48436	SOX9_HUMAN	transcription factor SOX9	444					cAMP-mediated signaling|negative regulation of transcription, DNA-dependent|positive regulation of branching involved in ureteric bud morphogenesis|protein complex assembly|renal vesicle induction	nucleus|protein complex	core promoter sequence-specific DNA binding|enhancer binding|protein kinase A catalytic subunit binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription				0		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			ACTACACCGACCACCAGAACT	0.627													105	141	---	---	---	---	PASS
RECQL5	9400	broad.mit.edu	37	17	73654527	73654527	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73654527A>C	uc010dgl.2	-	7	1156	c.1000T>G	c.(1000-1002)TGG>GGG	p.W334G	RECQL5_uc010dgk.2_Missense_Mutation_p.W307G|RECQL5_uc002jpb.1_Missense_Mutation_p.W334G|RECQL5_uc002joz.3_Missense_Mutation_p.W334G|RECQL5_uc002jpa.3_Missense_Mutation_p.W334G	NM_004259	NP_004250	O94762	RECQ5_HUMAN	RecQ protein-like 5 isoform 1	334	Helicase C-terminal.				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)			GCAATATTCCAATGGGCGACA	0.532								Other_identified_genes_with_known_or_suspected_DNA_repair_function					10	43	---	---	---	---	PASS
ANAPC11	51529	broad.mit.edu	37	17	79857246	79857246	+	Intron	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79857246G>A	uc002kbv.1	+						ANAPC11_uc002kbw.1_Intron|ANAPC11_uc002kbx.1_Intron|ANAPC11_uc002kby.1_Missense_Mutation_p.G80R|ANAPC11_uc002kbz.1_Intron|ANAPC11_uc002kca.1_Intron|ANAPC11_uc002kcb.1_Intron|ANAPC11_uc002kcc.1_Intron|ANAPC11_uc010dih.1_Intron|NPB_uc002kcd.2_5'Flank	NM_016476	NP_057560	Q9NYG5	APC11_HUMAN	APC11 anaphase promoting complex subunit 11						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	zinc ion binding				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			GCAGCACACCGGATCCCTGAT	0.612													25	22	---	---	---	---	PASS
ACSBG2	81616	broad.mit.edu	37	19	6177251	6177251	+	Missense_Mutation	SNP	T	G	G			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6177251T>G	uc002mef.1	+	8	977	c.750T>G	c.(748-750)ATT>ATG	p.I250M	ACSBG2_uc002mee.1_Missense_Mutation_p.I63M|ACSBG2_uc002meg.1_Missense_Mutation_p.I250M|ACSBG2_uc002meh.1_Missense_Mutation_p.I250M|ACSBG2_uc002mei.1_Missense_Mutation_p.I200M|ACSBG2_uc010xiz.1_Missense_Mutation_p.I250M	NM_030924	NP_112186	Q5FVE4	ACBG2_HUMAN	bubblegum-related acyl-CoA synthetase 2	250					cell differentiation|fatty acid metabolic process|multicellular organismal development|spermatogenesis	membrane|microsome|mitochondrion	acyl-CoA thioesterase activity|ATP binding|long-chain fatty acid-CoA ligase activity			ovary(1)	1						TCACGTGGATTGCAGGAGCAG	0.393													15	172	---	---	---	---	PASS
ACSBG2	81616	broad.mit.edu	37	19	6177276	6177276	+	Missense_Mutation	SNP	A	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6177276A>C	uc002mef.1	+	8	1002	c.775A>C	c.(775-777)AAA>CAA	p.K259Q	ACSBG2_uc002mee.1_Missense_Mutation_p.K72Q|ACSBG2_uc002meg.1_Missense_Mutation_p.K259Q|ACSBG2_uc002meh.1_Missense_Mutation_p.K259Q|ACSBG2_uc002mei.1_Missense_Mutation_p.K209Q|ACSBG2_uc010xiz.1_Missense_Mutation_p.K259Q	NM_030924	NP_112186	Q5FVE4	ACBG2_HUMAN	bubblegum-related acyl-CoA synthetase 2	259					cell differentiation|fatty acid metabolic process|multicellular organismal development|spermatogenesis	membrane|microsome|mitochondrion	acyl-CoA thioesterase activity|ATP binding|long-chain fatty acid-CoA ligase activity			ovary(1)	1						AAAGGACTTTAAACTGACAGA	0.463													10	176	---	---	---	---	PASS
HPN	3249	broad.mit.edu	37	19	35557111	35557111	+	Intron	SNP	A	G	G			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35557111A>G	uc002nxq.1	+						HPN_uc002nxr.1_Intron|HPN_uc002nxs.1_Intron|HPN_uc010xsh.1_3'UTR|HPN_uc002nxt.1_3'UTR|LOC100128675_uc010xsi.1_Intron	NM_002151	NP_002142	P05981	HEPS_HUMAN	hepsin						cell growth|proteolysis	cytoplasm|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	TGGGACGTGGAAGCCTCTCAG	0.617													8	27	---	---	---	---	PASS
YIF1B	90522	broad.mit.edu	37	19	38797598	38797598	+	Intron	SNP	A	G	G			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38797598A>G	uc002ohz.2	-						YIF1B_uc002ohw.2_Intron|YIF1B_uc002ohx.2_Intron|YIF1B_uc010xtx.1_Intron|YIF1B_uc010xty.1_Intron|YIF1B_uc002oia.2_Silent_p.A271A|YIF1B_uc002ohy.2_Intron|YIF1B_uc002oib.2_Silent_p.A271A	NM_001039672	NP_001034761	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B isoform 5							integral to membrane					0	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			tgggattacaagcatgagcca	0.000													7	67	---	---	---	---	PASS
YIF1B	90522	broad.mit.edu	37	19	38797601	38797601	+	Intron	SNP	A	G	G			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38797601A>G	uc002ohz.2	-						YIF1B_uc002ohw.2_Intron|YIF1B_uc002ohx.2_Intron|YIF1B_uc010xtx.1_Intron|YIF1B_uc010xty.1_Intron|YIF1B_uc002oia.2_Silent_p.H270H|YIF1B_uc002ohy.2_Intron|YIF1B_uc002oib.2_Silent_p.H270H	NM_001039672	NP_001034761	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B isoform 5							integral to membrane					0	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			gattacaagcatgagccaccg	0.000													8	64	---	---	---	---	PASS
YIF1B	90522	broad.mit.edu	37	19	38797609	38797609	+	Intron	SNP	C	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38797609C>A	uc002ohz.2	-						YIF1B_uc002ohw.2_Intron|YIF1B_uc002ohx.2_Intron|YIF1B_uc010xtx.1_Intron|YIF1B_uc010xty.1_Intron|YIF1B_uc002oia.2_Missense_Mutation_p.V268L|YIF1B_uc002ohy.2_Intron|YIF1B_uc002oib.2_Missense_Mutation_p.V268L	NM_001039672	NP_001034761	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B isoform 5							integral to membrane					0	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			gcatgagccaccgcgcccggc	0.000													5	70	---	---	---	---	PASS
CGB2	114336	broad.mit.edu	37	19	49535233	49535233	+	5'UTR	SNP	G	A	A	rs141047975	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49535233G>A	uc002plw.2	+	1					CGB_uc010yad.1_Intron|SNAR-G2_uc010yae.1_5'Flank|CGB2_uc010yaf.1_5'UTR|CGB2_uc010yag.1_5'Flank	NM_033378	NP_203696			chorionic gonadotropin, beta polypeptide 2												0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		GACTCCGGCCGGGTTCCCGTG	0.627													20	392	---	---	---	---	PASS
CGB2	114336	broad.mit.edu	37	19	49535314	49535314	+	5'UTR	SNP	C	T	T	rs149679637	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49535314C>T	uc002plw.2	+	1					CGB_uc010yad.1_Intron|SNAR-G2_uc010yae.1_5'Flank|CGB2_uc010yaf.1_5'UTR|CGB2_uc010yag.1_5'Flank	NM_033378	NP_203696			chorionic gonadotropin, beta polypeptide 2												0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		ATGTCCACATCCCCAGTGCTT	0.557													14	459	---	---	---	---	PASS
SLC17A7	57030	broad.mit.edu	37	19	49938510	49938510	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49938510C>T	uc002pnp.2	-	3	521	c.349G>A	c.(349-351)GGC>AGC	p.G117S	SLC17A7_uc002pnq.1_Missense_Mutation_p.G50S	NM_020309	NP_064705	Q9P2U7	VGLU1_HUMAN	solute carrier family 17, member 7	117	Helical; (Potential).				glutamate secretion|neurotransmitter secretion	cell junction|clathrin sculpted glutamate transport vesicle membrane|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|sodium-dependent phosphate transmembrane transporter activity|sodium:inorganic phosphate symporter activity			ovary(1)|pancreas(1)|skin(1)	3		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(486;0.0245)		TGTATGAGGCCGACAGTCTCT	0.527													4	73	---	---	---	---	PASS
LILRA3	11026	broad.mit.edu	37	19	54803946	54803946	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54803946C>T	uc002qfd.2	-	2	132	c.67G>A	c.(67-69)GCA>ACA	p.A23T	LILRA6_uc002qew.1_Intron|LILRA3_uc010erk.2_Missense_Mutation_p.A23T	NM_006865	NP_006856	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor,	23					defense response	extracellular region|plasma membrane	antigen binding|receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GACTCACCTGCCTGCACGTGG	0.632													19	7	---	---	---	---	PASS
CENPB	1059	broad.mit.edu	37	20	3765589	3765589	+	Silent	SNP	A	G	G			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3765589A>G	uc002wjk.2	-	1	1749	c.1542T>C	c.(1540-1542)AGT>AGC	p.S514S	CDC25B_uc010zqk.1_5'Flank|CDC25B_uc010zql.1_5'Flank|CDC25B_uc010zqm.1_5'Flank	NM_001810	NP_001801	P07199	CENPB_HUMAN	centromere protein B	514	Asp/Glu-rich (acidic).				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	chromatin binding|satellite DNA binding				0						cCTCTTCCTCACTGTCTGAAT	0.423													39	88	---	---	---	---	PASS
RBM39	9584	broad.mit.edu	37	20	34312531	34312531	+	Silent	SNP	T	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34312531T>C	uc002xeb.2	-	8	992	c.648A>G	c.(646-648)CAA>CAG	p.Q216Q	RBM39_uc002xdz.2_Silent_p.Q192Q|RBM39_uc002xea.2_Silent_p.Q59Q|RBM39_uc010gfn.2_Silent_p.Q59Q|RBM39_uc010zvm.1_Silent_p.Q194Q|RBM39_uc002xeg.2_Silent_p.Q194Q|RBM39_uc002xec.2_Silent_p.Q216Q|RBM39_uc002xed.2_5'UTR|RBM39_uc002xee.2_Silent_p.Q59Q|RBM39_uc002xef.2_Silent_p.Q59Q|RBM39_uc010zvn.1_Silent_p.Q59Q	NM_184234	NP_909122	Q14498	RBM39_HUMAN	RNA binding motif protein 39 isoform a	216	RRM 1.				mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	centrosome|nuclear speck	nucleotide binding|protein binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_epithelial(2;0.00295)|Lung NSC(9;0.00453)|Breast(12;0.00544)|all_lung(11;0.00676)					CTAAAACTCGTTGGCCAGTTA	0.418													28	58	---	---	---	---	PASS
KRTAP13-1	140258	broad.mit.edu	37	21	31768458	31768458	+	Silent	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31768458C>T	uc002yoa.2	+	1	67	c.54C>T	c.(52-54)TAC>TAT	p.Y18Y		NM_181599	NP_853630	Q8IUC0	KR131_HUMAN	keratin associated protein 13-1	18						intermediate filament				ovary(1)	1						GTGGTGGCTACCTGCACTACC	0.557													20	35	---	---	---	---	PASS
DSCR6	53820	broad.mit.edu	37	21	38390280	38390280	+	Missense_Mutation	SNP	T	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38390280T>C	uc002yvv.2	+	4	556	c.346T>C	c.(346-348)TCT>CCT	p.S116P	DSCR6_uc011aec.1_Silent_p.S2S|DSCR6_uc010gnd.2_Silent_p.S2S	NM_018962	NP_061835	P57055	DSCR6_HUMAN	Down syndrome critical region protein 6	116						nucleus				breast(1)	1		Myeloproliferative disorder(46;0.0632)				CGACGATGAGTCTACTGAGTC	0.567													4	11	---	---	---	---	PASS
DCAF8L2	347442	broad.mit.edu	37	X	27766775	27766775	+	Missense_Mutation	SNP	C	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27766775C>T	uc011mjy.1	+	1	1850	c.1763C>T	c.(1762-1764)ACG>ATG	p.T588M		NM_001136533	NP_001130005			DDB1 and CUL4 associated factor 8-like 2											central_nervous_system(1)|pancreas(1)	2						CGTCACGTGACGCAGAGAGGT	0.502													8	20	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	47657350	47657350	+	IGR	SNP	G	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47657350G>A								LOC100133957 (137574 upstream) : ZNF81 (38951 downstream)																							atgtccttcagttctccagga	0.000													21	96	---	---	---	---	PASS
HUWE1	10075	broad.mit.edu	37	X	53586385	53586385	+	Silent	SNP	G	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53586385G>T	uc004dsp.2	-	57	8247	c.7845C>A	c.(7843-7845)ATC>ATA	p.I2615I	HUWE1_uc004dsn.2_Silent_p.I1439I|uc004dss.2_5'Flank|MIRLET7F2_hsa-let-7f-2|MI0000068_5'Flank	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	2615					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17						AACGGGCGATGATGTGGACGT	0.572													4	16	---	---	---	---	PASS
KLHL13	90293	broad.mit.edu	37	X	117032810	117032810	+	3'UTR	SNP	G	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117032810G>T	uc004eql.2	-	7					KLHL13_uc004eqk.2_3'UTR|KLHL13_uc011mtn.1_3'UTR|KLHL13_uc011mto.1_3'UTR|KLHL13_uc011mtp.1_3'UTR|KLHL13_uc004eqm.2_3'UTR|KLHL13_uc011mtq.1_3'UTR	NM_033495	NP_277030	Q9P2N7	KLH13_HUMAN	kelch-like 13						cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex				kidney(1)|skin(1)	2						GGGGGAAAAAGAAGAGAATTT	0.353													6	54	---	---	---	---	PASS
KIAA1210	57481	broad.mit.edu	37	X	118217056	118217056	+	Missense_Mutation	SNP	G	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118217056G>C	uc004era.3	-	13	4876	c.4876C>G	c.(4876-4878)CCT>GCT	p.P1626A		NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481	1626										ovary(4)|skin(1)	5						ATCTTTTTAGGTTGGTTTTCA	0.388													43	128	---	---	---	---	PASS
CLIC2	1193	broad.mit.edu	37	X	154563725	154563725	+	Silent	SNP	C	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154563725C>A	uc004fnf.2	-	1	262	c.12G>T	c.(10-12)CTG>CTT	p.L4L	CLIC2_uc010nvj.1_Silent_p.L4L	NM_001289	NP_001280	O15247	CLIC2_HUMAN	chloride intracellular channel 2	4	N-terminal.|Required for insertion into the membrane (By similarity).				signal transduction	chloride channel complex|cytoplasm|nucleus	voltage-gated chloride channel activity			large_intestine(1)|ovary(1)|skin(1)	3	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					TGCCGGGCCGCAGGCCTGACA	0.418													21	32	---	---	---	---	PASS
HNRNPCL1	343069	broad.mit.edu	37	1	12908384	12908385	+	Intron	INS	-	A	A	rs143606605		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12908384_12908385insA	uc010obf.1	-						LOC649330_uc009vno.2_5'Flank	NM_001013631	NP_001013653	O60812	HNRCL_HUMAN	heterogeneous nuclear ribonucleoprotein C-like							ribonucleoprotein complex	nucleotide binding				0						ATTGCATTTAGAAAAAAAATCA	0.356													6	4	---	---	---	---	
HNRNPR	10236	broad.mit.edu	37	1	23660245	23660245	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23660245delA	uc001bgr.3	-						HNRNPR_uc001bgp.3_Intron|HNRNPR_uc009vqk.2_Intron|HNRNPR_uc001bgs.3_Intron|HNRNPR_uc010odw.1_Intron|HNRNPR_uc010odx.1_Intron|HNRNPR_uc009vql.2_Intron	NM_005826	NP_005817	O43390	HNRPR_HUMAN	heterogeneous nuclear ribonucleoprotein R							catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			upper_aerodigestive_tract(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00394)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;6.83e-27)|Colorectal(126;6.01e-08)|COAD - Colon adenocarcinoma(152;3.32e-06)|GBM - Glioblastoma multiforme(114;6.69e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00357)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0875)|LUSC - Lung squamous cell carcinoma(448;0.19)		ATGGTTAGGTAAAAAAAAAAG	0.318													5	3	---	---	---	---	
TESK2	10420	broad.mit.edu	37	1	45858374	45858374	+	Intron	DEL	A	-	-	rs111558684		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45858374delA	uc001cns.1	-						TESK2_uc009vxr.1_Intron|TESK2_uc010olo.1_Intron|TESK2_uc009vxs.1_Intron	NM_007170	NP_009101	Q96S53	TESK2_HUMAN	testis-specific protein kinase 2						actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)					actctgtctcaaaaaaaaaaa	0.000													2	5	---	---	---	---	
SLC35D1	23169	broad.mit.edu	37	1	67517487	67517487	+	Intron	DEL	A	-	-	rs66531736		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67517487delA	uc001ddk.2	-						SLC35D1_uc010oph.1_Intron	NM_015139	NP_055954	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-glucuronic						chondroitin sulfate biosynthetic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	integral to endoplasmic reticulum membrane	UDP-glucuronic acid transmembrane transporter activity|UDP-N-acetylgalactosamine transmembrane transporter activity				0					Lorazepam(DB00186)	AAACAAAAACAAAAAACTCCT	0.284													8	11	---	---	---	---	
ABCD3	5825	broad.mit.edu	37	1	94883978	94883980	+	5'UTR	DEL	GCC	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94883978_94883980delGCC	uc001dqn.3	+	1					ABCD3_uc001dqm.3_5'UTR|ABCD3_uc010oto.1_5'UTR|ABCD3_uc010otp.1_5'UTR|ABCD3_uc009wdr.2_5'UTR	NM_002858	NP_002849	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D, member 3						peroxisomal long-chain fatty acid import|peroxisome organization	cytosol|integral to peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(1)	1		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)		CAGTAAGGTAgccgccgccgccg	0.404													3	3	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145109259	145109260	+	Intron	INS	-	A	A	rs150048477	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145109259_145109260insA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						cactccagcccgggggcagagc	0.059													10	5	---	---	---	---	
NBPF9	400818	broad.mit.edu	37	1	145139601	145139602	+	Intron	INS	-	CCGGCCGCCGCCGTGGGGGC	CCGGCCGCCGCCGTGGGGGC	rs150282922		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145139601_145139602insCCGGCCGCCGCCGTGGGGGC	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron			Q3BBV1	NBPFK_HUMAN	RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0						ctgctgctgctCCGGCCGCCGC	0.649											OREG0013744	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	13	6	---	---	---	---	
TMOD4	29765	broad.mit.edu	37	1	151146702	151146702	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151146702delA	uc001exc.3	-						TMOD4_uc001exb.2_5'Flank|TMOD4_uc001exd.2_Intron|TMOD4_uc010pct.1_Intron	NM_013353	NP_037485	Q9NZQ9	TMOD4_HUMAN	tropomodulin 4 (muscle)						muscle contraction	cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			aaacaaaaagaaaaaaaaaag	0.234													4	3	---	---	---	---	
SSR2	6746	broad.mit.edu	37	1	155979572	155979572	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155979572delT	uc001fmx.2	-						SSR2_uc001fmv.2_Intron|SSR2_uc001fmw.2_Intron|SSR2_uc001fmy.2_Intron|SSR2_uc010pgv.1_Intron	NM_003145	NP_003136	P43308	SSRB_HUMAN	signal sequence receptor, beta precursor						cotranslational protein targeting to membrane	endoplasmic reticulum membrane|integral to membrane	signal sequence binding				0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					AAAGTCTTAGttttttttttt	0.199													8	6	---	---	---	---	
SLAMF6	114836	broad.mit.edu	37	1	160466322	160466323	+	Intron	INS	-	A	A	rs140116847	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160466322_160466323insA	uc001fwe.1	-						SLAMF6_uc001fwd.1_Intron|SLAMF6_uc010pjh.1_Intron|SLAMF6_uc010pji.1_Intron|SLAMF6_uc010pjj.1_Intron|SLAMF6_uc009wtm.1_Intron	NM_052931	NP_443163	Q96DU3	SLAF6_HUMAN	activating NK receptor precursor							integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	all_cancers(52;1.05e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0923)			TAGGAAAGGGTAGGAGATGTTT	0.475													4	5	---	---	---	---	
CD34	947	broad.mit.edu	37	1	208070654	208070655	+	Intron	INS	-	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208070654_208070655insT	uc001hgw.1	-						CD34_uc001hgx.1_Intron|CD34_uc010psj.1_Intron	NM_001025109	NP_001020280	P28906	CD34_HUMAN	CD34 antigen isoform a						cell-cell adhesion|leukocyte migration|regulation of immune response	integral to membrane	carbohydrate binding			ovary(1)	1						GTCTTTTTTGCCCACCAGATGG	0.371													11	6	---	---	---	---	
HEATR1	55127	broad.mit.edu	37	1	236755039	236755040	+	Intron	INS	-	A	A	rs150414828	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236755039_236755040insA	uc001hyd.1	-							NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28						rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GAATATCCCATACAAAATTCTC	0.371													2	4	---	---	---	---	
GRHL1	29841	broad.mit.edu	37	2	10139007	10139008	+	Intron	INS	-	AT	AT			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10139007_10139008insAT	uc002raa.2	+						GRHL1_uc002rab.2_Intron|GRHL1_uc002rad.2_Intron|GRHL1_uc010yjb.1_Intron	NM_198182	NP_937825	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1						cellular lipid metabolic process|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding			pancreas(1)|skin(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		tatatgtacacatatatataca	0.124													4	2	---	---	---	---	
LTBP1	4052	broad.mit.edu	37	2	33482160	33482160	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33482160delT	uc002ros.2	+						LTBP1_uc002rot.2_Intron|LTBP1_uc002rou.2_Intron|LTBP1_uc002rov.2_Intron|LTBP1_uc010ymz.1_Intron|LTBP1_uc010yna.1_Intron	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				AAAAGTTGGATTTTTTTCTTT	0.249													4	4	---	---	---	---	
VRK2	7444	broad.mit.edu	37	2	58362577	58362578	+	Intron	DEL	TT	-	-	rs72516644		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58362577_58362578delTT	uc002rzo.2	+						VRK2_uc010fcb.2_Intron|VRK2_uc002rzs.2_Intron|VRK2_uc002rzr.2_Intron|VRK2_uc010fcc.2_Intron|VRK2_uc002rzv.2_Intron|VRK2_uc010fcd.2_Intron|VRK2_uc002rzp.2_Intron|VRK2_uc010ypg.1_Intron|VRK2_uc002rzq.2_Intron|VRK2_uc002rzu.2_Intron|VRK2_uc002rzt.2_Intron	NM_001130482	NP_001123954	Q86Y07	VRK2_HUMAN	vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1						TGCTTAGTGCTTTTTTTTTTTT	0.317													6	3	---	---	---	---	
CCT7	10574	broad.mit.edu	37	2	73476774	73476774	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73476774delT	uc002siz.2	+						CCT7_uc002sja.2_Intron|CCT7_uc010yrf.1_Intron|CCT7_uc010feu.2_Intron|CCT7_uc010yrg.1_Intron|CCT7_uc010yrh.1_Intron|CCT7_uc010yri.1_Intron	NM_006429	NP_006420	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 isoform a						'de novo' posttranslational protein folding		ATP binding|unfolded protein binding				0						TTCTATTTTGTTTTTTTTTTG	0.463													4	4	---	---	---	---	
THSD7B	80731	broad.mit.edu	37	2	137748355	137748356	+	5'Flank	INS	-	G	G			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137748355_137748356insG	uc002tva.1	+						THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		ATGGAGATACTGATTAGGACAC	0.381													46	27	---	---	---	---	
LRP2	4036	broad.mit.edu	37	2	170128122	170128135	+	Intron	DEL	CACACACACACACA	-	-	rs146955000		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170128122_170128135delCACACACACACACA	uc002ues.2	-						LRP2_uc010zdf.1_Intron	NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	GCAAAacatgcacacacacacacacacacacaca	0.196													5	3	---	---	---	---	
PPIG	9360	broad.mit.edu	37	2	170463838	170463839	+	Intron	INS	-	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170463838_170463839insA	uc002uez.2	+						PPIG_uc010fpx.2_Intron|PPIG_uc010fpy.2_Intron|PPIG_uc002ufa.2_Intron|PPIG_uc002ufb.2_Intron|PPIG_uc002ufc.1_Intron|PPIG_uc002ufd.2_Intron	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G						protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)	GGTATTTTTTCTTCTTAGGACA	0.292													9	5	---	---	---	---	
HNRNPA3	220988	broad.mit.edu	37	2	178081963	178081963	+	Intron	DEL	G	-	-	rs10709241		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178081963delG	uc002ulb.1	+						HNRNPA3_uc002ulc.1_Intron|HNRNPA3_uc002uld.2_Intron|HNRNPA3_uc002ule.2_Intron	NM_194247	NP_919223	P51991	ROA3_HUMAN	heterogeneous nuclear ribonucleoprotein A3							catalytic step 2 spliceosome|nucleolus|nucleoplasm	nucleotide binding|protein binding|RNA binding			ovary(2)	2						ATCAGAAGATGGGTTACACAT	0.299													5	7	---	---	---	---	
TTN	7273	broad.mit.edu	37	2	179537655	179537655	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179537655delT	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron|TTN_uc010zfk.1_5'Flank|TTN_uc002una.1_Intron|TTN_uc010frf.1_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGTGCCATTCTTTTTTTTTTC	0.303													6	5	---	---	---	---	
PMS1	5378	broad.mit.edu	37	2	190656342	190656342	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190656342delA	uc002urh.3	+						PMS1_uc010zga.1_Intron|PMS1_uc010zgb.1_Intron|PMS1_uc002urk.3_Intron|PMS1_uc002uri.3_Intron|PMS1_uc010zgc.1_Intron|PMS1_uc010zgd.1_Intron|PMS1_uc002urj.2_Intron|PMS1_uc010fry.1_5'Flank|PMS1_uc010frz.2_5'Flank|PMS1_uc010zfz.1_Intron	NM_000534	NP_000525	P54277	PMS1_HUMAN	postmeiotic segregation 1 isoform a						mismatch repair|reciprocal meiotic recombination	MutLalpha complex	ATP binding|ATPase activity|mismatched DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			tttcatctccaaaaaaaaaaa	0.030			Mis|N			colorectal|endometrial|ovarian		Direct_reversal_of_damage|MMR					3	3	---	---	---	---	
HIGD1A	25994	broad.mit.edu	37	3	42835470	42835470	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42835470delA	uc003cma.3	-						HIGD1A_uc010hid.2_Intron|HIGD1A_uc003cmb.3_Intron	NM_001099669	NP_001093139	Q9Y241	HIG1A_HUMAN	HIG1 domain family, member 1A isoform b						response to stress	integral to membrane|protein complex	protein binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.217)		ctccaaaaagaaaaaaaaaGT	0.124													6	3	---	---	---	---	
PBRM1	55193	broad.mit.edu	37	3	52713877	52713877	+	5'Flank	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52713877delT	uc003des.2	-						PBRM1_uc003dex.2_5'Flank|PBRM1_uc003deq.2_5'Flank|PBRM1_uc003der.2_5'Flank|PBRM1_uc003det.2_5'Flank|PBRM1_uc003deu.2_5'Flank|PBRM1_uc003dev.2_5'Flank|PBRM1_uc003dew.2_5'Flank|PBRM1_uc010hmk.1_5'Flank|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_5'Flank|PBRM1_uc003dfb.1_5'Flank	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TAGCTATAAGTTTTTTTTTTT	0.363			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								9	4	---	---	---	---	
UBA3	9039	broad.mit.edu	37	3	69111333	69111334	+	Intron	DEL	AA	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69111333_69111334delAA	uc003dno.2	-						UBA3_uc003dnq.2_Intron|UBA3_uc011bfy.1_Intron|UBA3_uc011bfz.1_Intron	NM_003968	NP_003959	Q8TBC4	UBA3_HUMAN	ubiquitin-activating enzyme 3 isoform 1						protein neddylation|proteolysis	nucleus	acid-amino acid ligase activity|ATP binding|protein heterodimerization activity			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.98e-05)|Epithelial(33;0.000363)|LUSC - Lung squamous cell carcinoma(21;0.012)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.206)|Kidney(39;0.241)		AAATTAACCTAAAACCACAGTT	0.361													60	26	---	---	---	---	
SGEF	26084	broad.mit.edu	37	3	153935967	153935967	+	Intron	DEL	T	-	-	rs113879982		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153935967delT	uc011bog.1	+						SGEF_uc011boh.1_Intron	NM_015595	NP_056410	Q96DR7	ARHGQ_HUMAN	Src homology 3 domain-containing guanine						regulation of Rho protein signal transduction	intracellular|ruffle	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TAAGAAGCACTTTTTTTTTTC	0.383													16	7	---	---	---	---	
HTT	3064	broad.mit.edu	37	4	3134126	3134126	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3134126delT	uc011bvq.1	+							NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin						establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		ATCCTGAAACTTTTTTTTTTT	0.299													3	4	---	---	---	---	
TBC1D1	23216	broad.mit.edu	37	4	38029257	38029257	+	Intron	DEL	A	-	-	rs79921949		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38029257delA	uc003gtb.2	+						TBC1D1_uc011byd.1_Intron|TBC1D1_uc010ifd.2_Intron|TBC1D1_uc011byf.1_Intron	NM_015173	NP_055988	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family,							nucleus	Rab GTPase activator activity			ovary(1)	1						attccatgtcaaaaaaaaaaa	0.164													4	3	---	---	---	---	
RFC1	5981	broad.mit.edu	37	4	39304918	39304918	+	Intron	DEL	G	-	-	rs73238567	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39304918delG	uc003gty.1	-						RFC1_uc003gtx.1_Intron	NM_002913	NP_002904	P35251	RFC1_HUMAN	replication factor C large subunit						DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|telomere maintenance via telomerase|transcription, DNA-dependent|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|enzyme activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4						TGTTGTTAAAGAAAAAAAAAA	0.393													8	4	---	---	---	---	
CENPC1	1060	broad.mit.edu	37	4	68411006	68411006	+	Intron	DEL	C	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68411006delC	uc003hdd.1	-						CENPC1_uc010ihk.1_Intron|CENPC1_uc010ihm.1_Intron	NM_001812	NP_001803	Q03188	CENPC_HUMAN	centromere protein C 1						mitotic prometaphase	condensed chromosome kinetochore|condensed nuclear chromosome, centromeric region|cytosol	DNA binding			urinary_tract(1)|lung(1)	2						GGCGCCCGTGCCCCAGCCAGC	0.622													4	2	---	---	---	---	
TAF9	6880	broad.mit.edu	37	5	68662593	68662593	+	5'UTR	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68662593delT	uc003jwc.1	-	1					RAD17_uc003jwg.2_5'Flank|TAF9_uc003jwa.2_Intron|TAF9_uc003jwb.2_Intron|TAF9_uc003jwd.1_Intron|TAF9_uc003jwe.1_Intron|TAF9_uc003jwf.1_Intron	NM_003187	NP_003178	Q16594	TAF9_HUMAN	TAF9 RNA polymerase II, TATA box binding						histone H3 acetylation|negative regulation of apoptosis|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of cell growth|positive regulation of response to cytokine stimulus|positive regulation of transcription from RNA polymerase II promoter|response to interleukin-1|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	MLL1 complex|PCAF complex|pre-snoRNP complex|STAGA complex|transcription factor TFIID complex|transcription factor TFTC complex	activating transcription factor binding|C2H2 zinc finger domain binding|p53 binding|transcription coactivator activity|transcription regulatory region DNA binding				0		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.1e-56)|Epithelial(20;9.54e-53)|all cancers(19;2.2e-48)|Lung(70;0.0176)		ATATGTAAAAttttttttttg	0.169													3	4	---	---	---	---	
MTX3	345778	broad.mit.edu	37	5	79279310	79279311	+	3'UTR	INS	-	TGA	TGA	rs3841613		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79279310_79279311insTGA	uc010jag.2	-	9					MTX3_uc010jah.2_3'UTR|MTX3_uc003kge.3_3'UTR	NM_001010891	NP_001010891	Q5HYI7	MTX3_HUMAN	metaxin 3						protein targeting to mitochondrion	mitochondrial outer membrane					0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.63e-45)|Epithelial(54;2.9e-40)|all cancers(79;4.68e-35)		AGCATTCTCTTTGTTATTAAAA	0.366													3	6	---	---	---	---	
CAST	831	broad.mit.edu	37	5	96058638	96058639	+	Intron	INS	-	TTGTT	TTGTT			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96058638_96058639insTTGTT	uc003klz.1	+						CAST_uc003klt.2_Intron|CAST_uc003klu.2_Intron|CAST_uc003klv.2_Intron|CAST_uc003klw.2_Intron|CAST_uc003klx.2_Intron|CAST_uc003kly.2_Intron|CAST_uc011cuo.1_Intron|CAST_uc011cup.1_Intron|CAST_uc011cuq.1_Intron|CAST_uc011cur.1_Intron|CAST_uc011cus.1_Intron|CAST_uc003kma.1_Intron|CAST_uc011cut.1_Intron|CAST_uc003kmb.2_Intron|CAST_uc003kmc.2_Intron|CAST_uc003kmd.2_Intron|CAST_uc003kme.2_Intron|CAST_uc003kmf.2_Intron	NM_001042443	NP_001035908	P20810	ICAL_HUMAN	calpastatin isoform i								calcium-dependent cysteine-type endopeptidase inhibitor activity|protein binding			central_nervous_system(3)|ovary(1)|kidney(1)	5		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		GTCACCTAGAGttgttttgttt	0.178													6	5	---	---	---	---	
SEC24A	10802	broad.mit.edu	37	5	133984646	133984646	+	5'UTR	DEL	T	-	-	rs61421945		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133984646delT	uc003kzs.2	+	1					SEC24A_uc011cxu.1_5'UTR	NM_021982	NP_068817	O95486	SC24A_HUMAN	SEC24 related gene family, member A						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CGCCCCCCCCTCTTCTCCCAG	0.642													6	3	---	---	---	---	
KDM3B	51780	broad.mit.edu	37	5	137735917	137735917	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137735917delT	uc003lcy.1	+						KDM3B_uc010jew.1_Intron|KDM3B_uc011cys.1_Intron	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11						TTTTCCTTGGTTTTTtttttg	0.154													4	2	---	---	---	---	
SH3PXD2B	285590	broad.mit.edu	37	5	171821317	171821317	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171821317delT	uc003mbr.2	-						SH3PXD2B_uc003mbs.1_Intron	NM_001017995	NP_001017995	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B						adipose tissue development|bone development|cell communication|cell differentiation|eye development|heart development|podosome assembly	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-5-phosphate binding|SH2 domain binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			agcaacaaaattacacataca	0.000													8	4	---	---	---	---	
GPR111	222611	broad.mit.edu	37	6	47649747	47649747	+	Frame_Shift_Del	DEL	C	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47649747delC	uc010jzj.1	+	6	1453	c.1452delC	c.(1450-1452)CGCfs	p.R484fs	GPR111_uc010jzk.1_Frame_Shift_Del_p.R416fs|GPR111_uc003oyy.2_RNA	NM_153839	NP_722581	Q8IZF7	GP111_HUMAN	G-protein coupled receptor 111	484	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1						CCTATTTACGCCATGTGTGCA	0.468													38	21	---	---	---	---	
RHAG	6005	broad.mit.edu	37	6	49604650	49604650	+	5'Flank	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49604650delA	uc003ozk.3	-						RHAG_uc010jzl.2_5'Flank|RHAG_uc010jzm.2_5'Flank	NM_000324	NP_000315	Q02094	RHAG_HUMAN	Rh-associated glycoprotein						carbon dioxide transport|cellular ion homeostasis	integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			breast(1)|skin(1)	2	Lung NSC(77;0.0255)					ACATCACAAGAAAAAAAAAAT	0.403													9	5	---	---	---	---	
MYO6	4646	broad.mit.edu	37	6	76532235	76532237	+	Intron	DEL	CTT	-	-	rs151140767		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76532235_76532237delCTT	uc003pih.1	+						MYO6_uc003pig.1_Intron|MYO6_uc003pii.1_Intron	NM_004999	NP_004990	Q9UM54	MYO6_HUMAN	myosin VI						actin filament-based movement|DNA damage response, signal transduction by p53 class mediator|endocytosis|intracellular protein transport|positive regulation of transcription from RNA polymerase II promoter|regulation of secretion|sensory perception of sound|synaptic transmission	cell cortex|clathrin coated vesicle membrane|coated pit|cytosol|DNA-directed RNA polymerase II, holoenzyme|filamentous actin|Golgi apparatus|nuclear membrane|perinuclear region of cytoplasm|ruffle membrane|unconventional myosin complex	actin filament binding|ADP binding|ATP binding|calmodulin binding|minus-end directed microfilament motor activity|protein binding			kidney(1)|pancreas(1)	2		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		TTTTTTTGTCCTTCTTTAGGTGT	0.227													6	4	---	---	---	---	
AKD1	221264	broad.mit.edu	37	6	109913998	109913999	+	Intron	INS	-	T	T	rs145661031	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109913998_109913999insT	uc003ptn.2	-							NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	adenylate kinase domain containing 1 isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1						tgattttaggatttttttccct	0.000													3	3	---	---	---	---	
PDE7B	27115	broad.mit.edu	37	6	136468301	136468302	+	Intron	INS	-	A	A	rs149299885	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136468301_136468302insA	uc003qgp.2	+						uc003qgq.1_Intron|PDE7B_uc003qgr.2_Intron	NM_018945	NP_061818	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B						signal transduction|synaptic transmission	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(1)	1	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Dyphylline(DB00651)|Ketotifen(DB00920)	aagtaaaaattaaaaaaaaaaC	0.114													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	144522213	144522213	+	IGR	DEL	A	-	-	rs10782292	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144522213delA								STX11 (9138 upstream) : UTRN (85277 downstream)																							GCGAGCGGGGAAAAAAAAAAG	0.418													4	2	---	---	---	---	
RPS6KA2	6196	broad.mit.edu	37	6	166952429	166952429	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166952429delT	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)		TGtttttttcttttttttttc	0.224													5	3	---	---	---	---	
MICALL2	79778	broad.mit.edu	37	7	1491334	1491334	+	Intron	DEL	G	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1491334delG	uc003skj.3	-						MICALL2_uc003skl.1_RNA	NM_182924	NP_891554	Q8IY33	MILK2_HUMAN	MICAL-like 2 isoform 1							cytoplasm|cytoskeleton	zinc ion binding			central_nervous_system(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		CTCGGTCTCAGGGCCTCAGTC	0.652													4	2	---	---	---	---	
COL28A1	340267	broad.mit.edu	37	7	7413337	7413337	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7413337delT	uc003src.1	-						COL28A1_uc011jxe.1_Intron	NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN	collagen, type XXVIII precursor						cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity			skin(3)	3		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TTCTGGtttcttttttttttt	0.204													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	36013505	36013505	+	IGR	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36013505delT								SEPT7 (68590 upstream) : EEPD1 (179331 downstream)																							CTACATTTTCTTTTTTTTTTT	0.308													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	64800265	64800266	+	IGR	DEL	AG	-	-	rs138057727	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64800265_64800266delAG								INTS4L1 (105666 upstream) : ZNF92 (38502 downstream)																							AATTTAGCTTAGTGTTTCTGTT	0.327													4	2	---	---	---	---	
LOC729156	729156	broad.mit.edu	37	7	66305565	66305566	+	Intron	DEL	TA	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66305565_66305566delTA	uc003tvj.1	-							NR_003934				Homo sapiens cDNA FLJ36054 fis, clone TESTI2018290.												0						CATGTAAGTGTATATATATATG	0.312													4	4	---	---	---	---	
GTF2IP1	2970	broad.mit.edu	37	7	74766257	74766258	+	Intron	INS	-	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74766257_74766258insT	uc003ubw.2	-						uc003ubz.1_Intron|PMS2L2_uc011kfp.1_Intron|PMS2L2_uc011kfq.1_Intron|uc003ucd.2_Intron|uc010lck.2_Intron					SubName: Full=cDNA FLJ61347, highly similar to General transcription factor II-I;												0						CTCCGGATAAAttttttttttt	0.248													4	2	---	---	---	---	
SPDYE3	441272	broad.mit.edu	37	7	99909114	99909115	+	5'Flank	DEL	AA	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99909114_99909115delAA	uc003uug.1	+							NM_001004351	NP_001004351	A6NKU9	SPDE3_HUMAN	speedy homolog E3												0						gtctcgaaacaaaaaaaaaaaa	0.267													6	3	---	---	---	---	
POLR2J	5439	broad.mit.edu	37	7	102114989	102114990	+	Intron	INS	-	C	C	rs145000593		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102114989_102114990insC	uc003uzp.1	-							NM_006234	NP_006225	P52435	RPB11_HUMAN	DNA directed RNA polymerase II polypeptide J						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|LRR domain binding|protein dimerization activity			pancreas(1)	1						TTGTCTGAGGTCAGGGACAGAC	0.545													2	8	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	151949945	151949945	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151949945delT	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		GGGTACATGCttttttttttt	0.139			N		medulloblastoma								4	2	---	---	---	---	
TAF2	6873	broad.mit.edu	37	8	120809706	120809710	+	Intron	DEL	TTGAG	-	-	rs34955633		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120809706_120809710delTTGAG	uc003you.2	-							NM_003184	NP_003175	Q6P1X5	TAF2_HUMAN	TBP-associated factor 2						G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GATGAGCCTTTTGAGTTATCTCAAA	0.263													4	5	---	---	---	---	
COL14A1	7373	broad.mit.edu	37	8	121312689	121312689	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121312689delT	uc003yox.2	+						COL14A1_uc003yoz.2_Intron	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			GTAATCAAGATTTTTTTTTTG	0.338													4	2	---	---	---	---	
VLDLR	7436	broad.mit.edu	37	9	2639754	2639754	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2639754delT	uc003zhk.1	+						VLDLR_uc003zhl.1_Intron|VLDLR_uc003zhm.1_Intron|VLDLR_uc003zhn.1_Intron	NM_003383	NP_003374	P98155	VLDLR_HUMAN	very low density lipoprotein receptor isoform a						cholesterol metabolic process|endocytosis|lipid transport|memory|very-low-density lipoprotein particle clearance	coated pit|integral to membrane|membrane fraction|plasma membrane|very-low-density lipoprotein particle	apolipoprotein binding|calcium ion binding|low-density lipoprotein receptor activity|very-low-density lipoprotein particle receptor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		TTGACTCAGCTTTTTTTTAGA	0.388													11	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66545695	66545695	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66545695delA	uc010mnh.1	-						uc004aef.2_Intron					Homo sapiens cDNA FLJ20444 fis, clone KAT05128.																		CTGTAAGAGGAAAAAAAAACA	0.373													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	69443337	69443338	+	Intron	INS	-	TGAA	TGAA			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69443337_69443338insTGAA	uc010mnx.1	+							NM_001098806	NP_001092276			coiled-coil domain containing 29																		ATTCTGTTGACTTATGCATGTT	0.317													4	2	---	---	---	---	
ALDH1A1	216	broad.mit.edu	37	9	75554932	75554933	+	Intron	INS	-	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75554932_75554933insT	uc004ajd.2	-						ALDH1A1_uc011lsh.1_Intron	NM_000689	NP_000680	P00352	AL1A1_HUMAN	aldehyde dehydrogenase 1A1						cellular aldehyde metabolic process|ethanol oxidation|xenobiotic metabolic process	cytosol	aldehyde dehydrogenase (NAD) activity|androgen binding|Ras GTPase activator activity|retinal dehydrogenase activity			ovary(3)|lung(1)	4					NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)	AACTTAGACAATTTTCCTAAGC	0.386													23	11	---	---	---	---	
KIF27	55582	broad.mit.edu	37	9	86451766	86451767	+	3'UTR	INS	-	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86451766_86451767insT	uc004ana.2	-	18					KIF27_uc010mpw.2_3'UTR|KIF27_uc010mpx.2_3'UTR	NM_017576	NP_060046	Q86VH2	KIF27_HUMAN	kinesin family member 27						cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5						GAAGATGTACACATCTATAGCA	0.302													4	2	---	---	---	---	
KIF27	55582	broad.mit.edu	37	9	86451774	86451776	+	3'UTR	DEL	AGC	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86451774_86451776delAGC	uc004ana.2	-	18					KIF27_uc010mpw.2_3'UTR|KIF27_uc010mpx.2_3'UTR	NM_017576	NP_060046	Q86VH2	KIF27_HUMAN	kinesin family member 27						cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5						ACACATCTATAGCATATAAAAGA	0.300													4	2	---	---	---	---	
ZNF510	22869	broad.mit.edu	37	9	99537348	99537348	+	Intron	DEL	T	-	-	rs113196824		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99537348delT	uc004awn.1	-						ZNF510_uc004awo.1_Intron	NM_014930	NP_055745	Q9Y2H8	ZN510_HUMAN	zinc finger protein 510						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)				TGtttttttgttttttttttt	0.204													8	5	---	---	---	---	
CEP110	11064	broad.mit.edu	37	9	123924715	123924715	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123924715delT	uc004bkx.1	+						CEP110_uc004blb.1_Intron|CEP110_uc010mvp.1_Intron	NM_007018	NP_008949	Q7Z7A1	CNTRL_HUMAN	centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0						TCCTTCTAGCTTTTTTTTTTT	0.209													7	4	---	---	---	---	
GSN	2934	broad.mit.edu	37	9	124074857	124074857	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124074857delA	uc004blf.1	+						GSN_uc004bld.1_Intron|GSN_uc010mvq.1_Intron|GSN_uc010mvr.1_Intron|GSN_uc010mvu.1_Intron|GSN_uc010mvt.1_Intron|GSN_uc010mvs.1_Intron|GSN_uc004ble.1_Intron|GSN_uc010mvv.1_Intron|GSN_uc011lyh.1_Intron|GSN_uc011lyi.1_Intron|GSN_uc011lyj.1_Intron|GSN_uc004blg.1_Intron	NM_000177	NP_000168	P06396	GELS_HUMAN	gelsolin isoform a precursor						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3						GAATTTGAGGAAAAAAAAAAA	0.333													7	4	---	---	---	---	
FAM157B	100132403	broad.mit.edu	37	9	141107536	141107537	+	In_Frame_Ins	INS	-	GCA	GCA			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141107536_141107537insGCA	uc011mfe.1	+	2	218_219	c.218_219insGCA	c.(217-219)CGG>CGGCAG	p.85_86insQ		NM_001145249	NP_001138721	P0CG42	F157B_HUMAN	family with sequence similarity 157, member B	85_86	Gln-rich.										0						CGgcagcggcggcagcagcagc	0.386													24	18	---	---	---	---	
MCM10	55388	broad.mit.edu	37	10	13233564	13233567	+	Intron	DEL	AAGC	-	-	rs112703555		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13233564_13233567delAAGC	uc001ima.2	+						MCM10_uc001imb.2_Intron|MCM10_uc001imc.2_Intron	NM_182751	NP_877428	Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle	nucleoplasm	metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3						ATAAATAAATaagcaagcaagcaa	0.137													9	4	---	---	---	---	
ANKRD26	22852	broad.mit.edu	37	10	27332107	27332107	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27332107delA	uc001ith.2	-						ANKRD26_uc001itg.2_Intron|ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4						aattaaaatgaaaaaaaaaaa	0.000													4	4	---	---	---	---	
ANKRD26	22852	broad.mit.edu	37	10	27375697	27375697	+	Intron	DEL	G	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27375697delG	uc001ith.2	-						ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4						AAACttttttgtttttttttt	0.144													9	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42374902	42374902	+	IGR	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42374902delT								None (None upstream) : LOC441666 (452413 downstream)																							tccaatcgggttgatttcatt	0.000													4	2	---	---	---	---	
PRKG1	5592	broad.mit.edu	37	10	52751071	52751079	+	5'UTR	DEL	GCCGCCGCC	-	-	rs66567258		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52751071_52751079delGCCGCCGCC	uc001jjm.2	+	1					PRKG1_uc010qhp.1_5'UTR	NM_001098512	NP_001091982	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		tgccgtcccagccgccgccgccgccgccg	0.435													9	4	---	---	---	---	
ANK3	288	broad.mit.edu	37	10	61815229	61815229	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61815229delT	uc001jky.2	-						ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						TACTTGGAACTTTTTTTTTTA	0.284													9	4	---	---	---	---	
TMEM26	219623	broad.mit.edu	37	10	63195752	63195752	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63195752delT	uc001jlo.2	-						TMEM26_uc010qij.1_Intron|TMEM26_uc001jlq.2_Intron	NM_178505	NP_848600	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26							integral to membrane					0	Prostate(12;0.0112)					TTTATTGGAGTTTTTTTTTGG	0.338													14	8	---	---	---	---	
C10orf76	79591	broad.mit.edu	37	10	103716105	103716106	+	Intron	DEL	TC	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103716105_103716106delTC	uc009xwy.1	-						C10orf76_uc009xwx.1_Intron	NM_024541	NP_078817	Q5T2E6	CJ076_HUMAN	hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		GCCTCCCTATTCTCTCTCTCTC	0.446													4	2	---	---	---	---	
FAM175B	23172	broad.mit.edu	37	10	126515529	126515529	+	Intron	DEL	G	-	-	rs67721163		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126515529delG	uc001lib.3	+							NM_032182	NP_115558	Q15018	F175B_HUMAN	hypothetical protein LOC23172							BRISC complex	polyubiquitin binding				0						tgggtgtggtggcacgtggct	0.000													5	5	---	---	---	---	
SLC22A10	387775	broad.mit.edu	37	11	63065426	63065427	+	Intron	INS	-	T	T	rs137941419	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63065426_63065427insT	uc009yor.2	+						SLC22A10_uc010rmo.1_Intron|SLC22A10_uc001nwu.3_Intron|SLC22A10_uc010rmp.1_Intron	NM_001039752	NP_001034841	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10							integral to membrane	transmembrane transporter activity			ovary(2)	2						ATGATTCCATCTTTTTTTTACT	0.292													7	7	---	---	---	---	
ANO1	55107	broad.mit.edu	37	11	70028923	70028923	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70028923delA	uc001opj.2	+						ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_Intron|ANO1_uc010rql.1_Intron	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						AAGAAGAAGGAAAAAAAAAAA	0.249													14	9	---	---	---	---	
FCHSD2	9873	broad.mit.edu	37	11	72549650	72549650	+	3'UTR	DEL	A	-	-	rs113447165		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72549650delA	uc009ytl.2	-	20					FCHSD2_uc010rrg.1_3'UTR|FCHSD2_uc001oth.3_3'UTR|ATG16L2_uc009ytj.1_Intron	NM_014824	NP_055639	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2								protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			AAATGACAACAAAAAAAAAAG	0.453													8	5	---	---	---	---	
PDGFD	80310	broad.mit.edu	37	11	103870622	103870626	+	Intron	DEL	TCTTG	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103870622_103870626delTCTTG	uc001phq.2	-						PDGFD_uc001php.2_Intron	NM_025208	NP_079484	Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D isoform 1						positive regulation of cell division	endoplasmic reticulum lumen|extracellular region|Golgi membrane	growth factor activity			upper_aerodigestive_tract(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		GTCTACGCTATCTTGTCTGTTAGGG	0.434													9	4	---	---	---	---	
ASAM	79827	broad.mit.edu	37	11	123007147	123007147	+	Intron	DEL	C	-	-	rs35816690		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123007147delC	uc001pyt.2	-							NM_024769	NP_079045	Q9H6B4	CLMP_HUMAN	adipocyte-specific adhesion molecule precursor							integral to membrane|tight junction					0		Breast(109;0.0025)|Lung NSC(97;0.0179)|all_lung(97;0.0182)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.73e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		ccctccttgtccccccccacc	0.403													3	3	---	---	---	---	
NCAPD3	23310	broad.mit.edu	37	11	134086631	134086631	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134086631delA	uc001qhd.1	-						NCAPD3_uc010scm.1_Intron|NCAPD3_uc009zda.1_Intron	NM_015261	NP_056076	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3						cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	5	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		ACTTCGGATGAAAAAAAAAAG	0.443													4	3	---	---	---	---	
OVCH1	341350	broad.mit.edu	37	12	29586943	29586943	+	Intron	DEL	G	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29586943delG	uc001rix.1	-							NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor						proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TAAATATAATGGCAAATGTTT	0.328													9	5	---	---	---	---	
TSPAN11	441631	broad.mit.edu	37	12	31130231	31130232	+	Intron	INS	-	CCGCCAC	CCGCCAC	rs146938941	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31130231_31130232insCCGCCAC	uc010sju.1	+						TSPAN11_uc001rjp.2_Intron|TSPAN11_uc010sjv.1_Intron	NM_001080509	NP_001073978	A1L157	TSN11_HUMAN	tetraspanin 11							integral to membrane					0	all_lung(12;3.11e-10)|Lung NSC(12;5.24e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					CCCCCGCTCCGCCGCCACCCGC	0.634													7	4	---	---	---	---	
ACVR1B	91	broad.mit.edu	37	12	52345498	52345500	+	5'UTR	DEL	GCG	-	-	rs10540557		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52345498_52345500delGCG	uc001rzn.2	+	1					ACVR1B_uc001rzl.2_5'UTR|ACVR1B_uc001rzm.2_5'UTR|ACVR1B_uc010snn.1_5'UTR	NM_004302	NP_004293	P36896	ACV1B_HUMAN	activin A receptor, type IB isoform a precursor						G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|peptidyl-threonine phosphorylation|positive regulation of activin receptor signaling pathway|positive regulation of erythrocyte differentiation|protein autophosphorylation|transmembrane receptor protein serine/threonine kinase signaling pathway	cell surface	activin receptor activity, type I|ATP binding|metal ion binding|SMAD binding|transforming growth factor beta receptor activity|ubiquitin protein ligase binding			pancreas(4)|breast(2)|ovary(1)|lung(1)|kidney(1)	9				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	CTGCTGggctgcggcggcggcgg	0.310													2	7	---	---	---	---	
OSBPL8	114882	broad.mit.edu	37	12	76749943	76749943	+	Intron	DEL	G	-	-	rs66850526		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76749943delG	uc001sye.1	-						OSBPL8_uc001syf.1_Intron|OSBPL8_uc001syg.1_Intron	NM_020841	NP_065892	Q9BZF1	OSBL8_HUMAN	oxysterol-binding protein-like protein 8 isoform						lipid transport		lipid binding			ovary(1)	1						atgtaggggtgggggggggcg	0.100													14	11	---	---	---	---	
SYT1	6857	broad.mit.edu	37	12	79702391	79702392	+	Intron	DEL	AA	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79702391_79702392delAA	uc001sys.2	+						SYT1_uc001syt.2_Intron|SYT1_uc001syu.2_Intron|SYT1_uc001syv.2_Intron	NM_001135805	NP_001129277	P21579	SYT1_HUMAN	synaptotagmin I						detection of calcium ion|glutamate secretion|neurotransmitter secretion|protein homooligomerization	cell junction|chromaffin granule membrane|clathrin sculpted acetylcholine transport vesicle membrane|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|clathrin sculpted glutamate transport vesicle membrane|clathrin sculpted monoamine transport vesicle membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	1-phosphatidylinositol binding|low-density lipoprotein particle receptor binding|metal ion binding|syntaxin-1 binding|transporter activity			skin(3)|pancreas(2)|ovary(1)	6						agaaagaaagaaaaagaaagaa	0.109													6	3	---	---	---	---	
NTS	4922	broad.mit.edu	37	12	86270630	86270630	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86270630delT	uc001tag.2	+							NM_006183	NP_006174	P30990	NEUT_HUMAN	neurotensin/neuromedin N preproprotein						regulation of blood vessel size|signal transduction	extracellular region|soluble fraction|transport vesicle	neuropeptide hormone activity				0						TTTCTTTTAGTTAAAAGAAGT	0.284													3	5	---	---	---	---	
MTMR6	9107	broad.mit.edu	37	13	25823175	25823176	+	3'UTR	INS	-	AA	AA			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25823175_25823176insAA	uc001uqf.3	-	14					MTMR6_uc001uqe.1_Intron	NM_004685	NP_004676	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6							cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)|skin(2)	4		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		GAACTGAATGTCATTCCTTGCT	0.317													4	2	---	---	---	---	
MTMR6	9107	broad.mit.edu	37	13	25823176	25823177	+	3'UTR	INS	-	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25823176_25823177insA	uc001uqf.3	-	14					MTMR6_uc001uqe.1_Intron	NM_004685	NP_004676	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6							cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)|skin(2)	4		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		AACTGAATGTCATTCCTTGCTG	0.312													4	2	---	---	---	---	
B3GALTL	145173	broad.mit.edu	37	13	31821426	31821427	+	Intron	INS	-	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31821426_31821427insT	uc010aaz.2	+							NM_194318	NP_919299	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like						fucose metabolic process	endoplasmic reticulum membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		ATAGCtttttctttttttttgg	0.139													4	2	---	---	---	---	
CCNA1	8900	broad.mit.edu	37	13	37007569	37007571	+	Intron	DEL	TTC	-	-	rs66486755		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37007569_37007571delTTC	uc001uvr.3	+						CCNA1_uc010teo.1_Intron|CCNA1_uc010abq.2_Intron|CCNA1_uc010abp.2_Intron|CCNA1_uc001uvs.3_Intron|CCNA1_uc010abr.2_Intron	NM_003914	NP_003905	P78396	CCNA1_HUMAN	cyclin A1 isoform a						cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis	cytosol|microtubule cytoskeleton|nucleoplasm	protein kinase binding			lung(2)|skin(2)|ovary(1)	5		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		ctttctttctttctttctttcgt	0.074													4	2	---	---	---	---	
LMO7	4008	broad.mit.edu	37	13	76383654	76383655	+	Intron	INS	-	CTTTC	CTTTC			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76383654_76383655insCTTTC	uc001vjv.2	+						LMO7_uc010thv.1_Intron|LMO7_uc001vjt.1_Intron|LMO7_uc010thw.1_Intron|LMO7_uc001vjw.1_Intron	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		CTACATAGACTAAAATTCTGAT	0.282													6	6	---	---	---	---	
DZIP1	22873	broad.mit.edu	37	13	96271942	96271942	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96271942delA	uc001vmk.2	-						DZIP1_uc001vml.2_Intron	NM_198968	NP_945319	Q86YF9	DZIP1_HUMAN	DAZ interacting protein 1 isoform 2						germ cell development|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)	2	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			GTTTCATGAGAAAAAAAAAAA	0.254													7	4	---	---	---	---	
SNW1	22938	broad.mit.edu	37	14	78185057	78185058	+	Intron	DEL	TT	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78185057_78185058delTT	uc001xuf.2	-						SNW1_uc010tvm.1_Intron|SNW1_uc010asu.2_Intron|SNW1_uc010tvn.1_Intron	NM_012245	NP_036377	Q13573	SNW1_HUMAN	SKI-interacting protein						negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|regulation of transcription from RNA polymerase II promoter	catalytic step 2 spliceosome|nucleoplasm	Notch binding			ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CTTTGGAttctttttttttttt	0.153													4	2	---	---	---	---	
TTC8	123016	broad.mit.edu	37	14	89336340	89336341	+	Intron	INS	-	A	A			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89336340_89336341insA	uc010ath.2	+						TTC8_uc001xxl.2_Intron|TTC8_uc010ati.2_Intron|TTC8_uc001xxm.2_Intron|TTC8_uc010atj.2_Intron|TTC8_uc001xxi.2_Intron|TTC8_uc001xxj.2_Intron|TTC8_uc001xxk.2_Intron	NM_198309	NP_938051	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8 isoform B						cilium assembly|establishment of anatomical structure orientation|sensory processing	BBSome|centrosome|cilium membrane|microtubule basal body	protein binding				0						AAATCAGTCAGAAAAAAATAAT	0.153									Bardet-Biedl_syndrome				9	5	---	---	---	---	
DYNC1H1	1778	broad.mit.edu	37	14	102515747	102515750	+	Intron	DEL	CACC	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102515747_102515750delCACC	uc001yks.2	+							NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1						cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						TGAGAGCTGACACCCTGGGCTCTG	0.618													10	6	---	---	---	---	
ZNF839	55778	broad.mit.edu	37	14	102800802	102800803	+	Intron	INS	-	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102800802_102800803insT	uc001ylo.2	+						ZNF839_uc010awk.1_Intron|ZNF839_uc001ylp.2_Intron|ZNF839_uc001ylq.1_Intron|ZNF839_uc001ylr.2_Intron|ZNF839_uc001yls.2_Intron|ZNF839_uc001ylt.2_5'Flank	NM_018335	NP_060805	A8K0R7	ZN839_HUMAN	zinc finger protein 839							intracellular	zinc ion binding			ovary(1)|central_nervous_system(1)	2						AGAACTTTCTGTTTTTTATGTT	0.361													16	15	---	---	---	---	
SQRDL	58472	broad.mit.edu	37	15	45982862	45982863	+	Intron	INS	-	CCTGA	CCTGA	rs145687436	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45982862_45982863insCCTGA	uc001zvt.2	+						SQRDL_uc001zvu.2_Intron|SQRDL_uc001zvv.2_Intron	NM_021199	NP_067022	Q9Y6N5	SQRD_HUMAN	sulfide dehydrogenase like precursor								oxidoreductase activity			ovary(1)	1		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		gattgcaaaatcctACAGTTAA	0.163													4	3	---	---	---	---	
SEMA4B	10509	broad.mit.edu	37	15	90762951	90762952	+	Intron	INS	-	G	G	rs141287044	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90762951_90762952insG	uc002boy.2	+						SEMA4B_uc002boz.2_Intron|SEMA4B_uc010uqd.1_Intron|SEMA4B_uc002bpa.2_5'UTR|SEMA4B_uc010bnv.1_5'Flank	NM_020210	NP_064595			semaphorin 4B precursor											ovary(1)|breast(1)|kidney(1)	3	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			TGGGTGTGGAAGGGGGGGCTCG	0.639											OREG0023468	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	13	11	---	---	---	---	
ADAMTS17	170691	broad.mit.edu	37	15	100649465	100649466	+	Intron	INS	-	CAGCTCCTCTAAACACGCGGCA	CAGCTCCTCTAAACACGCGGCA	rs142688382	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100649465_100649466insCAGCTCCTCTAAACACGCGGCA	uc002bvv.1	-						ADAMTS17_uc002bvx.1_Intron	NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		GGTACGCGCTCCAGGAAGCGGA	0.564													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46386117	46386117	+	IGR	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46386117delT								None (None upstream) : ANKRD26P1 (117132 downstream)																							catttgatgattgtattcctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	46386121	46386121	+	IGR	DEL	A	-	-	rs28818909		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46386121delA								None (None upstream) : ANKRD26P1 (117128 downstream)																							tgatgattgtattcctttcct	0.000													4	2	---	---	---	---	
GPR114	221188	broad.mit.edu	37	16	57598779	57598780	+	Intron	INS	-	AGGCTGGG	AGGCTGGG	rs148143320	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57598779_57598780insAGGCTGGG	uc002elx.3	+						GPR114_uc010vhr.1_Intron|GPR114_uc002ely.2_Intron	NM_153837	NP_722579	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)	1						AGCACATGCAAaggctgggagg	0.441													6	7	---	---	---	---	
MTSS1L	92154	broad.mit.edu	37	16	70708094	70708111	+	Intron	DEL	AGTCTCAACAGCTATAGT	-	-	rs67662127		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70708094_70708111delAGTCTCAACAGCTATAGT	uc002ezj.2	-							NM_138383	NP_612392	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like						filopodium assembly|signal transduction		actin binding|cytoskeletal adaptor activity|SH3 domain binding			central_nervous_system(1)	1						CCTTCAGGCCAGTCTCAACAGCTATAGTAGTCTCAACA	0.367													6	6	---	---	---	---	
RABEP1	9135	broad.mit.edu	37	17	5286226	5286226	+	Intron	DEL	A	-	-	rs1058366	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5286226delA	uc002gbm.3	+						RABEP1_uc010vsw.1_Intron|RABEP1_uc002gbl.3_Intron|NUP88_uc002gbn.2_Intron	NM_004703	NP_004694	Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1						apoptosis|cellular membrane fusion|endocytosis|protein transport	centrosome|early endosome|endocytic vesicle|recycling endosome	growth factor activity|GTPase activator activity|protein homodimerization activity			large_intestine(1)|ovary(1)	2						TCTCCCCCCCAAAAAAAAATC	0.274													6	3	---	---	---	---	
ALOXE3	59344	broad.mit.edu	37	17	8017599	8017599	+	Intron	DEL	G	-	-	rs138589278		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8017599delG	uc010cnr.2	-						ALOXE3_uc002gka.2_Intron|ALOXE3_uc010vuo.1_Intron|ALOXE3_uc010vup.1_Intron	NM_021628	NP_067641	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3 isoform 2						leukotriene biosynthetic process		iron ion binding|lipoxygenase activity			skin(3)|lung(1)|central_nervous_system(1)	5						gggagcacaagggggagacaa	0.174													8	7	---	---	---	---	
ULK2	9706	broad.mit.edu	37	17	19703008	19703008	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19703008delA	uc002gwm.3	-						ULK2_uc002gwn.2_Intron	NM_001142610	NP_001136082	Q8IYT8	ULK2_HUMAN	unc-51-like kinase 2						signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					AGAAAATTTTAAGTAACAAAC	0.348													4	2	---	---	---	---	
ULK2	9706	broad.mit.edu	37	17	19703011	19703012	+	Intron	INS	-	TG	TG			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19703011_19703012insTG	uc002gwm.3	-						ULK2_uc002gwn.2_Intron	NM_001142610	NP_001136082	Q8IYT8	ULK2_HUMAN	unc-51-like kinase 2						signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					AAATTTTAAGTAACAAACGTTT	0.351													4	2	---	---	---	---	
PSMD11	5717	broad.mit.edu	37	17	30804285	30804285	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30804285delA	uc010cta.1	+						PSMD11_uc010wbz.1_Intron|PSMD11_uc002hhm.2_Intron	NM_002815	NP_002806	O00231	PSD11_HUMAN	proteasome 26S non-ATPase subunit 11						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	protein binding			ovary(1)	1		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.109)			ATGCTATATTAGGGTCGGTCT	0.398													6	5	---	---	---	---	
TNS4	84951	broad.mit.edu	37	17	38638837	38638838	+	Intron	INS	-	AC	AC			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38638837_38638838insAC	uc010cxb.2	-						TNS4_uc002huu.3_5'Flank	NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	tensin 4 precursor						apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			ctctactaaagacacacacaca	0.000													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	43675430	43675431	+	IGR	INS	-	A	A	rs1724389		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43675430_43675431insA								LRRC37A4 (79914 upstream) : LOC644172 (2060 downstream)																							TACACTGTTTTTTTTTTTTTTT	0.277													10	5	---	---	---	---	
HOXB2	3212	broad.mit.edu	37	17	46622334	46622335	+	5'UTR	INS	-	C	C	rs147329571	by1000genomes	TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46622334_46622335insC	uc002inm.2	-	1						NM_002145	NP_002136	P14652	HXB2_HUMAN	homeobox B2						blood circulation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GATCGGAAGGGACCCCCCTCCT	0.500													10	8	---	---	---	---	
C17orf82	388407	broad.mit.edu	37	17	59489871	59489877	+	Frame_Shift_Del	DEL	GGCCTCG	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59489871_59489877delGGCCTCG	uc002izh.1	+	1	760_766	c.535_541delGGCCTCG	c.(535-543)GGCCTCGGGfs	p.G179fs		NM_203425	NP_982249	Q86X59	CQ082_HUMAN	hypothetical protein LOC388407	179_181											0						AGCCCGCCCAGGCCTCGGGCCTCGGCA	0.734													4	7	---	---	---	---	
TANC2	26115	broad.mit.edu	37	17	61417855	61417855	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61417855delA	uc002jal.3	+						TANC2_uc010wpe.1_Intron	NM_025185	NP_079461	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and								binding			ovary(2)	2						TTTTACTTGCAAAAAAAAAAA	0.299													5	3	---	---	---	---	
TTYH2	94015	broad.mit.edu	37	17	72227404	72227404	+	Intron	DEL	G	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72227404delG	uc002jkc.2	+						TTYH2_uc010wqw.1_Intron	NM_032646	NP_116035	Q9BSA4	TTYH2_HUMAN	tweety 2 isoform 1							chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4						CCAACAAGCCGAACACTTTCT	0.473													4	2	---	---	---	---	
FBF1	85302	broad.mit.edu	37	17	73907069	73907079	+	Intron	DEL	CTCAATCCTGG	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73907069_73907079delCTCAATCCTGG	uc002jqc.2	-						FBF1_uc002jqa.1_Intron|FBF1_uc010wsp.1_Intron|MRPL38_uc002jpz.1_5'Flank|FBF1_uc002jqb.2_Intron|FBF1_uc010dgr.1_Intron	NM_001080542	NP_001074011	Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1												0						agaccacagtctcaatcctggcaaggttact	0.137													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	94412	94412	+	IGR	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:94412delT								None (None upstream) : USP14 (64071 downstream)																							CTAtcttttcttttttttttt	0.139													4	3	---	---	---	---	
ALPK2	115701	broad.mit.edu	37	18	56299168	56299168	+	5'Flank	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56299168delT	uc002lhj.3	-							NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase								ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						tagccccagctacttgagagg	0.000													5	3	---	---	---	---	
ALPK2	115701	broad.mit.edu	37	18	56299170	56299171	+	5'Flank	INS	-	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56299170_56299171insT	uc002lhj.3	-							NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase								ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						gccccagctacttgagaggctg	0.000													5	3	---	---	---	---	
IL27RA	9466	broad.mit.edu	37	19	14153191	14153191	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14153191delA	uc002mxx.2	+							NM_004843	NP_004834	Q6UWB1	I27RA_HUMAN	class I cytokine receptor precursor						cell surface receptor linked signaling pathway|immune response	integral to plasma membrane	transmembrane receptor activity				0						aaaacaaaggaaaaaaaaaaa	0.259													18	8	---	---	---	---	
CYP4F22	126410	broad.mit.edu	37	19	15648967	15648967	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15648967delT	uc002nbh.3	+							NM_173483	NP_775754	Q6NT55	CP4FN_HUMAN	cytochrome P450, family 4, subfamily F,							endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen			ovary(1)|pancreas(1)	2						tgagcttcactttttttttta	0.000													6	3	---	---	---	---	
ZNF492	57615	broad.mit.edu	37	19	22835890	22835890	+	Intron	DEL	A	-	-	rs62768461		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22835890delA	uc002nqw.3	+							NM_020855	NP_065906	Q9P255	ZN492_HUMAN	zinc finger protein 492						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				GAAGTATCATACTTACCTCGA	0.318													4	4	---	---	---	---	
ZNF492	57615	broad.mit.edu	37	19	22835892	22835893	+	Intron	INS	-	A	A	rs33953225		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22835892_22835893insA	uc002nqw.3	+							NM_020855	NP_065906	Q9P255	ZN492_HUMAN	zinc finger protein 492						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				AGTATCATACTTACCTCGATGT	0.322													4	4	---	---	---	---	
SBSN	374897	broad.mit.edu	37	19	36019467	36019468	+	5'Flank	INS	-	C	C			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36019467_36019468insC	uc002oae.1	-						SBSN_uc002oad.1_5'Flank	NM_198538	NP_940940	Q6UWP8	SBSN_HUMAN	suprabasin isoform 2 precursor							extracellular region				ovary(1)	1	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CCACCTCCTCTTTCATTCCTCA	0.559													4	2	---	---	---	---	
DHDH	27294	broad.mit.edu	37	19	49442536	49442536	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49442536delA	uc002ple.1	+							NM_014475	NP_055290	Q9UQ10	DHDH_HUMAN	dimeric dihydrodiol dehydrogenase						carbohydrate metabolic process		binding|D-xylose 1-dehydrogenase (NADP+) activity|electron carrier activity|NAD(P)+ transhydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		atctctattcaaaaaaaaaag	0.224													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	50005692	50005692	+	5'Flank	DEL	G	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50005692delG	uc010yaw.1	-						MIR150_hsa-mir-150|MI0000479_5'Flank					DM004425																		aaaaaaaaaagaTACCAGCCT	0.189													4	2	---	---	---	---	
SLC27A5	10998	broad.mit.edu	37	19	59021942	59021942	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59021942delA	uc002qtc.2	-							NM_012254	NP_036386	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid						bile acid and bile salt transport|bile acid biosynthetic process|very long-chain fatty acid metabolic process	endoplasmic reticulum membrane|integral to membrane	ATP binding|cholate-CoA ligase activity|long-chain fatty acid-CoA ligase activity				0		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		ctctgcctcgaaaaaaaaaac	0.169													4	2	---	---	---	---	
KIF16B	55614	broad.mit.edu	37	20	16362053	16362056	+	Intron	DEL	TTGG	-	-	rs33941499		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16362053_16362056delTTGG	uc002wpg.1	-						KIF16B_uc002wpe.1_5'Flank|KIF16B_uc002wpf.1_5'Flank|KIF16B_uc010gch.1_Intron|KIF16B_uc010gci.1_Intron|KIF16B_uc010gcj.1_Intron	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23						cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8						TGAATACATTTTGGTGTATTAAAT	0.270													3	4	---	---	---	---	
EDEM2	55741	broad.mit.edu	37	20	33760256	33760257	+	Intron	INS	-	TGG	TGG			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33760256_33760257insTGG	uc010zuv.1	-						PROCR_uc010zuw.1_Intron|PROCR_uc002xbt.2_Intron	NM_018217	NP_060687	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding				0			BRCA - Breast invasive adenocarcinoma(18;0.00936)			GCTAGGGGAAACAGGATGACTG	0.530													3	6	---	---	---	---	
HUNK	30811	broad.mit.edu	37	21	33312758	33312759	+	Intron	INS	-	T	T			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33312758_33312759insT	uc002yph.2	+							NM_014586	NP_055401	P57058	HUNK_HUMAN	hormonally upregulated Neu-associated kinase						multicellular organismal development|signal transduction		ATP binding|protein serine/threonine kinase activity			stomach(1)|skin(1)	2						GACCTTTTGTAGAATTTATTTT	0.327													9	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	38437653	38437653	+	IGR	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38437653delT								DSCR6 (45697 upstream) : PIGP (11 downstream)																							CTGACATTGATTTTTTTTTTT	0.323													4	2	---	---	---	---	
PCNT	5116	broad.mit.edu	37	21	47832027	47832027	+	Intron	DEL	C	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47832027delC	uc002zji.3	+						PCNT_uc002zjj.2_Intron	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					TTTTTACTCTCCTTTTCTCCT	0.587													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	23708620	23708620	+	IGR	DEL	A	-	-	rs34614850		TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23708620delA								BCR (48397 upstream) : ZDHHC8P1 (24173 downstream)																							AATAGGGAAGAAAAAAAAACC	0.403													8	5	---	---	---	---	
CSF2RA	1438	broad.mit.edu	37	X	1408883	1408883	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1408883delT	uc010nct.2	+						CSF2RA_uc011mhb.1_Intron|CSF2RA_uc004cpq.2_Intron|CSF2RA_uc004cpn.2_Intron|CSF2RA_uc004cpo.2_Intron|CSF2RA_uc010ncu.2_Intron|CSF2RA_uc011mhc.1_Intron|CSF2RA_uc004cpp.2_Intron|CSF2RA_uc010ncv.2_Intron|CSF2RA_uc004cpr.2_Intron	NM_001161529	NP_001155001	P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor alpha chain							extracellular region|integral to plasma membrane	cytokine receptor activity			ovary(2)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	tgtttttgtgtttttgttttg	0.000													39	34	---	---	---	---	
ARSD	414	broad.mit.edu	37	X	2840255	2840256	+	Intron	DEL	TC	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2840255_2840256delTC	uc004cqy.2	-						ARSD_uc004cqz.1_Intron|ARSD_uc004cra.1_Intron|ARSD_uc004crb.3_Intron	NM_001669	NP_001660	P51689	ARSD_HUMAN	arylsulfatase D isoform a precursor							lysosome	arylsulfatase activity|metal ion binding				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				atggatgacatctctctctctc	0.134													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	6340076	6340076	+	IGR	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6340076delT								NLGN4X (193370 upstream) : VCX3A (111584 downstream)																							tcttttattattttttttttG	0.254													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	11114136	11114138	+	Intron	DEL	AGG	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11114136_11114138delAGG	uc004cuh.2	-						uc004cui.1_Intron					Homo sapiens clone IMAGE:4081578, mRNA sequence.																		GATTGAGACCAGGGAGGCAAAGT	0.207													8	4	---	---	---	---	
BMX	660	broad.mit.edu	37	X	15554697	15554697	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15554697delA	uc004cww.2	+						BMX_uc004cwx.3_Intron|BMX_uc004cwy.3_Intron	NM_203281	NP_975010	P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase						cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)					GATTTTCTTTAAAAAAAAAAA	0.313													6	3	---	---	---	---	
TXLNG	55787	broad.mit.edu	37	X	16837192	16837192	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16837192delT	uc004cxq.1	+						TXLNG_uc010ney.1_Intron	NM_018360	NP_060830	Q9NUQ3	TXLNG_HUMAN	gamma-taxilin						cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane				lung(1)	1						GGACGCTTAGTTTTTTTTTTT	0.303													12	8	---	---	---	---	
CENPI	2491	broad.mit.edu	37	X	100356526	100356526	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100356526delT	uc004egx.2	+						CENPI_uc011mrg.1_Intron|CENPI_uc004egy.2_Intron	NM_006733	NP_006724	Q92674	CENPI_HUMAN	centromere protein I						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm	protein binding			skin(1)	1						cctttTTTTCTTTTTTTTTTT	0.095													6	3	---	---	---	---	
CXorf57	55086	broad.mit.edu	37	X	105905039	105905039	+	Intron	DEL	T	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105905039delT	uc004emi.3	+						CXorf57_uc004emj.3_Intron	NM_018015	NP_060485	Q6NSI4	CX057_HUMAN	hypothetical protein LOC55086											ovary(1)|lung(1)|breast(1)	3						TATTTTACGGTAAAAGTTTAT	0.239													6	3	---	---	---	---	
ATP11C	286410	broad.mit.edu	37	X	138864486	138864486	+	Intron	DEL	A	-	-			TCGA-B8-4143-01A-01D-1806-10	TCGA-B8-4143-11A-01D-1251-10									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138864486delA	uc004faz.2	-						ATP11C_uc004fay.2_Intron|ATP11C_uc004fba.2_Intron	NM_173694	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C isoform a						ATP biosynthetic process	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(5)|large_intestine(3)	8	Acute lymphoblastic leukemia(192;0.000127)					actctgtctcaaaaaaaaaaa	0.085													3	3	---	---	---	---	
