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
EFCAB7	84455	broad.mit.edu	37	1	63999825	63999825	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63999825A>C	uc001dbf.2	+	6	1036	c.742A>C	c.(742-744)ACA>CCA	p.T248P		NM_032437	NP_115813	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	248							calcium ion binding				0						TGTTTCCTTCACAGTTACCAT	0.358													64	121	---	---	---	---	PASS
DPYD	1806	broad.mit.edu	37	1	97564128	97564128	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97564128T>C	uc001drv.2	-	21	2820	c.2683A>G	c.(2683-2685)ATT>GTT	p.I895V		NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	895					'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)	TTCAGTCTAATCTTGTTTTCT	0.363													68	131	---	---	---	---	PASS
TSPAN2	10100	broad.mit.edu	37	1	115601593	115601593	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115601593G>T	uc001eft.2	-	5	417	c.355C>A	c.(355-357)CAT>AAT	p.H119N		NM_005725	NP_005716	O60636	TSN2_HUMAN	tetraspan 2	119	Extracellular (Potential).					integral to membrane					0	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		GTCTGAACATGTCGGATAGCC	0.418													6	325	---	---	---	---	PASS
CHD1L	9557	broad.mit.edu	37	1	146731533	146731533	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146731533G>T	uc001epm.3	+	6	600	c.537G>T	c.(535-537)TTG>TTT	p.L179F	uc001epp.2_RNA|CHD1L_uc001epn.3_Missense_Mutation_p.L66F|CHD1L_uc010ozo.1_RNA|CHD1L_uc009wjg.2_RNA|CHD1L_uc009wjh.2_Missense_Mutation_p.L179F|CHD1L_uc010ozp.1_5'UTR|CHD1L_uc001epo.3_Intron	NM_004284	NP_004275	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein	179	Helicase ATP-binding.				chromatin remodeling|DNA repair	cytoplasm|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(3)|lung(2)|upper_aerodigestive_tract(1)	6	all_hematologic(923;0.0487)					CTCACAGGTTGAAAAACCAAA	0.353													152	308	---	---	---	---	PASS
CFH	3075	broad.mit.edu	37	1	196658588	196658588	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196658588C>G	uc001gtj.3	+	8	1243	c.1003C>G	c.(1003-1005)CTA>GTA	p.L335V	CFH_uc001gti.3_Missense_Mutation_p.L335V|CFH_uc009wyw.2_Intron|CFH_uc009wyx.2_Missense_Mutation_p.L271V	NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	335	Sushi 6.				complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6						ACATGGAGGTCTATATCATGA	0.299													9	150	---	---	---	---	PASS
C1orf116	79098	broad.mit.edu	37	1	207195634	207195634	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207195634C>A	uc001hfd.2	-	4	1734	c.1475G>T	c.(1474-1476)AGC>ATC	p.S492I	C1orf116_uc009xcb.1_Missense_Mutation_p.S246I	NM_023938	NP_076427	Q9BW04	SARG_HUMAN	specifically androgen-regulated protein isoform	492						cytoplasm|plasma membrane	receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4	Prostate(682;0.19)					AAGGTAGCTGCTCAGTCCCAC	0.542													3	41	---	---	---	---	PASS
ZNF692	55657	broad.mit.edu	37	1	249151719	249151719	+	Intron	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249151719C>T	uc001ifc.1	-						ZNF692_uc001iez.1_5'Flank|ZNF692_uc001ifa.1_5'Flank|ZNF692_uc001ifb.1_5'UTR|ZNF692_uc001ifd.1_Intron|ZNF692_uc001ife.1_Intron|ZNF692_uc001iff.1_Intron|ZNF692_uc010pzr.1_Intron	NM_017865	NP_060335	Q9BU19	ZN692_HUMAN	zinc finger protein 692 isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			GGGAAGCAGTCAGGCTGAACT	0.592													23	47	---	---	---	---	PASS
PDIA6	10130	broad.mit.edu	37	2	10933278	10933278	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10933278G>C	uc002rau.2	-	5	535	c.397C>G	c.(397-399)CAG>GAG	p.Q133E	PDIA6_uc010yjg.1_Missense_Mutation_p.Q130E|PDIA6_uc002rav.2_Missense_Mutation_p.Q185E|PDIA6_uc010yjh.1_Missense_Mutation_p.Q138E|PDIA6_uc002raw.2_Missense_Mutation_p.Q181E	NM_005742	NP_005733	Q15084	PDIA6_HUMAN	protein disulfide isomerase A6 precursor	133	Thioredoxin 1.				cell redox homeostasis|glycerol ether metabolic process|protein folding	endoplasmic reticulum lumen|ER-Golgi intermediate compartment|melanosome|plasma membrane	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		TTCACGAGCTGGCGCAGAGCA	0.522													18	68	---	---	---	---	PASS
SPTBN1	6711	broad.mit.edu	37	2	54785805	54785805	+	Intron	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54785805C>A	uc002rxu.2	+						SPTBN1_uc002rxv.1_Intron|SPTBN1_uc002rxx.2_5'UTR	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1						actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)			CGGAATGGGGCTCGCCTAAGG	0.622													4	25	---	---	---	---	PASS
RNF149	284996	broad.mit.edu	37	2	101924707	101924707	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101924707C>T	uc002taz.1	-	1	446	c.344G>A	c.(343-345)CGT>CAT	p.R115H	RNF149_uc002tax.1_RNA	NM_173647	NP_775918	Q8NC42	RN149_HUMAN	ring finger protein 149 precursor	115	PA.					integral to membrane	ligase activity|zinc ion binding			ovary(1)|breast(1)	2						GCAGCCCCCACGAGCCACCAG	0.726													4	5	---	---	---	---	PASS
RAB3GAP1	22930	broad.mit.edu	37	2	135922225	135922225	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135922225G>A	uc002tuj.2	+	23	2693	c.2668G>A	c.(2668-2670)GCT>ACT	p.A890T	RAB3GAP1_uc010fnf.2_Missense_Mutation_p.A890T|RAB3GAP1_uc010fng.2_Missense_Mutation_p.A715T|RAB3GAP1_uc010fnh.1_RNA	NM_012233	NP_036365	Q15042	RB3GP_HUMAN	RAB3 GTPase-activating protein	890						centrosome|nucleus|soluble fraction	Rab GTPase activator activity|Rab GTPase binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.117)		AAGAGGACATGCTGGCAGGAT	0.488													20	44	---	---	---	---	PASS
FMNL2	114793	broad.mit.edu	37	2	153475624	153475624	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153475624C>T	uc002tye.2	+	14	1946	c.1579C>T	c.(1579-1581)CCC>TCC	p.P527S	FMNL2_uc010fob.2_5'Flank|FMNL2_uc002tyf.2_5'Flank	NM_052905	NP_443137	Q96PY5	FMNL2_HUMAN	formin-like 2	527	Pro-rich.				actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3						AGGACCCTTGCCCCCTCCTCC	0.532													22	43	---	---	---	---	PASS
SF3B1	23451	broad.mit.edu	37	2	198261032	198261032	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198261032G>T	uc002uue.2	-	23	3335	c.3287C>A	c.(3286-3288)ACA>AAA	p.T1096K		NM_012433	NP_036565	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1 isoform 1	1096					nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding			pancreas(3)|ovary(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GTTCAGAAGTGTAGCCAATAC	0.353													8	118	---	---	---	---	PASS
ERBB4	2066	broad.mit.edu	37	2	212251657	212251657	+	Silent	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212251657C>A	uc002veg.1	-	27	3500	c.3402G>T	c.(3400-3402)GTG>GTT	p.V1134V	ERBB4_uc002veh.1_Silent_p.V1118V|ERBB4_uc010zji.1_Silent_p.V1124V|ERBB4_uc010zjj.1_Silent_p.V1108V	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	1134	Cytoplasmic (Potential).				cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)		CTGGGGCAAACACGGTGGGGT	0.522										TSP Lung(8;0.080)			54	124	---	---	---	---	PASS
RHBDD1	84236	broad.mit.edu	37	2	227729679	227729679	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227729679G>A	uc002voi.2	+	2	391	c.270G>A	c.(268-270)TGG>TGA	p.W90*	RHBDD1_uc010fxc.2_Nonsense_Mutation_p.W90*	NM_032276	NP_115652	Q8TEB9	RHBD1_HUMAN	rhomboid domain containing 1	90						integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		CCATGCTCTGGAAAGGAATAA	0.423													7	329	---	---	---	---	PASS
RHBDD1	84236	broad.mit.edu	37	2	227729702	227729702	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227729702G>C	uc002voi.2	+	2	414	c.293G>C	c.(292-294)AGA>ACA	p.R98T	RHBDD1_uc010fxc.2_Missense_Mutation_p.R98T	NM_032276	NP_115652	Q8TEB9	RHBD1_HUMAN	rhomboid domain containing 1	98						integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		CTAGAAAGAAGACTGGGAAGT	0.423													8	330	---	---	---	---	PASS
ALPI	248	broad.mit.edu	37	2	233320967	233320967	+	Missense_Mutation	SNP	G	A	A	rs61736995	byFrequency	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233320967G>A	uc002vst.3	+	1	135	c.58G>A	c.(58-60)GTC>ATC	p.V20I	ALPI_uc002vsu.3_5'UTR	NM_001631	NP_001622	P09923	PPBI_HUMAN	intestinal alkaline phosphatase precursor	20					phosphorylation	anchored to membrane|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding|protein binding			central_nervous_system(1)	1		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;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		CTCCCTGGGCGTCATCCCAGG	0.657													29	82	---	---	---	---	PASS
CNTN4	152330	broad.mit.edu	37	3	2613235	2613235	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2613235C>A	uc003bpc.2	+	3	269	c.48C>A	c.(46-48)TGC>TGA	p.C16*	CNTN4_uc003bpb.1_5'UTR|CNTN4_uc003bpd.1_Nonsense_Mutation_p.C16*	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	16					axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		TCATTTTGTGCCTTGCAGGTA	0.393													66	111	---	---	---	---	PASS
SETD5	55209	broad.mit.edu	37	3	9482170	9482170	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9482170G>A	uc003brt.2	+	8	1033	c.598G>A	c.(598-600)GAG>AAG	p.E200K	SETD5_uc003brs.1_Missense_Mutation_p.E181K|SETD5_uc003bru.2_Missense_Mutation_p.E102K|SETD5_uc003brv.2_Missense_Mutation_p.E89K|SETD5_uc010hck.2_5'Flank|SETD5_uc003brw.1_5'Flank|SETD5_uc003brx.2_5'Flank	NM_001080517	NP_001073986	Q9C0A6	SETD5_HUMAN	SET domain containing 5	200										ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		GAATTTAGATGAGAATACAAC	0.433													15	39	---	---	---	---	PASS
SETD5	55209	broad.mit.edu	37	3	9482199	9482199	+	Silent	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9482199G>A	uc003brt.2	+	8	1062	c.627G>A	c.(625-627)CGG>CGA	p.R209R	SETD5_uc003brs.1_Silent_p.R190R|SETD5_uc003bru.2_Silent_p.R111R|SETD5_uc003brv.2_Silent_p.R98R|SETD5_uc010hck.2_5'Flank|SETD5_uc003brw.1_5'Flank|SETD5_uc003brx.2_5'Flank	NM_001080517	NP_001073986	Q9C0A6	SETD5_HUMAN	SET domain containing 5	209										ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		GGGAAAATCGGATAAGACTAT	0.413													4	50	---	---	---	---	PASS
SETD5	55209	broad.mit.edu	37	3	9482254	9482254	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9482254G>A	uc003brt.2	+	8	1117	c.682G>A	c.(682-684)GAT>AAT	p.D228N	SETD5_uc003brs.1_Missense_Mutation_p.D209N|SETD5_uc003bru.2_Missense_Mutation_p.D130N|SETD5_uc003brv.2_Missense_Mutation_p.D117N|SETD5_uc010hck.2_5'Flank|SETD5_uc003brw.1_5'Flank|SETD5_uc003brx.2_5'Flank	NM_001080517	NP_001073986	Q9C0A6	SETD5_HUMAN	SET domain containing 5	228										ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		GTACAGTGCAGATGTACAGAA	0.398													8	55	---	---	---	---	PASS
SETD5	55209	broad.mit.edu	37	3	9482262	9482262	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9482262G>C	uc003brt.2	+	8	1125	c.690G>C	c.(688-690)CAG>CAC	p.Q230H	SETD5_uc003brs.1_Missense_Mutation_p.Q211H|SETD5_uc003bru.2_Missense_Mutation_p.Q132H|SETD5_uc003brv.2_Missense_Mutation_p.Q119H|SETD5_uc010hck.2_5'Flank|SETD5_uc003brw.1_5'Flank|SETD5_uc003brx.2_5'Flank	NM_001080517	NP_001073986	Q9C0A6	SETD5_HUMAN	SET domain containing 5	230										ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		CAGATGTACAGAACGCGCTTG	0.393													11	53	---	---	---	---	PASS
SETD5	55209	broad.mit.edu	37	3	9482306	9482306	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9482306G>A	uc003brt.2	+	8	1169	c.734G>A	c.(733-735)GGC>GAC	p.G245D	SETD5_uc003brs.1_Missense_Mutation_p.G226D|SETD5_uc003bru.2_Missense_Mutation_p.G147D|SETD5_uc003brv.2_Missense_Mutation_p.G134D|SETD5_uc010hck.2_5'Flank|SETD5_uc003brw.1_5'Flank|SETD5_uc003brx.2_5'Flank	NM_001080517	NP_001073986	Q9C0A6	SETD5_HUMAN	SET domain containing 5	245										ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		GAATTTGTGGGCAAACCTACT	0.408													5	39	---	---	---	---	PASS
IRAK2	3656	broad.mit.edu	37	3	10268074	10268074	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10268074C>T	uc003bve.1	+	10	1305	c.1229C>T	c.(1228-1230)ACG>ATG	p.T410M		NM_001570	NP_001561	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	410	Protein kinase.				activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|endosome membrane|plasma membrane	ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity			lung(5)|breast(3)	8						GAGGTCCTCACGGGCATCCCT	0.537													26	46	---	---	---	---	PASS
TRANK1	9881	broad.mit.edu	37	3	36874132	36874132	+	Silent	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36874132C>T	uc003cgj.2	-	12	5462	c.5160G>A	c.(5158-5160)CTG>CTA	p.L1720L		NM_014831	NP_055646	O15050	TRNK1_HUMAN	lupus brain antigen 1	2270					DNA repair		ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|central_nervous_system(1)	2						CATTTTCAAACAGAAAGTGGA	0.468													103	98	---	---	---	---	PASS
RBM5	10181	broad.mit.edu	37	3	50147121	50147121	+	Silent	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50147121G>A	uc003cyg.2	+	15	1426	c.1278G>A	c.(1276-1278)CCG>CCA	p.P426P	RBM5_uc011bdj.1_Silent_p.P370P|RBM5_uc011bdk.1_Silent_p.P254P	NM_005778	NP_005769	P52756	RBM5_HUMAN	RNA binding motif protein 5	426	Required for interaction with U2AF2.				apoptosis|negative regulation of cell proliferation|positive regulation of apoptosis|regulation of alternative nuclear mRNA splicing, via spliceosome|spliceosome assembly	nucleoplasm|spliceosomal complex	DNA binding|mRNA binding|nucleotide binding|protein binding|zinc ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTGGCTCTCCGGTAATCCTGT	0.463													88	228	---	---	---	---	PASS
PARP9	83666	broad.mit.edu	37	3	122247075	122247075	+	3'UTR	SNP	G	A	A	rs114569472	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122247075G>A	uc010hri.2	-	11					PARP9_uc003eff.3_3'UTR|PARP9_uc011bjs.1_3'UTR|PARP9_uc003efg.2_3'UTR|PARP9_uc003efi.2_3'UTR|PARP9_uc003efh.2_3'UTR	NM_001146102	NP_001139574	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9						cell migration	cytosol|nucleus	NAD+ ADP-ribosyltransferase activity|protein binding			ovary(1)|pancreas(1)|prostate(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0519)		TATGTGGCTAGTCCTTTCAAT	0.428													6	15	---	---	---	---	PASS
SR140	23350	broad.mit.edu	37	3	142773862	142773862	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142773862C>T	uc003evh.1	+	27	2951	c.2852C>T	c.(2851-2853)TCG>TTG	p.S951L	SR140_uc003evi.1_Missense_Mutation_p.S542L|SR140_uc003evj.1_RNA|SR140_uc003evk.1_Missense_Mutation_p.S950L	NM_001080415	NP_001073884	O15042	SR140_HUMAN	U2-associated SR140 protein	951	Arg/Ser-rich.				RNA processing	nucleus	nucleotide binding|RNA binding				0						TCACCAAAATCGGAGCGATCA	0.488													10	13	---	---	---	---	PASS
ZIC1	7545	broad.mit.edu	37	3	147130364	147130364	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147130364G>A	uc003ewe.2	+	2	1761	c.1042G>A	c.(1042-1044)GAC>AAC	p.D348N		NM_003412	NP_003403	Q15915	ZIC1_HUMAN	zinc finger protein of the cerebellum 1	348	C2H2-type 4.				behavior|brain development|cell differentiation|inner ear morphogenesis|pattern specification process|positive regulation of protein import into nucleus|positive regulation of transcription, DNA-dependent|regulation of smoothened signaling pathway	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2						TAACAGCAGCGACCGCAAGAA	0.532													39	208	---	---	---	---	PASS
ZIC1	7545	broad.mit.edu	37	3	147131375	147131375	+	3'UTR	SNP	G	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147131375G>C	uc003ewe.2	+	3						NM_003412	NP_003403	Q15915	ZIC1_HUMAN	zinc finger protein of the cerebellum 1						behavior|brain development|cell differentiation|inner ear morphogenesis|pattern specification process|positive regulation of protein import into nucleus|positive regulation of transcription, DNA-dependent|regulation of smoothened signaling pathway	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2						CCCTATTTAAGAGACTGATCA	0.428													19	80	---	---	---	---	PASS
AADAC	13	broad.mit.edu	37	3	151545911	151545911	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151545911G>T	uc003eze.2	+	5	1241	c.1151G>T	c.(1150-1152)AGT>ATT	p.S384I		NM_001086	NP_001077	P22760	AAAD_HUMAN	arylacetamide deacetylase	384	Lumenal (Potential).				positive regulation of triglyceride catabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	carboxylesterase activity|deacetylase activity|serine hydrolase activity|triglyceride lipase activity			skin(2)	2		Myeloproliferative disorder(1037;0.0255)|all_neural(597;0.112)	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			CTTAAAATTAGTCACAGACTT	0.348													59	111	---	---	---	---	PASS
DRD5	1816	broad.mit.edu	37	4	9784478	9784478	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9784478C>A	uc003gmb.3	+	1	1221	c.825C>A	c.(823-825)AGC>AGA	p.S275R		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	275	Cytoplasmic (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane				skin(1)	1					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)	GCCGGAGCAGCGCAGCCTGCG	0.637													9	67	---	---	---	---	PASS
PPAT	5471	broad.mit.edu	37	4	57272694	57272694	+	Silent	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57272694G>A	uc003hbr.2	-	3	571	c.369C>T	c.(367-369)GGC>GGT	p.G123G		NM_002703	NP_002694	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	123	Glutamine amidotransferase type-2.				glutamine metabolic process|nucleoside metabolic process|purine base biosynthetic process|purine ribonucleoside monophosphate biosynthetic process	cytosol	4 iron, 4 sulfur cluster binding|amidophosphoribosyltransferase activity|metal ion binding				0	Glioma(25;0.08)|all_neural(26;0.101)				L-Glutamine(DB00130)|Thioguanine(DB00352)	TTACCAATTCGCCATTATGTG	0.393													81	170	---	---	---	---	PASS
LPHN3	23284	broad.mit.edu	37	4	62598777	62598777	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62598777C>T	uc010ihh.2	+	5	873	c.700C>T	c.(700-702)CGG>TGG	p.R234W	LPHN3_uc003hcq.3_Missense_Mutation_p.R234W|LPHN3_uc010ihg.1_Missense_Mutation_p.R302W|LPHN3_uc003hcs.1_Missense_Mutation_p.R63W	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	234	Extracellular (Potential).|Olfactomedin-like.				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18						GTTTGATTTGCGGACTAGGAT	0.468													15	41	---	---	---	---	PASS
CLGN	1047	broad.mit.edu	37	4	141317358	141317358	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141317358C>T	uc011chi.1	-	10	1104	c.886G>A	c.(886-888)GAT>AAT	p.D296N	CLGN_uc003iii.2_Missense_Mutation_p.D296N	NM_001130675	NP_001124147	O14967	CLGN_HUMAN	calmegin precursor	296	Lumenal (Potential).|1-2.				protein folding	endoplasmic reticulum membrane|integral to membrane	calcium ion binding|unfolded protein binding			ovary(2)|skin(1)	3	all_hematologic(180;0.162)					TCACTTTCATCCCTGTAAATA	0.338													63	246	---	---	---	---	PASS
FGA	2243	broad.mit.edu	37	4	155507194	155507194	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155507194T>G	uc003iod.1	-	5	1445	c.1387A>C	c.(1387-1389)AAA>CAA	p.K463Q	FGA_uc003ioe.1_Missense_Mutation_p.K463Q|FGA_uc003iof.1_Intron	NM_000508	NP_000499	P02671	FIBA_HUMAN	fibrinogen, alpha polypeptide isoform alpha-E	463	By similarity.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)|breast(1)	3	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	GTAACGGTTTTAGAGCATGAA	0.468													133	312	---	---	---	---	PASS
ARAP3	64411	broad.mit.edu	37	5	141052581	141052581	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141052581C>A	uc003llm.2	-	7	1170	c.1092G>T	c.(1090-1092)GAG>GAT	p.E364D	ARAP3_uc011dbe.1_Missense_Mutation_p.E26D|ARAP3_uc003lln.2_Missense_Mutation_p.E286D|ARAP3_uc003llo.1_Missense_Mutation_p.E364D	NM_022481	NP_071926	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	364	PH 1.				cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding			breast(5)|ovary(1)|large_intestine(1)	7						GGCCCTCACCCTCGCTCTCTG	0.607													3	37	---	---	---	---	PASS
DEK	7913	broad.mit.edu	37	6	18258550	18258550	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18258550A>C	uc003ncr.1	-	3	425	c.232T>G	c.(232-234)TTT>GTT	p.F78V	DEK_uc011djf.1_Intron|DEK_uc011djg.1_Intron	NM_003472	NP_003463	P35659	DEK_HUMAN	DEK oncogene isoform 1	78					chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|histone binding			kidney(1)	1	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			GCAATTGTAAATGGCTCTCTC	0.363			T	NUP214	AML								56	186	---	---	---	---	PASS
HLA-B	3106	broad.mit.edu	37	6	31323535	31323535	+	Intron	SNP	T	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31323535T>A	uc003nth.2	-						HLA-C_uc003ntb.2_5'Flank|HLA-C_uc003ntc.1_5'Flank|HLA-B_uc010jsm.1_5'Flank|HLA-B_uc011dnk.1_5'Flank|HLA-B_uc003ntf.2_Intron|HLA-B_uc003ntg.1_Intron|HLA-B_uc003nti.1_5'Flank|HLA-B_uc010jsn.1_RNA|HLA-B_uc010jso.2_3'UTR	NM_005514	NP_005505	P01889	1B07_HUMAN	major histocompatibility complex, class I, B						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0						CTCCTATTCATTGGAAAGTTC	0.552									Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				3	10	---	---	---	---	PASS
INTS1	26173	broad.mit.edu	37	7	1538175	1538175	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1538175G>A	uc003skn.2	-	10	1399	c.1298C>T	c.(1297-1299)GCG>GTG	p.A433V	INTS1_uc003skq.2_Missense_Mutation_p.A433V	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	433					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GTCCTTGTGCGCGCTCAGCAG	0.542													18	22	---	---	---	---	PASS
ZAN	7455	broad.mit.edu	37	7	100350275	100350275	+	Silent	SNP	A	G	G			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100350275A>G	uc003uwj.2	+	14	2712	c.2547A>G	c.(2545-2547)AAA>AAG	p.K849K	ZAN_uc003uwk.2_Silent_p.K849K|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	849	66 X heptapeptide repeats (approximate) (mucin-like domain).|Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			CCATGGAAAAACCCACCATCT	0.507													39	71	---	---	---	---	PASS
KCND2	3751	broad.mit.edu	37	7	120381668	120381668	+	Silent	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120381668C>A	uc003vjj.1	+	3	2324	c.1359C>A	c.(1357-1359)CTC>CTA	p.L453L		NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related	453	Cytoplasmic (Potential).				regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)					ATGGTTTACTCAGTAATCAGC	0.358													30	48	---	---	---	---	PASS
MGAM	8972	broad.mit.edu	37	7	141754596	141754596	+	Silent	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141754596C>T	uc003vwy.2	+	27	3256	c.3202C>T	c.(3202-3204)CTG>TTG	p.L1068L		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	1068	Glucoamylase.|Lumenal (Potential).				polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCCAGTCCCTCTGAACATACC	0.433													118	84	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	142424782	142424782	+	Intron	SNP	G	A	A	rs4726571	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142424782G>A	uc011krr.1	+						uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc011ksg.1_Intron|uc011ksj.1_RNA					SubName: Full=V_segment translation product; Flags: Fragment;																		TGGACTGGGCGACTCCAGGAA	0.323													3	1	---	---	---	---	PASS
CYP7A1	1581	broad.mit.edu	37	8	59409409	59409409	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59409409G>T	uc003xtm.3	-	3	725	c.662C>A	c.(661-663)GCA>GAA	p.A221E		NM_000780	NP_000771	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A,	221					bile acid biosynthetic process|cellular lipid metabolic process|cellular response to cholesterol|cellular response to glucose stimulus|cholesterol catabolic process|cholesterol homeostasis|regulation of bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	cholesterol 7-alpha-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)				GGGGAGGCCTGCTACCAGGGC	0.493									Neonatal_Giant_Cell_Hepatitis				10	145	---	---	---	---	PASS
C5	727	broad.mit.edu	37	9	123805397	123805397	+	Silent	SNP	C	T	T	rs151322743	byFrequency	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123805397C>T	uc004bkv.2	-	3	336	c.306G>A	c.(304-306)GTG>GTA	p.V102V	C5_uc010mvm.1_Silent_p.V102V|C5_uc010mvn.1_Silent_p.V102V	NM_001735	NP_001726	P01031	CO5_HUMAN	complement component 5 preproprotein	102					activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)	CTTCCAAATACACATAAGAAA	0.299													23	80	---	---	---	---	PASS
TPRN	286262	broad.mit.edu	37	9	140086590	140086590	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140086590G>A	uc004clt.2	-	3	2011	c.2011C>T	c.(2011-2013)CGC>TGC	p.R671C	TPRN_uc004clu.2_Missense_Mutation_p.R643C	NM_173691	NP_775962	Q4KMQ1	TPRN_HUMAN	hypothetical protein LOC286262 isoform 2	704					sensory perception of sound	stereocilium					0						GGCTCGCTGCGGAAGTCCGAG	0.627													18	40	---	---	---	---	PASS
TFAM	7019	broad.mit.edu	37	10	60148567	60148567	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60148567G>A	uc001jkf.2	+	4	561	c.429G>A	c.(427-429)ATG>ATA	p.M143I	TFAM_uc001jkg.2_RNA|TFAM_uc001jkh.2_Missense_Mutation_p.M143I	NM_003201	NP_003192	Q00059	TFAM_HUMAN	transcription factor A, mitochondrial precursor	143					DNA-dependent DNA replication|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase I promoter|transcription initiation from mitochondrial promoter	mitochondrial nucleoid	mitochondrial light strand promoter sense binding|protein binding|sequence-specific DNA binding transcription factor activity				0						GGAAAGCTATGACAAAAAAAA	0.269													46	83	---	---	---	---	PASS
PLA2G12B	84647	broad.mit.edu	37	10	74714479	74714479	+	5'UTR	SNP	A	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74714479A>C	uc001jtf.1	-	1					PLA2G12B_uc009xqt.1_5'UTR|PLA2G12B_uc010qjz.1_5'UTR	NM_032562	NP_115951	Q9BX93	PG12B_HUMAN	phospholipase A2, group XIIB precursor						lipid catabolic process	extracellular region	calcium ion binding|phospholipase A2 activity			ovary(1)	1	Prostate(51;0.0198)					CTCTCCTCAAACCCCAGCCAG	0.562													11	70	---	---	---	---	PASS
CHUK	1147	broad.mit.edu	37	10	101967081	101967081	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101967081A>C	uc001kqp.2	-	11	1192	c.1137T>G	c.(1135-1137)TGT>TGG	p.C379W		NM_001278	NP_001269	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	379					I-kappaB phosphorylation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|nucleus	ATP binding|identical protein binding|IkappaB kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|breast(1)	7		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)		TATAGCTATCACAGCCTCTCT	0.313													10	20	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1213119	1213119	+	Intron	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1213119C>T	uc009ycr.1	+						uc001lsz.2_RNA	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;						cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CTCCTACAACCAGCACGACCT	0.562													4	89	---	---	---	---	PASS
DGKZ	8525	broad.mit.edu	37	11	46401517	46401517	+	3'UTR	SNP	A	G	G	rs61882687	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46401517A>G	uc001ncn.1	+	32					DGKZ_uc001nch.1_3'UTR|DGKZ_uc001ncj.1_3'UTR|DGKZ_uc010rgr.1_3'UTR|DGKZ_uc001nck.1_3'UTR|DGKZ_uc001ncl.2_3'UTR|DGKZ_uc001ncm.2_3'UTR|DGKZ_uc009yky.1_3'UTR|DGKZ_uc010rgs.1_3'UTR|MDK_uc009ykz.1_5'Flank|MDK_uc001nco.2_5'Flank|MDK_uc001ncp.2_5'Flank|MDK_uc009yla.2_5'Flank|MDK_uc009ylb.2_5'Flank|MDK_uc001ncq.2_5'Flank|MDK_uc001ncr.2_5'Flank|MDK_uc001ncs.2_5'Flank	NM_001105540	NP_001099010	Q13574	DGKZ_HUMAN	diacylglycerol kinase zeta isoform 4						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell migration|intracellular signal transduction|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of mitotic cell cycle|platelet activation	cytoplasm|lamellipodium|nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|diacylglycerol kinase activity|lipid kinase activity|metal ion binding|protein binding|protein C-terminus binding			pancreas(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		CACGGGCAGCAGGAGGGACAA	0.682													3	12	---	---	---	---	PASS
HARBI1	283254	broad.mit.edu	37	11	46625305	46625305	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46625305A>C	uc001ncy.2	-	3	1073	c.825T>G	c.(823-825)GAT>GAG	p.D275E		NM_173811	NP_776172	Q96MB7	HARB1_HUMAN	harbinger transposase derived 1	275						cytoplasm|nucleus	metal ion binding|nuclease activity				0						CCTTGGATCCATCCAGGCAGC	0.517													15	33	---	---	---	---	PASS
KCNK4	50801	broad.mit.edu	37	11	64065643	64065643	+	Silent	SNP	C	T	T	rs143683020		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64065643C>T	uc001nzj.1	+	6	1046	c.723C>T	c.(721-723)CTC>CTT	p.L241L	KCNK4_uc001nzk.1_Missense_Mutation_p.R126W|KCNK4_uc010rnk.1_Silent_p.L69L|KCNK4_uc001nzl.1_Missense_Mutation_p.R126W|KCNK4_uc001nzm.3_RNA|KCNK4_uc001nzn.1_Silent_p.L241L|KCNK4_uc001nzo.2_Silent_p.L241L|KCNK4_uc001nzp.1_Silent_p.L127L|C11orf20_uc009ypm.2_5'Flank	NM_033310	NP_201567	Q9NYG8	KCNK4_HUMAN	TRAAK	241	Helical; (Potential).					integral to membrane	potassium channel activity|voltage-gated ion channel activity				0						GGATCCTGCTCGGCCTGGCTT	0.637													16	36	---	---	---	---	PASS
FZD4	8322	broad.mit.edu	37	11	86662613	86662613	+	Silent	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86662613G>A	uc001pce.2	-	2	1491	c.1185C>T	c.(1183-1185)CTC>CTT	p.L395L	PRSS23_uc001pcc.1_RNA	NM_012193	NP_036325	Q9ULV1	FZD4_HUMAN	frizzled 4 precursor	395	Helical; Name=5; (Potential).				canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|negative regulation of cell-substrate adhesion|neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|progesterone secretion|regulation of vascular endothelial growth factor receptor signaling pathway|substrate adhesion-dependent cell spreading|vasculogenesis|Wnt receptor signaling pathway, calcium modulating pathway	cell projection|cell surface|cytoplasm	cytokine binding|G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			large_intestine(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AATAAGTAAAGAGGGGAGCCA	0.453													8	182	---	---	---	---	PASS
FZD4	8322	broad.mit.edu	37	11	86662648	86662648	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86662648G>A	uc001pce.2	-	2	1456	c.1150C>T	c.(1150-1152)CTC>TTC	p.L384F	PRSS23_uc001pcc.1_RNA	NM_012193	NP_036325	Q9ULV1	FZD4_HUMAN	frizzled 4 precursor	384	Extracellular (Potential).				canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|negative regulation of cell-substrate adhesion|neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|progesterone secretion|regulation of vascular endothelial growth factor receptor signaling pathway|substrate adhesion-dependent cell spreading|vasculogenesis|Wnt receptor signaling pathway, calcium modulating pathway	cell projection|cell surface|cytoplasm	cytokine binding|G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			large_intestine(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AGGGCATCGAGATTTTGGTTT	0.483													10	150	---	---	---	---	PASS
FZD4	8322	broad.mit.edu	37	11	86662880	86662880	+	Silent	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86662880G>A	uc001pce.2	-	2	1224	c.918C>T	c.(916-918)TTC>TTT	p.F306F	PRSS23_uc001pcc.1_RNA	NM_012193	NP_036325	Q9ULV1	FZD4_HUMAN	frizzled 4 precursor	306	Helical; Name=3; (Potential).				canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|negative regulation of cell-substrate adhesion|neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|progesterone secretion|regulation of vascular endothelial growth factor receptor signaling pathway|substrate adhesion-dependent cell spreading|vasculogenesis|Wnt receptor signaling pathway, calcium modulating pathway	cell projection|cell surface|cytoplasm	cytokine binding|G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			large_intestine(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ACATCAGCAAGAAAATTATTG	0.448													3	86	---	---	---	---	PASS
FZD4	8322	broad.mit.edu	37	11	86663024	86663024	+	Silent	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86663024G>A	uc001pce.2	-	2	1080	c.774C>T	c.(772-774)CTC>CTT	p.L258L	PRSS23_uc001pcc.1_RNA	NM_012193	NP_036325	Q9ULV1	FZD4_HUMAN	frizzled 4 precursor	258	Helical; Name=2; (Potential).				canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|negative regulation of cell-substrate adhesion|neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|progesterone secretion|regulation of vascular endothelial growth factor receptor signaling pathway|substrate adhesion-dependent cell spreading|vasculogenesis|Wnt receptor signaling pathway, calcium modulating pathway	cell projection|cell surface|cytoplasm	cytokine binding|G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			large_intestine(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AGCACATACTGAGAAATATGA	0.458													7	61	---	---	---	---	PASS
PATE2	399967	broad.mit.edu	37	11	125647403	125647403	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125647403C>T	uc001qcu.2	-	4	262	c.216G>A	c.(214-216)ATG>ATA	p.M72I	PATE2_uc010sbj.1_Missense_Mutation_p.M29I	NM_212555	NP_997720	Q6UY27	PATE2_HUMAN	prostate and testis expressed 2 precursor	72						extracellular space					0						AATAATGATACATGCTCTGCC	0.423													33	100	---	---	---	---	PASS
B4GALNT3	283358	broad.mit.edu	37	12	665808	665808	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:665808G>T	uc001qii.1	+	15	2156	c.2156G>T	c.(2155-2157)GGC>GTC	p.G719V	B4GALNT3_uc001qik.1_Missense_Mutation_p.G268V	NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta	719	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			TTGGAACAAGGCCAGCGCGTG	0.617													5	74	---	---	---	---	PASS
VWF	7450	broad.mit.edu	37	12	6153556	6153556	+	Silent	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6153556C>A	uc001qnn.1	-	18	2593	c.2343G>T	c.(2341-2343)CTG>CTT	p.L781L	VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	781	Amino-terminal.|TIL 3.				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	CTTCAGCCCGCAGGTTGTCAG	0.577													3	50	---	---	---	---	PASS
SLC5A8	160728	broad.mit.edu	37	12	101588917	101588917	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101588917C>T	uc001thz.3	-	4	883	c.493G>A	c.(493-495)GCG>ACG	p.A165T		NM_145913	NP_666018	Q8N695	SC5A8_HUMAN	solute carrier family 5 (iodide transporter),	165	Helical; (Potential).				apoptosis|sodium ion transport	apical plasma membrane|integral to membrane	monocarboxylic acid transmembrane transporter activity|passive transmembrane transporter activity|symporter activity				0						GCCACTACCGCGCCCCACAGA	0.403													29	38	---	---	---	---	PASS
PPP2R5E	5529	broad.mit.edu	37	14	63858555	63858555	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63858555T>C	uc001xgd.1	-	10	1524	c.934A>G	c.(934-936)AAA>GAA	p.K312E	PPP2R5E_uc010tsf.1_Missense_Mutation_p.K236E|PPP2R5E_uc010tsg.1_Missense_Mutation_p.K236E|PPP2R5E_uc001xge.2_Missense_Mutation_p.K312E|PPP2R5E_uc010tsh.1_Missense_Mutation_p.K312E|PPP2R5E_uc001xgf.1_RNA	NM_006246	NP_006237	Q16537	2A5E_HUMAN	epsilon isoform of regulatory subunit B56,	312					signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		CTACATGTTTTAGGCCAAAAT	0.244													40	97	---	---	---	---	PASS
MIR376C	442913	broad.mit.edu	37	14	101506035	101506035	+	RNA	SNP	G	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101506035G>T	hsa-mir-376c|MI0000776	+			c.9G>T			uc010txn.1_RNA|MIR376A2_hsa-mir-376a-2|MI0003529_5'Flank|MIR654_hsa-mir-654|MI0003676_5'Flank|MIR376B_hsa-mir-376b|MI0002466_5'Flank|uc010awc.1_5'Flank|MIR376A1_hsa-mir-376a-1|MI0000784_5'Flank|MIR300_hsa-mir-300|MI0005525_5'Flank																	0						TTAAAAGGTGGATATTCCTTC	0.383													36	69	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107062402	107062402	+	RNA	SNP	G	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107062402G>C	uc010tyt.1	-	131		c.6193C>G								Parts of antibodies, mostly variable regions.												0						TCCTGGGCCCGACTCCTGCAG	0.597													3	69	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	28600002	28600002	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28600002T>A	uc010uaf.1	-	4	258	c.240A>T	c.(238-240)CAA>CAT	p.Q80H						SubName: Full=Putative uncharacterized protein ENSP00000383535; Flags: Fragment;																		TTCGTATGGTTTGAACCTGGG	0.493													5	206	---	---	---	---	PASS
AQR	9716	broad.mit.edu	37	15	35189161	35189161	+	Silent	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35189161C>A	uc001ziv.2	-	22	2578	c.2397G>T	c.(2395-2397)ACG>ACT	p.T799T		NM_014691	NP_055506	O60306	AQR_HUMAN	aquarius	799						catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TGAACTGAATCGTATTACTGC	0.338													3	87	---	---	---	---	PASS
SPATA5L1	79029	broad.mit.edu	37	15	45695108	45695108	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45695108G>A	uc001zve.2	+	1	590	c.481G>A	c.(481-483)GCT>ACT	p.A161T	uc001zvd.2_5'Flank|SPATA5L1_uc001zvf.2_RNA	NM_024063	NP_076968	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	161						cytoplasm	ATP binding|nucleoside-triphosphatase activity			ovary(3)|skin(1)	4		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		TGGCCTGGTGGCTGCCTTGCA	0.711													7	37	---	---	---	---	PASS
SPATA5L1	79029	broad.mit.edu	37	15	45695158	45695158	+	Silent	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45695158G>A	uc001zve.2	+	1	640	c.531G>A	c.(529-531)CTG>CTA	p.L177L	uc001zvd.2_5'Flank|SPATA5L1_uc001zvf.2_RNA	NM_024063	NP_076968	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	177						cytoplasm	ATP binding|nucleoside-triphosphatase activity			ovary(3)|skin(1)	4		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		CCGCTGGGCTGGTCACCCCTC	0.731													3	26	---	---	---	---	PASS
SPATA5L1	79029	broad.mit.edu	37	15	45695169	45695169	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45695169G>T	uc001zve.2	+	1	651	c.542G>T	c.(541-543)CGT>CTT	p.R181L	uc001zvd.2_5'Flank|SPATA5L1_uc001zvf.2_RNA	NM_024063	NP_076968	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	181						cytoplasm	ATP binding|nucleoside-triphosphatase activity			ovary(3)|skin(1)	4		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		GTCACCCCTCGTACCCGCGTC	0.736													3	23	---	---	---	---	PASS
MYO1E	4643	broad.mit.edu	37	15	59564611	59564611	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59564611T>G	uc002aga.2	-	2	413	c.41A>C	c.(40-42)CAC>CCC	p.H14P		NM_004998	NP_004989	Q12965	MYO1E_HUMAN	myosin IE	14	Myosin head-like.				actin filament-based movement	myosin complex	actin binding|ATP binding|ATPase activity, coupled|calmodulin binding|microfilament motor activity			central_nervous_system(3)	3				all cancers(107;0.207)		CTTGACATTGTGGCTTTGCCA	0.438													62	131	---	---	---	---	PASS
VPS33B	26276	broad.mit.edu	37	15	91549291	91549291	+	Splice_Site	SNP	T	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91549291T>A	uc002bqp.1	-	12	1207	c.853_splice	c.e12-1	p.V285_splice	VPS33B_uc002bqq.1_Splice_Site_p.V194_splice|VPS33B_uc010uqu.1_Splice_Site_p.V258_splice	NM_018668	NP_061138	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33B (yeast homolog))						cellular membrane fusion|lysosome localization|melanosome localization|platelet alpha granule organization|protein transport|vesicle docking involved in exocytosis	late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm|platelet alpha granule	protein binding			ovary(2)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)					ATTAAACACCTGTGAGGACAG	0.473													3	77	---	---	---	---	PASS
MEFV	4210	broad.mit.edu	37	16	3304573	3304573	+	Silent	SNP	G	T	T	rs224223	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3304573G>T	uc002cun.1	-	2	535	c.495C>A	c.(493-495)GCC>GCA	p.A165A		NM_000243	NP_000234	O15553	MEFV_HUMAN	Mediterranean fever protein	165					inflammatory response	cytoplasm|microtubule|microtubule associated complex|nucleus	actin binding|zinc ion binding			central_nervous_system(2)|skin(2)|ovary(1)|lung(1)	6					Colchicine(DB01394)	GGCCCTCCGAGGCCTTCTCTC	0.766													8	2	---	---	---	---	PASS
PRM3	58531	broad.mit.edu	37	16	11367307	11367307	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11367307G>A	uc002dat.1	-	1	146	c.146C>T	c.(145-147)GCG>GTG	p.A49V	C16orf75_uc002daq.1_Intron	NM_021247	NP_067070	Q9NNZ6	PRM3_HUMAN	protamine 3	49					cell differentiation|chromosome condensation|multicellular organismal development|spermatogenesis	nucleosome|nucleus	DNA binding				0						ttcctcGCCCGCTGATGACAA	0.423													7	3	---	---	---	---	PASS
GPT2	84706	broad.mit.edu	37	16	46943652	46943652	+	Silent	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46943652C>T	uc002eel.2	+	6	727	c.633C>T	c.(631-633)ATC>ATT	p.I211I	GPT2_uc002eem.2_Silent_p.I111I	NM_133443	NP_597700	Q8TD30	ALAT2_HUMAN	glutamic pyruvate transaminase 2 isoform 1	211					2-oxoglutarate metabolic process|cellular amino acid biosynthetic process|L-alanine metabolic process	mitochondrial matrix	L-alanine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)	GTGTGATGATCCCCATCCCAC	0.537													118	81	---	---	---	---	PASS
ITFG1	81533	broad.mit.edu	37	16	47189690	47189690	+	Intron	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47189690C>A	uc002eet.2	-						ITFG1_uc010vgg.1_Intron|ITFG1_uc010vgh.1_Intron	NM_030790	NP_110417	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)				CATCTGCTTTCTGAAAAAGAA	0.333													132	275	---	---	---	---	PASS
CLEC18B	497190	broad.mit.edu	37	16	74445808	74445808	+	Intron	SNP	T	C	C	rs146209466	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74445808T>C	uc002fct.2	-						CLEC18B_uc002fcu.2_Intron|CLEC18B_uc010vmu.1_3'UTR|CLEC18B_uc010vmv.1_Intron	NM_001011880	NP_001011880	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B							extracellular region	sugar binding				0						GGGTcaggagtgagctggtca	0.294													4	50	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7578526	7578526	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7578526C>A	uc002gim.2	-	5	598	c.404G>T	c.(403-405)TGC>TTC	p.C135F	TP53_uc002gig.1_Missense_Mutation_p.C135F|TP53_uc002gih.2_Missense_Mutation_p.C135F|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.C3F|TP53_uc010cng.1_Missense_Mutation_p.C3F|TP53_uc002gii.1_Missense_Mutation_p.C3F|TP53_uc010cnh.1_Missense_Mutation_p.C135F|TP53_uc010cni.1_Missense_Mutation_p.C135F|TP53_uc002gij.2_Missense_Mutation_p.C135F|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.C42F|TP53_uc002gio.2_Missense_Mutation_p.C3F|TP53_uc010vug.1_Missense_Mutation_p.C96F	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	135	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		C -> S (in sporadic cancers; somatic mutation).|C -> Y (in sporadic cancers; somatic mutation; decreased E6-mediated binding to E6-AP).|C -> T (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|C -> R (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> F (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.C135Y(51)|p.C135F(34)|p.C135W(19)|p.C135S(10)|p.C135fs*35(9)|p.0?(7)|p.C135*(7)|p.C135G(6)|p.C135R(6)|p.C135C(5)|p.C135fs*14(2)|p.N131fs*27(2)|p.F134_T140>S(1)|p.K132_A138delKMFCQLA(1)|p.S127_Q136del10(1)|p.C135T(1)|p.V73fs*9(1)|p.C135fs*36(1)|p.C135fs*15(1)|p.Y126fs*11(1)|p.C135_A138delCQLA(1)|p.C42Y(1)|p.C3Y(1)|p.M133fs*13(1)|p.C135_T140delCQLAKT(1)|p.Q136fs*13(1)|p.C135_Q136insXXXXXX(1)|p.C135_Q136insX(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GGCCAGTTGGCAAAACATCTT	0.572		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			23	30	---	---	---	---	PASS
LRRC37A4	55073	broad.mit.edu	37	17	43587708	43587708	+	Intron	SNP	A	G	G			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43587708A>G	uc002ije.2	-						uc010wjp.1_RNA					Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						AACAACCACCATCTCCAAATC	0.348													7	82	---	---	---	---	PASS
HOXB2	3212	broad.mit.edu	37	17	46622154	46622154	+	Silent	SNP	C	G	G			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46622154C>G	uc002inm.2	-	1	240	c.120G>C	c.(118-120)TCG>TCC	p.S40S		NM_002145	NP_002136	P14652	HXB2_HUMAN	homeobox B2	40					blood circulation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GAATTAATGTCGACTCCTTGA	0.557													11	126	---	---	---	---	PASS
SMARCD2	6603	broad.mit.edu	37	17	61909469	61909469	+	3'UTR	SNP	T	G	G			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61909469T>G	uc010deb.1	-	13					SMARCD2_uc010wpt.1_3'UTR|SMARCD2_uc010dea.1_3'UTR|SMARCD2_uc010dec.1_3'UTR	NM_001098426	NP_001091896	Q92925	SMRD2_HUMAN	SWI/SNF-related matrix-associated						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	SWI/SNF complex	protein binding|transcription coactivator activity				0						ATTTGGAAATTTCCAAACCTG	0.542													4	8	---	---	---	---	PASS
KIAA0802	23255	broad.mit.edu	37	18	8798101	8798101	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8798101C>A	uc002knr.2	+	10	2390	c.2248C>A	c.(2248-2250)CAT>AAT	p.H750N	KIAA0802_uc002knq.2_Missense_Mutation_p.H709N|KIAA0802_uc002kns.2_Missense_Mutation_p.H80N	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255	1060											0						TCAGGGTGAACATCCAGAGAC	0.547													3	59	---	---	---	---	PASS
SERPINB2	5055	broad.mit.edu	37	18	61558743	61558743	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61558743C>G	uc010xeu.1	+	3	398	c.65C>G	c.(64-66)GCA>GGA	p.A22G	SERPINB2_uc002ljo.2_Missense_Mutation_p.A22G|SERPINB2_uc010dqh.2_5'UTR	NM_001143818	NP_001137290	P05120	PAI2_HUMAN	serine (or cysteine) proteinase inhibitor, clade	22					anti-apoptosis|blood coagulation|fibrinolysis|regulation of proteolysis	extracellular space|Golgi apparatus|plasma membrane	serine-type endopeptidase inhibitor activity			lung(1)|skin(1)	2		Esophageal squamous(42;0.131)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	CTGGCAAAAGCAAGCCCCACC	0.502													41	36	---	---	---	---	PASS
DUS3L	56931	broad.mit.edu	37	19	5787682	5787682	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5787682C>T	uc002mdc.2	-	6	1227	c.1130G>A	c.(1129-1131)TGT>TAT	p.C377Y	PRR22_uc010xiv.1_5'Flank|DUS3L_uc002mdd.2_Missense_Mutation_p.C135Y|DUS3L_uc010duk.2_Missense_Mutation_p.C42Y	NM_020175	NP_064560	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like isoform 1	377					tRNA processing		flavin adenine dinucleotide binding|nucleic acid binding|tRNA dihydrouridine synthase activity|zinc ion binding				0						CAGCTCGGCACACTTGGTCAT	0.627													64	139	---	---	---	---	PASS
FAM125A	93343	broad.mit.edu	37	19	17535839	17535839	+	3'UTR	SNP	A	C	C			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17535839A>C	uc002ngo.1	+	9					FAM125A_uc002ngp.1_3'UTR|FAM125A_uc002ngq.1_3'UTR	NM_138401	NP_612410	Q96EY5	F125A_HUMAN	family with sequence similarity 125, member A						protein transport	late endosome membrane|microtubule organizing center|nucleus	SH3 domain binding				0						CCCTTACTCCACCTCCCCGCC	0.657											OREG0025346	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	42	---	---	---	---	PASS
ZNF536	9745	broad.mit.edu	37	19	30935719	30935719	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30935719G>A	uc002nsu.1	+	2	1388	c.1250G>A	c.(1249-1251)GGC>GAC	p.G417D	ZNF536_uc010edd.1_Missense_Mutation_p.G417D	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	417					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)					CCCATGGGCGGCATGTCCCAG	0.632													3	82	---	---	---	---	PASS
CYP2A6	1548	broad.mit.edu	37	19	41352896	41352896	+	Missense_Mutation	SNP	G	T	T	rs138978736	byFrequency	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41352896G>T	uc002opl.3	-	5	736	c.715C>A	c.(715-717)CAG>AAG	p.Q239K	CYP2A6_uc010ehe.1_Missense_Mutation_p.Q35K|CYP2A6_uc010ehf.1_RNA	NM_000762	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A,	239					coumarin catabolic process|exogenous drug catabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|coumarin 7-hydroxylase activity|electron carrier activity|enzyme binding|heme binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Chlorzoxazone(DB00356)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Formoterol(DB00983)|Halothane(DB01159)|Letrozole(DB01006)|Methoxsalen(DB00553)|Metyrapone(DB01011)|Nicotine(DB00184)|Pilocarpine(DB01085)|Tolbutamide(DB01124)|Tranylcypromine(DB00752)	TGCAGCAACTGAAAGGCCTGT	0.547													6	111	---	---	---	---	PASS
AXL	558	broad.mit.edu	37	19	41763458	41763458	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41763458G>A	uc010ehj.2	+	19	2447	c.2257G>A	c.(2257-2259)GTG>ATG	p.V753M	CYP2F1_uc010xvw.1_Intron|AXL_uc010ehk.2_Missense_Mutation_p.V744M	NM_021913	NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase isoform 1	753	Cytoplasmic (Potential).|Protein kinase.					integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	13						ATATCCGGGCGTGGAGAACAG	0.567													63	137	---	---	---	---	PASS
HIF3A	64344	broad.mit.edu	37	19	46800328	46800328	+	5'UTR	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46800328C>T	uc002peh.2	+	1					HIF3A_uc002pef.1_5'UTR|HIF3A_uc002peg.3_5'UTR|HIF3A_uc010xxx.1_5'Flank|HIF3A_uc002pei.3_5'Flank|HIF3A_uc002pej.1_5'Flank|HIF3A_uc002pek.2_5'Flank|HIF3A_uc010xxy.1_5'Flank	NM_152795	NP_690008	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		CGGCGACTGGCGAGCCATGGC	0.716													15	14	---	---	---	---	PASS
RPL13A	23521	broad.mit.edu	37	19	49994179	49994179	+	Intron	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49994179G>A	uc002pny.2	+						RPL13A_uc002pnz.2_Intron|RPL13A_uc002poa.2_Intron|SNORD34_uc010ena.1_RNA|SNORD35A_uc010enb.1_5'Flank	NM_012423	NP_036555	P40429	RL13A_HUMAN	ribosomal protein L13a						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|large ribosomal subunit	structural constituent of ribosome				0		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;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		ATGATGTTCCGCAACTACCTA	0.587													5	108	---	---	---	---	PASS
SRMS	6725	broad.mit.edu	37	20	62172641	62172641	+	Missense_Mutation	SNP	C	G	G			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62172641C>G	uc002yfi.1	-	7	1229	c.1188G>C	c.(1186-1188)GAG>GAC	p.E396D		NM_080823	NP_543013	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory	396	Protein kinase.						ATP binding|non-membrane spanning protein tyrosine kinase activity			stomach(1)|lung(1)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			AATTGGCCGCCTCAGGCGCTG	0.617													45	229	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11097590	11097590	+	Silent	SNP	G	A	A	rs57543194		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11097590G>A	uc002yit.1	-	2	280	c.72C>T	c.(70-72)TCC>TCT	p.S24S	BAGE_uc002yix.2_RNA	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tcaccacaggggactcctcct	0.139													5	92	---	---	---	---	PASS
U2AF1	7307	broad.mit.edu	37	21	44513243	44513243	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44513243G>A	uc002zda.1	-	8	776	c.692C>T	c.(691-693)TCG>TTG	p.S231L	U2AF1_uc002zcy.1_Missense_Mutation_p.S158L|U2AF1_uc002zcz.1_Missense_Mutation_p.S158L|U2AF1_uc002zdb.1_Missense_Mutation_p.S231L|U2AF1_uc010gpi.1_3'UTR	NM_001025203	NP_001020374	Q01081	U2AF1_HUMAN	U2 small nuclear RNA auxillary factor 1 isoform	231	Arg/Gly/Ser-rich (RS domain).				mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	Cajal body|catalytic step 2 spliceosome|nuclear speck	nucleotide binding|RNA binding|zinc ion binding				0						ACGATCTCTCGACCGCCTCCT	0.408													4	33	---	---	---	---	PASS
EP300	2033	broad.mit.edu	37	22	41575089	41575089	+	3'UTR	SNP	G	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41575089G>T	uc003azl.3	+	31						NM_001429	NP_001420	Q09472	EP300_HUMAN	E1A binding protein p300						apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64						TAAGAACTGTGCAGTAGCCGT	0.333			T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				3	9	---	---	---	---	PASS
NUDT10	170685	broad.mit.edu	37	X	51075901	51075901	+	Silent	SNP	G	A	A	rs2801627	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51075901G>A	uc004dph.2	+	2	304	c.84G>A	c.(82-84)GAG>GAA	p.E28E	NUDT10_uc004dpi.3_Silent_p.E28E	NM_153183	NP_694853	Q8NFP7	NUD10_HUMAN	nudix-type motif 10	28	Nudix hydrolase.					cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding				0	Ovarian(276;0.236)					TCCGGAGCGAGCGCGAGGACG	0.687													4	12	---	---	---	---	PASS
GPR174	84636	broad.mit.edu	37	X	78426887	78426887	+	Missense_Mutation	SNP	A	G	G			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:78426887A>G	uc004edg.1	+	1	419	c.383A>G	c.(382-384)GAC>GGC	p.D128G		NM_032553	NP_115942	Q9BXC1	GP174_HUMAN	putative purinergic receptor FKSG79	128	Cytoplasmic (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(1)|central_nervous_system(1)	2						CGCTTCCATGACTGCAAACAG	0.458										HNSCC(63;0.18)			124	63	---	---	---	---	PASS
BTK	695	broad.mit.edu	37	X	100630266	100630266	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100630266C>A	uc004ehg.2	-	2	200	c.7G>T	c.(7-9)GCA>TCA	p.A3S	BTK_uc010nnn.2_Missense_Mutation_p.A3S|BTK_uc010nno.2_Missense_Mutation_p.A37S|BTK_uc004ehi.2_Missense_Mutation_p.A3S	NM_000061	NP_000052	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	3	PH.				calcium-mediated signaling|induction of apoptosis by extracellular signals|mesoderm development	cytosol|membrane raft|nucleus|plasma membrane	ATP binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol-3,4,5-trisphosphate binding			lung(3)|central_nervous_system(2)|ovary(1)	6						AGAATCACTGCGGCCATAGCT	0.468									Agammaglobulinemia_X-linked				117	62	---	---	---	---	PASS
SLC25A5	292	broad.mit.edu	37	X	118605114	118605114	+	3'UTR	SNP	C	A	A	rs75063279	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118605114C>A	uc004erh.3	+	4					LOC100303728_uc004ere.1_5'Flank|LOC100303728_uc004erg.1_5'Flank	NM_001152	NP_001143	P05141	ADT2_HUMAN	adenine nucleotide translocator 2						chromosome segregation|energy reserve metabolic process|interspecies interaction between organisms|regulation of insulin secretion|viral reproduction	integral to plasma membrane|mitochondrial inner membrane|mitochondrial nucleoid|MMXD complex	adenine transmembrane transporter activity|protein binding			ovary(1)	1					Clodronate(DB00720)	CTGTCAGTTTCTCAGTGGCAA	0.378													6	20	---	---	---	---	PASS
PNMA5	114824	broad.mit.edu	37	X	152158951	152158951	+	Missense_Mutation	SNP	T	G	G			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152158951T>G	uc010ntw.2	-	3	1531	c.1192A>C	c.(1192-1194)AGT>CGT	p.S398R	PNMA5_uc004fha.3_Missense_Mutation_p.S398R|PNMA5_uc010ntx.2_Missense_Mutation_p.S398R|PNMA5_uc004fgy.3_Missense_Mutation_p.S398R	NM_001103151	NP_001096621	Q96PV4	PNMA5_HUMAN	paraneoplastic antigen like 5	398					apoptosis					ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(192;6.56e-05)					GTGCTTTCACTGCCTAACAGC	0.597													74	42	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14097	14097	+	RNA	SNP	C	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14097C>T	uc004cox.3	+	1		c.1761C>T			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		ATTAAACTTTACTTCCTCTCT	0.388													25	2	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	16885338	16885341	+	IGR	DEL	TGTC	-	-	rs60587152		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16885338_16885341delTGTC								CROCCL2 (66142 upstream) : NBPF1 (5071 downstream)																							tgtgtgtgtgtgtctggtgtctgt	0.000													4	2	---	---	---	---	
FAF1	11124	broad.mit.edu	37	1	50985130	50985133	+	Intron	DEL	GGAA	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50985130_50985133delGGAA	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron|FAF1_uc010onc.1_Intron	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity	p.0?(1)		ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		aaggagggagggaaggaaggaagg	0.123													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	121485344	121485347	+	IGR	DEL	TGTT	-	-	rs7415636		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121485344_121485347delTGTT								LOC647121 (171658 upstream) : None (None downstream)																							ggaaacactctgtttgtaaagtct	0.005													1238	8	---	---	---	---	
BAT2L2	23215	broad.mit.edu	37	1	171452398	171452398	+	5'Flank	DEL	A	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171452398delA	uc010pmg.1	+						BAT2L2_uc001ghq.1_5'Flank|BAT2L2_uc001ghr.1_5'Flank	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2								protein C-terminus binding				0						aggaaggaagaaaaggcaggc	0.000													4	2	---	---	---	---	
PLB1	151056	broad.mit.edu	37	2	28773037	28773038	+	Intron	INS	-	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28773037_28773038insT	uc002rmb.1	+						PLB1_uc010ezj.1_Intron|PLB1_uc002rmc.2_Intron	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor						lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)					CTTCCACGTGGttttttttttt	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64603286	64603288	+	IGR	DEL	CAC	-	-	rs141929982		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64603286_64603288delCAC								PELI1 (231681 upstream) : HSPC159 (78039 downstream)																							ccaccaccatcaccaccatcacc	0.000													6	3	---	---	---	---	
MARS2	92935	broad.mit.edu	37	2	198572076	198572077	+	3'UTR	INS	-	TTC	TTC	rs150680100	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198572076_198572077insTTC	uc002uuq.2	+	1					uc002uup.2_Intron	NM_138395	NP_612404	Q96GW9	SYMM_HUMAN	methionine-tRNA synthetase 2 precursor						methionyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|methionine-tRNA ligase activity			ovary(1)|central_nervous_system(1)|skin(1)	3					L-Methionine(DB00134)	GCCTGCTCCTATTCATTTCTCT	0.416													4	2	---	---	---	---	
ALS2CR8	79800	broad.mit.edu	37	2	203839300	203839316	+	Intron	DEL	TTAGGCCATCTGAATAA	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203839300_203839316delTTAGGCCATCTGAATAA	uc002uzo.2	+						ALS2CR8_uc010zia.1_Intron|ALS2CR8_uc010zib.1_Intron|ALS2CR8_uc010zic.1_Intron|ALS2CR8_uc002uzp.2_Intron	NM_001104586	NP_001098056	Q8N187	AL2S8_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)	2						ATGGCTAGTGTTAGGCCATCTGAATAACTGCAATATA	0.207													40	10	---	---	---	---	
FAM116A	201627	broad.mit.edu	37	3	57645136	57645139	+	Intron	DEL	AAGC	-	-	rs80026743		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57645136_57645139delAAGC	uc003dja.2	-							NM_152678	NP_689891	Q8IWF6	F116A_HUMAN	hypothetical protein LOC201627											pancreas(1)	1				BRCA - Breast invasive adenocarcinoma(55;0.000621)|KIRC - Kidney renal clear cell carcinoma(284;0.0485)|Kidney(284;0.0607)		ACTCCCTGAGAAGCAAGTATGTTG	0.358													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	78400340	78400341	+	IGR	INS	-	CTCT	CTCT	rs150160407	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78400340_78400341insCTCT								ROBO2 (703679 upstream) : ROBO1 (246047 downstream)																							ttccttccttcctttcttttgc	0.168													3	7	---	---	---	---	
EPHA3	2042	broad.mit.edu	37	3	89420872	89420873	+	Intron	DEL	AC	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89420872_89420873delAC	uc003dqy.2	+						EPHA3_uc003dqx.1_Intron|EPHA3_uc010hon.1_Intron	NM_005233	NP_005224	P29320	EPHA3_HUMAN	ephrin receptor EphA3 isoform a precursor							extracellular region|integral to plasma membrane	ATP binding			lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1)	33	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TGATacacatacacacacacac	0.272										TSP Lung(6;0.00050)			4	2	---	---	---	---	
POLN	353497	broad.mit.edu	37	4	2130784	2130785	+	Intron	DEL	AA	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2130784_2130785delAA	uc003ger.2	-						POLN_uc010icg.1_Intron|POLN_uc010ich.1_Intron	NM_181808	NP_861524	Q7Z5Q5	DPOLN_HUMAN	DNA-directed DNA polymerase nu						DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			ctcttgtctcaaaaaaaaaaaa	0.104								DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					4	2	---	---	---	---	
FIP1L1	81608	broad.mit.edu	37	4	54319248	54319249	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54319248_54319249delAG	uc003gzy.2	+	16	1633_1634	c.1447_1448delAG	c.(1447-1449)AGAfs	p.R483fs	PDGFRA_uc003haa.2_Intron|FIP1L1_uc011bzu.1_Frame_Shift_Del_p.R477fs|FIP1L1_uc003gzz.2_Frame_Shift_Del_p.R409fs|FIP1L1_uc003hab.2_Frame_Shift_Del_p.R448fs|FIP1L1_uc003hac.2_Frame_Shift_Del_p.R237fs|FIP1L1_uc010ign.2_RNA|FIP1L1_uc003had.2_Frame_Shift_Del_p.P67fs|FIP1L1_uc003hae.2_Frame_Shift_Del_p.P67fs	NM_030917	NP_112179	Q6UN15	FIP1_HUMAN	FIP1 like 1 isoform 1	483	Arg-rich.|Sufficient for interaction with CPSF1 and CSTF3.|Glu-rich.				mRNA processing	nucleus	RNA binding			ovary(1)|skin(1)	2			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			agaACGCACCAGAGAGAGAGAG	0.292			T	PDGFRA	idiopathic hypereosinophilic syndrome								120	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	69575658	69575659	+	IGR	INS	-	T	T	rs35227328		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69575658_69575659insT								UGT2B15 (39284 upstream) : UGT2B10 (106054 downstream)																							TTATATTTGAGTTTTTTGATAA	0.277													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	27491130	27491131	+	IGR	DEL	TC	-	-	rs71706046	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27491130_27491131delTC								ZNF184 (50233 upstream) : HIST1H2BL (284127 downstream)																							tgtgtgtgtgtctgtgtgtgtg	0.025													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	155028499	155028499	+	IGR	DEL	A	-	-	rs147940473		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155028499delA								CNKSR3 (196746 upstream) : RBM16 (26013 downstream)																							gactccatctaaaaaaaaaaa	0.169													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	98408891	98408893	+	IGR	DEL	TAG	-	-	rs140739561	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98408891_98408893delTAG								NPTX2 (149710 upstream) : TMEM130 (35219 downstream)																							gtggtggtgatagtggtggtggt	0.000													4	3	---	---	---	---	
SMURF1	57154	broad.mit.edu	37	7	98654600	98654601	+	Intron	INS	-	A	A	rs34738644		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98654600_98654601insA	uc003upu.1	-						SMURF1_uc003upv.1_Intron|SMURF1_uc003upt.2_Intron	NM_020429	NP_065162	Q9HCE7	SMUF1_HUMAN	Smad ubiquitination regulatory factor 1 isoform						BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|lung(1)	4	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			cactccatctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
CAPZA2	830	broad.mit.edu	37	7	116532873	116532874	+	Intron	INS	-	T	T	rs139698378		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116532873_116532874insT	uc003vil.2	+						CAPZA2_uc003vik.1_Intron|CAPZA2_uc011knk.1_Intron	NM_006136	NP_006127	P47755	CAZA2_HUMAN	capping protein (actin filament) muscle Z-line,						actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex	actin binding				0	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)			TAACCAAAACCTTTTTTTTTTT	0.307													4	3	---	---	---	---	
HTRA4	203100	broad.mit.edu	37	8	38836512	38836513	+	Intron	INS	-	A	A	rs34442629		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38836512_38836513insA	uc003xmj.2	+							NM_153692	NP_710159	P83105	HTRA4_HUMAN	HtrA serine peptidase 4 precursor						proteolysis|regulation of cell growth	extracellular region	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_lung(54;0.0344)|Hepatocellular(245;0.0512)|Lung NSC(58;0.0955)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)			gactccgtctcaaaaaaaaaaa	0.198													5	3	---	---	---	---	
CA1	759	broad.mit.edu	37	8	86250862	86250873	+	Intron	DEL	TTTCTTTCTTTC	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86250862_86250873delTTTCTTTCTTTC	uc003ydh.2	-						CA13_uc003ydf.1_Intron|CA1_uc010mae.1_Intron|CA1_uc003ydi.2_Intron	NM_001738	NP_001729	P00915	CAH1_HUMAN	carbonic anhydrase I						one-carbon metabolic process	Golgi apparatus	carbonate dehydratase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(136;4.89e-06)			Acetazolamide(DB00819)|Amlodipine(DB00381)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Dichlorphenamide(DB01144)|Ethinamate(DB01031)|Ethoxzolamide(DB00311)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Levetiracetam(DB01202)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)|Verapamil(DB00661)|Zonisamide(DB00909)	tttccttctttttctttctttctttctttctt	0.099													8	4	---	---	---	---	
RECK	8434	broad.mit.edu	37	9	36123173	36123173	+	3'UTR	DEL	T	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36123173delT	uc003zyv.2	+	21					RECK_uc003zyw.2_3'UTR|RECK_uc003zyx.2_RNA	NM_021111	NP_066934	O95980	RECK_HUMAN	RECK protein precursor							anchored to membrane|peripheral to membrane of membrane fraction|plasma membrane	metalloendopeptidase inhibitor activity|serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)	3			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			CCACACAGTATTTTTTTTTTT	0.353													9	4	---	---	---	---	
AUH	549	broad.mit.edu	37	9	93983057	93983058	+	Intron	INS	-	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93983057_93983058insA	uc004arf.3	-						AUH_uc004arg.3_Intron	NM_001698	NP_001689	Q13825	AUHM_HUMAN	AU RNA binding protein/enoyl-Coenzyme A						branched chain family amino acid catabolic process|mRNA catabolic process	mitochondrial matrix	enoyl-CoA hydratase activity|methylglutaconyl-CoA hydratase activity|mRNA 3'-UTR binding				0						CCTAAAATGAGAAAAAATAAAC	0.450													65	20	---	---	---	---	
TMEM38B	55151	broad.mit.edu	37	9	108521382	108521399	+	Intron	DEL	AAGTGATGATACGAATAA	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108521382_108521399delAAGTGATGATACGAATAA	uc004bcu.1	+						TMEM38B_uc010mtn.1_Intron	NM_018112	NP_060582	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B							integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			ovary(1)|skin(1)	2						ATTGGCCAAGAAGTGATGATACGAATAATCCAACTTAT	0.353													78	17	---	---	---	---	
GAPVD1	26130	broad.mit.edu	37	9	128122940	128122940	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128122940delC	uc010mwx.2	+	27	4558	c.4232delC	c.(4231-4233)GCCfs	p.A1411fs	GAPVD1_uc004bpp.2_Frame_Shift_Del_p.A1420fs|GAPVD1_uc004bpq.2_Frame_Shift_Del_p.A1393fs|GAPVD1_uc004bpr.2_Frame_Shift_Del_p.A1372fs|GAPVD1_uc004bps.2_Frame_Shift_Del_p.A1366fs|GAPVD1_uc004bpt.2_Frame_Shift_Del_p.A426fs	NM_015635	NP_056450	Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1411	VPS9.				endocytosis|regulation of protein transport|regulation of small GTPase mediated signal transduction|signal transduction	cytosol|endosome|membrane	GTPase activating protein binding|GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4						CTGAGCCTGGCCAATGAGGAC	0.468													200	93	---	---	---	---	
MLLT10	8028	broad.mit.edu	37	10	22022438	22022438	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22022438delA	uc001iqs.2	+	20	2809	c.2461delA	c.(2461-2463)ACTfs	p.T821fs	MLLT10_uc001iqt.2_Frame_Shift_Del_p.T805fs|MLLT10_uc001iqv.2_RNA|MLLT10_uc001iqy.2_Frame_Shift_Del_p.T805fs|MLLT10_uc001ira.2_Frame_Shift_Del_p.T262fs|MLLT10_uc001irb.2_RNA	NM_004641	NP_004632	P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	821					positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2						TCTAGCTCCTACTACTGATTC	0.318			T	MLL|PICALM|CDK6	AL								41	31	---	---	---	---	
CCDC6	8030	broad.mit.edu	37	10	61618990	61618991	+	Intron	INS	-	TA	TA	rs148577678	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61618990_61618991insTA	uc001jks.3	-							NM_005436	NP_005427	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6							cytoplasm|cytoskeleton	SH3 domain binding|structural constituent of cytoskeleton			ovary(3)|breast(1)	4				Kidney(211;0.0597)		gtgtgtgtgtgtgtgtatgAAG	0.223													4	3	---	---	---	---	
OIT3	170392	broad.mit.edu	37	10	74653469	74653469	+	5'UTR	DEL	A	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74653469delA	uc001jte.1	+	1					OIT3_uc009xqs.1_RNA	NM_152635	NP_689848	Q8WWZ8	OIT3_HUMAN	oncoprotein-induced transcript 3 precursor							nuclear envelope	calcium ion binding			ovary(2)	2	Prostate(51;0.0198)					TAGAGGCCTTAAAAAAAAAAG	0.463													117	7	---	---	---	---	
RRM1	6240	broad.mit.edu	37	11	4159297	4159298	+	Intron	INS	-	G	G			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4159297_4159298insG	uc001lyw.3	+						RRM1_uc009yej.2_Intron|RRM1_uc009yei.2_Intron|RRM1_uc010qyc.1_Intron|RRM1_uc010qyd.1_Intron	NM_001033	NP_001024	P23921	RIR1_HUMAN	ribonucleoside-diphosphate reductase M1 chain						deoxyribonucleotide biosynthetic process|DNA replication|nucleobase, nucleoside and nucleotide interconversion	cytosol|nucleoplasm|ribonucleoside-diphosphate reductase complex	ATP binding|ribonucleoside-diphosphate reductase activity			skin(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)	gctggccgggcgggggctgacc	0.089													3	3	---	---	---	---	
FADS1	3992	broad.mit.edu	37	11	61580507	61580508	+	Intron	INS	-	G	G	rs143226787	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61580507_61580508insG	uc010rlm.1	-						FADS1_uc001nsh.2_Intron|FADS1_uc010rln.1_Intron	NM_013402	NP_037534	O60427	FADS1_HUMAN	fatty acid desaturase 1						cell-cell signaling|cellular response to starvation|electron transport chain|icosanoid biosynthetic process|phospholipid biosynthetic process|regulation of cell differentiation|regulation of transcription, DNA-dependent|transport	endoplasmic reticulum membrane|integral to membrane|microsome	C-5 sterol desaturase activity|heme binding|protein binding			central_nervous_system(1)	1					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	TGGTAGTGGCAGCCTTGGGGGA	0.401													6	4	---	---	---	---	
AQP11	282679	broad.mit.edu	37	11	77314986	77314986	+	Intron	DEL	T	-	-	rs144276217		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77314986delT	uc001oyj.2	+						AQP11_uc009yuu.2_Intron	NM_173039	NP_766627	Q8NBQ7	AQP11_HUMAN	aquaporin 11							cell surface|integral to membrane	transporter activity				0	all_cancers(14;1.75e-17)|all_epithelial(13;4.7e-20)|Ovarian(111;0.249)		Epithelial(5;4.73e-49)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			AAAAATAATCTTTTTTTTTTT	0.323													3	3	---	---	---	---	
FZD4	8322	broad.mit.edu	37	11	86663230	86663231	+	Frame_Shift_Ins	INS	-	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86663230_86663231insT	uc001pce.2	-	2	873_874	c.567_568insA	c.(565-570)GATCAGfs	p.D189fs	PRSS23_uc001pcc.1_RNA	NM_012193	NP_036325	Q9ULV1	FZD4_HUMAN	frizzled 4 precursor	189_190	Extracellular (Potential).				canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|negative regulation of cell-substrate adhesion|neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|progesterone secretion|regulation of vascular endothelial growth factor receptor signaling pathway|substrate adhesion-dependent cell spreading|vasculogenesis|Wnt receptor signaling pathway, calcium modulating pathway	cell projection|cell surface|cytoplasm	cytokine binding|G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			large_intestine(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CAGATGTACTGATCAGAATTGG	0.515													234	7	---	---	---	---	
ING1	3621	broad.mit.edu	37	13	111367629	111367630	+	5'UTR	INS	-	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111367629_111367630insA	uc001vri.2	+	1					CARS2_uc010tjm.1_5'Flank|uc001vre.2_5'Flank|ING1_uc001vrf.2_Intron|ING1_uc001vrg.2_Intron|ING1_uc001vrh.2_Intron	NM_005537	NP_005528	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1 isoform D						cell cycle|negative regulation of cell growth|negative regulation of cell proliferation	nucleus	zinc ion binding			ovary(1)	1	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			TGGGTGGGGGCAAAAAAAAAAA	0.515													4	2	---	---	---	---	
C14orf135	64430	broad.mit.edu	37	14	60623036	60623037	+	Intron	INS	-	A	A			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60623036_60623037insA	uc001xeq.2	+						DHRS7_uc001xes.2_Intron|DHRS7_uc001xet.2_Intron|DHRS7_uc001xeu.2_Intron	NM_022495	NP_071940	Q63HM2	CN135_HUMAN	hepatitis C virus F protein-binding protein 2							integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)		CCTTCTTAACTAAAAAAAAAAA	0.262													4	2	---	---	---	---	
TRMT5	57570	broad.mit.edu	37	14	61439184	61439185	+	3'UTR	INS	-	GGC	GGC			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61439184_61439185insGGC	uc001xff.3	-	5						NM_020810	NP_065861	Q32P41	TRMT5_HUMAN	tRNA methyltransferase 5							cytoplasm	tRNA (guanine-N1-)-methyltransferase activity			central_nervous_system(2)|large_intestine(1)	3				OV - Ovarian serous cystadenocarcinoma(108;0.0873)		CTCTTGGGCATggcggcggcgg	0.500													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	100419365	100419367	+	IGR	DEL	TGA	-	-	rs113676314		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100419365_100419367delTGA								EML1 (10972 upstream) : EVL (18784 downstream)																							gtgatggtggtgatggtgatggt	0.118													7	4	---	---	---	---	
FSD2	123722	broad.mit.edu	37	15	83438317	83438318	+	Intron	INS	-	A	A	rs71455426		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83438317_83438318insA	uc002bjd.2	-						FSD2_uc010uol.1_Intron|FSD2_uc010uom.1_Intron	NM_001007122	NP_001007123	A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing											central_nervous_system(1)	1						ggactcatctcaaaaaaaaaaa	0.149													4	2	---	---	---	---	
LOC339047	339047	broad.mit.edu	37	16	16437571	16437572	+	Intron	DEL	TG	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16437571_16437572delTG	uc002dev.3	+						LOC339047_uc010vae.1_Intron|LOC339047_uc002dew.3_Intron	NM_178541	NP_848636			hypothetical protein LOC339047												0						TCTtgtgtgttgtgtgtgtgtg	0.035													7	4	---	---	---	---	
ITFG1	81533	broad.mit.edu	37	16	47189674	47189674	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47189674delC	uc002eet.2	-	18	1857	c.1795delG	c.(1795-1797)GAAfs	p.E599fs	ITFG1_uc010vgg.1_Frame_Shift_Del_p.E344fs|ITFG1_uc010vgh.1_3'UTR	NM_030790	NP_110417	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1	599						extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)				TGTCGTTTTTCTCTATCATCT	0.323													362	208	---	---	---	---	
NDRG4	65009	broad.mit.edu	37	16	58528736	58528737	+	Intron	INS	-	AA	AA			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58528736_58528737insAA	uc002enm.2	+						NDRG4_uc002enk.2_Intron|NDRG4_uc010vif.1_Intron	NM_001130487	NP_001123959	Q9ULP0	NDRG4_HUMAN	NDRG family member 4 isoform 2						cell differentiation|cell growth|multicellular organismal development|response to stress	cytoplasm				skin(1)	1						accctgtctctaaaaaaaaaaa	0.223													4	2	---	---	---	---	
GLG1	2734	broad.mit.edu	37	16	74514458	74514459	+	Intron	INS	-	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74514458_74514459insT	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139	Q92896	GSLG1_HUMAN	golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2						ttgttcttttgttttttttttt	0.163													6	3	---	---	---	---	
DVL2	1856	broad.mit.edu	37	17	7131298	7131299	+	Frame_Shift_Ins	INS	-	G	G	rs145282702		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7131298_7131299insG	uc002gez.1	-	10	1381_1382	c.1099_1100insC	c.(1099-1101)CGAfs	p.R367fs	DVL2_uc010vtr.1_Frame_Shift_Ins_p.R361fs	NM_004422	NP_004413	O14641	DVL2_HUMAN	dishevelled 2	367					canonical Wnt receptor signaling pathway involved in regulation of cell proliferation|intracellular signal transduction|neural tube closure|positive regulation of JUN kinase activity|positive regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|segment specification|transcription from RNA polymerase II promoter	cytosol|nucleus|plasma membrane	frizzled binding|identical protein binding|signal transducer activity			lung(1)|kidney(1)	2						TCACTCACTTCGGGGGAGAGTG	0.644													30	14	---	---	---	---	
CWC25	54883	broad.mit.edu	37	17	36962874	36962874	+	Intron	DEL	A	-	-	rs78213578		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36962874delA	uc002hqu.2	-						CWC25_uc010wdv.1_Intron|CWC25_uc010wdw.1_Intron	NM_017748	NP_060218	Q9NXE8	CWC25_HUMAN	coiled-coil domain containing 49												0						ATTGAGGTGGAAAAAAAAAAT	0.428													3	3	---	---	---	---	
EPN3	55040	broad.mit.edu	37	17	48617904	48617904	+	Intron	DEL	A	-	-	rs66736597		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48617904delA	uc002ira.3	+						SPATA20_uc002irc.2_5'Flank|EPN3_uc010wms.1_Intron|EPN3_uc010wmt.1_Intron|EPN3_uc010wmu.1_Intron	NM_017957	NP_060427	Q9H201	EPN3_HUMAN	epsin 3							clathrin-coated vesicle|nucleus|perinuclear region of cytoplasm	lipid binding			ovary(1)	1	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			GAAACGCAGCAAAATGTTCTC	0.577													1	5	---	---	---	---	
CDH7	1005	broad.mit.edu	37	18	63482006	63482006	+	Intron	DEL	A	-	-	rs146003873		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63482006delA	uc002ljz.2	+						CDH7_uc002lka.2_Intron|CDH7_uc002lkb.2_Intron	NM_033646	NP_387450	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4		Esophageal squamous(42;0.129)				ATCACCttttaaaaatatttt	0.239													3	6	---	---	---	---	
C3	718	broad.mit.edu	37	19	6708128	6708131	+	Intron	DEL	TTTC	-	-	rs151210064		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6708128_6708131delTTTC	uc002mfm.2	-							NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor						complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)		tccttctctttttctttcTCTTTC	0.157													2	4	---	---	---	---	
FARSA	2193	broad.mit.edu	37	19	13036039	13036039	+	Intron	DEL	T	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13036039delT	uc002mvs.2	-						FARSA_uc002mvt.2_Intron|FARSA_uc010xmv.1_Intron|FARSA_uc010dyy.1_Intron	NM_004461	NP_004452	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|phenylalanine-tRNA ligase activity|protein binding|tRNA binding			ovary(1)	1					L-Phenylalanine(DB00120)	TTCCCACCCCttttttttttt	0.299													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	42107406	42107409	+	IGR	DEL	CACG	-	-	rs111362097		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42107406_42107409delCACG								CEACAM21 (14210 upstream) : CEACAM4 (17935 downstream)																							CCCAGTAGGacacgcacgcacgcg	0.162													4	2	---	---	---	---	
TOMM40	10452	broad.mit.edu	37	19	45406538	45406539	+	3'UTR	INS	-	G	G	rs142675166	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45406538_45406539insG	uc002ozx.3	+	10					TOMM40_uc002ozy.3_3'UTR|TOMM40_uc002paa.3_3'UTR|TOMM40_uc002ozz.2_3'UTR|APOE_uc002pab.2_5'Flank	NM_006114	NP_006105	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40						protein targeting to mitochondrion	integral to membrane of membrane fraction|integral to mitochondrial outer membrane|mitochondrial outer membrane translocase complex|pore complex	porin activity|protein transmembrane transporter activity|voltage-gated anion channel activity				0	Lung NSC(12;0.0018)|all_lung(12;0.00481)			OV - Ovarian serous cystadenocarcinoma(262;0.0033)|Epithelial(262;0.176)		CCTTGGGGGTCGGGGGGGACAT	0.668													12	6	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15948080	15948080	+	Intron	DEL	T	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15948080delT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				TGAGTGGTTATTTTTAAAACG	0.338													15	9	---	---	---	---	
DHX35	60625	broad.mit.edu	37	20	37652159	37652159	+	Intron	DEL	T	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37652159delT	uc002xjh.2	+						DHX35_uc010zwa.1_Intron|DHX35_uc010zwb.1_Intron|DHX35_uc010zwc.1_Intron	NM_021931	NP_068750	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35							catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|nucleic acid binding			lung(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)				gccctgctgattttttttttt	0.000													6	3	---	---	---	---	
WFDC8	90199	broad.mit.edu	37	20	44190379	44190380	+	Intron	DEL	GT	-	-	rs113635448		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44190379_44190380delGT	uc002xow.2	-						WFDC8_uc002xox.2_Intron	NM_181510	NP_852611	Q8IUA0	WFDC8_HUMAN	WAP four-disulfide core domain 8 precursor							extracellular region	serine-type endopeptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)				TTAAACTtgcgtgtgtgtgtgt	0.149													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	46824300	46824302	+	IGR	DEL	CCT	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46824300_46824302delCCT								SULF2 (408940 upstream) : LOC284749 (164352 downstream)																							ATGCAATTCCcctcctcctcctc	0.502													4	2	---	---	---	---	
NTSR1	4923	broad.mit.edu	37	20	61391126	61391127	+	Intron	INS	-	A	A	rs71331957		TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61391126_61391127insA	uc002ydf.2	+							NM_002531	NP_002522	P30989	NTR1_HUMAN	neurotensin receptor 1							endoplasmic reticulum|Golgi apparatus|integral to plasma membrane	neurotensin receptor activity, G-protein coupled			skin(2)|lung(1)|central_nervous_system(1)	4	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)			gactccgtctcaaaaaaaaaaa	0.257													4	4	---	---	---	---	
PI4KA	5297	broad.mit.edu	37	22	21174921	21174922	+	Intron	INS	-	A	A	rs145024136	by1000genomes	TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21174921_21174922insA	uc002zsz.3	-						PI4KA_uc010gsq.1_Intron	NM_058004	NP_477352	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase type 3 alpha						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			AAGGAAACAAGAAAAAAAAAAC	0.238													100	7	---	---	---	---	
RPS6KA3	6197	broad.mit.edu	37	X	20204678	20204679	+	Intron	INS	-	T	T			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20204678_20204679insT	uc004czu.2	-						RPS6KA3_uc011mjk.1_Intron|RPS6KA3_uc004czv.2_Intron|RPS6KA3_uc011mjl.1_Intron|RPS6KA3_uc011mjm.1_Intron	NM_004586	NP_004577	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|central nervous system development|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|skeletal system development|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(4)|stomach(1)|ovary(1)|lung(1)|breast(1)	8						GAGCTATACAGTTTTTTTTTTT	0.168													4	2	---	---	---	---	
PHF6	84295	broad.mit.edu	37	X	133528164	133528165	+	Intron	DEL	TT	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133528164_133528165delTT	uc004exj.2	+						PHF6_uc004exk.2_Intron|PHF6_uc011mvk.1_Intron|PHF6_uc004exh.2_Intron|PHF6_uc010nrr.2_Intron|PHF6_uc004exi.2_Intron	NM_001015877	NP_001015877	Q8IWS0	PHF6_HUMAN	PHD finger protein 6 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					TCTGAACttctttttttttttt	0.139													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	9789276	9789277	+	IGR	DEL	GT	-	-			TCGA-CH-5761-01A-11D-1576-08	TCGA-CH-5761-11A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9789276_9789277delGT								TTTY22 (138422 upstream) : None (None downstream)																							GGAAGACAACgtgtgtgtgtgt	0.252													4	2	---	---	---	---	
