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
CROCCL1	84809	broad.mit.edu	37	1	16946434	16946434	+	RNA	SNP	C	T	T	rs367060		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16946434C>T	uc010ocf.1	-	3		c.464G>A			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						CTCAGCCTTCCGCCGGGCCAG	0.672													7	30	---	---	---	---	PASS
CROCCL1	84809	broad.mit.edu	37	1	16946438	16946438	+	RNA	SNP	G	A	A	rs28392876	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16946438G>A	uc010ocf.1	-	3		c.460C>T			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						GCCTTCCGCCGGGCCAGCAGC	0.672													7	27	---	---	---	---	PASS
GRIK3	2899	broad.mit.edu	37	1	37335385	37335385	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37335385C>T	uc001caz.2	-	5	885	c.750G>A	c.(748-750)ATG>ATA	p.M250I	GRIK3_uc001cba.1_Missense_Mutation_p.M250I	NM_000831	NP_000822	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	250	Extracellular (Potential).				negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)	ACTCAGTCATCATGCCCATGG	0.557													16	120	---	---	---	---	PASS
ASH1L	55870	broad.mit.edu	37	1	155491017	155491017	+	Silent	SNP	T	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155491017T>C	uc009wqq.2	-	2	774	c.294A>G	c.(292-294)AAA>AAG	p.K98K	ASH1L_uc001fkt.2_Silent_p.K98K|ASH1L_uc009wqr.1_Silent_p.K98K	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	98					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TCTTTGGAGGTTTTTTAGTTC	0.373													188	256	---	---	---	---	PASS
F13B	2165	broad.mit.edu	37	1	197008365	197008365	+	3'UTR	SNP	C	T	T	rs698859	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197008365C>T	uc001gtt.1	-	12						NM_001994	NP_001985	P05160	F13B_HUMAN	coagulation factor XIII B subunit precursor						blood coagulation	extracellular region				upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						TTATAAATAACGAAATGTTCA	0.229													4	41	---	---	---	---	PASS
PRELP	5549	broad.mit.edu	37	1	203452939	203452939	+	Silent	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203452939C>T	uc001gzs.2	+	2	827	c.627C>T	c.(625-627)GAC>GAT	p.D209D	PRELP_uc001gzt.2_Silent_p.D209D	NM_002725	NP_002716	P51888	PRELP_HUMAN	proline arginine-rich end leucine-rich repeat	209	LRR 6.				skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent			ovary(1)|central_nervous_system(1)|pancreas(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.109)			GGCTGAGCGACGGCGTCTTCA	0.597													47	224	---	---	---	---	PASS
PCNXL2	80003	broad.mit.edu	37	1	233386509	233386509	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233386509T>C	uc001hvl.2	-	8	2433	c.2198A>G	c.(2197-2199)AAT>AGT	p.N733S	PCNXL2_uc009xfu.2_RNA|PCNXL2_uc009xfv.1_RNA|PCNXL2_uc001hvq.1_Missense_Mutation_p.N32S	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	733						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)				ACAGTCATTATTTGATGGTAG	0.413													5	30	---	---	---	---	PASS
MTR	4548	broad.mit.edu	37	1	237061056	237061056	+	3'UTR	SNP	A	C	C	rs2853522	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237061056A>C	uc001hyi.3	+	33					MTR_uc010pxw.1_3'UTR|MTR_uc010pxx.1_3'UTR|MTR_uc010pxy.1_3'UTR	NM_000254	NP_000245	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine						nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	GCTGACACTTACCTGCTTCTG	0.428													4	40	---	---	---	---	PASS
ITGB1BP1	9270	broad.mit.edu	37	2	9548243	9548243	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9548243T>C	uc002qzj.2	-	5	557	c.380A>G	c.(379-381)TAT>TGT	p.Y127C	ITGB1BP1_uc002qzk.2_Missense_Mutation_p.Y127C|ITGB1BP1_uc002qzl.2_RNA|ITGB1BP1_uc002qzm.2_RNA|ITGB1BP1_uc010yiy.1_Missense_Mutation_p.Y83C|ITGB1BP1_uc002qzn.1_Missense_Mutation_p.Y127C	NM_004763	NP_004754	O14713	ITBP1_HUMAN	integrin cytoplasmic domain-associated protein 1	127	PID.				cell migration|cell-matrix adhesion|intracellular protein kinase cascade	cytosol|lamellipodium|membrane|ruffle	protein binding|protein binding				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.23)		ATTACTTACATATTGATCTGA	0.353													24	126	---	---	---	---	PASS
WDR35	57539	broad.mit.edu	37	2	20162080	20162080	+	Silent	SNP	G	A	A	rs142103808		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20162080G>A	uc002rdi.2	-	11	1311	c.1203C>T	c.(1201-1203)AAC>AAT	p.N401N	WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron	NM_001006657	NP_001006658	Q9P2L0	WDR35_HUMAN	WD repeat domain 35 isoform 1	401										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTCCATCTCGTTCTCCTCCT	0.333													22	147	---	---	---	---	PASS
NCAPH	23397	broad.mit.edu	37	2	97024978	97024978	+	Intron	SNP	A	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97024978A>C	uc002svz.1	+						NCAPH_uc010fhu.1_3'UTR|NCAPH_uc010fhv.1_Intron|NCAPH_uc010yum.1_Intron|NCAPH_uc010fhw.1_Intron|NCAPH_uc010yun.1_Intron|NCAPH_uc002swa.1_Intron	NM_015341	NP_056156	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|microtubule cytoskeleton|nucleus				urinary_tract(1)|skin(1)	2		Ovarian(717;0.0221)				AGTGTAGATGACCAGCCAGTC	0.498													12	35	---	---	---	---	PASS
C2orf55	343990	broad.mit.edu	37	2	99448880	99448880	+	Silent	SNP	G	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99448880G>A	uc002szf.1	-	5	765	c.471C>T	c.(469-471)GAC>GAT	p.D157D		NM_207362	NP_997245	Q6NV74	CB055_HUMAN	hypothetical protein LOC343990	157											0						GCAGCCCGTCGTCCTCAGAGC	0.587													15	141	---	---	---	---	PASS
FASTKD1	79675	broad.mit.edu	37	2	170416921	170416921	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170416921A>G	uc002uev.3	-	5	1335	c.947T>C	c.(946-948)ATT>ACT	p.I316T	FASTKD1_uc002uew.3_RNA|FASTKD1_uc002uex.3_Missense_Mutation_p.I302T|FASTKD1_uc002uey.2_Missense_Mutation_p.I279T	NM_024622	NP_078898	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	316					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(4)	4						AGGTCCTGCAATGGGTCCCAA	0.358													120	289	---	---	---	---	PASS
BMPR2	659	broad.mit.edu	37	2	203421005	203421005	+	Nonsense_Mutation	SNP	C	T	T	rs137852748		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203421005C>T	uc002uzf.3	+	12	3765	c.2617C>T	c.(2617-2619)CGA>TGA	p.R873*	BMPR2_uc010ftr.2_Intron	NM_001204	NP_001195	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor type II	873	Cytoplasmic (Potential).				anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9						TTTACTGAGACGAGAGCAACA	0.478													93	201	---	---	---	---	PASS
SPAG16	79582	broad.mit.edu	37	2	214239769	214239769	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214239769G>A	uc002veq.2	+	9	960	c.868G>A	c.(868-870)GGT>AGT	p.G290S	SPAG16_uc010fuz.1_Missense_Mutation_p.G141S|SPAG16_uc002ver.2_Missense_Mutation_p.G236S|SPAG16_uc010zjk.1_Missense_Mutation_p.G196S	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1	290					cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		TGCACCAGAAGGTCCTACTCA	0.318													27	55	---	---	---	---	PASS
IRS1	3667	broad.mit.edu	37	2	227662870	227662870	+	Silent	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227662870C>T	uc002voh.3	-	1	637	c.585G>A	c.(583-585)GTG>GTA	p.V195V		NM_005544	NP_005535	P35568	IRS1_HUMAN	insulin receptor substrate 1	195	IRS-type PTB.				fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity	caveola|cytosol|insulin receptor complex|microsome|nucleus	insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1)	12		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		AGTTCAGCTTCACGAAGCTGA	0.567											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	33	72	---	---	---	---	PASS
SRGAP3	9901	broad.mit.edu	37	3	9101809	9101809	+	Intron	SNP	C	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9101809C>A	uc003brf.1	-						SRGAP3_uc003brg.1_Intron|SRGAP3_uc003bri.1_Intron|SRGAP3_uc003brk.2_3'UTR|SRGAP3_uc003brj.1_Intron	NM_014850	NP_055665	O43295	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 3						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		GCTGTGGCTACCCGAGAATGT	0.567			T	RAF1	pilocytic astrocytoma								4	7	---	---	---	---	PASS
TRAK1	22906	broad.mit.edu	37	3	42251562	42251562	+	Intron	SNP	A	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42251562A>G	uc003cky.2	+						TRAK1_uc011azh.1_Missense_Mutation_p.E683G|TRAK1_uc011azi.1_Intron|TRAK1_uc011azj.1_Missense_Mutation_p.E609G|TRAK1_uc003cla.2_Missense_Mutation_p.E625G	NM_001042646	NP_001036111	Q9UPV9	TRAK1_HUMAN	OGT(O-Glc-NAc transferase)-interacting protein						endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1						GAGATGCAGGAGCCGCCAGCG	0.522													8	38	---	---	---	---	PASS
CCK	885	broad.mit.edu	37	3	42304784	42304784	+	Intron	SNP	A	G	G	rs1868522	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42304784A>G	uc003clc.1	-						CCK_uc003cld.1_Intron|CCK_uc011azk.1_3'UTR	NM_000729	NP_000720	P06307	CCKN_HUMAN	cholecystokinin preproprotein						axonogenesis|eating behavior|neuron migration		neuropeptide hormone activity			central_nervous_system(1)	1		Ovarian(412;0.0728)		KIRC - Kidney renal clear cell carcinoma(284;0.219)		GGACCGCCAGAAATCATGTTG	0.463													4	45	---	---	---	---	PASS
CYP8B1	1582	broad.mit.edu	37	3	42915969	42915969	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42915969A>T	uc003cmh.2	-	1	1665	c.1340T>A	c.(1339-1341)CTC>CAC	p.L447H	CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmg.2_Intron|CYP8B1_uc010hif.2_Missense_Mutation_p.L447H	NM_004391	NP_004382	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B,	447					bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity|electron carrier activity|heme binding|oxygen binding|sterol 12-alpha-hydroxylase activity			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		CACCTCACTGAGTGCAAAGAA	0.542													38	57	---	---	---	---	PASS
KIF15	56992	broad.mit.edu	37	3	44816791	44816791	+	Silent	SNP	T	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44816791T>C	uc003cnx.3	+	3	257	c.108T>C	c.(106-108)CCT>CCC	p.P36P	KIF15_uc010hiq.2_5'UTR	NM_020242	NP_064627	Q9NS87	KIF15_HUMAN	kinesin family member 15	36	Kinesin-motor.				blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		TTCGTCCTCCTGCAGAAAGAT	0.438													84	108	---	---	---	---	PASS
COL7A1	1294	broad.mit.edu	37	3	48607732	48607732	+	Silent	SNP	G	A	A	rs142651194	byFrequency	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48607732G>A	uc003ctz.2	-	97	7417	c.7416C>T	c.(7414-7416)GGC>GGT	p.G2472G		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	2472	Triple-helical region.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCCCACGCTCGCCTCGGGGCC	0.617													21	88	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52651419	52651419	+	Nonsense_Mutation	SNP	A	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52651419A>T	uc003des.2	-	14	1689	c.1677T>A	c.(1675-1677)TAT>TAA	p.Y559*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.Y559*|PBRM1_uc003der.2_Nonsense_Mutation_p.Y527*|PBRM1_uc003det.2_Nonsense_Mutation_p.Y574*|PBRM1_uc003deu.2_Nonsense_Mutation_p.Y574*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.Y559*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.Y559*|PBRM1_uc003dey.2_Nonsense_Mutation_p.Y559*|PBRM1_uc003dez.1_Nonsense_Mutation_p.Y559*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.Y472*|PBRM1_uc003dfc.2_5'Flank	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	559	Bromo 4.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AGATGATTTTATAATAATCAG	0.378			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								72	63	---	---	---	---	PASS
PARP14	54625	broad.mit.edu	37	3	122447574	122447574	+	3'UTR	SNP	A	C	C	rs3732832	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122447574A>C	uc003efq.3	+	17					PARP14_uc010hrk.2_RNA|PARP14_uc003efr.2_3'UTR	NM_017554	NP_060024	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)		TTTGTCGCTGAAGTCAGTCTT	0.303													2	18	---	---	---	---	PASS
ABCA11P	79963	broad.mit.edu	37	4	420664	420664	+	Missense_Mutation	SNP	G	T	T	rs1053401	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:420664G>T	uc003gae.2	-	5	777	c.242C>A	c.(241-243)CCT>CAT	p.P81H	ABCA11P_uc003gac.2_Missense_Mutation_p.P30H|ABCA11P_uc003gad.2_RNA|ABCA11P_uc011buv.1_3'UTR|ABCA11P_uc010ibd.1_Missense_Mutation_p.P81H					RecName: Full=Putative ATP-binding cassette sub-family A member 11;												0						ATCTTCTTCAGGCTCTTCTGG	0.423													5	40	---	---	---	---	PASS
CORIN	10699	broad.mit.edu	37	4	47597590	47597590	+	3'UTR	SNP	A	G	G	rs3749585	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47597590A>G	uc003gxm.2	-	22					CORIN_uc011bzf.1_3'UTR|CORIN_uc011bzg.1_3'UTR	NM_006587	NP_006578	Q9Y5Q5	CORIN_HUMAN	corin						peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2						AAATTAGTCCAAAACAAACAT	0.358													4	34	---	---	---	---	PASS
C4orf37	285555	broad.mit.edu	37	4	99049685	99049685	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99049685C>A	uc003htt.1	-	3	371	c.281G>T	c.(280-282)TGT>TTT	p.C94F		NM_174952	NP_777612	Q8N412	CD037_HUMAN	hypothetical protein LOC285555	94											0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)		TGACTTTCCACAAGAAGGAAT	0.348													22	107	---	---	---	---	PASS
GPM6A	2823	broad.mit.edu	37	4	176622807	176622807	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176622807G>A	uc003iuf.2	-	2	953	c.149C>T	c.(148-150)GCG>GTG	p.A50V	GPM6A_uc011ckj.1_Missense_Mutation_p.A43V|GPM6A_uc003iug.2_Missense_Mutation_p.A50V|GPM6A_uc003iuh.2_Missense_Mutation_p.A39V	NM_201591	NP_963885	P51674	GPM6A_HUMAN	glycoprotein M6A isoform 2	50	Extracellular (Potential).					cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		TCCAGAAAGCGCTTCATGACC	0.488													54	230	---	---	---	---	PASS
TRIML1	339976	broad.mit.edu	37	4	189064860	189064860	+	Intron	SNP	C	A	A	rs62351463	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189064860C>A	uc003izm.1	+						TRIML1_uc003izn.1_Translation_Start_Site	NM_178556	NP_848651	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1						multicellular organismal development		ligase activity|zinc ion binding			ovary(1)|pancreas(1)|breast(1)|skin(1)	4		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		TCTCTGCTCTCTGTGCTCCCA	0.443													8	132	---	---	---	---	PASS
RNF180	285671	broad.mit.edu	37	5	63509694	63509694	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63509694G>T	uc003jti.2	+	4	651	c.541G>T	c.(541-543)GCA>TCA	p.A181S	RNF180_uc003jth.3_Missense_Mutation_p.A181S|RNF180_uc010iws.2_Intron	NM_001113561	NP_001107033	Q86T96	RN180_HUMAN	ring finger protein 180 isoform 1	181	Cytoplasmic (Potential).					integral to membrane|nuclear envelope	zinc ion binding				0		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)		ATTAACAGAAGCACTCTGCCT	0.443													31	153	---	---	---	---	PASS
CMYA5	202333	broad.mit.edu	37	5	79031741	79031741	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79031741C>T	uc003kgc.2	+	2	7225	c.7153C>T	c.(7153-7155)CCA>TCA	p.P2385S		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2385						perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AGATAAGGTGCCACAACAGCC	0.353													40	72	---	---	---	---	PASS
PCDHGA11	56105	broad.mit.edu	37	5	140802703	140802703	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140802703G>C	uc003lkq.1	+	1	2167	c.1909G>C	c.(1909-1911)GAC>CAC	p.D637H	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lko.1_Missense_Mutation_p.D637H|PCDHGA11_uc003lkp.1_Intron	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	637	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGGACAGAGACGCGCTCAA	0.697													13	104	---	---	---	---	PASS
FAM50B	26240	broad.mit.edu	37	6	3850384	3850384	+	Silent	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3850384C>T	uc003mvu.2	+	2	451	c.339C>T	c.(337-339)CGC>CGT	p.R113R		NM_012135	NP_036267	Q9Y247	FA50B_HUMAN	family with sequence similarity 50, member B	113						nucleus				pancreas(1)	1	Ovarian(93;0.0925)	all_hematologic(90;0.108)				ggcGCGAGCGCAAGCGTAAGA	0.532													3	16	---	---	---	---	PASS
GABBR1	2550	broad.mit.edu	37	6	29573438	29573438	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29573438G>T	uc003nmt.3	-	20	2683	c.2347C>A	c.(2347-2349)CTG>ATG	p.L783M	GABBR1_uc003nmp.3_Missense_Mutation_p.L666M|GABBR1_uc003nms.3_Missense_Mutation_p.L666M|GABBR1_uc003nmu.3_Missense_Mutation_p.L721M|GABBR1_uc011dlr.1_Missense_Mutation_p.L606M	NM_001470	NP_001461	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor 1	783	Helical; Name=5; (Potential).				gamma-aminobutyric acid signaling pathway|negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|extracellular region|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(5)|liver(1)|skin(1)	7					Baclofen(DB00181)|Progabide(DB00837)	AAGATTCCCAGCAGCAGCAGC	0.512													29	89	---	---	---	---	PASS
PBX2	5089	broad.mit.edu	37	6	32156550	32156550	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32156550C>T	uc003oav.1	-	2	516	c.245G>A	c.(244-246)CGA>CAA	p.R82Q	PBX2_uc003oaw.2_Missense_Mutation_p.R82Q	NM_002586	NP_002577	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	82							transcription factor binding			ovary(1)	1						AGGCTTCATTCGGTGGCAGTT	0.537													37	214	---	---	---	---	PASS
RGL2	5863	broad.mit.edu	37	6	33259865	33259865	+	3'UTR	SNP	A	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33259865A>G	uc003odv.2	-	18					WDR46_uc003ods.2_5'Flank|WDR46_uc011dra.1_5'Flank|RGL2_uc003odu.2_3'UTR|RGL2_uc010jur.2_3'UTR|RGL2_uc003odw.2_3'UTR	NM_004761	NP_004752	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation						Ras protein signal transduction|regulation of small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity			skin(3)|lung(1)|breast(1)|pancreas(1)	6						CTGTAAGCCAACGGGGCTTCC	0.532													13	54	---	---	---	---	PASS
PLA2G7	7941	broad.mit.edu	37	6	46684241	46684241	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46684241G>C	uc010jzf.2	-	4	525	c.256C>G	c.(256-258)CCA>GCA	p.P86A	PLA2G7_uc010jzg.1_Missense_Mutation_p.P86A|PLA2G7_uc011dwd.1_Missense_Mutation_p.P41A|PLA2G7_uc011dwe.1_Intron	NM_005084	NP_005075	Q13093	PAFA_HUMAN	phospholipase A2, group VII	86					inflammatory response|lipid catabolic process	extracellular space	1-alkyl-2-acetylglycerophosphocholine esterase activity|phospholipid binding				0			Lung(136;0.192)			TCTTGGGATGGATAATATAAA	0.368													60	100	---	---	---	---	PASS
LAMA2	3908	broad.mit.edu	37	6	129799907	129799907	+	Silent	SNP	T	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129799907T>C	uc003qbn.2	+	53	7626	c.7521T>C	c.(7519-7521)AAT>AAC	p.N2507N	LAMA2_uc003qbo.2_Silent_p.N2503N	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	2507	Laminin G-like 2.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CTCCGTACAATATACTCAGTA	0.363													73	317	---	---	---	---	PASS
TNRC18	84629	broad.mit.edu	37	7	5391579	5391579	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5391579C>A	uc003soi.3	-	17	5690	c.5341G>T	c.(5341-5343)GGC>TGC	p.G1781C	TNRC18_uc003soj.2_Missense_Mutation_p.G163C	NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1781							DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GCCGCCAGGCCCCTCTTGGTC	0.647													12	34	---	---	---	---	PASS
TNRC18	84629	broad.mit.edu	37	7	5391580	5391580	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5391580C>A	uc003soi.3	-	17	5689	c.5340G>T	c.(5338-5340)AGG>AGT	p.R1780S	TNRC18_uc003soj.2_Missense_Mutation_p.R162S	NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1780							DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CCGCCAGGCCCCTCTTGGTCA	0.647													11	36	---	---	---	---	PASS
TNRC18	84629	broad.mit.edu	37	7	5427483	5427483	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5427483G>T	uc003soi.3	-	5	2321	c.1972C>A	c.(1972-1974)CCC>ACC	p.P658T	TNRC18_uc010ksx.1_Missense_Mutation_p.P584T	NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	658							DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GCGCTCTCGGGCCTCTCGGGG	0.736													5	18	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82430893	82430893	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82430893T>A	uc003uhx.2	-	22	15237	c.14948A>T	c.(14947-14949)CAG>CTG	p.Q4983L		NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	4906					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						TTGTCCATTCTGTCCCATCTT	0.338													60	59	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100685938	100685938	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100685938G>T	uc003uxp.1	+	3	11294	c.11241G>T	c.(11239-11241)ATG>ATT	p.M3747I	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	3747	Extracellular (Potential).|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					CTGTGTCAATGCCCATGGAAA	0.473													166	187	---	---	---	---	PASS
TMEM139	135932	broad.mit.edu	37	7	142984079	142984079	+	3'UTR	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142984079C>T	uc010lov.2	+	4					CASP2_uc003wco.2_5'Flank|CASP2_uc003wcp.2_5'Flank|CASP2_uc011kta.1_5'Flank|CASP2_uc003wcq.2_5'Flank|TMEM139_uc003wck.3_3'UTR|TMEM139_uc003wcl.2_3'UTR|TMEM139_uc003wcm.2_3'UTR|TMEM139_uc003wcn.2_RNA	NM_153345	NP_699176	Q8IV31	TM139_HUMAN	transmembrane protein 139 precursor							integral to membrane					0	Melanoma(164;0.059)					GTAAGCCCTTCCCAGCTGAGA	0.423													12	20	---	---	---	---	PASS
CNPY1	285888	broad.mit.edu	37	7	155301781	155301781	+	5'UTR	SNP	A	G	G	rs6947243	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155301781A>G	uc003wmc.1	-	2						NM_001103176	NP_001096646	Q3B7I2	CNPY1_HUMAN	canopy 1 homolog												0	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)		CCTCCGACTGAGCTAGGGGGA	0.478													6	90	---	---	---	---	PASS
RBM33	155435	broad.mit.edu	37	7	155473515	155473515	+	Silent	SNP	A	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155473515A>T	uc010lqk.1	+	5	848	c.480A>T	c.(478-480)ATA>ATT	p.I160I	RBM33_uc003wme.2_Silent_p.I160I	NM_053043	NP_444271	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	160	Glu-rich.						nucleotide binding|RNA binding			ovary(1)	1	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		AAGACCAAATAGAATATGTGG	0.403													13	75	---	---	---	---	PASS
ZDHHC2	51201	broad.mit.edu	37	8	17067943	17067943	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17067943C>T	uc003wxe.2	+	10	1301	c.904C>T	c.(904-906)CCT>TCT	p.P302S		NM_016353	NP_057437	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2	302						integral to membrane	acyltransferase activity|zinc ion binding				0				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		TAACCAGGATCCTGAACAAGC	0.343													13	55	---	---	---	---	PASS
SLC26A7	115111	broad.mit.edu	37	8	92406637	92406637	+	Intron	SNP	T	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92406637T>G	uc003yex.2	+						SLC26A7_uc003yey.2_Intron|SLC26A7_uc003yez.2_3'UTR|SLC26A7_uc003yfa.2_Intron	NM_052832	NP_439897	Q8TE54	S26A7_HUMAN	solute carrier family 26, member 7 isoform a							basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)			TTAAGTTTTTTCTGCTCTGAT	0.348													5	18	---	---	---	---	PASS
KIAA1432	57589	broad.mit.edu	37	9	5765320	5765320	+	Intron	SNP	C	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5765320C>A	uc003zji.2	+						KIAA1432_uc003zjh.2_Intron|KIAA1432_uc003zjl.3_Intron|KIAA1432_uc003zjj.1_Intron|ERMP1_uc011lme.1_RNA	NM_020829	NP_065880	Q4ADV7	RIC1_HUMAN	connexin 43-interacting protein 150 isoform a							integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		GGTGTGGCTACATTCTTTGAG	0.333													5	10	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68413570	68413570	+	RNA	SNP	G	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68413570G>A	uc004aex.2	+	1		c.125G>A								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		CCCCAGTGGCGCCGGATCTAG	0.562													3	5	---	---	---	---	PASS
FAM120AOS	158293	broad.mit.edu	37	9	96209937	96209937	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96209937T>G	uc004atu.3	-	3	1610	c.727A>C	c.(727-729)ACC>CCC	p.T243P	FAM120AOS_uc004atm.2_Intron|FAM120AOS_uc004atn.3_RNA|FAM120AOS_uc004ato.3_RNA|FAM120AOS_uc004atp.3_RNA|FAM120AOS_uc004atq.3_RNA|FAM120AOS_uc004atr.3_RNA|FAM120AOS_uc004ats.3_RNA|FAM120AOS_uc004att.3_RNA	NM_198841	NP_942138	Q5T036	F120S_HUMAN	hypothetical protein LOC158293	243											0						GGTTTTGTGGTTTTCTTTGAG	0.333													41	162	---	---	---	---	PASS
LOC387646	387646	broad.mit.edu	37	10	27538014	27538014	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27538014G>T	uc001its.2	-	1	3222	c.1379C>A	c.(1378-1380)ACT>AAT	p.T460N		NR_003525				SubName: Full=cDNA FLJ44924 fis, clone BRAMY3014555;												0						TTCTAGTTCAGTAGGTGGACC	0.502													84	134	---	---	---	---	PASS
TLL2	7093	broad.mit.edu	37	10	98127809	98127809	+	3'UTR	SNP	A	C	C	rs41291624	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98127809A>C	uc001kml.1	-	21						NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2 precursor						cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		CAAAACAAAAAAAATTCTCAG	0.373													6	70	---	---	---	---	PASS
ABLIM1	3983	broad.mit.edu	37	10	116201492	116201492	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116201492C>A	uc010qsg.1	-	18	2086	c.1987G>T	c.(1987-1989)GGG>TGG	p.G663W	ABLIM1_uc010qsh.1_Missense_Mutation_p.G631W|ABLIM1_uc010qsi.1_Missense_Mutation_p.G603W|ABLIM1_uc010qsk.1_Missense_Mutation_p.G540W|ABLIM1_uc009xyp.2_Missense_Mutation_p.G627W|ABLIM1_uc010qsf.1_Missense_Mutation_p.G340W|ABLIM1_uc009xyn.2_Missense_Mutation_p.G279W|ABLIM1_uc010qsj.1_Missense_Mutation_p.G258W|ABLIM1_uc009xyo.2_Missense_Mutation_p.G476W	NM_002313	NP_002304	O14639	ABLM1_HUMAN	actin-binding LIM protein 1 isoform a	663					axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		CGGTGAAGCCCATTTCTTCCA	0.428													25	102	---	---	---	---	PASS
SPTY2D1	144108	broad.mit.edu	37	11	18636763	18636763	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18636763G>A	uc001moy.2	-	3	1274	c.1058C>T	c.(1057-1059)CCT>CTT	p.P353L	SPTY2D1_uc010rdi.1_Missense_Mutation_p.P353L	NM_194285	NP_919261	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1	353	Ser-rich.									breast(1)	1						CATGGGCCCAGGCCTGGAATG	0.557													107	262	---	---	---	---	PASS
TTC17	55761	broad.mit.edu	37	11	43429097	43429097	+	Silent	SNP	A	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43429097A>G	uc001mxi.2	+	15	2048	c.2034A>G	c.(2032-2034)CTA>CTG	p.L678L	TTC17_uc001mxh.2_Silent_p.L678L|TTC17_uc010rfj.1_Silent_p.L621L|TTC17_uc001mxj.2_Silent_p.L448L	NM_018259	NP_060729	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	678							binding			ovary(5)	5						CTAAGCTGCTACTTCAAGCTT	0.388													24	83	---	---	---	---	PASS
OR4P4	81300	broad.mit.edu	37	11	55405910	55405910	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55405910T>C	uc010rij.1	+	1	77	c.77T>C	c.(76-78)TTT>TCT	p.F26S		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	26	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1						GTCCTCTGCTTTGTATTATTT	0.353													125	304	---	---	---	---	PASS
MS4A7	58475	broad.mit.edu	37	11	60150630	60150630	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60150630C>A	uc001npe.2	+	2	161	c.16C>A	c.(16-18)CAA>AAA	p.Q6K	MS4A7_uc001npf.2_Missense_Mutation_p.Q6K|MS4A7_uc001npg.2_Missense_Mutation_p.Q6K|MS4A7_uc001nph.2_Missense_Mutation_p.Q6K|MS4A14_uc001npi.2_Intron|MS4A7_uc009ymx.1_Missense_Mutation_p.Q6K	NM_206939	NP_996822	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member	6	Cytoplasmic (Potential).					integral to membrane	receptor activity			ovary(1)|central_nervous_system(1)	2						ATTACAATCCCAAACCATGGG	0.443													75	194	---	---	---	---	PASS
TMEM218	219854	broad.mit.edu	37	11	124972208	124972208	+	5'UTR	SNP	A	G	G	rs14065	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124972208A>G	uc001qbs.2	-	2					TMEM218_uc001qbr.2_5'UTR|TMEM218_uc010saw.1_Missense_Mutation_p.L12S|TMEM218_uc010sax.1_5'UTR|TMEM218_uc001qbt.2_Missense_Mutation_p.L12S|TMEM218_uc010say.1_RNA	NM_001080546	NP_001074015	A2RU14	TM218_HUMAN	transmembrane protein 218							integral to membrane					0						GCTCCAGTGCAACACACTCCC	0.567													3	18	---	---	---	---	PASS
PEX5	5830	broad.mit.edu	37	12	7360264	7360264	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7360264T>G	uc009zfu.1	+	12	1556	c.976T>G	c.(976-978)TTT>GTT	p.F326V	PEX5_uc001qsw.2_Missense_Mutation_p.F326V|PEX5_uc010sgc.1_Missense_Mutation_p.F341V|PEX5_uc001qsu.2_Missense_Mutation_p.F289V|PEX5_uc010sgd.1_Missense_Mutation_p.F347V|PEX5_uc001qsv.2_Missense_Mutation_p.F318V	NM_001131026	NP_001124498	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5 isoform d	326					protein import into peroxisome matrix, translocation|protein targeting to peroxisome|protein tetramerization|protein transport	cytosol|peroxisomal matrix|peroxisomal membrane	peroxisome matrix targeting signal-1 binding|protein C-terminus binding|protein N-terminus binding			ovary(1)	1						GGGGTACCAGTTTGAGGAGGA	0.557													83	181	---	---	---	---	PASS
ANO6	196527	broad.mit.edu	37	12	45810629	45810629	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45810629A>G	uc001roo.2	+	17	2494	c.2159A>G	c.(2158-2160)GAC>GGC	p.D720G	ANO6_uc010sld.1_Missense_Mutation_p.D720G|ANO6_uc010sle.1_Missense_Mutation_p.D720G|ANO6_uc010slf.1_Missense_Mutation_p.D741G|ANO6_uc010slg.1_Missense_Mutation_p.D702G	NM_001025356	NP_001020527	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform a	720	Cytoplasmic (Potential).				activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2						AAAGCCCAAGACATTGGAGCA	0.478													36	107	---	---	---	---	PASS
TBX3	6926	broad.mit.edu	37	12	115117393	115117393	+	Silent	SNP	A	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115117393A>G	uc001tvt.1	-	4	1745	c.781T>C	c.(781-783)TTG>CTG	p.L261L	TBX3_uc001tvu.1_Silent_p.L241L	NM_016569	NP_057653	O15119	TBX3_HUMAN	T-box 3 protein isoform 2	261	T-box; second part.				anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding			ovary(2)|skin(1)	3	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		GGGAGTTTCAAGATGTCATTG	0.438													62	303	---	---	---	---	PASS
ATP12A	479	broad.mit.edu	37	13	25272913	25272913	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25272913C>T	uc001upp.2	+	12	1817	c.1630C>T	c.(1630-1632)CCA>TCA	p.P544S	ATP12A_uc010aaa.2_Missense_Mutation_p.P550S	NM_001676	NP_001667	P54707	AT12A_HUMAN	hydrogen/potassium-exchanging ATPase 12A	544	Cytoplasmic (Potential).				ATP biosynthetic process	hydrogen:potassium-exchanging ATPase complex	ATP binding|hydrogen:potassium-exchanging ATPase activity|metal ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|breast(1)	6		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)	Esomeprazole(DB00736)|Pantoprazole(DB00213)	CGAGGAGCACCCACTGGACAA	0.637													28	121	---	---	---	---	PASS
TRPC4	7223	broad.mit.edu	37	13	38320157	38320157	+	Silent	SNP	G	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38320157G>T	uc001uws.2	-	3	1049	c.814C>A	c.(814-816)CGA>AGA	p.R272R	TRPC4_uc010abv.2_5'UTR|TRPC4_uc001uwt.2_Silent_p.R272R|TRPC4_uc010tey.1_Silent_p.R272R|TRPC4_uc010abw.2_Intron|TRPC4_uc010abx.2_Silent_p.R272R|TRPC4_uc010aby.2_Silent_p.R272R	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,	272	Cytoplasmic (Potential).|Multimerization domain (By similarity).				axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TTGTCATCTCGGTAATTAAGA	0.418													107	408	---	---	---	---	PASS
MYCBP2	23077	broad.mit.edu	37	13	77835374	77835374	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77835374A>T	uc001vkf.2	-	13	1761	c.1670T>A	c.(1669-1671)CTT>CAT	p.L557H	MYCBP2_uc010aev.2_5'UTR	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	557					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TGCAACTAAAAGGGCGTGAGA	0.403													36	157	---	---	---	---	PASS
HECTD1	25831	broad.mit.edu	37	14	31576011	31576011	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31576011C>T	uc001wrc.1	-	38	7556	c.7067G>A	c.(7066-7068)AGA>AAA	p.R2356K	HECTD1_uc001wra.1_Missense_Mutation_p.R482K|HECTD1_uc001wrb.1_Missense_Mutation_p.R482K	NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	2356	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		AAATCTGGCTCTGTGTGGGTT	0.358													19	163	---	---	---	---	PASS
LRFN5	145581	broad.mit.edu	37	14	42356025	42356025	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42356025T>G	uc001wvm.2	+	3	1395	c.197T>G	c.(196-198)ATT>AGT	p.I66S	LRFN5_uc010ana.2_Missense_Mutation_p.I66S	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	66	Extracellular (Potential).|LRR 1.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		GTTACAAATATTAAAAGGAAA	0.403										HNSCC(30;0.082)			27	73	---	---	---	---	PASS
CDKL1	8814	broad.mit.edu	37	14	50862598	50862598	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50862598A>G	uc010anu.1	-	5	559	c.559T>C	c.(559-561)TAT>CAT	p.Y187H	CDKL1_uc001wxz.2_5'UTR	NM_004196	NP_004187	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1	Error:Variant_position_missing_in_Q00532_after_alignment						cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(1)|stomach(1)	2	all_epithelial(31;0.000746)|Breast(41;0.0102)					ATAGAGGAATAAATCTTCTTA	0.219													26	46	---	---	---	---	PASS
BTBD7	55727	broad.mit.edu	37	14	93761005	93761005	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93761005C>A	uc001ybo.2	-	3	687	c.361G>T	c.(361-363)GCT>TCT	p.A121S	BTBD7_uc010aur.2_5'UTR|BTBD7_uc010two.1_Missense_Mutation_p.A36S|BTBD7_uc001ybp.2_Intron|BTBD7_uc001ybq.3_Missense_Mutation_p.A36S|BTBD7_uc001ybr.2_Missense_Mutation_p.A121S	NM_001002860	NP_001002860	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7 isoform 1	121										pancreas(1)	1		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		TCTGGTCTAGCCAAACTGGCT	0.408													12	88	---	---	---	---	PASS
SPG11	80208	broad.mit.edu	37	15	44858475	44858475	+	Silent	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44858475C>T	uc001ztx.2	-	37	6814	c.6783G>A	c.(6781-6783)CTG>CTA	p.L2261L	SPG11_uc010bdw.2_Silent_p.L391L|SPG11_uc010ueh.1_Silent_p.L2148L|SPG11_uc010uei.1_Intron	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	2261	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		GCAGTTGTTTCAGCTGGTGCC	0.502													14	47	---	---	---	---	PASS
RORA	6095	broad.mit.edu	37	15	60789779	60789779	+	Nonsense_Mutation	SNP	G	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60789779G>A	uc002agv.2	-	12	1702	c.1546C>T	c.(1546-1548)CGA>TGA	p.R516*	uc002ags.1_Intron|RORA_uc002agt.3_Nonsense_Mutation_p.R428*|RORA_uc002agw.2_Nonsense_Mutation_p.R508*|RORA_uc002agx.2_Nonsense_Mutation_p.R483*	NM_134260	NP_599022	P35398	RORA_HUMAN	RAR-related orphan receptor A isoform b	516	Ligand-binding.				positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2						TCTGTATGTCGTCCACATAAG	0.398													24	146	---	---	---	---	PASS
VPS13C	54832	broad.mit.edu	37	15	62241747	62241747	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62241747C>T	uc002agz.2	-	42	4728	c.4654G>A	c.(4654-4656)GAT>AAT	p.D1552N	VPS13C_uc002aha.2_Missense_Mutation_p.D1509N|VPS13C_uc002ahb.1_Missense_Mutation_p.D1552N|VPS13C_uc002ahc.1_Missense_Mutation_p.D1509N	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	1552					protein localization					ovary(2)	2						GATAAAAAATCCATGAAGGAA	0.408													54	117	---	---	---	---	PASS
BBS2	583	broad.mit.edu	37	16	56534715	56534715	+	Intron	SNP	G	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56534715G>A	uc002ejd.2	-						BBS2_uc010ccg.2_3'UTR	NM_031885	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2 protein						adult behavior|brain morphogenesis|cerebral cortex development|cilium morphogenesis|fat cell differentiation|hippocampus development|melanosome transport|negative regulation of multicellular organism growth|photoreceptor cell maintenance|protein localization to organelle|regulation of cilium beat frequency involved in ciliary motility|sperm axoneme assembly|striatum development	BBSome|cilium membrane|microtubule basal body|motile cilium	protein binding			ovary(1)	1						TATACATCTTGCCCTCCTCTA	0.453									Bardet-Biedl_syndrome				16	43	---	---	---	---	PASS
MT1E	4493	broad.mit.edu	37	16	56660686	56660686	+	Intron	SNP	A	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56660686A>G	uc002ejl.2	+						MT1A_uc002eji.2_Intron|MT1M_uc010vhe.1_Intron|MT1E_uc002ejm.2_Missense_Mutation_p.S113G	NM_175617	NP_783316	P04732	MT1E_HUMAN	metallothionein 1E							cytoplasm	cadmium ion binding|copper ion binding|zinc ion binding				0						GACGAAAAAAAGCATCCTCTG	0.542													17	40	---	---	---	---	PASS
PLCG2	5336	broad.mit.edu	37	16	81819486	81819486	+	Intron	SNP	C	G	G	rs4354929	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81819486C>G	uc002fgt.2	+						PLCG2_uc010chg.1_5'UTR	NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2						intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8						GAAGTTCATGCCCTGTTAACT	0.458													5	34	---	---	---	---	PASS
COTL1	23406	broad.mit.edu	37	16	84600669	84600669	+	Intron	SNP	G	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84600669G>C	uc002fid.2	-						COTL1_uc002fie.2_Intron|COTL1_uc010chk.2_Intron|COTL1_uc002fif.1_RNA	NM_021149	NP_066972	Q14019	COTL1_HUMAN	coactosin-like 1							cytoplasm|cytoskeleton	actin binding|enzyme binding			skin(1)	1						ACCCTGATGAGAGATGGAAAT	0.453													15	19	---	---	---	---	PASS
CPNE7	27132	broad.mit.edu	37	16	89657453	89657453	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89657453C>A	uc002fnp.2	+	14	1510	c.1380C>A	c.(1378-1380)GAC>GAA	p.D460E	CPNE7_uc002fnq.2_Missense_Mutation_p.D385E	NM_014427	NP_055242	Q9UBL6	CPNE7_HUMAN	copine 7 isoform b	460	VWFA.				lipid metabolic process		transporter activity				0		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		ACCCTGAGGACGATGAGTGTG	0.637													21	68	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11650990	11650990	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11650990C>T	uc002gne.2	+	32	6585	c.6517C>T	c.(6517-6519)CGG>TGG	p.R2173W	DNAH9_uc010coo.2_Missense_Mutation_p.R1467W	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	2173	AAA 2 (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GATCATGAAACGGCGCCCCGT	0.542													28	98	---	---	---	---	PASS
LRRC37B	114659	broad.mit.edu	37	17	30357718	30357718	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30357718T>G	uc002hgu.2	+	4	1878	c.1867T>G	c.(1867-1869)TTT>GTT	p.F623V	LRRC37B_uc010wbx.1_Missense_Mutation_p.F541V|LRRC37B_uc010csu.2_Intron	NM_052888	NP_443120	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B precursor	623	LRR 3.|Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				AAGACAAACATTTGAATCACT	0.254													2	6	---	---	---	---	PASS
AMAC1	146861	broad.mit.edu	37	17	33520557	33520557	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33520557C>T	uc002hjd.2	-	1	856	c.770G>A	c.(769-771)GGG>GAG	p.G257E		NM_152462	NP_689675	Q8N808	AMAC1_HUMAN	acyl-malonyl condensing enzyme 1	257	Helical; (Potential).					integral to membrane					0				BRCA - Breast invasive adenocarcinoma(366;0.0917)		CCCCACTGCCCCCACACAACT	0.627													61	124	---	---	---	---	PASS
BECN1	8678	broad.mit.edu	37	17	40970428	40970428	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40970428C>A	uc002ibo.3	-	7	629	c.494G>T	c.(493-495)TGT>TTT	p.C165F	BECN1_uc010whb.1_Missense_Mutation_p.C78F|BECN1_uc010whc.1_Missense_Mutation_p.C89F|BECN1_uc002ibn.2_Missense_Mutation_p.C165F	NM_003766	NP_003757	Q14457	BECN1_HUMAN	beclin 1	165	Potential.				anti-apoptosis|cell cycle|cellular defense response|cytokinesis|response to virus	membrane	protein binding			ovary(1)	1		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		GATCTCCAAACAGCGTCTGCC	0.502													60	240	---	---	---	---	PASS
SAMD14	201191	broad.mit.edu	37	17	48195543	48195543	+	Silent	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48195543C>T	uc002iqg.2	-	3	491	c.192G>A	c.(190-192)TCG>TCA	p.S64S	SAMD14_uc002iqd.2_5'Flank|SAMD14_uc002iqe.2_5'UTR|SAMD14_uc002iqf.2_Silent_p.S64S	NM_174920	NP_777580	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	64											0						CGGGCCCATCCGAGCCTTCAC	0.637													51	67	---	---	---	---	PASS
DTNA	1837	broad.mit.edu	37	18	32405233	32405233	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32405233A>T	uc010dmn.1	+	9	1005	c.1004A>T	c.(1003-1005)GAT>GTT	p.D335V	DTNA_uc002kxu.2_Missense_Mutation_p.D335V|DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Missense_Mutation_p.D335V|DTNA_uc002kxw.2_Missense_Mutation_p.D335V|DTNA_uc002kxx.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010dmk.1_Intron|DTNA_uc010dml.2_Intron|DTNA_uc002kyb.3_Intron|DTNA_uc010dmm.2_Missense_Mutation_p.D335V|DTNA_uc010xby.1_Intron|DTNA_uc010dmo.2_Intron|DTNA_uc002kyd.3_Intron|DTNA_uc010xbz.1_Intron|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Intron	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1	335					neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0						GCCAAAAGTGATACTTGGTAA	0.348													122	149	---	---	---	---	PASS
SKA1	220134	broad.mit.edu	37	18	47906545	47906545	+	Silent	SNP	C	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47906545C>A	uc002let.2	+	3	322	c.138C>A	c.(136-138)ATC>ATA	p.I46I	SKA1_uc002leu.2_Silent_p.I46I|SKA1_uc010xdl.1_Silent_p.I46I	NM_145060	NP_659497	Q96BD8	SKA1_HUMAN	spindle and KT associated 1	46					cell division|chromosome segregation|mitotic anaphase|mitotic prometaphase|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytosol|spindle microtubule	microtubule binding				0						GAGATGAGATCATTGTAATAA	0.294													69	84	---	---	---	---	PASS
NETO1	81832	broad.mit.edu	37	18	70417575	70417575	+	Silent	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70417575C>T	uc002lkw.2	-	9	1547	c.1263G>A	c.(1261-1263)CGG>CGA	p.R421R	NETO1_uc002lkx.1_Silent_p.R420R|NETO1_uc002lky.1_Silent_p.R421R	NM_138966	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin- and tolloid-like protein 1 isoform 3	421	Cytoplasmic (Potential).				memory|regulation of long-term neuronal synaptic plasticity|visual learning	cell junction|excitatory synapse|extracellular region|integral to membrane|postsynaptic density|postsynaptic membrane	receptor activity			ovary(2)|skin(2)	4		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		AAGATGACCTCCGCAGTTTAT	0.463													36	47	---	---	---	---	PASS
LSM7	51690	broad.mit.edu	37	19	2321719	2321719	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2321719T>A	uc002lvp.3	-	4	321	c.272A>T	c.(271-273)GAG>GTG	p.E91V	SPPL2B_uc010dsw.1_Intron	NM_016199	NP_057283	Q9UK45	LSM7_HUMAN	U6 snRNA-associated Sm-like protein LSm7	91					nuclear mRNA splicing, via spliceosome	nucleus|ribonucleoprotein complex	protein binding|U6 snRNA binding				0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGGATGGCCTCCATGCCGTC	0.701													5	4	---	---	---	---	PASS
FUT6	2528	broad.mit.edu	37	19	5832203	5832203	+	Missense_Mutation	SNP	G	A	A	rs111589452		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5832203G>A	uc002mdf.1	-	4	902	c.376C>T	c.(376-378)CGG>TGG	p.R126W	FUT6_uc002mdg.1_Missense_Mutation_p.R126W|FUT6_uc002mdh.1_Missense_Mutation_p.R126W|FUT6_uc010dul.1_Missense_Mutation_p.R126W	NM_001040701	NP_001035791	P51993	FUT6_HUMAN	fucosyltransferase 6	126	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity|alpha(1,3)-fucosyltransferase activity				0						TGCCCCTGCCGCCTCGGGGAG	0.617													11	55	---	---	---	---	PASS
ARHGEF18	23370	broad.mit.edu	37	19	7535249	7535249	+	Intron	SNP	C	A	A	rs12972299	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7535249C>A	uc002mgi.2	+						ARHGEF18_uc002mgh.2_Intron|ARHGEF18_uc002mgj.1_3'UTR	NM_001130955	NP_001124427	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)				TCTCTGGGGACCCCCATGGGG	0.637													3	17	---	---	---	---	PASS
PNPLA6	10908	broad.mit.edu	37	19	7605595	7605595	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7605595C>G	uc010xjq.1	+	8	1016	c.821C>G	c.(820-822)ACC>AGC	p.T274S	PNPLA6_uc002mgq.1_Missense_Mutation_p.T226S|PNPLA6_uc010xjp.1_Missense_Mutation_p.T226S|PNPLA6_uc002mgr.1_Missense_Mutation_p.T226S|PNPLA6_uc002mgs.2_Missense_Mutation_p.T265S	NM_006702	NP_006693	Q8IY17	PLPL6_HUMAN	neuropathy target esterase isoform b	265	cNMP 1.|Cytoplasmic (Potential).				cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3						GATGTCATCACCGTGAGTGAC	0.577													30	69	---	---	---	---	PASS
EMR2	30817	broad.mit.edu	37	19	14846897	14846897	+	3'UTR	SNP	T	A	A	rs1859257	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14846897T>A	uc002mzp.1	-	21					EMR2_uc010dzs.1_3'UTR|EMR2_uc010xnw.1_3'UTR|EMR2_uc002mzo.1_3'UTR|EMR2_uc002mzq.1_3'UTR|EMR2_uc002mzr.1_3'UTR|EMR2_uc002mzs.1_3'UTR|EMR2_uc002mzt.1_3'UTR|EMR2_uc002mzu.1_3'UTR	NM_013447	NP_038475	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone						cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			lung(2)|ovary(1)|skin(1)	4						ATTGAATGCCTAGCACGCCTT	0.453													5	46	---	---	---	---	PASS
SLC1A6	6511	broad.mit.edu	37	19	15075020	15075020	+	Intron	SNP	A	G	G	rs10407669	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15075020A>G	uc002naa.1	-						SLC1A6_uc010dzu.1_Intron|SLC1A6_uc010xod.1_Intron|SLC1A6_uc002nab.2_Intron|SLC1A6_uc002nac.2_Intron|SLC1A6_uc002nad.1_3'UTR	NM_005071	NP_005062	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity						synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|L-aspartate transmembrane transporter activity|sodium:dicarboxylate symporter activity			pancreas(3)|ovary(2)|skin(1)	6					L-Glutamic Acid(DB00142)	ACCCCTGCCCATTGCTCTGTC	0.498													13	240	---	---	---	---	PASS
TMEM145	284339	broad.mit.edu	37	19	42820894	42820894	+	Splice_Site	SNP	T	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42820894T>C	uc002otk.1	+	10	858	c.806_splice	c.e10+2	p.R269_splice		NM_173633	NP_775904	Q8NBT3	TM145_HUMAN	transmembrane protein 145							integral to membrane					0		Prostate(69;0.00682)				GGTGACACGGTGCCCGGGCAG	0.682													40	83	---	---	---	---	PASS
CGB	1082	broad.mit.edu	37	19	49527339	49527339	+	5'UTR	SNP	C	T	T	rs72626227	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49527339C>T	uc002plv.1	-	1					CGB_uc010yad.1_Intron|CGB_uc002plu.1_5'Flank	NM_000737	NP_000728	P01233	CGHB_HUMAN	chorionic gonadotropin beta 3 subunit precursor						apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Choriogonadotropin alfa(DB00097)	ACTAACCCCTCGGGGGGCAAG	0.667													7	76	---	---	---	---	PASS
ZNF525	170958	broad.mit.edu	37	19	53886286	53886286	+	3'UTR	SNP	T	C	C	rs4324256	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53886286T>C	uc010eqn.2	+	4					ZNF525_uc002qbl.2_Intron|ZNF765_uc010ydx.1_Intron	NR_003699				Homo sapiens cDNA FLJ39718 fis, clone SMINT2013695.												0						AAAGCTTGCATGTCATCATAG	0.393													6	53	---	---	---	---	PASS
NSFL1C	55968	broad.mit.edu	37	20	1424303	1424303	+	3'UTR	SNP	G	A	A	rs6891	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1424303G>A	uc002wfc.2	-	9					NSFL1C_uc002wfd.2_3'UTR|NSFL1C_uc002wfe.2_3'UTR|NSFL1C_uc002wff.2_RNA|NSFL1C_uc010gag.2_3'UTR	NM_016143	NP_057227	Q9UNZ2	NSF1C_HUMAN	p47 protein isoform a							chromosome|Golgi stack|nucleus	lipid binding|protein binding				0						ACTGCTGGGTGTGCACAAGGG	0.562													4	33	---	---	---	---	PASS
TGM6	343641	broad.mit.edu	37	20	2413340	2413340	+	3'UTR	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2413340C>T	uc002wfy.1	+	13					TGM6_uc010gal.1_3'UTR	NM_198994	NP_945345	O95932	TGM3L_HUMAN	transglutaminase 6						cell death|peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(3)|skin(1)	4					L-Glutamine(DB00130)	CCTCCTCCTGCCCATTCTTTG	0.338													17	87	---	---	---	---	PASS
KIF16B	55614	broad.mit.edu	37	20	16509021	16509021	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16509021A>C	uc002wpg.1	-	2	270	c.112T>G	c.(112-114)TTA>GTA	p.L38V	KIF16B_uc010gch.1_Missense_Mutation_p.L38V|KIF16B_uc010gci.1_Missense_Mutation_p.L38V|KIF16B_uc010gcj.1_Missense_Mutation_p.L38V	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23	38	Kinesin-motor.				cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8						CTTGCCTTTAAGTTTGTGATT	0.408													56	100	---	---	---	---	PASS
PISD	23761	broad.mit.edu	37	22	32058162	32058162	+	Silent	SNP	T	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32058162T>C	uc003alm.3	-	1	40	c.33A>G	c.(31-33)GGA>GGG	p.G11G	PISD_uc003aln.3_Silent_p.G11G	NM_014338	NP_055153	Q9UG56	PISD_HUMAN	phosphatidylserine decarboxylase	11					phospholipid biosynthetic process	mitochondrion	phosphatidylserine decarboxylase activity			central_nervous_system(2)|ovary(1)	3					Phosphatidylserine(DB00144)	CGTGCAGTAATCCCAGACATC	0.652											OREG0003531	type=REGULATORY REGION|Gene=PISD|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	34	236	---	---	---	---	PASS
L3MBTL2	83746	broad.mit.edu	37	22	41605635	41605635	+	Intron	SNP	T	C	C	rs139437	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41605635T>C	uc003azo.2	+						L3MBTL2_uc010gyi.1_Intron|L3MBTL2_uc003azn.2_Intron|uc003azp.1_RNA	NM_031488	NP_113676	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methylated histone residue binding|transcription corepressor activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3						GATCTGCAGCTTCTCCCCCCG	0.448													10	175	---	---	---	---	PASS
L3MBTL2	83746	broad.mit.edu	37	22	41605639	41605639	+	Intron	SNP	C	T	T	rs62889861	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41605639C>T	uc003azo.2	+						L3MBTL2_uc010gyi.1_Intron|L3MBTL2_uc003azn.2_Intron|uc003azp.1_RNA	NM_031488	NP_113676	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methylated histone residue binding|transcription corepressor activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3						TGCAGCTTCTCCCCCCGTGCA	0.443													11	184	---	---	---	---	PASS
NYX	60506	broad.mit.edu	37	X	41307152	41307152	+	Nonsense_Mutation	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41307152C>T	uc004dfh.2	+	1	440	c.10C>T	c.(10-12)CGA>TGA	p.R4*	NYX_uc011mku.1_5'UTR	NM_022567	NP_072089	Q9GZU5	NYX_HUMAN	nyctalopin precursor	4					response to stimulus|visual perception	intracellular|proteinaceous extracellular matrix				lung(2)	2						GATGAAAGGCCGAGGGATGTT	0.617													14	13	---	---	---	---	PASS
EDA	1896	broad.mit.edu	37	X	69255287	69255287	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69255287G>T	uc004dxs.2	+	8	1246	c.1004G>T	c.(1003-1005)AGC>ATC	p.S335I	EDA_uc004dxr.2_Missense_Mutation_p.S333I|EDA_uc011mpj.1_Missense_Mutation_p.S330I	NM_001399	NP_001390	Q92838	EDA_HUMAN	ectodysplasin A isoform EDA-A1	335	Extracellular (Potential).				cell differentiation|ectoderm development|immune response|positive regulation of NF-kappaB transcription factor activity|signal transduction	collagen|cytoskeleton|membrane fraction	tumor necrosis factor receptor binding			ovary(2)|large_intestine(1)	3						TGCACACGCAGCATCGAGACG	0.547													18	17	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	11928	11928	+	RNA	SNP	A	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:11928A>G	uc004cov.3	+	1		c.1351A>G			uc004cow.1_5'Flank|uc004cox.3_5'Flank|uc004coy.2_5'Flank					Homo sapiens potential LAG1 interactor mRNA, partial cds.																		CTCCTGATCAAATATCACTCT	0.463													4	5	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	12822	12822	+	RNA	SNP	A	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:12822A>G	uc004cox.3	+	1		c.486A>G			uc004coy.2_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		TACGCCCGAGCAGATGCCAAC	0.463													5	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	13129	13129	+	RNA	SNP	C	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:13129C>T	uc004cox.3	+	1		c.793C>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.																		TCCGCTTCCACCCCCTAGCAG	0.512													3	18	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	13710	13710	+	RNA	SNP	A	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:13710A>G	uc004cox.3	+	1		c.1374A>G			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.																		AAACGCCTGGCAGCCGGAAGC	0.483													5	5	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14233	14233	+	RNA	SNP	A	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14233A>G	uc004cox.3	+	1		c.1897A>G			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.																		CAACGCCCATAATCATACAAA	0.408													3	11	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14581	14581	+	RNA	SNP	T	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14581T>C	uc004cox.3	+	1		c.2245T>C			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.																		CTAACAATCAGTACTAAACCC	0.378													2	6	---	---	---	---	PASS
CAPZA1	829	broad.mit.edu	37	1	113202197	113202198	+	Intron	DEL	TC	-	-	rs113906793		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113202197_113202198delTC	uc001ecj.1	+							NM_006135	NP_006126	P52907	CAZA1_HUMAN	F-actin capping protein alpha-1 subunit						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|WASH complex	actin binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AATGACAGTTTCTCTCTCTCTC	0.396													8	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	200833330	200833330	+	IGR	DEL	A	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200833330delA								CAMSAP1L1 (3501 upstream) : GPR25 (8836 downstream)																							TGCTGTATGGAAAAAAAAAAA	0.249													11	5	---	---	---	---	
MOSC2	54996	broad.mit.edu	37	1	220953796	220953797	+	Intron	DEL	TT	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220953796_220953797delTT	uc001hmq.2	+						MOSC2_uc001hmr.2_Intron|MOSC2_uc009xdx.2_Intron	NM_017898	NP_060368	Q969Z3	MOSC2_HUMAN	MOCO sulphurase C-terminal domain containing 2							mitochondrial outer membrane|peroxisome	molybdenum ion binding|oxidoreductase activity|pyridoxal phosphate binding				0				GBM - Glioblastoma multiforme(131;0.00499)|all cancers(67;0.204)		TTGGATAAACtttttttttttt	0.218													4	2	---	---	---	---	
ADI1	55256	broad.mit.edu	37	2	3504893	3504894	+	Intron	INS	-	A	A	rs144556875	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3504893_3504894insA	uc002qxp.3	-						ADI1_uc010yiq.1_Intron	NM_018269	NP_060739	Q9BV57	MTND_HUMAN	acireductone dioxygenase 1						L-methionine salvage from methylthioadenosine	cytoplasm|nucleus|plasma membrane	acireductone dioxygenase (Ni2+-requiring) activity|metal ion binding|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0729)|Epithelial(75;0.173)|all cancers(51;0.228)		CCATAAAAATGAAACTACACTT	0.455													4	2	---	---	---	---	
RAD51AP2	729475	broad.mit.edu	37	2	17696274	17696275	+	Intron	INS	-	A	A	rs34060092		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17696274_17696275insA	uc002rcl.1	-						RAD51AP2_uc010exn.1_Intron	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CTTCTTGCTGGAAAAAAAAAAA	0.307													5	7	---	---	---	---	
NCOA1	8648	broad.mit.edu	37	2	24949704	24949704	+	Intron	DEL	A	-	-	rs71960773		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24949704delA	uc002rfk.2	+						NCOA1_uc010eye.2_Intron|NCOA1_uc002rfi.2_Intron|NCOA1_uc002rfj.2_Intron|NCOA1_uc002rfl.2_Intron	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1										PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AATACTTACTAAAAAAAAAAA	0.154			T	PAX3	alveolar rhadomyosarcoma								6	6	---	---	---	---	
LY75	4065	broad.mit.edu	37	2	160634565	160634566	+	Intron	DEL	CC	-	-	rs35013477		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160634565_160634566delCC	uc002ubb.3	-						LY75_uc010fos.2_Intron|CD302_uc002uba.2_Intron|CD302_uc010zco.1_Intron	NM_002349	NP_002340	O60449	LY75_HUMAN	lymphocyte antigen 75 precursor						endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding				0				COAD - Colon adenocarcinoma(177;0.132)		TAAAAATAAACCCTTTTATTAG	0.233													2	4	---	---	---	---	
LOC643387	643387	broad.mit.edu	37	2	239140426	239140427	+	5'UTR	INS	-	C	C	rs144646397		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239140426_239140427insC	uc010znu.1	+	1					LOC151174_uc002vxy.2_5'Flank|LOC151174_uc002vxx.3_5'Flank	NR_026923				Homo sapiens TAR DNA binding protein pseuodgene (LOC643387), non-coding RNA.												0						aaaaaaacaaaaaacaaacaaa	0.554													3	3	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10191580	10191580	+	Frame_Shift_Del	DEL	C	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10191580delC	uc003bvc.2	+	3	786	c.573delC	c.(571-573)CACfs	p.H191fs	VHL_uc003bvd.2_Frame_Shift_Del_p.H150fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	191					anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.H191fs*23(1)|p.D187_N193del(1)|p.H191fs*10(1)|p.H191fs*22(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TGGAAGACCACCCAAATGTGC	0.502		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				31	27	---	---	---	---	
TOP2B	7155	broad.mit.edu	37	3	25661230	25661231	+	Intron	DEL	AA	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25661230_25661231delAA	uc011awn.1	-						TOP2B_uc003cdj.2_Intron|TOP2B_uc011awm.1_Intron|TOP2B_uc010hff.1_Intron	NM_001068	NP_001059	Q02880	TOP2B_HUMAN	DNA topoisomerase II, beta isozyme						DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|resolution of meiotic recombination intermediates|sister chromatid segregation	cytosol|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex|WINAC complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5						GCAGGATGGGAAAAAAAAAAAA	0.356													5	4	---	---	---	---	
RBM6	10180	broad.mit.edu	37	3	50114316	50114316	+	Intron	DEL	A	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50114316delA	uc003cyc.2	+						RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768	P78332	RBM6_HUMAN	RNA binding motif protein 6						RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		gactccatctaaaaaaaaaaa	0.184													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	96472843	96472843	+	IGR	DEL	A	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96472843delA								None (None upstream) : EPHA6 (60582 downstream)																							ACTGCAAAGGAAACCTCTTTT	0.453													19	24	---	---	---	---	
CCNL1	57018	broad.mit.edu	37	3	156867954	156867954	+	Frame_Shift_Del	DEL	G	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156867954delG	uc003fbf.2	-	7	1378	c.779delC	c.(778-780)CCGfs	p.P260fs	CCNL1_uc003fbd.1_Frame_Shift_Del_p.P260fs|CCNL1_uc003fbe.2_Frame_Shift_Del_p.P54fs|CCNL1_uc003fbg.2_RNA|CCNL1_uc011bor.1_RNA|CCNL1_uc003fbi.1_Frame_Shift_Del_p.P105fs	NM_020307	NP_064703	Q9UK58	CCNL1_HUMAN	cyclin L1	260	Cyclin-like 2.				regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	nuclear speck	protein kinase binding			lung(3)|breast(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(72;0.0295)|Lung(72;0.0308)			AGTTGGCAACGGAATCTAAAC	0.343													44	34	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	180863907	180863907	+	IGR	DEL	A	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180863907delA								DNAJC19 (156377 upstream) : SOX2OT (417602 downstream)																							tagaaaatccaaaaaaaaaaa	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	104332523	104332524	+	IGR	DEL	CG	-	-	rs10611484		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104332523_104332524delCG								CENPE (212957 upstream) : TACR3 (178101 downstream)																							cacacacacacgcacacacacC	0.327													4	2	---	---	---	---	
C4orf21	55345	broad.mit.edu	37	4	113504970	113504970	+	Intron	DEL	A	-	-	rs140732512		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113504970delA	uc003iau.2	-						C4orf21_uc003iav.2_Intron	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like							integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		CTATATAATTAAAAAAAAAAA	0.080													4	2	---	---	---	---	
NDUFS4	4724	broad.mit.edu	37	5	52942409	52942410	+	Intron	DEL	AA	-	-	rs10571887		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52942409_52942410delAA	uc003jpe.2	+							NM_002495	NP_002486	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4						brain development|cAMP-mediated signaling|mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|positive regulation of fibroblast proliferation|reactive oxygen species metabolic process|regulation of protein phosphorylation|response to cAMP|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			central_nervous_system(1)	1		Lung NSC(810;8.27e-05)|Breast(144;0.0848)			NADH(DB00157)	ATATTCAGATAAGTGTGGCTTA	0.327													6	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	85703814	85703815	+	IGR	INS	-	AAGG	AAGG	rs149876942	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85703814_85703815insAAGG								NBPF22P (110452 upstream) : COX7C (209969 downstream)																							ggaaggaaggaaggaaggaagg	0.089													4	3	---	---	---	---	
LOC728554	728554	broad.mit.edu	37	5	177306168	177306168	+	Intron	DEL	T	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177306168delT	uc010jkr.2	+							NR_003615				Homo sapiens cDNA, FLJ17316.												0						TCATACTCCCtttttttttgt	0.144													4	2	---	---	---	---	
MTO1	25821	broad.mit.edu	37	6	74192512	74192513	+	Intron	INS	-	T	T	rs35121302		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74192512_74192513insT	uc003pgy.3	+						MTO1_uc010kav.2_Intron|MTO1_uc003pgz.3_Intron|MTO1_uc003pha.3_Intron|MTO1_uc003phb.3_Intron	NM_133645	NP_598400	Q9Y2Z2	MTO1_HUMAN	mitochondrial translation optimization 1 homolog						tRNA processing	mitochondrion	flavin adenine dinucleotide binding			ovary(3)|skin(2)|pancreas(1)	6						TTTtttctttcttttttttttt	0.158													7	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134747283	134747286	+	IGR	DEL	TCTT	-	-	rs67886112		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134747283_134747286delTCTT								SGK1 (108087 upstream) : ALDH8A1 (491243 downstream)																							tccctctccctctttctttctttc	0.034													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	7347247	7347247	+	IGR	DEL	T	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7347247delT								DEFB105A (175 upstream) : DEFB107A (6121 downstream)																							ACtttttttcttttttttttt	0.075													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	37363792	37363792	+	IGR	DEL	G	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37363792delG								KCNU1 (570151 upstream) : ZNF703 (189509 downstream)																							gagggagggagggggggagga	0.164													4	2	---	---	---	---	
NBN	4683	broad.mit.edu	37	8	90955480	90955481	+	Splice_Site	DEL	CC	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90955480_90955481delCC	uc003yej.1	-	14	2294	c.2184_splice	c.e14+1	p.E728_splice	NBN_uc003yei.1_Splice_Site_p.E646_splice|NBN_uc011lgb.1_Splice_Site_p.E728_splice	NM_002485	NP_002476	O60934	NBN_HUMAN	nibrin						cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance	Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm	protein N-terminus binding|transcription factor binding			central_nervous_system(3)|kidney(3)|lung(1)	7			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TTCCTACTAACCTCCATTTCCT	0.401								Direct_reversal_of_damage|Homologous_recombination	Nijmegen_Breakage_syndrome				72	59	---	---	---	---	
KIAA0368	23392	broad.mit.edu	37	9	114170786	114170786	+	Intron	DEL	A	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114170786delA	uc004bfe.1	-							NM_001080398	NP_001073867			KIAA0368 protein												0						AACTGCACCTAAAAAAAAAAA	0.348													4	4	---	---	---	---	
PPA1	5464	broad.mit.edu	37	10	71969126	71969127	+	Intron	INS	-	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71969126_71969127insT	uc001jqv.1	-							NM_021129	NP_066952	Q15181	IPYR_HUMAN	pyrophosphatase 1						diphosphate metabolic process|tRNA aminoacylation for protein translation	cytosol	inorganic diphosphatase activity|magnesium ion binding			breast(1)	1						AAGCCTGATACTTTGTCTCTTC	0.292													29	18	---	---	---	---	
CAMK2G	818	broad.mit.edu	37	10	75575127	75575128	+	Intron	INS	-	C	C	rs138806030	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75575127_75575128insC	uc001jvm.1	-						CAMK2G_uc001jvo.1_Intron|CAMK2G_uc001jvq.1_Intron|CAMK2G_uc001jvr.1_Intron|CAMK2G_uc001jvp.1_Intron|CAMK2G_uc001jvs.1_Intron|CAMK2G_uc001jvt.1_Intron|CAMK2G_uc001jvu.1_Intron|CAMK2G_uc009xrp.1_Intron	NM_172171	NP_751911	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II						insulin secretion|interferon-gamma-mediated signaling pathway|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding|calmodulin-dependent protein kinase activity			lung(1)|stomach(1)	2	Prostate(51;0.0112)					TCCAAGTACCGCCCCCCCCCAC	0.550													4	3	---	---	---	---	
CAPN5	726	broad.mit.edu	37	11	76833610	76833610	+	Intron	DEL	C	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76833610delC	uc001oxx.2	+						CAPN5_uc009yup.2_Intron|CAPN5_uc009yuq.2_Intron|CAPN5_uc001oxy.2_Intron|CAPN5_uc001oya.2_Intron	NM_004055	NP_004046	O15484	CAN5_HUMAN	calpain 5						proteolysis|signal transduction	intracellular	calcium-dependent cysteine-type endopeptidase activity				0						atctcccactcccTCTCCCTA	0.443													21	10	---	---	---	---	
PHLDB1	23187	broad.mit.edu	37	11	118487088	118487088	+	Intron	DEL	A	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118487088delA	uc001ptr.1	+						PHLDB1_uc010ryh.1_Intron|PHLDB1_uc001pts.2_Intron|PHLDB1_uc001ptt.2_Intron|PHLDB1_uc001ptu.1_Intron	NM_015157	NP_055972	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B,												0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		ACAACATCCCAAACCCTTTCA	0.512													6	4	---	---	---	---	
RACGAP1	29127	broad.mit.edu	37	12	50395167	50395168	+	Intron	DEL	TC	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50395167_50395168delTC	uc001rvt.2	-						RACGAP1_uc009zlm.1_Intron|RACGAP1_uc001rvs.2_Intron|RACGAP1_uc001rvu.2_Intron	NM_013277	NP_037409	Q9H0H5	RGAP1_HUMAN	Rac GTPase activating protein 1						blood coagulation|cytokinesis, actomyosin contractile ring assembly|cytokinesis, initiation of separation|embryo development|microtubule-based movement|neuroblast proliferation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|spermatogenesis|sulfate transport	acrosomal vesicle|cytosol|microtubule|midbody|nucleus|spindle	alpha-tubulin binding|beta-tubulin binding|gamma-tubulin binding|GTPase activator activity|metal ion binding			kidney(1)	1						AACAATGTGTTCTCTCTCTCTC	0.376													4	3	---	---	---	---	
USP15	9958	broad.mit.edu	37	12	62790336	62790336	+	Intron	DEL	T	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62790336delT	uc001src.1	+						USP15_uc001srb.1_Intron	NM_006313	NP_006304	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15						protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)	3			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		CTTTTGAACCttttttttttc	0.234													4	2	---	---	---	---	
THSD1P1	374500	broad.mit.edu	37	13	52803642	52803643	+	Intron	DEL	TT	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52803642_52803643delTT	uc001vgm.1	-						uc001vgn.2_Intron					Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						CAGTTTTCCCTTTTTTTTTTTT	0.332													6	4	---	---	---	---	
ARID4A	5926	broad.mit.edu	37	14	58768226	58768226	+	Intron	DEL	T	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58768226delT	uc001xdp.2	+						ARID4A_uc010apf.1_Intron|ARID4A_uc001xdo.2_Intron|ARID4A_uc001xdq.2_Intron	NM_002892	NP_002883	P29374	ARI4A_HUMAN	retinoblastoma-binding protein 1 isoform I						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	transcriptional repressor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|lung(1)	6						AAACACAACCTTTTAATGAGA	0.353													11	10	---	---	---	---	
ATXN3	4287	broad.mit.edu	37	14	92555366	92555366	+	Intron	DEL	T	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92555366delT	uc001yac.3	-						ATXN3_uc010aug.2_Intron|ATXN3_uc001yad.3_Intron|ATXN3_uc010auh.2_Intron|ATXN3_uc001yae.3_Intron|ATXN3_uc010twl.1_Intron	NM_004993	NP_004984	P54252	ATX3_HUMAN	ataxin 3 reference isoform						cell death|nervous system development|nucleotide-excision repair|regulation of transcription, DNA-dependent|synaptic transmission|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		TATTAAATACttttttttttt	0.134													8	4	---	---	---	---	
BNIP2	663	broad.mit.edu	37	15	59960956	59960957	+	Intron	INS	-	AC	AC	rs140314308	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59960956_59960957insAC	uc010uhc.1	-						BNIP2_uc002agi.3_Intron|BNIP2_uc010uhb.1_Intron	NM_004330	NP_004321	Q12982	BNIP2_HUMAN	BCL2/adenovirus E1B 19kD interacting protein 2						anti-apoptosis|apoptosis|positive regulation of muscle cell differentiation	nuclear envelope|perinuclear region of cytoplasm	calcium ion binding|GTPase activator activity|protein binding			ovary(1)	1						TTTTCTTTGTTACACACACACA	0.376													4	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	84946555	84946556	+	RNA	INS	-	T	T	rs71453238		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84946555_84946556insT	uc002bke.1	-	1		c.662_663insA								Homo sapiens cDNA FLJ34196 fis, clone FCBBF3019437.																		CGAAGGGAGGAttttttttttt	0.515													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26855912	26855912	+	IGR	DEL	A	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26855912delA								HS3ST4 (706904 upstream) : C16orf82 (222307 downstream)																							agactctgtcaaaaaaaaaaa	0.000													11	5	---	---	---	---	
XPO6	23214	broad.mit.edu	37	16	28167920	28167921	+	Intron	INS	-	AA	AA	rs150507094	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28167920_28167921insAA	uc002dpa.1	-						XPO6_uc002dpb.1_Intron|XPO6_uc010vcp.1_Intron	NM_015171	NP_055986	Q96QU8	XPO6_HUMAN	exportin 6						protein export from nucleus		protein binding|protein transporter activity			ovary(1)|skin(1)	2						AATTCTCCTTCAAAAAAatata	0.252													11	8	---	---	---	---	
ITGAX	3687	broad.mit.edu	37	16	31383487	31383487	+	Intron	DEL	G	-	-	rs67981265		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31383487delG	uc002ebu.1	+						ITGAX_uc002ebt.2_Intron	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor						blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4						cgggaggtctgggggggggga	0.144													4	2	---	---	---	---	
VPS35	55737	broad.mit.edu	37	16	46714944	46714945	+	Intron	INS	-	AC	AC	rs148688318	by1000genomes	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46714944_46714945insAC	uc002eef.3	-						VPS35_uc002eed.2_5'Flank|VPS35_uc002eee.2_Intron	NM_018206	NP_060676	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35						protein transport|retrograde transport, endosome to Golgi	cytosol|endosome|membrane	protein binding				0		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				AAAAAAACTATacacacacaca	0.223													4	4	---	---	---	---	
PAPD5	64282	broad.mit.edu	37	16	50263408	50263409	+	3'UTR	INS	-	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50263408_50263409insA	uc010vgo.1	+	13					PAPD5_uc010cbi.2_Intron|PAPD5_uc002efz.2_3'UTR|PAPD5_uc002ega.2_3'UTR	NM_001040284	NP_001035374	Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5 isoform a						cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)		CTGACAACTGCaaaaaaaacaa	0.332													4	4	---	---	---	---	
MYH8	4626	broad.mit.edu	37	17	10308044	10308045	+	Intron	DEL	AC	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10308044_10308045delAC	uc002gmm.2	-						uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,						muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						TGCAGGCTTTacacacacacac	0.307									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				5	3	---	---	---	---	
TOP3A	7156	broad.mit.edu	37	17	18211538	18211556	+	Intron	DEL	AAAAAAAAAAAAAAAAAAA	-	-	rs67569771		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18211538_18211556delAAAAAAAAAAAAAAAAAAA	uc002gsx.1	-						TOP3A_uc002gsw.1_5'Flank|TOP3A_uc010vxs.1_Intron|TOP3A_uc010cqa.1_Intron	NM_004618	NP_004609	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha						DNA topological change|meiosis	chromosome|PML body	ATP binding|DNA topoisomerase type I activity|protein binding|zinc ion binding			skin(3)	3						tgtctccaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaa	0.132													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	20468035	20468036	+	IGR	INS	-	G	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20468035_20468036insG								LGALS9B (97187 upstream) : CCDC144NL (298674 downstream)																							TGCCTTCGTGTGCGTCACCACG	0.525													6	3	---	---	---	---	
KRT33B	3884	broad.mit.edu	37	17	39523969	39523970	+	Intron	INS	-	A	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39523969_39523970insA	uc002hwl.2	-							NM_002279	NP_002270	Q14525	KT33B_HUMAN	type I hair keratin 3B							intermediate filament	protein binding|structural molecule activity				0		Breast(137;0.000496)				ataaaaaaattaaaaaaaaaaa	0.005													4	2	---	---	---	---	
EME1	146956	broad.mit.edu	37	17	48458137	48458138	+	Frame_Shift_Ins	INS	-	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48458137_48458138insT	uc002iqs.1	+	9	1623_1624	c.1550_1551insT	c.(1549-1551)TGTfs	p.C517fs	EME1_uc010dbp.1_Frame_Shift_Ins_p.C530fs|EME1_uc010dbq.1_RNA|uc010wmk.1_5'Flank	NM_152463	NP_689676	Q96AY2	EME1_HUMAN	essential meiotic endonuclease 1 homolog 1	517					DNA recombination|DNA repair	nucleolus	DNA binding|endonuclease activity|metal ion binding|protein binding				0	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			TATCAGCAGTGTTTTTCGGATA	0.515								Direct_reversal_of_damage|Homologous_recombination					140	76	---	---	---	---	
CA10	56934	broad.mit.edu	37	17	50234899	50234899	+	Intron	DEL	G	-	-	rs67822192		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50234899delG	uc002itw.3	-						CA10_uc002itv.3_Intron|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			ACCCCCCCCCGCAAAACACAC	0.522													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	18	11610673	11610674	+	IGR	INS	-	C	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11610673_11610674insC								FAM38B (908694 upstream) : GNAL (78462 downstream)																							AAGACTGAAGACaaaaaaaaaa	0.302													7	4	---	---	---	---	
EML2	24139	broad.mit.edu	37	19	46125008	46125009	+	Intron	INS	-	T	T	rs34741603		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46125008_46125009insT	uc002pcn.2	-						EML2_uc002pco.2_Intron|EML2_uc002pcp.2_Intron|EML2_uc010xxl.1_Intron|EML2_uc010xxm.1_Intron|EML2_uc010xxn.1_Intron|EML2_uc010xxo.1_Intron|EML2_uc010ekj.2_Intron	NM_012155	NP_036287	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like						sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		acttttccaccttttttttttt	0.203													6	3	---	---	---	---	
ZNF845	91664	broad.mit.edu	37	19	53849108	53849109	+	Intron	INS	-	T	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53849108_53849109insT	uc010ydv.1	+						ZNF845_uc010ydw.1_Intron	NM_138374	NP_612383	Q96IR2	ZN845_HUMAN	zinc finger protein 845						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						tacttttttagttttttttttt	0.000													6	3	---	---	---	---	
KIR2DL1	3802	broad.mit.edu	37	19	55286500	55286501	+	Intron	DEL	GA	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55286500_55286501delGA	uc002qhb.1	+						KIR2DS4_uc010yfj.1_Intron|KIR2DS4_uc010yfk.1_Intron|KIR2DL3_uc010erw.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR2DL3_uc002qha.1_Intron|KIR3DP1_uc010yfi.1_Intron|KIR2DL1_uc010erz.1_Intron	NM_014218	NP_055033	P43626	KI2L1_HUMAN	killer cell immunoglobulin-like receptor, two						immune response|natural killer cell inhibitory signaling pathway	integral to plasma membrane	protein binding|receptor activity				0				GBM - Glioblastoma multiforme(193;0.0192)		GGTagagggtgagagagagaga	0.431													7	4	---	---	---	---	
TNNT1	7138	broad.mit.edu	37	19	55646746	55646749	+	Intron	DEL	TTCC	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55646746_55646749delTTCC	uc002qjb.3	-						TNNT1_uc002qiz.3_Intron|TNNT1_uc002qja.3_Intron|TNNT1_uc002qjc.3_Intron|TNNT1_uc002qje.3_Intron|TNNT1_uc002qjd.3_Intron	NM_003283	NP_003274	P13805	TNNT1_HUMAN	troponin T1, skeletal, slow isoform a						muscle filament sliding|negative regulation of muscle contraction	cytosol|troponin complex	tropomyosin binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		aaacctacctttccttccttcctt	0.000													4	2	---	---	---	---	
MACROD2	140733	broad.mit.edu	37	20	15967343	15967343	+	Intron	DEL	T	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15967343delT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron|MACROD2_uc002wpd.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)				ATCACATTTCTTTTATTTTTC	0.358													41	23	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	15848642	15848643	+	IGR	INS	-	AAGG	AAGG			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15848642_15848643insAAGG								HSPA13 (93133 upstream) : SAMSN1 (8906 downstream)																							agaaagaaggaaaggaaggaag	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16920274	16920275	+	IGR	DEL	AT	-	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16920274_16920275delAT								OR11H1 (470470 upstream) : CCT8L2 (151373 downstream)																							TTATAGTGACATGTATGAAAAC	0.267													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	17071582	17071583	+	IGR	INS	-	A	A	rs78253844		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17071582_17071583insA								OR11H1 (621778 upstream) : CCT8L2 (65 downstream)																							ctccgtctctcaaaaaaaaaaa	0.129													4	3	---	---	---	---	
