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
ASH1L	55870	broad.mit.edu	37	1	155451980	155451980	+	Nonsense_Mutation	SNP	A	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155451980A>T	uc009wqq.2	-	3	1161	c.681T>A	c.(679-681)TGT>TGA	p.C227*	ASH1L_uc001fkt.2_Nonsense_Mutation_p.C227*|ASH1L_uc009wqr.1_Nonsense_Mutation_p.C227*	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	227					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)			TGGAAGGAGGACAGGTAGCAA	0.453													67	181	---	---	---	---	PASS
NUP133	55746	broad.mit.edu	37	1	229635527	229635527	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229635527G>C	uc001htn.2	-	5	644	c.552C>G	c.(550-552)ATC>ATG	p.I184M		NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	184					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GCCAATAGCGGATAGATCCTT	0.453													15	88	---	---	---	---	PASS
ATP6V1C2	245973	broad.mit.edu	37	2	10918726	10918726	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10918726A>C	uc002ras.2	+	12	1101	c.992A>C	c.(991-993)AAC>ACC	p.N331T	ATP6V1C2_uc002rat.2_Missense_Mutation_p.N285T	NM_001039362	NP_001034451	Q8NEY4	VATC2_HUMAN	vacuolar H+ ATPase C2 isoform a	331					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting V-type ATPase, V1 domain				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		CTCAAGGTGAACTTCAGTGAA	0.602													21	100	---	---	---	---	PASS
DDX11L2	84771	broad.mit.edu	37	2	114357543	114357543	+	3'UTR	SNP	T	A	A	rs114684815	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114357543T>A	uc010yxx.1	-	3										SubName: Full=DEAD/H box polypeptide 11 like 2;												0						CCTGTCAGGATGAGGCCTACT	0.572													5	23	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	132292791	132292791	+	RNA	SNP	T	C	C	rs3101988	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132292791T>C	uc002ttc.1	-	2		c.257A>G								full-length cDNA clone CS0DI014YM20 of Placenta Cot 25-normalized of Homo sapiens (human).																		GTGGATGCTCTGGGCACAGGT	0.627													3	2	---	---	---	---	PASS
PTH2R	5746	broad.mit.edu	37	2	209358096	209358096	+	Silent	SNP	G	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209358096G>T	uc002vdb.2	+	13	1578	c.1365G>T	c.(1363-1365)GTG>GTT	p.V455V	PTH2R_uc010zjb.1_Silent_p.V466V|PTH2R_uc010fuo.1_Intron	NM_005048	NP_005039	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor precursor	455	Cytoplasmic (Potential).					integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)		TCACCACCGTGACGCACAGCA	0.612													3	20	---	---	---	---	PASS
ACCN4	55515	broad.mit.edu	37	2	220396564	220396564	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220396564G>A	uc002vma.2	+	2	1062	c.1048G>A	c.(1048-1050)GGC>AGC	p.G350S	ACCN4_uc010fwi.1_Missense_Mutation_p.G350S|ACCN4_uc010fwj.1_Missense_Mutation_p.G350S|ACCN4_uc002vly.1_Missense_Mutation_p.G350S|ACCN4_uc002vlz.2_Missense_Mutation_p.G350S|ACCN4_uc002vmb.2_Missense_Mutation_p.G4S	NM_182847	NP_878267	Q96FT7	ACCN4_HUMAN	amiloride-sensitive cation channel 4 isoform 2	350	Extracellular (Potential).					integral to plasma membrane	sodium channel activity|sodium ion transmembrane transporter activity			ovary(2)	2		Renal(207;0.0183)		Epithelial(149;5.47e-10)|all cancers(144;9e-08)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.0086)|READ - Rectum adenocarcinoma(5;0.156)		CATGGGCAGTGGCCTGGAGAT	0.632													51	160	---	---	---	---	PASS
DOCK10	55619	broad.mit.edu	37	2	225717687	225717687	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225717687G>T	uc010fwz.1	-	17	2280	c.2041C>A	c.(2041-2043)CAC>AAC	p.H681N	DOCK10_uc002vob.2_Missense_Mutation_p.H675N	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	681	DHR-1.						GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TACTTGAGGTGTTTGGGGTAA	0.338													29	124	---	---	---	---	PASS
DUSP7	1849	broad.mit.edu	37	3	52088081	52088081	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52088081T>C	uc003dct.2	-	2	906	c.827A>G	c.(826-828)AAT>AGT	p.N276S	DUSP7_uc010hma.2_Missense_Mutation_p.N276S	NM_001947	NP_001938	Q16829	DUS7_HUMAN	dual specificity phosphatase 7	276					inactivation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein binding|protein tyrosine phosphatase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;5.14e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGGTGTGACATTGAGGATATA	0.582													47	169	---	---	---	---	PASS
ZBBX	79740	broad.mit.edu	37	3	167068219	167068219	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167068219T>C	uc003fep.2	-	9	840	c.517A>G	c.(517-519)ACT>GCT	p.T173A	ZBBX_uc011bpc.1_Missense_Mutation_p.T173A|ZBBX_uc003feq.2_Missense_Mutation_p.T144A	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	173	B box-type; atypical.					intracellular	zinc ion binding			ovary(2)	2						TGCAAAAGAGTTGTTCTGTGG	0.328													75	310	---	---	---	---	PASS
ARPM1	84517	broad.mit.edu	37	3	169486066	169486066	+	Silent	SNP	A	G	G			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169486066A>G	uc003ffs.1	-	2	648	c.273T>C	c.(271-273)TAT>TAC	p.Y91Y		NM_032487	NP_115876	Q9BYD9	ARPM1_HUMAN	actin related protein M1	91						cytoplasm|cytoskeleton					0	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;5.01e-59)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)			GCTTTAGGTTATAGTCATAGA	0.473													43	64	---	---	---	---	PASS
BOD1L	259282	broad.mit.edu	37	4	13629046	13629046	+	Missense_Mutation	SNP	T	C	C	rs138568321	byFrequency	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13629046T>C	uc003gmz.1	-	1	283	c.166A>G	c.(166-168)ATG>GTG	p.M56V	BOD1L_uc010idr.1_5'UTR|BOD1L_uc010ids.1_RNA	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	56							DNA binding			ovary(5)|breast(1)	6						TTCACGATCATGGCCACGAGC	0.378													6	2	---	---	---	---	PASS
DCHS2	54798	broad.mit.edu	37	4	155256174	155256174	+	Silent	SNP	C	G	G			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155256174C>G	uc003inw.2	-	8	1062	c.1062G>C	c.(1060-1062)GGG>GGC	p.G354G	DCHS2_uc003inx.2_Silent_p.G853G	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	354	Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CAGCTGTGAGCCCACCACCGT	0.423													28	132	---	---	---	---	PASS
AQPEP	206338	broad.mit.edu	37	5	115298232	115298232	+	5'UTR	SNP	G	C	C	rs9326980	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115298232G>C	uc003kro.2	+	1					AQPEP_uc003krp.2_RNA|uc003krn.1_Missense_Mutation_p.R29G	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin						proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0						GGCAGGGGTCGCAGCACTGAA	0.652													3	14	---	---	---	---	PASS
AQPEP	206338	broad.mit.edu	37	5	115298378	115298378	+	Silent	SNP	C	T	T	rs10062297	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115298378C>T	uc003kro.2	+	1	228	c.64C>T	c.(64-66)CTG>TTG	p.L22L	AQPEP_uc003krp.2_RNA|uc003krn.1_5'UTR	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin	22	Helical; Signal-anchor for type II membrane protein; (Potential).				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0						GCTGGCTGGGCTGGTAGCCGC	0.701													3	25	---	---	---	---	PASS
HSPA1B	3304	broad.mit.edu	37	6	31797488	31797488	+	Silent	SNP	C	G	G			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31797488C>G	uc003nxk.2	+	1	1977	c.1761C>G	c.(1759-1761)GCC>GCG	p.A587A		NM_005346	NP_005337	P08107	HSP71_HUMAN	heat shock 70kDa protein 1B	587					anti-apoptosis|mRNA catabolic process|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of inclusion body assembly|protein refolding|response to unfolded protein	cytosol|endoplasmic reticulum|inclusion body|mitochondrion|nuclear speck|perinuclear region of cytoplasm|ribonucleoprotein complex	ATP binding|protein binding involved in protein folding|protein N-terminus binding|receptor activity|ubiquitin protein ligase binding|unfolded protein binding			breast(1)	1						ACACCTTGGCCGAGAAGGACG	0.597													9	48	---	---	---	---	PASS
HLA-DMA	3108	broad.mit.edu	37	6	32920827	32920827	+	5'UTR	SNP	A	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32920827A>T	uc003ocm.2	-	1					HLA-DMA_uc011dqm.1_5'UTR	NM_006120	NP_006111	Q31604	Q31604_HUMAN	major histocompatibility complex, class II, DM							integral to membrane|MHC class II protein complex					0						TTCTTGCCACACAGTAGGTAG	0.547													27	116	---	---	---	---	PASS
PI16	221476	broad.mit.edu	37	6	36927000	36927000	+	Missense_Mutation	SNP	G	A	A	rs139393851		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36927000G>A	uc003ona.2	+	2	579	c.251G>A	c.(250-252)CGC>CAC	p.R84H	PI16_uc003omz.1_Missense_Mutation_p.R84H|PI16_uc003onb.2_Missense_Mutation_p.R84H|PI16_uc011dts.1_5'Flank	NM_153370	NP_699201	Q6UXB8	PI16_HUMAN	protease inhibitor 16 precursor	84	Extracellular (Potential).					extracellular region|integral to membrane	peptidase inhibitor activity				0						GAGCGCGGGCGCCGCGGCGAG	0.667													9	14	---	---	---	---	PASS
RAC1	5879	broad.mit.edu	37	7	6431629	6431629	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6431629A>G	uc003spx.2	+	3	423	c.182A>G	c.(181-183)CAA>CGA	p.Q61R	RAC1_uc003spw.2_Missense_Mutation_p.Q61R	NM_006908	NP_008839	P63000	RAC1_HUMAN	ras-related C3 botulinum toxin substrate 1	61	GTP (By similarity).			Q->L: Constitutively active. Interacts with PARD6 proteins.	actin filament polymerization|apoptosis|axon guidance|cell motility|cell-matrix adhesion|induction of apoptosis by extracellular signals|inflammatory response|lamellipodium assembly|localization within membrane|negative regulation of interleukin-23 production|negative regulation of receptor-mediated endocytosis|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of lamellipodium assembly|positive regulation of Rho protein signal transduction|regulation of cell migration|regulation of defense response to virus by virus|regulation of hydrogen peroxide metabolic process|regulation of respiratory burst|ruffle organization|small GTPase mediated signal transduction|T cell costimulation|viral reproduction	cytosol|melanosome|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity|thioesterase binding			lung(2)	2		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.104)	Pravastatin(DB00175)|Simvastatin(DB00641)	ACAGCTGGACAAGAAGATTAT	0.403													12	226	---	---	---	---	PASS
CDC14C	168448	broad.mit.edu	37	7	48965256	48965256	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48965256T>A	uc010kyv.1	+	1	1100	c.988T>A	c.(988-990)TTG>ATG	p.L330M		NR_003595				SubName: Full=Putative uncharacterized protein MGC26484;												0						GCAGCAGTTTTTGGTGATGAA	0.517													26	143	---	---	---	---	PASS
BRAF	673	broad.mit.edu	37	7	140501299	140501299	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140501299C>A	uc003vwc.3	-	6	834	c.773G>T	c.(772-774)GGT>GTT	p.G258V		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	258	Phorbol-ester/DAG-type.				activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding		KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	ACAGCGGAAACCCTGGAAAAG	0.368		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				11	75	---	---	---	---	PASS
MLLT3	4300	broad.mit.edu	37	9	20620724	20620724	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20620724T>C	uc003zoe.2	-	2	381	c.122A>G	c.(121-123)CAC>CGC	p.H41R	MLLT3_uc011lne.1_Missense_Mutation_p.H9R|MLLT3_uc011lnf.1_Missense_Mutation_p.H38R|MLLT3_uc003zof.2_5'UTR|MLLT3_uc011lng.1_Missense_Mutation_p.H9R	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	41	YEATS.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		TATGTTACTGTGCTCCGGACC	0.547			T	MLL	ALL								47	216	---	---	---	---	PASS
RFK	55312	broad.mit.edu	37	9	79002418	79002418	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79002418T>A	uc004akd.2	-	4	722	c.386A>T	c.(385-387)GAT>GTT	p.D129V	RFK_uc004ake.2_3'UTR	NM_018339	NP_060809	Q969G6	RIFK_HUMAN	riboflavin kinase	122					riboflavin biosynthetic process	cytosol	ATP binding|metal ion binding|riboflavin kinase activity				0					Riboflavin(DB00140)	TTCTTCAATATCACCTTGAAT	0.333													15	267	---	---	---	---	PASS
PTGR1	22949	broad.mit.edu	37	9	114325536	114325536	+	Intron	SNP	T	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114325536T>A	uc004bfh.2	-						ZNF483_uc004bfg.2_Intron|PTGR1_uc011lwr.1_Intron|PTGR1_uc004bfi.3_Intron|PTGR1_uc004bfj.3_3'UTR	NM_012212	NP_036344	Q14914	PTGR1_HUMAN	prostaglandin reductase 1 isoform 1						leukotriene metabolic process	cytoplasm	15-oxoprostaglandin 13-oxidase activity|2-alkenal reductase activity|alcohol dehydrogenase (NAD) activity|zinc ion binding				0						CAACAAATTTTAAAACTTAAT	0.323													5	74	---	---	---	---	PASS
TUBBP5	643224	broad.mit.edu	37	9	141071110	141071110	+	Silent	SNP	A	G	G			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141071110A>G	uc004com.2	+	4	774	c.513A>G	c.(511-513)CCA>CCG	p.P171P	TUBBP5_uc010ncq.2_3'UTR					RecName: Full=Putative tubulin beta-4q chain;												0						TGCGCTTCCCAGGCCAGCTGA	0.597													5	80	---	---	---	---	PASS
C1QL3	389941	broad.mit.edu	37	10	16562941	16562941	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16562941T>A	uc001ioj.1	-	1	1064	c.124A>T	c.(124-126)AGC>TGC	p.S42C		NM_001010908	NP_001010908	Q5VWW1	C1QL3_HUMAN	complement component 1, q subcomponent-like 3	42						collagen				ovary(1)	1						GCAGCGGTGCTGGGCGCCTTG	0.736													2	3	---	---	---	---	PASS
C10orf4	118924	broad.mit.edu	37	10	95429434	95429434	+	3'UTR	SNP	C	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95429434C>A	uc001kiz.1	-	14					C10orf4_uc001kiv.1_RNA|C10orf4_uc001kja.1_3'UTR	NM_145246	NP_660289	Q70Z53	F10C1_HUMAN	FRA10AC1 protein							nucleus	protein binding				0		Colorectal(252;0.122)				AAGCCTCTGACATTCTGAGAG	0.313													2	8	---	---	---	---	PASS
MS4A2	2206	broad.mit.edu	37	11	59861275	59861275	+	Intron	SNP	T	G	G			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59861275T>G	uc001nop.2	+						MS4A2_uc009ymu.2_3'UTR	NM_000139	NP_000130	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member						cell proliferation|humoral immune response	integral to plasma membrane	calcium channel activity			ovary(1)	1		all_epithelial(135;0.245)			Omalizumab(DB00043)	GTGCCtgtgtttgtgtgtgtg	0.368													3	5	---	---	---	---	PASS
NXF1	10482	broad.mit.edu	37	11	62566115	62566115	+	Intron	SNP	C	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62566115C>A	uc001nvf.1	-						NXF1_uc001nvg.1_3'UTR|NXF1_uc009yog.1_Intron|NXF1_uc010rmh.1_3'UTR	NM_006362	NP_006353	Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1 isoform 1						gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding			skin(3)	3						GCTCTAGGAGCAAATATACCA	0.577													10	35	---	---	---	---	PASS
FIBP	9158	broad.mit.edu	37	11	65655303	65655303	+	Intron	SNP	G	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65655303G>A	uc001ogd.2	-						FIBP_uc009yqu.2_Intron|FIBP_uc001oge.2_Intron|FIBP_uc010roq.1_Intron|FIBP_uc010ror.1_Missense_Mutation_p.S129L|CCDC85B_uc001ogf.2_5'Flank	NM_198897	NP_942600	O43427	FIBP_HUMAN	FGF intracellular binding protein isoform a						fibroblast growth factor receptor signaling pathway	endomembrane system|membrane|microsome|mitochondrion|nucleus	fibroblast growth factor binding			ovary(1)	1				READ - Rectum adenocarcinoma(159;0.166)		tcaactttctgatggctgggt	0.139													7	29	---	---	---	---	PASS
XRRA1	143570	broad.mit.edu	37	11	74618288	74618288	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74618288C>G	uc009yub.2	-	9	995	c.663G>C	c.(661-663)AAG>AAC	p.K221N	XRRA1_uc001ovm.2_RNA|XRRA1_uc001ovn.2_5'Flank|XRRA1_uc001ovo.2_5'UTR|XRRA1_uc001ovq.3_Missense_Mutation_p.K221N|XRRA1_uc001ovp.3_5'UTR|XRRA1_uc001ovr.2_5'UTR|XRRA1_uc001ovt.2_5'UTR	NM_182969	NP_892014	Q6P2D8	XRRA1_HUMAN	X-ray radiation resistance associated 1	221					response to X-ray	cytoplasm|nucleus				central_nervous_system(1)	1						GGATGTACCTCTTGCTTGTCA	0.542													20	105	---	---	---	---	PASS
USP35	57558	broad.mit.edu	37	11	77920864	77920864	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77920864A>C	uc009yva.1	+	10	2209	c.1963A>C	c.(1963-1965)ACC>CCC	p.T655P	USP35_uc001oze.2_Missense_Mutation_p.T411P|USP35_uc001ozc.2_Missense_Mutation_p.T223P|USP35_uc010rsp.1_Missense_Mutation_p.T87P|USP35_uc001ozd.2_Missense_Mutation_p.T266P|USP35_uc001ozf.2_Missense_Mutation_p.T386P	NM_020798	NP_065849	Q9P2H5	UBP35_HUMAN	ubiquitin specific protease 35	655					ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)	3	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			CACCCCCCCCACCAGCCTGTA	0.527													5	17	---	---	---	---	PASS
HEPHL1	341208	broad.mit.edu	37	11	93803647	93803647	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93803647T>C	uc001pep.2	+	6	1328	c.1171T>C	c.(1171-1173)TGG>CGG	p.W391R	uc001pen.1_Intron	NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor	391	Plastocyanin-like 3.|Extracellular (Potential).				copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				AAAAATTCTTTGGGATTATGC	0.438													15	33	---	---	---	---	PASS
BSX	390259	broad.mit.edu	37	11	122848489	122848489	+	Silent	SNP	G	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122848489G>A	uc010rzs.1	-	3	570	c.570C>T	c.(568-570)CGC>CGT	p.R190R		NM_001098169	NP_001091639	Q3C1V8	BSH_HUMAN	brain specific homeobox	190											0		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0361)		CCTCTGAACCGCGGGGGCTGC	0.657													3	21	---	---	---	---	PASS
OR4D5	219875	broad.mit.edu	37	11	123810477	123810477	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123810477G>A	uc001pzk.1	+	1	154	c.154G>A	c.(154-156)GAC>AAC	p.D52N		NM_001001965	NP_001001965	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D,	52	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		AGTGACCTCCGACCCACACCT	0.443													62	188	---	---	---	---	PASS
KRT73	319101	broad.mit.edu	37	12	53005086	53005086	+	Missense_Mutation	SNP	G	A	A	rs150273425		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53005086G>A	uc001sas.2	-	6	1047	c.1012C>T	c.(1012-1014)CGG>TGG	p.R338W		NM_175068	NP_778238	Q86Y46	K2C73_HUMAN	keratin 73	338	Rod.|Coil 2.					keratin filament	structural molecule activity			large_intestine(2)|ovary(2)|skin(2)	6				BRCA - Breast invasive adenocarcinoma(357;0.189)		TCCCCATGCCGGCCGGCTGCT	0.537													21	107	---	---	---	---	PASS
GPR84	53831	broad.mit.edu	37	12	54756338	54756338	+	3'UTR	SNP	A	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54756338A>T	uc001sfu.2	-	2						NM_020370	NP_065103	Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84							integral to membrane|plasma membrane	G-protein coupled receptor activity			breast(2)	2						CTGGGGAGAGATTGTTGTGAA	0.428													25	82	---	---	---	---	PASS
TIMELESS	8914	broad.mit.edu	37	12	56817470	56817470	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56817470C>T	uc001slf.2	-	17	2156	c.1988G>A	c.(1987-1989)CGT>CAT	p.R663H		NM_003920	NP_003911	Q9UNS1	TIM_HUMAN	timeless homolog	663	Glu-rich.				cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin				ovary(5)|breast(2)|pancreas(1)	8						ctcTGCCCCACGTTCCTCTGG	0.393													13	40	---	---	---	---	PASS
GPR133	283383	broad.mit.edu	37	12	131487352	131487352	+	Intron	SNP	C	T	T	rs144732392	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131487352C>T	uc001uit.3	+						GPR133_uc010tbm.1_Intron	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		GACCTGGGGGCGATCAGCCCC	0.642													7	32	---	---	---	---	PASS
LOC374491	374491	broad.mit.edu	37	13	25168501	25168501	+	RNA	SNP	G	A	A	rs4770716	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25168501G>A	uc001upm.2	+	10		c.1173G>A			LOC374491_uc001upn.2_RNA|LOC374491_uc001upo.2_RNA					Homo sapiens mRNA; cDNA DKFZp434J0717 (from clone DKFZp434J0717).												0						TTTTCTCTTCGGTGAGTAATC	0.388													4	56	---	---	---	---	PASS
NUFIP1	26747	broad.mit.edu	37	13	45523879	45523879	+	Silent	SNP	T	C	C			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45523879T>C	uc001uzp.2	-	8	1158	c.1116A>G	c.(1114-1116)TCA>TCG	p.S372S		NM_012345	NP_036477	Q9UHK0	NUFP1_HUMAN	nuclear fragile X mental retardation protein	372					box C/D snoRNP assembly|positive regulation of transcription from RNA polymerase II promoter|RNA processing	actin cytoskeleton|cytosolic ribosome|nuclear matrix|nucleolus|perichromatin fibrils|pre-snoRNP complex|presynaptic active zone|transcription elongation factor complex	DNA binding|identical protein binding|protein binding, bridging|RNA binding|zinc ion binding				0		Lung NSC(96;8.23e-05)|Breast(139;0.00378)|Prostate(109;0.0107)|all_hematologic(4;0.014)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)|Acute lymphoblastic leukemia(4;0.143)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000306)|BRCA - Breast invasive adenocarcinoma(63;0.125)		TCTCTGACCCTGAAAGACTGC	0.443													6	189	---	---	---	---	PASS
OR10G2	26534	broad.mit.edu	37	14	22102163	22102163	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22102163A>C	uc010tmc.1	-	1	836	c.836T>G	c.(835-837)GTG>GGG	p.V279G		NM_001005466	NP_001005466	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G,	279	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		AGTGTAAAACACAGCCGCTGC	0.512													19	102	---	---	---	---	PASS
FAM63B	54629	broad.mit.edu	37	15	59064095	59064095	+	Silent	SNP	T	G	G			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59064095T>G	uc002afj.2	+	1	703	c.501T>G	c.(499-501)CCT>CCG	p.P167P	FAM63B_uc002afi.2_Silent_p.P167P|FAM63B_uc002afk.2_RNA|FAM63B_uc002afl.2_RNA	NM_001040450	NP_001035540	Q8NBR6	FA63B_HUMAN	hypothetical protein LOC54629 isoform a	167										central_nervous_system(1)	1						CGAGCCCTCCTGGGGAATCTC	0.632													4	32	---	---	---	---	PASS
SLC7A5P2	387254	broad.mit.edu	37	16	21531681	21531681	+	Silent	SNP	C	G	G	rs42140	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21531681C>G	uc002djd.2	-	1	85	c.6G>C	c.(4-6)GCG>GCC	p.A2A	uc002diq.3_Intron|LOC100271836_uc002dja.2_RNA|LOC100271836_uc002djb.2_RNA	NR_002594				RecName: Full=Putative L-type amino acid transporter 1-like protein MLAS; AltName: Full=hLAT1 3-transmembrane protein MLAS;          Short=hLAT1 3TM MLAS;												0						GGCCCGCACCCGCCATGCTCT	0.771													2	4	---	---	---	---	PASS
SCNN1B	6338	broad.mit.edu	37	16	23360195	23360195	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23360195T>C	uc002dln.2	+	2	451	c.275T>C	c.(274-276)TTC>TCC	p.F92S		NM_000336	NP_000327	P51168	SCNNB_HUMAN	sodium channel, nonvoltage-gated 1, beta	92	Extracellular (By similarity).				excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(3)|breast(2)|large_intestine(1)|pancreas(1)	7				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	ACCATGGACTTCCCTGCCGTC	0.577													4	45	---	---	---	---	PASS
C16orf54	283897	broad.mit.edu	37	16	29755663	29755663	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29755663G>A	uc002dtp.2	-	2	719	c.610C>T	c.(610-612)CGG>TGG	p.R204W	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|uc002dtq.1_5'Flank	NM_175900	NP_787096	Q6UWD8	CP054_HUMAN	hypothetical protein LOC283897	204						integral to membrane					0						AAGGTGACCCGTGGCTGGAGG	0.667													6	31	---	---	---	---	PASS
ITGAD	3681	broad.mit.edu	37	16	31427932	31427932	+	Missense_Mutation	SNP	G	A	A	rs143518464		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31427932G>A	uc002ebv.1	+	20	2513	c.2464G>A	c.(2464-2466)GCA>ACA	p.A822T	ITGAD_uc010cap.1_Missense_Mutation_p.A823T	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor	822	Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1						CTACTATCCAGCAGGGCTGTC	0.622													41	132	---	---	---	---	PASS
CNOT1	23019	broad.mit.edu	37	16	58621140	58621140	+	Missense_Mutation	SNP	A	C	C			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58621140A>C	uc002env.2	-	6	691	c.398T>G	c.(397-399)CTG>CGG	p.L133R	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Missense_Mutation_p.L133R|CNOT1_uc002enx.2_Missense_Mutation_p.L133R|CNOT1_uc002enz.1_Intron	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	133					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		AGAATTCAACAGGGCAAGGCC	0.338													29	135	---	---	---	---	PASS
RTN4RL1	146760	broad.mit.edu	37	17	1840677	1840677	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1840677C>T	uc002ftp.2	-	2	458	c.439G>A	c.(439-441)GGC>AGC	p.G147S		NM_178568	NP_848663	Q86UN2	R4RL1_HUMAN	reticulon 4 receptor-like 1 precursor	147	LRR 4.				axon regeneration	anchored to plasma membrane	receptor activity				0						CTGTGCAGGCCGCCAAAGACG	0.622													11	49	---	---	---	---	PASS
LRRC37A4	55073	broad.mit.edu	37	17	43587708	43587708	+	Intron	SNP	A	G	G			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43587708A>G	uc002ije.2	-						uc010wjp.1_RNA					Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						AACAACCACCATCTCCAAATC	0.348													6	146	---	---	---	---	PASS
SPOP	8405	broad.mit.edu	37	17	47696688	47696688	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47696688T>G	uc010dbk.2	-	5	892	c.260A>C	c.(259-261)TAC>TCC	p.Y87S	SPOP_uc002ipb.2_Missense_Mutation_p.Y87S|SPOP_uc002ipc.2_Missense_Mutation_p.Y87S|SPOP_uc002ipd.2_Missense_Mutation_p.Y87S|SPOP_uc002ipe.2_Missense_Mutation_p.Y87S|SPOP_uc002ipf.2_Missense_Mutation_p.Y87S|SPOP_uc002ipg.2_Missense_Mutation_p.Y87S	NM_003563	NP_003554	O43791	SPOP_HUMAN	speckle-type POZ protein	87	MATH.|Required for nuclear localization.				mRNA processing	nucleus	protein binding			prostate(2)|ovary(2)|lung(2)	6						CAGTAACAGGTAAAGTGACAG	0.403										Prostate(2;0.17)			44	199	---	---	---	---	PASS
DNMT1	1786	broad.mit.edu	37	19	10265299	10265299	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10265299C>T	uc002mng.2	-	20	1927	c.1747G>A	c.(1747-1749)GAC>AAC	p.D583N	DNMT1_uc010xlc.1_Missense_Mutation_p.D599N|DNMT1_uc002mnh.2_Missense_Mutation_p.D478N|DNMT1_uc010xld.1_Missense_Mutation_p.D583N	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b	583	Interaction with the PRC2/EED-EZH2 complex (By similarity).				chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)	TTGATCAGGTCCCGCATGCAG	0.622													25	98	---	---	---	---	PASS
CYP2A6	1548	broad.mit.edu	37	19	41351368	41351368	+	Missense_Mutation	SNP	A	G	G	rs146206761	byFrequency	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41351368A>G	uc002opl.3	-	7	1013	c.992T>C	c.(991-993)ATT>ACT	p.I331T	CYP2A6_uc010ehe.1_Missense_Mutation_p.I127T	NM_000762	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A,	331					coumarin catabolic process|exogenous drug catabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|coumarin 7-hydroxylase activity|electron carrier activity|enzyme binding|heme binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Chlorzoxazone(DB00356)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Formoterol(DB00983)|Halothane(DB01159)|Letrozole(DB01006)|Methoxsalen(DB00553)|Metyrapone(DB01011)|Nicotine(DB00184)|Pilocarpine(DB01085)|Tolbutamide(DB01124)|Tranylcypromine(DB00752)	CACTCTGTCAATCTCCTCATG	0.537													5	173	---	---	---	---	PASS
CYP2A7	1549	broad.mit.edu	37	19	41383264	41383264	+	Missense_Mutation	SNP	A	G	G	rs138256878	byFrequency	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41383264A>G	uc002opm.2	-	7	1534	c.992T>C	c.(991-993)ATT>ACT	p.I331T	CYP2A7_uc002opo.2_Missense_Mutation_p.I331T|CYP2A7_uc002opn.2_Missense_Mutation_p.I280T	NM_000764	NP_000755	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A,	331						endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CACTCTGTCAATCTCCTCATG	0.527													16	186	---	---	---	---	PASS
LIG1	3978	broad.mit.edu	37	19	48654539	48654539	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48654539C>T	uc002pia.1	-	7	644	c.524G>A	c.(523-525)GGA>GAA	p.G175E	LIG1_uc010xze.1_5'UTR|LIG1_uc002phz.1_RNA|LIG1_uc002pib.1_RNA|LIG1_uc010xzf.1_Intron|LIG1_uc010xzg.1_Missense_Mutation_p.G144E|LIG1_uc010xzh.1_RNA	NM_000234	NP_000225	P18858	DNLI1_HUMAN	DNA ligase I	175					anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	CCCGTCTTCTCCTTCCTTCTC	0.567								NER					66	248	---	---	---	---	PASS
KDELR1	10945	broad.mit.edu	37	19	48893842	48893842	+	Intron	SNP	C	G	G	rs149176778	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48893842C>G	uc002pjb.1	-						KDELR1_uc002pja.1_5'UTR	NM_006801	NP_006792	P24390	ERD21_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum						intracellular protein transport|protein retention in ER lumen|vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|integral to membrane|membrane fraction	KDEL sequence binding|protein binding|receptor activity				0		all_epithelial(76;2.48e-06)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Prostate(7;0.122)|Breast(70;0.203)		all cancers(93;0.000114)|OV - Ovarian serous cystadenocarcinoma(262;0.000136)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.0145)		gagagacagacagacagacag	0.368													5	20	---	---	---	---	PASS
ADRA1D	146	broad.mit.edu	37	20	4202306	4202306	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4202306C>T	uc002wkr.2	-	2	1638	c.1583G>A	c.(1582-1584)CGC>CAC	p.R528H		NM_000678	NP_000669	P25100	ADA1D_HUMAN	alpha-1D-adrenergic receptor	528	Cytoplasmic (By similarity).			KPPSAFREWRLLGPFRRPTTQLRAKVSSLSHKIRAGGAQRA EAACAQRSEVEAVSLGVPHEVAEGATCQAYELADYSNLRET DI -> SHPAPSASGGCWGRSGDPRPSCAPKSPACRTRSPP GARSAQRQRAPSAQRWRLCP (in Ref. 1).	cell proliferation|cell-cell signaling|DNA metabolic process|G-protein signaling, coupled to cAMP nucleotide second messenger|multicellular organismal development|positive regulation of cell proliferation	integral to plasma membrane	alpha1-adrenergic receptor activity				0					Alfuzosin(DB00346)|Bethanidine(DB00217)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Doxazosin(DB00590)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Methotrimeprazine(DB01403)|Norepinephrine(DB00368)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)	TGCCTCTGCGCGCTGCGCGCC	0.716													18	62	---	---	---	---	PASS
RTN4R	65078	broad.mit.edu	37	22	20230164	20230164	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20230164G>T	uc002zrv.2	-	2	693	c.492C>A	c.(490-492)AAC>AAA	p.N164K	RTN4R_uc002zru.2_5'UTR	NM_023004	NP_075380	Q9BZR6	RTN4R_HUMAN	reticulon 4 receptor precursor	164	LRR 5.				axonogenesis|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	anchored to membrane|cell surface|endoplasmic reticulum|plasma membrane	protein binding|receptor activity				0	Colorectal(54;0.0993)					CCTGCAGCGCGTTGTCCTGCA	0.687													11	52	---	---	---	---	PASS
NUDT10	170685	broad.mit.edu	37	X	51075841	51075841	+	Silent	SNP	A	G	G	rs2625875	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51075841A>G	uc004dph.2	+	2	244	c.24A>G	c.(22-24)ACA>ACG	p.T8T	NUDT10_uc004dpi.3_Silent_p.T8T	NM_153183	NP_694853	Q8NFP7	NUD10_HUMAN	nudix-type motif 10	8						cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding				0	Ovarian(276;0.236)					CCAACCAGACACGGACCTACG	0.677													6	18	---	---	---	---	PASS
NAP1L2	4674	broad.mit.edu	37	X	72432915	72432915	+	3'UTR	SNP	C	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72432915C>T	uc004ebi.2	-	1					NAP1L2_uc011mqj.1_3'UTR	NM_021963	NP_068798	Q9ULW6	NP1L2_HUMAN	nucleosome assembly protein 1-like 2						nucleosome assembly	chromatin assembly complex				lung(1)	1	Renal(35;0.156)					ATATCTAGGGCAGTTAATTTC	0.343													13	22	---	---	---	---	PASS
RLIM	51132	broad.mit.edu	37	X	73811648	73811648	+	Missense_Mutation	SNP	G	A	A	rs147508371	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73811648G>A	uc004ebu.2	-	5	1792	c.1502C>T	c.(1501-1503)TCA>TTA	p.S501L	RLIM_uc004ebw.2_Missense_Mutation_p.S501L	NM_183353	NP_899196	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	501	Ser-rich.|Poly-Ser.				random inactivation of X chromosome|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytoplasm|transcriptional repressor complex	transcription corepressor activity|ubiquitin-protein ligase activity|zinc ion binding	p.S501L(1)		ovary(2)	2						GCCTGATGATGAGCTTCCTTC	0.378													5	37	---	---	---	---	PASS
HCFC1	3054	broad.mit.edu	37	X	153224170	153224170	+	Silent	SNP	A	C	C			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153224170A>C	uc004fjp.2	-	10	2181	c.1653T>G	c.(1651-1653)GCT>GCG	p.A551A		NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1	551					cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGCGGCCGCAGCGGCCAGTG	0.657													14	16	---	---	---	---	PASS
C1orf135	79000	broad.mit.edu	37	1	26164088	26164088	+	Intron	DEL	A	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26164088delA	uc001bkw.1	-							NM_024037	NP_076942	Q9H7T9	CA135_HUMAN	aurora A-binding protein												0		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00521)|all_lung(284;0.00764)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0675)|all_neural(195;0.117)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0429)|OV - Ovarian serous cystadenocarcinoma(117;3.28e-25)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;1.75e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000787)|BRCA - Breast invasive adenocarcinoma(304;0.00102)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)		TATTAATATTAAAAGACATAC	0.393													128	26	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	31128558	31128559	+	IGR	INS	-	TGG	TGG	rs150361136	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31128558_31128559insTGG								None (None upstream) : MATN1 (55567 downstream)																							ggtggtggtgatggtggtgatg	0.069													3	3	---	---	---	---	
DCDC2B	149069	broad.mit.edu	37	1	32680712	32680712	+	Intron	DEL	A	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32680712delA	uc001bun.2	+						C1orf91_uc001buo.3_Intron|C1orf91_uc001bup.3_Intron	NM_001099434	NP_001092904	A2VCK2	DCD2B_HUMAN	doublecortin domain containing 2B						intracellular signal transduction						0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				GACTGCCCGTAAAAAAAAAAA	0.458													9	4	---	---	---	---	
HDAC1	3065	broad.mit.edu	37	1	32768051	32768051	+	Intron	DEL	T	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32768051delT	uc001bvb.1	+						HDAC1_uc010ohd.1_Intron|HDAC1_uc010ohe.1_Intron|HDAC1_uc010ohf.1_Intron	NM_004964	NP_004955	Q13547	HDAC1_HUMAN	histone deacetylase 1						anti-apoptosis|blood coagulation|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|histone H3 deacetylation|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of androgen receptor signaling pathway|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	cytosol|NuRD complex|Sin3 complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|identical protein binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|RNA polymerase II transcription corepressor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|breast(1)	3		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)	GGGTCCCTGCTTTTTTTTTTT	0.423													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	53174728	53174729	+	IGR	DEL	AA	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53174728_53174729delAA								C1orf163 (10690 upstream) : ZYG11B (17402 downstream)																							cctgtctcagaaaaaaaaaaaa	0.233													4	2	---	---	---	---	
CELF3	11189	broad.mit.edu	37	1	151677284	151677285	+	Intron	INS	-	GT	GT	rs138717096	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151677284_151677285insGT	uc001eys.1	-						CELF3_uc010pdh.1_Intron|CELF3_uc001eyr.2_Intron|CELF3_uc009wmy.2_Intron|CELF3_uc009wmx.1_Intron	NM_007185	NP_009116	Q5SZQ8	CELF3_HUMAN	trinucleotide repeat containing 4						nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	mRNA binding|nucleotide binding			ovary(1)|central_nervous_system(1)	2						GGTCACGGAGGGTGTGTGTGTG	0.460													6	4	---	---	---	---	
UBAP2L	9898	broad.mit.edu	37	1	154209115	154209115	+	Intron	DEL	T	-	-	rs77740477		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154209115delT	uc001fep.3	+						UBAP2L_uc009wot.2_Intron|UBAP2L_uc010pek.1_Intron|UBAP2L_uc010pel.1_Intron|UBAP2L_uc001fen.1_Intron|UBAP2L_uc010pen.1_Intron	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a						binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			AGTGTCTTAATTTTTTTTCCC	0.388													350	8	---	---	---	---	
PPFIA4	8497	broad.mit.edu	37	1	203025097	203025097	+	Intron	DEL	T	-	-	rs5780137		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203025097delT	uc001gyz.2	+						PPFIA4_uc009xaj.2_Intron|PPFIA4_uc010pqf.1_Intron|PPFIA4_uc001gza.2_Intron|PPFIA4_uc001gzb.1_5'Flank	NM_015053	NP_055868	O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f						cell communication	cell surface|cytoplasm	protein binding			ovary(4)|skin(1)	5						CTAGGCCAGCTTTTTTTTTTT	0.502													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	237199267	237199270	+	IGR	DEL	TTCC	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237199267_237199270delTTCC								MTR (131987 upstream) : RYR2 (6432 downstream)																							ccttccctctttccttccttcctt	0.015													4	2	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245775408	245775413	+	Intron	DEL	GAGAGA	-	-	rs58523688		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245775408_245775413delGAGAGA	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron|KIF26B_uc001ibg.1_Intron	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			gtgtgtgtgtgagagagagagagaga	0.141													4	6	---	---	---	---	
ATAD2B	54454	broad.mit.edu	37	2	24110911	24110912	+	Intron	INS	-	A	A	rs145193037	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24110911_24110912insA	uc002rek.3	-						ATAD2B_uc010yki.1_Intron|ATAD2B_uc010exx.1_Intron	NM_017552	NP_060022	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B								ATP binding|nucleoside-triphosphatase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGACAGAAAAGAAAAAAAAAAT	0.282													8	8	---	---	---	---	
MCM6	4175	broad.mit.edu	37	2	136610223	136610223	+	Intron	DEL	A	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136610223delA	uc002tuw.2	-							NM_005915	NP_005906	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6						cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|identical protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.166)	Atorvastatin(DB01076)	GCTGTTCCAGAAAAAAAAAAA	0.284													6	3	---	---	---	---	
C2orf60	129450	broad.mit.edu	37	2	200800443	200800454	+	Intron	DEL	ACACACACACAC	-	-	rs10603476		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200800443_200800454delACACACACACAC	uc002uvi.3	-						C2orf60_uc002uvj.3_Intron|C2orf60_uc002uvk.3_Intron|C2orf60_uc010fss.2_Intron	NM_001039693	NP_001034782	A2RUC4	TYW5_HUMAN	hypothetical protein LOC129450						wybutosine biosynthetic process		iron ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein homodimerization activity|tRNA binding				0						CCTGCTTTAAacacacacacacacacacacac	0.250													3	7	---	---	---	---	
DOCK10	55619	broad.mit.edu	37	2	225719572	225719579	+	Intron	DEL	CCAACCAA	-	-	rs72305904		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225719572_225719579delCCAACCAA	uc010fwz.1	-						DOCK10_uc002vob.2_Intron	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10								GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		aaccaactagccaaccaaccaaccaacc	0.236													7	5	---	---	---	---	
ULK4	54986	broad.mit.edu	37	3	41939887	41939888	+	Intron	DEL	AG	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41939887_41939888delAG	uc003ckv.3	-						ULK4_uc003ckw.2_Intron|ULK4_uc003ckx.1_Intron	NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CTGTATACAAAGAGTCTACATG	0.302													241	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	109648950	109648953	+	IGR	DEL	TCCC	-	-	rs113948167		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109648950_109648953delTCCC								FLJ25363 (434936 upstream) : None (None downstream)																							cttccctccttccctccttccttc	0.000													4	4	---	---	---	---	
ALDH1L1	10840	broad.mit.edu	37	3	125878066	125878067	+	Intron	DEL	CA	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125878066_125878067delCA	uc003eim.1	-						ALDH1L1_uc010hse.1_Intron|ALDH1L1_uc011bki.1_Intron|ALDH1L1_uc003eio.2_5'Flank|ALDH1L1_uc010hsf.1_Intron|ALDH1L1_uc003eip.1_5'Flank|ALDH1L1_uc011bkj.1_Intron	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1						10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	cacatgcgtgcacacacacaca	0.000													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	170670639	170670640	+	IGR	INS	-	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170670639_170670640insA								EIF5A2 (44213 upstream) : SLC2A2 (43497 downstream)																							GTTTTTTAGATATGTTTCTTCA	0.495													79	13	---	---	---	---	
HRG	3273	broad.mit.edu	37	3	186393097	186393098	+	Intron	INS	-	GA	GA	rs59016663		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186393097_186393098insGA	uc003fqq.2	+							NM_000412	NP_000403	P04196	HRG_HUMAN	histidine-rich glycoprotein precursor						fibrinolysis|platelet activation|platelet degranulation	extracellular region|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding			ovary(1)|central_nervous_system(1)	2	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		tgtgtgtgtgtgagagagagag	0.173													25	7	---	---	---	---	
WDR53	348793	broad.mit.edu	37	3	196281881	196281882	+	Intron	INS	-	AGGTAGAATTA	AGGTAGAATTA	rs147559216	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196281881_196281882insAGGTAGAATTA	uc003fwt.2	-							NM_182627	NP_872433	Q7Z5U6	WDR53_HUMAN	WD repeat domain 53											breast(1)|skin(1)	2	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.6e-23)|all cancers(36;1.54e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.29e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		AGAGTGCGGTTAGGTAGAATTA	0.371													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	49512654	49512654	+	IGR	DEL	T	-	-	rs113012804		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49512654delT								CWH43 (448561 upstream) : None (None downstream)																							ACATTCTGCGTTTTTTTGGGG	0.368													5	3	---	---	---	---	
ADAMTS3	9508	broad.mit.edu	37	4	73280847	73280850	+	Intron	DEL	TAAT	-	-	rs146478222		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73280847_73280850delTAAT	uc003hgk.1	-							NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TAACTATCAATAATTAATTCATAT	0.260													9	6	---	---	---	---	
SEC31A	22872	broad.mit.edu	37	4	83775865	83775866	+	Intron	INS	-	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83775865_83775866insA	uc003hnf.2	-						SEC31A_uc003hne.2_Intron|SEC31A_uc011ccl.1_Intron|SEC31A_uc003hnl.2_Intron|SEC31A_uc003hng.2_Intron|SEC31A_uc003hnh.2_Intron|SEC31A_uc003hni.2_Intron|SEC31A_uc003hnj.2_Intron|SEC31A_uc011ccm.1_Intron|SEC31A_uc011ccn.1_Intron|SEC31A_uc003hnk.2_Intron|SEC31A_uc003hnm.2_Intron|SEC31A_uc003hnn.1_Intron	NM_001077207	NP_001070675	O94979	SC31A_HUMAN	SEC31 homolog A isoform 1						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)				CTAGTAGATTTAAAAAAAAAAA	0.129													4	2	---	---	---	---	
ODZ3	55714	broad.mit.edu	37	4	183522021	183522022	+	Intron	INS	-	AT	AT	rs141344153	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183522021_183522022insAT	uc003ivd.1	+							NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)		TGTGTATATACATATATATATA	0.297													3	6	---	---	---	---	
MTMR12	54545	broad.mit.edu	37	5	32268631	32268631	+	Intron	DEL	G	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32268631delG	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1						aaaaaaaaaaGATCACAGGAA	0.194													5	3	---	---	---	---	
NUP155	9631	broad.mit.edu	37	5	37349361	37349361	+	Intron	DEL	A	-	-	rs74712044		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37349361delA	uc003jku.1	-						NUP155_uc003jkt.1_Intron|NUP155_uc010iuz.1_Intron	NM_153485	NP_705618	O75694	NU155_HUMAN	nucleoporin 155kDa isoform 1						carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AAAGTAAGACAAAAAAAAAAA	0.279													6	3	---	---	---	---	
DCP2	167227	broad.mit.edu	37	5	112328171	112328171	+	Intron	DEL	T	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112328171delT	uc003kqh.2	+						DCP2_uc011cwa.1_Intron|DCP2_uc010jcc.2_Intron	NM_152624	NP_689837	Q8IU60	DCP2_HUMAN	DCP2 decapping enzyme						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus|RNA-induced silencing complex	exoribonuclease activity, producing 5'-phosphomonoesters|manganese ion binding|protein binding|protein binding|RNA binding				0		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		TGTTGAAGACTTTTTTTTTTT	0.348													3	4	---	---	---	---	
NME5	8382	broad.mit.edu	37	5	137474285	137474285	+	Intron	DEL	T	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137474285delT	uc003lce.2	-						BRD8_uc003lcc.1_Intron	NM_003551	NP_003542	P56597	NDK5_HUMAN	non-metastatic cells 5, protein expressed in						anti-apoptosis|CTP biosynthetic process|GTP biosynthetic process|multicellular organismal development|spermatid development|UTP biosynthetic process		ATP binding|nucleoside diphosphate kinase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TACATAAGCATTTTTTTTTTA	0.303													81	8	---	---	---	---	
EFHC1	114327	broad.mit.edu	37	6	52288788	52288803	+	Frame_Shift_Del	DEL	CTATGCAATTGTTCGA	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52288788_52288803delCTATGCAATTGTTCGA	uc003pap.3	+	2	323_338	c.108_123delCTATGCAATTGTTCGA	c.(106-123)GGCTATGCAATTGTTCGAfs	p.G36fs	EFHC1_uc011dwv.1_5'UTR|EFHC1_uc011dww.1_Frame_Shift_Del_p.G17fs	NM_018100	NP_060570	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	36_41						axoneme|neuronal cell body	calcium ion binding|protein C-terminus binding			ovary(2)|skin(1)	3	Lung NSC(77;0.109)					ACAGGAACGGCTATGCAATTGTTCGACGTCCAACAG	0.458													164	27	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	23604013	23604013	+	IGR	DEL	T	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23604013delT								TRA2A (32357 upstream) : CLK2P (20322 downstream)																							CCAAAATGGCttttttttttt	0.254													3	3	---	---	---	---	
C7orf46	340277	broad.mit.edu	37	7	23730803	23730803	+	Intron	DEL	T	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23730803delT	uc003swo.3	+						C7orf46_uc003swq.3_Intron|C7orf46_uc003swr.3_Intron|C7orf46_uc003swp.3_Intron|C7orf46_uc010kup.2_Intron	NM_199136	NP_954587	A4D161	CG046_HUMAN	hypothetical protein LOC340277 isoform 1												0						TGTTTTGCAGTTTTTTTTTTT	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	37860763	37860764	+	Intron	DEL	TA	-	-	rs71554525		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37860763_37860764delTA	uc003tfl.2	+											Homo sapiens, clone IMAGE:3881224, mRNA.																		AAGTTGTGGTTATATATATATA	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	57642327	57642327	+	IGR	DEL	T	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57642327delT								ZNF716 (109062 upstream) : None (None downstream)																							CTCTCTCACATATTTTTTCTG	0.308													4	3	---	---	---	---	
TFPI2	7980	broad.mit.edu	37	7	93519409	93519410	+	Intron	INS	-	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93519409_93519410insT	uc003umy.1	-						GNGT1_uc003umx.1_Intron|TFPI2_uc003umz.1_Intron|TFPI2_uc003una.1_Intron|TFPI2_uc003unb.1_Intron|TFPI2_uc010lfg.1_Intron	NM_006528	NP_006519	P48307	TFPI2_HUMAN	tissue factor pathway inhibitor 2 precursor						blood coagulation	proteinaceous extracellular matrix	extracellular matrix structural constituent|serine-type endopeptidase inhibitor activity			pancreas(1)	1	all_cancers(62;4.45e-10)|all_epithelial(64;2.92e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			GCCGCCGGCGCAAGGAGCGCGA	0.554													31	11	---	---	---	---	
FBXO43	286151	broad.mit.edu	37	8	101157157	101157158	+	Intron	INS	-	A	A	rs79122618		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101157157_101157158insA	uc003yjd.2	-						FBXO43_uc003yje.2_Intron|FBXO43_uc010mbp.1_Intron	NM_001029860	NP_001025031	Q4G163	FBX43_HUMAN	F-box protein 43 isoform b						meiosis		zinc ion binding			kidney(1)|skin(1)	2	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			gactccgtctcaaaaaaaaaaa	0.109													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	101438903	101438905	+	IGR	DEL	ACT	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101438903_101438905delACT								RNF19A (116576 upstream) : ANKRD46 (83082 downstream)																							caccaccaccactaccaccacca	0.000													4	2	---	---	---	---	
SMARCA2	6595	broad.mit.edu	37	9	2088641	2088641	+	Intron	DEL	T	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2088641delT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		AAGTTGTGGGTTTTTTTTTTC	0.343													140	9	---	---	---	---	
NXNL2	158046	broad.mit.edu	37	9	91150746	91150747	+	Intron	INS	-	C	C	rs150222723	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91150746_91150747insC	uc011ltj.1	+						NXNL2_uc004aqa.2_Intron	NM_001161625	NP_001155097	Q5VZ03	NXNL2_HUMAN	nucleoredoxin-like 2 isoform 1												0						TCTTTATGACGCCCCCCCCCAA	0.559													4	2	---	---	---	---	
TRIM14	9830	broad.mit.edu	37	9	100843027	100843028	+	Intron	INS	-	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100843027_100843028insA	uc004ayd.2	-						NANS_uc004ayb.2_Intron|NANS_uc004ayc.2_Intron|NANS_uc004aye.1_Intron	NM_033220	NP_150089	Q14142	TRI14_HUMAN	tripartite motif protein TRIM14 isoform alpha							cytoplasm|intracellular	zinc ion binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.0559)				ctcaaccagatacgcttcacCT	0.144													56	10	---	---	---	---	
C9orf5	23731	broad.mit.edu	37	9	111813112	111813112	+	Intron	DEL	A	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111813112delA	uc004bdt.3	-						C9orf5_uc004bds.3_Intron|C9orf5_uc004bdr.3_Intron	NM_032012	NP_114401	Q9H330	CI005_HUMAN	hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)		AATGAAAATTAAAAAAAAAAA	0.269													4	2	---	---	---	---	
RPL12	6136	broad.mit.edu	37	9	130210017	130210017	+	Intron	DEL	A	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130210017delA	uc004bqy.1	-						RPL12_uc004bqx.1_Intron|RPL12_uc004bqz.1_Intron	NM_000976	NP_000967	P30050	RL12_HUMAN	ribosomal protein L12						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	RNA binding|structural constituent of ribosome				0						TGTGGGAAAGAAAAAAAAAAT	0.413													269	13	---	---	---	---	
TTC16	158248	broad.mit.edu	37	9	130485247	130485247	+	Intron	DEL	A	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130485247delA	uc004brq.1	+						PTRH1_uc011mah.1_Intron|TTC16_uc011mai.1_Intron|TTC16_uc004brr.1_Intron|TTC16_uc010mxn.1_Intron	NM_144965	NP_659402	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16								binding				0						aatccatctcaaaaaaaaaaa	0.239													8	5	---	---	---	---	
AKR1C1	1645	broad.mit.edu	37	10	5011703	5011703	+	Intron	DEL	G	-	-	rs34344919		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5011703delG	uc001iho.2	+						AKR1E2_uc001ihl.1_Intron|AKR1C2_uc010qan.1_Intron|AKR1C3_uc001ihr.2_Intron|AKR1C1_uc001ihq.2_Intron	NM_001353	NP_001344	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1						bile acid and bile salt transport|bile acid metabolic process|cholesterol homeostasis|intestinal cholesterol absorption|protein homooligomerization|response to organophosphorus|xenobiotic metabolic process	cytosol	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity|aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid binding|indanol dehydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			ovary(2)	2					NADH(DB00157)	ACCTGTTTATGGGAGATATCT	0.448													4	2	---	---	---	---	
SMC3	9126	broad.mit.edu	37	10	112328525	112328526	+	Intron	INS	-	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112328525_112328526insT	uc001kze.2	+							NM_005445	NP_005436	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3						cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		ATAAAAGTACCTTTTTTTTTTT	0.282													4	4	---	---	---	---	
CARS	833	broad.mit.edu	37	11	3063660	3063661	+	Intron	INS	-	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3063660_3063661insT	uc001lxh.2	-						CARS_uc001lxe.2_Intron|CARS_uc001lxf.2_Intron|CARS_uc001lxg.2_Intron|CARS_uc010qxo.1_Intron|CARS_uc010qxp.1_Intron	NM_001751	NP_001742	P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase isoform b						cysteinyl-tRNA aminoacylation	cytoplasm|cytosol	ATP binding|cysteine-tRNA ligase activity|metal ion binding|protein homodimerization activity|protein homodimerization activity|tRNA binding|tRNA binding		CARS/ALK(5)	soft_tissue(5)|ovary(2)	7		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	ACAACTGCGtcttttttttttt	0.198			T	ALK	ALCL								4	3	---	---	---	---	
DYNC2H1	79659	broad.mit.edu	37	11	102996096	102996096	+	Intron	DEL	T	-	-	rs34114270		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102996096delT	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TGCTAAAGGCTTTTTTTTTTT	0.289													8	6	---	---	---	---	
CUL5	8065	broad.mit.edu	37	11	107904512	107904513	+	Intron	INS	-	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107904512_107904513insT	uc001pjv.2	+						CUL5_uc001pju.2_Intron	NM_003478	NP_003469	Q93034	CUL5_HUMAN	Vasopressin-activated calcium-mobilizing						cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		TCCCTTTTATCTTTTTTTTTTT	0.312													104	8	---	---	---	---	
MED13L	23389	broad.mit.edu	37	12	116549321	116549321	+	Intron	DEL	A	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116549321delA	uc001tvw.2	-							NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TCCACAACTGaaaaaaaaaag	0.313													160	10	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	21622710	21622711	+	IGR	DEL	GA	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21622710_21622711delGA								ZNF219 (49847 upstream) : OR5AU1 (386 downstream)																							ctcgggggtggagagagagaga	0.020													4	2	---	---	---	---	
HAUS4	54930	broad.mit.edu	37	14	23419361	23419361	+	Intron	DEL	C	-	-	rs59423232	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23419361delC	uc001whp.2	-						HAUS4_uc001who.2_Intron|HAUS4_uc001whq.2_Intron|HAUS4_uc001whr.2_Intron|HAUS4_uc001whs.2_Intron|HAUS4_uc001wht.2_Intron|HAUS4_uc001whu.2_Intron|HAUS4_uc001whv.2_Intron|HAUS4_uc001whw.2_Intron|HAUS4_uc001whx.2_Intron	NM_017815	NP_060285	Q9H6D7	HAUS4_HUMAN	HAUS augmin-like complex, subunit 4						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle				ovary(1)	1						aacaaaaaaacaaaaaGTCCT	0.149													5	3	---	---	---	---	
C14orf149	112849	broad.mit.edu	37	14	59946234	59946234	+	Intron	DEL	G	-	-	rs111912500		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59946234delG	uc001xee.1	-						C14orf149_uc010trx.1_Intron	NM_144581	NP_653182	Q96EM0	PRCM_HUMAN	proline racemase-like								proline racemase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.14)	L-Proline(DB00172)	AGCATCGAGTGAATAATAGCT	0.274													4	2	---	---	---	---	
PSMC1	5700	broad.mit.edu	37	14	90731688	90731688	+	Intron	DEL	A	-	-	rs34260220		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90731688delA	uc001xyf.2	+						PSMC1_uc001xyg.2_Intron|PSMC1_uc001xyh.2_Intron|PSMC1_uc010twh.1_Intron	NM_002802	NP_002793	P62191	PRS4_HUMAN	proteasome 26S ATPase subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding				0		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)		atactgatgGAAAAAAAAAAA	0.065													4	2	---	---	---	---	
NF1P1	440225	broad.mit.edu	37	15	22146377	22146378	+	5'Flank	DEL	GT	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22146377_22146378delGT	uc010tzs.1	-											Human NF1-related locus DNA in A9 mouse DNA background.												0						tTGAgtgtgggtgtgtgtgtgt	0.233													16	7	---	---	---	---	
DUOX2	50506	broad.mit.edu	37	15	45401551	45401552	+	Intron	INS	-	A	A	rs146500925		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45401551_45401552insA	uc010bea.2	-						DUOX2_uc001zun.2_Intron	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor						cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|skin(2)|pancreas(1)	5		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		GTAAATTAAGCAAAAAAAAAAA	0.366													6	3	---	---	---	---	
SPPL2A	84888	broad.mit.edu	37	15	51011931	51011931	+	Intron	DEL	G	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51011931delG	uc001zyv.2	-							NM_032802	NP_116191	Q8TCT8	PSL2_HUMAN	signal peptide peptidase-like 2A							integral to membrane	aspartic-type endopeptidase activity				0				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		TTTTTTTTTTGTAGTTTTGTC	0.363													4	2	---	---	---	---	
ADAM10	102	broad.mit.edu	37	15	58965331	58965332	+	Intron	INS	-	A	A			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58965331_58965332insA	uc002afd.1	-						ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron|ADAM10_uc002afg.2_Intron	NM_001110	NP_001101	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10 precursor						cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)		AGAGCATAAAGAAAAAAAAATa	0.302													4	2	---	---	---	---	
BNIP2	663	broad.mit.edu	37	15	59974852	59974853	+	Intron	INS	-	T	T			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59974852_59974853insT	uc010uhc.1	-						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						CAGGGTTGCAATTTTTTTTTTT	0.277													4	3	---	---	---	---	
MYOCD	93649	broad.mit.edu	37	17	12647692	12647694	+	In_Frame_Del	DEL	CAG	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12647692_12647694delCAG	uc002gnn.2	+	8	1209_1211	c.910_912delCAG	c.(910-912)CAGdel	p.Q310del	MYOCD_uc002gno.2_In_Frame_Del_p.Q310del|MYOCD_uc002gnp.1_In_Frame_Del_p.Q214del|MYOCD_uc002gnq.2_In_Frame_Del_p.Q29del	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin isoform 2	310	Gln-rich.				cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation	nucleus	nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding			central_nervous_system(2)|skin(2)|ovary(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		AATCCTCAGCcagcagcagcagc	0.527													52	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	25289230	25289233	+	IGR	DEL	TCTA	-	-	rs138697975		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25289230_25289233delTCTA								None (None upstream) : WSB1 (331873 downstream)																							GTTTGTTACCTCTATCTATTGACT	0.343													6	4	---	---	---	---	
NLE1	54475	broad.mit.edu	37	17	33469249	33469249	+	Intron	DEL	C	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33469249delC	uc002hiy.1	-						NLE1_uc010ctn.1_5'Flank|NLE1_uc002hiz.1_5'UTR	NM_018096	NP_060566	Q9NVX2	NLE1_HUMAN	Notchless gene homolog isoform a							nucleolus				breast(3)|ovary(1)	4		Ovarian(249;0.17)				cgcggcgacgccccccgcccc	0.597													4	2	---	---	---	---	
EFTUD2	9343	broad.mit.edu	37	17	42929595	42929595	+	Intron	DEL	T	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42929595delT	uc002ihn.2	-						EFTUD2_uc010wje.1_Intron|EFTUD2_uc010wjf.1_Intron	NM_004247	NP_004238	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain							Cajal body|catalytic step 2 spliceosome|cytoplasm|nuclear speck	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(33;0.109)				CTATTATTTCTTTTTTTTTTT	0.134													4	2	---	---	---	---	
BPTF	2186	broad.mit.edu	37	17	65905565	65905565	+	Intron	DEL	T	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65905565delT	uc002jgf.2	+						BPTF_uc002jge.2_Intron	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor						brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			GACCTTTGTCTTTTTTTTTTT	0.299													6	3	---	---	---	---	
MC5R	4161	broad.mit.edu	37	18	13825564	13825564	+	5'Flank	DEL	A	-	-	rs33981843		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13825564delA	uc010xaf.1	+							NM_005913	NP_005904	P33032	MC5R_HUMAN	melanocortin 5 receptor						G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocortin receptor activity|protein binding			ovary(3)|lung(2)|breast(1)	6						cctgtctcttaaaaaaaaaaa	0.224													9	5	---	---	---	---	
LMNB2	84823	broad.mit.edu	37	19	2433561	2433561	+	Intron	DEL	C	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2433561delC	uc002lvy.2	-						LMNB2_uc002lwa.1_Intron	NM_032737	NP_116126	Q03252	LMNB2_HUMAN	lamin B2							nuclear inner membrane	structural molecule activity			large_intestine(1)|ovary(1)	2		Hepatocellular(1079;0.137)		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)		ACCCTGGTCACCCCCATCAGC	0.682													1	5	---	---	---	---	
NLRP7	199713	broad.mit.edu	37	19	55452576	55452576	+	Intron	DEL	A	-	-	rs111382825		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55452576delA	uc002qih.3	-						NLRP7_uc002qig.3_Intron|NLRP7_uc002qii.3_Intron|NLRP7_uc010esk.2_Intron|NLRP7_uc010esl.2_Intron	NM_206828	NP_996611	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7								ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)		ctaaaaatacaaaaaaaaaaa	0.000													5	4	---	---	---	---	
ZIM3	114026	broad.mit.edu	37	19	57648045	57648046	+	Intron	INS	-	A	A	rs145532440	by1000genomes	TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57648045_57648046insA	uc002qnz.1	-							NM_052882	NP_443114	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		aaaaaaaaaagaaaaaaaaaaG	0.188													4	4	---	---	---	---	
RALGAPA2	57186	broad.mit.edu	37	20	20591999	20592002	+	Frame_Shift_Del	DEL	TTTA	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20591999_20592002delTTTA	uc002wrz.2	-	14	1900_1903	c.1757_1760delTAAA	c.(1756-1761)ATAAAGfs	p.I586fs	RALGAPA2_uc010gcx.2_Frame_Shift_Del_p.I290fs|RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	586_587					activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						AAACAAGTCCTTTATTTGTTTATC	0.382													773	8	---	---	---	---	
C20orf112	140688	broad.mit.edu	37	20	31035206	31035207	+	3'UTR	INS	-	AAAAA	AAAAA	rs149650216		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31035206_31035207insAAAAA	uc002wxu.3	-	8					C20orf112_uc010gec.2_3'UTR	NM_080616	NP_542183	Q96MY1	CT112_HUMAN	hypothetical protein LOC140688												0						GGTGAGATTCCaaaaaaaaaaa	0.510													5	3	---	---	---	---	
TSHZ2	128553	broad.mit.edu	37	20	51798634	51798635	+	Intron	INS	-	TTCC	TTCC			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51798634_51798635insTTCC	uc002xwo.2	+							NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)			CCTGccttcctttccttccttc	0.208													9	7	---	---	---	---	
LAMA5	3911	broad.mit.edu	37	20	60904422	60904426	+	Intron	DEL	CAGCC	-	-	rs3065756		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60904422_60904426delCAGCC	uc002ycq.2	-							NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor						angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	CTGGCAGCAGcagcccagcccagcc	0.600													5	5	---	---	---	---	
PIGP	51227	broad.mit.edu	37	21	38439272	38439273	+	Intron	DEL	GT	-	-	rs112008084		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38439272_38439273delGT	uc002yvw.1	-						PIGP_uc002yvy.1_Intron|PIGP_uc002yvx.1_Intron	NM_153681	NP_710148	P57054	PIGP_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity				0		Myeloproliferative disorder(46;0.0412)				TTTACTGTCCgtgtgtgtgtgt	0.139													4	3	---	---	---	---	
POLR2F	5435	broad.mit.edu	37	22	38355724	38355725	+	Intron	INS	-	A	A	rs145108295		TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38355724_38355725insA	uc003aul.2	+						POLR2F_uc010gxi.2_Intron|POLR2F_uc003aum.2_Intron	NM_021974	NP_068809	P61218	RPAB2_HUMAN	DNA directed RNA polymerase II polypeptide F						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase II promoter|transcription elongation from RNA polymerase III promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex|nucleolus	DNA binding|DNA-directed RNA polymerase activity			breast(1)	1	Melanoma(58;0.045)					AGAAAAACGATAAAAAAAAAAA	0.188													4	3	---	---	---	---	
ASMTL	8623	broad.mit.edu	37	X	1551100	1551100	+	Intron	DEL	C	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1551100delC	uc004cpx.1	-						ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGACACCCCACGTGTGAGGGT	0.597													6	4	---	---	---	---	
IL13RA1	3597	broad.mit.edu	37	X	117908116	117908116	+	Intron	DEL	T	-	-			TCGA-EJ-5505-01A-01D-1576-08	TCGA-EJ-5505-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117908116delT	uc004eqs.2	+						IL13RA1_uc004eqt.1_Intron	NM_001560	NP_001551	P78552	I13R1_HUMAN	interleukin 13 receptor, alpha 1 precursor							interleukin-13 receptor complex	cytokine receptor activity				0						ttttcttttcttttttttttt	0.204													8	4	---	---	---	---	
