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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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
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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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
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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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
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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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
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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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
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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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
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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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
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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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
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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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
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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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
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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	---	---	---	---	
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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	---	---	---	---	
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	81a818c2-0b58-46fa-a0a7-6f7cf020ba45	7756bd88-7802-41a3-abcb-aed3b0481164	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	---	---	---	---	
