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	pox	qox	pox_cutoff	isArtifactMode	oxoGCut	init_n_lod
MTHFR	4524	broad.mit.edu	37	1	11861224	11861224	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr1:11861224G>A	uc001atc.1	-	3	653	c.469C>T	c.(469-471)CGG>TGG	p.R157W	MTHFR_uc001atb.1_Missense_Mutation_p.R180W	NM_005957	NP_005948	P42898	MTHR_HUMAN	5,10-methylenetetrahydrofolate reductase	157			R -> Q (in MTHFRD).		blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)	ACACCTCCCCGCAGCGCCATG	0.587000													12	133					0	0	0.010729	0	0	
LHX8	431707	broad.mit.edu	37	1	75602794	75602794	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr1:75602794G>A	uc001dgo.2	+	4	779	c.115G>A	c.(115-117)GAG>AAG	p.E39K	LHX8_uc001dgq.2_5'UTR	NM_001001933	NP_001001933	Q68G74	LHX8_HUMAN	LIM homeobox 8	39						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						GGTGAGCCCCGAGGGAGCGGG	0.731000													9	58					0	0	0.004482	0	0	
CD101	9398	broad.mit.edu	37	1	117554317	117554317	+	Silent	SNP	A	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr1:117554317A>G	uc010oxb.1	+	3	628	c.570A>G	c.(568-570)GGA>GGG	p.G190G	CD101_uc009whd.2_Silent_p.G190G|CD101_uc010oxc.1_Silent_p.G190G|CD101_uc010oxd.1_Intron	NM_004258	NP_004249	Q93033	IGSF2_HUMAN	immunoglobulin superfamily, member 2 precursor	190	Extracellular (Potential).|Ig-like C2-type 2.				cell surface receptor linked signaling pathway	integral to membrane|plasma membrane	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4						CACAGGATGGAGGAGGAAGCC	0.512000													3	85					0	0	0.004672	0	0	
NBPF9	400818	broad.mit.edu	37	1	144619399	144619399	+	Silent	SNP	G	A	A	rs4067645	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr1:144619399G>A	uc009wig.1	+	7	622	c.546G>A	c.(544-546)GTG>GTA	p.V182V	NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Silent_p.V182V|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Silent_p.V113V|NBPF9_uc001eli.3_RNA|NBPF9_uc010oyf.1_Silent_p.V113V|NBPF9_uc010oyg.1_Silent_p.V147V|NBPF9_uc009wii.1_Intron	NM_001037675	NP_001032764	Q3BBV1	NBPFK_HUMAN	hypothetical protein LOC400818	182	NBPF 1.					cytoplasm					0						ATGAGAAAGTGCAGAAATCAT	0.413000													9	413					0	0	0.007413	0	0	
NBPF10	100132406	broad.mit.edu	37	1	145367739	145367739	+	Silent	SNP	A	G	G	rs146714035	by1000genomes	TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr1:145367739A>G	uc001end.3	+	85	10595	c.10560A>G	c.(10558-10560)AAA>AAG	p.K3520K	NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	3445											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ggaaggggaaaaaaagaaggg	0.244000													4	107					0	0	0.009096	0	0	
FLG	2312	broad.mit.edu	37	1	152283625	152283625	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr1:152283625C>A	uc001ezu.1	-	3	3773	c.3737G>T	c.(3736-3738)AGC>ATC	p.S1246I	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1246	Ser-rich.|Filaggrin 7.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTGTCTAGAGCTGTCAGCCCA	0.552000									Ichthyosis				19	427					2.40579e-17	2.98496e-17	0.006230	1	0	
FLG	2312	broad.mit.edu	37	1	152284540	152284540	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr1:152284540C>T	uc001ezu.1	-	3	2858	c.2822G>A	c.(2821-2823)CGC>CAC	p.R941H	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	941	Ser-rich.|Filaggrin 5.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGATCCCTGGCGCCTGCTTGT	0.562000									Ichthyosis				12	600					0	0	0.010729	0	0	
MUC1	4582	broad.mit.edu	37	1	155160774	155160774	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr1:155160774G>T	uc010pfj.1	-	2	784	c.378C>A	c.(376-378)AGC>AGA	p.S126R	RAG1AP1_uc010pey.1_Intron|MUC1_uc001fhy.2_5'UTR|MUC1_uc001fhz.2_5'UTR|MUC1_uc010pfb.1_Intron|MUC1_uc010pfc.1_Intron|MUC1_uc009wph.2_Intron|MUC1_uc010pfd.1_Intron|MUC1_uc010pfe.1_Intron|MUC1_uc010pff.1_Intron|MUC1_uc009wpi.2_Intron|MUC1_uc010pfg.1_Intron|MUC1_uc010pfh.1_Silent_p.L102L|MUC1_uc010pfi.1_Silent_p.L102L|MUC1_uc010pfk.1_Intron|MUC1_uc010pfl.1_Intron|MUC1_uc001fin.2_Intron|MUC1_uc009wpk.2_Intron|MUC1_uc001fip.2_Intron|MUC1_uc009wqg.2_Intron|MUC1_uc009wpo.2_Intron|MUC1_uc009wps.2_Intron|MUC1_uc009wpt.2_Intron|MUC1_uc001fic.2_Intron|MUC1_uc009wpu.2_Intron|MUC1_uc009wpq.2_Intron|MUC1_uc009wpv.2_Intron|MUC1_uc001fim.2_Intron|MUC1_uc001fib.2_Intron|MUC1_uc009wpw.2_Intron|MUC1_uc001fie.2_Intron|MUC1_uc009wpr.2_Intron|MUC1_uc001fig.2_Intron|MUC1_uc001fif.2_Intron|MUC1_uc009wpx.2_Intron|MUC1_uc001fid.2_Intron|MUC1_uc009wpj.2_Intron|MUC1_uc001fij.2_Intron|MUC1_uc009wpy.2_Intron|MUC1_uc010pfm.1_Intron|MUC1_uc001fiq.2_Intron|MUC1_uc009wpz.2_Intron|MUC1_uc010pfn.1_Intron|MUC1_uc009wqa.2_Missense_Mutation_p.S114R|MUC1_uc010pfo.1_Intron|MUC1_uc010pfp.1_Intron|MUC1_uc001fii.2_Intron|MUC1_uc001fih.2_Intron|MUC1_uc001fia.2_Intron|MUC1_uc009wqc.2_Silent_p.L28L|MUC1_uc009wqd.2_Missense_Mutation_p.S52R|MUC1_uc009wqb.2_Intron|MUC1_uc010pfq.1_Silent_p.L28L|MUC1_uc010pfr.1_Intron|MUC1_uc001fit.2_Intron|MUC1_uc009wqe.2_Intron|MUC1_uc001fil.2_Intron|MUC1_uc009wpm.2_Intron|MUC1_uc009wpp.2_Intron|MUC1_uc010pfs.1_Intron|MUC1_uc001fik.2_Intron|MUC1_uc001fio.2_Intron|MUC1_uc009wqf.2_Intron|MUC1_uc009wpl.2_Intron|MUC1_uc009wpn.2_Intron|MUC1_uc001fis.1_Intron			P15941	MUC1_HUMAN	SubName: Full=Mucin 1, cell surface associated;	1031	Extracellular (Potential).					apical plasma membrane|cell surface|cytoplasm|extracellular region|integral to plasma membrane|nucleus	protein binding			large_intestine(1)|pancreas(1)|breast(1)|skin(1)	4	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGGGAGAAGTGCTGTGATTGG	0.498000			T	IGH@	B-NHL								7	77					0.000157383	0.000184994	0.003080	1	0	
OR6N1	128372	broad.mit.edu	37	1	158735950	158735950	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr1:158735950G>C	uc010piq.1	-	1	523	c.523C>G	c.(523-525)CAG>GAG	p.Q175E		NM_001005185	NP_001005185	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N,	175	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)					AAGACGTGCTGAATGCGATTG	0.468000													6	146					0	0	0.001168	0	0	
ATRNL1	26033	broad.mit.edu	37	10	117061471	117061471	+	Silent	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr10:117061471G>A	uc001lcg.2	+	17	3122	c.2736G>A	c.(2734-2736)ACG>ACA	p.T912T	ATRNL1_uc010qsm.1_Silent_p.T87T|ATRNL1_uc010qsn.1_RNA	NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor	912	PSI 4.|Extracellular (Potential).					integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		GCAGCAGTACGAAACGATGTG	0.448000													17	69					0	0	0.004007	0	0	
MRGPRX2	117194	broad.mit.edu	37	11	19077900	19077900	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr11:19077900C>T	uc001mph.2	-	2	138	c.50G>A	c.(49-51)GGA>GAA	p.G17E		NM_054030	NP_473371	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	17	Extracellular (Potential).				sensory perception of pain|sleep	plasma membrane	G-protein coupled receptor activity|neuropeptide binding			ovary(1)	1						TTGGTCATTTCCATTCACTGT	0.522000													40	318					0	0	0.009718	0	0	
PDHX	8050	broad.mit.edu	37	11	35006231	35006231	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr11:35006231G>C	uc001mvt.2	+	9	1664	c.1138G>C	c.(1138-1140)GAT>CAT	p.D380H	PDHX_uc010rep.1_Missense_Mutation_p.D365H|PDHX_uc010req.1_Missense_Mutation_p.D153H	NM_003477	NP_003468	O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	380					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	acyltransferase activity			kidney(1)	1	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			AATCATAAAAGATGCTGCTGC	0.388000													10	109					0	0	0.006214	0	0	
MRPL21	219927	broad.mit.edu	37	11	68665460	68665460	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr11:68665460A>G	uc001ooi.2	-	3	192	c.167T>C	c.(166-168)CTG>CCG	p.L56P	MRPL21_uc001ooh.2_5'UTR|MRPL21_uc010rqe.1_Missense_Mutation_p.L56P	NM_181514	NP_852615	Q7Z2W9	RM21_HUMAN	mitochondrial ribosomal protein L21 isoform d	56					translation	mitochondrion|ribosome	RNA binding|structural constituent of ribosome				0			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TGGTGAACTCAGGGATGTTTT	0.478000													3	81					0	0	0.001168	0	0	
PDE2A	5138	broad.mit.edu	37	11	72288493	72288493	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr11:72288493C>T	uc010rrc.1	-	31	3004	c.2761G>A	c.(2761-2763)GAG>AAG	p.E921K	PDE2A_uc001oso.2_Missense_Mutation_p.E900K|PDE2A_uc010rra.1_Missense_Mutation_p.E914K|PDE2A_uc001osn.2_Missense_Mutation_p.E665K|PDE2A_uc010rrb.1_Missense_Mutation_p.E912K|PDE2A_uc010rrd.1_Missense_Mutation_p.E806K	NM_002599	NP_002590	O00408	PDE2A_HUMAN	phosphodiesterase 2A isoform 1	921					platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)	TCAGGCACCTCGTACTCCTCA	0.607000													7	86					0	0	0.004482	0	0	
NECAP1	25977	broad.mit.edu	37	12	8242546	8242546	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr12:8242546A>T	uc001qtx.2	+	2	188	c.110A>T	c.(109-111)AAA>ATA	p.K37I	NECAP1_uc001qty.2_5'UTR	NM_015509	NP_056324	Q8NC96	NECP1_HUMAN	NECAP endocytosis associated 1	37					endocytosis|protein transport	clathrin coated vesicle membrane|plasma membrane				ovary(1)	1				Kidney(36;0.0915)		TCTGACTGGAAATTAGACCAG	0.463000													15	149					0	0	0.006122	0	0	
RPL13AP20	387841	broad.mit.edu	37	12	13028751	13028751	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr12:13028751G>C	uc010sho.1	+	1	341	c.319G>C	c.(319-321)GGC>CGC	p.G107R		NR_003932				SubName: Full=Ribosomal protein L13a variant; Flags: Fragment;												0						GGTGTTTGACGGCATCCCACC	0.612000													6	17					0	0	0.003080	0	0	
SLC38A4	55089	broad.mit.edu	37	12	47172329	47172329	+	Silent	SNP	A	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr12:47172329A>G	uc001rpi.2	-	11	1347	c.948T>C	c.(946-948)CAT>CAC	p.H316H	SLC38A4_uc001rpj.2_Silent_p.H316H	NM_018018	NP_060488	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	316	Extracellular (Potential).				cellular nitrogen compound metabolic process|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Lung SC(27;0.192)|Renal(347;0.236)					TGTCATCACTATGAGCTTCAT	0.453000													7	69					0	0	0.001984	0	0	
ZCCHC8	55596	broad.mit.edu	37	12	122967235	122967235	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr12:122967235G>A	uc001ucn.2	-	8	810	c.679C>T	c.(679-681)CCT>TCT	p.P227S	ZCCHC8_uc001ucm.2_5'UTR|ZCCHC8_uc009zxp.2_5'UTR|ZCCHC8_uc009zxq.2_5'UTR	NM_017612	NP_060082	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	227	CCHC-type.					catalytic step 2 spliceosome	nucleic acid binding|protein binding|zinc ion binding				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		AAACAGTGAGGCTTTGGCCTA	0.308000													6	26					0	0	0.003080	0	0	
LOC284232	284232	broad.mit.edu	37	13	19415742	19415742	+	RNA	SNP	T	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr13:19415742T>C	uc010tcj.1	-	1		c.30368A>G				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						GCTGTTTTCCTAATCTTTCTT	0.313000													5	90					0	0	0.001984	0	0	
ADAM6	8755	broad.mit.edu	37	14	107099378	107099378	+	RNA	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr14:107099378G>A	uc010tyt.1	-	96		c.4385C>T								Parts of antibodies, mostly variable regions.												0						AGAGTCTCAGGGACCCCCCAG	0.567000													4	107					0	0	0.000602	0	0	
ZNF75A	7627	broad.mit.edu	37	16	3367328	3367328	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr16:3367328T>G	uc002cut.3	+	6	876	c.350T>G	c.(349-351)TTT>TGT	p.F117C	ZNF75A_uc002cuv.3_RNA	NM_153028	NP_694573	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	117					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1						GAAAATCATTTTGATATGCAC	0.393000													10	57					0	0	0.006214	0	0	
NDE1	54820	broad.mit.edu	37	16	15790648	15790648	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr16:15790648G>A	uc002ddt.1	+	7	921	c.878G>A	c.(877-879)CGG>CAG	p.R293Q	NDE1_uc010uzy.1_Missense_Mutation_p.R293Q|NDE1_uc002dds.2_Missense_Mutation_p.R293Q	NM_017668	NP_060138	Q9NXR1	NDE1_HUMAN	nuclear distribution gene E homolog 1	293					cell differentiation|cell division|centrosome duplication|establishment of chromosome localization|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|mitotic prometaphase|nervous system development	cleavage furrow|condensed chromosome kinetochore|cytosol|microtubule|spindle pole centrosome	microtubule binding			ovary(1)	1						GCCTCTGGGCGGAGCAGCAAG	0.577000													3	78					0	0	0.004672	0	0	
PAPD5	64282	broad.mit.edu	37	16	50258847	50258847	+	Silent	SNP	T	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr16:50258847T>C	uc010vgo.1	+	10	1544	c.1509T>C	c.(1507-1509)TAT>TAC	p.Y503Y	PAPD5_uc010cbi.2_RNA|PAPD5_uc002efz.2_Silent_p.Y294Y|PAPD5_uc002ega.2_Silent_p.Y294Y	NM_001040284	NP_001035374	Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5 isoform a	424					cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)		TTGCCACATATAGAGATTGGA	0.378000													21	140					0	0	0.002780	0	0	
PDP2	57546	broad.mit.edu	37	16	66918510	66918510	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr16:66918510G>A	uc002eqk.1	+	2	485	c.323G>A	c.(322-324)CGG>CAG	p.R108Q		NM_020786	NP_065837	Q9P2J9	PDP2_HUMAN	pyruvate dehydrogenase phosphatase isoenzyme 2	108					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity|metal ion binding			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)		TCAGTGTTGCGGTTTGAGAGC	0.522000													4	63					0	0	0.009096	0	0	
HYDIN	54768	broad.mit.edu	37	16	71054178	71054178	+	Missense_Mutation	SNP	T	C	C	rs6416709		TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr16:71054178T>C	uc002ezr.2	-	22	3357	c.3229A>G	c.(3229-3231)ATA>GTA	p.I1077V		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	1077										ovary(1)|skin(1)	2		Ovarian(137;0.0654)				ATGTTCTTTATGGCCAAGGGC	0.418000													3	44					0	0	0.004672	0	0	
ELAC2	60528	broad.mit.edu	37	17	12903546	12903546	+	Silent	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr17:12903546C>T	uc002gnz.3	-	15	1445	c.1350G>A	c.(1348-1350)GCG>GCA	p.A450A	ELAC2_uc002gnu.3_5'UTR|ELAC2_uc002gnv.3_Silent_p.A78A|ELAC2_uc002gnw.3_Silent_p.A108A|ELAC2_uc002gnx.3_Silent_p.A210A|ELAC2_uc010vvo.1_Silent_p.A248A|ELAC2_uc010vvp.1_Silent_p.A431A|ELAC2_uc010vvq.1_Silent_p.A449A|ELAC2_uc010vvr.1_Silent_p.A410A	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2 isoform 1	450					tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0						GAAGCTGCAGCGCCTCAACTA	0.572000									Hereditary_Prostate_Cancer				11	59					0	0	0.013537	0	0	
LOC162632	162632	broad.mit.edu	37	17	16701628	16701628	+	RNA	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr17:16701628C>T	uc010cpj.1	+	18		c.4159C>T			LOC162632_uc010cpk.1_RNA|LOC162632_uc010vwq.1_RNA|LOC162632_uc002gqm.2_RNA					Homo sapiens mRNA for KIAA0565 protein, partial cds.												0						CAAATTTCCTCGGGAAAGTTT	0.443000													11	126					0	0	0.013537	0	0	
FAM83G	644815	broad.mit.edu	37	17	18874692	18874692	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr17:18874692G>A	uc002guw.2	-	6	2619	c.2452C>T	c.(2452-2454)CGG>TGG	p.R818W	SLC5A10_uc002gur.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815	818										ovary(1)|central_nervous_system(1)	2						TTGCGGTCCCGGGGGGCTTGA	0.632000													16	109					0	0	0.004007	0	0	
Unknown	0	broad.mit.edu	37	17	20407426	20407426	+	RNA	SNP	A	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr17:20407426A>C	uc002gxb.2	-	1		c.369T>G								Homo sapiens similar to Keratin, type I cytoskeletal 16 (Cytokeratin-16) (CK-16) (Keratin-16) (K16), mRNA (cDNA clone IMAGE:4752428).																		caaagccaccacccaagccag	0.348000													10	46					0	0	0.005443	0	0	
TOP2A	7153	broad.mit.edu	37	17	38552660	38552660	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr17:38552660T>C	uc002huq.2	-	28	3721	c.3595A>G	c.(3595-3597)AAG>GAG	p.K1199E		NM_001067	NP_001058	P11388	TOP2A_HUMAN	DNA topoisomerase II, alpha isozyme	1199					apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation	cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding			ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	CCCTTGGCCTTCCCCCCTTTC	0.428000													4	130					0	0	0.009096	0	0	
KRTAP9-4	85280	broad.mit.edu	37	17	39406130	39406130	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr17:39406130G>A	uc002hwi.2	+	1	192	c.158G>A	c.(157-159)CGC>CAC	p.R53H	KRTAP9-9_uc010wfq.1_Intron	NM_033191	NP_149461	Q9BYQ2	KRA94_HUMAN	keratin associated protein 9-4	53	6.|15 X 5 AA repeats of C-C-[RQVGE]-[SPTN]- [TASPF].					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CCTTGCTGCCGCCCAACTTGC	0.642000													5	130					0	0	0.001168	0	0	
ZNRF4	148066	broad.mit.edu	37	19	5456633	5456633	+	Silent	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr19:5456633G>A	uc002mca.3	+	1	1208	c.1131G>A	c.(1129-1131)CCG>CCA	p.P377P		NM_181710	NP_859061	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4 precursor	377	Cytoplasmic (Potential).					integral to membrane	zinc ion binding	p.P377Q(1)		large_intestine(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		CCTCCCTACCGGGCCACCGGC	0.682000													11	79					0	0	0.008291	0	0	
KHSRP	8570	broad.mit.edu	37	19	6417055	6417055	+	Silent	SNP	G	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr19:6417055G>C	uc002mer.3	-	12	1235	c.1125C>G	c.(1123-1125)CCC>CCG	p.P375P		NM_003685	NP_003676	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	375	Gly-rich.|KH 3.				mRNA processing|mRNA transport|regulation of transcription, DNA-dependent|RNA splicing, via transesterification reactions|transcription, DNA-dependent	cytosol|nucleus	DNA binding|protein binding|RNA binding			skin(1)	1						ACCTGTCTGGGGGCCCCATTA	0.622000													11	96					0	0	0.013537	0	0	
C3	718	broad.mit.edu	37	19	6697719	6697719	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr19:6697719C>T	uc002mfm.2	-	20	2589	c.2527G>A	c.(2527-2529)GAG>AAG	p.E843K		NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor	843					complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)		TCCACCTGCTCGTTTCGAACA	0.587000													6	55					0	0	0.001168	0	0	
CPAMD8	27151	broad.mit.edu	37	19	17104353	17104353	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr19:17104353G>A	uc002nfb.2	-	12	1312	c.1280C>T	c.(1279-1281)ACG>ATG	p.T427M		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	380						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13						AATCTGGACCGTCACCCCCTC	0.443000													7	63					0	0	0.003080	0	0	
TMEM143	55260	broad.mit.edu	37	19	48836573	48836573	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr19:48836573A>G	uc002pix.1	-	8	1292	c.1283T>C	c.(1282-1284)ATG>ACG	p.M428T	TMEM143_uc002piw.1_RNA|TMEM143_uc002piy.1_Missense_Mutation_p.M393T|TMEM143_uc010xzn.1_Missense_Mutation_p.M363T|TMEM143_uc010elw.1_Missense_Mutation_p.M328T|TMEM143_uc010xzo.1_Missense_Mutation_p.M218T	NM_018273	NP_060743	Q96AN5	TM143_HUMAN	transmembrane protein 143	428						integral to membrane|mitochondrion					0		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000149)|all cancers(93;0.000198)|Epithelial(262;0.0151)|GBM - Glioblastoma multiforme(486;0.0157)		GTACAATCCCATGCTGGGGGT	0.627000													22	89					0	0	0.003330	0	0	
CGB7	94027	broad.mit.edu	37	19	49558229	49558229	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr19:49558229T>C	uc002pmd.2	-	2	417	c.52A>G	c.(52-54)ACA>GCA	p.T18A	CGB_uc010yad.1_Intron|CGB8_uc002pmc.2_Intron|CGB7_uc002pme.2_Missense_Mutation_p.T18A	NM_033142	NP_149133	P01233	CGHB_HUMAN	chorionic gonadotropin, beta polypeptide 7	18			T -> A.		apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Choriogonadotropin alfa(DB00097)	GATGCCCATGTCCCGCCCATG	0.657000													3	48					0	0	0.004672	0	0	
RGPD3	653489	broad.mit.edu	37	2	107049684	107049684	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr2:107049684C>T	uc010ywi.1	-	16	2320	c.2263G>A	c.(2263-2265)GAA>AAA	p.E755K		NM_001144013	NP_001137485	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	755					intracellular transport		binding			ovary(1)	1						CTATAGTTTTCGAGTTCCTGC	0.368000													28	506					0	0	0.005524	0	0	
NPRL2	10641	broad.mit.edu	37	3	50385317	50385317	+	Silent	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr3:50385317G>A	uc003daj.1	-	10	1351	c.948C>T	c.(946-948)TTC>TTT	p.F316F	ZMYND10_uc003dag.1_5'Flank|ZMYND10_uc010hll.1_5'Flank|ZMYND10_uc003dah.1_5'Flank|ZMYND10_uc010hlm.1_5'Flank|NPRL2_uc003dai.1_Silent_p.F196F|CYB561D2_uc003dak.2_5'Flank|CYB561D2_uc003dal.2_5'Flank|CYB561D2_uc003dam.2_5'Flank	NM_006545	NP_006536	Q8WTW4	NPRL2_HUMAN	tumor suppressor candidate 4	316					negative regulation of kinase activity		protein binding|protein kinase activity			lung(1)	1						TCATAAGCCCGAACTGGATCA	0.577000													5	153					0	0	0.003080	0	0	
ARMC8	25852	broad.mit.edu	37	3	137983022	137983022	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr3:137983022C>T	uc003esa.1	+	15	1592	c.1225C>T	c.(1225-1227)CAG>TAG	p.Q409*	TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_Nonsense_Mutation_p.Q392*|ARMC8_uc011bmg.1_Nonsense_Mutation_p.Q356*|ARMC8_uc011bmh.1_Nonsense_Mutation_p.Q350*|ARMC8_uc003esb.1_Nonsense_Mutation_p.Q381*|ARMC8_uc003esc.1_Nonsense_Mutation_p.Q181*|ARMC8_uc003esf.1_5'UTR	NM_015396	NP_056211	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8 isoform 2	423	ARM 9.						binding				0						AACCAGTTTCCAGGATCATGC	0.398000													12	71					0	0	0.001855	0	0	
MIER3	166968	broad.mit.edu	37	5	56234714	56234714	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr5:56234714T>A	uc003jrd.1	-	4	336	c.311A>T	c.(310-312)GAC>GTC	p.D104V	MIER3_uc003jqz.1_Missense_Mutation_p.D41V|MIER3_uc003jra.1_Missense_Mutation_p.D104V|MIER3_uc003jrb.1_5'UTR|MIER3_uc003jrc.1_Missense_Mutation_p.D109V	NM_152622	NP_689835	Q7Z3K6	MIER3_HUMAN	mesoderm induction early response 1, family	104					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0		Lung NSC(810;4.65e-05)|Prostate(74;0.0253)|Breast(144;0.0503)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;1.24e-37)		ACTTACTTTGTCTAGTGTCAT	0.353000													12	96					0	0	0.001855	0	0	
BRD8	10902	broad.mit.edu	37	5	137485477	137485477	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr5:137485477G>A	uc003lcf.1	-	23	3185	c.3130C>T	c.(3130-3132)CAG>TAG	p.Q1044*	BRD8_uc003lcc.1_Intron	NM_139199	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8 isoform 2	1044					cell surface receptor linked signaling pathway|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription from RNA polymerase II promoter	mitochondrion|NuA4 histone acetyltransferase complex	sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GATTCTTGCTGAGCCTCCCCC	0.453000													8	81					0	0	0.006214	0	0	
SPDEF	25803	broad.mit.edu	37	6	34508912	34508912	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr6:34508912C>T	uc003ojq.1	-	3	898	c.483G>A	c.(481-483)TGG>TGA	p.W161*	SPDEF_uc011dsq.1_Nonsense_Mutation_p.W161*	NM_012391	NP_036523	O95238	SPDEF_HUMAN	SAM pointed domain containing ets transcription	161	PNT.				negative regulation of survival gene product expression|negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(3)|ovary(1)|central_nervous_system(1)	5						GGTGCTCTGTCCACAGGAGCC	0.652000													6	15					0	0	0.001168	0	0	
Unknown	0	broad.mit.edu	37	7	39873287	39873287	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chr7:39873287T>C	uc010kxp.2	+	1	475	c.118T>C	c.(118-120)TTC>CTC	p.F40L						SubName: Full=Similar to sequence-specific single-stranded-DNA-binding protein;																		TGCAGAGACCTTCTTGTCGGA	0.502000													3	34					0	0	0.004672	0	0	
FRMPD4	9758	broad.mit.edu	37	X	12735849	12735849	+	Silent	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chrX:12735849G>A	uc004cuz.1	+	16	3410	c.2904G>A	c.(2902-2904)TCG>TCA	p.S968S	FRMPD4_uc011mij.1_Silent_p.S960S	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	968					positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13						CAAAGTCCTCGCACGCCCTGG	0.602000													26	151					0	0	0.003330	0	0	
OFD1	8481	broad.mit.edu	37	X	13753462	13753462	+	Silent	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chrX:13753462C>T	uc004cvp.3	+	2	467	c.108C>T	c.(106-108)CTC>CTT	p.L36L	OFD1_uc004cvr.3_5'UTR|OFD1_uc011mil.1_5'UTR|OFD1_uc004cvq.3_5'UTR|OFD1_uc010nen.2_Silent_p.L35L|OFD1_uc004cvs.3_RNA|OFD1_uc004cvu.3_Silent_p.L35L|OFD1_uc004cvv.3_Silent_p.L35L|TRAPPC2_uc010nek.1_5'Flank|TRAPPC2_uc010nel.1_5'Flank|TRAPPC2_uc010nem.1_5'Flank	NM_003611	NP_003602	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	36					cilium movement involved in determination of left/right asymmetry|G2/M transition of mitotic cell cycle	centriole|cilium|cytosol|microtubule basal body|nuclear membrane	alpha-tubulin binding|gamma-tubulin binding				0						TGGATACACTCAAGGTATCGG	0.393000													6	64					0	0	0.003080	0	0	
ZFX	7543	broad.mit.edu	37	X	24228401	24228401	+	Silent	SNP	G	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chrX:24228401G>A	uc004dbf.2	+	9	1584	c.1326G>A	c.(1324-1326)AGG>AGA	p.R442R	ZFX_uc004dbe.2_3'UTR|ZFX_uc011mjv.1_Silent_p.R481R|ZFX_uc010nfz.2_Silent_p.R98R	NM_003410	NP_003401	P17010	ZFX_HUMAN	zinc finger protein, X-linked	442	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(2)	2						TTTTGAAAAGGCACATGAAAA	0.403000													18	124					0	0	0.008871	0	0	
MED12	9968	broad.mit.edu	37	X	70357076	70357076	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chrX:70357076C>A	uc004dyy.2	+	39	5790	c.5591C>A	c.(5590-5592)CCA>CAA	p.P1864Q	MED12_uc011mpq.1_Missense_Mutation_p.P1864Q|MED12_uc004dyz.2_Missense_Mutation_p.P1864Q|MED12_uc004dza.2_Missense_Mutation_p.P1711Q|MED12_uc010nla.2_Missense_Mutation_p.P490Q	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	1864	Interaction with CTNNB1 and GLI3.				androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)					GTGCGCTTACCAATGCAGAAG	0.567000													10	70					7.48243e-07	9.11496e-07	0.006214	1	0	
ZCCHC13	389874	broad.mit.edu	37	X	73524180	73524180	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chrX:73524180C>T	uc004ebs.3	+	1	156	c.79C>T	c.(79-81)CGA>TGA	p.R27*		NM_203303	NP_976048	Q8WW36	ZCH13_HUMAN	zinc finger, CCHC domain containing 13	27							nucleic acid binding|zinc ion binding				0						AGCTGGAGGGCGAAGAGGTGG	0.552000													4	40					0	0	0.009096	0	0	
MCART6	401612	broad.mit.edu	37	X	103349655	103349655	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chrX:103349655A>T	uc004elu.2	-	2	467	c.286T>A	c.(286-288)TTT>ATT	p.F96I		NM_001012755	NP_001012773	Q5H9E4	MCAR6_HUMAN	mitochondrial carrier triple repeat 6	96	Helical; Name=2; (Potential).|Solcar 1.				transport	integral to membrane|mitochondrial inner membrane					0						TAAGTCCCAAACAGAAGAGTC	0.567000													15	108					0	0	0.003163	0	0	
AMOT	154796	broad.mit.edu	37	X	112035177	112035177	+	Silent	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chrX:112035177C>T	uc004epr.2	-	6	1809	c.1809G>A	c.(1807-1809)GTG>GTA	p.V603V	AMOT_uc004eps.2_Silent_p.V194V	NM_001113490	NP_001106962	Q4VCS5	AMOT_HUMAN	angiomotin isoform 1	603	Potential.				actin cytoskeleton organization|cell-cell junction assembly|negative regulation of angiogenesis|negative regulation of vascular permeability|positive regulation of blood vessel endothelial cell migration|positive regulation of cell size|positive regulation of stress fiber assembly|regulation of cell migration	actin filament|cell surface|cytoplasm|endocytic vesicle|external side of plasma membrane|integral to membrane|lamellipodium|ruffle|stress fiber|tight junction|tight junction	angiostatin binding|protein binding|receptor activity			ovary(1)	1						GCATCTTCTCCACCTTGTCAA	0.483000													10	129					0	0	0.006214	0	0	
DOCK11	139818	broad.mit.edu	37	X	117810670	117810670	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chrX:117810670G>T	uc004eqp.2	+	48	5493	c.5430G>T	c.(5428-5430)GAG>GAT	p.E1810D	DOCK11_uc004eqq.2_Missense_Mutation_p.E1589D	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1810	DHR-2.				blood coagulation	cytosol	GTP binding			ovary(3)	3						TTGGTACGGAGAATGTCAAAA	0.363000													6	63					8.12818e-05	9.72479e-05	0.001984	1	0	
SOX3	6658	broad.mit.edu	37	X	139586762	139586762	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-6564-01A-12D-1882-08	TCGA-BR-6564-11A-01D-1882-08									Somatic	Phase_I	Capture				Illumina GAIIx	2e66eb75-097c-4ad8-b2b3-9f5849dfd02f	ead5afab-44fa-4e35-ae10-89c8fdf61757	g.chrX:139586762C>T	uc004fbd.1	-	1	464	c.464G>A	c.(463-465)CGC>CAC	p.R155H		NM_005634	NP_005625	P41225	SOX3_HUMAN	SRY (sex determining region Y)-box 3	155	HMG box.				face development|hypothalamus development|negative regulation of neuron differentiation|pituitary gland development|regulation of transcription, DNA-dependent|sensory organ development|sex determination|transcription, DNA-dependent	nucleus	DNA binding			pancreas(1)	1	Acute lymphoblastic leukemia(192;7.65e-05)					GGCCATTTTGCGCCGCTGCCC	0.632000													4	93					0	0	0.009096	0	0	
