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_alt_allele	validation_method	validation_status	validation_tumor_sample	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
MUC16	94025	broad.mit.edu	37	19	8999459	8999459	+	Missense_Mutation	SNP	G	G	C			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr19:8999459G>C	ENST00000397910.4	-	56	40919	c.40716C>G	c.(40714-40716)agC>agG	p.S13572R	MUC16_ENST00000380951.5_Missense_Mutation_p.S213R	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13574	SEA 10.			Missing (in Ref. 3; AAK74120).	cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGTCAGCTGGCTCAGCTCCC	0.567000													4	263					0	0	1	0	0
PPARGC1A	10891	broad.mit.edu	37	4	23816227	23816227	+	Splice_Site	SNP	G	G	T			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr4:23816227G>T	ENST00000264867.2	-	8	998	c.877_splice	c.e8-1	p.G293_splice	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	293	Interaction with PPARG.				androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription cofactor activity|transcription factor binding			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				GTGGAGTTAGGCCTAAGGCAA	0.393000													7	26					0.00198382	0.00198382	1	1	0
SHANK2	22941	broad.mit.edu	37	11	70319087	70319087	+	Missense_Mutation	SNP	C	C	T			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr11:70319087C>T	ENST00000338508.4	-	33	5439	c.5440G>A	c.(5440-5442)Gat>Aat	p.D1814N	SHANK2_ENST00000449833.2_Missense_Mutation_p.D1218N|SHANK2_ENST00000423696.2_Missense_Mutation_p.D1434N|SHANK2_ENST00000409161.1_Missense_Mutation_p.D1217N			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	1434					intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			TGACTGCCATCGATCTCATTG	0.478000													4	107					0	0	1	0	0
RP11-417J8.6	0	broad.mit.edu	37	1	142713773	142713773	+	RNA	SNP	C	C	G			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr1:142713773C>G	ENST00000369381.2	-	0	832																											TCTTTTTCCACATTGTCATTT	0.284000													6	60					0	0	1	0	0
NGEF	25791	broad.mit.edu	37	2	233785226	233785226	+	Missense_Mutation	SNP	G	G	A			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr2:233785226G>A	ENST00000264051.3	-	5	874	c.596C>T	c.(595-597)gCa>gTa	p.A199V	NGEF_ENST00000409079.1_Missense_Mutation_p.A107V|NGEF_ENST00000373552.4_Missense_Mutation_p.A107V	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	199	Regulatory region; modulates activity toward RHOA, RAC1 and CDC42 (By similarity).				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		TTCTATTTCTGCATCCTGTTG	0.512000													4	78					0	0	1	0	0
TSSC2	0	broad.mit.edu	37	11	3427759	3427759	+	RNA	SNP	C	C	T			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr11:3427759C>T	ENST00000529482.1	+	0	876																											TGTCTGCACACGTCCTGCAGT	0.612000													4	34					0	0	1	0	0
ZNF814	730051	broad.mit.edu	37	19	58385546	58385546	+	Missense_Mutation	SNP	G	G	T			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr19:58385546G>T	ENST00000435989.2	-	3	1446	c.1212C>A	c.(1210-1212)gaC>gaA	p.D404E	ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	404					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding	p.D404E(10)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						AATGTTTTTTGTCAGTGTGAA	0.393000													4	7					0.00024832	0.000270895	1	1	0
ASUN	55726	broad.mit.edu	37	12	27067050	27067050	+	Silent	SNP	T	T	C			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr12:27067050T>C	ENST00000261191.7	-	13	1967	c.1431A>G	c.(1429-1431)ttA>ttG	p.L477L	ASUN_ENST00000539625.1_Silent_p.L376L	NM_018164.2	NP_060634.2	Q9NVM9	M89BB_HUMAN	asunder spermatogenesis regulator	477					cell division|mitosis|regulation of mitotic cell cycle		protein binding										TAACACTGGCTAATGGAACTA	0.289000													3	43					0	0	1	0	0
RP11-417J8.6	0	broad.mit.edu	37	1	142713774	142713774	+	RNA	SNP	A	A	G			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr1:142713774A>G	ENST00000369381.2	-	0	831																											CTTTTTCCACATTGTCATTTT	0.284000													6	60					0	0	1	0	0
FOXC1	2296	broad.mit.edu	37	6	1612142	1612144	+	In_Frame_Del	DEL	GCG	GCG	-			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr6:1612142_1612144delGCG	ENST00000380874.2	+	1	1462_1464	c.1462_1464delGCG	c.(1462-1464)del	p.A495del		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	495	Poly-Ala.				anti-apoptosis|artery morphogenesis|blood vessel remodeling|brain development|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|germ cell migration|glycosaminoglycan metabolic process|lacrimal gland development|lymphangiogenesis|metanephros development|negative regulation of mitotic cell cycle|neural crest cell fate commitment|Notch signaling pathway|odontogenesis of dentine-containing tooth|ossification|ovarian follicle development|paraxial mesodermal cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|regulation of blood vessel size|regulation of organ growth|regulation of sequence-specific DNA binding transcription factor activity|somitogenesis|ureteric bud development|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	nuclear heterochromatin|transcription factor complex	chromatin DNA binding|DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		CTTGGCGAGCgcggcggcggcgg	0.709													2	4	---	---	---	---					
MYO6	4646	broad.mit.edu	37	6	76599857	76599858	+	Frame_Shift_Ins	INS	-	-	A			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr6:76599857_76599858insA	ENST00000369981.3	+	26	3021_3022	c.2742_2743insA	c.(2740-2745)caaaaafs	p.QK914fs	MYO6_ENST00000369977.3_Frame_Shift_Ins_p.QK914fs|MYO6_ENST00000369985.4_Frame_Shift_Ins_p.QK914fs|MYO6_ENST00000369975.1_Frame_Shift_Ins_p.QK914fs			Q9UM54	MYO6_HUMAN	myosin VI	914					actin filament-based movement|DNA damage response, signal transduction by p53 class mediator|endocytosis|intracellular protein transport|positive regulation of transcription from RNA polymerase II promoter|regulation of secretion|sensory perception of sound|synaptic transmission	cell cortex|clathrin coated vesicle membrane|coated pit|cytosol|DNA-directed RNA polymerase II, holoenzyme|filamentous actin|Golgi apparatus|nuclear membrane|perinuclear region of cytoplasm|ruffle membrane|unconventional myosin complex	actin filament binding|ADP binding|ATP binding|calmodulin binding|minus-end directed microfilament motor activity|protein binding	p.K917fs*10(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		GTGCATTACAGAAAAAAAAACA	0.381													7	58	---	---	---	---					
CASP8AP2	9994	broad.mit.edu	37	6	90556397	90556398	+	RNA	INS	-	-	TTTTT			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr6:90556397_90556398insTTTTT	ENST00000551025.1	+	0	1492							Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2						cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		TTCTAAtttccttttttttttt	0.421													4	8	---	---	---	---					
PRKDC	5591	broad.mit.edu	37	8	48866910	48866910	+	Frame_Shift_Del	DEL	T	T	-			TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr8:48866910delT	ENST00000314191.2	-	5	552	c.496delA	c.(496-498)tafs	p.I166fs	PRKDC_ENST00000523565.1_5'UTR|PRKDC_ENST00000338368.3_Frame_Shift_Del_p.I166fs	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	166					cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				GTATCTGGTATTTTTTTTTTC	0.264								Non-homologous end-joining					2	4	---	---	---	---					
LYPD3	27076	broad.mit.edu	37	19	43969653	43969655	+	In_Frame_Del	DEL	AGC	AGC	-	rs141441894	byFrequency	TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr19:43969653_43969655delAGC	ENST00000244333.3	-	1	157_159	c.69_71delGCT	c.(67-72)ctt>ct	p.LL23del		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	23						anchored to plasma membrane				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				ACCTCCGCGAAGCAGCAGCAGCA	0.675													9	133	---	---	---	---					
TPTEP1	0	broad.mit.edu	37	22	17131536	17131537	+	RNA	INS	-	-	CTG	rs34452519		TCGA-WB-A80L-01A-11D-A35I-08	TCGA-WB-A80L-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	3af3804b-6214-4d23-ba0a-3b5d8f3243fd	4eec4f36-189f-462a-bcd1-462b39b578b2	g.chr22:17131536_17131537insCTG	ENST00000426585.1	+	0	2562_2563																											TGCCCACTCTTCTGGTCTCATG	0.540													2	4	---	---	---	---					
