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
TCEAL6	158931	broad.mit.edu	37	X	101396186	101396186	+	Missense_Mutation	SNP	C	C	T			TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chrX:101396186C>T	ENST00000372774.3	-	3	367	c.118G>A	c.(118-120)Ggg>Agg	p.G40R	TCEAL6_ENST00000372773.1_Missense_Mutation_p.G40R	NM_001006938.2	NP_001006939.2	Q6IPX3	TCAL6_HUMAN	transcription elongation factor A (SII)-like 6	40	Glu-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	14						tctgtcttcccctccgcgtct	0.507000													26	42					0	0	1	0	0
RAF1	5894	broad.mit.edu	37	3	12645671	12645671	+	Silent	SNP	G	G	A			TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr3:12645671G>A	ENST00000251849.4	-	7	1237	c.798C>T	c.(796-798)gtC>gtT	p.V266V	RAF1_ENST00000542177.1_Silent_p.V185V|RAF1_ENST00000534997.1_Silent_p.V51V|RAF1_ENST00000442415.2_Silent_p.V266V	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	v-raf-1 murine leukemia viral oncogene homolog 1	266					activation of MAPKK activity|apoptosis|axon guidance|cell proliferation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of peptidyl-serine phosphorylation|Ras protein signal transduction|synaptic transmission	cytosol|mitochondrial outer membrane|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity		ESRP1/RAF1(4)|RAF1/DAZL(2)|SRGAP3/RAF1(6)	biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	32					Sorafenib(DB00398)	GGGTGGTGCTGACCATGTGGA	0.517000			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome				7	78					0	0	1	0	0
HERC2P2	0	broad.mit.edu	37	15	23283128	23283128	+	RNA	SNP	C	C	T			TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr15:23283128C>T	ENST00000560464.1	-	0	5122																											ATGAAACCCACGTAGTCGGAC	0.537000													3	11					0	0	1	0	0
NRXN1	9378	broad.mit.edu	37	2	50765449	50765449	+	Missense_Mutation	SNP	C	C	A			TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr2:50765449C>A	ENST00000404971.1	-	11	3544	c.2205G>T	c.(2203-2205)tgG>tgT	p.W735C	NRXN1_ENST00000406316.2_Missense_Mutation_p.W695C|NRXN1_ENST00000405472.3_Missense_Mutation_p.W687C|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000401669.2_Missense_Mutation_p.W695C|NRXN1_ENST00000402717.3_Missense_Mutation_p.W687C|NRXN1_ENST00000406859.3_Missense_Mutation_p.W695C	NM_001135659.1	NP_001129131.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	695	Laminin G-like 4.				adult behavior|axon guidance|cell adhesion|grooming behavior|learning|neuromuscular process controlling balance|positive regulation of excitatory postsynaptic membrane potential|prepulse inhibition	cell surface|integral to plasma membrane	metal ion binding|protein binding|receptor activity			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CATATCTGTTCCACCCATCCC	0.488000													9	197					3.86212e-05	4.03004e-05	1	1	0
LRGUK	136332	broad.mit.edu	37	7	133821786	133821786	+	Missense_Mutation	SNP	A	A	T			TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr7:133821786A>T	ENST00000285928.2	+	2	377	c.308A>T	c.(307-309)gAt>gTt	p.D103V	LRGUK_ENST00000473068.1_3'UTR	NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	103							ATP binding|kinase activity			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						GAGGAATTTGATGGGGTCCTG	0.428000													9	16					0	0	1	0	0
TBP	6908	broad.mit.edu	37	6	170871094	170871094	+	Silent	SNP	G	G	A			TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr6:170871094G>A	ENST00000392092.2	+	3	549	c.270G>A	c.(268-270)caG>caA	p.Q90Q	TBP_ENST00000540980.1_Silent_p.Q70Q|TBP_ENST00000230354.6_Silent_p.Q90Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	90	Poly-Gln.				cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	repressing transcription factor binding|transcription regulatory region DNA binding			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagc	0.622000													4	42					0	0	1	0	0
ZNF646	9726	broad.mit.edu	37	16	31092931	31092931	+	Silent	SNP	C	C	T			TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr16:31092931C>T	ENST00000394979.2	+	1	5709	c.5286C>T	c.(5284-5286)acC>acT	p.T1762T	ZNF646_ENST00000300850.5_Silent_p.T1762T			O15015	ZN646_HUMAN	zinc finger protein 646	1762					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						GGCCTTTCACCTGCCCCCATT	0.701000													7	25					0	0	1	0	0
PMP22	5376	broad.mit.edu	37	17	15134175	15134175	+	Missense_Mutation	SNP	T	T	G	rs13422	by1000genomes	TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr17:15134175T>G	ENST00000494511.1	-	3	529	c.363A>C	c.(361-363)aaA>aaC	p.K121N	PMP22_ENST00000395936.1_3'UTR|PMP22_ENST00000395938.2_3'UTR|PMP22_ENST00000312280.3_3'UTR			Q01453	PMP22_HUMAN	peripheral myelin protein 22	0					peripheral nervous system development|synaptic transmission	integral to membrane				endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	8				UCEC - Uterine corpus endometrioid carcinoma (92;0.0884)|BRCA - Breast invasive adenocarcinoma(8;4.92e-06)		CTGCTTTCTGTTTTCCCTTCC	0.498000													3	42					0	0	1	0	0
KRTAP4-9	100132386	broad.mit.edu	37	17	39261693	39261693	+	Missense_Mutation	SNP	A	A	T	rs113059833	by1000genomes	TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr17:39261693A>T	ENST00000391415.1	+	1	110	c.53A>T	c.(52-54)gAc>gTc	p.D18V		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	18						keratin filament		p.D18V(1)		central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						TGCGGCCAAGACCTCTGTCAG	0.627000													4	33					0	0	1	0	0
PLEKHS1	79949	broad.mit.edu	37	10	115540477	115540477	+	Silent	SNP	G	G	A			TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr10:115540477G>A	ENST00000354462.3	+	6	692	c.534G>A	c.(532-534)ctG>ctA	p.L178L	PLEKHS1_ENST00000369309.1_Silent_p.L262L|PLEKHS1_ENST00000361048.1_3'UTR|PLEKHS1_ENST00000369312.4_Silent_p.L346L					pleckstrin homology domain containing, family S member 1																		AGCCTAGACTGAACAGAGCTC	0.532000													3	14					0	0	1	0	0
GPR125	166647	broad.mit.edu	37	4	22517165	22517165	+	Silent	SNP	G	G	A			TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr4:22517165G>A	ENST00000334304.5	-	1	512	c.243C>T	c.(241-243)aaC>aaT	p.N81N	GPR125_ENST00000502482.1_Silent_p.N81N	NM_145290.2	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	81					neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				TGACCGTGCGGTTGGGCAGAG	0.687000													4	12					0	0	1	0	0
SOX8	30812	broad.mit.edu	37	16	1034756	1034756	+	Silent	SNP	G	G	A			TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr16:1034756G>A	ENST00000293894.3	+	3	826	c.711G>A	c.(709-711)caG>caA	p.Q237Q		NM_014587.3	NP_055402.2	P57073	SOX8_HUMAN	SRY (sex determining region Y)-box 8	237					adipose tissue development|enteric nervous system development|fat cell differentiation|in utero embryonic development|metanephric nephron tubule formation|morphogenesis of a branching epithelium|negative regulation of apoptosis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|neural crest cell migration|oligodendrocyte differentiation|osteoblast differentiation|peripheral nervous system development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of gliogenesis|positive regulation of osteoblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone levels|renal vesicle induction|retinal rod cell differentiation|Sertoli cell development|signal transduction|spermatogenesis|ureter morphogenesis	cytoplasm|nucleus				central_nervous_system(1)|kidney(1)|lung(5)|prostate(2)|skin(1)	10		Hepatocellular(780;0.00308)				AGCTGCAGCAGGCGGGCGCCA	0.682000													3	11					0	0	1	0	0
DIP2C	22982	broad.mit.edu	37	10	375466	375466	+	Silent	SNP	G	G	T			TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr10:375466G>T	ENST00000280886.6	-	30	3747	c.3660C>A	c.(3658-3660)gcC>gcA	p.A1220A		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1220						nucleus	catalytic activity|transcription factor binding	p.A1220A(1)		breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		ACTGACTCACGGCAAGAAGCC	0.562000													9	20					3.86212e-05	4.03004e-05	1	1	0
POU4F2	5458	broad.mit.edu	37	4	147560457	147560458	+	In_Frame_Ins	INS	-	-	GGC	rs67907220		TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr4:147560457_147560458insGGC	ENST00000281321.3	+	1	413_414	c.165_166insGGC	c.(163-168)gggcgg>ggGGCgcgg	p.55_56GR>GAR	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	55	Poly-Gly.				estrogen receptor signaling pathway|MAPKKK cascade|negative regulation of transcription from RNA polymerase II promoter	nuclear speck	RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					ACGCTggtggtggcggcggcgg	0.762													2	4	---	---	---	---					
PNLIPRP2	5408	broad.mit.edu	37	10	118396277	118396278	+	RNA	INS	-	-	T	rs148140777	by1000genomes	TCGA-CE-A482-01A-11D-A23U-08	TCGA-CE-A482-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	36a7dd2c-a840-41b7-8b20-5b5d7fe9f20a	cd98f940-450f-4fe6-8c45-d6aa526e6494	g.chr10:118396277_118396278insT	ENST00000537242.1	+	0	962				PNLIPRP2_ENST00000298771.7_RNA|PNLIPRP2_ENST00000433618.4_RNA	NM_005396.4	NP_005387.2	P54317	LIPR2_HUMAN	pancreatic lipase-related protein 2						galactolipid catabolic process|lipid digestion|phospholipid catabolic process|triglyceride metabolic process	extracellular space	acylglycerol lipase activity|calcium ion binding|galactolipase activity|phospholipase activity|triglyceride lipase activity			endometrium(1)|large_intestine(1)|lung(11)|prostate(3)	16				all cancers(201;0.015)		GACAAATTATGGTTTTTTTTTT	0.421													4	3	---	---	---	---					
