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
PRTG	283659	broad.mit.edu	37	15	55933315	55933315	+	Silent	SNP	G	G	A			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr15:55933315G>A	ENST00000389286.4	-	12	2180	c.2133C>T	c.(2131-2133)tgC>tgT	p.C711C		NM_173814.4	NP_776175.2	Q2VWP7	PRTG_HUMAN	protogenin	711					multicellular organismal development	integral to membrane				breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		ACTTACACACGCATCCTGGAG	0.448000													3	26					0	0	1	0	0
BTN2A3P	0	broad.mit.edu	37	6	26422353	26422353	+	RNA	SNP	C	C	T	rs141013110		TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr6:26422353C>T	ENST00000466808.2	+	0	7																		p.P3S(2)									GCTCATGGAACCAGCTGCTGC	0.622000													4	90					0	0	1	0	0
TRPS1	7227	broad.mit.edu	37	8	116599567	116599567	+	Silent	SNP	G	G	A			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr8:116599567G>A	ENST00000395715.3	-	5	2938	c.2361C>T	c.(2359-2361)gaC>gaT	p.D787D	TRPS1_ENST00000220888.5_Silent_p.D774D|TRPS1_ENST00000519076.1_Silent_p.D528D|TRPS1_ENST00000520276.1_Silent_p.D778D|TRPS1_ENST00000519674.1_Silent_p.D774D	NM_014112.2	NP_054831.2	Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	774	Mediates interaction with GLI3.				negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CTTTGAGCCCGTCCTTCTCTT	0.507000									Langer-Giedion syndrome				4	179					0	0	1	0	0
CRAT	1384	broad.mit.edu	37	9	131860910	131860910	+	Missense_Mutation	SNP	G	G	A			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr9:131860910G>A	ENST00000318080.2	-	9	1399	c.1105C>T	c.(1105-1107)Cgg>Tgg	p.R369W	RP11-247A12.1_ENST00000434250.1_RNA	NM_000755.3|NM_001257363.1	NP_000746.2|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	369					energy derivation by oxidation of organic compounds|fatty acid beta-oxidation using acyl-CoA oxidase|transport	endoplasmic reticulum|mitochondrial inner membrane|peroxisomal matrix	carnitine O-acetyltransferase activity			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	AGGGGAGACCGCACAAGCTCG	0.607000													4	83					0	0	1	0	0
AMOT	154796	broad.mit.edu	37	X	112058796	112058796	+	Silent	SNP	C	C	T			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chrX:112058796C>T	ENST00000371959.3	-	2	1181	c.1182G>A	c.(1180-1182)caG>caA	p.Q394Q	AMOT_ENST00000524145.1_Silent_p.Q394Q|AMOT_ENST00000371962.1_Silent_p.Q162Q|AMOT_ENST00000304758.1_5'UTR|AMOT_ENST00000371958.1_Silent_p.Q162Q	NM_001113490.1	NP_001106962.1	Q4VCS5	AMOT_HUMAN	angiomotin	394					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	angiostatin binding|protein binding|receptor activity	p.Q394Q(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						gctgctgctgctgttgttggt	0.582000													3	43					0	0	1	0	0
UBBP4	0	broad.mit.edu	37	17	21730916	21730916	+	Missense_Mutation	SNP	G	G	T	rs111245273	by1000genomes	TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr17:21730916G>T	ENST00000584755.1	+	2	615	c.218G>T	c.(217-219)cGg>cTg	p.R73L	UBBP4_ENST00000578713.1_Missense_Mutation_p.R73L|UBBP4_ENST00000584398.1_Intron|UBBP4_ENST00000583708.1_Intron														p.R73L(24)		endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4)	24						GTCCTGCGTCGGAGAGGTGGT	0.552000													5	65					1.23904e-05	1.44555e-05	1	1	0
LTBP2	4053	broad.mit.edu	37	14	75022242	75022242	+	Nonsense_Mutation	SNP	G	G	A			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr14:75022242G>A	ENST00000261978.4	-	4	1371	c.985C>T	c.(985-987)Cag>Tag	p.Q329*	CTD-2207P18.1_ENST00000554552.1_lincRNA|LTBP2_ENST00000556690.1_Nonsense_Mutation_p.Q329*|LTBP2_ENST00000557425.1_Intron	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	329					protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		GGTACCGCCTGTTGGGTGCCA	0.627000													9	38					0	0	1	0	0
SIRPB1	10326	broad.mit.edu	37	20	1585397	1585397	+	Missense_Mutation	SNP	T	T	C	rs148754551	by1000genomes	TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr20:1585397T>C	ENST00000279477.7	-	3	806	c.742A>G	c.(742-744)Acc>Gcc	p.T248A	SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000381605.4_Intron|SIRPB1_ENST00000568365.1_Missense_Mutation_p.T248A|RP4-576H24.4_ENST00000564763.1_Intron	NM_001135844.2	NP_001129316.1	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	248					cell junction assembly|cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding	p.T248A(5)		central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						CCTCGGATGGTCTCAGACAAG	0.627000													4	22					0	0	1	0	0
OCA2	4948	broad.mit.edu	37	15	28231750	28231750	+	Missense_Mutation	SNP	C	C	T			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr15:28231750C>T	ENST00000354638.3	-	12	1377	c.1222G>A	c.(1222-1224)Gat>Aat	p.D408N	OCA2_ENST00000353809.5_Missense_Mutation_p.D384N|OCA2_ENST00000382996.2_Missense_Mutation_p.D408N	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	408					eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding	p.D408N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		GCACAATAATCGAAAAATCCC	0.294000									Oculocutaneous Albinism				28	46					0	0	1	0	0
TSHZ3	57616	broad.mit.edu	37	19	31768209	31768209	+	Silent	SNP	G	G	A			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr19:31768209G>A	ENST00000240587.4	-	2	2817	c.2490C>T	c.(2488-2490)gtC>gtT	p.V830V		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	830					negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					TGAATGATACGACGGCAGATG	0.527000													20	108					0	0	1	0	0
PMS2P3	0	broad.mit.edu	37	7	75142142	75142142	+	RNA	DEL	A	A	-	rs35519730		TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr7:75142142delA	ENST00000418756.1	-	0	991					NR_028059.1															lung(1)	1						tctcaaaaagaaaaaaaaaaa	0.418													2	4	---	---	---	---					
FAM66B	0	broad.mit.edu	37	8	7196263	7196264	+	RNA	DEL	AC	AC	-			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr8:7196263_7196264delAC	ENST00000606573.1	-	0	703																											ACTGAGGGGTacacacacacac	0.500													3	4	---	---	---	---					
MYRF	745	broad.mit.edu	37	11	61547022	61547022	+	Frame_Shift_Del	DEL	C	C	-			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr11:61547022delC	ENST00000278836.5	+	16	2323	c.2227delC	c.(2227-2229)ccfs	p.P744fs	TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000327797.1_Frame_Shift_Del_p.P388fs|MYRF_ENST00000265460.5_Frame_Shift_Del_p.P735fs|MYRF_ENST00000389602.4_Frame_Shift_Del_p.P135fs	NM_001127392.1	NP_001120864.1			myelin regulatory factor																		CAAGAAGAGGCCCCCCAAGGT	0.652													2	4	---	---	---	---					
HERC2P2	0	broad.mit.edu	37	15	23312380	23312380	+	RNA	DEL	T	T	-			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr15:23312380delT	ENST00000560464.1	-	0	3118																											TGTTAttttcttttttttttt	0.398													3	5	---	---	---	---					
DUOX2	50506	broad.mit.edu	37	15	45399034	45399034	+	Frame_Shift_Del	DEL	G	G	-			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr15:45399034delG	ENST00000389039.6	-	15	2212	c.1827delC	c.(1825-1827)ccfs	p.P609fs	DUOX2_ENST00000603300.1_Frame_Shift_Del_p.P609fs			Q9NRD8	DUOX2_HUMAN	dual oxidase 2	609					cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		GCTCACCTAAGGGAAGGCAGC	0.587													2	4	---	---	---	---					
UBE2Q2P1	0	broad.mit.edu	37	15	85081721	85081721	+	RNA	DEL	C	C	-			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr15:85081721delC	ENST00000339094.1	-	0	1678					NR_003661.2																						caaatatatacccccattcat	0.323													2	4	---	---	---	---					
C16orf74	404550	broad.mit.edu	37	16	85743879	85743881	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr16:85743879_85743881delGCT	ENST00000602583.1	-	1	575_577	c.25_27delAGC	c.(25-27)del	p.S9del	C16orf74_ENST00000602675.1_5'UTR|C16orf74_ENST00000602914.1_Intron|C16orf74_ENST00000602758.1_Intron|C16orf74_ENST00000284245.4_In_Frame_Del_p.S21del|C16orf74_ENST00000602719.1_In_Frame_Del_p.S21del|C16orf74_ENST00000602766.1_5'UTR			Q96GX8	CP074_HUMAN	chromosome 16 open reading frame 74	21																	CCTCGTCGTGGCTGCTGCTGCTG	0.635													3	6	---	---	---	---					
TNPO2	30000	broad.mit.edu	37	19	12830109	12830110	+	Frame_Shift_Ins	INS	-	-	T			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr19:12830109_12830110insT	ENST00000425528.1	-	4	497_498	c.140_141insA	c.(139-141)tctfs	p.S47fs	TNPO2_ENST00000356861.5_Frame_Shift_Ins_p.S47fs|TNPO2_ENST00000588216.1_Frame_Shift_Ins_p.S47fs|TNPO2_ENST00000441499.1_Frame_Shift_Ins_p.S47fs|TNPO2_ENST00000592287.1_Frame_Shift_Ins_p.S47fs|TNPO2_ENST00000589956.1_5'UTR|TNPO2_ENST00000450764.2_Frame_Shift_Ins_p.S47fs			O14787	TNPO2_HUMAN	transportin 2	47	Importin N-terminal.				intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CGAAAATCAGGTAGTTGTTGAA	0.545													10	23	---	---	---	---					
