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
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	byFrequency	TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr22:29091840T>C	ENST00000544772.1	-	12	1890	c.454A>G	c.(454-456)Aag>Gag	p.K152E	CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN	checkpoint kinase 2	373	FHA.				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418000			F			breast		Direct reversal of damage;Other conserved DNA damage response genes					4	22					0	0	1	0	0
HMGA2	8091	broad.mit.edu	37	12	66221789	66221789	+	Silent	SNP	C	C	T			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr12:66221789C>T	ENST00000541363.1	+	2	493	c.120C>T	c.(118-120)acC>acT	p.T40T	HMGA2_ENST00000536545.1_Silent_p.T40T|HMGA2_ENST00000393578.3_Silent_p.T40T|HMGA2_ENST00000403681.2_Silent_p.T40T|HMGA2_ENST00000425208.2_Silent_p.T40T|HMGA2_ENST00000393577.3_Silent_p.T40T|HMGA2_ENST00000354636.3_Silent_p.T40T			P52926	HMGA2_HUMAN	high mobility group AT-hook 2	40					cell division|chromatin organization|mitosis|multicellular organismal development|regulation of growth|transcription, DNA-dependent	chromatin	AT DNA binding		HMGA2/RAD51B(11)|HMGA2/CCNB1IP1(2)|HMGA2/WIF1_ENST00000286574(14)|HMGA2/ALDH2_ENST00000261733(2)|HMGA2/EBF1(2)|HMGA2/LHFP(2)|HMGA2/NFIB_ENST00000397581(8)|HMGA2/LPP(161)|HMGA2/FHIT_ENST00000476844(4)|HMGA2/COX6C(2)	lung(2)	2	all_cancers(1;5.78e-46)		GBM - Glioblastoma multiforme(1;0.00179)|LUSC - Lung squamous cell carcinoma(43;0.156)	GBM - Glioblastoma multiforme(28;0.0386)		AGGAACCAACCGGTGAGCCCT	0.448000			T	""" LHFP, RAD51L1, LPP, COX6C, CMKOR1, NFIB, ALDH2, CCNB1IP1, EBF1, WIF1, FHIT"""	"""lipoma, leiomyoma, pleiomorphic salivary gland adenoma"""								18	24					0	0	1	0	0
OR6K3	391114	broad.mit.edu	37	1	158687537	158687537	+	Silent	SNP	G	G	A			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr1:158687537G>A	ENST00000368146.1	-	1	416	c.417C>T	c.(415-417)taC>taT	p.Y139Y	OR6K3_ENST00000368145.1_Silent_p.Y123Y			Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K, member 3	139					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41	all_hematologic(112;0.0378)					AGATGGCAACGTATCTGTCAA	0.507000													4	81					0	0	1	0	0
ELANE	1991	broad.mit.edu	37	19	853364	853364	+	Silent	SNP	C	C	T			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr19:853364C>T	ENST00000590230.1	+	4	468	c.327C>T	c.(325-327)taC>taT	p.Y109Y	ELANE_ENST00000263621.1_Silent_p.Y109Y			P08246	ELNE_HUMAN	elastase, neutrophil expressed	109	Peptidase S1.				cellular calcium ion homeostasis|negative regulation of chemokine biosynthetic process|negative regulation of chemotaxis|negative regulation of inflammatory response|negative regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 biosynthetic process|positive regulation of MAP kinase activity|positive regulation of smooth muscle cell proliferation|protein catabolic process|proteolysis|response to UV	cell surface|extracellular region|stored secretory granule	bacterial cell surface binding|cytokine binding|heparin binding			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(1)|lung(4)|pancreas(1)	13					Alpha-1-proteinase inhibitor(DB00058)|Filgrastim(DB00099)|Pegfilgrastim(DB00019)	AAAACGGCTACGACCCCGTAA	0.706000													8	14					0	0	1	0	0
OPA3	80207	broad.mit.edu	37	19	46032458	46032458	+	Silent	SNP	G	G	A			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr19:46032458G>A	ENST00000323060.3	-	2	476	c.399C>T	c.(397-399)ctC>ctT	p.L133L		NM_001017989.2	NP_001017989.2	Q9H6K4	OPA3_HUMAN	optic atrophy 3 (autosomal recessive, with chorea and spastic paraplegia)	133					response to stimulus|visual perception	mitochondrion				cervix(1)|large_intestine(1)|lung(2)	4		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00778)|GBM - Glioblastoma multiforme(486;0.0976)|Epithelial(262;0.242)		GCAACTCCTCGAGCGCCAGCC	0.697000													13	13					0	0	1	0	0
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	byFrequency	TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr22:29091841G>A	ENST00000544772.1	-	12	1889	c.453C>T	c.(451-453)tcC>tcT	p.S151S	CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000403642.1_Silent_p.S281S	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN	checkpoint kinase 2	372	FHA.				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413000			F			breast		Direct reversal of damage;Other conserved DNA damage response genes					4	22					0	0	1	0	0
FAM221B	392307	broad.mit.edu	37	9	35819971	35819971	+	Missense_Mutation	SNP	G	G	T			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr9:35819971G>T	ENST00000423537.2	-	4	1038	c.769C>A	c.(769-771)Cat>Aat	p.H257N	TMEM8B_ENST00000377996.1_Intron	NM_001012446.3	NP_001012448.2	A6H8Z2	CI128_HUMAN	family with sequence similarity 221, member B	257										endometrium(2)|kidney(1)|lung(4)	7						CATAGGTAATGGGGGCAGCGC	0.483000													5	72					8.12818e-05	8.12818e-05	1	1	0
LONP1	9361	broad.mit.edu	37	19	5692054	5692054	+	Missense_Mutation	SNP	C	C	A			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr19:5692054C>A	ENST00000360614.3	-	18	3026	c.2869G>T	c.(2869-2871)Gtg>Ttg	p.V957L	LONP1_ENST00000590729.1_Missense_Mutation_p.V827L|LONP1_ENST00000593119.1_Missense_Mutation_p.V893L|LONP1_ENST00000540670.2_Missense_Mutation_p.V761L|LONP1_ENST00000585374.1_Missense_Mutation_p.V843L	NM_004793.2	NP_004784.2	P36776	LONM_HUMAN	lon peptidase 1, mitochondrial	957					cellular chaperone-mediated protein complex assembly|cellular response to oxidative stress|misfolded or incompletely synthesized protein catabolic process|mitochondrial DNA metabolic process|oxidation-dependent protein catabolic process|protein homooligomerization|response to hypoxia	mitochondrial nucleoid	ADP binding|ATP binding|ATP-dependent peptidase activity|DNA polymerase binding|G-quadruplex DNA binding|mitochondrial heavy strand promoter anti-sense binding|mitochondrial light strand promoter anti-sense binding|sequence-specific DNA binding|serine-type endopeptidase activity|single-stranded DNA binding|single-stranded RNA binding			breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CACCGTTCCACGGCCAGCGCC	0.687000													29	34					2.49675e-24	2.74642e-24	1	1	0
ARHGAP22	58504	broad.mit.edu	37	10	49667823	49667823	+	Missense_Mutation	SNP	A	A	T			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr10:49667823A>T	ENST00000249601.4	-	5	859	c.563T>A	c.(562-564)cTc>cAc	p.L188H	ARHGAP22_ENST00000374170.1_Missense_Mutation_p.L98H|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.L204H|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.L98H|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.L79H|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.L194H	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	188	Rho-GAP.				angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	GTPase activator activity			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CTCCTCAGTGAGCCCGCGCTC	0.642000													52	69					0	0	1	0	0
SEMA4G	57715	broad.mit.edu	37	10	102743064	102743066	+	In_Frame_Del	DEL	CCA	CCA	-			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr10:102743064_102743066delCCA	ENST00000210633.3	+	14	1786_1788	c.1708_1710delCCA	c.(1708-1710)del	p.P573del	MRPL43_ENST00000318325.2_Intron|MRPL43_ENST00000299179.5_Intron|MRPL43_ENST00000342071.1_Intron|MRPL43_ENST00000370241.3_Intron|SEMA4G_ENST00000517724.1_Intron|RP11-108L7.4_ENST00000447344.1_RNA|MRPL43_ENST00000370242.4_Intron|SEMA4G_ENST00000370250.4_In_Frame_Del_p.P568del			Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	568	Ig-like C2-type.				cell differentiation|nervous system development	integral to membrane	receptor activity			breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		CCCCACAGGGCCACCACCACCAC	0.616													2	4	---	---	---	---					
RRN3P2	653390	broad.mit.edu	37	16	29118702	29118704	+	RNA	DEL	AGC	AGC	-			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chr16:29118702_29118704delAGC	ENST00000564580.1	+	0	1448				CTB-134H23.3_ENST00000562618.1_RNA																							GCCAGGTCCAagcagcagcagca	0.660													2	4	---	---	---	---					
PLXNB3	5365	broad.mit.edu	37	X	153044463	153044463	+	Frame_Shift_Del	DEL	C	C	-			TCGA-P8-A6RY-01A-12D-A35D-08	TCGA-P8-A6RY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	68c49fd1-9ada-4ac7-963a-dc4bd8ccdf92	9019f5a7-57eb-44da-9368-4099e7314b2b	g.chrX:153044463delC	ENST00000538966.1	+	37	6039	c.5768delC	c.(5767-5769)gcfs	p.A1923fs	PLXNB3_ENST00000361971.5_Frame_Shift_Del_p.A1900fs|PLXNB3_ENST00000538776.1_Frame_Shift_Del_p.A1553fs|SRPK3_ENST00000489426.1_5'UTR	NM_001163257.1	NP_001156729.1	Q9ULL4	PLXB3_HUMAN	plexin B3	1900					axon guidance	integral to membrane|intracellular|plasma membrane	protein binding|receptor activity			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGTCGCCGCCCTGGTGGAA	0.647													2	4	---	---	---	---