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
PI3	5266	broad.mit.edu	37	20	43804501	43804501	+	Splice_Site	SNP	G	G	A			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr20:43804501G>A	ENST00000243924.3	+	2	126		c.e2-1			NM_002638.3	NP_002629.1	P19957	ELAF_HUMAN	peptidase inhibitor 3, skin-derived						copulation	proteinaceous extracellular matrix	serine-type endopeptidase inhibitor activity			large_intestine(1)|lung(5)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				TCTTTTAACAGTTCCTGTTAA	0.448000													5	75					0	0	1	0	0
IFITM3	10410	broad.mit.edu	37	11	320606	320606	+	Missense_Mutation	SNP	G	G	T	rs149004156	by1000genomes	TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr11:320606G>T	ENST00000399808.4	-	1	444	c.208C>A	c.(208-210)Ccc>Acc	p.P70T	IFITM3_ENST00000602735.1_Missense_Mutation_p.P49T|RP11-326C3.11_ENST00000602756.1_RNA|RP11-326C3.11_ENST00000602429.1_RNA|IFITM3_ENST00000526811.1_Missense_Mutation_p.P49T	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	70	Interaction with SPP1.				response to virus|type I interferon-mediated signaling pathway	integral to membrane|plasma membrane		p.P70T(3)		central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGGCAGCAGGGGTTCATGAAG	0.632000													6	73					0.000442599	0.000442599	1	1	0
HRAS	3265	broad.mit.edu	37	11	533874	533874	+	Missense_Mutation	SNP	T	T	C	rs121913233		TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr11:533874T>C	ENST00000417302.1	-	3	369	c.182A>G	c.(181-183)cAg>cGg	p.Q61R	HRAS_ENST00000397594.1_Missense_Mutation_p.Q61R|HRAS_ENST00000397596.2_Missense_Mutation_p.Q61R|HRAS_ENST00000468682.2_5'UTR|HRAS_ENST00000451590.1_Missense_Mutation_p.Q61R|HRAS_ENST00000311189.7_Missense_Mutation_p.Q61R	NM_176795.3	NP_789765.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	61			Q -> K (in follicular thyroid carcinoma samples; somatic mutation; increases transformation of cultured cell lines; dbSNP:rs28933406).|Q -> L (in melanoma; strongly reduced GTP hydrolysis in the presence of RAF1; increases transformation of cultured cell lines).		activation of MAPKK activity|axon guidance|blood coagulation|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|Ras protein signal transduction|synaptic transmission	cytosol|Golgi membrane|plasma membrane	GTP binding|GTPase activity|protein C-terminus binding	p.Q61R(136)|p.Q61L(117)|p.Q61P(3)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Sulindac(DB00605)	GTACTCCTCCTGGCCGGCGGT	0.597000	Q61L(KNS62_LUNG)|Q61L(KYSE30_OESOPHAGUS)|Q61L(NCIH1915_LUNG)	6	Mis		"""infrequent sarcomas, rare other types"""	"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""			Costello syndrome	HNSCC(11;0.0054)			18	34					0	0	1	0	0
PLEKHG4B	153478	broad.mit.edu	37	5	162009	162009	+	Missense_Mutation	SNP	A	A	G			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr5:162009A>G	ENST00000283426.6	+	10	1581	c.1531A>G	c.(1531-1533)Agg>Ggg	p.R511G		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	511					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GGCTGAGTGCAGGGAGGGAGA	0.632000													7	25					0	0	1	0	0
PLEKHM1P	440456	broad.mit.edu	37	17	62818136	62818136	+	RNA	SNP	G	G	C			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr17:62818136G>C	ENST00000582986.1	-	0	362					NR_024386.1																						CTGAAGAATGGGAAATGGAAT	0.572000													4	39					0	0	1	0	0
PTCHD4	442213	broad.mit.edu	37	6	48036151	48036151	+	Missense_Mutation	SNP	C	C	T			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr6:48036151C>T	ENST00000543600.1	-	1	229	c.190G>A	c.(190-192)Gcc>Acc	p.A64T	PTCHD4_ENST00000339488.4_Missense_Mutation_p.A81T			Q6ZW05	CF138_HUMAN	patched domain containing 4	81						integral to membrane	hedgehog receptor activity										TCGATCTTGGCCAGGCTGTGG	0.652000													3	44					0	0	1	0	0
LOC101927209	101927209	broad.mit.edu	37	1	142713944	142713944	+	RNA	SNP	C	C	T			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr1:142713944C>T	ENST00000369381.2	-	0	661																											TGATTACCTCCGAAGTTAAAG	0.308000													3	30					0	0	1	0	0
SAG	6295	broad.mit.edu	37	2	234243689	234243689	+	Silent	SNP	C	C	T			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr2:234243689C>T	ENST00000409110.1	+	11	1118	c.888C>T	c.(886-888)ggC>ggT	p.G296G	SAG_ENST00000449594.2_Silent_p.G162G	NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	296					rhodopsin mediated phototransduction|rhodopsin mediated signaling pathway		protein phosphatase inhibitor activity			cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		AAAGGAGAGGCATTGCCCTGG	0.542000													22	30					0	0	1	0	0
NBPF15	284565	broad.mit.edu	37	1	148594439	148594439	+	Silent	SNP	A	A	G	rs146739148	byFrequency	TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr1:148594439A>G	ENST00000442702.2	+	21	2879	c.1812A>G	c.(1810-1812)ttA>ttG	p.L604L	NBPF15_ENST00000369187.3_Silent_p.L604L	NM_001170755.1	NP_001164226.1	Q8N660	NBPFF_HUMAN	neuroblastoma breakpoint family, member 15	604	NBPF 6.					cytoplasm				NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12	all_hematologic(923;0.032)					CTGAAGTCTTACAGGACTCAC	0.463000													7	262					0	0	1	0	0
NBPF15	284565	broad.mit.edu	37	1	148594434	148594434	+	Missense_Mutation	SNP	G	G	A	rs143361250	byFrequency	TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr1:148594434G>A	ENST00000442702.2	+	21	2874	c.1807G>A	c.(1807-1809)Gtc>Atc	p.V603I	NBPF15_ENST00000369187.3_Missense_Mutation_p.V603I	NM_001170755.1	NP_001164226.1	Q8N660	NBPFF_HUMAN	neuroblastoma breakpoint family, member 15	603	NBPF 6.					cytoplasm				NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12	all_hematologic(923;0.032)					AGAGCCTGAAGTCTTACAGGA	0.458000													7	258					0	0	1	0	0
PTPN18	26469	broad.mit.edu	37	2	131129929	131129934	+	In_Frame_Del	DEL	GACGGG	GACGGG	-	rs112040677		TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr2:131129929_131129934delGACGGG	ENST00000175756.5	+	13	1214_1219	c.1113_1118delGACGGG	c.(1111-1119)cag>ca	p.QTG371del	PTPN18_ENST00000347849.3_In_Frame_Del_p.QTG264del	NM_014369.3	NP_055184.2	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type 18 (brain-derived)	371						cytoplasm|nucleus	non-membrane spanning protein tyrosine phosphatase activity	p.T378_G379delTG(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)	15	Colorectal(110;0.1)					gtgggacgcagacggggacggggacg	0.777													2	4	---	---	---	---					
THAP4	51078	broad.mit.edu	37	2	242545840	242545840	+	Frame_Shift_Del	DEL	C	C	-			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr2:242545840delC	ENST00000407315.1	-	3	1720	c.1289delG	c.(1288-1290)gcfs	p.G430fs	THAP4_ENST00000402136.1_Frame_Shift_Del_p.G18fs|THAP4_ENST00000402545.1_Frame_Shift_Del_p.G18fs	NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	430							DNA binding|metal ion binding			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)		CAGCCAGGTGCCCAGCATCCA	0.617													2	4	---	---	---	---					
RBPJ	3516	broad.mit.edu	37	4	26417145	26417146	+	Frame_Shift_Ins	INS	-	-	A			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr4:26417145_26417146insA	ENST00000342320.4	+	4	377_378	c.201_202insA	c.(199-204)aaaaaafs	p.KK67fs	RBPJ_ENST00000348160.4_Frame_Shift_Ins_p.KK68fs|RBPJ_ENST00000504907.1_Frame_Shift_Ins_p.KK67fs|RBPJ_ENST00000507561.1_Frame_Shift_Ins_p.KK46fs|RBPJ_ENST00000361572.6_Frame_Shift_Ins_p.KK81fs|RBPJ_ENST00000511401.1_3'UTR|RBPJ_ENST00000355476.3_Frame_Shift_Ins_p.KK67fs|RBPJ_ENST00000342295.1_Frame_Shift_Ins_p.KK81fs|RBPJ_ENST00000345843.3_Frame_Shift_Ins_p.KK66fs			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	81					DNA recombination|negative regulation of transcription, DNA-dependent|positive regulation of transcription of Notch receptor target	cytoplasm|nucleolus|nucleoplasm	DNA binding|protein binding|recombinase activity|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				GTGGATGGAAGAAAAAAAAAGA	0.371													9	111	---	---	---	---					
KIAA1958	158405	broad.mit.edu	37	9	115421618	115421627	+	Frame_Shift_Del	DEL	CTGGCCACCT	CTGGCCACCT	-			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr9:115421618_115421627delCTGGCCACCT	ENST00000337530.6	+	4	1716_1725	c.1420_1429delCTGGCCACCT	c.(1420-1431)cgfs	p.LATS474fs	KIAA1958_ENST00000536272.1_Frame_Shift_Del_p.LATS502fs	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	474										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						CTCGGACTTCCTGGCCACCTCGCTCCATGC	0.543													23	55	---	---	---	---