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
AHNAK	79026	broad.mit.edu	37	11	62287998	62287998	+	Missense_Mutation	SNP	C	C	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr11:62287998C>A	ENST00000378024.4	-	5	14165	c.13891G>T	c.(13891-13893)Gac>Tac	p.D4631Y	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	4631			D -> G (in dbSNP:rs12801123).	RD -> KG (in Ref. 2; AAA69898).	nervous system development	nucleus	protein binding			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				ACTTTGGGGTCCCTGATGTCA	0.522000													100	338					2.6645e-62	3.34771e-62	0.139131	1	0
LGI1	9211	broad.mit.edu	37	10	95557106	95557106	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr10:95557106G>A	ENST00000371418.4	+	8	1480	c.1220G>A	c.(1219-1221)cGt>cAt	p.R407H	LGI1_ENST00000371413.3_Intron|LGI1_ENST00000542308.1_Missense_Mutation_p.R359H	NM_005097.2	NP_005088.1	O95970	LGI1_HUMAN	leucine-rich, glioma inactivated 1	407					axon guidance|cell proliferation|positive regulation of cell growth|positive regulation of synaptic transmission	cell junction|extracellular space|synapse	receptor binding			central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(18)|ovary(2)|skin(1)	29		Colorectal(252;0.124)				AGTTCCCAGCGTCCTGTAATT	0.433000													113	82					0	0	0.139131	0	0
CMA1	1215	broad.mit.edu	37	14	24976583	24976583	+	Missense_Mutation	SNP	G	G	A	rs13306251	by1000genomes	TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr14:24976583G>A	ENST00000250378.3	-	2	217	c.188C>T	c.(187-189)aCg>aTg	p.T63M	CMA1_ENST00000206446.4_Intron|RP11-80A15.1_ENST00000555109.1_Intron	NM_001836.3	NP_001827.1	P23946	CMA1_HUMAN	chymase 1, mast cell	63	Peptidase S1.				interleukin-1 beta biosynthetic process|proteolysis	extracellular region	serine-type endopeptidase activity			kidney(1)|lung(8)|pancreas(1)|prostate(1)	11				GBM - Glioblastoma multiforme(265;0.0271)		ATGAGCAGCCGTCAGCACAAA	0.488000													83	163					0	0	0.139131	0	0
NEBL	10529	broad.mit.edu	37	10	21097515	21097515	+	Silent	SNP	G	G	A	rs140245727	byFrequency	TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr10:21097515G>A	ENST00000377122.4	-	26	3081	c.2685C>T	c.(2683-2685)gaC>gaT	p.D895D	NEBL_ENST00000377159.4_Intron|NEBL_ENST00000417816.2_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	895	Linker.				regulation of actin filament length		actin binding|structural constituent of muscle			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						CTGACCTGTCGTCTCCGAGAC	0.458000													7	331					0	0	0.038147	0	0
FYCO1	79443	broad.mit.edu	37	3	46014621	46014621	+	Silent	SNP	C	C	T	rs149291592	byFrequency	TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr3:46014621C>T	ENST00000296137.2	-	6	703	c.498G>A	c.(496-498)tcG>tcA	p.S166S	FYCO1_ENST00000535325.1_Silent_p.S166S	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	166	RUN.				transport	integral to membrane	metal ion binding|protein binding			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CAAAGCCCCTCGACGCCAGGT	0.483000													26	74					0	0	0.091800	0	0
CNGA1	1259	broad.mit.edu	37	4	47938995	47938995	+	Missense_Mutation	SNP	T	T	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr4:47938995T>A	ENST00000402813.3	-	10	1865	c.1723A>T	c.(1723-1725)Att>Ttt	p.I575F	CNGA1_ENST00000544810.1_Missense_Mutation_p.I506F|CNGA1_ENST00000514170.1_Missense_Mutation_p.I506F|CNGA1_ENST00000420489.2_Missense_Mutation_p.I506F|CNGA1_ENST00000358519.4_Missense_Mutation_p.I506F			P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1	506					response to stimulus|visual perception	integral to plasma membrane	cGMP binding|ion channel activity			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1)	28						TTCTTGCAAATATAATCTCCA	0.438000													16	283					0	0	0.160694	0	0
AKNA	80709	broad.mit.edu	37	9	117139492	117139492	+	Missense_Mutation	SNP	T	T	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr9:117139492T>C	ENST00000307564.4	-	3	756	c.595A>G	c.(595-597)Agg>Ggg	p.R199G	AKNA_ENST00000374075.5_Missense_Mutation_p.R118G|AKNA_ENST00000374088.3_Missense_Mutation_p.R199G|AKNA_ENST00000312033.3_Missense_Mutation_p.R199G	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	199					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						CTCCAGGACCTTGCCGGGCTG	0.612000													87	61					0	0	0.139131	0	0
PKHD1	5314	broad.mit.edu	37	6	51513908	51513908	+	Missense_Mutation	SNP	G	G	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr6:51513908G>T	ENST00000371117.3	-	62	11560	c.11285C>A	c.(11284-11286)cCa>cAa	p.P3762Q		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3762					cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TACCAATTGTGGCTGCACTGG	0.413000													82	132					1.55521e-42	1.85866e-42	0.139131	1	0
KLF11	8462	broad.mit.edu	37	2	10188340	10188340	+	Silent	SNP	G	G	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:10188340G>T	ENST00000535335.1	+	3	1041	c.825G>T	c.(823-825)gtG>gtT	p.V275V	KLF11_ENST00000540845.1_Silent_p.V275V|KLF11_ENST00000305883.1_Silent_p.V292V	NM_001177718.1	NP_001171189.1	O14901	KLF11_HUMAN	Kruppel-like factor 11	292					apoptosis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|regulation of transcription involved in S phase of mitotic cell cycle	nucleus	sequence-specific DNA binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.133)|OV - Ovarian serous cystadenocarcinoma(76;0.228)		TGATCCCTGTGACTGGACAAA	0.537000											OREG0014425	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	195					0.0381472	0.038942	0.038147	1	0
PHF3	23469	broad.mit.edu	37	6	64356551	64356551	+	Missense_Mutation	SNP	A	A	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr6:64356551A>G	ENST00000262043.3	+	2	435	c.95A>G	c.(94-96)gAg>gGg	p.E32G	PHF3_ENST00000393387.1_Missense_Mutation_p.E32G|PHF3_ENST00000509330.1_Missense_Mutation_p.E32G			Q92576	PHF3_HUMAN	PHD finger protein 3	32					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GAAGTCTGTGAGGATTTTAGT	0.393000													49	143					0	0	0.139131	0	0
PAX6	5080	broad.mit.edu	37	11	31815341	31815341	+	Missense_Mutation	SNP	A	A	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr11:31815341A>G	ENST00000419022.1	-	11	1285	c.817T>C	c.(817-819)Tct>Cct	p.S273P	PAX6_ENST00000241001.8_Missense_Mutation_p.S259P|PAX6_ENST00000379129.2_Missense_Mutation_p.S273P|PAX6_ENST00000379107.2_Missense_Mutation_p.S273P|PAX6_ENST00000379123.5_Missense_Mutation_p.S259P|PAX6_ENST00000379132.3_Missense_Mutation_p.S259P|PAX6_ENST00000379111.2_Missense_Mutation_p.S259P|PAX6_ENST00000379115.4_Missense_Mutation_p.S273P	NM_001127612.1|NM_001258462.1|NM_001258463.1	NP_001121084.1|NP_001245391.1|NP_001245392.1	P26367	PAX6_HUMAN	paired box 6	259					blood vessel development|central nervous system development|cornea development in camera-type eye|glucose homeostasis|iris morphogenesis|negative regulation of neurogenesis|neuron fate commitment|pancreatic A cell development|positive regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|ubiquitin-protein ligase activity			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)	35	Lung SC(675;0.225)					CTTCGATTAGAAAACCATACC	0.522000									Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation				78	5					0	0	0.139131	0	0
MAN2A2	4122	broad.mit.edu	37	15	91450665	91450665	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr15:91450665G>A	ENST00000360468.3	+	7	1154	c.1136G>A	c.(1135-1137)cGc>cAc	p.R379H	MAN2A2_ENST00000559717.1_Missense_Mutation_p.R379H|MAN2A2_ENST00000431652.2_5'UTR	NM_006122.2	NP_006113.2	P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	379					mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			CCTGGTGGGCGCATCAACTGC	0.567000													5	184					0	0	0.014758	0	0
STK3	6788	broad.mit.edu	37	8	99779474	99779474	+	Missense_Mutation	SNP	T	T	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr8:99779474T>C	ENST00000523601.1	-	5	716	c.317A>G	c.(316-318)gAc>gGc	p.D106G	STK3_ENST00000419617.2_Missense_Mutation_p.D78G	NM_001256312.1	NP_001243241.1	Q13188	STK3_HUMAN	serine/threonine kinase 3	78	Protein kinase.				apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)		TTCATACCTGTCACATTGCTG	0.313000													54	60					0	0	0.139131	0	0
NAT8	9027	broad.mit.edu	37	2	73868641	73868641	+	Missense_Mutation	SNP	G	G	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:73868641G>C	ENST00000272425.3	-	2	264	c.115C>G	c.(115-117)Ctg>Gtg	p.L39V		NM_003960.3|NM_016347.2	NP_003951.3|NP_057431.2	Q9UHE5	NAT8_HUMAN	N-acetyltransferase 8 (GCN5-related, putative)	39					gastrulation with mouth forming second|response to drug	integral to membrane	N-acetyltransferase activity			breast(1)|endometrium(2)|kidney(2)|lung(2)|ovary(1)|prostate(1)	9						GTTCGAGGCAGCTTCAGCAAT	0.622000													63	209					0	0	0.139131	0	0
ALMS1	7840	broad.mit.edu	37	2	73718168	73718168	+	Missense_Mutation	SNP	T	T	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:73718168T>G	ENST00000264448.6	+	10	9190	c.9079T>G	c.(9079-9081)Tgt>Ggt	p.C3027G	ALMS1_ENST00000409009.1_Missense_Mutation_p.C2985G	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3027					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CCCAAATCACTGTACATTAGC	0.378000													64	195					0	0	0.139131	0	0
CHAT	1103	broad.mit.edu	37	10	50901834	50901834	+	Nonstop_Mutation	SNP	G	G	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr10:50901834G>T	ENST00000455728.2	+	15	1748	c.1638G>T	c.(1636-1638)taG>taT	p.*546Y	C10orf53_ENST00000535836.1_Missense_Mutation_p.D38Y|C10orf53_ENST00000374113.3_Missense_Mutation_p.D38Y|C10orf53_ENST00000374112.3_Missense_Mutation_p.D38Y|C10orf53_ENST00000374111.3_Missense_Mutation_p.D38Y			P28329	CLAT_HUMAN	choline O-acetyltransferase	0					neurotransmitter biosynthetic process|neurotransmitter secretion	cytosol|nucleus	choline O-acetyltransferase activity			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)	GTTGGCCATAGATGGACATGA	0.463000													12	127					2.27111e-07	2.52919e-07	0.093190	1	0
PCSK5	5125	broad.mit.edu	37	9	78965754	78965754	+	Silent	SNP	G	G	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr9:78965754G>A	ENST00000545128.1	+	35	5434	c.4896G>A	c.(4894-4896)gcG>gcA	p.A1632A		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	797					anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						GAAAAGGAGCGTTGAATTGTT	0.448000													129	128					0	0	0.139131	0	0
COL25A1	84570	broad.mit.edu	37	4	109765700	109765700	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr4:109765700C>T	ENST00000399132.1	-	30	2134	c.1604G>A	c.(1603-1605)gGt>gAt	p.G535D	COL25A1_ENST00000399127.1_Missense_Mutation_p.G508D|COL25A1_ENST00000399126.1_Missense_Mutation_p.G535D	NM_198721.2	NP_942014.1	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1	535						collagen|extracellular space	beta-amyloid binding|heparin binding			NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		gccatggggacctggtgggcc	0.433000													48	100					0	0	0.139131	0	0
ETAA1	54465	broad.mit.edu	37	2	67631847	67631847	+	Missense_Mutation	SNP	A	A	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:67631847A>G	ENST00000272342.5	+	5	2163	c.2033A>G	c.(2032-2034)aAc>aGc	p.N678S	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	678						cytoplasm|nucleus				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						GGAGCCAAAAACATGTTTGCT	0.363000													90	110					0	0	0.139131	0	0
MMP19	4327	broad.mit.edu	37	12	56233333	56233333	+	Missense_Mutation	SNP	C	C	T	rs138516871		TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr12:56233333C>T	ENST00000322569.4	-	5	804	c.713G>A	c.(712-714)cGg>cAg	p.R238Q	MMP19_ENST00000548629.1_Missense_Mutation_p.R215Q|MMP19_ENST00000409200.3_Intron	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	238					angiogenesis|cell differentiation|collagen catabolic process|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26						AAAGTGGGGCCGGTAGCCCTC	0.617000													18	63					0	0	0.043863	0	0
KIAA1407	57577	broad.mit.edu	37	3	113761686	113761686	+	Silent	SNP	C	C	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr3:113761686C>T	ENST00000295878.3	-	4	425	c.279G>A	c.(277-279)gaG>gaA	p.E93E	KIAA1407_ENST00000545063.1_5'UTR|KIAA1407_ENST00000480588.1_5'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	93										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						CATTGACCAGCTCCTGAGCTA	0.333000													48	137					0	0	0.139131	0	0
GBP3	2635	broad.mit.edu	37	1	89486247	89486247	+	Missense_Mutation	SNP	T	T	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr1:89486247T>C	ENST00000370481.4	-	2	378	c.158A>G	c.(157-159)tAc>tGc	p.Y53C	GBP3_ENST00000475853.2_5'UTR	NM_018284.2	NP_060754.2	Q9H0R5	GBP3_HUMAN	guanylate binding protein 3	53						integral to membrane	GTP binding|GTPase activity			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		GTTCATCAGGTAGGATTTTCC	0.517000													30	159					0	0	0.116897	0	0
OSGIN1	29948	broad.mit.edu	37	16	83994303	83994303	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr16:83994303C>T	ENST00000343939.2	+	5	966	c.583C>T	c.(583-585)Cgg>Tgg	p.R195W	OSGIN1_ENST00000361711.3_Missense_Mutation_p.R112W|OSGIN1_ENST00000565123.1_Missense_Mutation_p.R112W|OSGIN1_ENST00000393306.1_Missense_Mutation_p.R112W			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	195					cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						CTGGAAGCACCGGAAGGAGCA	0.657000													21	101					0	0	0.069288	0	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393000			Mis		gliobastoma								107	83					0	0	0.139131	0	0
RPS6KA1	6195	broad.mit.edu	37	1	26898350	26898350	+	Missense_Mutation	SNP	G	G	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr1:26898350G>T	ENST00000374168.2	+	19	1917	c.1763G>T	c.(1762-1764)cGc>cTc	p.R588L	RPS6KA1_ENST00000526792.1_Missense_Mutation_p.R496L|RPS6KA1_ENST00000530003.1_Missense_Mutation_p.R572L|RPS6KA1_ENST00000374166.4_Missense_Mutation_p.R577L|RPS6KA1_ENST00000531382.1_Missense_Mutation_p.R597L|RPS6KA1_ENST00000374162.2_Missense_Mutation_p.R496L	NM_002953.3	NP_002944.2	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 1	588	Protein kinase 2.				axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		GTGCTGAAGCGCCAGGGCTAC	0.627000													27	35					3.00307e-07	3.27001e-07	0.134883	1	0
EPHA3	2042	broad.mit.edu	37	3	89448615	89448615	+	Nonsense_Mutation	SNP	G	G	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr3:89448615G>T	ENST00000336596.2	+	7	1804	c.1579G>T	c.(1579-1581)Gaa>Taa	p.E527*	EPHA3_ENST00000452448.2_Nonsense_Mutation_p.E527*|EPHA3_ENST00000494014.1_Nonsense_Mutation_p.E527*	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	527	Fibronectin type-III 2.					extracellular region|integral to plasma membrane	ATP binding			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		GTTTGAGTTTGAAACTAGTCC	0.448000										TSP Lung(6;0.00050)			30	92					1.57351e-24	1.79307e-24	0.064281	1	0
ALKBH6	84964	broad.mit.edu	37	19	36501795	36501795	+	Splice_Site	SNP	C	C	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr19:36501795C>T	ENST00000486389.1	-	4	1016		c.e4+1		ALKBH6_ENST00000485128.1_Splice_Site|ALKBH6_ENST00000252984.7_Splice_Site|ALKBH6_ENST00000378875.3_Splice_Site|ALKBH6_ENST00000495116.2_Intron|AC002116.8_ENST00000473572.2_RNA			Q3KRA9	ALKB6_HUMAN	alkB, alkylation repair homolog 6 (E. coli)							cytoplasm|nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1)	9	all_lung(56;1.35e-06)|Lung NSC(56;2.15e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TGTGTGGTTACCATGATGCCC	0.592000													35	88					0	0	0.183431	0	0
DPAGT1	1798	broad.mit.edu	37	11	118971495	118971495	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr11:118971495G>A	ENST00000409993.2	-	5	1892	c.341C>T	c.(340-342)gCg>gTg	p.A114V	DPAGT1_ENST00000354202.4_Missense_Mutation_p.A114V|DPAGT1_ENST00000432443.2_Missense_Mutation_p.A7V|DPAGT1_ENST00000445653.1_5'UTR			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	114					dolichol biosynthetic process|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|protein oligomerization	integral to endoplasmic reticulum membrane|microsome	phospho-N-acetylmuramoyl-pentapeptide-transferase activity|transferase activity, transferring glycosyl groups|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		TACATCATCCGCAAAGCCCAG	0.567000											OREG0021396	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	115					0	0	0.150653	0	0
CSMD3	114788	broad.mit.edu	37	8	113988170	113988170	+	Missense_Mutation	SNP	T	T	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr8:113988170T>C	ENST00000297405.5	-	7	1482	c.1238A>G	c.(1237-1239)gAc>gGc	p.D413G	CSMD3_ENST00000352409.3_Missense_Mutation_p.D413G|CSMD3_ENST00000343508.3_Missense_Mutation_p.D373G|CSMD3_ENST00000455883.2_Intron	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	413						integral to membrane|plasma membrane				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AGAGAGCCCGTCCTTGGACGT	0.478000										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			73	265					0	0	0.139131	0	0
ANKRD36	375248	broad.mit.edu	37	2	97875420	97875420	+	Missense_Mutation	SNP	T	T	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:97875420T>G	ENST00000420699.2	+	55	3512	c.3268T>G	c.(3268-3270)Tct>Gct	p.S1090A	ANKRD36_ENST00000461153.2_Missense_Mutation_p.S1090A	NM_001164315.1	NP_001157787.1	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	1090										endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						CTTTTCAGTGTCTTCTCGGAA	0.358000													14	95					0	0	0.043863	0	0
TP53	7157	broad.mit.edu	37	17	7578550	7578550	+	Missense_Mutation	SNP	G	G	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr17:7578550G>T	ENST00000420246.2	-	5	512	c.380C>A	c.(379-381)tCc>tAc	p.S127Y	TP53_ENST00000269305.4_Missense_Mutation_p.S127Y|TP53_ENST00000445888.2_Missense_Mutation_p.S127Y|TP53_ENST00000413465.2_Missense_Mutation_p.S127Y|TP53_ENST00000455263.2_Missense_Mutation_p.S127Y|TP53_ENST00000359597.4_Missense_Mutation_p.S127Y	NM_001126114.2|NM_001276696.1	NP_001119586.1|NP_001263625.1	P04637	P53_HUMAN	tumor protein p53	127	Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Required for interaction with FBXO42.		S -> C (in a sporadic cancer; somatic mutation).|S -> F (in sporadic cancers; somatic mutation).|S -> P (in sporadic cancers; somatic mutation).|S -> T (in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.S127F(23)|p.0?(8)|p.S127Y(8)|p.S127C(7)|p.Y126_K132delYSPALNK(6)|p.A129fs*20(3)|p.Y126_N131delYSPALN(3)|p.S34C(2)|p.P128fs*42(2)|p.V73fs*9(1)|p.S127fs*36(1)|p.P128fs*18(1)|p.Y126fs*11(1)|p.S127_Q136del10(1)|p.P13fs*18(1)|p.?(1)|p.S34F(1)|p.A36fs*20(1)|p.S127fs*42(1)|p.Y126fs*18(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GAGGGCAGGGGAGTACTGTAG	0.552000		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			44	0					1.00001e-27	1.16667e-27	0.111260	1	0
RINT1	60561	broad.mit.edu	37	7	105189063	105189063	+	Missense_Mutation	SNP	C	C	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr7:105189063C>A	ENST00000257700.2	+	7	1133	c.902C>A	c.(901-903)tCt>tAt	p.S301Y		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	301	RINT1/TIP20.				cell cycle|G2/M transition DNA damage checkpoint|protein transport|vesicle-mediated transport	endoplasmic reticulum membrane	protein binding			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GCCTCCCCTTCTGTCATCCTG	0.443000													98	347					9.15355e-43	1.12131e-42	0.139131	1	0
ABCB10	23456	broad.mit.edu	37	1	229685030	229685030	+	Silent	SNP	C	C	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr1:229685030C>G	ENST00000344517.4	-	2	711	c.669G>C	c.(667-669)ctG>ctC	p.L223L		NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	223	ABC transmembrane type-1.					integral to mitochondrial membrane|mitochondrial inner membrane	ATP binding|oligopeptide-transporting ATPase activity			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				CAGCACCACACAGAAACACGG	0.522000													15	68					0	0	0.062417	0	0
EIF2AK4	440275	broad.mit.edu	37	15	40258023	40258023	+	Silent	SNP	G	G	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr15:40258023G>A	ENST00000263791.5	+	8	1039	c.996G>A	c.(994-996)aaG>aaA	p.K332K	EIF2AK4_ENST00000382727.2_Silent_p.K332K|EIF2AK4_ENST00000559624.1_Silent_p.K332K	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	332	Protein kinase 1.				translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		AAAAAGAGAAGATTGATAAGT	0.443000													37	115					0	0	0.069456	0	0
ATRX	546	broad.mit.edu	37	X	76814313	76814313	+	Nonsense_Mutation	SNP	G	G	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chrX:76814313G>A	ENST00000373344.5	-	29	6545	c.6331C>T	c.(6331-6333)Cga>Tga	p.R2111*	ATRX_ENST00000395603.3_Nonsense_Mutation_p.R2073*|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2111	Helicase C-terminal.				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	p.R2111*(1)|p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145					Phosphatidylserine(DB00144)	ATAAATAATCGTCCTCTGAAA	0.274000			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome						69	1					0	0	0.139131	0	0
PLEC	5339	broad.mit.edu	37	8	145007212	145007212	+	Missense_Mutation	SNP	C	C	T			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr8:145007212C>T	ENST00000322810.4	-	14	2066	c.1897G>A	c.(1897-1899)Gtg>Atg	p.V633M	PLEC_ENST00000345136.3_Missense_Mutation_p.V496M|PLEC_ENST00000398774.2_Missense_Mutation_p.V464M|PLEC_ENST00000356346.3_Missense_Mutation_p.V482M|PLEC_ENST00000527096.1_Missense_Mutation_p.V519M|PLEC_ENST00000354589.3_Missense_Mutation_p.V496M|PLEC_ENST00000357649.2_Missense_Mutation_p.V500M|PLEC_ENST00000436759.2_Missense_Mutation_p.V523M|PLEC_ENST00000354958.2_Missense_Mutation_p.V474M	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	633	Globular 1.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GGGGCCGCCACGCCTGCCTTC	0.662000													3	4					0	0	0.069234	0	0
MAP3K5	4217	broad.mit.edu	37	6	136932510	136932510	+	Missense_Mutation	SNP	T	T	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr6:136932510T>C	ENST00000359015.4	-	18	2791	c.2431A>G	c.(2431-2433)Att>Gtt	p.I811V	MAP3K5_ENST00000355845.4_Missense_Mutation_p.I58V	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	811	Protein kinase.				activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		TAGGTATTAATCAACACATTG	0.368000													7	123					0	0	0.029380	0	0
KCNJ13	3769	broad.mit.edu	37	2	233633140	233633140	+	Missense_Mutation	SNP	A	A	G			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:233633140A>G	ENST00000233826.3	-	3	983	c.844T>C	c.(844-846)Tgc>Cgc	p.C282R	GIGYF2_ENST00000373563.4_Intron|GIGYF2_ENST00000452341.2_Intron|GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000409547.1_Intron|KCNJ13_ENST00000409779.1_3'UTR|GIGYF2_ENST00000373566.3_Intron|GIGYF2_ENST00000409451.3_Intron|KCNJ13_ENST00000410029.1_Missense_Mutation_p.C282R	NM_002242.4	NP_002233.2	O60928	IRK13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	282						voltage-gated potassium channel complex	inward rectifier potassium channel activity			endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		CTCCTTTGGCATATTTCTCCA	0.433000													131	120					0	0	0.139131	0	0
HECW2	57520	broad.mit.edu	37	2	197298053	197298053	+	Missense_Mutation	SNP	G	G	A			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr2:197298053G>A	ENST00000260983.3	-	2	277	c.95C>T	c.(94-96)gCc>gTc	p.A32V		NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						GCTCTGGGCGGCAAGGCTCTG	0.602000													5	231					0	0	0.014758	0	0
C3orf52	79669	broad.mit.edu	37	3	111835572	111835572	+	Frame_Shift_Del	DEL	G	G	-			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr3:111835572delG	ENST00000431717.2	+	4	553	c.480delG	c.(478-480)cagfs	p.Q160fs	C3orf52_ENST00000430855.1_Intron|C3orf52_ENST00000467942.2_3'UTR|C3orf52_ENST00000264848.5_3'UTR	NM_001171747.1	NP_001165218.1	Q5BVD1	TTMP_HUMAN	chromosome 3 open reading frame 52	0						endoplasmic reticulum membrane|integral to membrane				endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						CTGTTTTGCAGAAAAGATTCT	0.458													7	8	---	---	---	---					
CCNB3P1	100131678	broad.mit.edu	37	5	26740947	26740949	+	RNA	DEL	TTT	TTT	-			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr5:26740947_26740949delTTT	ENST00000506032.1	-	0	125																											AATCttcttcttttttttttttt	0.478													2	4	---	---	---	---					
RP11-436D23.1	0	broad.mit.edu	37	6	98715362	98715377	+	RNA	DEL	TCCTTCCTTCCTTCCT	TCCTTCCTTCCTTCCT	-	rs59041540		TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr6:98715362_98715377delTCCTTCCTTCCTTCCT	ENST00000607823.1	+	0	352																											AAAGAttctctccttccttccttccttccttccttc	0.375													3	5	---	---	---	---					
LOC100507283	100507283	broad.mit.edu	37	11	124672250	124672251	+	RNA	DEL	GT	GT	-	rs60473155		TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr11:124672250_124672251delGT	ENST00000499143.2	+	0	981				RP11-677M14.7_ENST00000529392.1_RNA	NR_103862.1																						CCAAAGAGGGgtgtgtgtgtgt	0.460													3	3	---	---	---	---					
RP11-314D7.1	0	broad.mit.edu	37	12	73525130	73525130	+	RNA	DEL	A	A	-			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr12:73525130delA	ENST00000551135.1	-	0	104																											accctgtctgaaaaaaaaaga	0.443													3	6	---	---	---	---					
DYNLL1	8655	broad.mit.edu	37	12	120935907	120935908	+	Frame_Shift_Ins	INS	-	-	TT	rs142458935	by1000genomes	TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr12:120935907_120935908insTT	ENST00000392509.2	+	3	425_426	c.164_165insTT	c.(163-168)cattgcfs	p.C56fs	DYNLL1_ENST00000548342.1_Frame_Shift_Ins_p.C56fs|DYNLL1_ENST00000549989.1_Frame_Shift_Ins_p.C56fs|DYNLL1_ENST00000392508.2_Frame_Shift_Ins_p.C56fs|DYNLL1_ENST00000552316.1_3'UTR|DYNLL1_ENST00000552870.1_Intron|DYNLL1_ENST00000242577.6_Frame_Shift_Ins_p.C56fs	NM_001037494.1	NP_001032583.1	P63167	DYL1_HUMAN	dynein, light chain, LC8-type 1	56					actin cytoskeleton organization|activation of pro-apoptotic gene products|anatomical structure morphogenesis|female gamete generation|G2/M transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|microtubule-based process|negative regulation of phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transport	centrosome|cytoplasmic dynein complex|cytosol|microtubule|mitochondrion|nucleus|plasma membrane	motor activity|protein binding					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCCACCTGGCATTGCATCGTGG	0.426													35	58	---	---	---	---					
TPTE2P1	646405	broad.mit.edu	37	13	25525716	25525716	+	RNA	DEL	A	A	-			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr13:25525716delA	ENST00000429698.1	-	0	282																											TGGAAGAAACAAAAAAAAGAA	0.383													6	3	---	---	---	---					
GSE1	23199	broad.mit.edu	37	16	85682289	85682290	+	Frame_Shift_Ins	INS	-	-	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chr16:85682289_85682290insC	ENST00000253458.7	+	3	534_535	c.358_359insC	c.(358-360)accfs	p.T120fs	GSE1_ENST00000405402.2_Frame_Shift_Ins_p.T16fs|GSE1_ENST00000393243.1_Frame_Shift_Ins_p.T47fs	NM_014615.2	NP_055430.1			Gse1 coiled-coil protein									p.V123fs*2(1)									CGTGCCCAGCACCCCCCCCGTG	0.688													8	197	---	---	---	---					
IRS4	8471	broad.mit.edu	37	X	107977802	107977803	+	Frame_Shift_Ins	INS	-	-	C			TCGA-E1-5304-01A-01D-1468-08	TCGA-E1-5304-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e6b925bf-a091-4254-ad24-d1581fa66cb1	81f4e278-bb3d-4621-886b-5e03e7205291	g.chrX:107977802_107977803insC	ENST00000372129.2	-	1	1848_1849	c.1772_1773insG	c.(1771-1773)ggcfs	p.G591fs		NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	591						plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						CTGAGCCTTTGCCCCCCCCAGA	0.545													8	421	---	---	---	---					
