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	Genome_Change	Annotation_Transcript	Transcript_Strand	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	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
TLL2	7093	broad.mit.edu	36	10	98145073	98145073	+	Silent	SNP	C	T	T			TCGA-06-0221-01	TCGA-06-0221-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:98145073C>T	uc001kml.1	-	c.1587G>A	c.(1585-1587)ACG>ACA	p.T529T	TLL2_uc009xvf.1_Silent_p.T507T	NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	529	CUB 2.				cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(252;0.0846)												0.397849	110.659556	111.507256	37	56	CC		KEEP	---	---	---	---	capture		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)	Silent	SNP	98145073	98145073	16476	10	C	T	T	23	23	TLL2	T	1	1
KRT2	3849	broad.mit.edu	36	12	51331909	51331909	+	Silent	SNP	A	G	G			TCGA-06-0221-01	TCGA-06-0221-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51331909A>G	uc001sat.1	-	c.285T>C	c.(283-285)GGT>GGC	p.G95G		NM_000423	NP_000414	P35908	K22E_HUMAN	keratin 2	95	Head.				keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton			ovary(2)	2														0.25	7.955234	8.901553	4	12	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.19)	Silent	SNP	51331909	51331909	8772	12	A	G	G	2	2	KRT2	G	4	4
KRT1	3848	broad.mit.edu	36	12	51358737	51358737	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0221-01	TCGA-06-0221-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51358737G>T	uc001sau.1	-	c.662C>A	c.(661-663)TCC>TAC	p.S221Y	KRT1_uc001sav.1_Missense_Mutation_p.S221Y	NM_006121	NP_006112	P04264	K2C1_HUMAN	keratin 1	221	Rod.|Linker 1.				complement activation, lectin pathway|epidermis development|fibrinolysis|regulation of angiogenesis|response to oxidative stress	plasma membrane	protein binding|receptor activity|structural constituent of cytoskeleton|sugar binding			ovary(1)	1														0.456	161.750772	161.962646	57	68	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51358737	51358737	8762	12	G	T	T	41	41	KRT1	T	3	3
MGA	23269	broad.mit.edu	36	15	39841668	39841668	+	Silent	SNP	A	G	G			TCGA-06-0221-01	TCGA-06-0221-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:39841668A>G	uc001zoh.1	+	c.7707A>G	c.(7705-7707)AAA>AAG	p.K2569K		NM_001080541	NP_001074010	Q8IWI9	MGAP_HUMAN	MAX gene associated	2481					regulation of transcription, DNA-dependent	MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|skin(1)	11		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)								606				0.232558	28.62738	31.443884	10	33	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Silent	SNP	39841668	39841668	9930	15	A	G	G	2	2	MGA	G	4	4
SALL1	6299	broad.mit.edu	36	16	49730567	49730567	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0221-01	TCGA-06-0221-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:49730567G>A	uc002egt.2	-	c.3067C>T	c.(3067-3069)CAT>TAT	p.H1023Y	SALL1_uc010cbt.1_Missense_Mutation_p.H926Y|SALL1_uc010cbu.1_Missense_Mutation_p.H1023Y|SALL1_uc010cbv.1_Intron	NM_001127892	NP_001121364	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform b	1023	C2H2-type 6.				adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription repressor activity|zinc ion binding			ovary(3)	3		all_cancers(37;0.0322)				GBM(103;1352 1446 1855 4775 8890)								0.333333	117.146654	120.398611	44	88	GG		KEEP	---	---	---	---	capture	COAD - Colon adenocarcinoma(2;0.24)		Missense_Mutation	SNP	49730567	49730567	14290	16	G	A	A	45	45	SALL1	A	2	2
MTSS1L	92154	broad.mit.edu	36	16	69271437	69271437	+	Silent	SNP	C	G	G			TCGA-06-0221-01	TCGA-06-0221-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69271437C>G	uc002ezj.1	-	c.228G>C	c.(226-228)TCG>TCC	p.S76S	MTSS1L_uc002ezk.1_5'UTR	NM_138383	NP_612392	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	76	IMD.				filopodium assembly|signal transduction		actin binding|cytoskeletal adaptor activity|SH3 domain binding			central_nervous_system(1)	1														0.428571	8.523792	8.554945	3	4	CC		KEEP	---	---	---	---	capture			Silent	SNP	69271437	69271437	10356	16	C	G	G	23	23	MTSS1L	G	3	3
CALR3	125972	broad.mit.edu	36	19	16454329	16454329	+	Missense_Mutation	SNP	C	T	T	rs10404156	by-cluster,by-hapmap	TCGA-06-0221-01	TCGA-06-0221-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:16454329C>T	uc002ned.2	-	c.850G>A	c.(850-852)GAC>AAC	p.D284N	MED26_uc002nee.2_Non-coding_Transcript	NM_145046	NP_659483	Q96L12	CALR3_HUMAN	calreticulin 3	284	P-domain.				protein folding	endoplasmic reticulum lumen	calcium ion binding|sugar binding|unfolded protein binding				0														0.407821	222.088907	223.403632	73	106	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16454329	16454329	2710	19	C	T	T	31	31	CALR3	T	1	1
HOMER3	9454	broad.mit.edu	36	19	18910592	18910592	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0221-01	TCGA-06-0221-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18910592T>C	uc002nku.1	-	c.116A>G	c.(115-117)TAT>TGT	p.Y39C	HOMER3_uc010eby.1_Missense_Mutation_p.Y39C|HOMER3_uc010ebz.1_Missense_Mutation_p.Y39C|HOMER3_uc002nkv.1_Missense_Mutation_p.Y39C|HOMER3_uc002nkw.1_Missense_Mutation_p.Y39C	NM_004838	NP_004829	Q9NSC5	HOME3_HUMAN	Homer, neuronal immediate early gene, 3	39	WH1.				metabotropic glutamate receptor signaling pathway|protein targeting	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	protein binding				0														0.25	8.924422	9.602619	3	9	TT		KEEP	---	---	---	---	capture	Epithelial(12;0.0107)		Missense_Mutation	SNP	18910592	18910592	7572	19	T	C	C	49	49	HOMER3	C	4	4
ZNF254	9534	broad.mit.edu	36	19	24102506	24102506	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0221-01	TCGA-06-0221-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:24102506A>G	uc002nru.1	+	c.1864A>G	c.(1864-1866)AGA>GGA	p.R622G		NM_203282	NP_975011	O75437	ZN254_HUMAN	zinc finger protein 254	622	C2H2-type 15.				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)												0.6	451.858677	453.650539	123	82	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24102506	24102506	18389	19	A	G	G	11	11	ZNF254	G	4	4
C19orf29	58509	broad.mit.edu	36	19	3564138	3564138	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0221-01	TCGA-06-0221-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3564138C>G	uc002lyh.1	-	c.1704G>C	c.(1702-1704)GAG>GAC	p.E568D	C19orf29_uc010dtn.1_Missense_Mutation_p.E416D|C19orf29_uc002lyi.2_Missense_Mutation_p.E568D|C19orf29_uc010dto.1_Non-coding_Transcript	NM_001080543	NP_001074012	Q8WUQ7	CS029_HUMAN	chromosome 19 open reading frame 29	568					nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome	protein binding				0		Hepatocellular(1079;0.137)												0.444444	8.24999	8.280517	4	5	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	3564138	3564138	1981	19	C	G	G	28	28	C19orf29	G	3	3
LYPD5	284348	broad.mit.edu	36	19	48994512	48994512	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0221-01	TCGA-06-0221-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:48994512G>C	uc002oxm.2	-	c.452C>G	c.(451-453)TCC>TGC	p.S151C	LYPD5_uc002oxn.2_Missense_Mutation_p.S108C	NM_001031749	NP_001026919	Q6UWN5	LYPD5_HUMAN	LY6/PLAUR domain containing 5 isoform A	151	UPAR/Ly6.					anchored to membrane|plasma membrane					0		Prostate(69;0.0352)												0.147059	11.735923	19.856587	10	58	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48994512	48994512	9490	19	G	C	C	41	41	LYPD5	C	3	3
PRR12	57479	broad.mit.edu	36	19	54788411	54788411	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0221-01	TCGA-06-0221-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54788411C>G	uc002poo.2	+	c.102C>G	c.(100-102)AGC>AGG	p.S34R		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	Error:Variant_position_missing_in_Q9ULL5_after_alignment							DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)												0.5	10.063017	10.063017	5	5	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)	Missense_Mutation	SNP	54788411	54788411	13027	19	C	G	G	28	28	PRR12	G	3	3
SIGLEC11	114132	broad.mit.edu	36	19	55153518	55153518	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0221-01	TCGA-06-0221-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55153518C>A	uc002pre.1	-	c.1449G>T	c.(1447-1449)GAG>GAT	p.E483D	SIGLEC11_uc010enr.1_Intron	NM_052884	NP_443116	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11 isoform 1	495	Extracellular (Potential).				cell adhesion	integral to membrane	sugar binding			ovary(3)|central_nervous_system(2)|pancreas(1)	6		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)												0.347826	20.492248	20.962687	8	15	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)	Missense_Mutation	SNP	55153518	55153518	14802	19	C	A	A	24	24	SIGLEC11	A	3	3
BCAS2	10286	broad.mit.edu	36	1	114925727	114925727	+	Silent	SNP	G	C	C			TCGA-06-0221-01	TCGA-06-0221-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:114925727G>C	uc001efa.1	-	c.9C>G	c.(7-9)GGC>GGG	p.G3G	DENND2C_uc001eez.2_Intron	NM_005872	NP_005863	O75934	SPF27_HUMAN	breast carcinoma amplified sequence 2	3					mRNA processing|RNA splicing, via transesterification reactions	nucleolus|spliceosomal complex	protein binding			large_intestine(1)	1	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)												0.25	6.717782	7.400909	3	9	GG		KEEP	---	---	---	---	capture		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Silent	SNP	114925727	114925727	1372	1	G	C	C	46	46	BCAS2	C	3	3
FCRL1	115350	broad.mit.edu	36	1	156037894	156037894	+	Silent	SNP	G	A	A			TCGA-06-0221-01	TCGA-06-0221-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156037894G>A	uc001frg.1	-	c.984C>T	c.(982-984)TAC>TAT	p.Y328Y	FCRL1_uc001frf.1_Non-coding_Transcript|FCRL1_uc001frh.1_Silent_p.Y328Y|FCRL1_uc001fri.1_Intron|FCRL1_uc001frj.1_Non-coding_Transcript	NM_052938	NP_443170	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	328	Helical; (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(3)	3	all_hematologic(112;0.0378)					GBM(54;482 1003 11223 30131 35730)								0.342105	107.880877	110.396498	39	75	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.24)		Silent	SNP	156037894	156037894	6031	1	G	A	A	40	40	FCRL1	A	1	1
F5	2153	broad.mit.edu	36	1	167754315	167754315	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0221-01	TCGA-06-0221-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:167754315G>A	uc001ggg.1	-	c.6304C>T	c.(6304-6306)CGT>TGT	p.R2102C		NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	2102	F5/8 type C 2.		R -> H (in THR-APCR).|R -> C (in FA5D; impairs both factor V secretion and activity).		cell adhesion|oxidation-reduction process|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)	5	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)									0.359551	97.47823	99.022766	32	57	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	167754315	167754315	5542	1	G	A	A	39	39	F5	A	1	1
WDR65	149465	broad.mit.edu	36	1	43437651	43437651	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0221-01	TCGA-06-0221-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:43437651T>A	uc001cip.1	+	c.1432T>A	c.(1432-1434)TCC>ACC	p.S478T	EBNA1BP2_uc001cio.1_Intron|WDR65_uc001ciq.1_Missense_Mutation_p.S478T	NM_152498	NP_689711	Q96MR6	WDR65_HUMAN	WD repeat domain 65	478	WD 7.										0	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)												0.38	263.079642	266.231488	95	155	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43437651	43437651	17889	1	T	A	A	62	62	WDR65	A	4	4
PAX1	5075	broad.mit.edu	36	20	21643242	21643242	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0221-01	TCGA-06-0221-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:21643242C>G	uc002wsj.2	+	c.1124C>G	c.(1123-1125)GCG>GGG	p.A375G		NM_006192	NP_006183	P15863	PAX1_HUMAN	paired box 1	469					regulation of transcription, DNA-dependent|skeletal system development|transcription from RNA polymerase II promoter	nucleus	DNA binding			kidney(1)	1														0.333333	6.520326	6.74257	3	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21643242	21643242	11898	20	C	G	G	27	27	PAX1	G	3	3
DUSP15	128853	broad.mit.edu	36	20	29918553	29918553	+	Silent	SNP	T	G	G			TCGA-06-0221-01	TCGA-06-0221-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:29918553T>G	uc002wwx.1	-	c.120A>C	c.(118-120)TCA>TCC	p.S40S	DUSP15_uc002wwu.1_Silent_p.S37S|DUSP15_uc002wwv.1_5'UTR|DUSP15_uc002www.1_5'UTR	NM_080611	NP_817130	Q9H1R2	DUS15_HUMAN	dual specificity phosphatase 15 isoform a	37						cytoplasm|plasma membrane	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1														0.571429	6.968199	6.995148	4	3	TT		KEEP	---	---	---	---	capture	Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)		Silent	SNP	29918553	29918553	5000	20	T	G	G	59	59	DUSP15	G	4	4
ELFN2	114794	broad.mit.edu	36	22	36100849	36100849	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0221-01	TCGA-06-0221-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:36100849G>T	uc003asq.2	-	c.672C>A	c.(670-672)TAC>TAA	p.Y224*	ELFN2_uc010gxg.1_Nonsense_Mutation_p.Y224*	NM_052906	NP_443138	Q5R3F8	LRFN6_HUMAN	leucine rich repeat containing 62	224	LRRCT.|Extracellular (Potential).					cell surface|integral to membrane				ovary(1)	1	Melanoma(58;0.0574)													0.217391	6.697221	8.384454	5	18	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	36100849	36100849	5250	22	G	T	T	44	44	ELFN2	T	5	3
IDH1	3417	broad.mit.edu	36	2	208821358	208821358	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0221-01	TCGA-06-0221-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:208821358G>C	uc002vcs.1	-	c.394C>G	c.(394-396)CGT>GGT	p.R132G	IDH1_uc002vct.1_Missense_Mutation_p.R132G|IDH1_uc002vcu.1_Missense_Mutation_p.R132G	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132		Substrate.	R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|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).|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 -> 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).		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(296)|p.R132C(292)|p.R132?(210)|p.R132G(95)|p.R132S(69)|p.R132L(6)|p.R132V(1)|p.G131_R132>VL(1)		central_nervous_system(1848)|haematopoietic_and_lymphoid_tissue(593)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2451						Pancreas(158;264 1958 3300 35450 36047)			p.R132C(SNU1079-Tumor)|p.R132C(HT1080-Tumor)	134				0.34188	126.274693	128.854564	40	77	GG		KEEP	---	---	---	---	capture		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	Missense_Mutation	SNP	208821358	208821358	7794	2	G	C	C	37	37	IDH1	C	3	3
BSN	8927	broad.mit.edu	36	3	49664230	49664230	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0221-01	TCGA-06-0221-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49664230G>A	uc003cxe.2	+	c.2237G>A	c.(2236-2238)AGC>AAC	p.S746N		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	746					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	zinc ion binding			ovary(5)|central_nervous_system(1)|pancreas(1)	7														0.148936	6.982077	12.563665	7	40	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)	Missense_Mutation	SNP	49664230	49664230	1561	3	G	A	A	34	34	BSN	A	2	2
CCDC149	91050	broad.mit.edu	36	4	24447967	24447967	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0221-01	TCGA-06-0221-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:24447967C>T	uc003grc.1	-	c.643G>A	c.(643-645)GCC>ACC	p.A215T	CCDC149_uc003grb.1_Non-coding_Transcript|CCDC149_uc003grd.1_Intron|CCDC149_uc003gre.1_Missense_Mutation_p.A160T	NM_173463	NP_775734	B4DZG3	B4DZG3_HUMAN	coiled-coil domain containing 149 isoform 1	215											0		Breast(46;0.173)												0.414286	81.99755	82.43628	29	41	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24447967	24447967	2903	4	C	T	T	27	27	CCDC149	T	1	1
SLCO6A1	133482	broad.mit.edu	36	5	101841372	101841372	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0221-01	TCGA-06-0221-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:101841372T>C	uc003knn.2	-	c.709A>G	c.(709-711)ACT>GCT	p.T237A	SLCO6A1_uc003kno.2_Intron|SLCO6A1_uc003knp.1_Missense_Mutation_p.T237A|SLCO6A1_uc003knq.1_Intron	NM_173488	NP_775759	Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family,	237	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)|central_nervous_system(1)	4		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)												0.442308	402.608448	403.359455	115	145	TT		KEEP	---	---	---	---	capture		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)	Missense_Mutation	SNP	101841372	101841372	15229	5	T	C	C	58	58	SLCO6A1	C	4	4
CCDC112	153733	broad.mit.edu	36	5	114660105	114660105	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0221-01	TCGA-06-0221-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:114660105G>C	uc003kqz.2	-	c.35C>G	c.(34-36)GCG>GGG	p.A12G	CCDC112_uc003kqy.2_5'Flank|CCDC112_uc003kra.2_Missense_Mutation_p.A12G	NM_001040440	NP_689762	Q8NEF3	CC112_HUMAN	coiled-coil domain containing 112 isoform 1	Error:Variant_position_missing_in_Q8NEF3_after_alignment											0		all_cancers(142;0.000523)|all_epithelial(76;6.44e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)												0.571429	6.455428	6.481123	4	3	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(64;4.09e-08)|Epithelial(69;5.28e-08)|all cancers(49;7.06e-06)	Missense_Mutation	SNP	114660105	114660105	2869	5	G	C	C	38	38	CCDC112	C	3	3
HEATR7B2	133558	broad.mit.edu	36	5	41034516	41034516	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0221-01	TCGA-06-0221-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:41034516T>G	uc003jmj.2	-	c.4606A>C	c.(4606-4608)ACC>CCC	p.T1536P	HEATR7B2_uc003jmi.2_Missense_Mutation_p.T1091P	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	1536							binding			ovary(6)|central_nervous_system(2)	8														0.3	6.818075	7.177463	3	7	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41034516	41034516	7318	5	T	G	G	58	58	HEATR7B2	G	4	4
RSPO3	84870	broad.mit.edu	36	6	127513287	127513287	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0221-01	TCGA-06-0221-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:127513287T>A	uc003qas.1	+	c.313T>A	c.(313-315)TGT>AGT	p.C105S	RSPO3_uc003qar.1_Missense_Mutation_p.C105S	NM_032784	NP_116173	Q9BXY4	RSPO3_HUMAN	R-spondin 3	105	FU 2.					extracellular region	heparin binding				0														0.446809	199.90805	200.255579	63	78	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(226;0.0555)	Missense_Mutation	SNP	127513287	127513287	14191	6	T	A	A	55	55	RSPO3	A	4	4
PLEKHG1	57480	broad.mit.edu	36	6	151193575	151193575	+	Silent	SNP	C	T	T			TCGA-06-0221-01	TCGA-06-0221-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:151193575C>T	uc003qny.1	+	c.1635C>T	c.(1633-1635)AGC>AGT	p.S545S	PLEKHG1_uc003qnz.1_Silent_p.S545S	NM_001029884	NP_001025055	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G	545					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2														0.138298	19.508666	31.402058	13	81	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)	Silent	SNP	151193575	151193575	12494	6	C	T	T	26	26	PLEKHG1	T	2	2
ZFP57	346171	broad.mit.edu	36	6	29748882	29748882	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0221-01	TCGA-06-0221-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:29748882A>G	uc003nnl.2	-	c.925T>C	c.(925-927)TCC>CCC	p.S309P		NM_001109809	NP_001103279	Q9NU63	ZFP57_HUMAN	zinc finger protein 57 homolog	245					DNA methylation involved in embryo development|regulation of gene expression by genetic imprinting|transcription, DNA-dependent		DNA binding|zinc ion binding			ovary(3)	3														0.350282	189.303348	192.800371	62	115	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29748882	29748882	18239	6	A	G	G	10	10	ZFP57	G	4	4
KCNU1	157855	broad.mit.edu	36	8	36782971	36782971	+	Silent	SNP	G	A	A			TCGA-06-0221-01	TCGA-06-0221-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:36782971G>A	uc010lvw.1	+	c.495G>A	c.(493-495)AAG>AAA	p.K165K	KCNU1_uc003xjw.2_Non-coding_Transcript	NM_001031836	NP_001027006	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	165	Helical; Name=Segment S3; (Potential).					voltage-gated potassium channel complex	binding|catalytic activity|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1														0.428571	36.895576	37.020179	12	16	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)	Silent	SNP	36782971	36782971	8398	8	G	A	A	36	36	KCNU1	A	2	2
ABCD1	215	broad.mit.edu	36	X	152661982	152661982	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0221-01	TCGA-06-0221-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152661982G>A	uc004fif.1	+	c.1979G>A	c.(1978-1980)CGG>CAG	p.R660Q	ABCD1_uc004fig.1_Missense_Mutation_p.R160Q|ABCD1_uc004fih.1_Silent_p.P30P	NM_000033	NP_000024	P33897	ABCD1_HUMAN	ATP-binding cassette, sub-family D (ALD), member	660	ABC transporter.		R -> W (in X-ALD; CALD, ALMD and AS- types).|R -> P (in X-ALD; CALD-type).		fatty acid beta-oxidation using acyl-CoA oxidase|peroxisomal membrane transport|peroxisome organization	cytosol|integral to peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|identical protein binding|peroxisomal fatty-acyl-CoA transporter activity				0	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.3125	14.670779	15.170641	5	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152661982	152661982	61	23	G	A	A	39	39	ABCD1	A	1	1
HSD17B10	3028	broad.mit.edu	36	X	53475930	53475930	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0221-01	TCGA-06-0221-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:53475930C>T	uc004dsl.1	-	c.347G>A	c.(346-348)CGA>CAA	p.R116Q	HSD17B10_uc004dsm.1_Missense_Mutation_p.R116Q	NM_004493	NP_004484	Q99714	HCD2_HUMAN	hydroxysteroid (17-beta) dehydrogenase 10	116					branched chain family amino acid catabolic process|lipid metabolic process|oxidation-reduction process|tRNA processing	mitochondrial matrix|plasma membrane	3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity|3-hydroxyacyl-CoA dehydrogenase activity|cholate 7-alpha-dehydrogenase activity				0					NADH(DB00157)									0.619048	42.679158	42.939956	13	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53475930	53475930	7674	23	C	T	T	31	31	HSD17B10	T	1	1
MED12	9968	broad.mit.edu	36	X	70273587	70273587	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0221-01	TCGA-06-0221-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70273587A>C	uc004dyy.1	+	c.5534A>C	c.(5533-5535)AAC>ACC	p.N1845T	MED12_uc004dyz.1_Missense_Mutation_p.N1845T|MED12_uc004dza.1_Missense_Mutation_p.N1692T|MED12_uc010nla.1_Missense_Mutation_p.N471T	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	1845	Interaction with CTNNB1 and GLI3.				androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)													0.444444	6.692783	6.731623	4	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70273587	70273587	9817	23	A	C	C	2	2	MED12	C	4	4
KRTAP5-5	439915	broad.mit.edu	36	11	1607767	1607775	+	In_Frame_Del	DEL	GGCTGTGGA	-	-			TCGA-06-0221-01	TCGA-06-0221-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:1607767_1607775delGGCTGTGGA	uc001lty.1	+	c.121_129delGGCTGTGGA	c.(121-129)GGCTGTGGAdel	p.GCG47del		NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	47_49						keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)										0.33			7	14				---	---	---	---	capture_indel			In_Frame_Del	DEL	1607767	1607775	8886	11	GGCTGTGGA	-	-	39	39	KRTAP5-5	-	5	5
TP53	7157	broad.mit.edu	36	17	7519237	7519238	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-06-0221-01	TCGA-06-0221-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7519237_7519238delTC	uc002gim.2	-	c.417_418delGA	c.(415-420)AAGACCfs	p.K139fs	TP53_uc002gig.1_Frame_Shift_Del_p.K139fs|TP53_uc002gih.1_Frame_Shift_Del_p.K139fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.K7fs|TP53_uc010cng.1_Frame_Shift_Del_p.K7fs|TP53_uc002gii.1_Frame_Shift_Del_p.K7fs|TP53_uc010cnh.1_Frame_Shift_Del_p.K139fs|TP53_uc010cni.1_Frame_Shift_Del_p.K139fs|TP53_uc002gij.2_Frame_Shift_Del_p.K139fs|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Frame_Shift_Del_p.K46fs|TP53_uc002gio.2_Frame_Shift_Del_p.K7fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	139_140	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		T -> S (in sporadic cancers; somatic mutation).|T -> P (in a sporadic cancer; somatic mutation).|T -> N (in a sporadic cancer; somatic mutation).|T -> A (in sporadic cancers; somatic mutation).|T -> I (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 gene-specific transcription from RNA polymerase II promoter|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 gene-specific transcription from RNA polymerase II promoter|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	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|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|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.K139N(8)|p.K139K(7)|p.0?(6)|p.N131fs*27(2)|p.K139_C141>N(1)|p.L137_W146del10(1)|p.C135_T140delCQLAKT(1)|p.K139fs*9(1)|p.K139fs*29(1)|p.K139fs*4(1)|p.F134_T140>S(1)|p.Q136_K139delQLAK(1)|p.A138_V143delAKTCPV(1)|p.T140fs*9(1)|p.A138_P142delAKTCP(1)|p.K139fs*10(1)|p.T140fs*30(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		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)		Pancreas(47;798 1329 9957 10801)		111	p.K139fs(HCC1438-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.82			58	13				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	7519237	7519238	16923	17	TC	-	-	58	58	TP53	-	5	5
