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
CRB1	23418	broad.mit.edu	37	1	197313415	197313415	+	Silent	SNP	A	A	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr1:197313415A>G	ENST00000367400.3	+	3	792	c.657A>G	c.(655-657)gtA>gtG	p.V219V	CRB1_ENST00000535699.1_Silent_p.V150V|CRB1_ENST00000367399.2_Intron|CRB1_ENST00000538660.1_Silent_p.V219V|CRB1_ENST00000543483.1_5'UTR	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs homolog 1 (Drosophila)	219	EGF-like 5; calcium-binding (Potential).				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding	p.V219V(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TAAAAGGTGTAAACTGTGAAT	0.398													6	397	---	---	---	---
BCL11A	53335	broad.mit.edu	37	2	60773250	60773250	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr2:60773250C>T	ENST00000335712.6	-	2	468	c.241G>A	c.(241-243)Gtg>Atg	p.V81M	BCL11A_ENST00000538214.1_Missense_Mutation_p.V81M|BCL11A_ENST00000537768.1_De_novo_Start_InFrame|BCL11A_ENST00000356842.4_Missense_Mutation_p.V81M|BCL11A_ENST00000358510.4_Missense_Mutation_p.V81M|BCL11A_ENST00000359629.5_Missense_Mutation_p.V81M	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	81	Required for nuclear body formation and for SUMO1 recruitment (By similarity).				negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding	p.V81M(3)		NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			GGCTTATCCACAGCTTTTTCT	0.483			T	IGH@	B-CLL								5	133	---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141473639	141473639	+	Missense_Mutation	SNP	A	A	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr2:141473639A>C	ENST00000389484.3	-	37	6897	c.5926T>G	c.(5926-5928)Tta>Gta	p.L1976V		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1976					protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding	p.L1976V(1)		NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ACTTCAATTAAGTTGAAACCA	0.343										TSP Lung(27;0.18)			92	216	---	---	---	---
CUL3	8452	broad.mit.edu	37	2	225379456	225379456	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr2:225379456T>C	ENST00000264414.4	-	4	750	c.412A>G	c.(412-414)Aac>Gac	p.N138D	CUL3_ENST00000344951.4_Missense_Mutation_p.N72D|CUL3_ENST00000432260.2_5'UTR|CUL3_ENST00000409096.1_Missense_Mutation_p.N114D|CUL3_ENST00000409777.1_Missense_Mutation_p.N114D	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	138					cell cycle arrest|cell migration|cyclin catabolic process|cytokinesis|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|mitotic anaphase|negative regulation of Rho protein signal transduction|positive regulation of cell proliferation|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|Golgi apparatus|nucleus|polar microtubule	ubiquitin protein ligase binding	p.N138D(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TTGTAGACGTTCTCCACATTA	0.338													27	79	---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51101984	51101984	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr3:51101984G>A	ENST00000266037.9	+	6	444	c.421G>A	c.(421-423)Gag>Aag	p.E141K		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	141						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding	p.E130K(1)|p.E141K(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		TCAGGTGCGGGAGGTTAAGCG	0.453													28	120	---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51101986	51101986	+	Silent	SNP	G	G	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr3:51101986G>A	ENST00000266037.9	+	6	446	c.423G>A	c.(421-423)gaG>gaA	p.E141E		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	141						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding	p.E141E(2)|p.E130E(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		AGGTGCGGGAGGTTAAGCGGC	0.453													27	122	---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51102013	51102013	+	Silent	SNP	G	G	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr3:51102013G>A	ENST00000266037.9	+	6	473	c.450G>A	c.(448-450)ctG>ctA	p.L150L		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	150						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding	p.L150L(2)|p.L139L(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		CCGTGCGCCTGGACTGGGGTA	0.463													26	123	---	---	---	---
RYBP	23429	broad.mit.edu	37	3	72428496	72428496	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr3:72428496T>C	ENST00000477973.2	-	2	505	c.506A>G	c.(505-507)gAa>gGa	p.E169G		NM_012234.5	NP_036366.3	Q8N488	RYBP_HUMAN	RING1 and YY1 binding protein		Interaction with E4TF1B.				apoptosis|histone H2A monoubiquitination|multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleoplasm	DNA binding|protein binding|transcription corepressor activity|zinc ion binding	p.K169R(2)		prostate(1)|upper_aerodigestive_tract(1)	2		Prostate(10;0.00174)|Lung NSC(201;0.0659)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;0.000197)|Epithelial(33;0.00068)|LUSC - Lung squamous cell carcinoma(21;0.00228)|Lung(16;0.00677)|KIRC - Kidney renal clear cell carcinoma(39;0.198)|Kidney(39;0.232)		ACTTTCTCCTTCTTCTCCTTT	0.408													65	193	---	---	---	---
CDKL3	51265	broad.mit.edu	37	5	133634385	133634385	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr5:133634385C>T	ENST00000265334.4	-	13	1854	c.1736G>A	c.(1735-1737)tGc>tAc	p.C579Y	CDKL3_ENST00000536186.1_Intron|CTD-2410N18.4_ENST00000518409.1_RNA|CDKL3_ENST00000609654.1_Intron|CDKL3_ENST00000609383.1_Intron|CDKL3_ENST00000435240.2_Intron|CDKL3_ENST00000523054.1_3'UTR	NM_001113575.1	NP_001107047.1	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3	579						cytoplasm	ATP binding|cyclin-dependent protein kinase activity	p.C579Y(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(3)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTTCCCCTCGCAATGGCCATC	0.348													37	125	---	---	---	---
PSD2	84249	broad.mit.edu	37	5	139189047	139189047	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr5:139189047T>C	ENST00000274710.3	+	2	227	c.22T>C	c.(22-24)Tct>Cct	p.S8P		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	8					regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity	p.S8P(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAAGCTCTTATCTGCAGTGCC	0.627													3	21	---	---	---	---
ATP10B	23120	broad.mit.edu	37	5	159992774	159992774	+	Missense_Mutation	SNP	C	C	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr5:159992774C>G	ENST00000327245.5	-	26	4918	c.4072G>C	c.(4072-4074)Gtc>Ctc	p.V1358L		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	1358					ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity	p.V1358L(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACTTCGGGGACAGGGGCAGGC	0.517													58	234	---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100345786	100345786	+	RNA	SNP	G	G	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr7:100345786G>T	ENST00000542585.1	+	0	1198				ZAN_ENST00000349350.6_RNA|ZAN_ENST00000348028.3_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000421100.1_RNA	NM_003386.1	NP_003377.1	Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane		p.K350N(3)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			TTTTTGGAAAGACCCCAGAGC	0.597													12	59	---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	7169914	7169914	+	Missense_Mutation	SNP	G	G	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr9:7169914G>C	ENST00000381306.3	+	21	3583	c.3018G>C	c.(3016-3018)ttG>ttC	p.L1006F	KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000428870.2_Intron|KDM4C_ENST00000381309.3_Intron	NM_001146694.1	NP_001140166.1	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	0					positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding	p.L1006F(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						GATGCCACTTGGGGACCTGCC	0.448													12	53	---	---	---	---
IKBKAP	8518	broad.mit.edu	37	9	111662626	111662626	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr9:111662626C>T	ENST00000374647.5	-	19	2351	c.2044G>A	c.(2044-2046)Gtg>Atg	p.V682M	IKBKAP_ENST00000537196.1_Missense_Mutation_p.V333M	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	682					immune response|protein complex assembly|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding|signal transducer activity	p.V682M(1)		NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CCATGGGACACATGATTGCTG	0.458													22	108	---	---	---	---
WDR38	401551	broad.mit.edu	37	9	127618187	127618187	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr9:127618187C>A	ENST00000373574.1	+	4	411	c.355C>A	c.(355-357)Cag>Aag	p.Q119K		NM_001045476.1|NM_001276374.1	NP_001038941.1|NP_001263303.1	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	119								p.Q119K(1)		breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						TGACTCGAGACAGCTGGCATC	0.622											OREG0019485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	139	---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	113105824	113105824	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr11:113105824C>T	ENST00000316851.7	+	13	1733	c.1733C>T	c.(1732-1734)gCg>gTg	p.A578V	NCAM1_ENST00000533760.1_Missense_Mutation_p.A460V|NCAM1_ENST00000397957.4_3'UTR|NCAM1_ENST00000401611.2_Missense_Mutation_p.A587V	NM_001242607.1|NM_181351.4	NP_001229536.1|NP_851996.2	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	588	Fibronectin type-III 1.				axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane		p.A587V(2)|p.A578V(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		AGGCTGGCGGCGCTCAATGGC	0.587													9	15	---	---	---	---
KMT2A	4297	broad.mit.edu	37	11	118343971	118343971	+	Silent	SNP	T	T	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr11:118343971T>C	ENST00000534358.1	+	3	2120	c.2097T>C	c.(2095-2097)gcT>gcC	p.A699A	KMT2A_ENST00000354520.4_Silent_p.A699A|KMT2A_ENST00000389506.5_Silent_p.A699A	NM_001197104.1|NM_005933.3	NP_001184033.1|NP_005924.2			lysine (K)-specific methyltransferase 2A									p.A699A(2)									TTCTGAGAGCTCCAAGATTTA	0.453													33	124	---	---	---	---
OR10G9	219870	broad.mit.edu	37	11	123893785	123893785	+	Silent	SNP	C	C	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr11:123893785C>T	ENST00000375024.1	+	1	66	c.66C>T	c.(64-66)gaC>gaT	p.D22D		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	22					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.D22D(2)|p.D22E(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		CAGGGCTGGACGCCCCACTCT	0.587													18	416	---	---	---	---
OR10G7	390265	broad.mit.edu	37	11	123909643	123909643	+	Silent	SNP	G	G	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr11:123909643G>A	ENST00000330487.5	-	1	74	c.66C>T	c.(64-66)gaC>gaT	p.D22D		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	22					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.D22D(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		AGAGGGGGGCGTCCAGCCCTG	0.562													12	129	---	---	---	---
BARX2	8538	broad.mit.edu	37	11	129312807	129312807	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr11:129312807A>G	ENST00000281437.4	+	3	662	c.566A>G	c.(565-567)aAg>aGg	p.K189R	BARX2_ENST00000526127.1_Missense_Mutation_p.K44R|BARX2_ENST00000531946.1_Missense_Mutation_p.K67R	NM_003658.4	NP_003649.2	Q9UMQ3	BARX2_HUMAN	BARX homeobox 2	189								p.K189R(1)		breast(1)|central_nervous_system(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	20	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.00929)|Lung(977;0.0245)|LUSC - Lung squamous cell carcinoma(976;0.0253)		ATGAAATGGAAGAAAATGGTA	0.498													7	125	---	---	---	---
SPIC	121599	broad.mit.edu	37	12	101876611	101876611	+	Silent	SNP	A	A	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr12:101876611A>G	ENST00000551346.1	+	5	411	c.252A>G	c.(250-252)caA>caG	p.Q84Q	SPIC_ENST00000299272.5_Silent_p.Q84Q			Q8N5J4	SPIC_HUMAN	Spi-C transcription factor (Spi-1/PU.1 related)	84						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	p.Q84Q(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	22						ATATTCATCAATCTCTGCAGA	0.403													131	332	---	---	---	---
FERMT2	10979	broad.mit.edu	37	14	53385917	53385917	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr14:53385917G>T	ENST00000395631.2	-	3	531	c.315C>A	c.(313-315)aaC>aaA	p.N105K	FERMT2_ENST00000341590.3_Missense_Mutation_p.N105K|FERMT2_ENST00000343279.4_Missense_Mutation_p.N105K|FERMT2_ENST00000553373.1_Missense_Mutation_p.N105K|FERMT2_ENST00000399304.3_Missense_Mutation_p.N105K			Q96AC1	FERM2_HUMAN	fermitin family member 2	105					actin cytoskeleton organization|cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytosol|focal adhesion|stress fiber	binding	p.N105K(1)	ERO1L/FERMT2(2)	NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	20	Breast(41;0.0342)					CATACTTCATGTTGGGAAGCT	0.398													6	288	---	---	---	---
HYPK	25764	broad.mit.edu	37	15	44094002	44094002	+	Nonstop_Mutation	SNP	T	T	G			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr15:44094002T>G	ENST00000406925.1	+	5	4499	c.388T>G	c.(388-390)Tga>Gga	p.*130G	SERF2_ENST00000594896.1_Nonstop_Mutation_p.*176G|HYPK_ENST00000442995.2_Nonstop_Mutation_p.*130G|HYPK_ENST00000458412.1_3'UTR|SERF2_ENST00000600633.1_Nonstop_Mutation_p.*130G					huntingtin interacting protein K														all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		GBM - Glioblastoma multiforme(94;8.1e-07)		CCTAACCAACTGATGCGTGCT	0.413													31	92	---	---	---	---
ZSCAN32	54925	broad.mit.edu	37	16	3440104	3440104	+	Silent	SNP	T	T	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr16:3440104T>A	ENST00000396852.4	-	5	964	c.657A>T	c.(655-657)gtA>gtT	p.V219V	ZSCAN32_ENST00000439568.2_Intron|ZSCAN32_ENST00000573830.1_Intron|ZSCAN32_ENST00000422427.2_Silent_p.V7V|ZSCAN32_ENST00000574940.1_Silent_p.V219V|ZSCAN32_ENST00000396846.3_Silent_p.V219V|ZSCAN32_ENST00000304926.3_Silent_p.V7V	NM_001284527.1|NM_001284529.1	NP_001271456.1|NP_001271458.1			zinc finger and SCAN domain containing 32									p.V7V(1)									GACAGAGGGATACAGCTCTGT	0.582													13	39	---	---	---	---
ZNF521	25925	broad.mit.edu	37	18	22804338	22804338	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr18:22804338G>A	ENST00000361524.3	-	4	3692	c.3544C>T	c.(3544-3546)Ccc>Tcc	p.P1182S	ZNF521_ENST00000584787.1_Missense_Mutation_p.P962S|ZNF521_ENST00000538137.2_Missense_Mutation_p.P1182S	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1182					cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CTGATTCTGGGCATTGGTGAT	0.478			T	PAX5	ALL								4	191	---	---	---	---
CATSPERD	257062	broad.mit.edu	37	19	5768180	5768180	+	Splice_Site	SNP	A	A	C			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr19:5768180A>C	ENST00000381624.3	+	18	1622	c.1561A>C	c.(1561-1563)Aaa>Caa	p.K521Q	CATSPERD_ENST00000381614.2_Splice_Site_p.K179Q|CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	TM146_HUMAN	catsper channel auxiliary subunit delta	521						integral to membrane		p.K521Q(1)									TGCTTGCAGCAAAGTTTCCGC	0.537													39	104	---	---	---	---
LDLR	3949	broad.mit.edu	37	19	11227612	11227612	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr19:11227612C>T	ENST00000558518.1	+	12	1970	c.1783C>T	c.(1783-1785)Cgg>Tgg	p.R595W	LDLR_ENST00000545707.1_Missense_Mutation_p.R468W|LDLR_ENST00000535915.1_Missense_Mutation_p.R554W|LDLR_ENST00000557933.1_Missense_Mutation_p.R595W|LDLR_ENST00000558013.1_Missense_Mutation_p.R595W|LDLR_ENST00000455727.2_Missense_Mutation_p.R427W	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	595					cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity	p.R595W(1)|p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Methyl aminolevulinate(DB00992)|Porfimer(DB00707)	CGGGGGCAACCGGAAGACCAT	0.542													73	342	---	---	---	---
JAK3	3718	broad.mit.edu	37	19	17950419	17950419	+	Silent	SNP	T	T	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr19:17950419T>A	ENST00000458235.1	-	10	1407	c.1308A>T	c.(1306-1308)ggA>ggT	p.G436G	JAK3_ENST00000534444.1_Silent_p.G436G|JAK3_ENST00000526008.1_5'UTR|JAK3_ENST00000527670.1_Silent_p.G436G	NM_000215.3	NP_000206.2	P52333	JAK3_HUMAN	Janus kinase 3	436	SH2; atypical.				B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding	p.G436G(2)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147						GAAGGAAGGTTCCTGTGGGGC	0.612		2	Mis		"""acute megakaryocytic leukemia, ETP ALL"""								5	30	---	---	---	---
TSKS	60385	broad.mit.edu	37	19	50248602	50248602	+	Silent	SNP	C	C	T			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr19:50248602C>T	ENST00000246801.3	-	7	1126	c.1044G>A	c.(1042-1044)gtG>gtA	p.V348V	TSKS_ENST00000358830.3_Silent_p.V148V	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	348							protein binding	p.V348V(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		GGGCTTCCTGCACCGCCCCCT	0.706													3	8	---	---	---	---
SNX12	29934	broad.mit.edu	37	X	70280884	70280884	+	Silent	SNP	C	C	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chrX:70280884C>A	ENST00000374274.3	-	4	587	c.471G>T	c.(469-471)ccG>ccT	p.P157P	SNX12_ENST00000465030.1_5'UTR|SNX12_ENST00000276105.3_Silent_p.P153P	NM_001256185.1|NM_001256188.1|NM_013346.3	NP_001243114.1|NP_001243117.1|NP_037478.2	Q9UMY4	SNX12_HUMAN	sorting nexin 12	157					cell communication|protein transport	membrane	phosphatidylinositol binding|protein binding	p.P157P(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	8	Renal(35;0.156)					GCACCTTCCCCGGGACGTAGT	0.512													3	22	---	---	---	---
MT-CO1	4512	broad.mit.edu	37	M	7026	7026	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chrM:7026G>A	ENST00000361624.2	+	1	1123	c.1123G>A	c.(1123-1125)Gcc>Acc	p.A375T						mitochondrially encoded cytochrome c oxidase I											breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						ACTACGTTGTAGCTCACTTCC	0.448													4	2	---	---	---	---
MBD6	114785	broad.mit.edu	37	12	57920425	57920425	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CH-5744-01A-11D-1576-08	TCGA-CH-5744-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	79e46606-ecb4-4a53-acaf-e9e46855fe4d	84029535-3038-490b-b904-910d79fce5c8	g.chr12:57920425delG	ENST00000355673.3	+	7	1853	c.1497delG	c.(1495-1497)ctgfs	p.L499fs	MBD6_ENST00000431731.2_Frame_Shift_Del_p.L499fs	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	499	Pro-rich.					chromosome|nucleus	chromatin binding|DNA binding			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|urinary_tract(1)	31						CCGAAGGACTGGGGATGGGGG	0.647													51	217	---	---	---	---
