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	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	ref_context	gc_content	COSMIC_n_overlapping_mutations	ESP_AvgAAsampleReadDepth	ESP_AvgEAsampleReadDepth	ESP_AvgSampleReadDepth	ESP_Chromosome	ESP_Position	ESP_TotalAAsamplesCovered	ESP_TotalEAsamplesCovered	ESP_TotalSamplesCovered	Ensembl_so_accession	Ensembl_so_term	HGNC_AccessionNumbers	HGNC_CCDSIDs	HGNC_Chromosome	HGNC_DateModified	HGNC_DateNameChanged	HGNC_DateSymbolChanged	HGNC_EnsemblGeneID	HGNC_EnsemblIDsuppliedbyEnsembl	HGNC_Genefamilydescription	HGNC_HGNCID	HGNC_LocusGroup	HGNC_LocusType	HGNC_NameSynonyms	HGNC_OMIMIDsuppliedbyNCBI	HGNC_PreviousNames	HGNC_PreviousSymbols	HGNC_PubmedIDs	HGNC_RecordType	HGNC_RefSeqsuppliedbyNCBI	HGNC_Status	HGNC_Synonyms	HGNC_UCSCIDsuppliedbyUCSC	HGNC_UniProtIDsuppliedbyUniProt	HGNC_VEGAIDs	HGVS_coding_DNA_change	HGVS_genomic_change	HGVS_protein_change	UniProt_alt_uniprot_accessions	annotation_transcript	build	ccds_id	dbNSFP_1000Gp1_AC	dbNSFP_1000Gp1_AF	dbNSFP_1000Gp1_AFR_AC	dbNSFP_1000Gp1_AFR_AF	dbNSFP_1000Gp1_AMR_AC	dbNSFP_1000Gp1_AMR_AF	dbNSFP_1000Gp1_ASN_AC	dbNSFP_1000Gp1_ASN_AF	dbNSFP_1000Gp1_EUR_AC	dbNSFP_1000Gp1_EUR_AF	dbNSFP_Ancestral_allele	dbNSFP_CADD_phred	dbNSFP_CADD_raw	dbNSFP_CADD_raw_rankscore	dbNSFP_ESP6500_AA_AF	dbNSFP_ESP6500_EA_AF	dbNSFP_Ensembl_geneid	dbNSFP_Ensembl_transcriptid	dbNSFP_FATHMM_pred	dbNSFP_FATHMM_rankscore	dbNSFP_FATHMM_score	dbNSFP_GERP_NR	dbNSFP_GERP_RS	dbNSFP_GERP_RS_rankscore	dbNSFP_Interpro_domain	dbNSFP_LRT_Omega	dbNSFP_LRT_converted_rankscore	dbNSFP_LRT_pred	dbNSFP_LRT_score	dbNSFP_LR_pred	dbNSFP_LR_rankscore	dbNSFP_LR_score	dbNSFP_MutationAssessor_pred	dbNSFP_MutationAssessor_rankscore	dbNSFP_MutationAssessor_score	dbNSFP_MutationTaster_converted_rankscore	dbNSFP_MutationTaster_pred	dbNSFP_MutationTaster_score	dbNSFP_Polyphen2_HDIV_pred	dbNSFP_Polyphen2_HDIV_rankscore	dbNSFP_Polyphen2_HDIV_score	dbNSFP_Polyphen2_HVAR_pred	dbNSFP_Polyphen2_HVAR_rankscore	dbNSFP_Polyphen2_HVAR_score	dbNSFP_RadialSVM_pred	dbNSFP_RadialSVM_rankscore	dbNSFP_RadialSVM_score	dbNSFP_Reliability_index	dbNSFP_SIFT_converted_rankscore	dbNSFP_SIFT_pred	dbNSFP_SIFT_score	dbNSFP_SLR_test_statistic	dbNSFP_SiPhy_29way_logOdds	dbNSFP_SiPhy_29way_logOdds_rankscore	dbNSFP_SiPhy_29way_pi	dbNSFP_UniSNP_ids	dbNSFP_Uniprot_aapos	dbNSFP_Uniprot_acc	dbNSFP_Uniprot_id	dbNSFP_aaalt	dbNSFP_aapos	dbNSFP_aapos_FATHMM	dbNSFP_aapos_SIFT	dbNSFP_aaref	dbNSFP_cds_strand	dbNSFP_codonpos	dbNSFP_folddegenerate	dbNSFP_genename	dbNSFP_hg18_pos1coor	dbNSFP_phastCons100way_vertebrate	dbNSFP_phastCons100way_vertebrate_rankscore	dbNSFP_phastCons46way_placental	dbNSFP_phastCons46way_placental_rankscore	dbNSFP_phastCons46way_primate	dbNSFP_phastCons46way_primate_rankscore	dbNSFP_phyloP100way_vertebrate	dbNSFP_phyloP100way_vertebrate_rankscore	dbNSFP_phyloP46way_placental	dbNSFP_phyloP46way_placental_rankscore	dbNSFP_phyloP46way_primate	dbNSFP_phyloP46way_primate_rankscore	dbNSFP_refcodon	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_type	havana_transcript	init_n_lod	init_t_lod	isArtifactMode	n_alt_count	n_ref_count	oxoGCut	pox	pox_cutoff	qox	refseq_mrna_id	t_alt_count	t_lod_fstar	t_ref_count	tumor_f
ARID2	196528	broad.mit.edu	hg19	12	46287220	46287220	+	Missense_Mutation	SNP	G	G	A			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr12:46287220G>A	ENST00000334344.6	+	19	5337	c.5165G>A	c.(5164-5166)gGc>gAc	p.G1722D	ARID2_ENST00000422737.1_Missense_Mutation_p.G1573D|ARID2_ENST00000444670.1_Missense_Mutation_p.G1332D|ARID2_ENST00000457135.1_Missense_Mutation_p.G330D|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1722		chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding	NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)	ACTGTAGGGGGCACAAGCTCA	0.483	0	71.0	60.0	64.0	12	46287220	2203	4300	6503	SO:0001583	missense		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079	"""-"""	18037	protein-coding gene	gene with protein product		609539				Standard	NM_152641	Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.5165G>A	12.37:g.46287220G>A	ENSP00000335044:p.Gly1722Asp	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.910338	0.52439	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670;ENST00000457135	T	0.32272	1.46	5.4	5.4	0.78164	.	0.187530	0.48286	D	0.000183	T	0.26521	0.0648	L	0.29908	0.895	0.41564	D	0.988649	B;B;B	0.34290	0.447;0.447;0.242	B;B;B	0.36244	0.22;0.147;0.054	T	0.06427	-1.0827	10	0.49607	T	0.09	-1.9611	14.718	0.69284	0.0:0.2665:0.7335:0.0	.	1722;1332;1722	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	D	1722;839;839;1573;1332;330	ENSP00000335044:G1722D	ENSP00000335044:G1722D	G	+	2	0	ARID2	44573487	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.618000	0.54188	2.536000	0.85505	0.591000	0.81541	GGC	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2		1.415661	0	2	26	0	0	1	0	XM_350875	3	6.711165	29	0.093750
TMEM44	93109	broad.mit.edu	hg19	3	194346636	194346636	+	Silent	SNP	C	C	T			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr3:194346636C>T	ENST00000392432.2	-	3	553	c.348G>A	c.(346-348)aaG>aaA	p.K116K	TMEM44_ENST00000273580.7_Silent_p.K116K|TMEM44_ENST00000330115.3_Silent_p.K13K|TMEM44_ENST00000381975.3_Silent_p.K116K|TMEM44_ENST00000347147.4_Silent_p.K116K|TMEM44_ENST00000473092.1_Silent_p.K116K	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	116			integral to membrane		breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|urinary_tract(1)	8	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;9.06e-06)	CTGAATTAGACTTGAATTTGG	0.468	0	208.0	192.0	197.0	3	194346636	2203	4300	6503	SO:0001819	synonymous_variant	AL833026	CCDS3308.1, CCDS33921.1, CCDS3308.2, CCDS54698.1, CCDS54699.1	3q29	2005-08-16			ENSG00000145014	ENSG00000145014		25120	protein-coding gene	gene with protein product						Standard	NM_138399	Approved	DKFZp686O18124	uc010hzn.3	Q2T9K0	OTTHUMG00000156023	ENST00000347147.4:c.348G>A	3.37:g.194346636C>T		A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	ENST00000347147.4	37	CCDS33921.1																																																																																			TMEM44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342749.1		165.109768	0	9	111	0	0	1	0	NM_138399	49	171.209756	10	0.830508
SPARCL1	8404	broad.mit.edu	hg19	4	88414959	88414959	+	Silent	SNP	C	C	T	rs145736129		TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr4:88414959C>T	ENST00000418378.1	-	5	1564	c.993G>A	c.(991-993)acG>acA	p.T331T	SPARCL1_ENST00000282470.6_Silent_p.T331T|SPARCL1_ENST00000503414.1_Silent_p.T206T	NM_001128310.1	NP_001121782.1	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	331		signal transduction	extracellular space|proteinaceous extracellular matrix	calcium ion binding	breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)	GATTTCTGGGCGTGGTATTAC	0.483	0	191.0	159.0	170.0	4	88414959	2203	4300	6503	SO:0001819	synonymous_variant	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583	"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""		8488563, 7600298, 16844696	Standard	NM_001128310	Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000503414.1:c.618G>A	4.37:g.88414959C>T		B4E2Z0|E7ESU2|Q14800	ENST00000503414.1	37																																																																																				SPARCL1-005	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363611.2		193.929610	0	11	141	0	0	1	0		63	194.310057	49	0.562500
PRDM2	7799	hgsc.bcm.edu	hg19	1	14106463	14106463	+	Missense_Mutation	SNP	A	A	G	rs139578720	byFrequency	TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450																										TCCTGCATCAATGTTGCCTGT	0.473	0	101.0	99.0	100.0	1	14106463	2203	4300	6503	SO:0001583	missense	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731	"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196			7538672	Standard	NM_012231	Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.2173A>G	1.37:g.14106463A>G	ENSP00000235372:p.Met725Val	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	ENST00000235372.7	37	CCDS150.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	A	0.065	-1.215976	0.01542	6.81E-4	1.16E-4	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.01388	5.07;4.95;4.96;4.96	5.61	1.97	0.26223	.	0.405138	0.30911	N	0.008629	T	0.00724	0.0024	N	0.14661	0.345	0.20638	N	0.999876	B;B;B;B	0.20368	0.015;0.0;0.044;0.026	B;B;B;B	0.17979	0.009;0.0;0.009;0.02	T	0.47824	-0.9087	10	0.02654	T	1	.	1.7173	0.02904	0.5704:0.1423:0.1506:0.1368	.	725;583;725;725	A8MW16;Q5THJ0;Q13029;Q13029-2	.;.;PRDM2_HUMAN;.	V	725;725;725;524;524	ENSP00000235372:M725V;ENSP00000312352:M725V;ENSP00000411103:M524V;ENSP00000341621:M524V	ENSP00000235372:M725V	M	+	1	0	PRDM2	13979050	0.019000	0.18553	0.572000	0.28498	0.961000	0.63080	0.313000	0.19415	0.465000	0.27167	0.533000	0.62120	ATG	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2				-7	107					NM_012231	55		43	
CNOT1	23019	broad.mit.edu	hg19	16	58610395	58610395	+	Missense_Mutation	SNP	C	C	A			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr16:58610395C>A	ENST00000317147.5	-	14	2008	c.1676G>T	c.(1675-1677)cGa>cTa	p.R559L	CNOT1_ENST00000441024.2_Missense_Mutation_p.R559L|CNOT1_ENST00000569240.1_Missense_Mutation_p.R559L	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	559		nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol		breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)	ATCAAGTATTCGAGACAATTT	0.478	0	187.0	141.0	156.0	16	58610395	2198	4300	6498	SO:0001583	missense	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107		7877	protein-coding gene	gene with protein product		604917		NOT1	14702039	Standard	NM_016284	Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.1676G>T	16.37:g.58610395C>A	ENSP00000320949:p.Arg559Leu	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	C	37	6.308562	0.97462	.	.	ENSG00000125107	ENST00000317147;ENST00000394200;ENST00000441024	T;T	0.17054	2.3;2.3	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.53932	0.1827	M	0.91818	3.245	0.80722	D	1	D;D;D	0.89917	0.992;1.0;1.0	D;D;D	0.91635	0.979;0.997;0.999	T	0.61978	-0.6951	9	.	.	.	11.9105	19.9986	0.97401	0.0:1.0:0.0:0.0	.	559;559;559	A5YKK6-4;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	L	559	ENSP00000320949:R559L;ENSP00000413113:R559L	.	R	-	2	0	CNOT1	57167896	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.733000	0.93635	0.650000	0.86243	CGA	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3		-10.436814	1	-4	119	0	1	1	1	NM_016284	3	6.382469	71	0.040541
HERC2	8924	broad.mit.edu	hg19	15	28441638	28441638	+	Nonsense_Mutation	SNP	C	C	A			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr15:28441638C>A	ENST00000261609.7	-	51	8197	c.8089G>T	c.(8089-8091)Gag>Tag	p.E2697*		NM_004667.5	NP_004658.3	O95714	HERC2_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 2	2697		DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding	NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)	GGTACCAACTCCATTTCTGAT	0.408	0	107.0	106.0	106.0	15	28441638	2203	4300	6503	SO:0001587	stop_gained	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731		4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""		9949213	Standard	NM_004667	Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.8089G>T	15.37:g.28441638C>A	ENSP00000261609:p.Glu2697*		ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	48	14.590650	0.99802	.	.	ENSG00000128731	ENST00000261609	.	.	.	5.3	5.3	0.74995	.	0.120957	0.56097	D	0.000040	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.3101	0.94184	0.0:1.0:0.0:0.0	.	.	.	.	X	2697	.	ENSP00000261609:E2697X	E	-	1	0	HERC2	26115233	1.000000	0.71417	1.000000	0.80357	0.061000	0.15899	7.776000	0.85560	2.649000	0.89929	0.484000	0.47621	GAG	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2		161.638271	1	25	119	0	1.72039e-30	1	2.21193e-30	NM_004667	54	161.690306	49	0.524272
TOP2B	7155	broad.mit.edu	hg19	3	25665189	25665189	+	Missense_Mutation	SNP	C	C	A			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr3:25665189C>A	ENST00000435706.2	-	21	2730	c.2529G>T	c.(2527-2529)aaG>aaT	p.K843N	TOP2B_ENST00000264331.4_Missense_Mutation_p.K848N			Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	848		DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|resolution of meiotic recombination intermediates|sister chromatid segregation	cytosol|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex|WINAC complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity	breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					CATAAAGGAACTTAAGGAGGT	0.388	0	69.0	62.0	64.0	3	25665189	1853	4091	5944	SO:0001583	missense	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097		11990	protein-coding gene	gene with protein product		126431	"""topoisomerase (DNA) II beta (180kD)"""		1309226, 1333583	Standard	NM_001068	Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000435706.2:c.2529G>T	3.37:g.25665189C>A	ENSP00000396704:p.Lys843Asn	Q13600|Q9UMG8|Q9UQP8	ENST00000435706.2	37	CCDS46776.1	.	.	.	.	.	.	.	.	.	.	C	12.04	1.817903	0.32145	.	.	ENSG00000077097	ENST00000435706;ENST00000264331;ENST00000424225	T;T	0.44881	0.91;0.91	5.43	1.41	0.22369	.	0.000000	0.85682	D	0.000000	T	0.23492	0.0568	N	0.16016	0.355	0.80722	D	1	B	0.14438	0.01	B	0.21360	0.034	T	0.05402	-1.0887	10	0.21014	T	0.42	-11.3882	10.7836	0.46393	0.0:0.6438:0.0:0.3562	.	843	Q02880-2	.	N	843;848;843	ENSP00000396704:K843N;ENSP00000264331:K848N	ENSP00000264331:K848N	K	-	3	2	TOP2B	25640193	0.999000	0.42202	0.998000	0.56505	0.965000	0.64279	0.698000	0.25571	0.028000	0.15324	0.557000	0.71058	AAG	TOP2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340821.1		2.202463	1	-8	22	0	6.4e-05	1	7.2e-05		3	6.744387	26	0.103448
ATP2A3	489	broad.mit.edu	hg19	17	3833685	3833685	+	Missense_Mutation	SNP	C	C	T			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr17:3833685C>T	ENST00000309890.7	-	18	2804	c.2654G>A	c.(2653-2655)gGc>gAc	p.G885D	ATP2A3_ENST00000352011.3_Missense_Mutation_p.G885D|ATP2A3_ENST00000397039.1_Missense_Mutation_p.G69D|ATP2A3_ENST00000397041.3_Missense_Mutation_p.G885D|ATP2A3_ENST00000397043.3_Missense_Mutation_p.G885D|ATP2A3_ENST00000397035.3_Missense_Mutation_p.G885D|ATP2A3_ENST00000359983.3_Missense_Mutation_p.G885D	NM_174953.2|NM_174954.2|NM_174955.2|NM_174956.2	NP_777613.1|NP_777614.1|NP_777615.1|NP_777616.1	Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	885		ATP biosynthetic process|platelet activation	integral to membrane|nuclear membrane|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding	breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)	ACAGTCGATGCCGGCAAAGAG	0.612	0	99.0	76.0	84.0	17	3833685	2203	4299	6502	SO:0001583	missense		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929			8809064	Standard	NM_005173	Approved	SERCA3	uc002fwy.2	Q93084		ENST00000397043.3:c.2654G>A	17.37:g.3833685C>T	ENSP00000380236:p.Gly885Asp	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	ENST00000397043.3	37	CCDS45580.1	.	.	.	.	.	.	.	.	.	.	C	6.993	0.553332	0.13374	.	.	ENSG00000074370	ENST00000397043;ENST00000397039;ENST00000352011;ENST00000359983;ENST00000397041;ENST00000397045;ENST00000309890;ENST00000397035	D;D;D;D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43	3.78	1.37	0.22104	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.379891	0.28736	N	0.014319	T	0.82254	0.4997	L	0.45470	1.425	0.54753	D	0.999982	B;B;B;B;B;B	0.12013	0.0;0.0;0.0;0.005;0.002;0.001	B;B;B;B;B;B	0.13407	0.001;0.004;0.006;0.009;0.009;0.009	T	0.72030	-0.4413	10	0.30854	T	0.27	.	8.1506	0.31139	0.0:0.7576:0.0:0.2424	.	885;885;885;885;885;885	Q93084-4;Q93084-2;Q93084;Q93084-6;G3XAE1;Q93084-3	.;.;AT2A3_HUMAN;.;.;.	D	885;69;885;885;885;885;885;885	ENSP00000380236:G885D;ENSP00000380232:G69D;ENSP00000301387:G885D;ENSP00000353072:G885D;ENSP00000380234:G885D;ENSP00000312577:G885D;ENSP00000380229:G885D	ENSP00000312577:G885D	G	-	2	0	ATP2A3	3780434	0.019000	0.18553	0.016000	0.15963	0.077000	0.17291	1.418000	0.34782	0.357000	0.24183	0.467000	0.42956	GGC	ATP2A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438402.1		2.102147	0	-14	24	0	0	1	0	NM_174953	3	6.644526	26	0.103448
CYLD	1540	broad.mit.edu	hg19	16	50788282	50788282	+	Missense_Mutation	SNP	G	G	T			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr16:50788282G>T	ENST00000540145.1	+	6	1275	c.860G>T	c.(859-861)aGt>aTt	p.S287I	CYLD_ENST00000568704.2_Missense_Mutation_p.S287I|CYLD_ENST00000427738.3_Missense_Mutation_p.S287I|CYLD_ENST00000566206.1_Missense_Mutation_p.S287I|CYLD_ENST00000569418.1_Missense_Mutation_p.S287I|CYLD_ENST00000398568.2_Missense_Mutation_p.S287I|CYLD_ENST00000311559.9_Missense_Mutation_p.S287I|CYLD_ENST00000564326.1_Missense_Mutation_p.S287I			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	287	Interaction with TRIP.	cell cycle|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K63-linked deubiquitination|regulation of microtubule cytoskeleton organization|regulation of mitotic cell cycle|translation|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	cytosol|extrinsic to internal side of plasma membrane|microtubule|perinuclear region of cytoplasm|ribosome	proline-rich region binding|protein kinase binding|structural constituent of ribosome|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding	central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)			CAGCTTTGTAGTTTTGCGTGT	0.308	0	161.0	149.0	152.0	16	50788282	1846	4093	5939	SO:0001583	missense	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17						2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1	7493027	Standard	NM_015247	Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000398568.2:c.860G>T	16.37:g.50788282G>T	ENSP00000381574:p.Ser287Ile	O94934|Q7L3N6|Q96EH0|Q9NZX9	ENST00000398568.2	37	CCDS42164.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.916209	0.52546	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	T;T;T;T	0.19806	2.12;2.12;2.12;2.12	5.98	5.98	0.97165	Cytoskeleton-associated protein, Gly-rich domain (3);	0.042476	0.85682	D	0.000000	T	0.22898	0.0553	L	0.38175	1.15	0.53688	D	0.999972	P;P;P;P	0.39352	0.669;0.617;0.617;0.669	B;B;B;B	0.38106	0.265;0.173;0.173;0.265	T	0.00787	-1.1566	10	0.51188	T	0.08	-17.329	20.4447	0.99122	0.0:0.0:1.0:0.0	.	287;287;287;287	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	I	287	ENSP00000445447:S287I;ENSP00000308928:S287I;ENSP00000392025:S287I;ENSP00000381574:S287I	ENSP00000308928:S287I	S	+	2	0	CYLD	49345783	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	6.808000	0.75206	2.834000	0.97654	0.655000	0.94253	AGT	CYLD-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000422997.1		-4.119380	1	-1	54	0	1	1	1		3	6.552900	49	0.057692
CDC40	51362	broad.mit.edu	hg19	6	110540993	110540993	+	Missense_Mutation	SNP	G	G	A			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr6:110540993G>A	ENST00000368932.1	+	13	1362	c.1261G>A	c.(1261-1263)Gtc>Atc	p.V421I	CDC40_ENST00000368930.1_Missense_Mutation_p.V421I|CDC40_ENST00000307731.1_Missense_Mutation_p.V421I			O60508	PRP17_HUMAN	cell division cycle 40	421		mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|nucleoplasm		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)	TTTGGGAGCTGTCAACACCAT	0.408	0	211.0	190.0	197.0	6	110540993	2203	4300	6503	SO:0001583	missense	AF015044	CCDS5081.1	6q22.1	2013-01-17	2013-01-17		ENSG00000168438	ENSG00000168438	"""WD repeat domain containing"""	17350	protein-coding gene	gene with protein product		605585	"""cell division cycle 40 homolog (yeast)"", ""cell division cycle 40 homolog (S. cerevisiae)"""		9769104, 9830021	Standard	NM_015891	Approved	PRP17, EHB3, PRPF17, FLJ10564	uc003pua.3	O60508	OTTHUMG00000015358	ENST00000368932.1:c.1261G>A	6.37:g.110540993G>A	ENSP00000357928:p.Val421Ile	B2RBC5|O75471|Q5SRN0|Q9UPG1	ENST00000368932.1	37	CCDS5081.1	.	.	.	.	.	.	.	.	.	.	G	30	5.057298	0.93846	.	.	ENSG00000168438	ENST00000368932;ENST00000368933;ENST00000368930;ENST00000307731	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	5.51	5.51	0.81932	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.67297	0.2878	L	0.41573	1.285	0.80722	D	1	P	0.41848	0.763	P	0.55999	0.789	T	0.64063	-0.6495	10	0.34782	T	0.22	-6.1007	19.43	0.94760	0.0:0.0:1.0:0.0	.	421	O60508	PRP17_HUMAN	I	421	ENSP00000357928:V421I;ENSP00000357929:V421I;ENSP00000357926:V421I;ENSP00000304370:V421I	ENSP00000304370:V421I	V	+	1	0	CDC40	110647686	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.476000	0.97823	2.589000	0.87451	0.591000	0.81541	GTC	CDC40-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041791.1		62.296152	0	1	105	0	0	1	0	NM_015891	26	68.033302	77	0.252427
CHML	1122	broad.mit.edu	hg19	1	241797963	241797963	+	Missense_Mutation	SNP	C	C	T			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr1:241797963C>T	ENST00000366553.1	-	1	1269	c.1106G>A	c.(1105-1107)cGg>cAg	p.R369Q	OPN3_ENST00000366554.2_Intron|OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	369		intracellular protein transport|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity	breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)		GTTGCCAAACCGTCCGAGACA	0.418	0	95.0	96.0	96.0	1	241797963	2203	4299	6502	SO:0001583	missense	X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668		1941	protein-coding gene	gene with protein product		118825			7981670	Standard	NM_001821	Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.1106G>A	1.37:g.241797963C>T	ENSP00000355511:p.Arg369Gln	B2RAB9|Q17RE0|Q9H1Y4	ENST00000366553.1	37	CCDS31073.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.362737	0.61403	2.27E-4	0.0	ENSG00000203668	ENST00000366553	D	0.88124	-2.34	4.96	3.1	0.35709	.	0.187243	0.47852	U	0.000213	D	0.87309	0.6145	.	.	.	0.48452	D	0.999651	D	0.60160	0.987	P	0.49683	0.619	D	0.87755	0.2594	9	0.87932	D	0	-2.4762	9.5703	0.39425	0.0:0.8242:0.0:0.1758	.	369	P26374	RAE2_HUMAN	Q	369	ENSP00000355511:R369Q	ENSP00000355511:R369Q	R	-	2	0	CHML	239864586	1.000000	0.71417	0.847000	0.33407	0.840000	0.47671	3.008000	0.49544	1.469000	0.48083	0.655000	0.94253	CGG	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1		41.407861	0	13	65	0	0	1	0	NM_001821	15	43.645932	38	0.283019
SIGLEC1	6614	broad.mit.edu	hg19	20	3674277	3674277	+	Missense_Mutation	SNP	C	C	T			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr20:3674277C>T	ENST00000344754.4	-	13	3324	c.3325G>A	c.(3325-3327)Gtg>Atg	p.V1109M	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.V1109M	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1109	Ig-like C2-type 11.	cell-cell adhesion|cell-matrix adhesion|endocytosis|inflammatory response	extracellular region|integral to membrane|plasma membrane	sugar binding	NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70					GTGGTCCACACAAGGCAGGTC	0.652	0	71.0	49.0	57.0	20	3674277	2203	4300	6503	SO:0001583	missense	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827	"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN	8530048	Standard	XM_006723610	Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.3325G>A	20.37:g.3674277C>T	ENSP00000341141:p.Val1109Met	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	ENST00000344754.4	37	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822182	0.71028	.	.	ENSG00000088827	ENST00000344754;ENST00000202578	T;T	0.13901	2.55;2.55	5.52	5.52	0.82312	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.206543	0.24314	N	0.039618	T	0.45498	0.1345	M	0.88842	2.985	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.989	T	0.46091	-0.9216	10	0.72032	D	0.01	.	16.9389	0.86210	0.0:1.0:0.0:0.0	.	1109;1109	Q9BZZ2;Q9BZZ2-3	SN_HUMAN;.	M	1109	ENSP00000341141:V1109M;ENSP00000202578:V1109M	ENSP00000202578:V1109M	V	-	1	0	SIGLEC1	3622277	0.106000	0.21978	0.061000	0.19648	0.941000	0.58515	2.243000	0.43115	2.612000	0.88384	0.655000	0.94253	GTG	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2		36.398940	0	-1	27	0	0	1	0	NM_023068	12	36.398940	12	0.500000
HOXB2	3212	broad.mit.edu	hg19	17	46620496	46620496	+	Silent	SNP	A	A	G			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr17:46620496A>G	ENST00000330070.4	-	2	2172	c.1005T>C	c.(1003-1005)ccT>ccC	p.P335P	HOXB2_ENST00000504772.3_5'UTR	NM_002145.3	NP_002136.1	P14652	HXB2_HUMAN	homeobox B2	335		blood circulation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	11					CCTCGGAAAAAGGGACCGGGC	0.587	2	80.0	83.0	82.0	17	46620496	2203	4300	6503	SO:0001819	synonymous_variant		CCDS11527.1	17q21.32	2012-02-22	2005-12-22		ENSG00000173917	ENSG00000173917	"""Homeoboxes / ANTP class : HOXL subclass"""	5113	protein-coding gene	gene with protein product		142967	"""homeo box B2"""	HOX2, HOX2H	1973146, 1358459	Standard	XM_005257276	Approved		uc002inm.3	P14652	OTTHUMG00000159930	ENST00000330070.4:c.1005T>C	17.37:g.46620496A>G		P10913|P17485	ENST00000330070.4	37	CCDS11527.1																																																																																			HOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358384.2		-68.455214	0	24	239	0	0	1	0		4	6.716725	276	0.014286
DHTKD1	55526	broad.mit.edu	hg19	10	12160871	12160871	+	Silent	SNP	G	G	A	rs143353830	byFrequency	TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr10:12160871G>A	ENST00000263035.4	+	15	2588	c.2526G>A	c.(2524-2526)ccG>ccA	p.P842P		NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	842		glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding	breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)		GCCCCTTCCCGTTGGATTCTT	0.443	0	144.0	140.0	142.0	10	12160871	2203	4300	6503	SO:0001819	synonymous_variant	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192		23537	protein-coding gene	gene with protein product		614984			10997877	Standard	NM_018706	Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2526G>A	10.37:g.12160871G>A		Q68CU5|Q9BUM8|Q9HCE2	ENST00000263035.4	37	CCDS7087.1																																																																																			DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1		-19.194786	0	-11	177	0	0	1	0	NM_018706	4	6.464803	106	0.036364
BAP1	8314	broad.mit.edu	hg19	3	52437899	52437899	+	Frame_Shift_Del	DEL	T	T	-			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr3:52437899delT	ENST00000460680.1	-	13	1733	c.1262delA	c.(1261-1263)aagfs	p.K421fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.K403fs	NM_004656.2	NP_004647.1	Q92560	BAP1_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	421		monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	CCCTGTTCCCTTCCCCTTATA	0.557	0	77.0	81.0	80.0	3	52437899	2203	4300	6503	SO:0001589	frameshift_variant	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930		950	protein-coding gene	gene with protein product		603089			9528852	Standard	NM_004656	Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1262delA	3.37:g.52437899delT	ENSP00000417132:p.Lys421fs	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	ENST00000460680.1	37	CCDS2853.1																																																																																			BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	.	.		9	81						38		11	0.78
BAP1	8314	broad.mit.edu	hg19	3	52437898	52437899	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-YZ-A984-01A-11D-A39W-08	TCGA-YZ-A984-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5de40e2-d2f6-4027-a8ad-f910915e22e7	5111a54d-a424-4c60-b712-670f14bb3450	g.chr3:52437898_52437899delCT	ENST00000460680.1	-	13	1733_1734	c.1262_1263delAG	c.(1261-1263)aagfs	p.K421fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.K403fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0		anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	TCCCTGTTCCCTTCCCCTTATA	0.554	0									SO:0001589	frameshift_variant	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930		950	protein-coding gene	gene with protein product		603089			9528852	Standard	NM_004656	Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1262_1263delAG	3:g.52437898_52437899delCT	ENSP00000417132:p.Lys421fs	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	ENST00000460680.1		CCDS2853.1																																																																																			BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	1.985000e+01	1.015700e+02		9	80						37		10	8.160000e-01