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
DSCR10	0	broad.mit.edu	hg19	21	39580548	39580548	+	RNA	SNP	C	C	T			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chr21:39580548C>T	ENST00000432141.1	+	0	670					NR_027695.1																TGTGGGTTTGCCATCGAAGGA	0.413	0	259.0	253.0	255.0	21	39580548	2203	4300	6503			AB066291		21q22.13	2012-10-16	2011-02-24		ENSG00000233316	ENSG00000233316	"""Long non-coding RNAs"""	16302	non-coding RNA	RNA, long non-coding			"""Down syndrome critical region gene 10"""		12168953	Standard	NR_027695	Approved		uc010gnt.2	P59022	OTTHUMG00000090611		21.37:g.39580548C>T		Q52LN2	ENST00000432141.1	37																																																																																				DSCR10-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000207199.1		-45.484558	0	-32	227	0	0	1	0	NR_027695.1	4	7.077458	199	0.019704
TRIM68	55128	broad.mit.edu	hg19	11	4626372	4626372	+	Missense_Mutation	SNP	G	G	C			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chr11:4626372G>C	ENST00000300747.5	-	2	652	c.363C>G	c.(361-363)agC>agG	p.S121R		NM_018073.6	NP_060543.5	Q6AZZ1	TRI68_HUMAN	tripartite motif containing 68	121		protein autoubiquitination|regulation of androgen receptor signaling pathway	Golgi apparatus|nucleolus|perinuclear region of cytoplasm	androgen receptor binding|histone acetyltransferase binding|ubiquitin-protein ligase activity|zinc ion binding	breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)	CTGGGGACTGGCTGCAGGCCT	0.552	0	117.0	100.0	106.0	11	4626372	2201	4298	6499	SO:0001583	missense	AF360739	CCDS31356.1	11p15.4	2013-01-09	2011-01-25	2004-11-17		ENSG00000167333	"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	21161	protein-coding gene	gene with protein product		613184	"""ring finger protein 137"", ""tripartite motif-containing 68"""	RNF137	11597395	Standard	NM_018073	Approved	SS-56, FLJ10369	uc001lzf.2	Q6AZZ1		ENST00000300747.5:c.363C>G	11.37:g.4626372G>C	ENSP00000300747:p.Ser121Arg	A6NI19|A8K551|B3KPM5|B4DVK4|Q8WZ70|Q96LE5|Q96PF7|Q9H9C2|Q9NW18	ENST00000300747.5	37	CCDS31356.1	.	.	.	.	.	.	.	.	.	.	G	0.026	-1.371813	0.01225	.	.	ENSG00000167333	ENST00000300747;ENST00000533021	T;T	0.41758	0.99;0.99	4.67	0.224	0.15297	Zinc finger, B-box (3);	0.911108	0.09364	N	0.812418	T	0.18718	0.0449	N	0.12611	0.24	0.09310	N	1	B;B	0.13594	0.008;0.006	B;B	0.16289	0.01;0.015	T	0.26052	-1.0114	10	0.14656	T	0.56	.	1.7882	0.03046	0.1864:0.2892:0.3766:0.1477	.	121;121	E9PR29;Q6AZZ1	.;TRI68_HUMAN	R	121	ENSP00000300747:S121R;ENSP00000436112:S121R	ENSP00000300747:S121R	S	-	3	2	TRIM68	4582948	0.000000	0.05858	0.004000	0.12327	0.244000	0.25665	-0.114000	0.10757	-0.044000	0.13491	0.549000	0.68633	AGC	TRIM68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385948.1		74.479091	0	-28	66	0	0	1	0	NM_018073	24	76.248790	48	0.333333
CALD1	800	broad.mit.edu	hg19	7	134620492	134620492	+	Silent	SNP	C	C	T			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chr7:134620492C>T	ENST00000361388.2	+	6	1141	c.675C>T	c.(673-675)gaC>gaT	p.D225D	CALD1_ENST00000495522.1_Silent_p.D219D|CALD1_ENST00000424922.1_Intron|CALD1_ENST00000422748.1_Silent_p.D225D|CALD1_ENST00000543443.1_Intron|CALD1_ENST00000361675.2_Silent_p.D454D|CALD1_ENST00000417172.1_Intron|CALD1_ENST00000393118.2_Silent_p.D219D|CALD1_ENST00000361901.2_Intron	NM_033138.3|NM_033157.3	NP_149129.2|NP_149347.2	Q05682	CALD1_HUMAN	caldesmon 1	454		cellular component movement|muscle contraction	cytosol|focal adhesion|myofibril	actin binding|calmodulin binding|myosin binding|tropomyosin binding	NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43					TCCAAGAAGACAAGCCTACCT	0.368	0	79.0	72.0	75.0	7	134620492	2203	4300	6503	SO:0001819	synonymous_variant	M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786		1441	protein-coding gene	gene with protein product		114213			1885618	Standard	NM_004342	Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.1362C>T	7.37:g.134620492C>T		A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	ENST00000361675.2	37	CCDS5835.1																																																																																			CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1		20.921556	0	5	20	0	0	1	0	NM_033138	7	21.037248	10	0.411765
MUC4	4585	broad.mit.edu	hg19	3	195484122	195484122	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chr3:195484122C>T	ENST00000463781.3	-	18	15523	c.15064G>A	c.(15064-15066)Ggc>Agc	p.G5022S	MUC4_ENST00000475231.1_Missense_Mutation_p.G4970S|MUC4_ENST00000349607.4_Missense_Mutation_p.G735S|MUC4_ENST00000346145.4_Missense_Mutation_p.G786S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1779		cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity	NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)	GATGCCAAGCCAATCTTGGCA	0.552	0	106.0	94.0	98.0	3	195484122	2203	4300	6503	SO:0001583	missense	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113	"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""		1673336	Standard	NM_004532	Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.2356G>A	3.37:g.195484122C>T	ENSP00000304207:p.Gly786Ser	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	ENST00000346145.4	37	CCDS3310.1	.	.	.	.	.	.	.	.	.	.	.	9.460	1.092823	0.20471	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.41400	1.0;1.36;1.26;1.32	5.01	0.987	0.19790	.	1.227080	0.05637	N	0.582679	T	0.20740	0.0499	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;P	0.39352	0.411;0.113;0.113;0.079;0.079;0.669	B;B;B;B;B;B	0.35039	0.194;0.044;0.044;0.031;0.031;0.19	T	0.06588	-1.0818	10	0.06236	T	0.91	-1.0229	6.4887	0.22103	0.0:0.5022:0.0:0.4978	.	4894;735;786;5022;4970;1727	E7ESK3;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;.;.;.;.;.	S	735;786;5022;4970;1522	ENSP00000338109:G735S;ENSP00000304207:G786S;ENSP00000417498:G5022S;ENSP00000420243:G4970S	ENSP00000304207:G786S	G	-	1	0	MUC4	196969793	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.313000	0.08103	-0.127000	0.11661	0.556000	0.70494	GGC	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1		77.296999	0	-14	68	0	0	1	0	NM_018406	24	77.335350	27	0.470588
NPAS1	4861	broad.mit.edu	hg19	19	47542770	47542770	+	Missense_Mutation	SNP	A	A	T			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chr19:47542770A>T	ENST00000602212.1	+	8	1130	c.910A>T	c.(910-912)Atg>Ttg	p.M304L	NPAS1_ENST00000449844.2_Missense_Mutation_p.M304L|NPAS1_ENST00000602189.1_Missense_Mutation_p.M129L|NPAS1_ENST00000439365.2_Missense_Mutation_p.M128L			Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	304	PAS 2.	central nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity	endometrium(2)|kidney(1)|large_intestine(2)|lung(1)	6		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)	CCATGGACACATGATCGTCTT	0.672	0	33.0	32.0	33.0	19	47542770	2203	4296	6499	SO:0001583	missense	U77968	CCDS12694.1	19q13.2-q13.3	2013-05-21				ENSG00000130751	"""Basic helix-loop-helix proteins"""	7894	protein-coding gene	gene with protein product	"""neuronal PAS1"", ""member of PAS superfamily 5"""	603346			9012850, 9079689	Standard	NM_002517	Approved	MOP5, PASD5, bHLHe11	uc002pfy.3	Q99742		ENST00000602212.1:c.910A>T	19.37:g.47542770A>T	ENSP00000469142:p.Met304Leu	B4DR69|Q99632|Q9BY83	ENST00000602212.1	37	CCDS12694.1	.	.	.	.	.	.	.	.	.	.	A	18.24	3.580722	0.65992	.	.	ENSG00000130751	ENST00000449844;ENST00000439365	T;T	0.21734	1.99;1.99	4.56	4.56	0.56223	PAS (1);	0.197400	0.41605	D	0.000853	T	0.22781	0.0550	M	0.68317	2.08	0.44985	D	0.998006	B;B	0.28055	0.033;0.199	B;B	0.23852	0.015;0.049	T	0.04440	-1.0951	10	0.52906	T	0.07	.	10.298	0.43635	1.0:0.0:0.0:0.0	.	128;304	B4DR69;Q99742	.;NPAS1_HUMAN	L	304;128	ENSP00000405290:M304L;ENSP00000398689:M128L	ENSP00000398689:M128L	M	+	1	0	NPAS1	52234610	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.989000	0.70587	1.703000	0.51240	0.459000	0.35465	ATG	NPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466658.1		84.254559	0	-21	32	0	0	1	0	NM_002517	26	84.424875	20	0.565217
SCLT1	132320	ucsc.edu	hg19	4	129880901	129880901	+	Silent	SNP	A	A	G			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae																										TCGGTTCTTAATTGGTTGGCT	0.363	0	145.0	135.0	139.0	4	129880901	2203	4300	6503	SO:0001819	synonymous_variant	AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466		26406	protein-coding gene	gene with protein product		611399			15797711	Standard	XM_005262732	Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.901T>C	4.37:g.129880901A>G		A4QN04|Q0VAH2|Q6P2M4	ENST00000281142.5	37	CCDS3740.1																																																																																			SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2				-13	68					NM_144643	4		33	
GNAQ	2776	broad.mit.edu	hg19	9	80409488	80409488	+	Missense_Mutation	SNP	T	T	A	rs121913492		TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chr9:80409488T>A	ENST00000286548.4	-	5	848	c.626A>T	c.(625-627)cAa>cTa	p.Q209L	GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7L	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	209		activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity	NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302					CTCTGACCTTTGGCCCCCTAC	0.348	153	108.0	105.0	106.0	9	80409488	2203	4300	6503	SO:0001583	missense		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052		4390	protein-coding gene	gene with protein product		600998			8825633	Standard	NM_002072	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.626A>T	9.37:g.80409488T>A	ENSP00000286548:p.Gln209Leu	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	ENST00000286548.4	37	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.985495	0.93044	.	.	ENSG00000156052	ENST00000286548;ENST00000397476	D;D	0.91237	-2.81;-2.81	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.97573	0.9205	H	0.99347	4.525	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99402	1.0928	10	0.87932	D	0	.	15.9502	0.79827	0.0:0.0:0.0:1.0	.	209	P50148	GNAQ_HUMAN	L	209;7	ENSP00000286548:Q209L;ENSP00000443197:Q7L	ENSP00000286548:Q209L	Q	-	2	0	GNAQ	79599308	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.040000	0.89188	2.167000	0.68274	0.460000	0.39030	CAA	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1		153.725937	0	-33	79	0	0	1	0	NM_002072	47	153.728276	46	0.505376
POLR1B	84172	broad.mit.edu	hg19	2	113332606	113332606	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chr2:113332606C>T	ENST00000263331.5	+	15	3288	c.2708C>T	c.(2707-2709)cCt>cTt	p.P903L	POLR1B_ENST00000417433.2_Missense_Mutation_p.P847L|POLR1B_ENST00000541869.1_Missense_Mutation_p.P941L|POLR1B_ENST00000409894.3_Missense_Mutation_p.P720L|POLR1B_ENST00000537335.1_Missense_Mutation_p.P692L	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	903		termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding	breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42					GAGGACATGCCTTTTACTGAG	0.502	0	139.0	135.0	137.0	2	113332606	2203	4300	6503	SO:0001583	missense	AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630	"""RNA polymerase subunits"""	20454	protein-coding gene	gene with protein product		602000				Standard	NM_001137604	Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000417433.2:c.2540C>T	2.37:g.113332606C>T	ENSP00000405358:p.Pro847Leu	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	ENST00000417433.2	37	CCDS46395.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.948577	0.92593	.	.	ENSG00000125630	ENST00000263331;ENST00000541869;ENST00000409894;ENST00000537335;ENST00000417433;ENST00000458012;ENST00000536096	D;D;D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11;-3.11;-3.11	5.91	5.91	0.95273	DNA-directed RNA polymerase, subunit 2, domain 6 (2);	0.000000	0.85682	D	0.000000	D	0.97601	0.9214	H	0.95884	3.735	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	D	0.98218	1.0476	10	0.72032	D	0.01	-19.2794	19.07	0.93130	0.0:1.0:0.0:0.0	.	941;720;847;903	F5GZX4;F8W898;Q9H9Y6-2;Q9H9Y6	.;.;.;RPA2_HUMAN	L	903;941;720;692;847;288;262	ENSP00000263331:P903L;ENSP00000444136:P941L;ENSP00000387143:P720L;ENSP00000437914:P692L;ENSP00000405358:P847L;ENSP00000394408:P288L	ENSP00000263331:P903L	P	+	2	0	POLR1B	113049077	1.000000	0.71417	0.974000	0.42286	0.984000	0.73092	7.438000	0.80431	2.793000	0.96121	0.655000	0.94253	CCT	POLR1B-005	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000330626.1		96.377266	0	-9	101	0	0	1	0	NM_019014	32	97.816508	56	0.363636
SPHKAP	80309	broad.mit.edu	hg19	2	228883588	228883588	+	Missense_Mutation	SNP	T	T	A			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chr2:228883588T>A	ENST00000392056.3	-	7	2028	c.1982A>T	c.(1981-1983)aAt>aTt	p.N661I	SPHKAP_ENST00000344657.5_Missense_Mutation_p.N661I	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	661			cytoplasm	protein binding	NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)	CCTGACGACATTTTCTGAGCA	0.443	0	180.0	165.0	170.0	2	228883588	2203	4300	6503	SO:0001583	missense		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820	"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646			12080051, 11214970	Standard	NM_030623	Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.1982A>T	2.37:g.228883588T>A	ENSP00000375909:p.Asn661Ile	Q68DA3|Q68DR8|Q9C0I5	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	T	15.85	2.954257	0.53293	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.51071	0.72;0.72	5.54	0.14	0.14804	.	0.616477	0.18172	N	0.149421	T	0.52500	0.1738	M	0.63843	1.955	0.09310	N	1	P;D	0.54397	0.766;0.966	B;P	0.56823	0.174;0.807	T	0.43540	-0.9385	10	0.59425	D	0.04	.	5.6187	0.17446	0.1157:0.2735:0.0:0.6108	.	661;661	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	I	661	ENSP00000375909:N661I;ENSP00000339886:N661I	ENSP00000339886:N661I	N	-	2	0	SPHKAP	228591832	0.913000	0.31002	0.031000	0.17742	0.988000	0.76386	1.595000	0.36708	-0.124000	0.11724	0.533000	0.62120	AAT	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1		241.323817	0	5	171	0	0	1	0	NM_030623	76	241.323817	76	0.500000
PLSCR5	389158	broad.mit.edu	hg19	3	146309609	146309609	+	Silent	SNP	G	G	C			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chr3:146309609G>C	ENST00000443512.1	-	5	1516	c.513C>G	c.(511-513)ccC>ccG	p.P171P	PLSCR5_ENST00000492200.1_Silent_p.P171P|PLSCR5_ENST00000482567.1_Silent_p.P159P	NM_001085420.1	NP_001078889.1	A0PG75	PLS5_HUMAN	phospholipid scramblase family, member 5	171					endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12					TAGGCAGAAAGGGGTCCCACT	0.378	0	65.0	61.0	62.0	3	146309609	1840	4097	5937	SO:0001819	synonymous_variant	AY436642	CCDS46931.1	3q24	2004-06-28			ENSG00000231213	ENSG00000231213		19952	protein-coding gene	gene with protein product						Standard	NM_001085420	Approved		uc010hvc.3	A0PG75	OTTHUMG00000159437	ENST00000443512.1:c.513C>G	3.37:g.146309609G>C		B2RXK5	ENST00000443512.1	37	CCDS46931.1																																																																																			PLSCR5-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355365.1		29.746800	0	-2	14	0	0	1	0	XM_371670	10	29.964771	15	0.400000
C17orf47	284083	broad.mit.edu	hg19	17	56620130	56620130	+	Missense_Mutation	SNP	A	A	G			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chr17:56620130A>G	ENST00000321691.3	-	1	1599	c.1418T>C	c.(1417-1419)cTg>cCg	p.L473P	RP11-112H10.4_ENST00000580589.1_RNA|RP11-112H10.4_ENST00000578022.1_RNA|RP11-112H10.4_ENST00000580769.1_RNA	NM_001038704.2	NP_001033793	Q8NEP4	CQ047_HUMAN	chromosome 17 open reading frame 47	473					NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	24	Medulloblastoma(34;0.127)|all_neural(34;0.237)				CTGGAACTTCAGATCCTCACA	0.493	0	207.0	217.0	214.0	17	56620130	2203	4300	6503	SO:0001583	missense		CCDS32691.1	17q23.2	2012-10-11			ENSG00000181013	ENSG00000181013		26844	protein-coding gene	gene with protein product						Standard	NM_001038704	Approved	FLJ40121	uc002iwq.2	Q8NEP4	OTTHUMG00000179244	ENST00000321691.3:c.1418T>C	17.37:g.56620130A>G	ENSP00000354874:p.Leu473Pro	Q8N821	ENST00000321691.3	37	CCDS32691.1	.	.	.	.	.	.	.	.	.	.	A	5.368	0.253205	0.10185	.	.	ENSG00000181013	ENST00000321691	T	0.40225	1.04	5.76	3.53	0.40419	.	1.197710	0.06144	N	0.672897	T	0.28928	0.0718	N	0.17082	0.46	0.19575	N	0.999965	B	0.32382	0.368	B	0.32677	0.15	T	0.29088	-1.0023	10	0.48119	T	0.1	5.0836	6.0145	0.19594	0.7513:0.1648:0.0839:0.0	.	473	Q8NEP4	CQ047_HUMAN	P	473	ENSP00000354874:L473P	ENSP00000354874:L473P	L	-	2	0	C17orf47	53975129	0.001000	0.12720	0.001000	0.08648	0.024000	0.10985	0.883000	0.28200	0.443000	0.26582	-0.466000	0.05196	CTG	C17orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445443.1		-45.686738	0	-47	212	0	0	1	0	NM_001038704	4	6.302427	197	0.019900
EIF1AX	1964	broad.mit.edu	hg19	X	20156740	20156740	+	Splice_Site	SNP	C	C	T			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chrX:20156740C>T	ENST00000379607.5	-	2	220	c.17G>A	c.(16-18)gGt>gAt	p.G6D	EIF1AX_ENST00000379593.1_Intron	NM_001412.3	NP_001403.1	P47813	IF1AX_HUMAN	eukaryotic translation initiation factor 1A, X-linked	6			cytosol	translation initiation factor activity	endometrium(2)|lung(1)|ovary(1)|prostate(1)	5					ACCTCCTTTACCTGATGGTTT	0.299	0	130.0	120.0	123.0	X	20156740	2203	4300	6503	SO:0001630	splice_region_variant	L18960	CCDS14196.1	Xp22.13	2014-02-19	2002-11-28	2004-05-26	ENSG00000173674	ENSG00000173674		3250	protein-coding gene	gene with protein product		300186	"""eukaryotic translation initiation factor 1A, X chromosome"""	EIF4C, EIF1A	8106356, 9381176	Standard	NM_001412	Approved	eIF-1A, eIF-4C	uc004czt.3	P47813	OTTHUMG00000022704	ENST00000379607.5:c.17-1G>A	X.37:g.20156740C>T		B2R5U5|Q0VGC2|Q5JPS5|Q5JPS6	ENST00000379607.5	37	CCDS14196.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.689024	0.68271	.	.	ENSG00000173674	ENST00000379607	T	0.45668	0.89	4.84	4.84	0.62591	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	.	.	.	.	T	0.73885	0.3644	H	0.95780	3.72	0.80722	D	1	D	0.55800	0.973	D	0.63703	0.917	D	0.83652	0.0156	9	0.87932	D	0	.	17.4345	0.87547	0.0:1.0:0.0:0.0	.	6	P47813	IF1AX_HUMAN	D	6	ENSP00000368927:G6D	ENSP00000368927:G6D	G	-	2	0	EIF1AX	20066661	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	7.237000	0.78164	2.129000	0.65627	0.600000	0.82982	GGT	EIF1AX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058913.1		94.077512	0	-79	74	0	0	1	0		27	98.716581	2	0.931034
CSPG4	1464	broad.mit.edu	hg19	15	75977618	75977618	+	Missense_Mutation	SNP	G	G	A			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chr15:75977618G>A	ENST00000308508.5	-	4	4306	c.4214C>T	c.(4213-4215)gCc>gTc	p.A1405V		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1405	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1 (By similarity).	angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity	breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48					CTTCTGCAGGGCTCCATGCTG	0.667	0	32.0	36.0	34.0	15	75977618	2196	4288	6484	SO:0001583	missense	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546	"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""		8790396, 16407841	Standard	NM_001897	Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.4214C>T	15.37:g.75977618G>A	ENSP00000312506:p.Ala1405Val	D3DW77|Q92675	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	2.794	-0.250600	0.05867	.	.	ENSG00000173546	ENST00000308508	T	0.45668	0.89	4.76	2.74	0.32292	.	0.805243	0.11285	N	0.579940	T	0.33352	0.0860	L	0.51422	1.61	0.32270	N	0.569036	B	0.13145	0.007	B	0.09377	0.004	T	0.35798	-0.9774	10	0.16896	T	0.51	.	7.9412	0.29959	0.0936:0.1614:0.745:0.0	.	1405	Q6UVK1	CSPG4_HUMAN	V	1405	ENSP00000312506:A1405V	ENSP00000312506:A1405V	A	-	2	0	CSPG4	73764673	0.213000	0.23551	0.950000	0.38849	0.069000	0.16628	0.432000	0.21461	1.133000	0.42147	0.505000	0.49811	GCC	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1		-5.623958	0	-8	45	0	0	1	0	NM_001897	3	6.430147	54	0.052632
TMC2	117532	broad.mit.edu	hg19	20	2597933	2597933	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-A880-01A-11D-A39W-08	TCGA-WC-A880-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0e3e20e6-94c6-4561-b023-9ebd11545994	0714c842-679d-47ab-85b2-b3f269b2c2ae	g.chr20:2597933C>T	ENST00000358864.1	+	16	2171	c.2156C>T	c.(2155-2157)cCc>cTc	p.P719L	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	719			integral to membrane		NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35					TCCCTCCCACCCTCCTTTGAC	0.622	0	103.0	73.0	84.0	20	2597933	2203	4300	6503	SO:0001583	missense	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488		16527	protein-coding gene	gene with protein product		606707	"""transmembrane, cochlear expressed, 2"""	C20orf145	11850618, 12906855	Standard	XM_005260660	Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.2156C>T	20.37:g.2597933C>T	ENSP00000351732:p.Pro719Leu	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	ENST00000358864.1	37	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	C	29.5	5.011478	0.93346	.	.	ENSG00000149488	ENST00000358864	T	0.74842	-0.88	5.35	5.35	0.76521	.	0.049001	0.85682	N	0.000000	D	0.88074	0.6339	M	0.86740	2.835	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89780	0.3960	10	0.87932	D	0	-21.2049	16.9454	0.86228	0.0:1.0:0.0:0.0	.	719	Q8TDI7	TMC2_HUMAN	L	719	ENSP00000351732:P719L	ENSP00000351732:P719L	P	+	2	0	TMC2	2545933	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.666000	0.90696	0.650000	0.86243	CCC	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2		37.204177	0	-5	48	0	0	1	0		14	38.514641	30	0.318182