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
FSHR	0	broad.mit.edu	hg19	2	49381416	49381416	+	Silent	SNP	A	A	G			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr2:49381416A>G	ENST00000406846.2	-	1	260	c.141T>C	c.(139-141)aaT>aaC	p.N47N	FSHR_ENST00000346173.3_Silent_p.N47N|FSHR_ENST00000304421.4_Silent_p.N47N	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	47		female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding	NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		GTTCAATGGCATTCCTCGGGA	0.463	0	70.0	69.0	69.0	2	49381416	2203	4300	6503	SO:0001819	synonymous_variant		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820	"""GPCR / Class A : Gonadotropin and TSH receptors"""	3969	protein-coding gene	gene with protein product		136435		ODG1	8230163, 8855829	Standard	NM_000145	Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.141T>C	2.37:g.49381416A>G		A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	ENST00000406846.2	37	CCDS1843.1																																																																																			FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2		25.729183	0	-8	36	0	0	1	0		10	28.003147	30	0.250000
STK4	6789	broad.mit.edu	hg19	20	43653753	43653753	+	Silent	SNP	G	G	A			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr20:43653753G>A	ENST00000372806.3	+	10	1382	c.1287G>A	c.(1285-1287)caG>caA	p.Q429Q	STK4_ENST00000396731.4_Silent_p.Q429Q|STK4_ENST00000372801.1_Silent_p.Q429Q|STK4_ENST00000499879.2_Silent_p.Q374Q	NM_006282.2	NP_006273.1	Q13043	STK4_HUMAN	serine/threonine kinase 4	429		apoptosis|cell morphogenesis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of apoptosis|protein autophosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein homodimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity|transcription factor binding	NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Myeloproliferative disorder(115;0.0122)			AAATACCACAGGATGGAGACT	0.363	0	104.0	100.0	101.0	20	43653753	2203	4300	6503	SO:0001819	synonymous_variant		CCDS13341.1	20q11.2-q13.2	2014-09-17			ENSG00000101109	ENSG00000101109		11408	protein-coding gene	gene with protein product	"""mammalian sterile 20-like 1"", ""yeast Ste20-like"", ""kinase responsive to stress 2"""	604965			8816758, 9545236, 11517310	Standard	NM_006282	Approved	MST1, KRS2, YSK3	uc002xnb.3	Q13043	OTTHUMG00000033059	ENST00000372806.3:c.1287G>A	20.37:g.43653753G>A		B2RCR8|Q15802|Q4G156|Q5H982|Q6PD60|Q9BR32|Q9NTZ4	ENST00000372806.3	37	CCDS13341.1																																																																																			STK4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080401.4		14.098175	0	8	62	0	0	1	0	NM_006282	7	18.522913	35	0.166667
PSAP	5660	broad.mit.edu	hg19	10	73588803	73588803	+	Missense_Mutation	SNP	T	T	C			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr10:73588803T>C	ENST00000394936.3	-	5	554	c.407A>G	c.(406-408)aAc>aGc	p.N136S	PSAP_ENST00000394934.1_Missense_Mutation_p.N136S			P07602	SAP_HUMAN	prosaposin	136	Saposin B-type 1.	glycosphingolipid metabolic process|lipid transport|platelet activation|platelet degranulation	extracellular space|Golgi apparatus|integral to membrane|lysosomal lumen	enzyme activator activity|lipid binding	endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13					CTCGCAGAGGTTGAGAGCAGA	0.552	0	73.0	72.0	73.0	10	73588803	2203	4300	6503	SO:0001583	missense	BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746	"""Endogenous ligands"""	9498	protein-coding gene	gene with protein product	"""variant Gaucher disease and variant metachromatic leukodystrophy"""	176801	"""sphingolipid activator protein-1"""	SAP1, GLBA	2717620	Standard	NM_001042465	Approved		uc001jsm.3	P07602	OTTHUMG00000018429	ENST00000394936.3:c.407A>G	10.37:g.73588803T>C	ENSP00000378394:p.Asn136Ser	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	ENST00000394936.3	37	CCDS7311.1	.	.	.	.	.	.	.	.	.	.	T	6.204	0.405741	0.11754	2.27E-4	0.0	ENSG00000197746	ENST00000394936;ENST00000373120;ENST00000357471;ENST00000394934;ENST00000404083;ENST00000394940	T;T	0.74106	-0.81;-0.81	5.0	-1.83	0.07833	Saposin-like (2);Saposin-like type B, 2 (1);Saposin B (2);	0.596935	0.18687	N	0.133984	T	0.44871	0.1314	N	0.03608	-0.345	0.23401	N	0.997756	B	0.09022	0.002	B	0.11329	0.006	T	0.34950	-0.9808	10	0.37606	T	0.19	-8.1092	7.1844	0.25791	0.0:0.4344:0.2114:0.3542	.	136	P07602	SAP_HUMAN	S	136;136;136;136;139;61	ENSP00000378394:N136S;ENSP00000378392:N136S	ENSP00000350063:N136S	N	-	2	0	PSAP	73258809	0.000000	0.05858	0.993000	0.49108	0.888000	0.51559	-0.356000	0.07661	0.018000	0.15052	-0.736000	0.03550	AAC	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1		26.325878	0	-40	87	0	0	1	0	NM_002778	13	35.435608	69	0.158537
LAMA5	3911	ucsc.edu	hg19	20	60885315	60885315	+	Silent	SNP	G	G	T			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf																										TGACTGCCAGGGGCCGCACCT	0.652	0	33.0	39.0	37.0	20	60885315	2201	4294	6495	SO:0001819	synonymous_variant	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702	"""Laminins"""	6485	protein-coding gene	gene with protein product		601033			9271224	Standard	NM_005560	Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.10653C>A	20.37:g.60885315G>T		Q8TDF8|Q8WZA7|Q9H1P1	ENST00000252999.3	37	CCDS33502.1																																																																																			LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2				-3	62					NM_005560	4		37	
LYPD4	147719	broad.mit.edu	hg19	19	42342289	42342289	+	Silent	SNP	C	C	T			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr19:42342289C>T	ENST00000330743.3	-	4	1469	c.258G>A	c.(256-258)tcG>tcA	p.S86S	LYPD4_ENST00000343055.4_Silent_p.S51S|LYPD4_ENST00000601246.1_Silent_p.S51S	NM_173506.4	NP_775777.3	Q6UWN0	LYPD4_HUMAN	LY6/PLAUR domain containing 4	86	Poly-Ser.		anchored to membrane|plasma membrane		breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12					CAGGGTAAGACGAAGACGAGC	0.557	0	98.0	89.0	92.0	19	42342289	2203	4300	6503	SO:0001819	synonymous_variant	AY358726	CCDS12587.1	19q13.2	2008-02-05				ENSG00000273111		28659	protein-coding gene	gene with protein product					12975309	Standard	XM_005278383	Approved	MGC42718	uc002orp.1	Q6UWN0		ENST00000330743.3:c.258G>A	19.37:g.42342289C>T		Q8IYW0	ENST00000330743.3	37	CCDS12587.1																																																																																			LYPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463039.1		1.802766	0	-13	34	0	0	1	0	NM_173506	3	6.598771	27	0.100000
OR1L1	26737	broad.mit.edu	hg19	9	125424359	125424359	+	Missense_Mutation	SNP	G	G	A			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr9:125424359G>A	ENST00000373686.1	+	1	515	c.515G>A	c.(514-516)cGc>cAc	p.R172H	OR1L1_ENST00000309623.1_Missense_Mutation_p.R122H			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1	172		sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	breast(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)	17					GCCATTGACCGCTATGTGGCC	0.458	0	260.0	235.0	243.0	9	125424359	2203	4300	6503	SO:0001583	missense		CCDS35127.1, CCDS35127.2	9q33.2	2013-09-20			ENSG00000173679	ENSG00000173679	"""GPCR / Class A : Olfactory receptors"""	8213	protein-coding gene	gene with protein product				OR1L2		Standard	NM_001005236	Approved	OR9-C	uc022bmz.1	Q8NH94	OTTHUMG00000020618	ENST00000309623.1:c.365G>A	9.37:g.125424359G>A	ENSP00000310773:p.Arg122His	Q5T7Z3|Q6IFN2	ENST00000309623.1	37	CCDS35127.2	.	.	.	.	.	.	.	.	.	.	G	13.83	2.353302	0.41700	.	.	ENSG00000173679	ENST00000373686;ENST00000309623	T;T	0.77489	-1.1;-1.1	3.11	2.2	0.27929	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.73273	0.3566	M	0.61703	1.905	0.27518	N	0.951488	B	0.21520	0.057	B	0.20184	0.028	T	0.66968	-0.5789	9	0.72032	D	0.01	.	9.2331	0.37450	0.1151:0.0:0.8849:0.0	.	172	Q8NH94	OR1L1_HUMAN	H	172;122	ENSP00000362790:R172H;ENSP00000310773:R122H	ENSP00000310773:R122H	R	+	2	0	OR1L1	124464180	0.996000	0.38824	0.317000	0.25265	0.010000	0.07245	7.528000	0.81941	0.623000	0.30267	0.313000	0.20887	CGC	OR1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053949.1		-21.064550	0	-24	154	0	0	1	0		4	7.403119	116	0.033333
KCNH5	27133	broad.mit.edu	hg19	14	63269191	63269191	+	Missense_Mutation	SNP	G	G	A			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr14:63269191G>A	ENST00000322893.7	-	9	1946	c.1678C>T	c.(1678-1680)Cgc>Tgc	p.R560C	KCNH5_ENST00000394968.1_Missense_Mutation_p.R502C|KCNH5_ENST00000420622.2_Missense_Mutation_p.R560C	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	560		regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)	GCCAAGGCGCGCAGACACCCA	0.512	0	82.0	77.0	79.0	14	63269191	2203	4300	6503	SO:0001583	missense	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015	"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716			9738473, 16382104	Standard	NM_139318	Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.1678C>T	14.37:g.63269191G>A	ENSP00000321427:p.Arg560Cys	C9JP98	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.948501	0.73787	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968	D;D;D	0.96940	-4.18;-4.18;-4.18	5.13	4.22	0.49857	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.000000	0.85682	D	0.000000	D	0.98413	0.9472	M	0.91038	3.17	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99564	1.0969	10	0.87932	D	0	.	15.7242	0.77740	0.0:0.1373:0.8627:0.0	.	502;560;560	Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;KCNH5_HUMAN	C	560;560;502	ENSP00000321427:R560C;ENSP00000395439:R560C;ENSP00000378419:R502C	ENSP00000321427:R560C	R	-	1	0	KCNH5	62338944	1.000000	0.71417	0.977000	0.42913	0.897000	0.52465	5.628000	0.67791	1.265000	0.44215	0.563000	0.77884	CGC	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1		9.419160	0	0	68	0	0	1	0	NM_139318	6	15.053430	38	0.136364
GNA11	2767	broad.mit.edu	hg19	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr19:3118942A>T	ENST00000078429.4	+	5	868	c.626A>T	c.(625-627)cAg>cTg	p.Q209L	AC005262.3_ENST00000587701.1_RNA|GNA11_ENST00000586180.1_3'UTR	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	209		activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)	GTGGGGGGCCAGCGGTCGGAG	0.612	82	104.0	89.0	94.0	19	3118942	2203	4300	6503	SO:0001583	missense	AF493900	CCDS12103.1	19p13.3	2014-02-04			ENSG00000088256	ENSG00000088256		4379	protein-coding gene	gene with protein product		139313	"""hypocalciuric hypercalcemia 2"""	HHC2	1302014, 23802516	Standard	NM_002067	Approved	FBH, FBH2, FHH2	uc002lxd.3	P29992	OTTHUMG00000180631	ENST00000078429.4:c.626A>T	19.37:g.3118942A>T	ENSP00000078429:p.Gln209Leu	O15109|Q14350|Q6IB00	ENST00000078429.4	37	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	.	15.05	2.718086	0.48622	.	.	ENSG00000088256	ENST00000078429	D	0.91237	-2.81	3.26	3.26	0.37387	.	0.000000	0.64402	U	0.000006	D	0.96950	0.9004	H	0.99357	4.53	0.80722	D	1	D	0.59767	0.986	D	0.68483	0.958	D	0.96823	0.9605	10	0.87932	D	0	.	10.7338	0.46113	1.0:0.0:0.0:0.0	.	209	P29992	GNA11_HUMAN	L	209	ENSP00000078429:Q209L	ENSP00000078429:Q209L	Q	+	2	0	GNA11	3069942	1.000000	0.71417	0.438000	0.26821	0.027000	0.11550	9.104000	0.94239	1.256000	0.44068	0.379000	0.24179	CAG	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2		17.309185	0	-15	66	0	0	1	0	NM_002067	7	19.449272	24	0.225806
RNF167	26001	broad.mit.edu	hg19	17	4846548	4846548	+	Missense_Mutation	SNP	G	G	A			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr17:4846548G>A	ENST00000262482.6	+	7	1201	c.545G>A	c.(544-546)gGa>gAa	p.G182E	RNF167_ENST00000572430.1_Missense_Mutation_p.G182E|RNF167_ENST00000576229.1_Missense_Mutation_p.G147E|RNF167_ENST00000570492.1_Intron|RNF167_ENST00000571816.1_Missense_Mutation_p.G182E|RNF167_ENST00000575111.1_Missense_Mutation_p.G182E	NM_015528.1	NP_056343.1	Q9H6Y7	RN167_HUMAN	ring finger protein 167	182		negative regulation of cell cycle|protein polyubiquitination	cytoplasm|endomembrane system|integral to membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding	endometrium(1)|large_intestine(2)|lung(1)	4					GGGATTGTGGGACTGCTGGTT	0.547	0	83.0	72.0	76.0	17	4846548	2203	4300	6503	SO:0001583	missense	AL050060	CCDS11060.1	17p13.3	2013-02-21			ENSG00000108523	ENSG00000108523	"""RING-type (C3HC4) zinc fingers"""	24544	protein-coding gene	gene with protein product		610431			23129617, 23353890	Standard	NM_015528	Approved	DKFZP566H073	uc002fzs.3	Q9H6Y7	OTTHUMG00000099397	ENST00000262482.6:c.545G>A	17.37:g.4846548G>A	ENSP00000262482:p.Gly182Glu	D3DTK8|Q6XYE0|Q8NDC1|Q9Y3V1	ENST00000262482.6	37	CCDS11060.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.763871	0.69878	.	.	ENSG00000108523	ENST00000262482	T	0.04156	3.69	5.9	5.9	0.94986	.	0.168939	0.52532	D	0.000076	T	0.18467	0.0443	M	0.76170	2.325	0.44587	D	0.997552	D	0.58620	0.983	D	0.63703	0.917	T	0.00036	-1.2256	10	0.41790	T	0.15	-0.3361	13.364	0.60674	0.0:0.1579:0.8421:0.0	.	182	Q9H6Y7	RN167_HUMAN	E	182	ENSP00000262482:G182E	ENSP00000262482:G182E	G	+	2	0	RNF167	4787293	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.290000	0.59019	2.793000	0.96121	0.563000	0.77884	GGA	RNF167-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216854.3		16.307772	0	-3	51	0	0	1	0	NM_015528	7	18.835121	26	0.212121
EIF2B5	8893	broad.mit.edu	hg19	3	183856019	183856019	+	Silent	SNP	C	C	T			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr3:183856019C>T	ENST00000273783.3	+	5	872	c.750C>T	c.(748-750)agC>agT	p.S250S	EIF2B5_ENST00000444495.1_Silent_p.S250S	NM_003907.2	NP_003898.2	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa	250		astrocyte development|myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|positive regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus|RNA metabolic process	cytosol|eukaryotic translation initiation factor 2B complex|nucleus	guanyl-nucleotide exchange factor activity|transferase activity|translation initiation factor activity|translation initiation factor binding	cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(5)|urinary_tract(1)	27	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		GTCATATCAGCATCTGTTCTC	0.468	0	161.0	147.0	152.0	3	183856019	2203	4300	6503	SO:0001819	synonymous_variant	U23028	CCDS3252.1	3q27.3	2006-07-18	2002-08-29		ENSG00000145191	ENSG00000145191		3261	protein-coding gene	gene with protein product		603945	"""eukaryotic translation initiation factor 2B, subunit 5 (epsilon, 82kD)"""		8688466	Standard	NM_003907	Approved	EIF2Bepsilon, EIF-2B	uc003fmp.3	Q13144	OTTHUMG00000156840	ENST00000273783.3:c.750C>T	3.37:g.183856019C>T		Q541Z1|Q96D04	ENST00000273783.3	37	CCDS3252.1																																																																																			EIF2B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346168.1		23.928331	0	-15	77	0	0	1	0		10	26.379962	31	0.243902
PLAU	5328	broad.mit.edu	hg19	10	75673396	75673396	+	Missense_Mutation	SNP	T	T	C			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr10:75673396T>C	ENST00000446342.1	+	6	991	c.509T>C	c.(508-510)aTc>aCc	p.I170T	C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000494287.1_3'UTR|PLAU_ENST00000372764.3_Missense_Mutation_p.I187T|C10orf55_ENST00000409178.1_Intron|PLAU_ENST00000372762.4_Missense_Mutation_p.I151T	NM_001145031.1	NP_001138503	P00749	UROK_HUMAN	plasminogen activator, urokinase	187	Connecting peptide.	blood coagulation|chemotaxis|fibrinolysis|proteolysis|regulation of cell adhesion mediated by integrin|regulation of receptor activity|regulation of smooth muscle cell migration|regulation of smooth muscle cell-matrix adhesion|signal transduction	cell surface|extracellular space|plasma membrane	serine-type endopeptidase activity	cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(3)|ovary(2)	16	Prostate(51;0.0112)				TTCACCACCATCGAGAACCAG	0.547	0	99.0	117.0	111.0	10	75673396	2203	4300	6503	SO:0001583	missense	BC013575	CCDS7339.1, CCDS44442.1	10q24	2012-10-02			ENSG00000122861	ENSG00000122861		9052	protein-coding gene	gene with protein product		191840			2415429	Standard	NM_002658	Approved	URK, UPA	uc001jwa.3	P00749	OTTHUMG00000018494	ENST00000372764.3:c.560T>C	10.37:g.75673396T>C	ENSP00000361850:p.Ile187Thr	B4DPZ2|Q15844|Q16618|Q53XS3|Q5SWW9|Q969W6	ENST00000372764.3	37	CCDS7339.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.248166	0.39697	.	.	ENSG00000122861	ENST00000446342;ENST00000372764;ENST00000372762;ENST00000372761	D;D;D	0.88509	-2.39;-2.39;-2.39	5.25	0.244	0.15507	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.454666	0.26255	N	0.025427	D	0.83737	0.5319	L	0.52206	1.635	0.09310	N	1	B;B;B;B	0.20368	0.021;0.044;0.034;0.001	B;B;B;B	0.27380	0.079;0.049;0.064;0.002	T	0.73228	-0.4049	10	0.49607	T	0.09	.	8.0973	0.30835	0.0:0.2628:0.0:0.7372	.	170;151;187;187	E7ET40;E7ESM2;B2R7F2;P00749	.;.;.;UROK_HUMAN	T	170;187;151;151	ENSP00000388474:I170T;ENSP00000361850:I187T;ENSP00000361848:I151T	ENSP00000361847:I151T	I	+	2	0	PLAU	75343402	0.071000	0.21146	0.000000	0.03702	0.969000	0.65631	1.239000	0.32719	-0.135000	0.11495	0.528000	0.53228	ATC	PLAU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048727.1		-10.791646	0	-27	176	0	0	1	0	NM_002658	9	6.945374	93	0.088235
TRIML1	339976	broad.mit.edu	hg19	4	189068325	189068325	+	Silent	SNP	G	G	A			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr4:189068325G>A	ENST00000332517.3	+	6	1346	c.1206G>A	c.(1204-1206)gaG>gaA	p.E402E	TRIML1_ENST00000507581.1_3'UTR	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	402	B30.2/SPRY.	multicellular organismal development		ligase activity|zinc ion binding	NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)	ACGTCAGAGAGCCTGTGTGTA	0.493	0	152.0	136.0	141.0	4	189068325	2203	4300	6503	SO:0001819	synonymous_variant	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108	"""RING-type (C3HC4) zinc fingers"""	26698	protein-coding gene	gene with protein product					12477932	Standard	NM_178556	Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.1206G>A	4.37:g.189068325G>A		Q96BE5	ENST00000332517.3	37	CCDS3851.1																																																																																			TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1		59.751651	0	-21	119	0	0	1	0	NM_178556	24	64.688427	69	0.258065
PPARD	5467	broad.mit.edu	hg19	6	35393805	35393805	+	Silent	SNP	C	C	G			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr6:35393805C>G	ENST00000311565.4	+	9	1624	c.1275C>G	c.(1273-1275)acC>acG	p.T425T	PPARD_ENST00000540939.1_Silent_p.T322T|PPARD_ENST00000448077.2_Silent_p.T386T|PPARD_ENST00000360694.3_Silent_p.T425T|PPARD_ENST00000418635.2_Silent_p.T327T	NM_001171818.1	NP_001165289.1	Q03181	PPARD_HUMAN	peroxisome proliferator-activated receptor delta	425	Ligand-binding.	apoptosis|axon ensheathment|cholesterol metabolic process|decidualization|embryo implantation|fatty acid beta-oxidation|fatty acid transport|generation of precursor metabolites and energy|glucose metabolic process|glucose transport|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fat cell differentiation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|linoleic acid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding	autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(4)|liver(2)|lung(9)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23					AGACCGAAACCGAGACCTCGC	0.607	0	100.0	84.0	89.0	6	35393805	2203	4300	6503	SO:0001819	synonymous_variant	L07592	CCDS4803.1, CCDS4804.1, CCDS54994.1, CCDS54995.1	6p21.2	2013-01-16	2006-10-17		ENSG00000112033	ENSG00000112033	"""Nuclear hormone receptors"""	9235	protein-coding gene	gene with protein product		600409	"""peroxisome proliferative activated receptor, delta"""		1333051	Standard	NM_177435	Approved	NUC1, NUCII, FAAR, NR1C2	uc003okm.3	Q03181	OTTHUMG00000014567	ENST00000311565.4:c.1275C>G	6.37:g.35393805C>G		A8K6J6|B4E3V3|B6ZGS1|B7Z3W1|E9PE18|Q5D1P0|Q7Z5K0|Q9BUD4	ENST00000311565.4	37	CCDS4803.1																																																																																			PPARD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040288.1		10.356799	0	-25	27	0	0	1	0	NM_006238	5	13.738804	26	0.161290
DRG1	4733	broad.mit.edu	hg19	22	31816310	31816310	+	Missense_Mutation	SNP	A	A	G			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr22:31816310A>G	ENST00000331457.4	+	5	642	c.481A>G	c.(481-483)Att>Gtt	p.I161V	DRG1_ENST00000433341.1_3'UTR	NM_004147.3	NP_004138.1	Q9Y295	DRG1_HUMAN	developmentally regulated GTP binding protein 1	161	G.	multicellular organismal development|transcription, DNA-dependent	cytoplasm|intermediate filament cytoskeleton|nucleus	GTP binding|transcription factor binding	breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	11					TAAGAAGATAATTGAAAATGA	0.428	0	81.0	76.0	78.0	22	31816310	2203	4300	6503	SO:0001583	missense	AJ005940	CCDS13897.1	22q12.2	2010-02-26	2001-11-28		ENSG00000185721	ENSG00000185721		3029	protein-coding gene	gene with protein product		603952	"""developmentally regulated GTP-binding protein 1"""	NEDD3	7929244, 1449490	Standard	NM_004147	Approved		uc003aku.3	Q9Y295	OTTHUMG00000030792	ENST00000331457.4:c.481A>G	22.37:g.31816310A>G	ENSP00000329715:p.Ile161Val	B2RDS8|Q6FGP8|Q8WW69|Q9UGF2	ENST00000331457.4	37	CCDS13897.1	.	.	.	.	.	.	.	.	.	.	A	18.84	3.709524	0.68730	.	.	ENSG00000185721	ENST00000331457	T	0.16897	2.31	5.2	5.2	0.72013	Small GTP-binding protein domain (1);GTP-binding domain, HSR1-related (1);	0.000000	0.85682	D	0.000000	T	0.32704	0.0838	M	0.67397	2.05	0.80722	D	1	P	0.40681	0.727	P	0.50570	0.644	T	0.05699	-1.0869	10	0.87932	D	0	-27.6891	14.5399	0.67984	1.0:0.0:0.0:0.0	.	161	Q9Y295	DRG1_HUMAN	V	161	ENSP00000329715:I161V	ENSP00000329715:I161V	I	+	1	0	DRG1	30146310	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.648000	0.91062	2.082000	0.62665	0.533000	0.62120	ATT	DRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075680.5		30.870118	0	13	88	0	0	1	0	NM_004147	12	35.090373	44	0.214286
EIF1B	10289	broad.mit.edu	hg19	3	40353009	40353010	+	Frame_Shift_Ins	INS	-	-	T			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr3:40353009_40353010insT	ENST00000232905.3	+	3	502_503	c.244_245insT	c.(244-246)gttfs	p.V82fs		NM_005875.2	NP_005866.1	O60739	EIF1B_HUMAN	eukaryotic translation initiation factor 1B	82		regulation of translational initiation		protein binding|translation initiation factor activity	central_nervous_system(1)|lung(3)	4				KIRC - Kidney renal clear cell carcinoma(284;0.0509)|Kidney(284;0.064)	ATACGGAGAGGTTATTCAGCTT	0.361	0									SO:0001589	frameshift_variant	BC006996	CCDS2690.1	3p22.1	2006-02-03			ENSG00000114784	ENSG00000114784		30792	protein-coding gene	gene with protein product					7904817	Standard	NM_005875	Approved	GC20	uc003ckc.3	O60739	OTTHUMG00000131388	ENST00000232905.3:c.246dupT	3.37:g.40353011_40353011dupT	ENSP00000232905:p.Val82fs	Q9UQF8	ENST00000232905.3	37	CCDS2690.1																																																																																			EIF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254177.1	.	.		-11	65					NM_005875	10		44	0.19
BAP1	8314	broad.mit.edu	hg19	3	52439229	52439229	+	Frame_Shift_Del	DEL	G	G	-			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr3:52439229delG	ENST00000460680.1	-	11	1484	c.1013delC	c.(1012-1014)cctfs	p.P339fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.P321fs	NM_004656.2	NP_004647.1	Q92560	BAP1_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	339		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)	GCTGCCTGGAGGCTTCACCAC	0.587	1	113.0	120.0	117.0	3	52439229	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.1013delC	3.37:g.52439229delG	ENSP00000417132:p.Pro339fs	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	ENST00000460680.1	37	CCDS2853.1																																																																																			BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	.	.		-23	154						25		63	0.28
CCAR2	57805	broad.mit.edu	hg19	8	22475962	22475963	+	Frame_Shift_Ins	INS	-	-	A			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr8:22475962_22475963insA	ENST00000308511.4	+	17	2423_2424	c.2174_2175insA	c.(2173-2178)ttagagfs	p.E726fs	CCAR2_ENST00000520861.1_Frame_Shift_Ins_p.E401fs|CCAR2_ENST00000389279.3_Frame_Shift_Ins_p.E726fs					cell cycle and apoptosis regulator 2	726											CGGCGAGACTTAGAGAGGATCC	0.564	0									SO:0001589	frameshift_variant	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941		23360	protein-coding gene	gene with protein product	"""deleted in breast cancer"""	607359	"""KIAA1967"""	KIAA1967	12370419	Standard	NM_021174	Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.2175dupA	8.37:g.22475963_22475963dupA	ENSP00000310670:p.Glu726fs	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	ENST00000308511.4	37	CCDS34863.1																																																																																			CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	.	.		-20	105					NM_021174	17		51	0.25
BAP1	8314	broad.mit.edu	hg19	3	52439228	52439229	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-YZ-A980-01A-11D-A39W-08	TCGA-YZ-A980-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2acd7e08-0c2b-46ce-b3bb-9a2087f87ec5	40222640-92e6-45b0-9b35-b35133e45faf	g.chr3:52439228_52439229delAG	ENST00000460680.1	-	11	1484_1485	c.1013_1014delCT	c.(1012-1014)cctfs	p.P339fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.P321fs	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)	TGCTGCCTGGAGGCTTCACCAC	0.589	1									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.1013_1014delCT	3:g.52439228_52439229delAG	ENSP00000417132:p.Pro339fs	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	ENST00000460680.1		CCDS2853.1																																																																																			BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1	3.912000e+01	5.691000e+01		-23	154						24		61	2.900000e-01
