#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_name_source	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
ABCB4	5244	genome.wustl.edu	37	7	87074281	87074282	+	Frame_Shift_Ins	INS	-	-	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr7:87074281_87074282insA	ENST00000265723.4	-	10	1126_1127	c.1015_1016insT	c.(1015-1017)tcafs	p.S339fs	ABCB4_ENST00000545634.1_Frame_Shift_Ins_p.S339fs|ABCB4_ENST00000453593.1_Frame_Shift_Ins_p.S339fs|ABCB4_ENST00000358400.3_Frame_Shift_Ins_p.S339fs|ABCB4_ENST00000359206.3_Frame_Shift_Ins_p.S339fs	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	339	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)	p.S339fs*3(1)		breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	AATTAGGATTGAAAAAAAAACC	0.347																																																	1	Deletion - Frameshift(1)	lung(1)	GRCh37	CD034702|CI034710	ABCB4	D|I																																				SO:0001589	frameshift_variant	5244			M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"""ATP binding cassette transporters / subfamily B"""	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.1016dupT	7.37:g.87074290_87074290dupA	ENSP00000265723:p.Ser339fs		A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Frame_Shift_Ins	INS	pfam_ABC_transptr_TM_dom,pfam_ABC_transporter-like,pfam_ABC_ATPase_put,pfam_Zeta_toxin_domain,superfamily_ABC_transptrTM_dom_typ1,smart_AAA+_ATPase,pfscan_ABC_transporter-like,pfscan_ABC_transporter_type1	p.S339fs	ENST00000265723.4	37	c.1016_1015	CCDS5606.1	7																																																																																			ABCB4	-	pfam_ABC_transptr_TM_dom,superfamily_ABC_transptrTM_dom_typ1,pfscan_ABC_transporter_type1		0.347	ABCB4-002	KNOWN	basic|CCDS	protein_coding	ABCB4	HGNC	protein_coding	OTTHUMT00000336083.1	-	NM_000443		87074282	-1	no_errors	ENST00000265723	ensembl	human	known	70_37	frame_shift_ins	INS	1.000:1.000	A
ASCL4	121549	genome.wustl.edu	37	12	108169229	108169229	+	Silent	SNP	C	C	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr12:108169229C>T	ENST00000342331.4	+	1	1068	c.237C>T	c.(235-237)aaC>aaT	p.N79N		NM_203436.2	NP_982260.2	Q6XD76	ASCL4_HUMAN	achaete-scute family bHLH transcription factor 4	78	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|skin development (GO:0043588)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(1)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	13						GCAAGCGCAACGAGCGCGAGC	0.716																																					GBM(170;776 3695 11650)												0													5.0	5.0	5.0					12																	108169229		1920	3859	5779	SO:0001819	synonymous_variant	121549			AY238895	CCDS31894.2	12q24.11	2013-10-17	2013-10-17		ENSG00000187855	ENSG00000187855		"""Basic helix-loop-helix proteins"""	24311	protein-coding gene	gene with protein product		609155	"""achaete-scute complex-like 4 (Drosophila)"", ""achaete-scute complex homolog 4 (Drosophila)"""				Standard	NM_203436		Approved	HASH4, bHLHa44	uc001tmr.3	Q6XD76	OTTHUMG00000156964	ENST00000342331.4:c.237C>T	12.37:g.108169229C>T			Q7RTS2	Silent	SNP	pfam_HLH_dom,superfamily_HLH_dom,smart_HLH_dom,pfscan_HLH_dom	p.N79	ENST00000342331.4	37	c.237	CCDS31894.2	12																																																																																			ASCL4	-	pfam_HLH_dom,superfamily_HLH_dom,smart_HLH_dom,pfscan_HLH_dom		0.716	ASCL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ASCL4	HGNC	protein_coding	OTTHUMT00000346845.1	C	NM_203436		108169229	+1	no_errors	ENST00000342331	ensembl	human	known	70_37	silent	SNP	1.000	T
BATF2	116071	genome.wustl.edu	37	11	64756991	64756991	+	Silent	SNP	A	A	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr11:64756991A>T	ENST00000301887.4	-	3	565	c.435T>A	c.(433-435)tcT>tcA	p.S145S	BATF2_ENST00000527716.1_Silent_p.S121S|BATF2_ENST00000435842.2_Silent_p.S60S	NM_138456.3	NP_612465.3	Q8N1L9	BATF2_HUMAN	basic leucine zipper transcription factor, ATF-like 2	145					defense response to protozoan (GO:0042832)|myeloid dendritic cell differentiation (GO:0043011)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(1)|skin(1)	9						GGAGGCTGGGAGAATCATGAG	0.642																																																	0													34.0	17.0	23.0					11																	64756991		2181	4257	6438	SO:0001819	synonymous_variant	116071			AK092453	CCDS8087.1, CCDS73317.1	11q13.1	2013-01-10			ENSG00000168062	ENSG00000168062		"""basic leucine zipper proteins"""	25163	protein-coding gene	gene with protein product		614983					Standard	NM_138456		Approved	MGC20410	uc001ocf.1	Q8N1L9	OTTHUMG00000165633	ENST00000301887.4:c.435T>A	11.37:g.64756991A>T			D9IC56|Q8NAF4|Q8NAL8|Q96EH4	Silent	SNP	pfam_bZIP,superfamily_Euk_TF_DNA-bd,smart_bZIP,pfscan_bZIP	p.S145	ENST00000301887.4	37	c.435	CCDS8087.1	11																																																																																			BATF2	-	NULL		0.642	BATF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BATF2	HGNC	protein_coding	OTTHUMT00000385478.2	A	NM_138456		64756991	-1	no_errors	ENST00000301887	ensembl	human	known	70_37	silent	SNP	0.002	T
C1orf61	10485	genome.wustl.edu	37	1	156379734	156379735	+	Intron	INS	-	-	T	rs112262029|rs397861750|rs561039298	byFrequency	TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr1:156379734_156379735insT	ENST00000368243.1	-	5	288				C1orf61_ENST00000488498.2_5'Flank	NM_006365.1	NP_006356.1	Q13536	CROC4_HUMAN	chromosome 1 open reading frame 61							nucleus (GO:0005634)				large_intestine(2)|lung(2)|skin(1)	5	Hepatocellular(266;0.158)					ttctttctttcttttttttttt	0.49													|||unknown(HR)	1247	0.249002	0.1445	0.3473	5008	,	,		15734	0.3353		0.2187	False		,,,				2504	0.2628																0																																										SO:0001627	intron_variant	10485				CCDS1142.1	1q22	2014-03-17			ENSG00000125462	ENSG00000125462			30780	protein-coding gene	gene with protein product	"""contingent replication of cDNA-4"", ""transcriptional activator of the c fos promoter"""					10995546, 23012322	Standard	XM_005244832		Approved	CROC4	uc001fou.1	Q13536	OTTHUMG00000031022	ENST00000368243.1:c.172-1967->A	1.37:g.156379745_156379745dupT			B1ALL5|B1ALL8	RNA	INS	-	NULL	ENST00000368243.1	37	NULL	CCDS1142.1	1																																																																																			C1orf61	-	-		0.490	C1orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C1orf61	HGNC	protein_coding	OTTHUMT00000075988.1	-	NM_006365		156379735	-1	no_errors	ENST00000488498	ensembl	human	known	70_37	rna	INS	0.003:0.004	T
CCNO	10309	genome.wustl.edu	37	5	54529143	54529143	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr5:54529143C>T	ENST00000282572.4	-	1	365	c.209G>A	c.(208-210)gGc>gAc	p.G70D	RP11-506H20.1_ENST00000506435.1_RNA	NM_021147.3	NP_066970.3	P22674	CCNO_HUMAN	cyclin O	70					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cell cycle (GO:0007049)|cell division (GO:0051301)|cilium assembly (GO:0042384)|depyrimidination (GO:0045008)|DNA repair (GO:0006281)|embryo development (GO:0009790)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	uracil DNA N-glycosylase activity (GO:0004844)			endometrium(1)|lung(3)|skin(1)	5		Lung NSC(810;4.08e-05)|Breast(144;0.0735)|Prostate(74;0.183)	LUSC - Lung squamous cell carcinoma(15;0.142)|Lung(15;0.161)			GCTCTCTGCGCCGTCTGAGCC	0.716																																																	0													9.0	10.0	10.0					5																	54529143		2177	4268	6445	SO:0001583	missense	10309			M87499	CCDS34157.1	5q11.2	2010-11-15	2007-07-26	2007-07-26	ENSG00000152669	ENSG00000152669			18576	protein-coding gene	gene with protein product		607752	"""cyclin U"""	CCNU			Standard	NR_125346		Approved	UDG2, FLJ22422, UNG2	uc003jpw.3	P22674	OTTHUMG00000162598	ENST00000282572.4:c.209G>A	5.37:g.54529143C>T	ENSP00000282572:p.Gly70Asp		A8K1W5|Q0P6J2|Q9H6B0|Q9UMD5	Missense_Mutation	SNP	pfam_Cyclin_N,pfam_Cyclin_C,superfamily_Cyclin-like,smart_Cyclin-like,pirsf_Cyclin_A/B/D/E	p.G70D	ENST00000282572.4	37	c.209	CCDS34157.1	5	.	.	.	.	.	.	.	.	.	.	C	8.444	0.851490	0.17034	.	.	ENSG00000152669	ENST00000282572	T	0.18502	2.21	5.37	0.182	0.15077	.	1.208020	0.05981	N	0.644196	T	0.08935	0.0221	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.37549	-0.9701	10	0.11794	T	0.64	.	2.7552	0.05291	0.261:0.2428:0.3829:0.1134	.	70	P22674	CCNO_HUMAN	D	70	ENSP00000282572:G70D	ENSP00000282572:G70D	G	-	2	0	CCNO	54564900	0.003000	0.15002	0.013000	0.15412	0.012000	0.07955	0.768000	0.26590	0.236000	0.21180	-1.083000	0.02208	GGC	CCNO	-	pirsf_Cyclin_A/B/D/E		0.716	CCNO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CCNO	HGNC	protein_coding	OTTHUMT00000369707.1	C	NM_021147		54529143	-1	no_errors	ENST00000282572	ensembl	human	known	70_37	missense	SNP	0.000	T
CROCCP2	84809	genome.wustl.edu	37	1	16946090	16946090	+	lincRNA	SNP	T	T	C	rs200611073		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr1:16946090T>C	ENST00000412962.1	-	0	1429				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											TGGGAGAATATGGAACAGCTT	0.577																																																	0																																												84809			AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16946090T>C			Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	-	NULL	ENST00000412962.1	37	NULL		1																																																																																			CROCCP2	-	-		0.577	CROCCP2-003	KNOWN	basic	lincRNA	CROCCP2	HGNC	lincRNA	OTTHUMT00000092784.1	T	NR_026752.1		16946090	-1	no_errors	ENST00000412962	ensembl	human	known	70_37	rna	SNP	0.000	C
DDX11	1663	genome.wustl.edu	37	12	31242861	31242861	+	Silent	SNP	A	A	C	rs200751040|rs531309221	byFrequency	TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr12:31242861A>C	ENST00000407793.2	+	9	1173	c.922A>C	c.(922-924)Agg>Cgg	p.R308R	DDX11_ENST00000350437.4_Silent_p.R308R|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000542838.1_Silent_p.R308R|DDX11_ENST00000545668.1_Silent_p.R308R|DDX11_ENST00000228264.6_Silent_p.R282R	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	308	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.R308R(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					AAAGAGGAGGAGGCAGGAGAA	0.587										Multiple Myeloma(12;0.14)				29	0.00579073	0.0038	0.0043	5008	,	,		20906	0.0099		0.007	False		,,,				2504	0.0041																2	Substitution - coding silent(2)	kidney(2)											5.0	7.0	6.0					12																	31242861		2036	4038	6074	SO:0001819	synonymous_variant	1663			U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.922A>C	12.37:g.31242861A>C			Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	pfam_DEAD_2,smart_Helicase-like_DEXD_c2,smart_ATP-dep_Helicase_C,pfscan_Helic_SF1/SF2_ATP-bd_DinG/Rad3,tigrfam_DNA_helicase_DNA-repair_Rad3	p.R308	ENST00000407793.2	37	c.922	CCDS44856.1	12																																																																																			DDX11	-	pfam_DEAD_2,smart_Helicase-like_DEXD_c2,pfscan_Helic_SF1/SF2_ATP-bd_DinG/Rad3,tigrfam_DNA_helicase_DNA-repair_Rad3		0.587	DDX11-202	KNOWN	basic|CCDS	protein_coding	DDX11	HGNC	protein_coding	OTTHUMT00000399728.1	A	NM_030653		31242861	+1	no_errors	ENST00000407793	ensembl	human	known	70_37	silent	SNP	0.001	C
DOK2	9046	genome.wustl.edu	37	8	21767414	21767414	+	Missense_Mutation	SNP	C	C	T	rs200168233		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr8:21767414C>T	ENST00000276420.4	-	5	905	c.647G>A	c.(646-648)cGc>cAc	p.R216H	DOK2_ENST00000544659.1_Missense_Mutation_p.R62H	NM_003974.2	NP_003965.2	O60496	DOK2_HUMAN	docking protein 2, 56kDa	216	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|leukocyte migration (GO:0050900)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	receptor signaling protein activity (GO:0005057)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(3)|skin(1)	26				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		AGAGACGCAGCGACGGCCTGC	0.527																																																	0								C	HIS/ARG	0,4404		0,0,2202	45.0	42.0	43.0		647	4.7	1.0	8		43	1,8587	1.2+/-3.3	0,1,4293	yes	missense	DOK2	NM_003974.2	29	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	216/413	21767414	1,12991	2202	4294	6496	SO:0001583	missense	9046			AF034970	CCDS6016.1	8p21.3	2008-08-07	2002-08-29		ENSG00000147443	ENSG00000147443			2991	protein-coding gene	gene with protein product		604997	"""docking protein 2, 56kD"""			9478921, 14645010	Standard	NM_003974		Approved	p56dok-2, Dok-2	uc003wzy.1	O60496	OTTHUMG00000131075	ENST00000276420.4:c.647G>A	8.37:g.21767414C>T	ENSP00000276420:p.Arg216His		Q8N5A4	Missense_Mutation	SNP	pfam_Insln_rcpt_S1,smart_Pleckstrin_homology,smart_Insln_rcpt_S1,pfscan_Pleckstrin_homology,pfscan_Insln_rcpt_S1	p.R216H	ENST00000276420.4	37	c.647	CCDS6016.1	8	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.77|16.77	3.215588|3.215588	0.58452|0.58452	0.0|0.0	1.16E-4|1.16E-4	ENSG00000147443|ENSG00000147443	ENST00000523932|ENST00000276420;ENST00000544659;ENST00000518197	T|D;D;D	0.43688|0.86164	0.94|-2.08;-2.08;-2.08	4.73|4.73	4.73|4.73	0.59995|0.59995	.|Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.94341|0.94341	0.8181|0.8181	M|M	0.89214|0.89214	3.015|3.015	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	D|D	0.95319|0.95319	0.8419|0.8419	7|10	0.72032|0.66056	D|D	0.01|0.02	.|.	16.5224|16.5224	0.84320|0.84320	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|216;216	.|O60496;A8K7W1	.|DOK2_HUMAN;.	T|H	209|216;62;62	ENSP00000429224:A209T|ENSP00000276420:R216H;ENSP00000443602:R62H;ENSP00000430729:R62H	ENSP00000429224:A209T|ENSP00000276420:R216H	A|R	-|-	1|2	0|0	DOK2|DOK2	21823360|21823360	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.494000|0.494000	0.33585|0.33585	7.096000|7.096000	0.76960|0.76960	2.187000|2.187000	0.69744|0.69744	0.449000|0.449000	0.29647|0.29647	GCT|CGC	DOK2	-	pfam_Insln_rcpt_S1,smart_Insln_rcpt_S1,pfscan_Insln_rcpt_S1		0.527	DOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DOK2	HGNC	protein_coding	OTTHUMT00000253735.3	C	NM_003974		21767414	-1	no_errors	ENST00000276420	ensembl	human	known	70_37	missense	SNP	1.000	T
EBPL	84650	genome.wustl.edu	37	13	50235160	50235160	+	Missense_Mutation	SNP	G	G	C			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr13:50235160G>C	ENST00000242827.6	-	4	615	c.565C>G	c.(565-567)Cta>Gta	p.L189V	EBPL_ENST00000378284.2_3'UTR|EBPL_ENST00000378272.5_3'UTR|EBPL_ENST00000495963.2_5'UTR|EBPL_ENST00000378270.5_3'UTR	NM_032565.3	NP_115954.1	Q9BY08	EBPL_HUMAN	emopamil binding protein-like	189					sterol metabolic process (GO:0016125)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholestenol delta-isomerase activity (GO:0047750)	p.L189V(9)		endometrium(8)|kidney(6)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Lung NSC(96;0.000468)|Breast(56;0.0011)|Prostate(109;0.00243)|Hepatocellular(98;0.0556)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.06e-09)		TTGAGTTCTAGCCATGACTGC	0.418																																					NSCLC(39;857 1083 36109 42364 51411)												9	Substitution - Missense(9)	endometrium(6)|kidney(3)											67.0	67.0	67.0					13																	50235160		2203	4300	6503	SO:0001583	missense	84650			AF243433	CCDS9420.1, CCDS61334.1	13q12-q13	2008-02-05			ENSG00000123179	ENSG00000123179			18061	protein-coding gene	gene with protein product							Standard	NM_032565		Approved	EBRP	uc001vdg.3	Q9BY08	OTTHUMG00000016920	ENST00000242827.6:c.565C>G	13.37:g.50235160G>C	ENSP00000242827:p.Leu189Val		A6NJ59|Q569H7|Q5JVN2|Q5JVN3|Q5JVN4|Q5JVN5|Q5JVN6	Missense_Mutation	SNP	pfam_EBP	p.L189V	ENST00000242827.6	37	c.565	CCDS9420.1	13	.	.	.	.	.	.	.	.	.	.	C	3.076	-0.189988	0.06299	.	.	ENSG00000123179	ENST00000242827	D	0.97850	-4.57	5.61	2.84	0.33178	.	0.689671	0.14945	N	0.289287	D	0.88179	0.6367	N	0.00621	-1.32	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.79482	-0.1785	10	0.25751	T	0.34	-0.2032	8.3049	0.32036	0.0:0.4998:0.3595:0.1406	.	189	Q9BY08	EBPL_HUMAN	V	189	ENSP00000242827:L189V	ENSP00000242827:L189V	L	-	1	2	EBPL	49133161	0.000000	0.05858	0.303000	0.25071	0.899000	0.52679	-1.071000	0.03437	0.397000	0.25310	-0.127000	0.14921	CTA	EBPL	-	pfam_EBP		0.418	EBPL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	EBPL	HGNC	protein_coding	OTTHUMT00000044932.2	G	NM_032565		50235160	-1	no_errors	ENST00000242827	ensembl	human	known	70_37	missense	SNP	0.264	C
KIAA0556	23247	genome.wustl.edu	37	16	27673314	27673314	+	Intron	SNP	C	C	T	rs8053696|rs66487783|rs56350763|rs370380914		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr16:27673314C>T	ENST00000261588.4	+	6	559				AC016597.1_ENST00000408601.1_RNA|KIAA0556_ENST00000567894.1_Intron	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556							extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						tatacacatacatatatatat	0.139																																																	0																																										SO:0001627	intron_variant	0			AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.540+13258C>T	16.37:g.27673314C>T			A7E2C2	RNA	SNP	-	NULL	ENST00000261588.4	37	NULL	CCDS32415.1	16																																																																																			AC016597.1	-	-		0.139	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000221528	Clone_based_ensembl_gene	protein_coding	OTTHUMT00000433724.1	C	NM_015202		27673314	+1	no_errors	ENST00000408601	ensembl	human	novel	70_37	rna	SNP	0.000	T
LOC101928298	101928298	genome.wustl.edu	37	10	10101345	10101345	+	lincRNA	SNP	G	G	A	rs573757632		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr10:10101345G>A	ENST00000429539.1	+	0	169																											CTTTCCTTCCGCCATCTCTGC	0.453													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19463	0.0		0.0	False		,,,				2504	0.0																0																																												0																															10.37:g.10101345G>A				RNA	SNP	-	NULL	ENST00000429539.1	37	NULL		10																																																																																			RP5-933E2.1	-	-		0.453	RP5-933E2.1-001	KNOWN	basic	lincRNA	ENSG00000224788	Clone_based_vega_gene	lincRNA	OTTHUMT00000046738.1	G			10101345	+1	no_errors	ENST00000429539	ensembl	human	known	70_37	rna	SNP	0.000	A
GTF2IP7	101927126	genome.wustl.edu	37	7	75720936	75720936	+	RNA	SNP	C	C	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr7:75720936C>T	ENST00000434037.1	-	0	1211																											gctggtactacgctttttttt	0.512																																																	0																																												0																															7.37:g.75720936C>T				RNA	SNP	-	NULL	ENST00000434037.1	37	NULL		7																																																																																			AC005077.12	-	-		0.512	AC005077.12-002	KNOWN	basic	processed_transcript	ENSG00000227038	Clone_based_vega_gene	pseudogene	OTTHUMT00000344843.1	C			75720936	-1	no_errors	ENST00000434037	ensembl	human	known	70_37	rna	SNP	0.058	T
RP11-138M12.1	0	genome.wustl.edu	37	6	125752346	125752346	+	lincRNA	SNP	G	G	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr6:125752346G>T	ENST00000430672.1	-	0	164																											ATAGATATTTGGTCTTAGAAA	0.343																																																	0																																												0																															6.37:g.125752346G>T				RNA	SNP	-	NULL	ENST00000430672.1	37	NULL		6																																																																																			RP11-138M12.1	-	-		0.343	RP11-138M12.1-001	KNOWN	basic	lincRNA	ENSG00000228704	Clone_based_vega_gene	lincRNA	OTTHUMT00000042071.1	G			125752346	-1	no_errors	ENST00000430672	ensembl	human	known	70_37	rna	SNP	0.062	T
RP11-268G12.1	0	genome.wustl.edu	37	X	27193166	27193166	+	lincRNA	SNP	C	C	T	rs371640635		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chrX:27193166C>T	ENST00000422048.1	-	0	1749				RP11-268G12.3_ENST00000436019.2_lincRNA																							tacaggtgcgcgccaccacac	0.468													c|||	3	0.000794702	0.0008	0.0	3775	,	,		12421	0.001		0.0	False		,,,				2504	0.001																0																																												0																															X.37:g.27193166C>T				RNA	SNP	-	NULL	ENST00000422048.1	37	NULL		X																																																																																			RP11-268G12.1	-	-		0.468	RP11-268G12.1-001	KNOWN	basic	lincRNA	ENSG00000228933	Clone_based_vega_gene	lincRNA	OTTHUMT00000056136.1	C			27193166	-1	no_errors	ENST00000422048	ensembl	human	known	70_37	rna	SNP	0.000	T
PGM5P2	595135	genome.wustl.edu	37	9	69083139	69083139	+	lincRNA	SNP	T	T	C			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr9:69083139T>C	ENST00000412376.1	-	0	1429				PGM5P2_ENST00000591037.1_RNA																							tcattaaaaattttaGTATCT	0.254																																																	0																																												0																															9.37:g.69083139T>C				RNA	SNP	-	NULL	ENST00000412376.1	37	NULL		9																																																																																			RP11-87H9.3	-	-		0.254	RP11-87H9.3-001	KNOWN	basic	lincRNA	ENSG00000231242	Clone_based_vega_gene	lincRNA	OTTHUMT00000143173.1	T			69083139	-1	no_errors	ENST00000412376	ensembl	human	known	70_37	rna	SNP	0.008	C
RP11-308N19.1	0	genome.wustl.edu	37	9	109262674	109262674	+	lincRNA	SNP	C	C	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr9:109262674C>A	ENST00000435485.1	+	0	334																											GTGTCTTAAGCTGGGTCATTG	0.468																																																	0																																												0																															9.37:g.109262674C>A				RNA	SNP	-	NULL	ENST00000435485.1	37	NULL		9																																																																																			RP11-308N19.1	-	-		0.468	RP11-308N19.1-002	KNOWN	basic	lincRNA	ENSG00000234323	Clone_based_vega_gene	lincRNA	OTTHUMT00000053526.1	C			109262674	+1	no_errors	ENST00000435485	ensembl	human	known	70_37	rna	SNP	0.000	A
RP11-435B5.7	0	genome.wustl.edu	37	1	143527557	143527557	+	lincRNA	SNP	C	C	A	rs368565679		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr1:143527557C>A	ENST00000418607.2	-	0	811																											AATTACTTTTCTTTTTGGTAT	0.348																																																	0																																												0																															1.37:g.143527557C>A				RNA	SNP	-	NULL	ENST00000418607.2	37	NULL		1																																																																																			BX004987.7	-	-		0.348	RP11-435B5.7-001	KNOWN	not_best_in_genome_evidence|basic	lincRNA	ENSG00000235566	Clone_based_vega_gene	lincRNA	OTTHUMT00000037982.2	C			143527557	-1	no_errors	ENST00000418607	ensembl	human	known	70_37	rna	SNP	0.000	A
NHS	4810	genome.wustl.edu	37	X	17604191	17604191	+	Intron	SNP	C	C	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chrX:17604191C>T	ENST00000380060.3	+	2	903				RP1-60N8.1_ENST00000433228.1_RNA	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)						cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					GTGGtagagtcagagcaccca	0.438																																																	0																																										SO:0001627	intron_variant	0				CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.566-101671C>T	X.37:g.17604191C>T			B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	RNA	SNP	-	NULL	ENST00000380060.3	37	NULL	CCDS14181.1	X																																																																																			RP1-60N8.1	-	-		0.438	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000235834	Clone_based_vega_gene	protein_coding	OTTHUMT00000059120.1	C	NM_198270		17604191	+1	no_errors	ENST00000433228	ensembl	human	known	70_37	rna	SNP	0.103	T
RP11-634B22.4	0	genome.wustl.edu	37	11	123539734	123539734	+	lincRNA	SNP	T	T	C			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr11:123539734T>C	ENST00000532961.1	+	0	526																											tgctgaactgtgagtcaatta	0.448																																																	0																																												0																															11.37:g.123539734T>C				Splice_Site	SNP	-	NULL	ENST00000532961.1	37	c.NULL		11																																																																																			RP11-634B22.4	-	-		0.448	RP11-634B22.4-001	KNOWN	basic	lincRNA	ENSG00000254467	Clone_based_vega_gene	lincRNA	OTTHUMT00000387416.1	T			123539734	+1	no_errors	ENST00000532961	ensembl	human	known	70_37	splice_site	SNP	0.161	C
RP11-20G6.2	0	genome.wustl.edu	37	16	23034721	23034722	+	lincRNA	INS	-	-	ACAC	rs13335004|rs147289151|rs67478567|rs398029019		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr16:23034721_23034722insACAC	ENST00000567395.1	+	0	721_722																											cacacacacatacacacacaca	0.441																																																	0																																												0																															16.37:g.23034726_23034729dupACAC				RNA	INS	-	NULL	ENST00000567395.1	37	NULL		16																																																																																			RP11-20G6.2	-	-		0.441	RP11-20G6.2-001	KNOWN	basic	lincRNA	ENSG00000261090	Clone_based_vega_gene	lincRNA	OTTHUMT00000436061.1	-			23034722	+1	no_errors	ENST00000567395	ensembl	human	known	70_37	rna	INS	0.026:0.065	ACAC
ZNF267	10308	genome.wustl.edu	37	16	31924622	31924622	+	Intron	SNP	G	G	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr16:31924622G>T	ENST00000300870.10	+	4	435				ZNF267_ENST00000394846.3_Intron	NM_001265588.1|NM_003414.5	NP_001252517.1|NP_003405	Q14586	ZN267_HUMAN	zinc finger protein 267						multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(5)|kidney(1)|large_intestine(14)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	41						gtttcttccagacgaatggaa	0.458																																																	0																																										SO:0001627	intron_variant	0			X78925	CCDS32440.1	16p11.2	2013-01-08			ENSG00000185947	ENSG00000185947		"""Zinc fingers, C2H2-type"", ""-"""	13060	protein-coding gene	gene with protein product		604752				7865130	Standard	NM_003414		Approved	HZF2	uc002ecs.5	Q14586		ENST00000300870.10:c.227-1175G>T	16.37:g.31924622G>T			A0JNZ9|Q8NE41|Q9NRJ0	RNA	SNP	-	NULL	ENST00000300870.10	37	NULL	CCDS32440.1	16																																																																																			RP11-170L3.8	-	-		0.458	ZNF267-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000262657	Clone_based_vega_gene	protein_coding	OTTHUMT00000432446.2	G	NM_003414		31924622	+1	no_errors	ENST00000575471	ensembl	human	known	70_37	rna	SNP	0.048	T
LOC100130950	100130950	genome.wustl.edu	37	17	5144571	5144571	+	lincRNA	SNP	T	T	C	rs372004880|rs200898855		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr17:5144571T>C	ENST00000575056.1	-	0	267				RP11-333E1.1_ENST00000573772.1_RNA																							cctaccctaattaatccatcc	0.483																																																	0																																												0																															17.37:g.5144571T>C				RNA	SNP	-	NULL	ENST00000575056.1	37	NULL		17																																																																																			RP11-333E1.2	-	-		0.483	RP11-333E1.2-001	KNOWN	basic	lincRNA	ENSG00000263164	Clone_based_vega_gene	lincRNA	OTTHUMT00000439347.1	T			5144571	-1	no_errors	ENST00000575056	ensembl	human	known	70_37	rna	SNP	0.102	C
TPM4	7171	genome.wustl.edu	37	19	16176846	16176847	+	5'Flank	INS	-	-	GTGT	rs71964633		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr19:16176846_16176847insGTGT	ENST00000344824.6	+	0	0				CTD-2231E14.4_ENST00000585520.1_lincRNA|TPM4_ENST00000538887.1_5'Flank	NM_001145160.1	NP_001138632.1	P67936	TPM4_HUMAN	tropomyosin 4						cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|osteoblast differentiation (GO:0001649)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|membrane (GO:0016020)|muscle thin filament tropomyosin (GO:0005862)|podosome (GO:0002102)|stress fiber (GO:0001725)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)		TPM4/ALK(12)	breast(1)|large_intestine(3)	4						taggcagCGAAgtgtgtgtgtg	0.49			T	ALK	ALCL																																			Dom	yes		19	19p13.1	7171	tropomyosin 4		L	0																																										SO:0001631	upstream_gene_variant	0				CCDS12338.1, CCDS46007.1	19p13.1	2013-03-11			ENSG00000167460	ENSG00000167460		"""Tropomyosins"""	12013	protein-coding gene	gene with protein product		600317				8641132	Standard	NM_003290		Approved		uc002ndi.2	P67936	OTTHUMG00000182134		19.37:g.16176851_16176854dupGTGT	Exception_encountered		P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Splice_Site	INS	-	NULL	ENST00000344824.6	37	c.NULL	CCDS46007.1	19																																																																																			CTD-2231E14.4	-	-		0.490	TPM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000267517	Clone_based_vega_gene	protein_coding	OTTHUMT00000459672.2	-	NM_003290		16176847	+1	no_errors	ENST00000585520	ensembl	human	known	70_37	splice_site_ins	INS	0.000:0.000	GTGT
FAM153B	202134	genome.wustl.edu	37	5	175558737	175558737	+	3'UTR	SNP	G	G	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr5:175558737G>A	ENST00000508356.1	+	0	2104				RP11-844P9.1_ENST00000504629.1_lincRNA			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B											endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	16	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		AGCATATTTTGTTTGTGtgag	0.269																																																	0																																										SO:0001624	3_prime_UTR_variant	202134			AK055006	CCDS43401.1, CCDS43401.2	5q35.2	2010-05-12			ENSG00000182230	ENSG00000182230			27323	protein-coding gene	gene with protein product							Standard	NM_001265615		Approved		uc031smb.1	P0C7A2	OTTHUMG00000163181	ENST00000508356.1:c.*2101G>A	5.37:g.175558737G>A			A8MTI1	RNA	SNP	-	NULL	ENST00000508356.1	37	NULL		5																																																																																			FAM153B	-	-		0.269	FAM153B-010	KNOWN	basic	processed_transcript	FAM153B	HGNC	protein_coding	OTTHUMT00000371929.1	G	NM_001079529		175558737	+1	no_errors	ENST00000508356	ensembl	human	known	70_37	rna	SNP	0.257	A
FAM182B	728882	genome.wustl.edu	37	20	25831374	25831374	+	Intron	SNP	A	A	T	rs201792208		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr20:25831374A>T	ENST00000376403.1	-	2	142				FAM182B_ENST00000478164.1_Intron|FAM182B_ENST00000376404.2_Intron			Q5T319	F182B_HUMAN	family with sequence similarity 182, member B											lung(1)	1						caggttggtgaactgtcatca	0.408																																																	0																																										SO:0001627	intron_variant	728882					20p11.1	2010-07-14			ENSG00000175170	ENSG00000175170			34503	pseudogene	pseudogene							Standard	NR_027061		Approved			Q5T319	OTTHUMG00000032136	ENST00000376403.1:c.237-1790T>A	20.37:g.25831374A>T			Q4G0Q1	RNA	SNP	-	NULL	ENST00000376403.1	37	NULL		20																																																																																			FAM182B	-	-		0.408	FAM182B-003	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	FAM182B	HGNC	protein_coding	OTTHUMT00000078463.2	A	NR_026714		25831374	-1	no_errors	ENST00000582267	ensembl	human	known	70_37	rna	SNP	0.000	T
FBXL2	25827	genome.wustl.edu	37	3	33406150	33406150	+	De_novo_Start_OutOfFrame	SNP	G	G	A	rs370862715		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr3:33406150G>A	ENST00000542085.1	+	0	440				FBXL2_ENST00000538181.1_Intron|FBXL2_ENST00000507198.1_Missense_Mutation_p.G77S|FBXL2_ENST00000283627.6_3'UTR|FBXL2_ENST00000484457.1_Missense_Mutation_p.G77S|FBXL2_ENST00000446237.3_De_novo_Start_OutOfFrame|FBXL2_ENST00000538892.1_Missense_Mutation_p.G77S					F-box and leucine-rich repeat protein 2											endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|urinary_tract(1)	15						GAAGCGATGCGGTGGATTCCT	0.448																																																	0								G	SER/GLY,SER/GLY	0,4406		0,0,2203	216.0	194.0	201.0		229,229	4.8	0.9	3		201	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FBXL2	NM_001171713.1,NM_012157.3	56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	77/356,77/424	33406150	1,13005	2203	4300	6503			25827			AF174589	CCDS2658.1, CCDS54560.1	3p22.3	2011-06-09			ENSG00000153558	ENSG00000153558		"""F-boxes / Leucine-rich repeats"""	13598	protein-coding gene	gene with protein product		605652				10508920, 10531035	Standard	NM_012157		Approved	FBL2, FBL3	uc003cfp.3	Q9UKC9	OTTHUMG00000130745	ENST00000542085.1:c.-642G>A	3.37:g.33406150G>A				Missense_Mutation	SNP	pfam_Leu-rich_rpt,pfam_F-box_dom_cyclin-like,smart_F-box_dom_cyclin-like,smart_Leu-rich_rpt_Cys-con_subtyp,pfscan_F-box_dom_cyclin-like	p.G77S	ENST00000542085.1	37	c.229		3	.	.	.	.	.	.	.	.	.	.	G	22.7	4.324600	0.81580	0.0	1.16E-4	ENSG00000153558	ENST00000484457;ENST00000538892;ENST00000507198	T;T;T	0.22743	4.4;1.94;1.94	4.8	4.8	0.61643	.	0.112080	0.64402	D	0.000008	T	0.22437	0.0541	L	0.45051	1.395	0.80722	D	1	D	0.61080	0.989	B	0.43052	0.406	T	0.02053	-1.1222	10	0.29301	T	0.29	.	18.8066	0.92040	0.0:0.0:1.0:0.0	.	77	Q9UKC9	FBXL2_HUMAN	S	77	ENSP00000417601:G77S;ENSP00000441228:G77S;ENSP00000426163:G77S	ENSP00000408895:G77S	G	+	1	0	FBXL2	33381154	1.000000	0.71417	0.862000	0.33874	0.977000	0.68977	9.357000	0.97099	2.621000	0.88768	0.650000	0.86243	GGT	FBXL2	-	smart_Leu-rich_rpt_Cys-con_subtyp		0.448	FBXL2-204	KNOWN	basic	protein_coding	FBXL2	HGNC	protein_coding		G	NM_012157		33406150	+1	no_errors	ENST00000484457	ensembl	human	known	70_37	missense	SNP	1.000	A
FGF18	8817	genome.wustl.edu	37	5	170876248	170876248	+	Silent	SNP	C	C	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr5:170876248C>T	ENST00000274625.5	+	4	892	c.348C>T	c.(346-348)ctC>ctT	p.L116L		NM_003862.2	NP_003853.1	O76093	FGF18_HUMAN	fibroblast growth factor 18	116					anatomical structure morphogenesis (GO:0009653)|angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|chondrocyte development (GO:0002063)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intramembranous ossification (GO:0001957)|lung development (GO:0030324)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleolus (GO:0005730)	growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	9	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AAGGCAAGCTCGTGGGGAAGG	0.572																																																	0													102.0	81.0	88.0					5																	170876248		2203	4300	6503	SO:0001819	synonymous_variant	8817			AB007422	CCDS4378.1	5q34	2008-02-05			ENSG00000156427	ENSG00000156427			3674	protein-coding gene	gene with protein product		603726				9660775, 9742123	Standard	NM_003862		Approved	FGF-18, ZFGF5	uc003mbk.3	O76093	OTTHUMG00000130464	ENST00000274625.5:c.348C>T	5.37:g.170876248C>T			D3DQL7|Q6UWF1	Silent	SNP	pfam_IL1_HBGF,superfamily_Cytokine_IL1-like,smart_IL1_HBGF,prints_IL1_HBGF	p.L116	ENST00000274625.5	37	c.348	CCDS4378.1	5																																																																																			FGF18	-	pfam_IL1_HBGF,superfamily_Cytokine_IL1-like,smart_IL1_HBGF,prints_IL1_HBGF		0.572	FGF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FGF18	HGNC	protein_coding	OTTHUMT00000252857.2	C	NM_033649, NM_003862		170876248	+1	no_errors	ENST00000274625	ensembl	human	known	70_37	silent	SNP	0.701	T
GTF3C1	2975	genome.wustl.edu	37	16	27471985	27471986	+	IGR	INS	-	-	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr16:27471985_27471986insT	ENST00000356183.4	-	0	7018				GTF3C1_ENST00000567806.1_5'UTR|GTF3C1_ENST00000561623.1_3'UTR	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa						5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						TCCACAGGGACTTTTTTTTTTT	0.356																																																	0																																										SO:0001628	intergenic_variant	2975			U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789			16.37:g.27471996_27471996dupT			B2RP21|Q12838|Q6DKN9|Q9Y4W9	RNA	INS	-	NULL	ENST00000356183.4	37	NULL	CCDS32414.1	16																																																																																			GTF3C1	-	-		0.356	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GTF3C1	HGNC	protein_coding	OTTHUMT00000433856.1	-	NM_001520		27471986	-1	no_errors	ENST00000567806	ensembl	human	known	70_37	rna	INS	0.603:0.466	T
GYLTL1B	120071	genome.wustl.edu	37	11	45949830	45949830	+	Silent	SNP	C	C	T	rs140565103	byFrequency	TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr11:45949830C>T	ENST00000531526.1	+	13	1968	c.1857C>T	c.(1855-1857)taC>taT	p.Y619Y	GYLTL1B_ENST00000536139.1_Silent_p.Y588Y|GYLTL1B_ENST00000401752.1_Silent_p.Y619Y|GYLTL1B_ENST00000325468.5_Silent_p.Y619Y|GYLTL1B_ENST00000529052.1_Silent_p.Y588Y	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	619					muscle cell cellular homeostasis (GO:0046716)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(35;0.226)		ATGAACCCTACGTGGTGGTGC	0.637																																																	0								C		1,4405	2.1+/-5.4	0,1,2202	164.0	158.0	160.0		1857	-11.1	0.2	11	dbSNP_134	160	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	GYLTL1B	NM_152312.3		0,3,6499	TT,TC,CC		0.0233,0.0227,0.0231		619/722	45949830	3,13001	2203	4299	6502	SO:0001819	synonymous_variant	120071				CCDS31473.1	11p11.12	2013-02-22			ENSG00000165905	ENSG00000165905		"""Glycosyltransferase family 8 domain containing"""	16522	protein-coding gene	gene with protein product		609709				15661757, 15958417	Standard	XM_005252785		Approved	PP5656, FLJ35207, LARGE2	uc001nbv.1	Q8N3Y3	OTTHUMG00000167037	ENST00000531526.1:c.1857C>T	11.37:g.45949830C>T			A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Silent	SNP	pfam_Glyco_trans_8	p.Y619	ENST00000531526.1	37	c.1857	CCDS31473.1	11																																																																																			GYLTL1B	-	NULL		0.637	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	GYLTL1B	HGNC	protein_coding	OTTHUMT00000392572.1	C	NM_152312		45949830	+1	no_errors	ENST00000325468	ensembl	human	known	70_37	silent	SNP	0.691	T
INHBA-AS1	285954	genome.wustl.edu	37	7	41816584	41816584	+	RNA	SNP	C	C	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr7:41816584C>A	ENST00000415848.2	+	0	603					NR_027118.1				INHBA antisense RNA 1																		gccaggatcccagctggtaga	0.517																																																	0																																												285954					7p14.1	2012-10-12	2012-08-15		ENSG00000224116	ENSG00000224116		"""Long non-coding RNAs"""	40303	non-coding RNA	RNA, long non-coding			"""INHBA antisense RNA 1 (non-protein coding)"""				Standard	NR_027118		Approved		uc003tht.4		OTTHUMG00000155114		7.37:g.41816584C>A				RNA	SNP	-	NULL	ENST00000415848.2	37	NULL		7																																																																																			INHBA-AS1	-	-		0.517	INHBA-AS1-001	KNOWN	basic	antisense	INHBA-AS1	HGNC	antisense	OTTHUMT00000338451.2	C	NR_027118		41816584	+1	no_errors	ENST00000415848	ensembl	human	known	70_37	rna	SNP	0.004	A
JAG1	182	genome.wustl.edu	37	20	10629352	10629352	+	Missense_Mutation	SNP	G	G	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr20:10629352G>A	ENST00000254958.5	-	12	1929	c.1414C>T	c.(1414-1416)Cgc>Tgc	p.R472C	JAG1_ENST00000423891.2_Missense_Mutation_p.R313C|JAG1_ENST00000488480.1_RNA	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	472	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						CAGATACAGCGATAACCATTA	0.473									Alagille Syndrome																																								0													77.0	73.0	74.0					20																	10629352		2203	4300	6503	SO:0001583	missense	182	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.1414C>T	20.37:g.10629352G>A	ENSP00000254958:p.Arg472Cys		A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	pfam_EG-like_dom,pfam_Notch_ligand_N,pfam_DSL,pfam_EGF_extracell,pfam_EGF-like_Ca-bd,smart_DSL,smart_EG-like_dom,smart_EGF-like_Ca-bd,smart_VWC_out,smart_VWF_C,pfscan_DSL,pfscan_EG-like_dom	p.R472C	ENST00000254958.5	37	c.1414	CCDS13112.1	20	.	.	.	.	.	.	.	.	.	.	G	24.0	4.483543	0.84854	.	.	ENSG00000101384	ENST00000254958;ENST00000423891	T;T	0.61274	0.12;0.12	5.93	5.93	0.95920	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	T	0.78817	0.4343	M	0.84219	2.685	0.80722	D	1	D	0.89917	1.0	D	0.65443	0.935	T	0.80063	-0.1539	10	0.66056	D	0.02	.	20.3437	0.98782	0.0:0.0:1.0:0.0	.	472	P78504	JAG1_HUMAN	C	472;313	ENSP00000254958:R472C;ENSP00000389519:R313C	ENSP00000254958:R472C	R	-	1	0	JAG1	10577352	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.815000	0.96918	0.561000	0.74099	CGC	JAG1	-	pfam_EG-like_dom,pfam_EGF_extracell,smart_EGF-like_Ca-bd,smart_EG-like_dom,pfscan_EG-like_dom		0.473	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	JAG1	HGNC	protein_coding		G	NM_000214		10629352	-1	no_errors	ENST00000254958	ensembl	human	known	70_37	missense	SNP	1.000	A
KIR3DL1	3811	genome.wustl.edu	37	19	55333103	55333103	+	Silent	SNP	C	C	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr19:55333103C>A	ENST00000391728.4	+	5	772	c.739C>A	c.(739-741)Cgg>Agg	p.R247R	KIR3DL1_ENST00000541392.1_Silent_p.R247R|KIR3DL1_ENST00000358178.4_Silent_p.R152R|KIR3DL1_ENST00000326542.7_Silent_p.R247R|KIR3DL1_ENST00000402254.2_Silent_p.R247R|KIR3DL1_ENST00000538269.1_Silent_p.R247R	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	247	Ig-like C2-type 3.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		CTGTAGCTCCCGGAGCTCCTA	0.572																																																	0																																										SO:0001819	synonymous_variant	3811			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.739C>A	19.37:g.55333103C>A			O43473|Q14946|Q16541	Silent	SNP	pfam_Immunoglobulin,smart_Ig_sub	p.R247	ENST00000391728.4	37	c.739	CCDS42621.1	19																																																																																			KIR3DL1	-	pfam_Immunoglobulin,smart_Ig_sub		0.572	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	KIR3DL1	HGNC	protein_coding	OTTHUMT00000141238.1	C	NM_013289		55333103	+1	no_errors	ENST00000402254	ensembl	human	known	70_37	silent	SNP	0.000	A
LINC00162	378825	genome.wustl.edu	37	21	46419224	46419224	+	lincRNA	SNP	G	G	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr21:46419224G>A	ENST00000422199.1	-	0	631					NR_024089.1		P0C852	CU113_HUMAN	long intergenic non-protein coding RNA 162																		GCAGGCACCTGCAGGCTGCCC	0.552																																																	0																																												378825			BC027456		21q22.2	2014-07-18	2011-08-11	2011-08-11	ENSG00000224930	ENSG00000275874		"""-"""	19725	non-coding RNA	RNA, long non-coding	"""narcolepsy candidate region 1 gene C"""		"""chromosome 21 open reading frame 113"", ""non-protein coding RNA 162"""	C21orf113, NCRNA00162		16826516	Standard	NR_024089		Approved	PRED74, NLC1-C	uc002zgo.3	P0C852	OTTHUMG00000090292		21.37:g.46419224G>A				RNA	SNP	-	NULL	ENST00000422199.1	37	NULL		21																																																																																			LINC00162	-	-		0.552	LINC00162-001	KNOWN	basic	lincRNA	LINC00162	HGNC	lincRNA	OTTHUMT00000206637.1	G			46419224	-1	no_errors	ENST00000422199	ensembl	human	known	70_37	rna	SNP	0.141	A
LINC00266-1	140849	genome.wustl.edu	37	20	62934716	62934716	+	RNA	SNP	G	G	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr20:62934716G>A	ENST00000279067.3	+	0	732					NR_040415.1				long intergenic non-protein coding RNA 266-1																		CTGAATGTACGTATAAAATAT	0.353																																																	0																																												140849			BC118988		20q13.33	2012-10-12	2011-08-11	2011-08-11	ENSG00000149656	ENSG00000149656		"""Long non-coding RNAs"""	16202	non-coding RNA	RNA, long non-coding			"""chromosome 20 open reading frame 69"", ""non-protein coding RNA 266"", ""non-protein coding RNA 266-1"""	C20orf69, NCRNA00266, NCRNA00266-1			Standard	NR_040415		Approved	bA476I15.3	uc002yio.1		OTTHUMG00000033036		20.37:g.62934716G>A				RNA	SNP	-	NULL	ENST00000279067.3	37	NULL		20																																																																																			LINC00266-1	-	-		0.353	LINC00266-1-001	KNOWN	basic	processed_transcript	LINC00266-1	HGNC	processed_transcript	OTTHUMT00000080304.2	G			62934716	+1	no_errors	ENST00000279067	ensembl	human	known	70_37	rna	SNP	0.000	A
NINJ2	4815	genome.wustl.edu	37	12	772689	772689	+	De_novo_Start_OutOfFrame	SNP	G	G	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr12:772689G>A	ENST00000305108.4	-	0	256				RP11-218M22.1_ENST00000543884.1_RNA	NM_016533.4	NP_057617.2	Q9NZG7	NINJ2_HUMAN	ninjurin 2						nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|tissue regeneration (GO:0042246)	integral component of plasma membrane (GO:0005887)				large_intestine(3)|lung(1)|ovary(2)	6	all_cancers(10;0.0101)|all_epithelial(11;0.0174)|Ovarian(42;0.0512)|all_lung(10;0.103)|Lung NSC(10;0.185)		OV - Ovarian serous cystadenocarcinoma(31;3.26e-05)|BRCA - Breast invasive adenocarcinoma(9;0.0508)			TGGGATGCCCGTCTTGGCTGC	0.607																																																	0													51.0	54.0	53.0					12																	772689		2203	4300	6503			100049716			AF205633	CCDS8505.1, CCDS73418.1	12p13	2008-08-05			ENSG00000171840	ENSG00000171840			7825	protein-coding gene	gene with protein product		607297				10627596	Standard	XM_005253689		Approved		uc001qil.3	Q9NZG7	OTTHUMG00000090311	ENST00000305108.4:c.-25C>T	12.37:g.772689G>A				RNA	SNP	-	NULL	ENST00000305108.4	37	NULL	CCDS8505.1	12																																																																																			RP11-218M22.1	-	-		0.607	NINJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LOC100049716	Clone_based_vega_gene	protein_coding	OTTHUMT00000206673.2	G	NM_016533		772689	+1	no_errors	ENST00000543884	ensembl	human	known	70_37	rna	SNP	0.029	A
CACNA1B	774	genome.wustl.edu	37	9	140785082	140785082	+	Intron	SNP	G	G	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr9:140785082G>A	ENST00000371372.1	+	3	675				CACNA1B_ENST00000371357.1_Intron|CACNA1B_ENST00000277549.5_Intron|CACNA1B_ENST00000277551.2_Intron|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371363.1_Intron|CACNA1B_ENST00000371355.4_Intron	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit						calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	CGGGCTCCAGGGATGGGCGGT	0.637																																																	0																																										SO:0001627	intron_variant	100133077			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.530+7747G>A	9.37:g.140785082G>A			B1AQK5	RNA	SNP	-	NULL	ENST00000371372.1	37	NULL	CCDS59522.1	9																																																																																			RP11-188C12.3	-	-		0.637	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	LOC100133077	Clone_based_vega_gene	protein_coding	OTTHUMT00000055380.1	G	NM_000718		140785082	-1	no_errors	ENST00000371390	ensembl	human	known	70_37	rna	SNP	0.000	A
LOC100505782	100505782	genome.wustl.edu	37	17	39565702	39565702	+	RNA	SNP	C	C	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr17:39565702C>T	ENST00000432258.1	+	0	1116				AC003958.2_ENST00000430006.1_RNA																							GAAATTGCTTCAAGAAAGGAA	0.433																																																	0																																												100505782																															17.37:g.39565702C>T				RNA	SNP	-	NULL	ENST00000432258.1	37	NULL		17																																																																																			AC003958.2	-	-		0.433	AC003958.2-002	KNOWN	basic	antisense	LOC100505782	Clone_based_vega_gene	antisense	OTTHUMT00000257900.2	C			39565702	+1	no_errors	ENST00000430006	ensembl	human	known	70_37	rna	SNP	0.001	T
LOC283194	283194	genome.wustl.edu	37	11	58746612	58746612	+	RNA	SNP	G	G	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr11:58746612G>T	ENST00000525714.1	-	0	146				RP11-142C4.6_ENST00000532098.1_RNA|RP11-142C4.6_ENST00000533954.1_RNA																							TGTGAGTTCTGCCTACTTGAT	0.443																																																	0																																												283194																															11.37:g.58746612G>T				RNA	SNP	-	NULL	ENST00000525714.1	37	NULL		11																																																																																			RP11-142C4.6	-	-		0.443	RP11-142C4.6-002	KNOWN	basic|exp_conf	antisense	LOC283194	Clone_based_vega_gene	antisense	OTTHUMT00000394604.1	G			58746612	-1	no_errors	ENST00000533954	ensembl	human	known	70_37	rna	SNP	0.101	T
LOXL1	4016	genome.wustl.edu	37	15	74218664	74218664	+	5'Flank	SNP	C	C	G			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr15:74218664C>G	ENST00000261921.7	+	0	0				LOXL1-AS1_ENST00000564963.1_RNA|LOXL1-AS1_ENST00000562965.1_RNA|LOXL1-AS1_ENST00000562130.1_RNA|LOXL1-AS1_ENST00000564194.1_RNA|LOXL1-AS1_ENST00000567257.1_RNA|LOXL1-AS1_ENST00000565416.1_RNA|LOXL1-AS1_ENST00000568229.1_RNA|LOXL1-AS1_ENST00000562739.1_RNA|LOXL1-AS1_ENST00000565756.1_RNA|LOXL1-AS1_ENST00000568087.1_RNA|LOXL1-AS1_ENST00000566675.1_RNA|LOXL1-AS1_ENST00000567644.1_RNA	NM_005576.2	NP_005567.2	Q08397	LOXL1_HUMAN	lysyl oxidase-like 1						extracellular matrix organization (GO:0030198)|oxidation-reduction process (GO:0055114)|protein deamination (GO:0018277)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor (GO:0016641)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						GCTGGGAACTCCAGGGACTGA	0.677																																																	0																																										SO:0001631	upstream_gene_variant	100287616			L21186	CCDS10253.1	15q24-q25	2008-07-18			ENSG00000129038	ENSG00000129038			6665	protein-coding gene	gene with protein product		153456				7689553	Standard	NM_005576		Approved	LOXL, LOL	uc002awc.1	Q08397	OTTHUMG00000137595		15.37:g.74218664C>G	Exception_encountered		Q6NUL3|Q96BW7	RNA	SNP	-	NULL	ENST00000261921.7	37	NULL	CCDS10253.1	15																																																																																			LOXL1-AS1	-	-		0.677	LOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LOXL1-AS1	HGNC	protein_coding	OTTHUMT00000268995.2	C	NM_005576		74218664	-1	no_errors	ENST00000562130	ensembl	human	known	70_37	rna	SNP	0.002	G
LPHN1	22859	genome.wustl.edu	37	19	14261736	14261736	+	Silent	SNP	C	C	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr19:14261736C>T	ENST00000340736.6	-	24	4671	c.4374G>A	c.(4372-4374)gaG>gaA	p.E1458E	CTB-55O6.12_ENST00000588658.1_RNA|CTB-55O6.12_ENST00000588387.1_RNA|LPHN1_ENST00000361434.3_Silent_p.E1453E	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	1458					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GCCCTGGCCCCTCAAGGCCTG	0.716																																																	0													16.0	16.0	16.0					19																	14261736		2142	4204	6346	SO:0001819	synonymous_variant	22859			AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"""-"", ""GPCR / Class B : Orphans"""	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.4374G>A	19.37:g.14261736C>T			Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	pfam_GPCR_2_latrophilin_rcpt_C,pfam_Olfac-like,pfam_DUF3497,pfam_GPCR_2_secretin-like,pfam_Lectin_gal-bd_dom,pfam_GPS_dom,pfam_GPCR_2_extracellular_dom,smart_Olfac-like,smart_GPCR_2_extracellular_dom,smart_GPS_dom,pfscan_GPS_dom,pfscan_Lectin_gal-bd_dom,pfscan_Olfac-like,pfscan_GPCR_2_extracellular_dom,pfscan_GPCR_2-like,prints_GPCR_2_latrophilin,prints_GPCR_2_secretin-like	p.E1458	ENST00000340736.6	37	c.4374	CCDS32928.1	19																																																																																			LPHN1	-	pfam_GPCR_2_latrophilin_rcpt_C		0.716	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	LPHN1	HGNC	protein_coding	OTTHUMT00000459696.1	C	NM_014921		14261736	-1	no_errors	ENST00000340736	ensembl	human	known	70_37	silent	SNP	1.000	T
MAP7D2	256714	genome.wustl.edu	37	X	20030618	20030618	+	Missense_Mutation	SNP	C	C	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chrX:20030618C>A	ENST00000379651.3	-	14	1816	c.1798G>T	c.(1798-1800)Ggt>Tgt	p.G600C	MAP7D2_ENST00000443379.3_Missense_Mutation_p.G555C|MAP7D2_ENST00000452324.3_Missense_Mutation_p.G548C|MAP7D2_ENST00000379643.5_Missense_Mutation_p.G641C|MAP7D2_ENST00000543767.1_Missense_Mutation_p.G485C	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	600					microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						TGATCCACACCATTAACTTCC	0.423																																																	0													131.0	118.0	123.0					X																	20030618		2203	4300	6503	SO:0001583	missense	256714			BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.1798G>T	X.37:g.20030618C>A	ENSP00000368972:p.Gly600Cys		B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Missense_Mutation	SNP	pfam_E-MAP-115	p.G641C	ENST00000379651.3	37	c.1921	CCDS14195.1	X	.	.	.	.	.	.	.	.	.	.	C	12.67	2.007955	0.35415	.	.	ENSG00000184368	ENST00000379651;ENST00000379643;ENST00000543767;ENST00000443379;ENST00000544957;ENST00000452324	T;T;T;T;T	0.25085	2.15;3.5;3.5;1.82;2.15	5.39	1.55	0.23275	.	0.935908	0.09083	N	0.851029	T	0.36744	0.0978	L	0.47716	1.5	0.09310	N	1	D;D;D;D;P	0.76494	0.999;0.999;0.999;0.999;0.728	D;D;D;D;P	0.74348	0.921;0.964;0.983;0.946;0.487	T	0.19910	-1.0291	10	0.66056	D	0.02	1.0703	1.462	0.02398	0.1422:0.3996:0.1365:0.3217	.	555;548;641;600;485	B7Z3S7;C9JYW0;Q96T17-2;Q96T17;F5GYC2	.;.;.;MA7D2_HUMAN;.	C	600;641;485;555;283;548	ENSP00000368972:G600C;ENSP00000368964:G641C;ENSP00000440691:G485C;ENSP00000388239:G555C;ENSP00000413301:G548C	ENSP00000368964:G641C	G	-	1	0	MAP7D2	19940539	0.029000	0.19370	0.002000	0.10522	0.537000	0.34900	0.131000	0.15870	0.116000	0.18110	0.525000	0.51046	GGT	MAP7D2	-	NULL		0.423	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MAP7D2	HGNC	protein_coding	OTTHUMT00000056001.1	C	NM_152780		20030618	-1	no_errors	ENST00000379643	ensembl	human	known	70_37	missense	SNP	0.001	A
MED1	5469	genome.wustl.edu	37	17	37563901	37563902	+	Frame_Shift_Ins	INS	-	-	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr17:37563901_37563902insT	ENST00000300651.6	-	17	4795_4796	c.4572_4573insA	c.(4570-4575)aaatctfs	p.S1525fs	MED1_ENST00000394287.3_Intron|CTB-131K11.1_ENST00000582842.1_RNA	NM_004774.3	NP_004765.2	O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		ATGCTATGAGATTTTTTCTtgt	0.421										HNSCC(31;0.082)																											Pancreas(21;279 768 2492 4877 24026)												0																																										SO:0001589	frameshift_variant	5469			L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"""PPAR binding protein"""	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000300651.6:c.4573dupA	17.37:g.37563907_37563907dupT	ENSP00000300651:p.Ser1525fs		B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Frame_Shift_Ins	INS	pfam_Mediator_Med1_met/fun	p.S1524fs	ENST00000300651.6	37	c.4573_4572	CCDS11336.1	17																																																																																			MED1	-	NULL		0.421	MED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MED1	HGNC	protein_coding	OTTHUMT00000256943.3	-	NM_004774		37563902	-1	no_errors	ENST00000300651	ensembl	human	known	70_37	frame_shift_ins	INS	1.000:1.000	T
MED1	5469	genome.wustl.edu	37	17	37563901	37563902	+	Frame_Shift_Ins	INS	-	-	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr17:37563901_37563902insT	ENST00000300651.6	-	17	4795_4796	c.4572_4573insA	c.(4570-4575)aaatctfs	p.S1525fs	MED1_ENST00000394287.3_Intron|CTB-131K11.1_ENST00000582842.1_RNA	NM_004774.3	NP_004765.2	O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		ATGCTATGAGATTTTTTCTtgt	0.421										HNSCC(31;0.082)																											Pancreas(21;279 768 2492 4877 24026)												0																																										SO:0001589	frameshift_variant	5469			L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"""PPAR binding protein"""	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000300651.6:c.4573dupA	17.37:g.37563907_37563907dupT	ENSP00000300651:p.Ser1525fs		B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Frame_Shift_Ins	INS	pfam_Mediator_Med1_met/fun	p.S1524fs	ENST00000300651.6	37	c.4573_4572	CCDS11336.1	17																																																																																			MED1	-	NULL		0.421	MED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MED1	HGNC	protein_coding	OTTHUMT00000256943.3	-	NM_004774		37563902	-1	no_errors	ENST00000300651	ensembl	human	known	70_37	frame_shift_ins	INS	1.000:1.000	T
MEGF10	84466	genome.wustl.edu	37	5	126705681	126705681	+	Silent	SNP	C	C	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr5:126705681C>A	ENST00000274473.6	+	6	666	c.399C>A	c.(397-399)acC>acA	p.T133T	MEGF10_ENST00000418761.2_Silent_p.T133T|MEGF10_ENST00000508365.1_Silent_p.T133T|MEGF10_ENST00000503335.2_Silent_p.T133T	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	133	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		GGGGAGGGACCAACTGCTCCA	0.522																																																	0													190.0	152.0	165.0					5																	126705681		2203	4300	6503	SO:0001819	synonymous_variant	84466			AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.399C>A	5.37:g.126705681C>A			Q68DE5|Q8WUL3	Silent	SNP	pfam_EGF_laminin,pfam_EGF_extracell,superfamily_Proteinase_amylase_inhib_dom,smart_EG-like_dom,smart_EGF_laminin,pfscan_EG-like_dom,pfscan_EMI_domain	p.T133	ENST00000274473.6	37	c.399	CCDS4142.1	5																																																																																			MEGF10	-	smart_EG-like_dom		0.522	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MEGF10	HGNC	protein_coding	OTTHUMT00000250973.2	C	NM_032446		126705681	+1	no_errors	ENST00000274473	ensembl	human	known	70_37	silent	SNP	1.000	A
MIAT	440823	genome.wustl.edu	37	22	27066924	27066925	+	lincRNA	INS	-	-	T	rs531961689|rs568998572	byFrequency	TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr22:27066924_27066925insT	ENST00000382641.1	-	0	977				MIAT_ENST00000423278.1_lincRNA|CTA-211A9.5_ENST00000437071.1_lincRNA																							AGCTTGATGCGTTTTTTTTTTT	0.515																																																	0																																												440823																															22.37:g.27066935_27066935dupT				RNA	INS	-	NULL	ENST00000382641.1	37	NULL		22																																																																																			MIAT	-	-		0.515	CTA-373H7.7-001	KNOWN	basic|exp_conf	lincRNA	MIAT	HGNC	lincRNA	OTTHUMT00000320776.1	-			27066925	+1	no_errors	ENST00000421151	ensembl	human	known	70_37	rna	INS	0.001:0.000	T
MT-CO1	4512	genome.wustl.edu	37	M	6297	6297	+	Silent	SNP	T	T	C			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chrM:6297T>C	ENST00000361624.2	+	1	394	c.394T>C	c.(394-396)Tta>Cta	p.L132L	MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TW_ENST00000387382.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-TQ_ENST00000387372.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TL1_ENST00000386347.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TM_ENST00000387377.1_RNA			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	132					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						TCTACCCTCCCTTAGCAGGGA	0.522																																																	0																																										SO:0001819	synonymous_variant	4512					mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.394T>C	M.37:g.6297T>C			Q34770	Silent	SNP	pfam_Cyt_c_Oxase_su1,superfamily_Cyt_c_Oxase_su1_dom,pfscan_Cyt_c_Oxase_su1_dom,prints_Cyt_c_Oxase_su1	p.L132	ENST00000361624.2	37	c.394		MT																																																																																			MT-CO1	-	pfam_Cyt_c_Oxase_su1,superfamily_Cyt_c_Oxase_su1_dom,pfscan_Cyt_c_Oxase_su1_dom,prints_Cyt_c_Oxase_su1		0.522	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	MT-CO1	HGNC	protein_coding		T	YP_003024028		6297	+1	no_errors	ENST00000361624	ensembl	human	known	70_37	silent	SNP	NULL	C
NBPF10	100132406	genome.wustl.edu	37	1	145298168	145298168	+	Missense_Mutation	SNP	G	G	A	rs12124464		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr1:145298168G>A	ENST00000342960.5	+	5	615	c.580G>A	c.(580-582)Gct>Act	p.A194T	NBPF10_ENST00000369338.1_Intron|RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	194	NBPF 1. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GGTGCAGAAGGCTGAAGAGAG	0.532																																																	0																																										SO:0001583	missense	100132406			BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.580G>A	1.37:g.145298168G>A	ENSP00000345684:p.Ala194Thr		Q5RHC0|Q9NWN6	Missense_Mutation	SNP	pfam_NBPF_dom	p.A194T	ENST00000342960.5	37	c.580	CCDS53355.1	1	.	.	.	.	.	.	.	.	.	.	.	9.671	1.146604	0.21288	.	.	ENSG00000163386	ENST00000369339;ENST00000448873;ENST00000342960	T	0.07567	3.18	1.18	-2.35	0.06684	.	.	.	.	.	T	0.02342	0.0072	L	0.52126	1.63	0.09310	N	1	.	.	.	.	.	.	T	0.43048	-0.9415	7	0.23891	T	0.37	.	3.9478	0.09355	0.1922:0.4783:0.3295:0.0	rs28610541	.	.	.	T	194;119;194	ENSP00000345684:A194T	ENSP00000345684:A194T	A	+	1	0	NBPF10	144009525	0.010000	0.17322	0.000000	0.03702	0.009000	0.06853	0.472000	0.22116	-1.101000	0.03027	-1.043000	0.02367	GCT	NBPF10	-	pfam_NBPF_dom		0.532	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NBPF10	HGNC	protein_coding		G	NM_001039703		145298168	+1	no_errors	ENST00000342960	ensembl	human	known	70_37	missense	SNP	0.000	A
NEDD4L	23327	genome.wustl.edu	37	18	56034976	56034976	+	Splice_Site	SNP	A	A	C			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr18:56034976A>C	ENST00000400345.3	+	22	2346		c.e22-1		NEDD4L_ENST00000456986.1_Splice_Site|NEDD4L_ENST00000256832.7_Splice_Site|NEDD4L_ENST00000256830.9_Splice_Site|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000357895.5_Splice_Site|NEDD4L_ENST00000431212.2_Splice_Site|NEDD4L_ENST00000435432.2_Splice_Site|NEDD4L_ENST00000586263.1_Splice_Site|NEDD4L_ENST00000456173.2_Splice_Site|NEDD4L_ENST00000382850.4_Splice_Site|NEDD4L_ENST00000356462.6_Splice_Site	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase						cellular sodium ion homeostasis (GO:0006883)|excretion (GO:0007588)|gene expression (GO:0010467)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cation channel activity (GO:2001259)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of sodium ion transport (GO:0010765)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane depolarization (GO:0003254)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of protein catabolic process (GO:0042176)|regulation of tight junction assembly (GO:2000810)|response to metal ion (GO:0010038)|response to salt stress (GO:0009651)|sodium ion transport (GO:0006814)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|ventricular cardiac muscle cell action potential (GO:0086005)|viral life cycle (GO:0019058)|viral process (GO:0016032)|water homeostasis (GO:0030104)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ion channel binding (GO:0044325)|ligase activity (GO:0016874)|potassium channel inhibitor activity (GO:0019870)|potassium channel regulator activity (GO:0015459)|sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4)	37						TCTCCTCAAAAGGGACAACTA	0.428																																																	0													113.0	103.0	106.0					18																	56034976		1901	4123	6024	SO:0001630	splice_region_variant	23327			AF210730	CCDS45872.1, CCDS45873.1, CCDS45874.1, CCDS45875.1, CCDS45876.1, CCDS58632.1, CCDS59323.1	18q21.31	2014-08-12	2012-02-23		ENSG00000049759				7728	protein-coding gene	gene with protein product		606384	"""neural precursor cell expressed, developmentally down-regulated 4-like"""			10594025, 11244092, 18322022	Standard	NM_001144965		Approved	KIAA0439, RSP5, NEDD4-2	uc002lgy.3	Q96PU5	OTTHUMG00000179875	ENST00000400345.3:c.2064-1A>C	18.37:g.56034976A>C			O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Splice_Site	SNP	-	e22-2	ENST00000400345.3	37	c.2064-2	CCDS45872.1	18	.	.	.	.	.	.	.	.	.	.	A	23.9	4.467901	0.84533	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7612	0.78082	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NEDD4L	54185956	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.287000	0.95975	2.182000	0.69389	0.528000	0.53228	.	NEDD4L	-	-		0.428	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NEDD4L	HGNC	protein_coding	OTTHUMT00000448749.1	A		Intron	56034976	+1	no_errors	ENST00000400345	ensembl	human	known	70_37	splice_site	SNP	1.000	C
NPTX1	4884	genome.wustl.edu	37	17	78449464	78449464	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr17:78449464G>A	ENST00000306773.4	-	2	656	c.499C>T	c.(499-501)Cag>Tag	p.Q167*	NPTX1_ENST00000575212.1_5'UTR	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	167					axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			ATCTTGCTCTGCAGCAGATCC	0.642																																																	0													60.0	53.0	55.0					17																	78449464		2203	4300	6503	SO:0001587	stop_gained	4884			U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246			7952	protein-coding gene	gene with protein product		602367				8884281	Standard	NM_002522		Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.499C>T	17.37:g.78449464G>A	ENSP00000307549:p.Gln167*		B3KXH3|Q5FWE6	Nonsense_Mutation	SNP	pfam_Pentaxin,superfamily_ConA-like_lec_gl_sf,smart_Pentaxin,prints_Pentaxin	p.Q167*	ENST00000306773.4	37	c.499	CCDS32762.1	17	.	.	.	.	.	.	.	.	.	.	G	38	6.786124	0.97837	.	.	ENSG00000171246	ENST00000306773	.	.	.	3.7	3.7	0.42460	.	0.066354	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	-20.6591	14.7467	0.69494	0.0:0.0:1.0:0.0	.	.	.	.	X	167	.	ENSP00000307549:Q167X	Q	-	1	0	NPTX1	76064059	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.038000	0.93771	2.068000	0.61886	0.561000	0.74099	CAG	NPTX1	-	NULL		0.642	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPTX1	HGNC	protein_coding	OTTHUMT00000438051.1	G			78449464	-1	no_errors	ENST00000306773	ensembl	human	known	70_37	nonsense	SNP	1.000	A
PDZD2	23037	genome.wustl.edu	37	5	32089653	32089653	+	Silent	SNP	C	C	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr5:32089653C>T	ENST00000438447.1	+	20	6487	c.6099C>T	c.(6097-6099)tcC>tcT	p.S2033S	PDZD2_ENST00000282493.3_Silent_p.S2033S			O15018	PDZD2_HUMAN	PDZ domain containing 2	2033					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						GTGCTGACTCCGGGCCGGTGA	0.642																																																	0													123.0	136.0	131.0					5																	32089653		2203	4300	6503	SO:0001819	synonymous_variant	23037			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.6099C>T	5.37:g.32089653C>T			Q9BXD4	Silent	SNP	pfam_PDZ,superfamily_PDZ,smart_PDZ,pfscan_PDZ	p.S2033	ENST00000438447.1	37	c.6099	CCDS34137.1	5																																																																																			PDZD2	-	NULL		0.642	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PDZD2	HGNC	protein_coding	OTTHUMT00000366608.1	C			32089653	+1	no_errors	ENST00000282493	ensembl	human	known	70_37	silent	SNP	0.000	T
PIGO	84720	genome.wustl.edu	37	9	35095707	35095707	+	Intron	SNP	T	T	C			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr9:35095707T>C	ENST00000378617.3	-	2	394				PIGO_ENST00000492770.1_Intron|RP11-182N22.8_ENST00000431804.1_RNA|PIGO_ENST00000361778.2_Intron|PIGO_ENST00000341666.3_Intron|PIGO_ENST00000298004.5_Intron	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O						C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			CCCCTCGCAATATTACTCTCC	0.542											OREG0019166	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0																																										SO:0001627	intron_variant	84720			AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"""Phosphatidylinositol glycan anchor biosynthesis"""	23215	protein-coding gene	gene with protein product		614730	"""phosphatidylinositol glycan, class O"""			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.1-144A>G	9.37:g.35095707T>C		852	B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	RNA	SNP	-	NULL	ENST00000378617.3	37	NULL	CCDS6575.1	9																																																																																			PIGO	-	-		0.542	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PIGO	HGNC	protein_coding	OTTHUMT00000052284.1	T	NM_032634		35095707	-1	no_errors	ENST00000474436	ensembl	human	known	70_37	rna	SNP	0.000	C
PROCA1	147011	genome.wustl.edu	37	17	27038050	27038051	+	5'UTR	INS	-	-	G			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr17:27038050_27038051insG	ENST00000579650.1	-	0	266_267				PROCA1_ENST00000301039.2_Intron|PROCA1_ENST00000581289.1_Intron|PROCA1_ENST00000439862.3_5'UTR			Q8NCQ7	PRCA1_HUMAN	protein interacting with cyclin A1						lipid catabolic process (GO:0016042)		calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			breast(1)|cervix(1)|endometrium(1)|large_intestine(7)|lung(4)|ovary(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					taggagaggaaggagggaagag	0.639																																																	0																																										SO:0001623	5_prime_UTR_variant	147011			BC029574	CCDS11239.1	17q11.2	2009-04-20	2009-04-20		ENSG00000167525	ENSG00000167525			28600	protein-coding gene	gene with protein product	"""proline-rich cyclin A1-interacting protein"""					15159402	Standard	NM_152465		Approved	MGC39650	uc002hca.1	Q8NCQ7	OTTHUMG00000132682	ENST00000579650.1:c.-741->C	17.37:g.27038052_27038052dupG			B4DX95|G5E9R8	RNA	INS	-	NULL	ENST00000579650.1	37	NULL		17																																																																																			PROCA1	-	-		0.639	PROCA1-003	KNOWN	basic	processed_transcript	PROCA1	HGNC	protein_coding	OTTHUMT00000255971.3	-	NM_152465		27038051	-1	no_errors	ENST00000422880	ensembl	human	known	70_37	rna	INS	0.000:0.000	G
SFPQ	6421	genome.wustl.edu	37	1	35645341	35645341	+	5'UTR	SNP	G	G	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr1:35645341G>T	ENST00000468598.1	-	0	905							P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich						alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)		SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				TAAAGTTCCTGAAGTCCATAT	0.358			T	TFE3	papillary renal cell																																			Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	0																																										SO:0001623	5_prime_UTR_variant	6421			X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"""RNA binding motif (RRM) containing"""	10774	protein-coding gene	gene with protein product	"""polypyrimidine tract binding protein associated"", ""protein phosphatase 1, regulatory subunit 140"""	605199	"""splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"""			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000468598.1:c.-1930C>A	1.37:g.35645341G>T			P30808|Q5SZ71	RNA	SNP	-	NULL	ENST00000468598.1	37	NULL		1																																																																																			SFPQ	-	-		0.358	SFPQ-004	KNOWN	basic	processed_transcript	SFPQ	HGNC	protein_coding	OTTHUMT00000011997.2	G	NM_005066		35645341	-1	no_errors	ENST00000468598	ensembl	human	known	70_37	rna	SNP	0.070	T
SHOC2	8036	genome.wustl.edu	37	10	112679831	112679831	+	Intron	SNP	G	G	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr10:112679831G>T	ENST00000369452.4	+	1	111				BBIP1_ENST00000448814.1_5'Flank|BBIP1_ENST00000436562.1_5'Flank|SHOC2_ENST00000265277.5_Intron|BBIP1_ENST00000423273.1_5'Flank|BBIP1_ENST00000447005.1_5'Flank|SHOC2_ENST00000489390.1_Intron|BBIP1_ENST00000454061.1_5'Flank|BBIP1_ENST00000605742.1_5'Flank	NM_007373.3	NP_031399.2	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog (C. elegans)						fibroblast growth factor receptor signaling pathway (GO:0008543)|positive regulation of Ras protein signal transduction (GO:0046579)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase binding (GO:0019903)|protein phosphatase regulator activity (GO:0019888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(2)	17				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)		CTGGGCCCCCGGGCCCAGTCC	0.781																																																	0																																										SO:0001627	intron_variant	8036			AB020669	CCDS7568.1, CCDS58095.1	10q25	2014-09-17	2001-11-28		ENSG00000108061	ENSG00000108061			15454	protein-coding gene	gene with protein product		602775	"""soc-2 (suppressor of clear, C.elegans) homolog"""			9618511, 9674433, 10783161	Standard	NM_007373		Approved	KIAA0862, SOC2, SUR-8, SOC-2, SUR8	uc001kzl.4	Q9UQ13	OTTHUMG00000019047	ENST00000369452.4:c.-235+416G>T	10.37:g.112679831G>T			A8K9W8|B3KR23|O76063|Q5VZS8|Q5VZS9	RNA	SNP	-	NULL	ENST00000369452.4	37	NULL	CCDS7568.1	10																																																																																			SHOC2	-	-		0.781	SHOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SHOC2	HGNC	protein_coding	OTTHUMT00000050355.1	G	NM_007373		112679831	+1	no_errors	ENST00000489783	ensembl	human	known	70_37	rna	SNP	0.005	T
SNHG14	104472715	genome.wustl.edu	37	15	25477868	25477868	+	RNA	SNP	G	G	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr15:25477868G>A	ENST00000453082.2	+	0	1711				SNORD115-33_ENST00000363723.1_RNA|SNORD115-35_ENST00000365122.1_RNA|SNORD115-34_ENST00000362441.1_RNA	NR_003343.1				small nucleolar RNA host gene 14 (non-protein coding)																		TGAGCTCTTCGGCCCAAGTGG	0.597																																																	0																																												0					15q11.2	2014-01-17	2011-08-22	2011-08-22	ENSG00000224078	ENSG00000224078		"""Long non-coding RNAs"""	37462	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 214"""		"""UBE3A antisense RNA 1 (non-protein coding)"""	UBE3A-AS1		23771028	Standard			Approved	NCRNA00214, UBE3A-AS			OTTHUMG00000056661		15.37:g.25477868G>A				RNA	SNP	-	NULL	ENST00000453082.2	37	NULL		15																																																																																			SNHG14	-	-		0.597	SNHG14-003	KNOWN	non_canonical_TEC|basic	antisense	SNHG14	HGNC	processed_transcript	OTTHUMT00000126730.2	G			25477868	+1	no_errors	ENST00000453082	ensembl	human	known	70_37	rna	SNP	0.000	A
SSBP3	23648	genome.wustl.edu	37	1	54692356	54692356	+	3'UTR	SNP	A	A	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr1:54692356A>T	ENST00000371320.3	-	0	2025				SSBP3_ENST00000326956.7_5'UTR|SSBP3_ENST00000417664.2_3'UTR|SSBP3_ENST00000371319.3_3'UTR	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3						head morphogenesis (GO:0060323)|hematopoietic progenitor cell differentiation (GO:0002244)|midbrain-hindbrain boundary initiation (GO:0021547)|positive regulation of anterior head development (GO:2000744)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prechordal plate formation (GO:0021501)|protein complex assembly (GO:0006461)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|protein complex (GO:0043234)	single-stranded DNA binding (GO:0003697)			central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	11						ttttttttttAAGAAGAAAGC	0.388																																																	0																																										SO:0001624	3_prime_UTR_variant	23648				CCDS590.1, CCDS591.1, CCDS30726.1	1p32.3	2008-02-05	2001-11-28		ENSG00000157216	ENSG00000157216			15674	protein-coding gene	gene with protein product		607390	"""single-stranded DNA-binding protein 3"""			12079286	Standard	NM_145716		Approved	CSDP, SSDP, FLJ10355, SSDP1	uc001cxe.4	Q9BWW4	OTTHUMG00000008264	ENST00000371320.3:c.*448T>A	1.37:g.54692356A>T			A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	RNA	SNP	-	NULL	ENST00000371320.3	37	NULL	CCDS591.1	1																																																																																			SSBP3	-	-		0.388	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	SSBP3	HGNC	protein_coding	OTTHUMT00000022721.1	A	NM_018070		54692356	-1	no_errors	ENST00000326956	ensembl	human	known	70_37	rna	SNP	0.992	T
STARD13	90627	genome.wustl.edu	37	13	33738477	33738477	+	Intron	SNP	G	G	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr13:33738477G>T	ENST00000336934.5	-	3	440				STARD13_ENST00000399365.3_Intron|STARD13_ENST00000255486.4_Intron|STARD13-IT1_ENST00000456087.1_RNA|STARD13_ENST00000487412.1_Intron	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13						regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		AATGTGCGTTGATCGCTCCTG	0.328																																																	0																																										SO:0001627	intron_variant	100874373			AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.323+996C>A	13.37:g.33738477G>T			A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	RNA	SNP	-	NULL	ENST00000336934.5	37	NULL	CCDS9348.1	13																																																																																			STARD13-IT1	-	-		0.328	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	STARD13-IT1	HGNC	protein_coding	OTTHUMT00000276118.2	G	NM_001243466		33738477	-1	no_errors	ENST00000456087	ensembl	human	known	70_37	rna	SNP	0.000	T
SUPT7L	9913	genome.wustl.edu	37	2	27876450	27876450	+	Missense_Mutation	SNP	C	C	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr2:27876450C>A	ENST00000337768.5	-	6	1716	c.1147G>T	c.(1147-1149)Gac>Tac	p.D383Y	SUPT7L_ENST00000404798.2_Missense_Mutation_p.D248Y|SUPT7L_ENST00000405491.1_Missense_Mutation_p.D381Y|SUPT7L_ENST00000464789.2_Missense_Mutation_p.D381Y|SUPT7L_ENST00000406540.1_Missense_Mutation_p.D381Y	NM_001282729.1|NM_014860.1	NP_001269658.1|NP_055675.1	O94864	ST65G_HUMAN	suppressor of Ty 7 (S. cerevisiae)-like	383					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|maintenance of protein location in nucleus (GO:0051457)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)					CTATCTGAGTCATCAGGGCTC	0.517																																																	0													136.0	141.0	139.0					2																	27876450		2008	4179	6187	SO:0001583	missense	9913			AF197954	CCDS42667.1, CCDS62885.1, CCDS62886.1	2p23.3	2008-02-05			ENSG00000119760	ENSG00000119760			30632	protein-coding gene	gene with protein product		612762				9872452, 11564863	Standard	NM_001282732		Approved	STAF65, gamma, KIAA0764, SPT7L	uc002rli.1	O94864	OTTHUMG00000151947	ENST00000337768.5:c.1147G>T	2.37:g.27876450C>A	ENSP00000336750:p.Asp383Tyr		B4E3W3|Q6IB21|Q9H2T6	Missense_Mutation	SNP	pfam_BTP,smart_BTP	p.D383Y	ENST00000337768.5	37	c.1147	CCDS42667.1	2	.	.	.	.	.	.	.	.	.	.	C	18.12	3.553830	0.65425	.	.	ENSG00000119760	ENST00000337768;ENST00000406540;ENST00000405491;ENST00000464789;ENST00000404798	.	.	.	5.96	5.96	0.96718	.	0.141043	0.64402	D	0.000005	T	0.46833	0.1413	N	0.08118	0	0.43453	D	0.995649	P;P;P	0.37276	0.454;0.589;0.454	B;B;B	0.41036	0.121;0.346;0.188	T	0.51172	-0.8739	9	0.49607	T	0.09	-24.2369	20.422	0.99049	0.0:1.0:0.0:0.0	.	248;381;383	B4E3W3;O94864-2;O94864	.;.;ST65G_HUMAN	Y	383;381;381;381;248	.	ENSP00000336750:D383Y	D	-	1	0	SUPT7L	27729954	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.904000	0.69886	2.832000	0.97577	0.655000	0.94253	GAC	SUPT7L	-	NULL		0.517	SUPT7L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SUPT7L	HGNC	protein_coding	OTTHUMT00000324568.1	C	NM_014860		27876450	-1	no_errors	ENST00000337768	ensembl	human	known	70_37	missense	SNP	1.000	A
TGFBR2	7048	genome.wustl.edu	37	3	30732976	30732976	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr3:30732976C>T	ENST00000295754.5	+	7	1971	c.1589C>T	c.(1588-1590)aCa>aTa	p.T530I	TGFBR2_ENST00000359013.4_Missense_Mutation_p.T555I	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	530	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						GCCCGTCTCACAGCCCAGTGT	0.592																																																	0													73.0	70.0	71.0					3																	30732976		2203	4300	6503	SO:0001583	missense	7048				CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513			11773	protein-coding gene	gene with protein product		190182	"""transforming growth factor, beta receptor II (70-80kD)"""	MFS2		1319842, 15235604	Standard	NM_001024847		Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.1589C>T	3.37:g.30732976C>T	ENSP00000295754:p.Thr530Ile		B4DTV5|Q15580|Q6DKT6|Q99474	Missense_Mutation	SNP	pfam_Transforming_GF_b_rcpt_2_ecto,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Transform_growth_fac-b_typ-2,prints_Activin_II/TGFBeta-II_recpt,pfscan_Prot_kinase_cat_dom	p.T555I	ENST00000295754.5	37	c.1664	CCDS2648.1	3	.	.	.	.	.	.	.	.	.	.	C	33	5.236087	0.95240	.	.	ENSG00000163513	ENST00000295754;ENST00000359013;ENST00000439925	D;D	0.94828	-3.53;-3.53	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98175	0.9397	M	0.93283	3.4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98548	1.0635	10	0.87932	D	0	.	20.2857	0.98533	0.0:1.0:0.0:0.0	.	530;555	P37173;D2JYI1	TGFR2_HUMAN;.	I	530;555;360	ENSP00000295754:T530I;ENSP00000351905:T555I	ENSP00000295754:T530I	T	+	2	0	TGFBR2	30707980	1.000000	0.71417	0.984000	0.44739	0.992000	0.81027	7.818000	0.86416	2.803000	0.96430	0.650000	0.86243	ACA	TGFBR2	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Transform_growth_fac-b_typ-2,pfscan_Prot_kinase_cat_dom		0.592	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TGFBR2	HGNC	protein_coding	OTTHUMT00000252994.2	C			30732976	+1	no_errors	ENST00000359013	ensembl	human	known	70_37	missense	SNP	1.000	T
THSD7A	221981	genome.wustl.edu	37	7	11446665	11446665	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr7:11446665G>A	ENST00000423059.4	-	21	4185	c.3934C>T	c.(3934-3936)Cga>Tga	p.R1312*	AC004160.4_ENST00000425837.1_RNA|AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1312	TSP type-1 13. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		GTCACTGTTCGTCTTCGGATC	0.453										HNSCC(18;0.044)																																							0													109.0	104.0	106.0					7																	11446665		1940	4142	6082	SO:0001587	stop_gained	221981				CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.3934C>T	7.37:g.11446665G>A	ENSP00000406482:p.Arg1312*			Nonsense_Mutation	SNP	pfam_Thrombospondin_1_rpt,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,pfscan_Thrombospondin_1_rpt	p.R1312*	ENST00000423059.4	37	c.3934	CCDS47543.1	7	.	.	.	.	.	.	.	.	.	.	G	46	12.335071	0.99658	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	.	.	.	5.71	2.83	0.33086	.	0.052613	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4285	0.75072	0.0:0.0:0.3545:0.6455	.	.	.	.	X	1312	.	ENSP00000262042:R1312X	R	-	1	2	THSD7A	11413190	0.997000	0.39634	1.000000	0.80357	0.987000	0.75469	1.707000	0.37888	0.395000	0.25257	0.644000	0.83932	CGA	THSD7A	-	pfam_Thrombospondin_1_rpt,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,pfscan_Thrombospondin_1_rpt		0.453	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	THSD7A	HGNC	protein_coding	OTTHUMT00000325944.4	G	XM_928187.2		11446665	-1	no_errors	ENST00000423059	ensembl	human	known	70_37	nonsense	SNP	0.996	A
TNFRSF21	27242	genome.wustl.edu	37	6	47251881	47251881	+	Missense_Mutation	SNP	T	T	C			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr6:47251881T>C	ENST00000296861.2	-	3	1429	c.1036A>G	c.(1036-1038)Atc>Gtc	p.I346V		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	346					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			TGCTCATTGATGTCAAAATGC	0.537																																																	0													181.0	170.0	174.0					6																	47251881		2203	4300	6503	SO:0001583	missense	27242			AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	13469	protein-coding gene	gene with protein product	"""death receptor 6"""	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1036A>G	6.37:g.47251881T>C	ENSP00000296861:p.Ile346Val		B2RDI9|Q0D2P5|Q96D86	Missense_Mutation	SNP	pfam_Death,superfamily_DEATH-like,smart_TNFR/NGFR_Cys_rich_reg,smart_Death,pfscan_Death,pfscan_TNFR/NGFR_Cys_rich_reg,prints_TNFR_21	p.I346V	ENST00000296861.2	37	c.1036	CCDS4921.1	6	.	.	.	.	.	.	.	.	.	.	T	23.8	4.463599	0.84425	.	.	ENSG00000146072	ENST00000296861;ENST00000419206	T	0.71698	-0.59	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.79610	0.4475	M	0.63843	1.955	0.80722	D	1	D	0.65815	0.995	D	0.78314	0.991	T	0.81913	-0.0715	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	346	O75509	TNR21_HUMAN	V	346;35	ENSP00000296861:I346V	ENSP00000296861:I346V	I	-	1	0	TNFRSF21	47359840	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.440000	0.80464	2.371000	0.80710	0.533000	0.62120	ATC	TNFRSF21	-	prints_TNFR_21		0.537	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TNFRSF21	HGNC	protein_coding	OTTHUMT00000040814.1	T	NM_014452		47251881	-1	no_errors	ENST00000296861	ensembl	human	known	70_37	missense	SNP	1.000	C
USP42	84132	genome.wustl.edu	37	7	6182606	6182606	+	Missense_Mutation	SNP	C	C	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr7:6182606C>T	ENST00000306177.5	+	8	997	c.839C>T	c.(838-840)cCg>cTg	p.P280L		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	280	USP.				cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		TTTGTGAAGCCGGAACAGCTT	0.542																																																	0													170.0	178.0	176.0					7																	6182606		2126	4247	6373	SO:0001583	missense	84132			AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"""Ubiquitin-specific peptidases"""	20068	protein-coding gene	gene with protein product			"""ubiquitin specific protease 42"""			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.839C>T	7.37:g.6182606C>T	ENSP00000301962:p.Pro280Leu		A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Missense_Mutation	SNP	pfam_Peptidase_C19,pfscan_Peptidase_C19	p.P280L	ENST00000306177.5	37	c.839	CCDS47535.1	7	.	.	.	.	.	.	.	.	.	.	C	32	5.108395	0.94292	.	.	ENSG00000106346	ENST00000306177;ENST00000465073;ENST00000426246	T;T;T	0.02916	4.11;4.11;4.11	5.56	5.56	0.83823	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.64402	D	0.000006	T	0.16896	0.0406	M	0.76433	2.335	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.992;0.996;0.998;0.998	T	0.00050	-1.2196	10	0.87932	D	0	.	19.5344	0.95244	0.0:1.0:0.0:0.0	.	243;280;280;280	A4D2N7;Q9H9J4-2;Q9H9J4;A4D2N6	.;.;UBP42_HUMAN;.	L	280;213;126	ENSP00000301962:P280L;ENSP00000430568:P213L;ENSP00000408217:P126L	ENSP00000301962:P280L	P	+	2	0	USP42	6149132	1.000000	0.71417	0.968000	0.41197	0.878000	0.50629	7.385000	0.79763	2.622000	0.88805	0.563000	0.77884	CCG	USP42	-	pfam_Peptidase_C19,pfscan_Peptidase_C19		0.542	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	USP42	HGNC	protein_coding	OTTHUMT00000324262.3	C	XM_166526		6182606	+1	no_errors	ENST00000306177	ensembl	human	known	70_37	missense	SNP	1.000	T
WBP4	11193	genome.wustl.edu	37	13	41639425	41639426	+	Splice_Site	DEL	TA	TA	-	rs78988439|rs58699334		TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	TA	TA					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr13:41639425_41639426delTA	ENST00000379487.3	+	4	662		c.e4+2		WBP4_ENST00000542082.1_Splice_Site	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4						mRNA cis splicing, via spliceosome (GO:0045292)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	nucleic acid binding (GO:0003676)|proline-rich region binding (GO:0070064)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|prostate(1)|skin(1)	12		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		TAGAGTCAGGTaaaaaaaaaaa	0.376																																																	0																																										SO:0001630	splice_region_variant	11193			AF071185	CCDS9375.1	13q13.3	2012-10-17	2012-10-17		ENSG00000120688	ENSG00000120688			12739	protein-coding gene	gene with protein product	"""formin binding protein 21"""	604981				9724750	Standard	NM_007187		Approved	FBP21, MGC117310	uc001uxt.3	O75554	OTTHUMG00000016784	ENST00000379487.3:c.262+2TA>-	13.37:g.41639425_41639426delTA			B7Z4M2|Q32P29	Splice_Site	DEL	-	e4+2	ENST00000379487.3	37	c.262+2_262+1	CCDS9375.1	13																																																																																			WBP4	-	-		0.376	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WBP4	HGNC	protein_coding	OTTHUMT00000044655.2	TA	NM_007187	Intron	41639426	+1	no_errors	ENST00000379487	ensembl	human	known	70_37	splice_site_del	DEL	1.000:0.999	-
WTIP	126374	genome.wustl.edu	37	19	34973057	34973058	+	Missense_Mutation	DNP	GA	GA	TT			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G|A	G|A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr19:34973057_34973058GA>TT	ENST00000590071.2	+	1	515_516	c.178_179GA>TT	c.(178-180)GAg>TTg	p.E60L	WTIP_ENST00000270288.6_Missense_Mutation_p.E284L	NM_001080436.1	NP_001073905.1	A6NIX2	WTIP_HUMAN	Wilms tumor 1 interacting protein	60	Gly-rich.				cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|negative regulation of hippo signaling (GO:0035331)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)	4	all_lung(56;5.94e-07)|Lung NSC(56;9.35e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			CGGCGGCCCCGAGGCCGGGGCG	0.837																																																	0																																										SO:0001583	missense	126374			AK130059	CCDS59375.1	19q13.11	2012-03-16			ENSG00000142279	ENSG00000142279			20964	protein-coding gene	gene with protein product	"""WT1-interacting protein"""	614790				14736876	Standard	NM_001080436		Approved		uc002nvm.3	A6NIX2		Exception_encountered	19.37:g.34973057_34973058delinsTT	ENSP00000466953:p.Glu60Leu			Nonsense_Mutation|Missense_Mutation	SNP	pfam_Znf_LIM,smart_Znf_LIM,pfscan_Znf_LIM	p.E284*|p.E284V	ENST00000590071.2	37	c.850|c.851	CCDS59375.1	19																																																																																			WTIP	-	NULL		0.837	WTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WTIP	HGNC	protein_coding	OTTHUMT00000459381.3	G|A	XM_059037		34973057|34973058	+1	no_errors	ENST00000270288	ensembl	human	known	70_37	nonsense|missense	SNP	1.000	T
XIRP2	129446	genome.wustl.edu	37	2	168100990	168100990	+	Missense_Mutation	SNP	G	G	T			TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr2:168100990G>T	ENST00000409195.1	+	9	3177	c.3088G>T	c.(3088-3090)Gat>Tat	p.D1030Y	XIRP2_ENST00000295237.9_Missense_Mutation_p.D1030Y|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.D808Y|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	855					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TGACCAGTTTGATGAAAGCAT	0.363																																																	0													59.0	55.0	56.0					2																	168100990		1832	4081	5913	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.3088G>T	2.37:g.168100990G>T	ENSP00000386840:p.Asp1030Tyr		A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	pfam_Actin-binding_Xin_repeat,superfamily_FH2_actin-bd	p.D1030Y	ENST00000409195.1	37	c.3088	CCDS42769.1	2	.	.	.	.	.	.	.	.	.	.	G	16.17	3.048196	0.55110	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.03272	3.99;3.99;3.99	6.08	6.08	0.98989	.	0.106971	0.64402	D	0.000004	T	0.16471	0.0396	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.988;0.995;0.995	T	0.00003	-1.2596	10	0.87932	D	0	-24.6652	19.4349	0.94788	0.0:0.0:1.0:0.0	.	855;855;808	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Y	1030;1030;808	ENSP00000386840:D1030Y;ENSP00000295237:D1030Y;ENSP00000387255:D808Y	ENSP00000295237:D1030Y	D	+	1	0	XIRP2	167809236	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.280000	0.72626	2.894000	0.99253	0.655000	0.94253	GAT	XIRP2	-	NULL		0.363	XIRP2-001	KNOWN	basic|CCDS	protein_coding	XIRP2	HGNC	protein_coding	OTTHUMT00000333547.1	G	NM_152381		168100990	+1	no_errors	ENST00000295237	ensembl	human	known	70_37	missense	SNP	1.000	T
ZNF295-AS1	150142	genome.wustl.edu	37	21	43443259	43443260	+	lincRNA	INS	-	-	A	rs544526744|rs200856198|rs572259890	byFrequency	TCGA-EK-A2RE-01A-11D-A18J-09	TCGA-EK-A2RE-10A-01D-A18J-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	96ea0b20-0da0-4bdd-bbf0-799b981e778b	e472c85c-6544-4277-a4f5-64e8199980e1	g.chr21:43443259_43443260insA	ENST00000596595.1	+	0	1068_1069							Q8N0V1	ZNAS1_HUMAN	ZNF295 antisense RNA 1																		gtgagaccctgaaaaaaaaaaa	0.554																																																	0																																												150142					21q22.3	2012-10-12	2012-08-15	2011-08-11	ENSG00000237232	ENSG00000237232		"""Long non-coding RNAs"""	23130	non-coding RNA	RNA, long non-coding			"""chromosome 21 open reading frame 121"", ""non-protein coding RNA 318"", ""ZNF295 antisense RNA 1 (non-protein coding)"""	C21orf121, NCRNA00318			Standard	NR_119384		Approved	PRED87	uc011aeu.1	Q8N0V1	OTTHUMG00000086787		21.37:g.43443270_43443270dupA				RNA	INS	-	NULL	ENST00000596595.1	37	NULL		21																																																																																			ZNF295-AS1	-	-		0.554	ZNF295-AS1-201	KNOWN	basic	lincRNA	ZNF295-AS1	HGNC	lincRNA		-	NR_027273		43443260	+1	no_errors	ENST00000596595	ensembl	human	known	70_37	rna	INS	0.015:0.019	A
