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TFEB (transcription factor EB)

Written2004-05Roland P Kuiper
Dept of Human Genetics-417, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)TCFEB
bHLHe35
HGNC (Hugo) TFEB
LocusID (NCBI) 7942
Atlas_Id 531
Location 6p21.1  [Link to chromosome band 6p21]
Location_base_pair Starts at 41651716 and ends at 41703997 bp from pter ( according to hg19-Feb_2009)  [Mapping TFEB.png]
Fusion genes
(updated 2016)
CLTC (17q23.1) / TFEB (6p21.1)COL21A1 (6p12.1) / TFEB (6p21.1)MALAT1 (11q13.1) / TFEB (6p21.1)
MCM2 (3q21.3) / TFEB (6p21.1)PRKAA1 (5p13.1) / TFEB (6p21.1)TFE3 (Xp11.23) / TFEB (6p21.1)
TFEB (6p21.1) / ACTN3 (11q13.2)TFEB (6p21.1) / ALPHA ()TFEB (6p21.1) / CADM2 (3p12.1)
TFEB (6p21.1) / DIP2B (12q13.12)TFEB (6p21.1) / MCM2 (3q21.3)TFEB (6p21.1) / PGC (6p21.1)
TFEB (6p21.1) / PRKAA1 (5p13.1)TFEB (6p21.1) / TRERF1 (6p21.1)
Note Member of the basic-helix-loop-helix leucine-zipper transcription factor MiTF/TFE family (also known as the MiT family), which also contains MiTF, TFEC, and TFE3. The four members form homo- and/or heterodimers to bind the Ebox core sequence CAYGTG.

DNA/RNA

 
  Genomic organization of TFEB gene.
Description TFEB gene contains 8 coding exons and 7 alternative first exons that are differentially expressed.
Transcription Alternative first exon usage points towards the existence of up to seven alternative promoters. Alternative splicing of exon 3 (encoding an acidic activation domain) similar to the closely related TFE3, TFEC, and MiTF genes.

Protein

 
  Functional domains in the TFEB protein.
Description 490 amino acids; 65 kDa; N-terminal Gln-rich stretch (Gln, exon 2), N-term acidic transcriptional activation domain (AAD, exon 3), basic helix-loop-helix region (bHLH, exon 6-8), leucine zipper (LZ, exon 8), proline-rich activation domain ( ProAD, exon 9), Ser-rich stretch (Ser)
Expression Wide in fetal and adult tissues, although the various TFEB transcript variants are expressed in a tissue-restricted manner: TFEB-A is enriched in placenta, TFEB-F in spleen, and TFEB-E and TFEB-G in brain.
Localisation Nucleus
Function Transcription factor; member of the basic-helix-loop-helix leucine-zipper transcription factor MiTF/TFE family (also known as the MiT family), which also contains MiTF, TFEC, and TFE3. The four members form homo- and/or heterodimers to bind the Ebox core sequence CAYGTG; the helix-loop-helix - leucine zipper region is implicated in DNA binding and dimerization (homo and heterodimerizations); mice which lack TFEB die due to defects in placental vascularization.
Homology High homology to the other MiTF/TFE members TFE3, TFEC and MiTF, homologous to myc family of bHLH transcription factors.

Implicated in

Note
Entity Renal cell carcinoma with t(6;11)(p21;q13) -> Alpha/TFEB gene fusion
Disease Clear cell renal cell carcinomas
Prognosis Limited follow-up available, prognosis appears to be good; no reports of developed metastases
Cytogenetics t(6;11)(p21;q13), usually as the sole cytogenetic anomaly.
Hybrid/Mutated Gene Alpha/TFEB, both fusion genes are expressed; 5'-Alpha-TFEB-3' fusion transcript contains the entire open reading frame of TFEB.
Abnormal Protein No fusion protein, the Alpha gene is a non-protein-encoding transcript.
Oncogenesis Highly induced expression of full-length TFEB protein due to promoter substitution in the Alpha-TFEB fusion gene.
  

Bibliography

A distinctive pediatric renal neoplasm characterized by epithelioid morphology, basement membrane production, focal HMB45 immunoreactivity, and t(6;11)(p21.1;q12) chromosome translocation.
Argani P, Hawkins A, Griffin CA, Goldstein JD, Haas M, Beckwith JB, Mankinen CB, Perlman EJ
The American journal of pathology. 2001 ; 158 (6) : 2089-2096.
PMID 11395386
 
Distinctive neoplasms characterised by specific chromosomal translocations comprise a significant proportion of paediatric renal cell carcinomas.
Argani P, Ladanyi M
Pathology. 2003 ; 35 (6) : 492-498.
PMID 14660099
 
A helix-loop-helix protein related to the immunoglobulin E box-binding proteins.
Carr CS, Sharp PA
Molecular and cellular biology. 1990 ; 10 (8) : 4384-4388.
PMID 2115126
 
Cloning of an Alpha-TFEB fusion in renal tumors harboring the t(6;11)(p21;q13) chromosome translocation.
Davis IJ, Hsi BL, Arroyo JD, Vargas SO, Yeh YA, Motyckova G, Valencia P, Perez-Atayde AR, Argani P, Ladanyi M, Fletcher JA, Fisher DE
Proceedings of the National Academy of Sciences of the United States of America. 2003 ; 100 (10) : 6051-6056.
PMID 12719541
 
TFEB has DNA-binding and oligomerization properties of a unique helix-loop-helix/leucine-zipper family.
Fisher DE, Carr CS, Parent LA, Sharp PA
Genes & development. 1991 ; 5 (12A) : 2342-2352.
PMID 1748288
 
microphthalmia, a critical factor in melanocyte development, defines a discrete transcription factor family.
Hemesath TJ, Steingrímsson E, McGill G, Hansen MJ, Vaught J, Hodgkinson CA, Arnheiter H, Copeland NG, Jenkins NA, Fisher DE
Genes & development. 1994 ; 8 (22) : 2770-2780.
PMID 7958932
 
Upregulation of the transcription factor TFEB in t(6;11)(p21;q13)-positive renal cell carcinomas due to promoter substitution.
Kuiper RP, Schepens M, Thijssen J, van Asseldonk M, van den Berg E, Bridge J, Schuuring E, Schoenmakers EF, van Kessel AG
Human molecular genetics. 2003 ; 12 (14) : 1661-1669.
PMID 12837690
 
The bHLH-Zip transcription factor Tfeb is essential for placental vascularization.
Steingrímsson E, Tessarollo L, Reid SW, Jenkins NA, Copeland NG
Development (Cambridge, England). 1998 ; 125 (23) : 4607-4616.
PMID 9806910
 

Citation

This paper should be referenced as such :
Kuiper, RP
TFEB (transcription factor EB)
Atlas Genet Cytogenet Oncol Haematol. 2004;8(3):206-207.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/TFEBID531.html


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 7 ]
  Kidney: Renal cell carcinoma with inv(X)(p11q12) NONO/TFE3
Kidney: Renal cell carcinomas with MiT family translocation
Kidney: Renal cell carcinoma with t(X;17)(p11;q25) ASPSCR1/TFE3
Kidney: Renal cell carcinoma with t(6;11)(p21;q12) MALAT1/TFEB
Kidney: Renal cell carcinoma with t(X;17)(p11;q23) CLTC/TFE3
Kidney: Renal cell carcinoma with t(X;1)(p11;q21) PRCC/TFE3
Kidney: Renal cell carcinoma with t(X;1)(p11;p34) SFPQ/TFE3


External links

Nomenclature
HGNC (Hugo)TFEB   11753
Cards
AtlasTFEBID531
Entrez_Gene (NCBI)TFEB  7942  transcription factor EB
AliasesALPHATFEB; BHLHE35; TCFEB
GeneCards (Weizmann)TFEB
Ensembl hg19 (Hinxton)ENSG00000112561 [Gene_View]  chr6:41651716-41703997 [Contig_View]  TFEB [Vega]
Ensembl hg38 (Hinxton)ENSG00000112561 [Gene_View]  chr6:41651716-41703997 [Contig_View]  TFEB [Vega]
ICGC DataPortalENSG00000112561
TCGA cBioPortalTFEB
AceView (NCBI)TFEB
Genatlas (Paris)TFEB
WikiGenes7942
SOURCE (Princeton)TFEB
Genetics Home Reference (NIH)TFEB
Genomic and cartography
GoldenPath hg19 (UCSC)TFEB  -     chr6:41651716-41703997 -  6p21   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)TFEB  -     6p21   [Description]    (hg38-Dec_2013)
EnsemblTFEB - 6p21 [CytoView hg19]  TFEB - 6p21 [CytoView hg38]
Mapping of homologs : NCBITFEB [Mapview hg19]  TFEB [Mapview hg38]
OMIM600744   
Gene and transcription
Genbank (Entrez)AA235980 AJ608786 AJ608787 AJ608788 AJ608789
RefSeq transcript (Entrez)NM_001167827 NM_001271943 NM_001271944 NM_001271945 NM_007162
RefSeq genomic (Entrez)NC_000006 NC_018917 NT_007592 NW_004929326
Consensus coding sequences : CCDS (NCBI)TFEB
Cluster EST : UnigeneHs.485360 [ NCBI ]
CGAP (NCI)Hs.485360
Alternative Splicing GalleryENSG00000112561
Gene ExpressionTFEB [ NCBI-GEO ]   TFEB [ EBI - ARRAY_EXPRESS ]   TFEB [ SEEK ]   TFEB [ MEM ]
Gene Expression Viewer (FireBrowse)TFEB [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)7942
GTEX Portal (Tissue expression)TFEB
Protein : pattern, domain, 3D structure
UniProt/SwissProtP19484   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP19484  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP19484
Splice isoforms : SwissVarP19484
PhosPhoSitePlusP19484
Domaine pattern : Prosite (Expaxy)BHLH (PS50888)   
Domains : Interpro (EBI)bHLH_dom    MiT/TFE_C    MiT/TFE_N    TFEB   
Domain families : Pfam (Sanger)DUF3371 (PF11851)    HLH (PF00010)    MITF_TFEB_C_3_N (PF15951)   
Domain families : Pfam (NCBI)pfam11851    pfam00010    pfam15951   
Domain families : Smart (EMBL)HLH (SM00353)  
Conserved Domain (NCBI)TFEB
DMDM Disease mutations7942
Blocks (Seattle)TFEB
SuperfamilyP19484
Human Protein AtlasENSG00000112561
Peptide AtlasP19484
HPRD02847
IPIIPI00465427   IPI00385436   IPI00643397   IPI00647494   IPI00641758   IPI00640180   IPI00893531   IPI00642910   IPI00646065   IPI00641818   IPI00853484   
Protein Interaction databases
DIP (DOE-UCLA)P19484
IntAct (EBI)P19484
FunCoupENSG00000112561
BioGRIDTFEB
STRING (EMBL)TFEB
ZODIACTFEB
Ontologies - Pathways
QuickGOP19484
Ontology : AmiGOembryonic placenta development  adaptive immune response  transcription factor activity, sequence-specific DNA binding  transcription factor activity, sequence-specific DNA binding  nucleus  nucleus  cytoplasm  transcription, DNA-templated  regulation of transcription, DNA-templated  autophagy  humoral immune response  lysosome organization  positive regulation of autophagy  transcription regulatory region DNA binding  positive regulation of transcription from RNA polymerase II promoter  protein dimerization activity  
Ontology : EGO-EBIembryonic placenta development  adaptive immune response  transcription factor activity, sequence-specific DNA binding  transcription factor activity, sequence-specific DNA binding  nucleus  nucleus  cytoplasm  transcription, DNA-templated  regulation of transcription, DNA-templated  autophagy  humoral immune response  lysosome organization  positive regulation of autophagy  transcription regulatory region DNA binding  positive regulation of transcription from RNA polymerase II promoter  protein dimerization activity  
NDEx NetworkTFEB
Atlas of Cancer Signalling NetworkTFEB
Wikipedia pathwaysTFEB
Orthology - Evolution
OrthoDB7942
GeneTree (enSembl)ENSG00000112561
Phylogenetic Trees/Animal Genes : TreeFamTFEB
HOVERGENP19484
HOGENOMP19484
Homologs : HomoloGeneTFEB
Homology/Alignments : Family Browser (UCSC)TFEB
Gene fusions - Rearrangements
Fusion : MitelmanCLTC/TFEB [17q23.1/6p21.1]  [t(6;17)(p21;q23)]  
Fusion : MitelmanMALAT1/TFEB [11q13.1/6p21.1]  [t(6;11)(p21;q13)]  
Fusion : MitelmanTFEB/DIP2B [6p21.1/12q13.12]  [t(6;12)(p21;q13)]  
Fusion : MitelmanTFEB/PGC [6p21.1/6p21.1]  [t(6;6)(p21;p21)]  
Fusion : MitelmanTFEB/TRERF1 [6p21.1/6p21.1]  [t(6;6)(p21;p21)]  
Fusion: TCGATFEB 6p21.1 DIP2B 12q13.12 GBM
Fusion: TCGATFEB 6p21.1 PGC 6p21.1 OV
Fusion : TICdbMALAT1 [11q13.1]  -  TFEB [6p21.1]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerTFEB [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TFEB
dbVarTFEB
ClinVarTFEB
1000_GenomesTFEB 
Exome Variant ServerTFEB
ExAC (Exome Aggregation Consortium)TFEB (select the gene name)
Genetic variants : HAPMAP7942
Genomic Variants (DGV)TFEB [DGVbeta]
DECIPHER (Syndromes)6:41651716-41703997  ENSG00000112561
CONAN: Copy Number AnalysisTFEB 
Mutations
ICGC Data PortalTFEB 
TCGA Data PortalTFEB 
Broad Tumor PortalTFEB
OASIS PortalTFEB [ Somatic mutations - Copy number]
Cancer Gene: CensusTFEB 
Somatic Mutations in Cancer : COSMICTFEB  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDTFEB
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch TFEB
DgiDB (Drug Gene Interaction Database)TFEB
DoCM (Curated mutations)TFEB (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)TFEB (select a term)
intoGenTFEB
NCG5 (London)TFEB
Cancer3DTFEB(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600744   
Orphanet21643   
MedgenTFEB
Genetic Testing Registry TFEB
NextProtP19484 [Medical]
TSGene7942
GENETestsTFEB
Huge Navigator TFEB [HugePedia]
snp3D : Map Gene to Disease7942
BioCentury BCIQTFEB
ClinGenTFEB
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD7942
Chemical/Pharm GKB GenePA36468
Clinical trialTFEB
Miscellaneous
canSAR (ICR)TFEB (select the gene name)
Probes
Litterature
PubMed44 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineTFEB
EVEXTFEB
GoPubMedTFEB
iHOPTFEB
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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