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TFE3 (transcription factor E3)

Written1999-01Jean-Loup Huret, François Desangles
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France
Updated2001-08Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France
Updated2004-05Roland 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)TFEA
bHLHe33
Other alias
HGNC (Hugo) TFE3
LocusID (NCBI) 7030
Atlas_Id 86
Location Xp11.23  [Link to chromosome band Xp11]
Location_base_pair Starts at 49028726 and ends at 49043517 bp from pter ( according to hg19-Feb_2009)  [Mapping TFE3.png]
Fusion genes
(updated 2016)
ASPSCR1 (17q25.3) / TFE3 (Xp11.23)CBX5 (12q13.13) / TFE3 (Xp11.23)CLTC (17q23.1) / TFE3 (Xp11.23)
DVL2 (17p13.1) / TFE3 (Xp11.23)NONO (Xq13.1) / TFE3 (Xp11.23)PARP14 (3q21.1) / TFE3 (Xp11.23)
PRCC (1q23.1) / TFE3 (Xp11.23)RBM10 (Xp11.23) / TFE3 (Xp11.23)RREB1 (6p24.3) / TFE3 (Xp11.23)
SFPQ (16q24.1) / TFE3 (Xp11.23)TFE3 (Xp11.23) / ASPSCR1 (17q25.3)TFE3 (Xp11.23) / CLTC (17q23.1)
TFE3 (Xp11.23) / CYP11A1 (15q24.1)TFE3 (Xp11.23) / LINC01545 (Xp11.23)TFE3 (Xp11.23) / NONO (Xq13.1)
TFE3 (Xp11.23) / PRCC (1q23.1)TFE3 (Xp11.23) / SFPQ (16q24.1)TFE3 (Xp11.23) / TFEB (6p21.1)
YAP1 (11q22.1) / TFE3 (Xp11.23)

DNA/RNA

 
Description 8 exons
Transcription differential splicing removing exon 3 (with dominant negative activity of the resulting protein)

Protein

 
Description 743 amino acids; 80 kDa; N-term acidic transcriptional activation domain (domain 260-271, exon 3), helix-loop-helix (344 -400), leucine zipper (409-430), and a proline/arginine rich sequence (575-743) C-term
Expression wide; in fetal and adult tissues
Localisation nucleus
Function transcription factor; member of the basic helix-loop-helix family (b-HLH) of transcription factors primarily found to bind to the immunoglobulin enchancer muE3 motif, Ig K enhancers and Ig H variable regions promotors; the helix-loop-helix - leucine zipper region is implicated in DNA binding and dimerization (homo and heterodimerizations); mice which lack TFE3 in their B and T lymphocytes reconstitute the B- and T-cell compartments, but IgM levels are reduced
Homology to other members of the myc family of helix-loop-helix transcription factors

Implicated in

Note
  
Entity t(X;1)(p11.2;q21.2) in renal cell carcinoma --> PRCC/TFE3
Prognosis overall 5-yr survival rate around 85%
Hybrid/Mutated Gene 5' PRCC- 3' TFE3; variable breakpoint in PRCC; breakpoint in the 1st intron of TFE3
Abnormal Protein N-term PRCC with the proline rich sequence fused to most of TFE3, including the acidic transcriptional activation domain, the helix-loop-helix, and the leucine zipper; the reciprocal TFE3-PRCC is expressed; it is to be noted that the normal TFE3 transcript is lost in female patients
 
Oncogenesis PRCCTFE3 appears to be the fusion product that is most critical for the development of papillary renal cell carcinomas; it is a three-fold better transactivator than wild-type TFE3 and shows the characteristics associated with malignant trannsformation
  
  
Entity t(X;1)(p11.2;p34) in renal cell carcinoma --> PSF/TFE3
Disease t(X;1)(p11.2;p34) has only been found in a handfull cases of papillary renal cell carcinoma
Hybrid/Mutated Gene 5' PSF- 3' TFE3
 
Abnormal Protein N-term PSF and most of it fused to the DNA binding domains of TFE3 (excluding the acidic transcriptional activation domain, including the C-term helix-loop-helix, and the leucine zipper); no TFE3-PSF reciprocal transcript, as the der(X) t(X;1) is missing; the normal TFE3 transcript is found
  
  
Entity inv(X)(p11.2q12) in renal cell carcinoma --> NonO/TFE3
Disease only one case of papillary renal cell carcinoma
Hybrid/Mutated Gene 5' NONO- 3' TFE3
 
Abnormal Protein N-term NONO and most of it except the C-term proline rich sequence fused to the DNA binding domains of TFE3 (excluding the acidic transcriptional activation domain, including the C-term helix-loop-helix, and the leucine zipper); the reciprocal transcript is found
  
  
Entity Alveolar soft part sarcoma with ASPSCR1 -TFE3 fusion
Cytogenetics der(X)t(X;17)(p11;q25) is consistently involved; it implicates: 1- the formation of a hybrid gene at the breakpoint, and also, 2- gain in Xp11-pter sequences, and loss of heterozygocity in 11q25-qter, with possible implications
Hybrid/Mutated Gene 5' ASPSCR1-3' TFE3; the reciprocal 5' TFE3 - 3' ASPSCR1 is most often absent. ASPSCR1 is fused in frame to TFE3 exon 3 or 4
Abnormal Protein NH2 term ASPSCR1, fused to the C term of TFE3
Oncogenesis might combine the effect of a fusion protein to that of gene(s) dosage
  
  
Entity primary renal ASPSCR1-TFE3 tumour
Disease a subset of renal cell carcinoma, which presents with a combination of alveolar soft part sarcoma-like features and epithelial features is found to carry this anomaly
Cytogenetics balanced t(X;17)(p11.2;q25), in contrast with what is found in the alveolar soft part sarcoma (see above)
Hybrid/Mutated Gene 5' ASPSCR1-3' TFE3
Abnormal Protein NH2 term ASPSCR1, fused to the C term of TFE3
  
  
Entity other Xp11 involvements in renal cell carcinoma (t(X;10)(p11;q23), etc ...) are likely to implicate TFE3
  

Breakpoints

 

Bibliography

Primary renal neoplasms with the ASPL-TFE3 gene fusion of alveolar soft part sarcoma: a distinctive tumor entity previously included among renal cell carcinomas of children and adolescents.
Argani P, Antonescu CR, Illei PB, Lui MY, Timmons CF, Newbury R, Reuter VE, Garvin AJ, Perez-Atayde AR, Fletcher JA, Beckwith JB, Bridge JA, Ladanyi M
The American journal of pathology. 2001 ; 159 (1) : 179-192.
PMID 11438465
 
The leucine zipper of TFE3 dictates helix-loop-helix dimerization specificity.
Beckmann H, Kadesch T
Genes & development. 1991 ; 5 (6) : 1057-1066.
PMID 2044953
 
Fusion of splicing factor genes PSF and NonO (p54nrb) to the TFE3 gene in papillary renal cell carcinoma.
Clark J, Lu YJ, Sidhar SK, Parker C, Gill S, Smedley D, Hamoudi R, Linehan WM, Shipley J, Cooper CS
Oncogene. 1997 ; 15 (18) : 2233-2239.
PMID 9393982
 
Fusion of a novel gene, RCC17, to the TFE3 gene in t(X;17)(p11.2;q25.3)-bearing papillary renal cell carcinomas.
Heimann P, El Housni H, Ogur G, Weterman MA, Petty EM, Vassart G
Cancer research. 2001 ; 61 (10) : 4130-4135.
PMID 11358836
 
The der(17)t(X;17)(p11;q25) of human alveolar soft part sarcoma fuses the TFE3 transcription factor gene to ASPL, a novel gene at 17q25.
Ladanyi M, Lui MY, Antonescu CR, Krause-Boehm A, Meindl A, Argani P, Healey JH, Ueda T, Yoshikawa H, Meloni-Ehrig A, Sorensen PH, Mertens F, Mandahl N, van den Berghe H, Sciot R, Cin PD, Bridge J
Oncogene. 2001 ; 20 (1) : 48-57.
PMID 11244503
 
The absence of the transcription activator TFE3 impairs activation of B cells in vivo.
Merrell K, Wells S, Henderson A, Gorman J, Alt F, Stall A, Calame K
Molecular and cellular biology. 1997 ; 17 (6) : 3335-3344.
PMID 9154832
 
A dominant negative form of transcription activator mTFE3 created by differential splicing.
Roman C, Cohn L, Calame K
Science (New York, N.Y.). 1991 ; 254 (5028) : 94-97.
PMID 1840705
 
The t(X;1)(p11.2;q21.2) translocation in papillary renal cell carcinoma fuses a novel gene PRCC to the TFE3 transcription factor gene.
Sidhar SK, Clark J, Gill S, Hamoudi R, Crew AJ, Gwilliam R, Ross M, Linehan WM, Birdsall S, Shipley J, Cooper CS
Human molecular genetics. 1996 ; 5 (9) : 1333-1338.
PMID 8872474
 
Transformation capacities of the papillary renal cell carcinoma-associated PRCCTFE3 and TFE3PRCC fusion genes.
Weterman MA, van Groningen JJ, den Hartog A, Geurts van Kessel A
Oncogene. 2001 ; 20 (12) : 1414-1424.
PMID 11313885
 
Nuclear localization and transactivating capacities of the papillary renal cell carcinoma-associated TFE3 and PRCC (fusion) proteins.
Weterman MJ, van Groningen JJ, Jansen A, van Kessel AG
Oncogene. 2000 ; 19 (1) : 69-74.
PMID 10644981
 

Citation

This paper should be referenced as such :
Kuiper, RP
TFE3 (transcription factor E3)
Atlas Genet Cytogenet Oncol Haematol. 2004;8(3):203-205.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/TFE3ID86.html
History of this paper:
Huret, JL ; Desangles, F. TFE3 (transcription factor E3). Atlas Genet Cytogenet Oncol Haematol. 1999;3(2):61-62.
http://documents.irevues.inist.fr/bitstream/handle/2042/37503/01-1999-TFE3ID86.pdf
Huret, JL. TFE3 (transcription factor E3). Atlas Genet Cytogenet Oncol Haematol. 2001;5(4):268-270.
http://documents.irevues.inist.fr/bitstream/handle/2042/37783/08-2001-TFE3ID86.pdf


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 12 ]
  Soft Tissues: Alveolar soft part sarcoma with t(X;17)(p11;q25) ASPSCR1/TFE3
Kidney: Renal cell carcinoma with inv(X)(p11q12) NONO/TFE3
Kidney: Papillary renal cell carcinoma
Kidney: Renal cell carcinomas with MiT family translocation
Kidney: Renal cell carcinoma with t(X;17)(p11;q25) ASPSCR1/TFE3
Kidney: Renal cell carcinoma: an overview
Kidney: Renal cell carcinoma with t(6;11)(p21;q12) MALAT1/TFEB
Kidney: Renal cell carcinoma with t(X;17)(p11;q23) CLTC/TFE3
Soft tissue tumors: an overview
Kidney: Renal cell carcinoma with t(X;1)(p11;q21) PRCC/TFE3
Kidney: Renal cell carcinoma with t(X;1)(p11;p34) SFPQ/TFE3
Bone: Vascular Tumors


External links

Nomenclature
HGNC (Hugo)TFE3   11752
Cards
AtlasTFE3ID86
Entrez_Gene (NCBI)TFE3  7030  transcription factor binding to IGHM enhancer 3
AliasesRCCP2; RCCX1; TFEA; bHLHe33
GeneCards (Weizmann)TFE3
Ensembl hg19 (Hinxton)ENSG00000068323 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000068323 [Gene_View]  chrX:49028726-49043517 [Contig_View]  TFE3 [Vega]
ICGC DataPortalENSG00000068323
GNOMAD BrowserENSG00000068323
TCGA cBioPortalTFE3
AceView (NCBI)TFE3
Genatlas (Paris)TFE3
WikiGenes7030
SOURCE (Princeton)TFE3
Genetics Home Reference (NIH)TFE3
Genomic and cartography
GoldenPath hg38 (UCSC)TFE3  -     chrX:49028726-49043517 -  Xp11.23   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)TFE3  -     Xp11.23   [Description]    (hg19-Feb_2009)
EnsemblTFE3 - Xp11.23 [CytoView hg19]  TFE3 - Xp11.23 [CytoView hg38]
Mapping of homologs : NCBITFE3 [Mapview hg19]  TFE3 [Mapview hg38]
OMIM300854   314310   
Gene and transcription
Genbank (Entrez)AK295497 AK310095 AK313540 AL161985 BC001532
RefSeq transcript (Entrez)NM_001282142 NM_006521
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)TFE3
Cluster EST : UnigeneHs.730740 [ NCBI ]
CGAP (NCI)Hs.730740
Alternative Splicing GalleryENSG00000068323
Gene ExpressionTFE3 [ NCBI-GEO ]   TFE3 [ EBI - ARRAY_EXPRESS ]   TFE3 [ SEEK ]   TFE3 [ MEM ]
Gene Expression Viewer (FireBrowse)TFE3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)7030
GTEX Portal (Tissue expression)TFE3
Protein : pattern, domain, 3D structure
UniProt/SwissProtP19532   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP19532  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP19532
Splice isoforms : SwissVarP19532
PhosPhoSitePlusP19532
Domaine pattern : Prosite (Expaxy)BHLH (PS50888)   
Domains : Interpro (EBI)bHLH_dom    MiT/TFE_C    MiT/TFE_N    TFE3   
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)TFE3
DMDM Disease mutations7030
Blocks (Seattle)TFE3
SuperfamilyP19532
Human Protein AtlasENSG00000068323
Peptide AtlasP19532
HPRD02439
IPIIPI00873893   IPI00552083   
Protein Interaction databases
DIP (DOE-UCLA)P19532
IntAct (EBI)P19532
FunCoupENSG00000068323
BioGRIDTFE3
STRING (EMBL)TFE3
ZODIACTFE3
Ontologies - Pathways
QuickGOP19532
Ontology : AmiGORNA polymerase II core promoter proximal region sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  adaptive immune response  transcription factor activity, sequence-specific DNA binding  nucleus  nucleoplasm  cytosol  transcription from RNA polymerase II promoter  humoral immune response  transcription regulatory region DNA binding  regulation of osteoclast differentiation  positive regulation of cell adhesion  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  protein dimerization activity  
Ontology : EGO-EBIRNA polymerase II core promoter proximal region sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  adaptive immune response  transcription factor activity, sequence-specific DNA binding  nucleus  nucleoplasm  cytosol  transcription from RNA polymerase II promoter  humoral immune response  transcription regulatory region DNA binding  regulation of osteoclast differentiation  positive regulation of cell adhesion  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  protein dimerization activity  
Pathways : KEGGTranscriptional misregulation in cancer   
NDEx NetworkTFE3
Atlas of Cancer Signalling NetworkTFE3
Wikipedia pathwaysTFE3
Orthology - Evolution
OrthoDB7030
GeneTree (enSembl)ENSG00000068323
Phylogenetic Trees/Animal Genes : TreeFamTFE3
HOVERGENP19532
HOGENOMP19532
Homologs : HomoloGeneTFE3
Homology/Alignments : Family Browser (UCSC)TFE3
Gene fusions - Rearrangements
Fusion : MitelmanASPSCR1/TFE3 [17q25.3/Xp11.23]  [t(X;17)(p11;q25)]  
Fusion : MitelmanCLTC/TFE3 [17q23.1/Xp11.23]  [t(X;17)(p11;q23)]  
Fusion : MitelmanNONO/TFE3 [Xq13.1/Xp11.23]  [inv(X)(p11q13)]  [t(X;X)(p11;q13)]  
Fusion : MitelmanPARP14/TFE3 [3q21.1/Xp11.23]  [t(X;3)(p11;q21)]  
Fusion : MitelmanPRCC/TFE3 [1q23.1/Xp11.23]  [t(X;1)(p11;q23)]  
Fusion : MitelmanRREB1/TFE3 [6p24.3/Xp11.23]  [t(X;6)(p11;p24)]  
Fusion : MitelmanSFPQ/TFE3 [16q24.1/Xp11.23]  [t(X;1)(p11;p34)]  
Fusion : MitelmanTFE3/LINC01545 [Xp11.23/Xp11.23]  [t(X;X)(p11;p11)]  
Fusion : MitelmanTFE3/NONO [Xp11.23/Xq13.1]  [t(X;X)(p11;q13)]  
Fusion : MitelmanTFE3/SFPQ [Xp11.23/16q24.1]  [t(X;1)(p11;p34)]  
Fusion : MitelmanYAP1/TFE3 [11q22.1/Xp11.23]  [t(X;11)(p11;q22)]  
Fusion : COSMICASPSCR1 [17q25.3]  -  TFE3 [Xp11.23]  [fusion_393]  [fusion_394]  [fusion_395]  [fusion_396]  [fusion_814]  
Fusion : COSMICCLTC [17q23.1]  -  TFE3 [Xp11.23]  [fusion_799]  [fusion_800]  
Fusion : COSMICNONO [Xq13.1]  -  TFE3 [Xp11.23]  [fusion_865]  [fusion_866]  
Fusion : COSMICPRCC [1q23.1]  -  TFE3 [Xp11.23]  [fusion_805]  [fusion_806]  [fusion_807]  [fusion_808]  [fusion_809]  [fusion_810]  [fusion_811]  
[fusion_812]  [fusion_813]  
Fusion : COSMICSFPQ [1p34.3]  -  TFE3 [Xp11.23]  [fusion_801]  [fusion_802]  [fusion_803]  [fusion_804]  [fusion_914]  [fusion_915]  
Fusion : COSMICTFE3 [Xp11.23]  -  ASPSCR1 [17q25.3]  [fusion_769]  [fusion_782]  [fusion_797]  [fusion_798]  [fusion_838]  [fusion_875]  
Fusion : COSMICTFE3 [Xp11.23]  -  PRCC [1q23.1]  [fusion_839]  [fusion_874]  
Fusion: TCGASFPQ 16q24.1 TFE3 Xp11.23 KIRC
Fusion: TCGATFE3 Xp11.23 CXorf31 BRCA
Fusion: TCGATFE3 Xp11.23 SFPQ 16q24.1 KIRC
Fusion : TICdbASPSCR1 [17q25.3]  -  TFE3 [Xp11.23]
Fusion : TICdbCLTC [17q23.1]  -  TFE3 [Xp11.23]
Fusion : TICdbNONO [Xq13.1]  -  TFE3 [Xp11.23]
Fusion : TICdbSFPQ [1p34.3]  -  TFE3 [Xp11.23]
Fusion : TICdbYAP1 [11q22.1]  -  TFE3 [Xp11.23]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerTFE3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TFE3
dbVarTFE3
ClinVarTFE3
1000_GenomesTFE3 
Exome Variant ServerTFE3
ExAC (Exome Aggregation Consortium)TFE3 (select the gene name)
Genetic variants : HAPMAP7030
Genomic Variants (DGV)TFE3 [DGVbeta]
DECIPHERTFE3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisTFE3 
Mutations
ICGC Data PortalTFE3 
TCGA Data PortalTFE3 
Broad Tumor PortalTFE3
OASIS PortalTFE3 [ Somatic mutations - Copy number]
Cancer Gene: CensusTFE3 
Somatic Mutations in Cancer : COSMICTFE3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDTFE3
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
LOVD (Leiden Open Variation Database)X-chromosome gene database
BioMutasearch TFE3
DgiDB (Drug Gene Interaction Database)TFE3
DoCM (Curated mutations)TFE3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)TFE3 (select a term)
intoGenTFE3
NCG5 (London)TFE3
Cancer3DTFE3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM300854    314310   
Orphanet17527    17144    21643   
MedgenTFE3
Genetic Testing Registry TFE3
NextProtP19532 [Medical]
TSGene7030
GENETestsTFE3
Target ValidationTFE3
Huge Navigator TFE3 [HugePedia]
snp3D : Map Gene to Disease7030
BioCentury BCIQTFE3
ClinGenTFE3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD7030
Chemical/Pharm GKB GenePA36467
Clinical trialTFE3
Miscellaneous
canSAR (ICR)TFE3 (select the gene name)
Probes
Litterature
PubMed110 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineTFE3
EVEXTFE3
GoPubMedTFE3
iHOPTFE3
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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