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TCF12 (transcription factor 12)

Written2003-07Goran Stenman
Lundberg Laboratory for Cancer Research, Department of Pathology, Goteborg University, Sahlgrenska University Hospital, SE-413 45 Goteborg, Sweden

(Note : for Links provided by Atlas : click)

Identity

Alias (NCBI)HTF4
HEB
HGNC (Hugo) TCF12
HGNC Alias symbHEB
HTF4
HsT17266
bHLHb20
p64
HGNC Alias namehelix-loop-helix transcription factor 4
LocusID (NCBI) 6938
Atlas_Id 406
Location 15q21.3  [Link to chromosome band 15q21]
Location_base_pair Starts at 57219430 and ends at 57289853 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping TCF12.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
CGNL1 (15q21.3)::TCF12 (15q21.3)FMNL2 (2q23.3)::TCF12 (15q21.3)KMT2A (11q23.3)::TCF12 (15q21.3)
MAP3K5 (6q23.3)::TCF12 (15q21.3)MIR548H3 (6q16.1)::TCF12 (15q21.3)NR4A3 (9q22.33)::TCF12 (15q21.3)
OSCP1 (1p34.3)::TCF12 (15q21.3)RNF111 (15q22.1)::TCF12 (15q21.3)RREB1 (6p24.3)::TCF12 (15q21.3)
RUNX1 (21q22.12)::TCF12 (15q21.3)TCF12 (15q21.3)::CMAS (12p12.1)TCF12 (15q21.3)::DDX39B (6p21.33)
TCF12 (15q21.3)::FTL (19q13.33)TCF12 (15q21.3)::KMT2A (11q23.3)TCF12 (15q21.3)::MGST2 (4q31.1)
TCF12 (15q21.3)::NPAS1 (19q13.32)TCF12 (15q21.3)::NR4A3 (9q22.33)TCF12 (15q21.3)::NR4A3 (9q31.1)
TCF12 (15q21.3)::OSCP1 (1p34.3)TCF12 (15q21.3)::TCF12 (15q21.3)TCF12 (15q21.3)::TEX9 (15q21.3)
TCF12 (15q21.3)::TMEM255B (13q34)

DNA/RNA

Description spans 370 kb; 21 exons.
Transcription two alternatively spliced transcripts of 4745 bp and 4077 bp.

Protein

Description 682 aa, 73 kDa; serine rich N-terminus containing a potential leuzine zipper domain; C-terminus containing a bHLH-domain as well as a class A-specific domain.
Expression ubiquitous
Localisation nuclear
Function basic helix-loop-helix (bHLH) transcription factor belonging to the class A family; acts as a general negative regulator of cell proliferation; binds specifically to oligomers of E-box motifs; forms heterodimers with other bHLH proteins of both class A and class B, e.g. E2A, TAL1, myogenin and MyoD; implicated in myogenesis, hematopoiesis and neurogenesis.
Homology TCF3 and TCF4

Implicated in

Note
  
Entity Extraskeletal myxoid chondrosarcoma with t(9;15)(q22;q21).
Disease rare type of sarcoma (2.3% of all soft tissue sarcomas) characteristically involving the deep, soft tissues of the extremities; morphological resemblance to embryonic cartilage.
Hybrid/Mutated Gene TCF12-TEC
Abnormal Protein N-terminal domain of TCF12 fused to the entire TEC protein; the translocation separates the N-terminal of TCF12 from the bHLH domain as well as from a potential leucine zipper domain; the N-terminal of TCF12 shows no sequence homology to the N-terminals of EWSR1 or TAF2N.
  

Bibliography

Muscle differentiation: more complexity to the network of myogenic regulators.
Arnold HH, Winter B
Current opinion in genetics & development. 1998 ; 8 (5) : 539-544.
PMID 9794824
 
Distinguishable patterns of protein-DNA interactions involving complexes of basic helix-loop-helix proteins.
Doyle K, Zhang Y, Baer R, Bina M
The Journal of biological chemistry. 1994 ; 269 (16) : 12099-12105.
PMID 8163514
 
Genomic organization of human TCF12 gene and spliced mRNA variants producing isoforms of transcription factor HTF4.
Gan TI, Rowen L, Nesbitt R, Roe BA, Wu H, Hu P, Yao Z, Kim UJ, O'Sickey T, Bina M
Cytogenetic and genome research. 2002 ; 98 (4) : 245-248.
PMID 12826747
 
HEB, a helix-loop-helix protein related to E2A and ITF2 that can modulate the DNA-binding ability of myogenic regulatory factors.
Hu JS, Olson EN, Kingston RE
Molecular and cellular biology. 1992 ; 12 (3) : 1031-1042.
PMID 1312219
 
bHLH transcription factors and mammalian neuronal differentiation.
Kageyama R, Ishibashi M, Takebayashi K, Tomita K
The international journal of biochemistry & cell biology. 1997 ; 29 (12) : 1389-1399.
PMID 9570134
 
Oncogenic conversion of a novel orphan nuclear receptor by chromosome translocation.
Labelle Y, Zucman J, Stenman G, Kindblom LG, Knight J, Turc-Carel C, Dockhorn-Dworniczak B, Mandahl N, Desmaze C, Peter M
Human molecular genetics. 1995 ; 4 (12) : 2219-2226.
PMID 8634690
 
Class A helix-loop-helix proteins are positive regulators of several cyclin-dependent kinase inhibitors' promoter activity and negatively affect cell growth.
Pagliuca A, Gallo P, De Luca P, Lania L
Cancer research. 2000 ; 60 (5) : 1376-1382.
PMID 10728702
 
A heterodimer of HEB and an E12-related protein interacts with the CD4 enhancer and regulates its activity in T-cell lines.
Sawada S, Littman DR
Molecular and cellular biology. 1993 ; 13 (9) : 5620-5628.
PMID 8355705
 
Fusion of the NH2-terminal domain of the basic helix-loop-helix protein TCF12 to TEC in extraskeletal myxoid chondrosarcoma with translocation t(9;15)(q22;q21).
Sjögren H, Wedell B, Meis-Kindblom JM, Kindblom LG, Stenman G
Cancer research. 2000 ; 60 (24) : 6832-6835.
PMID 11156374
 
HTF4: a new human helix-loop-helix protein.
Zhang Y, Babin J, Feldhaus AL, Singh H, Sharp PA, Bina M
Nucleic acids research. 1991 ; 19 (16) : page 4555.
PMID 1886779
 
The nucleotide sequence of the human transcription factor HTF4a cDNA.
Zhang Y, Bina M
DNA sequence : the journal of DNA sequencing and mapping. 1992 ; 2 (6) : 397-403.
PMID 1446075
 
Localization of the human HTF4 transcription factors 4 gene (TCF12) to chromosome 15q21.
Zhang Y, Flejter WL, Barcroft CL, Rivière M, Szpirer J, Szpirer C, Bina M
Cytogenetics and cell genetics. 1995 ; 68 (3-4) : 235-238.
PMID 7842744
 

Citation

This paper should be referenced as such :
Stenman, G
TCF12 (transcription factor 12)
Atlas Genet Cytogenet Oncol Haematol. 2003;7(3):174-175.
Free journal version : [ pdf ]   [ DOI ]


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 3 ]
  TAL1 (1p32) deletion in lymphoid malignancies
t(11;15)(q23;q21) KMT2A::TCF12
t(15;21)(q21;q22) RUNX1::TCF12


External links

 

Nomenclature
HGNC (Hugo)TCF12   11623
Cards
AtlasTCF12ID406
Entrez_Gene (NCBI)TCF12    transcription factor 12
AliasesCRS3; HEB; HTF4; HsT17266; 
TCF-12; bHLHb20; p64
GeneCards (Weizmann)TCF12
Ensembl hg19 (Hinxton)ENSG00000140262 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000140262 [Gene_View]  ENSG00000140262 [Sequence]  chr15:57219430-57289853 [Contig_View]  TCF12 [Vega]
ICGC DataPortalENSG00000140262
TCGA cBioPortalTCF12
AceView (NCBI)TCF12
Genatlas (Paris)TCF12
SOURCE (Princeton)TCF12
Genetics Home Reference (NIH)TCF12
Genomic and cartography
GoldenPath hg38 (UCSC)TCF12  -     chr15:57219430-57289853 +  15q21.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)TCF12  -     15q21.3   [Description]    (hg19-Feb_2009)
GoldenPathTCF12 - 15q21.3 [CytoView hg19]  TCF12 - 15q21.3 [CytoView hg38]
ImmunoBaseENSG00000140262
Genome Data Viewer NCBITCF12 [Mapview hg19]  
OMIM600480   615314   
Gene and transcription
Genbank (Entrez)AI269491 AK022018 AK056961 AK294617 AK294991
RefSeq transcript (Entrez)NM_001306219 NM_001306220 NM_001322151 NM_001322152 NM_001322154 NM_001322156 NM_001322157 NM_001322158 NM_001322159 NM_001322161 NM_001322162 NM_001322164 NM_001322165 NM_003205 NM_207036 NM_207037 NM_207038 NM_207040
Consensus coding sequences : CCDS (NCBI)TCF12
Gene ExpressionTCF12 [ NCBI-GEO ]   TCF12 [ EBI - ARRAY_EXPRESS ]   TCF12 [ SEEK ]   TCF12 [ MEM ]
Gene Expression Viewer (FireBrowse)TCF12 [ Firebrowse - Broad ]
GenevisibleExpression of TCF12 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6938
GTEX Portal (Tissue expression)TCF12
Human Protein AtlasENSG00000140262-TCF12 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ99081   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ99081  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ99081
PhosPhoSitePlusQ99081
Domaine pattern : Prosite (Expaxy)BHLH (PS50888)   
Domains : Interpro (EBI)bHLH_dom    HLH_DNA-bd_sf   
Domain families : Pfam (Sanger)HLH (PF00010)   
Domain families : Pfam (NCBI)pfam00010   
Domain families : Smart (EMBL)HLH (SM00353)  
Conserved Domain (NCBI)TCF12
PDB (RSDB)2KNH    4JOL   
PDB Europe2KNH    4JOL   
PDB (PDBSum)2KNH    4JOL   
PDB (IMB)2KNH    4JOL   
Structural Biology KnowledgeBase2KNH    4JOL   
SCOP (Structural Classification of Proteins)2KNH    4JOL   
CATH (Classification of proteins structures)2KNH    4JOL   
SuperfamilyQ99081
AlphaFold pdb e-kbQ99081   
Human Protein Atlas [tissue]ENSG00000140262-TCF12 [tissue]
HPRD02725
Protein Interaction databases
DIP (DOE-UCLA)Q99081
IntAct (EBI)Q99081
BioGRIDTCF12
STRING (EMBL)TCF12
ZODIACTCF12
Ontologies - Pathways
QuickGOQ99081
Ontology : AmiGOchromatin  chromatin  transcription cis-regulatory region binding  RNA polymerase II cis-regulatory region sequence-specific DNA binding  RNA polymerase II cis-regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  cis-regulatory region sequence-specific DNA binding  DNA-binding transcription activator activity, RNA polymerase II-specific  DNA-binding transcription factor activity  protein binding  nucleus  nucleoplasm  nucleoplasm  transcription regulator complex  cytoplasm  regulation of transcription by RNA polymerase II  immune response  nervous system development  muscle organ development  transcription factor binding  positive regulation of gene expression  nuclear speck  cell differentiation  cAMP response element binding  intracellular membrane-bounded organelle  bHLH transcription factor binding  positive regulation of neuron differentiation  positive regulation of transcription by RNA polymerase II  SMAD binding  protein heterodimerization activity  E-box binding  HMG box domain binding  RNA polymerase II transcription regulator complex  regulation of hematopoietic stem cell differentiation  sequence-specific double-stranded DNA binding  
Ontology : EGO-EBIchromatin  chromatin  transcription cis-regulatory region binding  RNA polymerase II cis-regulatory region sequence-specific DNA binding  RNA polymerase II cis-regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  cis-regulatory region sequence-specific DNA binding  DNA-binding transcription activator activity, RNA polymerase II-specific  DNA-binding transcription factor activity  protein binding  nucleus  nucleoplasm  nucleoplasm  transcription regulator complex  cytoplasm  regulation of transcription by RNA polymerase II  immune response  nervous system development  muscle organ development  transcription factor binding  positive regulation of gene expression  nuclear speck  cell differentiation  cAMP response element binding  intracellular membrane-bounded organelle  bHLH transcription factor binding  positive regulation of neuron differentiation  positive regulation of transcription by RNA polymerase II  SMAD binding  protein heterodimerization activity  E-box binding  HMG box domain binding  RNA polymerase II transcription regulator complex  regulation of hematopoietic stem cell differentiation  sequence-specific double-stranded DNA binding  
REACTOMEQ99081 [protein]
REACTOME PathwaysR-HSA-8939236 [pathway]   
NDEx NetworkTCF12
Atlas of Cancer Signalling NetworkTCF12
Wikipedia pathwaysTCF12
Orthology - Evolution
OrthoDB6938
GeneTree (enSembl)ENSG00000140262
Phylogenetic Trees/Animal Genes : TreeFamTCF12
Homologs : HomoloGeneTCF12
Homology/Alignments : Family Browser (UCSC)TCF12
Gene fusions - Rearrangements
Fusion : MitelmanCGNL1::TCF12 [15q21.3/15q21.3]  
Fusion : MitelmanMAP3K5::TCF12 [6q23.3/15q21.3]  
Fusion : MitelmanRNF111::TCF12 [15q22.1/15q21.3]  
Fusion : MitelmanTCF12::MGST2 [15q21.3/4q31.1]  
Fusion : MitelmanTCF12::NPAS1 [15q21.3/19q13.32]  
Fusion : MitelmanTCF12::NR4A3 [15q21.3/9q22.33]  
Fusion : MitelmanTCF12::TEX9 [15q21.3/15q21.3]  
Fusion : MitelmanTCF12::TMEM255B [15q21.3/13q34]  
Fusion : COSMICTCF12 [15q21.3]  -  NR4A3 [9q31.1]  [fusion_754]  
Fusion : QuiverTCF12
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerTCF12 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TCF12
dbVarTCF12
ClinVarTCF12
MonarchTCF12
1000_GenomesTCF12 
Exome Variant ServerTCF12
GNOMAD BrowserENSG00000140262
Varsome BrowserTCF12
ACMGTCF12 variants
VarityQ99081
Genomic Variants (DGV)TCF12 [DGVbeta]
DECIPHERTCF12 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisTCF12 
Mutations
ICGC Data PortalTCF12 
TCGA Data PortalTCF12 
Broad Tumor PortalTCF12
OASIS PortalTCF12 [ Somatic mutations - Copy number]
Cancer Gene: CensusTCF12 
Somatic Mutations in Cancer : COSMICTCF12  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DTCF12
Mutations and Diseases : HGMDTCF12
intOGen PortalTCF12
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaTCF12
DgiDB (Drug Gene Interaction Database)TCF12
DoCM (Curated mutations)TCF12
CIViC (Clinical Interpretations of Variants in Cancer)TCF12
OncoKBTCF12
NCG (London)TCF12
Cancer3DTCF12
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600480    615314   
Orphanet18668    10369    10368   
DisGeNETTCF12
MedgenTCF12
Genetic Testing Registry TCF12
NextProtQ99081 [Medical]
GENETestsTCF12
Target ValidationTCF12
Huge Navigator TCF12 [HugePedia]
ClinGenTCF12 (curated)
Clinical trials, drugs, therapy
MyCancerGenomeTCF12
Protein Interactions : CTDTCF12
Pharm GKB GenePA36381
PharosQ99081
Clinical trialTCF12
Miscellaneous
canSAR (ICR)TCF12
HarmonizomeTCF12
DataMed IndexTCF12
Probes
Litterature
PubMed106 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXTCF12
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Oct 8 21:29:09 CEST 2021

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