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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

Other namesHTF4
HEB
HGNC (Hugo) TCF12
LocusID (NCBI) 6938
Atlas_Id 406
Location 15q21.3  [Link to chromosome band 15q21]
Location_base_pair Starts at 57511628 and ends at 57580730 bp from pter ( according to hg19-Feb_2009)  [Mapping TCF12.png]
Fusion genes
(updated 2016)		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)
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) / OSCP1 (1p34.3)TCF12 (15q21.3) / TCF12 (15q21.3)
TCF12 (15q21.3) / TEC (4p12)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 ]
On line version : http://AtlasGeneticsOncology.org/Genes/TCF12ID406.html

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  Bone: Chondrosarcoma
Soft Tissues: Extraskeletal myxoid chondrosarcoma
Soft tissue tumors: an overview

External links

Nomenclature
HGNC (Hugo)TCF12   11623
Cards
AtlasTCF12ID406
Entrez_Gene (NCBI)TCF12  6938  transcription factor 12
AliasesCRS3; HEB; HTF4; HsT17266; 
TCF-12; bHLHb20
GeneCards (Weizmann)TCF12
Ensembl hg19 (Hinxton)ENSG00000140262 [Gene_View]  chr15:57511628-57580730 [Contig_View]  TCF12 [Vega]
Ensembl hg38 (Hinxton)ENSG00000140262 [Gene_View]  chr15:57511628-57580730 [Contig_View]  TCF12 [Vega]
ICGC DataPortalENSG00000140262
TCGA cBioPortalTCF12
AceView (NCBI)TCF12
Genatlas (Paris)TCF12
WikiGenes6938
SOURCE (Princeton)TCF12
Genomic and cartography
GoldenPath hg19 (UCSC)TCF12  -     chr15:57511628-57580730 +  15q21   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)TCF12  -     15q21   [Description]    (hg38-Dec_2013)
EnsemblTCF12 - 15q21 [CytoView hg19]  TCF12 - 15q21 [CytoView hg38]
Mapping of homologs : NCBITCF12 [Mapview hg19]  TCF12 [Mapview hg38]
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
RefSeq genomic (Entrez)NC_000015 NC_018926 NG_033851 NT_010194 NW_004929398
Consensus coding sequences : CCDS (NCBI)TCF12
Cluster EST : UnigeneHs.511504 [ NCBI ]
CGAP (NCI)Hs.511504
Alternative Splicing GalleryENSG00000140262
Gene ExpressionTCF12 [ NCBI-GEO ]   TCF12 [ EBI - ARRAY_EXPRESS ]   TCF12 [ SEEK ]   TCF12 [ MEM ]
Gene Expression Viewer (FireBrowse)TCF12 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6938
GTEX Portal (Tissue expression)TCF12
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ99081 (Uniprot)
NextProtQ99081  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ99081
Splice isoforms : SwissVarQ99081 (Swissvar)
PhosPhoSitePlusQ99081
Domaine pattern : Prosite (Expaxy)BHLH (PS50888)   
Domains : Interpro (EBI)bHLH_dom   
Domain families : Pfam (Sanger)HLH (PF00010)   
Domain families : Pfam (NCBI)pfam00010   
Domain families : Smart (EMBL)HLH (SM00353)  
DMDM Disease mutations6938
Blocks (Seattle)TCF12
PDB (SRS)2KNH    4JOL   
PDB (PDBSum)2KNH    4JOL   
PDB (IMB)2KNH    4JOL   
PDB (RSDB)2KNH    4JOL   
Structural Biology KnowledgeBase2KNH    4JOL   
SCOP (Structural Classification of Proteins)2KNH    4JOL   
CATH (Classification of proteins structures)2KNH    4JOL   
SuperfamilyQ99081
Human Protein AtlasENSG00000140262
Peptide AtlasQ99081
HPRD02725
IPIIPI00012966   IPI00384979   IPI00384333   IPI01010229   IPI01013422   IPI01018775   IPI00940466   IPI01009406   IPI00883875   
Protein Interaction databases
DIP (DOE-UCLA)Q99081
IntAct (EBI)Q99081
FunCoupENSG00000140262
BioGRIDTCF12
STRING (EMBL)TCF12
ZODIACTCF12
Ontologies - Pathways
QuickGOQ99081
Ontology : AmiGOnuclear chromatin  RNA polymerase II core promoter proximal region sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  transcription factor activity, sequence-specific DNA binding  protein binding  nucleus  cytoplasm  regulation of transcription from RNA polymerase II promoter  transcription from RNA polymerase II promoter  immune response  muscle organ development  transcription factor binding  enhancer binding  cAMP response element binding  protein homodimerization activity  bHLH transcription factor binding  transcription regulatory region DNA binding  positive regulation of neuron differentiation  positive regulation of transcription from RNA polymerase II promoter  SMAD binding  protein heterodimerization activity  E-box binding  HMG box domain binding  RNA polymerase II transcription factor complex  
Ontology : EGO-EBInuclear chromatin  RNA polymerase II core promoter proximal region sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  transcription factor activity, sequence-specific DNA binding  protein binding  nucleus  cytoplasm  regulation of transcription from RNA polymerase II promoter  transcription from RNA polymerase II promoter  immune response  muscle organ development  transcription factor binding  enhancer binding  cAMP response element binding  protein homodimerization activity  bHLH transcription factor binding  transcription regulatory region DNA binding  positive regulation of neuron differentiation  positive regulation of transcription from RNA polymerase II promoter  SMAD binding  protein heterodimerization activity  E-box binding  HMG box domain binding  RNA polymerase II transcription factor complex  
REACTOMEQ99081 [protein]
REACTOME PathwaysR-HSA-375170 CDO in myogenesis [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]  [t(15;15)(q21;q21)]  
Fusion : MitelmanMAP3K5/TCF12 [6q23.3/15q21.3]  [t(6;15)(q23;q21)]  
Fusion : MitelmanRNF111/TCF12 [15q22.1/15q21.3]  [t(15;15)(q21;q22)]  
Fusion : MitelmanTCF12/MGST2 [15q21.3/4q31.1]  [t(4;15)(q31;q21)]  
Fusion : MitelmanTCF12/NPAS1 [15q21.3/19q13.32]  [t(15;19)(q21;q13)]  
Fusion : MitelmanTCF12/NR4A3 [15q21.3/9q22.33]  [t(9;15)(q31;q21)]  
Fusion : MitelmanTCF12/TEX9 [15q21.3/15q21.3]  [t(15;15)(q21;q21)]  
Fusion : MitelmanTCF12/TMEM255B [15q21.3/13q34]  [t(13;15)(q34;q21)]  
Fusion : COSMICTCF12 [15q21.3]  -  NR4A3 [9q22.33]  [fusion_754]  [fusion_755]  
Fusion: TCGACGNL1 15q21.3 TCF12 15q21.3 BRCA
Fusion: TCGARNF111 15q22.1 TCF12 15q21.3 BRCA
Fusion: TCGATCF12 15q21.3 FAM70B BRCA
Fusion: TCGATCF12 15q21.3 MGST2 4q31.1 BRCA
Fusion: TCGATCF12 15q21.3 NPAS1 19q13.32 PRAD
Fusion: TCGATCF12 15q21.3 TEX9 15q21.3 BRCA
Polymorphisms : SNP, variants
NCBI Variation ViewerTCF12 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TCF12
dbVarTCF12
ClinVarTCF12
1000_GenomesTCF12 
Exome Variant ServerTCF12
ExAC (Exome Aggregation Consortium)TCF12 (select the gene name)
Genetic variants : HAPMAP6938
Genomic Variants (DGV)TCF12 [DGVbeta]
Mutations
ICGC Data PortalTCF12 
TCGA Data PortalTCF12 
Broad Tumor PortalTCF12
OASIS PortalTCF12 [ Somatic mutations - Copy number]
Cancer Gene: CensusTCF12 
Somatic Mutations in Cancer : COSMICTCF12 
intOGen PortalTCF12
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 TCF12
DgiDB (Drug Gene Interaction Database)TCF12
DoCM (Curated mutations)TCF12 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)TCF12 (select a term)
intoGenTCF12
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)15:57511628-57580730  ENSG00000140262
CONAN: Copy Number AnalysisTCF12 
Mutations and Diseases : HGMDTCF12
OMIM600480    615314   
MedgenTCF12
Genetic Testing Registry TCF12
NextProtQ99081 [Medical]
TSGene6938
GENETestsTCF12
Huge Navigator TCF12 [HugePedia]
snp3D : Map Gene to Disease6938
BioCentury BCIQTCF12
ClinGenTCF12 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6938
Chemical/Pharm GKB GenePA36381
Clinical trialTCF12
Miscellaneous
canSAR (ICR)TCF12 (select the gene name)
Probes
Litterature
PubMed67 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineTCF12
EVEXTCF12
GoPubMedTCF12
iHOPTCF12
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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