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TCF12 (transcription factor 12)

Identity

Other namesCRS3
HEB
HTF4
HsT17266
TCF-12
bHLHb20
HGNC (Hugo) TCF12
LocusID (NCBI) 6938
Atlas_Id 406
Location 15q21.3
Location_base_pair Starts at 57511628 and ends at 57580730 bp from pter ( according to hg19-Feb_2009)  [Mapping]
Fusion genes (updated 2015)TCF12/TEC (15q21.3/-)TCF12/NR4A3 (15q21.3/9q22.33)

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

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.
  

Other Solid tumors implicated (Data extracted from papers in the Atlas)

Solid Tumors chondrosarcID5063 ExtraMyxChondroID5025 softissuTumID5042

External links

Nomenclature
HGNC (Hugo)TCF12   11623
Cards
AtlasTCF12ID406
Entrez_Gene (NCBI)TCF12  6938  transcription factor 12
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_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 : Fast-db (Paris)GSHG0009884
Alternative Splicing GalleryENSG00000140262
Gene ExpressionTCF12 [ NCBI-GEO ]     TCF12 [ SEEK ]   TCF12 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ99081 (Uniprot)
NextProtQ99081  [Medical]  [Publications]
With graphics : InterProQ99081
Splice isoforms : SwissVarQ99081 (Swissvar)
Domaine pattern : Prosite (Expaxy)BHLH (PS50888)   
Domains : Interpro (EBI)bHLH_dom   
Related proteins : CluSTrQ99081
Domain families : Pfam (Sanger)HLH (PF00010)   
Domain families : Pfam (NCBI)pfam00010   
Domain families : Smart (EMBL)HLH (SM00353)  
DMDM Disease mutations6938
Blocks (Seattle)Q99081
PDB (SRS)2KNH    4JOL   
PDB (PDBSum)2KNH    4JOL   
PDB (IMB)2KNH    4JOL   
PDB (RSDB)2KNH    4JOL   
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
IntegromeDBTCF12
STRING (EMBL)TCF12
ZODIACTCF12
Ontologies - Pathways
QuickGOQ99081
Ontology : AmiGOnuclear chromatin  RNA polymerase II core promoter proximal region sequence-specific DNA binding  RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription  sequence-specific DNA binding transcription factor activity  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  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  RNA polymerase II transcription factor complex  
Ontology : EGO-EBInuclear chromatin  RNA polymerase II core promoter proximal region sequence-specific DNA binding  RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription  sequence-specific DNA binding transcription factor activity  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  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  RNA polymerase II transcription factor complex  
REACTOMEQ99081 [protein]
REACTOME PathwaysREACT_111045 Developmental Biology [pathway]
Protein Interaction DatabaseTCF12
Atlas of Cancer Signalling NetworkTCF12
Wikipedia pathwaysTCF12
Gene fusion - Rearrangements
Fusion : COSMICTCF12 [15q21.3]  -  NR4A3 [9q22.33]  [fusion_754]  [fusion_755]  
Fusion: TCGATCF12 TEX9  TCF12 FAM70B  TCF12 MGST2  TCF12 NPAS1  CGNL1 TCF12  
RNF111 TCF12  
Fusion Cancer (Beijing)TCF12 [15q21.3]  -  MAP3K5 [6q23.3]  [FUSC004567]
Polymorphisms : SNP, variants
NCBI Variation ViewerTCF12 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TCF12
dbVarTCF12
ClinVarTCF12
1000_GenomesTCF12 
Exome Variant ServerTCF12
SNP (GeneSNP Utah)TCF12
SNP : HGBaseTCF12
Genetic variants : HAPMAPTCF12
Genomic Variants (DGV)TCF12 [DGVbeta]
Mutations
ICGC Data PortalTCF12 
TCGA Data PortalTCF12 
Tumor PortalTCF12
Cancer Gene: CensusTCF12 
Somatic Mutations in Cancer : COSMICTCF12 
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
DoCM (Curated mutations) TCF12
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)15:57511628-57580730
CONAN: Copy Number AnalysisTCF12 
Mutations and Diseases : HGMDTCF12
OMIM600480    615314   
MedgenTCF12
NextProtQ99081 [Medical]
GENETestsTCF12
Disease Genetic AssociationTCF12
Huge Navigator TCF12 [HugePedia]  TCF12 [HugeCancerGEM]
snp3D : Map Gene to Disease6938
DGIdb (Drug Gene Interaction db)TCF12
BioCentury BCIQTCF12
General knowledge
Homologs : HomoloGeneTCF12
Homology/Alignments : Family Browser (UCSC)TCF12
Phylogenetic Trees/Animal Genes : TreeFamTCF12
Chemical/Protein Interactions : CTD6938
Chemical/Pharm GKB GenePA36381
Clinical trialTCF12
Cancer Resource (Charite)ENSG00000140262
Other databases
Probes
Litterature
PubMed59 Pubmed reference(s) in Entrez
CoreMineTCF12
GoPubMedTCF12
iHOPTCF12

Bibliography

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
 
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
 
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
 
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
 
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
 
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
 
Localization of the human HTF4 transcription factors 4 gene (TCF12) to chromosome 15q21.
Zhang Y, Flejter WL, Barcroft CL, Riviˆ®re M, Szpirer J, Szpirer C, Bina M
Cytogenetics and cell genetics. 1995 ; 68 (3-4) : 235-238.
PMID 7842744
 
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
 
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
 
Fusion of the EWS-related gene TAF2N to TEC in extraskeletal myxoid chondrosarcoma.
Sjˆgren H, Meis-Kindblom J, Kindblom LG, Aman P, Stenman G
Cancer research. 1999 ; 59 (20) : 5064-5067.
PMID 10537274
 
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
 
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).
Sjˆgren H, Wedell B, Meis-Kindblom JM, Kindblom LG, Stenman G
Cancer research. 2000 ; 60 (24) : 6832-6835.
PMID 11156374
 
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
 
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Contributor(s)

Written07-2003Goran Stenman

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

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indexed on : Fri Aug 28 20:00:39 CEST 2015

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