TCF12 (transcription factor 12)

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TCF12 (transcription factor 12)

Written	2003-07	Goran 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_symbol (synonym)	HEB
	HTF4
	HsT17266
	bHLHb20
Other alias
HGNC (Hugo)	TCF12
LocusID (NCBI)	6938
Atlas_Id	406
Location	15q21.3 [Link to chromosome band 15q21]
Location_base_pair	Starts at 57219430 and ends at 57288516 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) [ 3 ]

Bone: Chondrosarcoma
Soft Tissues: Extraskeletal myxoid chondrosarcoma
Soft tissue tumors: an overview

External links

	Nomenclature
HGNC (Hugo)	TCF12 11623
	Cards
Atlas	TCF12ID406
Entrez_Gene (NCBI)	TCF12 6938 transcription factor 12
Aliases	CRS3; HEB; HTF4; HsT17266;
	TCF-12; bHLHb20
GeneCards (Weizmann)	TCF12
Ensembl hg19 (Hinxton)	ENSG00000140262 [Gene_View]
Ensembl hg38 (Hinxton)	ENSG00000140262 [Gene_View] chr15:57219430-57288516 [Contig_View] TCF12 [Vega]
ICGC DataPortal	ENSG00000140262
TCGA cBioPortal	TCF12
AceView (NCBI)	TCF12
Genatlas (Paris)	TCF12
WikiGenes	6938
SOURCE (Princeton)	TCF12
Genetics Home Reference (NIH)	TCF12
	Genomic and cartography
GoldenPath hg38 (UCSC)	TCF12 - chr15:57219430-57288516 + 15q21.3 [Description] (hg38-Dec_2013)
GoldenPath hg19 (UCSC)	TCF12 - 15q21.3 [Description] (hg19-Feb_2009)
Ensembl	TCF12 - 15q21.3 [CytoView hg19] TCF12 - 15q21.3 [CytoView hg38]
Mapping of homologs : NCBI	TCF12 [Mapview hg19] TCF12 [Mapview hg38]
OMIM	600480 615314
	Gene and transcription
Genbank (Entrez)	###############################################################################################################################################################################################################################################################
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)
Consensus coding sequences : CCDS (NCBI)	TCF12
Cluster EST : Unigene	Hs.511504 [ NCBI ]
CGAP (NCI)	Hs.511504
Alternative Splicing Gallery	ENSG00000140262
Gene Expression	TCF12 [ 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]
Genevisible	Expression in : [tissues] [cell-lines] [cancer] [perturbations]
BioGPS (Tissue expression)	6938
GTEX Portal (Tissue expression)	TCF12
	Protein : pattern, domain, 3D structure
UniProt/SwissProt	Q99081 [function] [subcellular_location] [family_and_domains] [pathology_and_biotech] [ptm_processing] [expression] [interaction]
NextProt	Q99081 [Sequence] [Exons] [Medical] [Publications]
With graphics : InterPro	Q99081
Splice isoforms : SwissVar	Q99081
PhosPhoSitePlus	Q99081
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)
Conserved Domain (NCBI)	TCF12
DMDM Disease mutations	6938
Blocks (Seattle)	TCF12
PDB (SRS)	2KNH 4JOL
PDB (PDBSum)	2KNH 4JOL
PDB (IMB)	2KNH 4JOL
PDB (RSDB)	2KNH 4JOL
Structural Biology KnowledgeBase	2KNH 4JOL
SCOP (Structural Classification of Proteins)	2KNH 4JOL
CATH (Classification of proteins structures)	2KNH 4JOL
Superfamily	Q99081
Human Protein Atlas	ENSG00000140262
Peptide Atlas	Q99081
HPRD	02725
IPI	IPI00012966 IPI00384979 IPI00384333 IPI01010229 IPI01013422 IPI01018775 IPI00940466 IPI01009406 IPI00883875
	Protein Interaction databases
DIP (DOE-UCLA)	Q99081
IntAct (EBI)	Q99081
FunCoup	ENSG00000140262
BioGRID	TCF12
STRING (EMBL)	TCF12
ZODIAC	TCF12
	Ontologies - Pathways
QuickGO	Q99081
Ontology : AmiGO	nuclear 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 nucleoplasm cytoplasm regulation of transcription from RNA polymerase II promoter transcription from RNA polymerase II promoter immune response muscle organ development transcription factor binding nuclear speck enhancer binding cAMP response element binding protein homodimerization activity intracellular membrane-bounded organelle 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-EBI	nuclear 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 nucleoplasm cytoplasm regulation of transcription from RNA polymerase II promoter transcription from RNA polymerase II promoter immune response muscle organ development transcription factor binding nuclear speck enhancer binding cAMP response element binding protein homodimerization activity intracellular membrane-bounded organelle 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
REACTOME	Q99081 [protein]
REACTOME Pathways	R-HSA-375170 [pathway]
NDEx Network	TCF12
Atlas of Cancer Signalling Network	TCF12
Wikipedia pathways	TCF12
	Orthology - Evolution
OrthoDB	6938
GeneTree (enSembl)	ENSG00000140262
Phylogenetic Trees/Animal Genes : TreeFam	TCF12
HOVERGEN	Q99081
HOGENOM	Q99081
Homologs : HomoloGene	TCF12
Homology/Alignments : Family Browser (UCSC)	TCF12
	Gene fusions - Rearrangements
Fusion : Mitelman	CGNL1/TCF12 [15q21.3/15q21.3] [t(15;15)(q21;q21)]
Fusion : Mitelman	MAP3K5/TCF12 [6q23.3/15q21.3] [t(6;15)(q23;q21)]
Fusion : Mitelman	RNF111/TCF12 [15q22.1/15q21.3] [t(15;15)(q21;q22)]
Fusion : Mitelman	TCF12/MGST2 [15q21.3/4q31.1] [t(4;15)(q31;q21)]
Fusion : Mitelman	TCF12/NPAS1 [15q21.3/19q13.32] [t(15;19)(q21;q13)]
Fusion : Mitelman	TCF12/NR4A3 [15q21.3/9q22.33] [t(9;15)(q31;q21)]
Fusion : Mitelman	TCF12/TEX9 [15q21.3/15q21.3] [t(15;15)(q21;q21)]
Fusion : Mitelman	TCF12/TMEM255B [15q21.3/13q34] [t(13;15)(q34;q21)]
Fusion : COSMIC	TCF12 [15q21.3] - NR4A3 [9q22.33] [fusion_754] [fusion_755]
Fusion: TCGA	CGNL1 15q21.3 TCF12 15q21.3 BRCA
Fusion: TCGA	RNF111 15q22.1 TCF12 15q21.3 BRCA
Fusion: TCGA	TCF12 15q21.3 FAM70B BRCA
Fusion: TCGA	TCF12 15q21.3 MGST2 4q31.1 BRCA
Fusion: TCGA	TCF12 15q21.3 NPAS1 19q13.32 PRAD
Fusion: TCGA	TCF12 15q21.3 TEX9 15q21.3 BRCA
	Polymorphisms : SNP and Copy number variants
NCBI Variation Viewer	TCF12 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)	TCF12
dbVar	TCF12
ClinVar	TCF12
1000_Genomes	TCF12
Exome Variant Server	TCF12
ExAC (Exome Aggregation Consortium)	TCF12 (select the gene name)
Genetic variants : HAPMAP	6938
Genomic Variants (DGV)	TCF12 [DGVbeta]
DECIPHER	TCF12 [patients] [syndromes] [variants] [genes]
CONAN: Copy Number Analysis	TCF12
	Mutations
ICGC Data Portal	TCF12
TCGA Data Portal	TCF12
Broad Tumor Portal	TCF12
OASIS Portal	TCF12 [ Somatic mutations - Copy number]
Cancer Gene: Census	TCF12
Somatic Mutations in Cancer : COSMIC	TCF12 [overview] [genome browser] [tissue] [distribution]
Mutations and Diseases : HGMD	TCF12
intOGen Portal	TCF12
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
BioMuta	search 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)
intoGen	TCF12
NCG5 (London)	TCF12
Cancer3D	TCF12(select the gene name)
Impact of mutations	[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
	Diseases
OMIM	600480 615314
Orphanet	18668 10369 10368
Medgen	TCF12
Genetic Testing Registry	TCF12
NextProt	Q99081 [Medical]
TSGene	6938
GENETests	TCF12
Target Validation	TCF12
Huge Navigator	TCF12 [HugePedia]
snp3D : Map Gene to Disease	6938
BioCentury BCIQ	TCF12
ClinGen	TCF12 (curated)
	Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD	6938
Chemical/Pharm GKB Gene	PA36381
Clinical trial	TCF12
	Miscellaneous
canSAR (ICR)	TCF12 (select the gene name)
	Probes
	Litterature
PubMed	72 Pubmed reference(s) in Entrez
GeneRIFs	Gene References Into Functions (Entrez)
CoreMine	TCF12
EVEX	TCF12
GoPubMed	TCF12
iHOP	TCF12

REVIEW articles	automatic search in PubMed
Last year publications	automatic search in PubMed

Search in all EBI NCBI

indexed on : Mon May 22 09:24:43 CEST 2017

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