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Aliases for TCF12 Gene

Aliases for TCF12 Gene

  • Transcription Factor 12 2 3 3 5
  • Class B Basic Helix-Loop-Helix Protein 20 3 4
  • Helix-Loop-Helix Transcription Factor 4 2 3
  • Transcription Factor HTF-4 3 4
  • DNA-Binding Protein HTF4 3 4
  • E-Box-Binding Protein 3 4
  • BHLHb20 3 4
  • TCF-12 3 4
  • HTF4 3 4
  • HEB 3 4
  • HsT17266 3
  • BHLHB20 4
  • CRS3 3
  • P64 3

External Ids for TCF12 Gene

Previous GeneCards Identifiers for TCF12 Gene

  • GC15P052769
  • GC15P050257
  • GC15P054789
  • GC15P054926
  • GC15P054998
  • GC15P057210
  • GC15P034034

Summaries for TCF12 Gene

Entrez Gene Summary for TCF12 Gene

  • The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for TCF12 Gene

TCF12 (Transcription Factor 12) is a Protein Coding gene. Diseases associated with TCF12 include Craniosynostosis 3 and Isolated Plagiocephaly. Among its related pathways are ERK Signaling and Wnt / Hedgehog / Notch. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and protein heterodimerization activity. An important paralog of this gene is TCF4.

UniProtKB/Swiss-Prot for TCF12 Gene

  • Transcriptional regulator. Involved in the initiation of neuronal differentiation. Activates transcription by binding to the E box (5-CANNTG-3).

Gene Wiki entry for TCF12 Gene

Additional gene information for TCF12 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TCF12 Gene

Genomics for TCF12 Gene

GeneHancer (GH) Regulatory Elements for TCF12 Gene

Promoters and enhancers for TCF12 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15J056917 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.8 843 4.1 MLX DMAP1 IRF4 YY1 SLC30A9 ZNF213 ZNF143 SP3 NFYC ZNF610 ENSG00000285253 ENSG00000285331 LOC145783 TCF12 LINC00926 RFX7 GC15M057779
GH15J057215 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.1 +300.2 300183 6.7 PKNOX1 FEZF1 ZNF335 ZFP91 RCOR1 FOS ATF7 ZNF362 PRDM6 SMARCA4 TCF12 LINC00926 GC15M057874 GC15P057133
GH15J056885 Promoter/Enhancer 1.6 Ensembl ENCODE 12.9 -30.9 -30906 3 HDGF PKNOX1 ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B E2F8 ZNF207 PIR32785 TCF12 ZNF280D LINC00926 LOC105370833 ENSG00000285253 ENSG00000285331 LOC145783
GH15J056037 Enhancer 1.5 FANTOM5 Ensembl ENCODE 12.6 -877.3 -877308 6.5 PKNOX1 CLOCK FOXA2 MLX FEZF1 DMAP1 ZNF2 YY1 ZNF766 ZNF213 ZNF280D RFX7 RSL24D1 TEX9 PYGO1 PRTG MNS1 TCF12 PIGBOS1 RN7SL568P
GH15J057035 Enhancer 0.8 dbSUPER 15.8 +123.4 123432 13.1 HDGF PKNOX1 INSM2 FEZF1 BATF ZNF2 ZNF213 ZSCAN5C SCRT2 ETV6 TCF12 LINC00926 ZNF280D GC15P057009 GC15M057890
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TCF12 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TCF12 gene promoter:
  • Nkx2-5
  • SRF
  • SRF (504 AA)

Genomic Locations for TCF12 Gene

Genomic Locations for TCF12 Gene
380,993 bases
Plus strand
380,659 bases
Plus strand

Genomic View for TCF12 Gene

Genes around TCF12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TCF12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TCF12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TCF12 Gene

Proteins for TCF12 Gene

  • Protein details for TCF12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Transcription factor 12
    Protein Accession:
    Secondary Accessions:
    • B4E1W1
    • Q7Z3D9
    • Q86TC1
    • Q86VM2

    Protein attributes for TCF12 Gene

    682 amino acids
    Molecular mass:
    72965 Da
    Quaternary structure:
    • Efficient DNA binding requires dimerization with another bHLH protein. Forms homo- or heterooligomers with myogenin, E12 and ITF2 proteins. Interacts with PTF1A. Interacts with NEUROD2 (By similarity). Interacts with RUNX1T1. Interacts with AML1-MTG8/ETO (via nervy homology region 2 in oligomerized form) (PubMed:23812588). Interacts with BHLHA9 (PubMed:25466284).

    Three dimensional structures from OCA and Proteopedia for TCF12 Gene

    Alternative splice isoforms for TCF12 Gene


neXtProt entry for TCF12 Gene

Post-translational modifications for TCF12 Gene

  • Ubiquitination at posLast=571571, posLast=151151, and posLast=110110
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TCF12 Gene

Domains & Families for TCF12 Gene

Gene Families for TCF12 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted secreted proteins
  • Transcription factors

Protein Domains for TCF12 Gene

Graphical View of Domain Structure for InterPro Entry



  • the 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.
  • the 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.
genes like me logo Genes that share domains with TCF12: view

Function for TCF12 Gene

Molecular function for TCF12 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional regulator. Involved in the initiation of neuronal differentiation. Activates transcription by binding to the E box (5-CANNTG-3).
GENATLAS Biochemistry:
transcription factor 12,involved in differentiation of muscle cells and in regulation of gene expression during hematopoiesis

Phenotypes From GWAS Catalog for TCF12 Gene

Gene Ontology (GO) - Molecular Function for TCF12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 11802795
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IDA 11802795
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IDA 11802795
genes like me logo Genes that share ontologies with TCF12: view
genes like me logo Genes that share phenotypes with TCF12: view

Human Phenotype Ontology for TCF12 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TCF12 Gene

MGI Knock Outs for TCF12:

Animal Model Products

CRISPR Products

Targeted motifs for TCF12 Gene
HOMER Transcription Factor Regulatory Elements motif TCF12
  • Consensus sequence: ACAGCTGCTG Submotif: canonical Cell Type: GM12878 GEO ID: GSE32465

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TCF12

Clone Products

  • Addgene plasmids for TCF12

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for TCF12 Gene

Localization for TCF12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TCF12 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TCF12 gene
Compartment Confidence
nucleus 5
plasma membrane 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TCF12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IDA 21828274
GO:0005634 nucleus IDA 21828274
GO:0005654 nucleoplasm TAS --
GO:0005667 transcription factor complex IBA,IEA --
GO:0005737 cytoplasm IDA 21828274
genes like me logo Genes that share ontologies with TCF12: view

Pathways & Interactions for TCF12 Gene

genes like me logo Genes that share pathways with TCF12: view

Pathways by source for TCF12 Gene

SIGNOR curated interactions for TCF12 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for TCF12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II TAS 8163514
GO:0006366 transcription by RNA polymerase II IEA --
GO:0006955 immune response TAS 1312219
genes like me logo Genes that share ontologies with TCF12: view

Drugs & Compounds for TCF12 Gene

No Compound Related Data Available

Transcripts for TCF12 Gene

mRNA/cDNA for TCF12 Gene

(28) REFSEQ mRNAs :
(18) Additional mRNA sequences :
(3) Selected AceView cDNA sequences:
(28) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TCF12 Gene

Transcription factor 12:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TCF12

Clone Products

  • Addgene plasmids for TCF12

Alternative Splicing Database (ASD) splice patterns (SP) for TCF12 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e ^ 3a · 3b · 3c · 3d · 3e ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a ·
SP1: - - - - - - -
SP2: - - - - - -
SP3: - - - - - -
SP4: - - - - - - -
SP6: - - - - - - - - -
SP7: -
SP8: - -
SP9: - -
SP12: - - -
SP13: -

ExUns: 17b ^ 18 ^ 19a · 19b ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26a · 26b ^ 27a · 27b · 27c
SP1: - - -
SP2: - - -
SP3: - - - -
SP4: - - - -
SP5: - - - -
SP11: -

Relevant External Links for TCF12 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for TCF12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TCF12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TCF12 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (56.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TCF12 Gene

NURSA nuclear receptor signaling pathways regulating expression of TCF12 Gene:


SOURCE GeneReport for Unigene cluster for TCF12 Gene:


mRNA Expression by UniProt/SwissProt for TCF12 Gene:

Tissue specificity: Expressed in several tissues and cell types including skeletal muscle, thymus, and a B-cell line.

Evidence on tissue expression from TISSUES for TCF12 Gene

  • Nervous system(4.9)
  • Muscle(4.4)
  • Liver(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TCF12 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • skull
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with TCF12: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for TCF12 Gene

Orthologs for TCF12 Gene

This gene was present in the common ancestor of animals.

Orthologs for TCF12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia TCF12 34 33
  • 99.72 (n)
(Monodelphis domestica)
Mammalia TCF12 34
  • 96 (a)
(Canis familiaris)
Mammalia TCF12 34 33
  • 95.9 (n)
(Bos Taurus)
Mammalia TCF12 34 33
  • 95.41 (n)
(Rattus norvegicus)
Mammalia Tcf12 33
  • 91.83 (n)
(Mus musculus)
Mammalia Tcf12 16 34 33
  • 91.45 (n)
(Ornithorhynchus anatinus)
Mammalia TCF12 34
  • 87 (a)
(Gallus gallus)
Aves TCF12 34 33
  • 83.39 (n)
(Anolis carolinensis)
Reptilia TCF12 34
  • 78 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia tcf12 33
  • 79.99 (n)
Str.13108 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.8165 33
(Danio rerio)
Actinopterygii tcf12 34 33
  • 69.8 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10475 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008814 33
  • 48.95 (n)
fruit fly
(Drosophila melanogaster)
Insecta da 34 35
  • 25 (a)
(Caenorhabditis elegans)
Secernentea hlh-2 34
  • 25 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 26 (a)
Cin.4501 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4501 33
Species where no ortholog for TCF12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TCF12 Gene

Gene Tree for TCF12 (if available)
Gene Tree for TCF12 (if available)
Evolutionary constrained regions (ECRs) for TCF12: view image

Paralogs for TCF12 Gene

Paralogs for TCF12 Gene

(2) SIMAP similar genes for TCF12 Gene using alignment to 20 proteins:

  • B4E1W1_HUMAN
  • F5GY10_HUMAN
genes like me logo Genes that share paralogs with TCF12: view

Variants for TCF12 Gene

Sequence variations from dbSNP and Humsavar for TCF12 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1057518720 uncertain-significance, Craniosynostosis 3 57,263,249(+) A/C coding_sequence_variant, missense_variant
rs36060670 benign, not provided, Craniosynostosis 3 (CRS3) [MIM:615314] 57,262,146(+) T/G coding_sequence_variant, missense_variant
rs398122381 pathogenic, Craniosynostosis 3 57,232,327(+) C/G coding_sequence_variant, intron_variant, stop_gained
rs730880015 pathogenic, Craniosynostosis 3 57,243,507(+) G/ coding_sequence_variant, frameshift
rs730880016 pathogenic, Craniosynostosis 3 57,273,122(+) G/A coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for TCF12 Gene

Variant ID Type Subtype PubMed ID
dgv742e212 CNV loss 25503493
dgv743e212 CNV loss 25503493
esv2749733 CNV deletion 23290073
esv3330040 CNV insertion 20981092
esv3569642 CNV gain 25503493
esv3581725 CNV loss 25503493
esv3636602 CNV loss 21293372
esv3636603 CNV loss 21293372
esv3636606 CNV gain 21293372
esv9081 CNV gain 19470904
nsv1045611 CNV gain 25217958
nsv1069859 CNV deletion 25765185
nsv1113714 CNV deletion 24896259
nsv1127434 CNV deletion 24896259
nsv1546 CNV insertion 18451855
nsv457162 CNV gain 19166990
nsv457164 CNV loss 19166990
nsv472273 CNV novel sequence insertion 20440878
nsv526342 CNV gain 19592680
nsv569577 CNV gain 21841781
nsv569578 CNV loss 21841781
nsv833020 CNV gain+loss 17160897
nsv833021 CNV gain 17160897
nsv94799 CNV insertion 16902084
nsv94818 CNV insertion 16902084
nsv94861 CNV deletion 16902084
nsv974581 CNV duplication 23825009

Variation tolerance for TCF12 Gene

Residual Variation Intolerance Score: 11.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.40; 54.24% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TCF12 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TCF12 Gene

Disorders for TCF12 Gene

MalaCards: The human disease database

(10) MalaCards diseases for TCF12 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
craniosynostosis 3
  • crs3
isolated plagiocephaly
  • craniosynostosis
chondrosarcoma, extraskeletal myxoid
  • emc
isolated brachycephaly
  • non-syndromic bicoronal synostosis
  • craniostenosis
- elite association - COSMIC cancer census association via MalaCards
Search TCF12 in MalaCards View complete list of genes associated with diseases


  • Craniosynostosis 3 (CRS3) [MIM:615314]: A primary abnormality of skull growth involving premature fusion of one or more cranial sutures. The growth velocity of the skull often cannot match that of the developing brain resulting in an abnormal head shape and, in some cases, increased intracranial pressure, which must be treated promptly to avoid permanent neurodevelopmental disability. {ECO:0000269 PubMed:23354436, ECO:0000269 PubMed:25271085}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TCF12

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TCF12: view

No data available for Genatlas for TCF12 Gene

Publications for TCF12 Gene

  1. Genomic organization of human TCF12 gene and spliced mRNA variants producing isoforms of transcription factor HTF4. (PMID: 12826747) Gan TI … Bina M (Cytogenetic and genome research 2002) 3 4 22 58
  2. HEB, a helix-loop-helix protein related to E2A and ITF2 that can modulate the DNA-binding ability of myogenic regulatory factors. (PMID: 1312219) Hu JS … Kingston RE (Molecular and cellular biology 1992) 3 4 22 58
  3. HTF4: a new human helix-loop-helix protein. (PMID: 1886779) Zhang Y … Bina M (Nucleic acids research 1991) 2 3 4 58
  4. Expanding the mutation spectrum in 182 Spanish probands with craniosynostosis: identification and characterization of novel TCF12 variants. (PMID: 25271085) Paumard-Hernández B … Heath KE (European journal of human genetics : EJHG 2015) 3 4 58
  5. Mutations affecting the BHLHA9 DNA-binding domain cause MSSD, mesoaxial synostotic syndactyly with phalangeal reduction, Malik-Percin type. (PMID: 25466284) Malik S … Grzeschik KH (American journal of human genetics 2014) 3 4 58

Products for TCF12 Gene

Sources for TCF12 Gene

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