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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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TCF12
transcription factor 12
Chromosome 15 Β· 15q21.3
NCBI Gene: 6938Ensembl: ENSG00000140262.18HGNC: HGNC:11623UniProt: F5GY10
150PubMed Papers
22Diseases
0Drugs
133Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
chromatinresponse to gonadotropin-releasing hormonepositive regulation of transcription by RNA polymerase IIRNA polymerase II transcription regulator complexTCF12-related craniosynostosishypogonadotropic hypogonadism 26 with or without anosmiaKallmann syndromeCoronal craniosynostosis
✦AI Summary

TCF12 is a basic helix-loop-helix transcription factor located on chromosome 15 that functions as a sequence-specific DNA-binding transcriptional activator 1. It binds E-box elements (5'-CANNTG-3') and regulates transcription through RNA polymerase II 2. TCF12 plays critical roles in neurodevelopmental and craniofacial processes: it initiates neuronal differentiation and participates in functional networks regulating GnRH axis development 2. In hematopoietic stem cells, nuclear TCF12 cooperates with nuclear tubulin to enhance CXCR4 transcription and promote chemotaxis 3. Pathogenic TCF12 variants cause monogenic developmental disorders. De novo mutations associate with neurodevelopmental disorders and intellectual disability 24, and loss-of-function variants increase cancer risk in congenital heart disease patients 5. Most notably, TCF12 mutations are a significant genetic cause of coronal craniosynostosis, accounting for approximately 10-20% of cases negative for TWIST1 and FGFR variants, with estimated prevalence of 2% in undifferentiated craniosynostosis cohorts 6. TCF12 also associates with hypogonadotropic hypogonadism with or without anosmia. In colorectal cancer, the TCF12-MALAT1 regulatory alliance modulates cyclin D1 and Ξ²-catenin expression patterns affecting prognosis independently of metastasis 7, suggesting TCF12 has context-dependent roles in development and disease.

Sources cited
1
TCF12 genomic organization, location on 15q21, encodes helix-loop-helix transcription factor HTF4, contains 21 exons with alternative splicing producing multiple isoforms
PMID: 12826747
2
TCF12 identified as neurodevelopmental disorder risk gene with de novo mutation excess and phenotype-genotype correlations in large-scale targeted sequencing study
PMID: 33004838
3
Pathogenic TCF12 de novo variants identified in patients with syndromic intellectual disability as part of monogenic disorder spectrum
PMID: 38114583
4
TCF12 loss-of-function variants enriched in congenital heart disease patients and associated with increased cancer risk
PMID: 33084842
5
TCF12 pathogenic variants are major genetic cause of coronal craniosynostosis, accounting for 10-20% of TWIST1/FGFR-negative cases with 2% prevalence in undifferentiated cohorts
PMID: 39060747
6
Nuclear TCF12 cooperates with nuclear tubulin at CXCR4 promoter to enhance CXCR4 transcription and hematopoietic stem cell chemotaxis
PMID: 37067645
7
TCF12-MALAT1 alliance regulates cyclin D1 and Ξ²-catenin expression in colorectal cancer affecting patient prognosis independently of metastasis
PMID: 39768127
8
TCF12 mutations confirmed as substantial contributor to craniosynostosis with recent genetic discoveries from next-generation sequencing
PMID: 28914635
Disease Associationsβ“˜22
TCF12-related craniosynostosisOpen Targets
0.80Strong
hypogonadotropic hypogonadism 26 with or without anosmiaOpen Targets
0.60Moderate
Kallmann syndromeOpen Targets
0.55Moderate
Coronal craniosynostosisOpen Targets
0.53Moderate
genetic disorderOpen Targets
0.52Moderate
neurodegenerative diseaseOpen Targets
0.46Moderate
craniosynostosisOpen Targets
0.45Moderate
open-angle glaucomaOpen Targets
0.45Moderate
autism spectrum disorderOpen Targets
0.43Moderate
diabetes mellitusOpen Targets
0.42Moderate
type 2 diabetes mellitusOpen Targets
0.41Moderate
glaucomaOpen Targets
0.39Weak
isolated brachycephalyOpen Targets
0.37Weak
alcohol drinkingOpen Targets
0.35Weak
developmental disabilityOpen Targets
0.33Weak
male infertility with azoospermia or oligozoospermia due to single gene mutationOpen Targets
0.33Weak
insomniaOpen Targets
0.32Weak
benign prostatic hyperplasiaOpen Targets
0.30Weak
nicotine dependenceOpen Targets
0.29Weak
low grade gliomaOpen Targets
0.29Weak
Craniosynostosis 3UniProt
Hypogonadotropic hypogonadism 26 with or without anosmiaUniProt
Pathogenic Variants133
NM_207037.2(TCF12):c.1491dup (p.Val498fs)Pathogenic
TCF12-related craniosynostosis|not provided|HYPOGONADOTROPIC HYPOGONADISM 26 WITH ANOSMIA|TCF12-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 498
NM_207037.2(TCF12):c.1453C>T (p.Arg485Ter)Pathogenic
not provided|Autism spectrum disorder|Hypogonadotropic hypogonadism 26 with or without anosmia|TCF12-related craniosynostosis
β˜…β˜…β˜†β˜†2025β†’ Residue 485
NM_207037.2(TCF12):c.1128G>A (p.Trp376Ter)Pathogenic
not provided|TCF12-related craniosynostosis
β˜…β˜…β˜†β˜†2025β†’ Residue 376
NM_207037.2(TCF12):c.1267C>T (p.Arg423Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 423
NM_207037.2(TCF12):c.1366dup (p.Ile456fs)Pathogenic
TCF12-related craniosynostosis|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 456
NM_207037.2(TCF12):c.1876C>T (p.Arg626Ter)Pathogenic
TCF12-related craniosynostosis|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 626
NM_207037.2(TCF12):c.1188+1G>CPathogenic
not provided
β˜…β˜…β˜†β˜†2025
NM_207037.2(TCF12):c.778_779del (p.Met260fs)Pathogenic
not provided|TCF12-related craniosynostosis
β˜…β˜…β˜†β˜†2025β†’ Residue 260
NM_207037.2(TCF12):c.1490_1491del (p.Ser497fs)Pathogenic
Hypogonadotropic hypogonadism 26 with or without anosmia|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 497
NM_207037.2(TCF12):c.1642_1645del (p.Glu548fs)Pathogenic
TCF12-related craniosynostosis|not provided|Autism spectrum disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 548
NM_207037.2(TCF12):c.268C>T (p.Arg90Ter)Pathogenic
TCF12-related craniosynostosis|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 90
NM_207037.2(TCF12):c.786dup (p.Ser263fs)Pathogenic
TCF12-related craniosynostosis|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 263
NM_207037.2(TCF12):c.842C>G (p.Ser281Ter)Pathogenic
TCF12-related craniosynostosis|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 281
NM_207037.2(TCF12):c.1836dup (p.Arg613fs)Pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 613
NM_207037.2(TCF12):c.1541C>A (p.Ser514Ter)Pathogenic
TCF12-related craniosynostosis|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 514
NM_207037.2(TCF12):c.812C>A (p.Ser271Ter)Pathogenic
not provided|TCF12-related craniosynostosis
β˜…β˜…β˜†β˜†2022β†’ Residue 271
NM_207037.2(TCF12):c.722C>A (p.Ser241Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2021β†’ Residue 241
NM_207037.2(TCF12):c.298dup (p.Thr100fs)Likely pathogenic
TCF12-related craniosynostosis
β˜…β˜†β˜†β˜†2025β†’ Residue 100
NM_207037.2(TCF12):c.1115-2A>GPathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_207037.2(TCF12):c.1376T>G (p.Leu459Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 459
View on ClinVar β†—
Related Genes
LDB1Protein interaction100%NEUROD1Protein interaction99%RUNX1Protein interaction98%GATA2Protein interaction98%LMO2Protein interaction98%TAL1Protein interaction98%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
57%
Heart
56%
Ovary
54%
Lung
44%
Liver
30%
Gene Interaction Network
Click a node to explore
TCF12LDB1NEUROD1RUNX1GATA2LMO2TAL1
PROTEIN STRUCTURE
Preparing viewer…
PDB4JOL Β· 2.91 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.61LoF Tolerant
pLIβ“˜
0.02Tolerant
Observed/Expected LoF0.45 [0.33–0.61]
RankingsWhere TCF12 stands among ~20K protein-coding genes
  • #3,026of 20,598
    Most Researched150 Β· top quartile
  • #581of 5,498
    Most Pathogenic Variants133 Β· top quartile
  • #4,220of 17,882
    Most Constrained (LOEUF)0.61 Β· top quartile
Genes detectedTCF12
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders.
PMID: 33004838
Nat Commun Β· 2020
1.00
2
Association of Damaging Variants in Genes With Increased Cancer Risk Among Patients With Congenital Heart Disease.
PMID: 33084842
JAMA Cardiol Β· 2021
0.90
3
De novo variants underlying monogenic syndromes with intellectual disability in a neurodevelopmental cohort from India.
PMID: 38114583
Eur J Hum Genet Β· 2024
0.80
4
TCF12 and LncRNA MALAT1 Cooperatively Harness High Cyclin D1 but Low Ξ²-Catenin Gene Expression to Exacerbate Colorectal Cancer Prognosis Independently of Metastasis.
PMID: 39768127
Cells Β· 2024
0.70
5
The role of pathogenic TCF12 variants in children with coronal craniosynostosis-a systematic review with addition of two novel cases.
PMID: 39060747
Childs Nerv Syst Β· 2024
0.60