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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
ZFHX3
zinc finger homeobox 3
Chromosome 16 Β· 16q22.2-q22.3
NCBI Gene: 463Ensembl: ENSG00000140836.17HGNC: HGNC:777UniProt: Q15911
137PubMed Papers
22Diseases
0Drugs
38Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
RNA polymerase II cis-regulatory region sequence-specific DNA bindingtranscription regulator complexpositive regulation of DNA-templated transcriptionnuclear bodyprostate carcinomaatrial fibrillationNeurodevelopmental disordercardioembolic stroke
✦AI Summary

ZFHX3 (zinc finger homeobox 3) is a transcriptional regulator that functions as both an activator and repressor of gene expression, playing critical roles in cardiac function, neuronal development, and disease pathogenesis. The protein binds to AT-rich DNA sequences and regulates diverse biological processes through chr16 remodeling complexes 1. In cardiac tissue, ZFHX3 is essential for normal atrial function, with loss-of-function variants causing atrial fibrillation through dysregulation of cardiac pathways and altered calcium handling 2. The gene is significantly associated with atrial fibrillation risk, particularly in Caucasian populations, where specific polymorphisms increase disease susceptibility 34. ZFHX3 also plays a crucial role in neuronal development, with haploinsufficiency causing syndromic intellectual disability characterized by developmental delays, autism spectrum disorder, and distinctive facial features 1. Additionally, GGC repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4 (SCA4), a neurodegenerative disorder featuring cerebellar ataxia, dysautonomia, and motor neuron involvement 5. The protein's widespread expression in developing brain tissue and its interaction with chr16 remodeling complexes underscore its fundamental importance in both cardiac and neurological function.

Sources cited
1
ZFHX3 haploinsufficiency causes syndromic intellectual disability and the protein interacts with chromatin remodeling complexes
PMID: 38412861
2
ZFHX3 is essential for normal atrial function and its loss causes atrial fibrillation through cardiac pathway dysregulation
PMID: 37449401
3
Rs7193343 polymorphism in ZFHX3 is associated with atrial fibrillation risk in Caucasian populations
PMID: 26112950
4
ZFHX3 is one of the shared loci associated with atrial fibrillation across different populations
PMID: 40645996
5
GGC repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4 with cerebellar ataxia and motor neuron involvement
PMID: 38973251
Disease Associationsβ“˜22
prostate carcinomaOpen Targets
0.58Moderate
atrial fibrillationOpen Targets
0.58Moderate
Neurodevelopmental disorderOpen Targets
0.52Moderate
cardioembolic strokeOpen Targets
0.52Moderate
heart failureOpen Targets
0.52Moderate
type 2 diabetes mellitusOpen Targets
0.52Moderate
cardiac arrhythmiaOpen Targets
0.51Moderate
atrial flutterOpen Targets
0.50Moderate
diabetes mellitusOpen Targets
0.48Moderate
spinocerebellar ataxia type 4Open Targets
0.48Moderate
obesityOpen Targets
0.47Moderate
prostate adenocarcinomaOpen Targets
0.46Moderate
syndromic intellectual disabilityOpen Targets
0.44Moderate
Epidermal Inclusion CystOpen Targets
0.43Moderate
heart diseaseOpen Targets
0.43Moderate
gastroesophageal reflux diseaseOpen Targets
0.43Moderate
cardiomyopathyOpen Targets
0.43Moderate
endometrial cancerOpen Targets
0.42Moderate
occlusion precerebral arteryOpen Targets
0.42Moderate
esophageal diseaseOpen Targets
0.41Moderate
Atrial fibrillation, familial, 8UniProt
Spinocerebellar ataxia 4UniProt
Pathogenic Variants38
NM_006885.4(ZFHX3):c.6850C>T (p.Arg2284Ter)Pathogenic
not specified|Neurodevelopmental disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 2284
NM_006885.4(ZFHX3):c.1149_1171dup (p.Gln391fs)Likely pathogenic
Neurodevelopmental delay
β˜…β˜†β˜†β˜†2026β†’ Residue 391
NM_006885.4(ZFHX3):c.1604T>A (p.Leu535Ter)Pathogenic
not specified
β˜…β˜†β˜†β˜†2025β†’ Residue 535
NM_006885.4(ZFHX3):c.3663+1G>TLikely pathogenic
not specified
β˜…β˜†β˜†β˜†2025
NM_006885.4(ZFHX3):c.5512C>T (p.Gln1838Ter)Pathogenic
not specified
β˜…β˜†β˜†β˜†2025β†’ Residue 1838
NM_006885.4(ZFHX3):c.314dup (p.Pro106fs)Pathogenic
not specified
β˜…β˜†β˜†β˜†2025β†’ Residue 106
NM_006885.4(ZFHX3):c.5689G>T (p.Glu1897Ter)Pathogenic
not specified
β˜…β˜†β˜†β˜†2025β†’ Residue 1897
NM_006885.4(ZFHX3):c.5858G>T (p.Gly1953Val)Likely pathogenic
not specified
β˜…β˜†β˜†β˜†2025β†’ Residue 1953
NM_006885.4(ZFHX3):c.2655del (p.Gln885fs)Pathogenic
ZFHX3-related disorder
β˜…β˜†β˜†β˜†2025β†’ Residue 885
NM_006885.4(ZFHX3):c.2095_2096delinsTGC (p.Gly699fs)Pathogenic
not specified
β˜…β˜†β˜†β˜†2025β†’ Residue 699
NM_006885.4(ZFHX3):c.4834G>T (p.Glu1612Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1612
NM_006885.4(ZFHX3):c.5396_5397del (p.Pro1799fs)Likely pathogenic
Intellectual disability
β˜…β˜†β˜†β˜†2025β†’ Residue 1799
NM_006885.4(ZFHX3):c.2047C>T (p.Gln683Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 683
NM_006885.4(ZFHX3):c.3767del (p.Leu1256fs)Pathogenic
not specified
β˜…β˜†β˜†β˜†2025β†’ Residue 1256
NM_006885.4(ZFHX3):c.8289dup (p.Ile2764fs)Likely pathogenic
ZFHX3-associated disorder
β˜…β˜†β˜†β˜†2025β†’ Residue 2764
NM_006885.4(ZFHX3):c.10778C>G (p.Ser3593Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 3593
NM_006885.4(ZFHX3):c.4132C>T (p.Gln1378Ter)Pathogenic
Neurodevelopmental disorder
β˜…β˜†β˜†β˜†2025β†’ Residue 1378
NM_006885.4(ZFHX3):c.8295dup (p.Asp2766Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 2766
NM_006885.4(ZFHX3):c.10231_10234del (p.Asp3411fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 3411
NM_006885.4(ZFHX3):c.709C>T (p.Arg237Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 237
View on ClinVar β†—
Related Genes
RUNX3Protein interaction86%POU1F1Protein interaction85%CDKN1AProtein interaction85%PIAS3Protein interaction79%PITX2Protein interaction78%KCNN3Protein interaction72%
Tissue Expression6 tissues
Lung
100%
Brain
94%
Heart
79%
Liver
59%
Ovary
57%
Bone Marrow
24%
Gene Interaction Network
Click a node to explore
ZFHX3RUNX3POU1F1CDKN1APIAS3PITX2KCNN3
PROTEIN STRUCTURE
Preparing viewer…
PDB2DA1 Β· NMR
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.19Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.15 [0.11–0.19]
RankingsWhere ZFHX3 stands among ~20K protein-coding genes
  • #3,396of 20,598
    Most Researched137 Β· top quartile
  • #1,587of 5,498
    Most Pathogenic Variants38
  • #387of 17,882
    Most Constrained (LOEUF)0.19 Β· top 5%
Genes detectedZFHX3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies.
PMID: 38181741
Cell Β· 2024
1.00
2
Haploinsufficiency of ZFHX3, encoding a key player in neuronal development, causes syndromic intellectual disability.
PMID: 38412861
Am J Hum Genet Β· 2024
0.90
3
Loss of the Atrial Fibrillation-Related Gene,
PMID: 37449401
Circ Res Β· 2023
0.80
4
Spinocerebellar ataxia type 4 is caused by a GGC expansion in the ZFHX3 gene and is associated with prominent dysautonomia and motor neuron signs.
PMID: 38973251
J Intern Med Β· 2024
0.70
5
An Update on the Adult-Onset Hereditary Cerebellar Ataxias: Novel Genetic Causes and New Diagnostic Approaches.
PMID: 38760634
Cerebellum Β· 2024
0.60