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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.
KCTD3
potassium channel tetramerization domain containing 3
Chromosome 1 Β· 1q41
NCBI Gene: 51133Ensembl: ENSG00000136636.14HGNC: HGNC:21305UniProt: B4DJX2
64PubMed Papers
20Diseases
0Drugs
1Pathogenic Variants
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingplasma membraneprotein homooligomerizationgenetic disorderdevelopmental and epileptic encephalopathyEpileptic encephalopathyneurodegenerative disease
✦AI Summary

KCTD3 is an accessory subunit that specifically regulates the hyperpolarization-activated cyclic nucleotide-gated channel 3 (HCN3). KCTD3 directly interacts with HCN3 through the channel's C-terminal domain, profoundly increasing cell surface expression and current density without affecting the channel's voltage dependence or kinetics 1. KCTD3 is widely expressed in brain and kidney tissues 2, where it likely participates in ion channel modulation and cellular signaling. Biallelic loss-of-function mutations in KCTD3 cause a distinct neurological syndrome characterized by developmental epileptic encephalopathy, global developmental delay, central hypotonia with progressive peripheral hypertonia, and posterior fossa abnormalities including cerebellar vermis hypoplasia and Dandy-Walker malformation 2. KCTD3 mutations have been identified as disease-causing in consanguineous families through exome sequencing studies 34. The gene has also been associated with lateral ventricular enlargement in childhood, a structural brain abnormality linked to schizophrenia risk 5, and may contribute to neurodevelopmental disorders when deleted in conjunction with other genomic aberrations 6. KCTD3 represents an important member of the KCTD protein family implicated in neurodevelopmental and neuropsychiatric disorders 7.

Sources cited
1
KCTD3 is an HCN3-interacting accessory subunit that up-regulates cell surface expression and current density without affecting voltage dependence
PMID: 23382386
2
Biallelic KCTD3 mutations cause developmental epileptic encephalopathy with cerebellar abnormalities and developmental delay
PMID: 29406573
3
KCTD3 identified as a disease gene in consanguineous families with neurological disorders via whole-exome sequencing
PMID: 25558065
4
KCTD3 validated as a causative gene in clinical exome sequencing of 1000 diagnostic cases
PMID: 27848944
5
KCTD3 DNA methylation at birth prospectively associates with lateral ventricular volume in childhood
PMID: 37469193
6
KCTD3 is part of the KCTD gene family involved in neurodevelopmental and neuropsychiatric disorders
PMID: 31197948
7
KCTD3 hemizygous deletion may contribute to autism spectrum disorder when occurring with additional genomic aberrations
PMID: 19582487
Disease Associationsβ“˜20
genetic disorderOpen Targets
0.41Moderate
developmental and epileptic encephalopathyOpen Targets
0.37Weak
Epileptic encephalopathyOpen Targets
0.37Weak
neurodegenerative diseaseOpen Targets
0.34Weak
esophageal cancerOpen Targets
0.32Weak
SeizureOpen Targets
0.26Weak
isolated cerebellar hypoplasia/agenesisOpen Targets
0.26Weak
Severe global developmental delayOpen Targets
0.26Weak
female reproductive system diseaseOpen Targets
0.14Weak
autismOpen Targets
0.12Weak
lysosomal storage diseaseOpen Targets
0.10Weak
placental retentionOpen Targets
0.08Suggestive
amyotrophic lateral sclerosisOpen Targets
0.07Suggestive
ocular hypotensionOpen Targets
0.07Suggestive
hypertrophic cardiomyopathyOpen Targets
0.06Suggestive
skin cancerOpen Targets
0.06Suggestive
frozen shoulderOpen Targets
0.06Suggestive
Abruptio PlacentaeOpen Targets
0.06Suggestive
hemoglobin D diseaseOpen Targets
0.05Suggestive
lung diseaseOpen Targets
0.05Suggestive
Pathogenic Variants1
NM_016121.5(KCTD3):c.648G>A (p.Trp216Ter)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2022β†’ Residue 216
View on ClinVar β†—
Related Genes
KCTD4Shared pathway100%KCTD18Shared pathway100%SAMD1Shared pathway100%KCTD15Shared pathway100%KCTD14Shared pathway100%IKZF4Shared pathway100%
Tissue Expression6 tissues
Liver
100%
Brain
74%
Ovary
50%
Bone Marrow
48%
Heart
47%
Lung
33%
Gene Interaction Network
Click a node to explore
KCTD3KCTD4KCTD18SAMD1KCTD15KCTD14IKZF4
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9Y597
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.72LoF Tolerant
pLIβ“˜
0.01Tolerant
Observed/Expected LoF0.49 [0.35–0.72]
RankingsWhere KCTD3 stands among ~20K protein-coding genes
  • #7,281of 20,598
    Most Researched64
  • #5,027of 5,498
    Most Pathogenic Variants1
  • #5,516of 17,882
    Most Constrained (LOEUF)0.72
Genes detectedKCTD3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families.
PMID: 25558065
Cell Rep Β· 2015
1.00
2
Clinical exome sequencing: results from 2819 samples reflecting 1000 families.
PMID: 27848944
Eur J Hum Genet Β· 2017
0.90
3
Phenotypic characterization of KCTD3-related developmental epileptic encephalopathy.
PMID: 29406573
Clin Genet Β· 2018
0.80
4
Genetic analysis of intracapillary glomerular lipoprotein deposits in aging mice.
PMID: 25353171
PLoS One Β· 2014
0.70
5
KCTD: A new gene family involved in neurodevelopmental and neuropsychiatric disorders.
PMID: 31197948
CNS Neurosci Ther Β· 2019
0.60