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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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CLCN4
Cl-/H+ antiporter 4
Chromosome X Β· Xp22.2
NCBI Gene: 1183Ensembl: ENSG00000073464.14HGNC: HGNC:2022UniProt: P51793
36PubMed Papers
21Diseases
0Drugs
68Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTransporter
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
chloride transportchloride channel activityprotein bindingantiporter activityX-linked non-syndromic intellectual disabilityclcn4-related disordernon-syndromic X-linked intellectual disabilitygenetic disorder
✦AI Summary

CLCN4 encodes a chloride/proton antiporter (ClC-4) that mediates electrogenic exchange of chloride ions against protons 1. The protein functions as a strongly outwardly rectifying H+/Cl- exchanger with conserved gating glutamate residues typical of antiporter family members 2. ClC-4 localizes to multiple intracellular compartments including endosomes, lysosomes, and synaptic vesicles, where it associates with other chloride-proton antiporters like CLCN3 and CLCN5 2. Pathogenic CLCN4 variants cause Raynaud-Claes syndrome, an X-linked neurodevelopmental disorder characterized by global developmental delay, intellectual disability, and drug-resistant epilepsy 3. Seizures develop in approximately 55% of patients, often within the first year of life, with myoclonic seizures being most common 4. Most variants result in loss-of-function through reduced anion exchange capacity, altered protein trafficking, or disrupted oligomerization with other ClC proteins 3. Functional analyses reveal that 25% of variants cause voltage-dependent activation shifts, while others produce toxic gain-of-function allowing inward transport at negative voltages 5. CLCN4 dysfunction impairs synaptic plasticity and dendritic development; Clcn4 knockout mice exhibit autism-spectrum behaviors with reduced dendritic branching and decreased synaptic phosphorylation markers 6. Lamotrigine shows therapeutic promise in select patients 4.

Sources cited
1
CLCN4 identified as novel X-linked intellectual disability gene; variants impair protein function as shown by electrophysiological studies
PMID: 25644381
2
CLCN4 functions as chloride-proton antiporter; associates with TMEM9/TMEM9B subunits in endosomal complexes
PMID: 40437099
3
CLCN4 variants cause neurodevelopmental disorder with global developmental delay and seizures; variants compromise anion exchange function, protein expression, or heterodimerization
PMID: 38758281
4
CLCN4 encodes 2Cl-/H+ exchanger prominently expressed in hippocampus and cerebellum; loss-of-function variants cause Raynaud-Claes syndrome
PMID: 37271660
5
CLCN4 variants demonstrate complex pathophysiology including loss-of-function with voltage activation shifts and toxic gain-of-function with disrupted gating
PMID: 36385166
6
CLCN4-related epilepsy affects 54.55% of patients with CLCN4 disorders; drug-resistant seizures most common; myoclonic seizures predominate; lamotrigine shows therapeutic benefit
PMID: 33951195
7
Clcn4 knockout mice exhibit autism-spectrum behaviors with reduced dendritic branching, impaired synaptic plasticity, and decreased synaptic phosphorylation markers
PMID: 39863599
Disease Associationsβ“˜21
X-linked non-syndromic intellectual disabilityOpen Targets
0.84Strong
clcn4-related disorderOpen Targets
0.53Moderate
non-syndromic X-linked intellectual disabilityOpen Targets
0.48Moderate
genetic disorderOpen Targets
0.47Moderate
SeizureOpen Targets
0.27Weak
Intellectual disabilityOpen Targets
0.15Weak
Neurodevelopmental disorderOpen Targets
0.15Weak
intellectual disability, X-linked 81Open Targets
0.12Weak
schizophreniaOpen Targets
0.12Weak
microcephalyOpen Targets
0.11Weak
Global developmental delayOpen Targets
0.11Weak
Rare genetic intellectual disabilityOpen Targets
0.11Weak
neoplasmOpen Targets
0.08Suggestive
atypical teratoid rhabdoid tumorOpen Targets
0.04Suggestive
epilepsyOpen Targets
0.03Suggestive
esophageal adenocarcinomaOpen Targets
0.03Suggestive
cancerOpen Targets
0.02Suggestive
Retinal NeoplasmOpen Targets
0.02Suggestive
ependymomaOpen Targets
0.02Suggestive
childhood supratentorial ependymomaOpen Targets
0.02Suggestive
Raynaud-Claes syndromeUniProt
Pathogenic Variants68
NM_001830.4(CLCN4):c.949G>A (p.Val317Ile)Pathogenic
not provided|Intellectual disability|Inborn genetic diseases|Intellectual disability, X-linked 49
β˜…β˜…β˜†β˜†2025β†’ Residue 317
NM_001830.4(CLCN4):c.1664C>T (p.Ala555Val)Pathogenic
CLCN4-related disorder|Inborn genetic diseases|not provided|Intellectual disability, X-linked 49
β˜…β˜…β˜†β˜†2025β†’ Residue 555
NM_001830.4(CLCN4):c.2191G>A (p.Gly731Arg)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 731
NM_001830.4(CLCN4):c.1399G>A (p.Gly467Ser)Likely pathogenic
Intellectual disability, X-linked 49|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 467
NM_001830.4(CLCN4):c.265G>A (p.Asp89Asn)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 89
NM_001830.4(CLCN4):c.1630G>A (p.Gly544Arg)Pathogenic
Intellectual disability, X-linked 49|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 544
NM_001830.4(CLCN4):c.823G>A (p.Val275Met)Pathogenic
CLCN4-related disorder|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 275
NM_001830.4(CLCN4):c.2152C>T (p.Arg718Trp)Pathogenic
CLCN4-related disorder|Intellectual disability, X-linked 49|not provided|See cases
β˜…β˜…β˜†β˜†2023β†’ Residue 718
NM_001830.4(CLCN4):c.1807C>T (p.Arg603Trp)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 603
NM_001830.4(CLCN4):c.957_958del (p.Phe319fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 319
NM_001830.4(CLCN4):c.844-1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_001830.4(CLCN4):c.592T>C (p.Tyr198His)Likely pathogenic
Intellectual disability, X-linked 49
β˜…β˜†β˜†β˜†2025β†’ Residue 198
NM_001830.4(CLCN4):c.369del (p.Phe123fs)Pathogenic
Intellectual disability, X-linked 49
β˜…β˜†β˜†β˜†2025β†’ Residue 123
NM_001830.4(CLCN4):c.1319_1320insCGACC (p.Ala441fs)Pathogenic
Intellectual disability, X-linked 49
β˜…β˜†β˜†β˜†2025β†’ Residue 441
NM_001830.4(CLCN4):c.405G>A (p.Trp135Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 135
NM_001830.4(CLCN4):c.281G>A (p.Trp94Ter)Likely pathogenic
Intellectual disability, X-linked 49
β˜…β˜†β˜†β˜†2025β†’ Residue 94
NM_001830.4(CLCN4):c.1490G>A (p.Trp497Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 497
NM_001830.4(CLCN4):c.497dup (p.Leu166fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 166
NM_001830.4(CLCN4):c.985_986dup (p.Met329fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 329
NM_001830.4(CLCN4):c.555+1G>TLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
View on ClinVar β†—
Related Genes
CLCA4Shared pathway100%CLCA2Shared pathway100%CLCA1Shared pathway75%TTYH3Shared pathway75%AMELXProtein interaction71%TMC4Shared pathway67%
Tissue Expression6 tissues
Brain
100%
Heart
57%
Bone Marrow
10%
Lung
6%
Liver
6%
Ovary
2%
Gene Interaction Network
Click a node to explore
CLCN4CLCA4CLCA2CLCA1TTYH3AMELXTMC4
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt P51793
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.11Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.02 [0.01–0.11]
RankingsWhere CLCN4 stands among ~20K protein-coding genes
  • #10,757of 20,598
    Most Researched36
  • #1,074of 5,498
    Most Pathogenic Variants68 Β· top quartile
  • #93of 17,882
    Most Constrained (LOEUF)0.11 Β· top 1%
Genes detectedCLCN4
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes.
PMID: 25644381
Mol Psychiatry Β· 2016
1.00
2
EndoMAP.v1 charts the structural landscape of human early endosome complexes.
PMID: 40437099
Nature Β· 2025
0.90
3
Expanding the genetic and phenotypic relevance of CLCN4 variants in neurodevelopmental condition: 13 new patients.
PMID: 38758281
J Neurol Β· 2024
0.80
4
Developmental and epileptic encephalopathy in a young Italian woman with a de novo missense variant in the CLCN4 gene: A case report.
PMID: 37271660
Brain Dev Β· 2023
0.70
5
Comprehensive analysis and experimental validation reveal elevated CLCN4 is a promising biomarker in endometrial cancer.
PMID: 37671947
Aging (Albany NY) Β· 2023
0.60