CLCN4

Gene Facts

• HGNC Symbol: CLCN4 (HGNC:2022)
• HGNC Name: chloride voltage-gated channel 4
• Gene type: protein-coding gene
• Locus type: gene with protein product
• Previous symbols: No previous names found
• Alias symbols: CLC4, ClC-4
• %HI: 28.47
• pLI: 1
• LOEUF: 0.15
• Cytoband: Xp22.2
• Genomic Coordinates:

  GRCh37/hg19:	chrX:10125015-10205700
  GRCh38/hg38:	chrX:10156975-10237660

• MANE Select Transcript: NM_001830.4 ENST00000380833.9
• Function: Strongly outwardly rectifying, electrogenic H(+)/Cl(-)exchanger which mediates the exchange of chloride ions against protons (PubMed:18063579, PubMed:28972156, PubMed:23647072, PubMed:27550844, PubMed:25644381). The CLC channel family contains both chloride channels and proton-coupled anion transporters that exchange chloride or another anion for protons (PubMed:29845874). The presence of conserved gating glutamate residues is typical for family members that function as antiporters (PubMed:29845... (Source: Uniprot)

Dosage Sensitivity Summary (Gene)

• Dosage ID: ISCA-9681
• ClinGen Curation ID: CCID:006874
• Curation Status: Complete
• Issue Type: Dosage Curation - Gene
• Haploinsufficiency: Little Evidence for Haploinsufficiency (1)
• Triplosensitivity: No Evidence for Triplosensitivity (0)
• Last Evaluated: 07/27/2022

Haploinsufficiency (HI) Score Details

• HI Score: 1
• HI Evidence Strength: Little Evidence for Haploinsufficiency

HI Disease

• intellectual disability, X-linked 49

HI Evidence

• PUBMED: 25644381
  Hu et al. (2016) reported five unrelated families with variants in CLCN4; four of the families had missense variants, and one family (referred to as MRX49) had a frameshift variant. The frameshift variant segregated with four affected males in the family (a fifth affected male was not tested). Unaffected brothers of these affected individuals were shown not to have the variant. The phenotype of the affected individuals was relatively non-specific; within family MRX49, the degree of intellectual disability ranged from borderline to moderate. The family was said to have no other distinguishing features aside from head circumference over the 97th percentile in 3 of the 5 affected individuals. The authors did perform some functional assays to demonstrate that CLCN4 variants "impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4− / − mice or after mRNA knock-down."
• PUBMED: 27550844
  Palmer et al. (2018) described 10 previously unreported families and reviewed 6 previously reported families with X-linked intellectual disability due to pathogenic variant in CLCN4, including 5 females with de novo variants, a frameshift variant (Family B), and a deletion of exon 12 (Family J). The authors summarized phenotypic and molecular genetic information on 52 individuals from 16 families. In family B, the frameshift variant was found in three affected brothers and their unaffected sister and mother. A fourth brother, who is reportedly unaffected, was also found to have the variant; this individual is known to have Klinefelter syndrome, and the authors postulate that the presence of the extra X chromosome contributes to his unaffected status. In family J, the deletion was found in two affected brothers and their unaffected mother. The authors comment that the individuals in the study with variants predicted to result in loss of function are (in general) more mildly affected than those individuals with missense variants, suggesting that "an abnormally functioning CIC-4 antiporter is more deleterious than a reduction in its levels or a complete absence." They also note that "no potential dominant negative effect of CLCN4 missense variants was observed when equal amounts of wild-type and mutant ClC-4 were expressed in Xenopus oocytes."

• HI Evidence Comments: CLCN4 encodes the voltage-dependent 2Cl_/H+-exchanger ClC-4. In humans, CIC-4 is widely expressed across tissues with particularly high expression in the brain. Pathogenic variants in CLCN4 cause an X-linked form of intellectual disability (referred to by OMIM as Raynaud-Claes syndrome) characterized by borderline to severe intellectual disability and impaired language development. Additional features include behavioral problems, psychiatric disorders, seizures (variable forms), progressive ataxia, brain abnormalities, and unremarkable facial features (OMIM 300114). Per GeneReviews ((Palmer EE, Nguyen MH, Forwood C, et al. CLCN4-Related Neurodevelopmental Disorder. 2021 Dec 16. Available from: https://www.ncbi.nlm.nih.gov/books/NBK575836/): "The X-linked CLCN4-related neurodevelopmental disorder (CLCN4-NDD) has been characterized in 36 males reported to date by developmental delay, intellectual disability, autism spectrum disorder, behavioral issues (e.g., anxiety, hyperactivity, and bipolar disorder), epilepsy, and gastrointestinal dysfunction. The five heterozygous females with a de novo CLCN4 variant reported to date had findings very similar to those of affected males. However, 22 of 25 heterozygous females identified in family studies were unaffected or had only mild specific learning difficulties and/or mental health concerns, whereas three were more severely affected. No genotype-phenotype correlations have been identified to date. Significant phenotypic variability has been observed both between individuals from different families with a recurrent variant and among individuals from a single family who have the same variant. The phenotypes of males with haploinsufficiency (due to exon deletions or frameshift variants) were noted to be relatively milder than the phenotypes of individuals with missense variants The CLCN4 related conditions show complete penetrance but variable expressivity in males, and incomplete penetrance and variable expressivity in females. The pathogenic variant spectrum includes missense (mostly), framehshift, splice site, and one single-exon deletion. All missense variants were predicted to affect CLCN4’s function based on in silico tools and either segregated with the phenotype in the family or were de novo. Several variants are likely to result in a complete loss of ClC-4 function in hemizygous males; frameshift variants in exons 3 and 11, and deletion of exon 12. Phenotypes of males and females with frameshifts or exonic deletion are relatively mild compared with most affected individuals with missense variants. No potential dominant negative effect of CLCN4 missense variants was observed when equal amounts of wild-type and mutant ClC-4 were expressed in Xenopus oocytes. (summary by Palmer et al. (2018), PMID: 27550844). Additional relevant literature: Veeramah et al (2013) (PMID: 23647072) reported a de novo missense variant (p.G544R) of CLCN4 in a 14-month-old boy with severe developmental delay, epileptic encephalopathy,microcephaly, delayed psychomotor development, hypotonia, and dystonia. In vitro analyses using cell-based assays revealed that the CLCN4 variant greatly impaired ion transport by the ClC-4 2Cl-/H+-exchanger, acted as a loss of function variant. Guzman et al (2022) (PMID: 35721313) examined the functional consequences of previously reported 12 CLCN4 missense variants using biochemical, microscopy, and electrophysiological approaches. They categorized the variants into three groups: one group with only subtle changes in transport properties and almost normal subcellular localization (D15N, V275M, V536M, G544R, A555V, and R718W), a second group causing pronounced reductions in endosomal ClC-4 transport (G78S, L221P, L221V, and S534L), and a third mainly affecting transporter biogenesis or trafficking group (V212G and G731R). The authors used SDS-PAGE and confocal imaging to describe protein expression, stability, and subcellular distribution of WT and mutant ClC-4. While D15N, G78S, V275M, V536M, R718W, and G731R ClC-4 were indistinguishable from WT in these analyses, they observed reduced full-length expression levels of V212G, L221P, S534L, G544R, and A555V ClC-4. They suggest that L221V variant leads to complete loss of function of ClC-4. The exact mechanisms by which variants in CLCN4 cause neurodevelopmental disorders are unclear. Functional evidence is emerging, but it has not been definitively demonstrated loss of function is a true disease mechanism. No focal deletions involving CLCN4 have been reported at this time. Additional information is necessary to clarify the role of loss of function variants in this phenotype.

NOTE

The loss-of-function and triplosensitivity ratings for genes on the X chromosome are made in the context of a male genome to account for the effects of hemizygous duplications or nullizygous deletions. In contrast, disruption of some genes on the X chromosome causes male lethality and the ratings of dosage sensitivity instead take into account the phenotype in female individuals. Factors that may affect the severity of phenotypes associated with X-linked disorders include the presence of variable copies of the X chromosome (i.e. 47,XXY or 45,X) and skewed X-inactivation in females.

Triplosensitivity (TS) Score Details

• TS Score: 0
• TS Evidence Strength: No Evidence for Triplosensitivity
• TS Evidence Comments: At this time there is no evidence that supports the triplosensitivity of CLCN4.

NOTE

The loss-of-function and triplosensitivity ratings for genes on the X chromosome are made in the context of a male genome to account for the effects of hemizygous duplications or nullizygous deletions. In contrast, disruption of some genes on the X chromosome causes male lethality and the ratings of dosage sensitivity instead take into account the phenotype in female individuals. Factors that may affect the severity of phenotypes associated with X-linked disorders include the presence of variable copies of the X chromosome (i.e. 47,XXY or 45,X) and skewed X-inactivation in females.