Genotype-phenotype correlation in CLCN4-related developmental and epileptic encephalopathy

Area of Science:

• Neurogenetics
• Ion Channel Function
• X-linked Disorders

Background:

• CLCN4-related disorder is a rare X-linked neurodevelopmental condition with an unclear pathogenic mechanism.
• CLCN4 encodes the vesicular 2Cl-/H+ exchanger ClC-4, and its variants often alter transport activity.
• ClC-4, along with ClC-3, is implicated in endosomal ion homeostasis and intracellular trafficking.

Purpose of the Study:

• Investigate the pathogenic mechanisms of CLCN4 variants in patients with epilepsy.
• Characterize the functional consequences of identified CLCN4 variants on ClC-4 transport activity.
• Correlate genotype with phenotype in male patients presenting with developmental and epileptic encephalopathy.

Main Methods:

• Patient identification through database review and thorough phenotyping.
• Functional analysis of CLCN4 variants in mammalian cells using patch-clamp electrophysiology.
• Protein biochemistry and confocal fluorescence microscopy to assess variant effects.

Main Results:

• Three male patients with developmental and epileptic encephalopathy and distinct phenotypes were identified.
• The p.(Gly342Arg) variant impaired ClC-4 heterodimerization with ClC-3 and suppressed anion currents.
• The p.(Ile549Leu) and p.(Asp89Asn) variants altered voltage-dependent activation of ClC-4 transport, with p.(Asp89Asn) showing increased activity.

Conclusions:

• CLCN4 variants p.(Gly342Arg) and p.(Ile549Leu) impair ClC-4 transport function, while p.(Asp89Asn) results in gain-of-transport function.
• All three variants lead to epilepsy and global developmental impairment.
• Phenotypic variability, including epilepsy presentation, growth parameters, and brain malformations, is observed among patients with different CLCN4 variants.