Identification of a novel CLCN2 homozygous variant in a man with leukoencephalopathy and infertility: a case report and literature review

TL;DR

A new CLCN2 gene variant was found in a man with brain and fertility issues, offering insights into a rare disorder.

Contribution

A novel biallelic CLCN2 variant, p.A506V, is identified and its impact on ClC-2 function is analyzed.

Findings

The A506V variant disrupts hydrogen bonds at chloride-binding sites in ClC-2.

The variant affects ClC-2 interaction with GlialCAM, altering its function in glial cells.

The study expands the known genetic spectrum of CLCN2-related leukoencephalopathy.

Abstract

Leukoencephalopathy with ataxia (LKPAT), also known as CLCN2-related leukoencephalopathy, is a rare autosomal recessive disorder caused by pathogenic variants in CLCN2, which encodes ClC-2, a ubiquitously expressed chloride channel protein. However, due to high variability in clinical presentation leading to underdiagnosis, very few cases have been reported since its first description in 2013. The prevalence and genotype–phenotype correlations of LKPAT remain unclear, as do the pathogenic mechanisms of CLCN2 variants. In this study, we reported a Chinese man who presented with dizziness, weakness of the left lower limb, and mild cerebellar ataxia. Notably, the patient had a history of azoospermia. Brain MRI showed symmetrical and confluent white matter abnormalities with hypointense signals on T1-weighted images and hyperintense signals on T2-weighted images. In this patient, a novel biallelic missense variant p.A506V was identified in CLCN2. Through in silico analysis, we observed that substitution of A506 with V506 altered hydrogen bond formation at chloride-binding sites. In addition, the A506V variant impacted the interaction of ClC-2 with GlialCAM, a ClC-2 auxiliary subunit that can physically bind ClC-2 and regulate its biophysical properties and subcellular localization in glial cells. Furthermore, we reviewed the literature and identified potential genotype–phenotype correlations in CLCN2-related diseases. Our results highlight the need for CLCN2 genetic analysis to establish a definitive diagnosis when strong diagnostic clues are present. This study expands the genotypic spectrum of LKPAT, indicates the potential pathogenesis of the CLCN2 A506V variant, and provides valuable insights into further investigation into therapeutics of CLCN2-related leukoencephalopathy.

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