Dent Disease 1 Associated with a Rare Novel Renal Chloride Channel 5 Variant in a Chinese Family

Abstract

Dent disease 1, an X-linked recessive proximal tubulopathy most commonly caused by CLCN5 variants, often presents with heterogeneous and nonspecific phenotypes that hinder clinical diagnosis in the absence of molecular data. We investigated a Chinese kindred with suspected hereditary renal disease using whole-exome sequencing and comprehensive in silico analyses and identified a novel frameshift variant in CLCN5 (NM_001127899: c.2359dupG/p.R788Afs*24). Segregation analysis showed the proband to be hemizygous, with his mother and daughter as heterozygous carriers. Pathogenicity prediction, domain mapping against published CLCN5 variants, and literature review indicate that this variant lies within a functionally critical, variant-hotspot region of the protein where truncating variants correlate with classic Dent disease 1 phenotypes. Molecular docking and structural modeling further predict destabilization of the H⁺/Cl⁻ exchange transporter 5 (CLC-5) dimer and reduced adenosine triphosphate (ATP)/adenosine diphosphate (ADP) binding affinity attributable to the frameshift, providing mechanistic plausibility for impaired channel function. Collectively, genetic, bioinformatic, and structural evidence support the p.R788Afs24 mutant as a likely pathogenic allele underlying the proband’s renal phenotype, expanding the variant spectrum of CLCN5 and underscoring the necessity of genetic testing for accurate diagnosis and management of Dent disease 1.