SLC12A1 variant c.1684+1 G>A causes Bartter syndrome type 1 by promoting exon 13 skipping

BackgroundBartter syndrome type 1, an autosomal recessive genetic disorder, is caused by pathogenic loss‐of‐function variants in the SLC12A1 gene. It is characterized by metabolic alkalosis and prenatal‐onset polyuria leading to polyhydramnios.MethodsWe identified pathogenic gene in a 12‐day‐old newborn boy with Bartter syndrome type 1 using whole‐exome sequencing. Sanger sequencing validated the identified variants. A minigene assay was performed to investigate the effect of a novel splice site variant on pre‐mRNA splicing.ResultsWe found a compound heterozygous variants in the SLC12A1 gene, consisting of a known pathogenic missense mutation (NM_000338: c.769 G>A; p.Gly257Ser) and a novel splice site variant (c.1684+1 G>A). In silico predictions and an in vitro minigene splicing assay demonstrated that the splicing variant c.1684+1 G>A abolished a consensus splice donor site of SLC12A1 intron 13, resulting in complete exon 13 skipping, translational frameshift, and premature termination codon, ultimately leading to loss of SLC12A1 function.ConclusionUsing a cell‐based in vitro assay, we revealed the aberrant effect of the pathogenic splicing variant SLC12A1 c.1684+1 G>A on pre‐mRNA splicing. Our findings expand the gene mutation spectrum of Bartter syndrome type 1, providing a basis for genetic diagnosis and the development of genetic medicines.image