Intronic variants impacting SLC12A1 gene splicing in Bartter syndrome type 1: Characterization of a novel deep intronic variant via Whole-genome sequencing and minigene analysis

Abstract

Background: Bartter syndrome type 1 (BS1) is a rare autosomal recessive disorder characterized by renal salt wasting, hypokalemia, metabolic alkalosis, and hyperreninemic hyperaldosteronism. Variants in the SLC12A1 gene, which encodes the Na-K-2Cl cotransporter NKCC2, are responsible for this condition.

Methods: To investigate the genetic underpinnings of BS1 in an index case with clinical features indicative of the disease, we performed whole-exome sequencing (WES), followed by whole-genome sequencing (WGS) to identify potential causative variants. Functional characterization of a novel deep intronic variant was achieved through minigene analysis to assess its impact on pre-mRNA splicing.

Results: WES identified a heterozygous missense variant (c.1391G > T, p.Gly464Val) in the SLC12A1 gene. Subsequent WGS uncovered a second, previously unreported deep intronic variant (c.629-527 T > C). Minigene assays revealed that the c.629-527 T > C variant altered splicing patterns, resulting in two mRNA isoforms: one with aberrant retention of intron 4 causing a frameshift mutation leading to premature termination codon (p.Leu214IlefsTer31), and another indistinguishable from wild-type splicing. This compound heterozygosity provided molecular confirmation of BS1 diagnosis.

Conclusion: Our study characterizes a novel intronic variant impacting SLC12A1 gene splicing in BS1, expanding the mutational spectrum of this gene. The findings underscore the utility of integrating genomic sequencing with functional assays for precise diagnosis and personalized medical management.

Keywords: Bartter syndrome type 1; Minigene assay; SLC12A1 gene; Whole-genome sequencing.