Long-Read Sequencing Identifies Novel Pathogenic Intronic Variants in Gitelman Syndrome

Area of Science:

• Genetics
• Molecular Biology
• Renal Physiology

Background:

• Gitelman syndrome is a salt-losing tubulopathy.
• It is caused by variants in SLC12A3, encoding the Na+-Cl- cotransporter (NCC).
• Genetic diagnosis remains incomplete in up to 10% of patients.

Purpose of the Study:

• To identify a second pathogenic variant in introns, splice sites, or promoters of SLC12A3.
• To increase the diagnostic yield for Gitelman syndrome.

Main Methods:

• Long-read sequencing of SLC12A3 in 95 individuals with suspected Gitelman syndrome.
• Midigene splice assays to assess pathogenicity of intronic variants.

Main Results:

• A second likely pathogenic/pathogenic variant was found in 67% of patients.
• Intronic variants, including deep intronic and novel ones, were identified.
• Aberrant splicing patterns were confirmed for intronic variants.

Conclusions:

• Intronic pathogenic variants contribute significantly to the missing heritability in Gitelman syndrome.
• Long-read sequencing should be integrated into diagnostic workflows for Gitelman syndrome.