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Detecting pathogenic deep intronic variants in Gitelman syndrome.

Rini Rossanti^1,2, Tomoko Horinouchi¹, Nana Sakakibara¹

¹Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.

American Journal of Medical Genetics. Part A

|July 5, 2022

Summary

Gitelman syndrome (GS) genetic testing often reveals one mutated SLC12A3 allele. Deep intronic variant screening identified a pathogenic variant in intron 4, partially explaining these cases.

Keywords:

GS deep intronic variant minigene assay

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Area of Science:

Genetics
Molecular Biology
Nephrology

Background:

Gitelman syndrome (GS) is a rare salt-losing tubulopathy.
It is typically caused by biallelic loss-of-function variants in the SLC12A3 gene.
However, a significant percentage of GS patients present with only one identified SLC12A3 variant.

Purpose of the Study:

To investigate the role of deep intronic variants in SLC12A3.
To screen for pathogenic deep intronic variants in patients with suspected GS and monoallelic SLC12A3 mutations.

Main Methods:

Screening of SLC12A3 deep intronic regions and promoter in 13 patients with suspected GS and one mutated allele.
Utilized HaloPlex Target Enrichment System for whole intron and promoter capture.
Variant analysis with SureCall and pathogenicity assessment using a minigene system.

Main Results:

Seven rare SLC12A3 intronic variants were identified in six patients.
One pathogenic variant (c.602-16G>A, intron 4) was detected, activating a cryptic acceptor site.
No pathogenic variants were found in the promoter region.

Conclusions:

Deep intronic variant screening identified a pathogenic variant in a subset of GS patients with monoallelic SLC12A3 mutations.
Deep intronic variants partially explain the genetic basis of Gitelman syndrome in patients with only one identified mutated allele.