Molecular characterization of a novel synonymous variant in a Mexican patient with Pompe disease

Introduction

Pompe disease (PD) is an autosomal recessive disorder caused by a deficiency of lysosomal acid alpha-1,4-glucosidase (GAA; EC 3.2.1.20), encoded by the GAA gene, leading to progressive neuromuscular deterioration. The mutational spectrum of GAA is expanding, particularly with recognition of splicing-impacting synonymous variants. Here, we report the molecular characterization and reclassification of a novel synonymous GAA variant in a female Mexican patient with enzymatically confirmed infantile-onset PD (IOPD).

Methods

DNA and RNA were extracted from peripheral blood. Next-generation sequencing of a clinical exome panel identified variants in the GAA gene. The whole coding sequence of the GAA was amplified from cDNA, subcloned, and analyzed by Sanger sequencing to assess splicing alterations.

Results

The pathogenic variant c.1979G > A (p.Arg660His) and a novel VUS c.2799G > A (p.Lys933=) were detected. The variant c.2799G > A is predicted to affect splicing. mRNA analysis revealed three isoforms, one corresponding to c.1979G > A and two others caused by alternative splicing of c.2799G > A (isoforms 1 and 2). The isoform-1 showed c.2799G > A, followed by 61 bp retention of intron 19, predicted to cause a frameshift p.(A934fs). Isoform 2 has a 90 bp deletion in exon 19, resulting in a p.V904_K933del in-frame deletion.

Discussion

This study demonstrates that the synonymous variant c.2799G > A is pathogenic due to its impact on RNA splicing. Our findings highlight the importance of transcript analysis for VUS reclassification and stress the clinical relevance of evaluating synonymous variants in genetic diagnostics and patient management.