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

Area of Science:

• Genetics and Molecular Biology
• Rare Diseases
• Biochemistry

Background:

• Pompe disease (PD) is an autosomal recessive disorder caused by deficiency of lysosomal acid alpha-1,4-glucosidase (GAA).
• The mutational spectrum of the GAA gene is expanding, with increasing recognition of splicing-altering synonymous variants.
• Infantile-onset PD (IOPD) presents with severe, progressive neuromuscular deterioration.

Purpose of the Study:

• To molecularly characterize and reclassify a novel synonymous GAA variant in a patient with IOPD.
• To investigate the impact of the synonymous variant on RNA splicing and protein function.
• To highlight the clinical relevance of evaluating synonymous variants in genetic diagnostics.

Main Methods:

• DNA and RNA were extracted from peripheral blood of a female Mexican patient with IOPD.
• Next-generation sequencing identified variants in the GAA gene.
• Sanger sequencing of amplified cDNA assessed splicing alterations, and mRNA analysis identified different isoforms.

Main Results:

• A pathogenic variant (c.1979G>A) and a novel variant of uncertain significance (VUS) (c.2799G>A) in the GAA gene were detected.
• The synonymous variant c.2799G>A was predicted and confirmed to affect RNA splicing, leading to three mRNA isoforms.
• Two novel isoforms resulted from alternative splicing due to c.2799G>A, including a frameshift and an in-frame deletion.

Conclusions:

• The synonymous variant c.2799G>A is pathogenic, demonstrating a significant impact on RNA splicing.
• Transcript analysis is crucial for the reclassification of VUS and accurate genetic diagnosis.
• Evaluating synonymous variants is clinically relevant for Pompe disease diagnostics and patient management.