From Past to Present: Pompe Disease, Pseudodeficiency Alleles, and Diagnostic Challenges

Pompe disease is an autosomal recessive disorder caused by GAA variants leading to acid alpha-glucosidase deficiency. Diagnosis is challenging due to the variable phenotypic presentation and overlap with other conditions. Traditionally, diagnosis relies on measuring enzyme activity, but next-generation sequencing (NGS) advancements have improved accuracy. However, interpreting variants is complex, especially because pseudodeficiency alleles mimic disease-causing variants. We present two patients harboring the pseudodeficiency allele NM_000152.5( GAA ):c.271G>A, p.Asp91Asn, which is confusing due to inaccurate reports and results related to enzymatic activity. The first case was a recently published controversial case of a 700-year-old mummy in which the authors classified the variant as pathogenic. The second patient had symptoms compatible with late-onset Pompe disease and was homozygous for the variant. We aimed to determine the correct variant classification using GAA :c.271G>A as a model and to achieve a genetic diagnosis of the second patient. This variant was analyzed following international guidelines (ACMG-AMP) and reviewed with the Lysosomal Diseases Variant Curation Expert Panel. The second patient underwent NGS. We demonstrated that GAA :c.271G>A meets the criterion of being classified as benign for Pompe. Additionally, the second patient carried a heterozygous pathogenic PABPN1 variant associated with oculopharyngeal muscular dystrophy, which better explained the clinical features. This underscores the importance of expanding the genetic analysis in the presence of pseudodeficiency alleles that can mask the true cause of the disease and highlights the fact that an accurate diagnosis should adhere to guidelines on variant curation to reduce the risk of misdiagnosis, which could result in inadequate care and risky medical decisions.