Pompe disease (glycogen storage disease type II) is an inherited disorder of glycogen metabolism, caused by a deficiency of the enzyme alpha-glucosidase (also called acid-maltase). Pompe disease is a type of lysosomal storage disease. Individuals with Pompe disease are unable to use the glycogen stored in the lysosomes for energy, resulting in the progressive storage of glycogen in the heart, liver, and skeletal muscle. Pompe disease can present in infancy with profound hypotonia, cardiomegaly and cardiomyopathy or later in childhood and adulthood with progressive muscle weakness and respiratory insufficiency. Late onset Pompe disease presenting in the second to seventh decade of life can appear similar to a limb-girdle muscular dystrophy with lower limb proximal weakness.

The alpha-glucosidase enzyme is encoded by the GAA gene. Full gene sequencing will identify two causative mutations in 83-93% of individuals with confirmed reduced or absent enzyme activity. Most mutations are point mutations but deletion of exon 18 accounts for 5-7% of alleles.