GAA and glycogen storage disease II: The presence of large glycogen-filled lysosomes and massive autophagic buildup in muscles are hallmarks of GSDII.12, 13 Complete GAA deficiency causes the severe form of GSDII with infantile onset (Pompe disease), whereas partial enzyme defects induce late-onset milder forms of the disease, that are mainly characterized by progressive skeletal muscle weakness, while cardiac muscle is spared.