While most glycogen is cytosolic, glycogen granules are also found in lysosomes, which they are thought to enter by autophagy. Once in lysosomes, the polysaccharide component of the granules is degraded by a single enzyme, lysosomal alpha-glucosidase (GAA), which hydrolyzes both alpha(1,4) and alpha(1,6) linkages to yield free glucose (Brown et al. 1970). The fate of the glycogenin protein component of the granules has not been studied; it is thought to be degraded by the diverse lysosomal proteases (Muller et al. 2012).
Mutations that reduce the activity of GAA are associated with glycogen storage disease type II (Pompe disease) (Leslie & Tinkle).