Glycogen branching enzyme leads to increased osmotic pressure resulting in cellular swelling and death. The tissues most affected by this disease are the liver, heart, and neuromuscular system, areas with the greatest levels of glycogen accumulation. Abnormal glycogen buildup in the liver interferes with liver functioning and can result in an enlarged liver and liver disease. In muscles, the inability of cells to efficiently breakdown glycogen due to the severe reduction or absence of branching can lead to muscle weakness and atrophy. At least three mutations in the GBE1 gene have been found to cause another disease called adult polyglucosan body disease (APBD).
Glucose 6-phosphate an allosteric activator of glycogen synthase, which makes sense because when the level of glucose is high the body should store the excess glucose as glycogen. On the other hand, glycogen synthase is inhibited when it is phosphorylated by protein kinase during times of high stress or low levels of blood glucose, via hormone induction by glucagon or adrenaline. When the body needs glucose for energy, glycogen phosphorylase, with the help of an orthophosphate, can cleave away a molecule from the glycogen chain. The cleaved molecule is in the form of glucose-1-phosphate, which can be converted into G6P by phosphoglucomutase.