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PPT1 mutations are the root cause of several diseases, specifically those where mutations cause a decrease or depletion of PPT1. Infantile neuronal ceroid lipofuscinosis (INCF) is characterized by impaired mental and motor development, including difficulty with walking, speaking, and intellectual function, beginning around the first or second year of life. The PPT1 mutation involved in INCF replaces an arginine with a stop signal in the instructions to make the enzyme. This mutation leads to a vast reduction in the production of PPT1, which impairs the removal of fatty acids from proteins. This impaired removal leads to fatty acid accumulations throughout the body, particularly in neuronal cells in the brain. Late-infantile neuronal ceroid lipofuscinosis has the same characteristics as INCF, but the mutation varies slightly. This leads to a slight reduction in the activity of PPT1 instead of completely wiping it out.   

Mutations can also cause premature stop signals to be added to the instructions to create PPT1, resulting in Kufs disease. This is characterized by seizures, problems with movement, and a decline of intellectual function, usually beginning in early adulthood. Although premature stop signals are added, these mutations allow enough PPT1 to be produced so that the onset is later on in life and the life expectancy is higher.