Vitamin D deficiency: This condition can lead to low alkaline phosphatase levels due to decreased bone turnover. Although AST and ALT are liver enzymes, their levels can be influenced by overall metabolic health, which might be indirectly affected by vitamin D status.

Hypothyroidism: This condition can affect liver enzyme production and bone metabolism, potentially leading to low levels of these enzymes.
Malnutrition or starvation: Prolonged malnutrition can lead to decreased production of enzymes, including AST, ALT, and alkaline phosphatase, due to the lack of necessary substrates and building blocks for enzyme synthesis.
Chronic kidney disease: Advanced kidney disease can lead to alterations in vitamin D metabolism, affecting bone health and potentially leading to low alkaline phosphatase levels. It may also influence liver function indirectly.

Wilson's Disease: Although it typically presents with elevated liver enzymes due to liver damage, in its early stages or with certain presentations, enzyme levels might not be elevated. It's crucial to consider this diagnosis due to its potential for severe liver damage and the importance of early treatment.
Hemochromatosis: This genetic disorder leads to iron overload, which can cause liver damage. Early in the disease, liver enzymes might not be elevated, making it a "do not miss" diagnosis due to its potential for severe complications if untreated.

Osteogenesis imperfecta: A genetic disorder affecting bone health, potentially leading to low alkaline phosphatase levels due to impaired bone turnover. Its impact on liver enzymes is less direct but could be considered in the context of overall metabolic health.
Certain genetic disorders affecting enzyme production: Rare genetic conditions can directly impact the production or function of AST, ALT, and alkaline phosphatase, leading to their low levels. These would be considered based on additional clinical findings and family history.