Vitamin D deficiency: This is the most straightforward explanation, as low vitamin D can lead to decreased calcium absorption from the gut, resulting in low calcium levels. Low alkaline phosphatase can be seen in severe vitamin D deficiency due to its role in bone mineralization.

Malabsorption: Conditions like celiac disease, Crohn's disease, or pancreatic insufficiency can lead to malabsorption of fat-soluble vitamins, including vitamin D, and calcium. This would explain the low levels of both calcium and vitamin D. Alkaline phosphatase might be low due to the lack of substrate for bone mineralization.
Chronic kidney disease (CKD): CKD can lead to impaired activation of vitamin D, resulting in low active vitamin D levels, which in turn causes low calcium absorption. Alkaline phosphatase can be low in early stages of CKD due to impaired bone turnover.

Hypoparathyroidism: Although less common, hypoparathyroidism can cause low calcium levels. Vitamin D levels might be low due to secondary effects on bone health and mineralization. Alkaline phosphatase can be low in the context of decreased bone turnover.
Osteomalacia: A condition characterized by softening of the bones due to impaired bone mineralization. It can present with low calcium, low vitamin D, and low alkaline phosphatase, especially in the early stages or in cases of malabsorption.

Pseudohypoparathyroidism: A rare genetic disorder characterized by resistance to parathyroid hormone (PTH), which can lead to low calcium levels. Vitamin D levels might be affected indirectly, and alkaline phosphatase can be low due to the underlying metabolic bone disease.
Phosphate deficiency: Although phosphate levels are not directly mentioned, a severe phosphate deficiency can lead to low alkaline phosphatase and indirectly affect calcium and vitamin D metabolism, particularly in the context of malnutrition or specific genetic disorders.