Subnormal cystathionine is usually a nutritional condition that is readily corrected by adequate provision of serine and B-6/P-5-P. If dietary cysteine intake is concomitantly insufficient, there could also be a cysteine deficiency that could be associated with subnormal intracellular glutathione and decreased antioxidant and detoxification (chemical and heavy metal) capacity.

Cystathionine is an intermediary metabolite of the essential amino acid methionine. Cystathionine is preceded by homocysteine, and it leads to cysteine and alpha-ketobutyric acid. Cystathionine formation from homocysteine requires the amino acid serine and vitamin B6 as coenzyme pyridoxal 5-phosphate (P 5-P).

Low cystathionine with normal (or high) methionine and normal homocystine may indicate limited serine but usually indicates increased need for vitamin B6 or pyridoxal phosphate. Depending upon need for and levels of cysteine, cystine and taurine, this problem may or may not have associated symptoms and may only be a transient physiological imbalance. However, if low cystathionine reflects a significant weakness in the activity of its formation enzyme (cystathionine beta-synthase), then clinical abnormalities could be associated with this finding. Pathologies associated with impaired cystathionine beta-synthase include: ectopia lentis, myopia, osteoporosis, scoliosis, CNS disorders, and arterial and venous thromboemboli.

There might be a B6 functional deficit as B6 or P-5-P is required for the conversion of cystathionine to cysteine. Hence low cysteine can result.