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Homocystinuria (HCU) is an inherited disorder of amino acid metabolism, caused by an enzymatic defect in a metabolic pathway that leads to increased levels of methionine.
Cystinuria is a genetic kidney defect. Since normal urine does not contain cystine, the presence of cystine in the urine tells you the dog has cystinuria. The only exception would be if the dog was on certain antibiotics at the time of the test. Other than that, a urine test that is positive for cystine means your dog has cystinuria.