Hematuria: This condition, characterized by the presence of blood in the urine, can cause urine discoloration without necessarily affecting liver function tests (LFTs). The blood can come from anywhere in the urinary tract, including the kidneys, ureters, bladder, or urethra.

Myoglobinuria: This condition occurs when myoglobin, a protein found in muscles, is present in the urine, often due to muscle injury (rhabdomyolysis). It can cause urine discoloration, typically brown or tea-colored, without abnormal LFTs.
Bilirubinuria: Although less common, if there's a significant increase in unconjugated bilirubin, it might not be reflected in LFTs as abnormal but could potentially discolor urine.
Medication or Food-Induced Urine Discoloration: Certain medications (like rifampicin) or foods (beets, rhubarb) can change the color of urine without affecting liver function.

Alkaptonuria: A rare genetic disorder that leads to the accumulation of homogentisic acid in the body, which can cause urine to turn dark or black upon standing. Although rare, missing this diagnosis could lead to significant morbidity due to the associated arthritis and other systemic complications.
Porphyrias: A group of disorders that can lead to the accumulation of porphyrins, which may cause urine discoloration. Some forms of porphyria can have severe neurological and abdominal manifestations, making them critical not to miss.

Melanuria: The presence of melanin in the urine, which could be due to melanoma or other conditions affecting melanin production. This is extremely rare and usually associated with other significant clinical findings.
Pseudomelanosis: Certain conditions or substances can mimic melanin in the urine, causing discoloration. This is more of a curiosity and rarely of clinical significance.