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Birth prevalence is estimated at around 1/250,000 to 1/1,000,000 in most ethnic groups. The condition is more common in Slovakia and the Dominican republic where it affects up to 1 in 19,000 newborns.

Many affected individuals are asymptomatic and unaware of their condition until adulthood, however, homogentisic aciduria may be recognized early in infancy by dark-stained diapers. After the third decade, unusual pigmentation of the sclera and the skin overlying cartilage begins to be observed, as well as muscular-skeletal symptoms such as back pain and stiffness. Involvement of the large peripheral joints usually occurs several years after spinal changes, often leading to end-stage joint disease. Ochronotic peripheral arthropathy is generally degenerative in nature. From the fourth decade, joint mobility diminishes. Ankylosis may be present. Fractures of the vertebrae and long bones are also possible. Other features may include genitourinary (e.g. renal, bladder, prostatic stones) and cardiac (mitral valvulitis, arrhythmias) complications as well as respiratory insufficiency due to musculoskeletal involvement.

Patients are homozygous or compound heterozygous for loss-of-function mutations (more than 200 different variants described worldwide) in the HGD gene, encoding homogentisate 1,2-dioxygenase, an enzyme of the phenylalanine and tyrosine catabolic pathway. The inability to break down HGA leads to its accumulation. Tissue damage results from the deposition of a melanin-like pigment, which is a polymerized form of BQA, that has a high affinity for connective tissue. This pigment is able to trigger numerous redox reactions and induce free radical production, causing further damage to the connective tissue.

Diagnosis is suspected upon clinical examination and is based on the amount of HGA found in the urine using gas chromatography-mass spectroscopy. As many patients present without dark urine, it may be advisable to look for HGA in all patients with radiographic evidence of osteoarthritis. A spinal x-ray will reveal disk degeneration combined with dense calcification, particularly in the lumbar area. Genetic testing confirms the diagnosis.

Differential diagnosis includes acute intermittent porphyria, rheumatoid arthritis, ankylosing spondylitis and osteoarthritis.

Transmission is autosomal recessive, there is a 25% risk of disease transmission to offspring where both parents are unaffected carriers.

Treatment is palliative. Dietary restriction (low protein diet) is beneficial, but compliance is often limited. Medical therapy (paracetamol, non-steroidal anti-inflammatory drugs) associated with physiotherapy help to minimize pain and improve the range of joint motion. Older individuals may require removal and fusion of lumbar discs. Hip or knee joint replacement may be necessary. Therapeutic strategies aimed at perturbing the altered phenylalanine-tyrosine pathway have been devised (e.g. nitisinone). Off-label usage of nitisinone has been shown to slow the rate of disease progression; however, the long-term effectiveness and safety in adult patients with alkaptonuria, as well as the most suitable age for intervention, remains to be evaluated (currently an open-label clinical trial and observation study are under way).

Life expectancy is not significantly reduced but pain can be constant and progressive functional decline is observed with a loss of mobility; patients often require the use of physical aids (crutches, wheelchair). Cardiac complications are often life-threatening and may worsen the prognosis.