Alpha-oxidation of phytanic acid is believed to take place entirely within peroxisomes.
(Propionyl-CoA is released as a result of beta oxidation when the beta carbon is substituted)
Enzymatic deficiency in alpha-oxidation (most frequently in phytanoyl-CoA dioxygenase) leads to Refsum's disease, in which the accumulation of phytanic acid and its derivatives leads to neurological damage. Other disorders of peroxisome biogenesis also prevent alpha-oxidation from occurring.