We have compared the substitution pattern of the glucocerebrosidase gene (GBA) 
and the glucocerebrosidase pseudogene (psGBA), two highly homologous regions 
under different selective pressures and within the same genomic background. 
Mutations in GBA may lead to Gaucher disease, an inborn metabolic disorder. 
Disease-causing mutations and neutral variation in the gene have been compared 
to neutral variation in the pseudogene. This comparison offers a unique 
opportunity to better understand the action of purifying selection, since the 
differences between mutational patterns can be attributed to different selective 
pressures. A similar frequency of CpG dinucleotides was observed in GBA and in 
psGBA, and CpG pairs were mutated with the same high frequency in both regions. 
However, nucleotides not in CpG pairs were more likely to contribute to 
disease-causing mutation than to accepted polymorphisms. This pattern, which 
resulted in a lower transition to transversion ratio in the gene, may be due to 
CpG avoidance on critical regions within exons.