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Historical aspects of a local cluster of individuals with lysinuric protein intolerance (LPI) were studied in a sample of patients and in a massscreened population in a northern area of Japan. The historical aspects were investigated by estimating the mutation age and analyses of haplotype diversity of the chromosome carrying the R410X mutation. This mutation occurred over 1000 years ago, and its fixation in the local cluster suggests that LPI had been a nearly neutral phenotype. The present results also give an estimate of the geographical distribution of the R410X mutation, providing a basis for targeting populations for mass screening for LPI.