The dataset allows direct characterization of the pattern of haplotypic coding sequence variation of individual X chromosomes. Although ascertained from individuals with XLMR, only a small fraction of the observed variants is likely to cause mental retardation and, therefore, the set predominantly represents background population variation. Of the 1,769 coding sequence variants from the X-specific part of the X chromosome, 914 were nonrecurrent (that is, observed in only one XLMR-affected family) and 855 were recurrent (observed in multiple XLMR-affected families, Table 2). We identified 63% of the recurrent and 16% of the nonrecurrent variants in the dbSNP database. The sequences of any two individuals differed on average by 109 variants. Of these, six were nonrecurrent, including four missense and two synonymous variants, and 103 were recurrent, including 40 missense, 60 synonymous and two in-frame insertions/deletions. The results illustrate that most coding sequence differences between individuals are recurrent (‘common’) variants despite the existence of a larger number of different nonrecurrent (‘rare’) variants.
