As a further strategy to identify missense variants causing mental retardation, we investigated the number of variants in each gene. Genes that show more amino acid variation in a human population than expected from their rate of evolution are identifiable by the McDonald-Kreitman test24. Application of this test to a random population sample identifies positively selected genes. Application to X-chromosome genes in a sample ascertained for XLMR, however, would be expected to identify both positively selected genes and those with excess missense variants that cause mental retardation. We restricted application of the McDonald-Kreitman test to nonrecurrent variants, as recurrent variants are less likely to be implicated in mental retardation. The results highlighted ZFX (P = 0.0014) and G6PD (P = 0.008), both of which have previously been identified as strong candidates for recent positive selection25,26. It also highlighted, however, four known genes involved in XLMR at similar levels of significance: HUWE1 (P = 0.007), OPHN1 (P = 0.001), MED12 (0.004) and PGK1 (P = 0.002). As these genes do not show evidence of recent positive selection25, their excess variation may
