Gene-based association, performed using the VEGAS2 algorithm, tested the significance of 17,322 genes (Bonferroni threshold P < 2.89 × 10−6) (see Additional file 5). No gene-level associations were significant after Bonferroni correction. The minimum P value achieved, P = 7 × 10−6, was for 3 genes from chromosome 6p21.1 (ENPP4, ENPP5, and CLIC5) and was driven by association of rs7762549, the 4th ranked association interval. To the best of our knowledge, none of these genes have previously been implicated in ASD or ASD-related traits.
