To assess the possible involvement of CNVs disrupting X-chromosomal genes in the etiology of ID, we initially screened 246 males with intellectual disability and probable X-linked inheritance using a custom-designed NimbleGen 385K array with probes targeting the X chromosome. A 90 Kb deletion encompassing the entire PTCHD1 gene and 5’ exons of the ncRNAs (but no other known coding genes) was found in a male ID patient (Family 2). The deletion was validated using qPCR revealing that the deletion was maternally inherited in two affected brothers and their affected uncle (Fig. 2). XCI analysis revealed allele ratios of 51:49 and 75:25 from lymphocytes of 2 obligate female carriers.
