In addition, we have found another 11deletions that map to regions upstream of PTCHD1. The region 5’ and distal to PTCHD1 is relatively gene poor. Within this upstream region, a coding gene, DDX53, encoding DEAD Box 53, lies ~335 Kb 5’ to PTCHD1. Five of the 11 upstream deletions span DDX53. However, based on the function of DDX53 protein and the expression pattern of this gene (which is restricted mainly to testis and tumor cells (21)), it is unlikely to contribute to the ASD or ID phenotype. Additionally, within the gene-poor region between PTCHD1 and DDX53, there is a putative pseudogene of FAM3C, FAM3C2, which is disrupted by five of the 10 upstream deletions. FAM3C, a cytokine-like gene on 7q31.31, consists of 10 exons (22) whereas FAM3C2, although 99% identical, has no intron/exon structure and is interrupted by a short interspersed nuclear element (SINE). It appears to have inserted on Xp22 after human/chimp evolutionary divergence. Since no mRNA or EST matches exactly to FAM3C2, it is most likely an untranscribed processed pseudogene.
