We analyzed SNP microarray data from 10,246 control individuals (4,829 male; 5,417 female), for CNVs at PTCHD1 and the upstream region. In a 1.4-Mb region spanning from PTCHD1 to adjacent genes PRDX4 (proximal) and ZNF645 (proximal), we identified 15 CNVs (7 duplications and 8 deletions); however, it is notable that only 1 male control with a deletion was identified, which was 20.6 Kb in length and did not disrupt any known exons of any genes or non-coding RNAs, or any of the identified conserved or putative regulatory sequences. The remaining 7 deletions were all identified among female controls, consistent with the X-linked recessive inheritance observed for the PTCHD1 mutations. Thus, PTCHD1 and upstream deletions were not observed in 4,829 male controls, or in the Database of Genomic Variants (18), which suggests that the CNV directly disrupting PTCHD1 and the 6 CNVs located just upstream in unrelated ASD probands are associated with autism (male ASD cases N=7, out of 1,185; male controls N=0 out of 4,829; Fisher’s exact test: p =1.2×10-5).
