Genomic copy number variation (CNV) in the human population is a well-documented source of genetic variation covering at least 10-12% of the genome. Here we identify a new CNV of ~90kb at chromosome 10p12.1 encompassing the PTCHD3 gene. This CNV was originally detected as deletion in a number of patients diagnosed with Autism Spectrum Disorder. However, further investigations demonstrate that the CNV is likely not disease-associated but instead a rare variant mainly in Caucasian populations appearing at frequency of ~0.5-1%. The deletion is mainly heterozygous, although homozygous deletions at this locus appear to be tolerated without obvious phenotypic effect. The presence of apparently healthy individuals null for PTCHD3 suggests it may be a non-essential human gene, a somewhat surprising observation given its high evolutionary conservation amongst divergent species. The human PTCHD3 gene is composed of four exons covering ~16kb of genomic DNA with an mRNA transcript of ~2.4kb in size. The protein product is 767 amino acids in length with a 595 residue patched domain that is highly conserved in vertebrates. Based on its amino acid composition and similarity comparisons, it is modelled as a transmembrane protein with hedgehog receptor activity. Our work reveals the gene is expressed as at least two mRNA splice variants. A longer isoform of ~2.4kb and a shorter variant of ~1.6kb are expressed in many tissues as demonstrated by multiple tissue northern blotting. The shorter isoform is the result of truncation of the last exon (exon 4) of the full length isoform. This shorter isoform codes for a protein consisting of 533 amino acids that shares its first 510 amino acids with the longer isoform. The 5'-UTR of PTCHD3 (common to both isoforms) is relatively short and consists of ~300bp, as demonstrated by RACE. Although predicted to be ~87kDa, the full length PTCHD3 runs at ~120kDa, demonstrated by SDS-PAGE. Immunostaining of COS-7, expressing this protein from a plasmid vector, suggests that it may be localised to the endoplasmic reticulum. Further investigations on the cloning and expression of shorter isoform are also being conducted amongst other experiments to characterise the functional role of this interesting human gene.

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