Molecular characterization of CTNS deletions in nephropathic cystinosis: Development of a PCR-based detection assay

Nephropathic cystinosis is an autosomal recessive disorder that is characte rized by accumulation of intralysosomal cystine and is caused by a defect i n the transport of cystine across the lysosomal membrane. Using a positiona l cloning strategy, we recently cloned the causative gene, CTNS, and identi fied pathogenic mutations, including deletions, that span the cystinosis lo cus. Two types of deletions were detected-one of 9.5-16 kb, which was seen in a single family, and one of similar to 65 kb, which is the most frequent mutation found in the homozygous state in nearly one-third of cystinotic i ndividuals. We present here characterization of the deletion breakpoints an d demonstrate that, although both deletions occur in regions of repetitive sequences, they are the result of nonhomologous recombination. This type of mechanism suggests that the similar to 65-kb deletion is not a recurrent m utation, and our results confirm that it is identical in all patients. Hapl otype analysis shows that this large deletion is due to a founder effect th at occurred in a white individual and that probably arose in the middle of the first millenium. We also describe a rapid PCR-based assay that will acc urately detect both homozygous and heterozygous deletions, and we use it to show that the similar to 65-kb deletion is present in either the homozygou s or the heterozygous state in 76% of cystinotic patients of European origi n.