Identification and detection of the common 65-kb deletion breakpoint in the nephropathic cystinosis gene (CTNS)

The most common mutation in the cystinosis gene, CTNS, is a 65-kb deletion thought to have originated in Germany. Although homozygotes for this deleti on are detectable by the absence of the D17S829 polymorphic marker, no meth od exists to identify heterozygotes. We identified the 65-kb deletion break points and used flanking PCR primers to amplify a 423-bp fragment present o nly in the deletion alleles. Using this method, we determined that 121 of 2 16 (56%) cystinosis alleles examined bore the 65-kb deletion. We found no n on-Europeans with the deletion, and the deletion size and breakpoints appea red identical in all patients studied, supporting the concept of a founder effect. The addition of D17S829 primers (266 bp apart) to the PCR created a multiplex PCR system useful for diagnosing cystinosis patients homozygous and heterozygous for the 65-kb deletion.