A homemade MLPA assay detects known CTNS mutations and identifies a novel deletion in a previously unresolved cystinosis family

► Cystinosis can be caused by hard-to-detect copy number mutations in CTNS. ► MLPA represents an appropriate tool for unraveling this class of mutations. ► We developed and validated a CTNS-specific MLPA assay. ► Our assay identified a novel CTNS-deletion in a previously unresolved case. ► This deletion, as the first of its kind, does not affect the coding sequence.