Variants inABCA4are responsible for autosomal-recessive Stargardt disease and cone-rod dystrophy. Sequence analysis ofABCA4exons previously revealed one causative variant in each of 45 probands. To identify the “missing” variants in these cases, we performed multiplex ligation-dependent probe amplification-based deletion scanning ofABCA4. In addition, we sequenced the promoter region, fragments containing five deep-intronic splice variants, and 15 deep-intronic regions containing weak splice sites. Heterozygous deletions spanningABCA4exon 5 or exons 20–22 were found in two probands, heterozygous deep-intronic variants were identified in six probands, and a deep-intronic variant was found together with an exon 20–22 deletion in one proband. Based on ophthalmologic findings and characteristics of the identified exonic variants present intrans, the deep-intronic variants V1 and V4 were predicted to be relatively mild and severe, respectively. These findings are important for proper genetic counseling and for the development of variant-specific therapies.
A person with Stargardt disease (STGD1) carries a deletion of exons 20-22 in one of two ABCA4 gene copies and a deep-intronic mutation (c.5196+1137G>A) in the other copy. Both types of mutations cannot be identified using standard Sanger sequencing of the protein coding segments of the gene and require specific analyses. Deletions and deep-intronic variants in ABCA4 can constitute up to 20% of ABCA4 mutations.