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We investigated the prevalence of reported deep-intronic variants in a French cohort of 70 patients with Stargardt disease harboring a monoallelic pathogenic variant on the exonic regions of <i>ABCA4</i>. Direct Sanger sequencing of selected intronic regions of <i>ABCA4</i> was conducted. Complete phenotypic analysis and correlation with the genotype was performed in case a known intronic pathogenic variant was identified. All other variants found on the analyzed sequences were queried for minor allele frequency and possible pathogenicity by <i>in silico</i> predictions. The second mutated allele was found in 14 (20%) subjects. The three known deep-intronic variants found were c.5196+1137G&gt;A in intron 36 (6 subjects), c.4539+2064C&gt;T in intron 30 (4 subjects) and c.4253+43G&gt;A in intron 28 (4 subjects). Even though the phenotype depends on the compound effect of the biallelic variants, a genotype-phenotype correlation suggests that the c.5196+1137G&gt;A was mostly associated with a mild phenotype and the c.4539+2064C&gt;T with a more severe one. A variable effect was instead associated with the variant c.4253+43G&gt;A. In addition, two novel variants, c.768+508A&gt;G and c.859-245_859-243delinsTGA never associated with Stargardt disease before, were identified and a possible splice defect was predicted <i>in silico</i>. Our study calls for a larger cohort analysis including targeted locus sequencing and 3D protein modeling to better understand phenotype-genotype correlations associated with deep-intronic changes and patients&#8217; selection for clinical trials.