Prevalence of ABCA4 Deep-Intronic Variants and Related Phenotype in An Unsolved “One-Hit” Cohort with Stargardt Disease

Abstract

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 ABCA4. Direct Sanger sequencing of selected intronic regions of ABCA4 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 in silico predictions. The second mutated allele was found in 14 (20%) subjects. The three known deep-intronic variants found were c.5196+1137G>A in intron 36 (6 subjects), c.4539+2064C>T in intron 30 (4 subjects) and c.4253+43G>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>A was mostly associated with a mild phenotype and the c.4539+2064C>T with a more severe one. A variable effect was instead associated with the variant c.4253+43G>A. In addition, two novel variants, c.768+508A>G and c.859-245_859-243delinsTGA never associated with Stargardt disease before, were identified and a possible splice defect was predicted in silico. 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’ selection for clinical trials.

Detailed Phenotyping and Therapeutic Strategies for Intronic ABCA4 Variants in Stargardt Disease

“…In addition, a recent study on deep-intronic ABCA4 variants in a French cohort also concluded that the c.5196+1137G>A variant was mostly associated with a milder phenotype, based on six subjects harboring this allele. 32 It should also be noted, however, that evidence is emerging that some variants that were long considered pathogenic or benign by themselves, such as c.2588G>C; p.[G863A,G863del] and c.5603A>T; p.(N1868I), are fully penetrant only when in combination on the same allele. The same is true for the cis configuration of p.(N1868I) with a recently identified intronic mutation, c.769-784C>T. 9 , 33 , 34 In addition, modifier variants, either within or outside of ABCA4 , as well as environmental factors will likely play a role in determining disease outcome.…”

Increasing the Genetic Diagnosis Yield in Inherited Retinal Dystrophies: Assigning Pathogenicity to Novel Non-canonical Splice Site Variants

“…A step further in genetic diagnosis has been attained when deep-intronic variants that alter the splicing pattern have been identified, as is the case in Stargardt disease, a macular disorder with a very well defined clinical phenotype and a major causative gene, ABCA4. In fact, the introduction of the whole ABCA4 locus in the target NGS panels clearly helps to increase the genetic yield in Stargardt disease patients [16,17].…”

Clinical spectrum, genetic complexity and therapeutic approaches for retinal disease caused by ABCA4 mutations

“…There is a clustering of different deep-intronic variants in introns 7 (n = 4), 13 (n = 4), 30 (n = 6) and 36 (n = 4). The total number of alleles carrying deep-intronic and near-exon variants is 355 ( Table 4 ) ( Bauwens et al, 2015 ; Bauwens et al, 2019 ; Bax et al, 2015 ; Braun et al, 2013 ; Khan et al (2020) ; Khan et al, 2019 ; Nassisi et al, 2019 ; Sangermano et al., 2019 ; Schulz et al, 2017 ; Zernant et al, 2018 ; Zernant et al, 2014b ). Only seven variants were found in more than 10 alleles, i.e.…”