Phenotype–genotype correlations in a pseudodominant Stargardt disease pedigree due to a novel ABCA4 deletion–insertion variant causing a splicing defect

• Main Authors: Di Huang, Jennifer A. Thompson, Jason Charng, Enid Chelva, Samuel McLenachan, Shang‐Chih Chen, Dan Zhang, Terri L. McLaren, Tina M. Lamey, Ian J. Constable, John N. De Roach, May Thandar Aung‐Htut, Abbie Adams, Sue Fletcher, Steve D. Wilton, Fred K. Chen
• Format: Article
• Language: English
• Published: Wiley 2020-07-01
• Series: Molecular Genetics & Genomic Medicine
• Subjects: ATP‐binding cassette subfamily A member 4 (ABCA4); genotype‐phenotype correlations; pseudodominant inheritance; splicing defect; variant pathogenicity
• Online Access: https://doi.org/10.1002/mgg3.1259

Abstract Background Deletion–insertion (delins) variants in the retina‐specific ATP‐binding cassette transporter gene, subfamily A, member 4 (ABCA4) accounts for <1% in Stargardt disease. The consequences of these delins variants on splicing cannot be predicted with certainty without supporting in vitro data. Methods Candidate ABCA4 variants were revealed by genetic and segregation analysis of a family with pseudodominant Stargardt disease using a commercial panel and Sanger sequencing. RNA extracted from patient‐derived fibroblasts was analyzed by RT‐PCR to evaluate splicing behavior of the ABCA4 variants. Results Affected members carrying the novel c.6031_6044delinsAGTATTTAACCAATATTT variant in exon 44 presented with contrasting phenotypes; from early‐onset cone‐rod dystrophy to late‐onset macular dystrophy. This variant resulted in a 56‐nucleotide deletion in the mutant allele by activation of a cryptic splice acceptor site which disrupts the reading frame and results in a premature termination codon (p.Ile2003LeufsTer41). If translated, the crucial functional domains near the C‐terminus would be truncated from the ABCA4 protein. Conclusion This work demonstrates the intrafamilial phenotypic variability in a pseudodominant Stargardt disease pedigree and the use of patient‐derived fibroblasts to evaluate the effect of a novel ABCA4 delins variant on splicing to complement in silico pathogenicity assessment.