Novel ABCA4 mutation leads to loss of a conserved C-terminal motif: implications for predicting pathogenicity based on genetic testing

Potential CRISPR Base Editing Therapeutic Options in a Sorsby Fundus Dystrophy Patient

TIMP3 mutations are associated with early-onset macular choroidal neovascularisation for which no treatment currently exists. CRISPR base editing, with its ability to irreversibly correct point mutations by chemical modification of nucleobases at DNA level, may be a therapeutic option. We report a bioinformatic analysis of potential therapeutic options in a patient presenting with Sorsby fundus dystrophy. Genetic testing in a 35-year-old gentleman with bilateral macular choroidal neovascularisation revealed the patient to be heterozygous for a TIMP3 variant c.610A>T, p.(Ser204Cys). Using a glycosylase base editor (GBE), another DNA-edit could be introduced that would revert the variant back to wild-type on amino acid level. Alternatively, the mutated residue could be changed to another amino acid that would be better tolerated, and for that, an available 'NG'-PAM site was found to be available for the SpCas9-based adenine base editor (ABE) that would introduce p.(Ser204Arg). In silico analyses predicted this variant to be non-pathogenic; however, a bystander edit, p.Ile205Thr, would be introduced. This case report highlights the importance of considering genetic testing in young patients with choroidal neovascularisation, particularly within the context of a strong family history of presumed wet age-related macular degeneration, and describes potential therapeutic options.

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

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.

Functional significance of the conserved C-Terminal VFVNFA motif in the retina-specific ABC transporter, ABCA4, and its role in inherited visual disease

The human retina-specific ATP binding cassette transporter, ABCA4, plays a significant role in the visual cycle. Mutations in the ABCA4 gene result in a broad spectrum of severe, blinding, retinal degenerative diseases, including Stargardt macular dystrophy, fundus flavimaculatus, autosomal recessive (ar)-retinitis pigmentosa, and ar-cone-rod dystrophy. Genetic testing frequently yields novel variants of unknown significance, making accurate prognosis and therapeutic approaches difficult. Recently, we have reported a novel variant of ABCA4 corresponding to a four-nucleotide deletion which led to a premature stop codon and loss of the last 161 amino acids, including the highly-conserved VFVNFA motif. Despite the presence of this motif among other ABCA proteins, knowledge of the functional significance of this sequence remains limited. In this study, we have conducted structural and functional analyses of recombinant ABCA4 polypeptides with altered VFVNFA motifs to evaluate the importance of this sequence. Further investigation of ABCA4 subdomain interactions, using Fluorescence Resonance Energy Transfer, demonstrated a loss of interaction between nucleotide binding domains in the absence of the VFVNFA motif.