Mild deep-intronic ABCA4 variants explain genetically unsolved cases of very late-onset Stargardt disease

Abstract

Purpose : To describe the phenotypic features, to assess the penetrance, and to investigate the effect on splicing in patient-derived photoreceptor precursor cells (PPCs) of two Stargardt disease (STGD1)-associated intronic ABCA4 variants that were found to show a partial splice defect in vitro.

Methods : Segregation-analysis was performed in 13/15 families carrying c.769-784C>T or c.4253+43G>A. Retrospective ophthalmologic data were assessed of all 15 probands and their affected siblings. The penetrances of c.769-784C>T and c.4253+43G>A were calculated using ABCA4 allele frequency data of one European and two Dutch population databases. Reverse-transcription PCR was performed on mRNA isolated from patient-derived PPCs carrying these variants in a heterozygous manner.

Results : Subjects who harbor c.4253+43G>A or c.769-784C>T mostly manifest late-onset STGD1, with a median age of onset of 52.0 and 54.5 years, respectively. A slowly progressive decline in visual acuity was observed in the majority of the patients, due to the gradual progression of macular atrophy in a foveal sparing pattern. We calculated the penetrances of c.4253+43G>A and c.769-784C>T, in trans with a severe variant, to be reduced to 43.1% and 20.5%, respectively, based on the allele frequencies of these intronic variants in the Dutch population. In patient-derived PPCs, variant c.769-784C>T resulted in partial pseudo-exon insertion, and variant c.4253+43G>A in partial deletion of exon 28.

Conclusions : ABCA4 variants c.4253+43G>A and c.769-784C>T were associated with late-onset, slowly progressive, STGD1 due to mild splice defects. Both variants were calculated to be reduced penetrant when not taking into account the effect of known, and yet unidentified, factors in cis. We hypothesize that several genetic or non-genetic factors influence the expression and the penetrance of these mild variants.

This abstract was presented at the 2019 ARVO Annual Meeting, held in Vancouver, Canada, April 28 - May 2, 2019.