Exploring the role of putative cis-regulatory variants within the 5’UTR of the ABCA4 gene in ~6,900 cases with inherited retinal disease

Abstract

Purpose : ABCA4-retinopathy (including Stargardt, STGD1) is by far the most common single-gene inherited retinal disease (IRD). Although a plethora of pathogenic coding and an increasing number of noncoding splicing ABCA4 variants are known, a significant fraction of STGD1 cases remains genetically unexplained. It is becoming clear that noncoding variants in ABCA4 represent an emerging source of missing heritability in STGD1. Here we explored one of such regions, the 5’ untranslated region (5’UTR) of ABCA4 in IRD cohorts, in search of rare potentially pathogenic cis-regulatory variants.

Methods : Data derived from ~6,900 IRD probands from three cohorts – (i) ERDC4000, a targeted IRD gene sequencing project of the European Retinal Disease Consortium (n=3,200), (ii) ABCA4 locus (re)sequencing of STGD1 cases (n=1,054), and (iii) WGS data from a Genomics England IRD cohort (n=2,615), were mined to search for 5’UTR variants of ABCA4. Candidate variants were evaluated for potential effects on gene regulation by means of computational tools and interrogation of retina-derived epigenomic datasets.

Results : We identified eight rare (MAF < 0.001) ABCA4 5’UTR variants, three of which are ultra-rare (absent from public databases). All variants were heterozygous and found in IRD cases for which an ABCA4-associated disease was suspected, 4 of which are monoallelic for ABCA4 variants. Most variants were predicted to significantly disrupt secondary structure formation and/or affect motifs representing retina-specific transcription factor binding. Furthermore, two variants were found to create an upstream open reading frame in a favorable Kozak sequence context. Validation and segregation analysis of these alleles, and luciferase assays to assess their functional activity are ongoing.

Conclusions : Although often under-recognized, 5’UTR variants are known to influence post-transcriptional and translational regulation. Thus far, no (likely) pathogenic cis-regulatory variants within the 5’UTR of ABCA4 have been reported. Here we present a comprehensive analysis of the ABCA4 5’UTR in ~6,900 IRD cases. Exploring the functional consequences of these eight rare and other putative regulatory noncoding ABCA4 variants will not only expand our understanding of its cis-regulation but also provide mechanistic insight into STDG1.

This is a 2021 ARVO Annual Meeting abstract.