Frequent hypomorphic alleles solve 80% of late-onset ABCA4 disease and distinguish it from age-related macular degeneration

Abstract

Purpose : Variation in the ABCA4 gene is causal for, or associated with, a wide range of phenotypes from early-onset Mendelian retinal dystrophies to late-onset complex disorders such as age-related macular degeneration (AMD). However, a significant fraction of the disease-associated genetic variation has remained elusive thereby complicating assessment of the role of monoallelic and biallelic variants in clinically confirmed disease.

Methods : All 645 study subjects diagnosed with ABCA4 disease underwent complete ophthalmic examinations, including autofluorescence (AF) imaging with cSLO and SD-OCT scans. The ABCA4 gene and locus sequencing were performed using the Illumina TruSeq Custom Amplicon protocol followed by confirmation of variants by Sanger sequencing. The possible effect of ABCA4 variants was assessed with prediction algorithms via Alamut and the allele frequencies of all variants were compared to the gnomAD database or the 1000 Genomes Project database. Protein unfolding propensities for selected ABCA4 variants were evaluated with the unfolding mutation screen.

Results : We determined that some ABCA4 variants, previously considered benign due to high minor allele frequency (MAF 2-7%) in the general population, account for a large fraction of missing pathogenic alleles, particularly in monoallelic cases. We show that a hypomorphic c.5603A>T (p.Asn1868Ile) variant with MAF ~7% in the general population accounts for a large fraction of missing pathogenic alleles. It explains >50% of monoallelic cases, ~80% of late-onset cases and distinguishes ABCA4 disease from AMD. We also identify intragenic modifying effects of another, c.2588G>C (p.Gly863Ala), allele and describe distinct clinical phenotype(s) conferred by these alleles.

Conclusions : Our findings substantiate the causality of frequent missense variants and their phenotypic outcomes as a significant contribution to ABCA4 disease and its clinical presentation.

This is an abstract that was submitted for the 2017 ARVO Annual Meeting, held in Baltimore, MD, May 7-11, 2017.