ABCA4-associated disease as a model for missing heritability in autosomal recessive disorders: novel non-coding splice, cis-regulatory, structural and recurrent hypomorphic variants

Abstract

Purpose : Stargardt disease (STGD1) is one of the most common inherited retinal diseases (IRD), with an estimated prevalence of 1/8,000 – 1/10,000. The underlying disease gene for STGD1 is ABCA4. Apart from STGD1, biallelic ABCA4 variants have been linked to a spectrum of autosomal recessive retinal dystrophies, jointly named ABCA4-associated disease (AAD). AAD is hallmarked by a large proportion of patients with only one pathogenic variant in the disease gene ABCA4, suggestive for missing heritability.

Methods : Locus-specific genotyping of ABCA4, combined with extensive functional studies such as in vitro splice assays and luciferase assays allowed to unravel the missing alleles in a cohort of 67 AAD patients, with one (n=64) or no (n=3) identified coding ABCA4 variant.

Results : We identified eight pathogenic (deep-)intronic ABCA4 variants and six structural variants, five and four of which, respectively, are novel, including the first duplications to be described. Together, these variants account for the missing alleles in 40.3% of patients. Furthermore, two novel variants with a putative cis-regulatory effect were identified. The common hypomorphic variant c.5603A>T p.(Asn1868Ile) was found as a candidate second allele in 43.3% of patients. Overall, we have elucidated the missing heritability in 83.6% of our cohort.

Conclusions : This study demonstrates that a locus-specific integrated approach combining genomics with downstream tailored functional studies is powerful for elucidating a major portion of missing heritability in ABCA4-associated disease. The discovery of novel pathogenic variants in non-coding regions and the development of AONs can be envisaged for personalized therapies. Overall, this ABCA4-oriented study can be regarded as a model for missing heritability in other autosomal recessive diseases with a recognizable phenotype and with an incomplete molecular diagnosis.

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