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

Miriam Bauwens, Alejandro Garanto, Riccardo Sangermano, Sarah Naessens, Nicole Weisschuh, Julie De Zaeytijd, Mubeen Khan, Françoise Sadler, Irina Balikova, Caroline Van Cauwenbergh, Toon Rosseel, Jim Bauwens, Kim De Leeneer, Sarah De Jaegere, Thalia Van Laethem, Meindert De Vries, Keren Carss, Gavin Arno, Ana Fakin, Andrew R. WebsterThomy J.L. de Ravel de l’Argentière, Yves Sznajer, Marnik Vuylsteke, Susanne Kohl, Bernd Wissinger, Timothy Cherry, Rob W.J. Collin, Frans P.M. Cremers, Bart P. Leroy, Elfride De Baere

Research output: Contribution to specialist/vulgarizing publicationArticleSpecialist

37 Citations (Scopus)

Abstract

Purpose: ABCA4-associated disease, a recessive retinal dystrophy, is hallmarked by a large proportion of patients with only one pathogenic ABCA4 variant, suggestive for missing heritability. Methods: By locus-specific analysis of ABCA4, combined with extensive functional studies, we aimed to unravel the missing alleles in a cohort of 67 patients (p), with one (p = 64) or no (p = 3) identified coding pathogenic variants of ABCA4. Results: We identified eight pathogenic (deep-)intronic ABCA4 splice variants, of which five are novel and six structural variants, four of which are novel, including two duplications. 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. In addition, we successfully rescued three deep-intronic variants using antisense oligonucleotide (AON)-mediated treatment in HEK 293-T cells and in patient-derived fibroblast cells. Conclusion: Noncoding pathogenic variants, novel structural variants, and a common hypomorphic allele of the ABCA4 gene explain the majority of unsolved cases with ABCA4-associated disease, rendering this retinopathy a model for missing heritability in autosomal recessive disorders.

Original languageEnglish
Pages1761-1771
Number of pages11
Volume21
Specialist publicationGenetics in Medicine
PublisherNature Publishing Group
DOIs
Publication statusPublished - 23 Jan 2019

Keywords

  • ABCA4-associated disease
  • AON
  • deep-intronic
  • missing heritability
  • noncoding

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