Cevik, SenemJones, Jazzlyn S.Biswas, Subhasis B.Biswas-Fiss, Esther E.2026-01-242026-01-24202597804432941439780443193507978032385317097801281391659780323988957978012410523297801281556159780443294105978032399229997801281684481876-1623https://doi.org/10.1016/bs.apcsb.2024.12.003https://hdl.handle.net/20.500.12868/4611Variants in the ABCA4 gene are a fundamental cause of several inherited retinal degenerations (IRDs), including Stargardt macular dystrophy, retinitis pigmentosa, and cone-rod dystrophy. These three ABCA4-driven diseases are estimated to cause blindness in 1.4 million people worldwide. As a result, genetic testing of ABCA4 is increasingly common in clinical settings. Of the 4111 identified variants in ABCA4, 1668 are missense, of which 47 % are of unknown pathogenicity (variants of unknown significance, VUS). This genetic uncertainty leads to three fundamental problems: (i) for IRD patients with multiple unclassified ABCA4 mutations, it is impossible to predict which variant will cause disease in relatives who have not yet developed it; (ii) development of variant-specific therapies remains limited; and (iii) these variants cannot be used to predict disease prospectively, which is essential for life-planning decisions and for directing patients to new clinical trials. This chapter describes approaches to deciphering the impact of ABCA4 genetic variants of unknown significance (VUS) using a combination of in silico and in vitro analyses. By leveraging complementary fields—protein biochemistry and computational biology—to create a “sequence-structure-function” workflow, where in silico 3D protein structural analysis of ABCA4 sequence variants serves as a tool to predict disease severity and clinical pathogenicity in conjunction with first-line bioinformatic tools and functional analysis. This approach represents a helpful step forward in understanding how ABCA4 variants affect structure and function and in evaluating their potential to cause inherited retinal diseases. © 2025eninfo:eu-repo/semantics/closedAccessABC transporterABCA4ATPaseBioinformaticsGenetic variantsInherited retinal degenerationProtein structure computational modelingVariants of unknown significanceVirus-like particleVisual diseaseBook Chapter10.1016/bs.apcsb.2024.12.003147423460409734092-s2.0-105007036285Q2