Abstract
The transmembrane protein ABCA4, found in the photoreceptor outer segment discs, functions to transport retinoids-a process essential to the visual transduction cycle. Variants in the ABCA4 gene, now numbering over 4000, give rise to impaired protein function, ultimately leading to various inherited retinal dystrophies (IRDs). The binding and clearance of retinoids rely on the functionality of ABCA4, and recent studies point to the role of its extracytoplasmic domain (ECD2) in retinoid binding and transport. In this study, we asked whether ABCA4 missense variants map to specific clusters within ECD2, how these residues influence retinoid interaction, and how this correlates with the 3D structure of the domain. First, ECD2 variants reported in the ClinVar database were analyzed using pathogenicity prediction tools (PolyPhen2, Provean, SIFT). Variants classified as pathogenic across all tools (PAAT) were mapped to the ECD2 domain, particularly the conserved regions or critical conserved motifs (CCMs). Most interestingly, 54% of PAAT variants are mapped to the CCMs. The convergence of these clusters in the cryo-EM structures supported the significance of the CCMs in retinoid interaction, emphasizing their relevance in understanding the pathophysiology of IRDs. Tryptophan fluorescence demonstrated that these CCM residues (specifically P1395L) were indeed crucial for retinoid interaction. By employing in silico and function-based methods, we have presented an integrated approach to delineate the functions of the ECD2 domain of ABCA4.