Abstract Background Succinic semialdehyde dehydrogenase deficiency (SSADHD), caused by variants in ALDH5A1 , is a rare inherited neurometabolic disorder with phenotypic heterogeneity. To clarify the pathogenicity of ALDH5A1 variants, we systematically investigated their effects on succinic semialdehyde dehydrogenase (SSADH) structure and function. Methods We obtained the clinical and molecular characteristics of 12 probands. We further augmented the pathogenicity dataset for 14 variants using multiple in silico tools under the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guideline. More importantly, we provided quantitative data on protein expression and residual enzyme activity for SSADH, enabling robust assignment of ACMG PS3/BS3 codes. Finally, we integrated 3D structural modelling with changes in physicochemical properties to butter elucidate how individual variants impair SSADH function. Results Patients with SSADHD exhibit varying degrees of epilepsy, intellectual disorders, developmental delay, and hypotonia. Among the 14 variants, 9 affect SSADH expression level of protein, and 9 affect SSADH enzyme activity. After acquiring functional experiments’ results, PS3 was assigned to 10 variants and BS3 to 1; more notably, 8 variants obtained more plentiful pathogenic evidence. Intriguingly, we also investigated the underlying mechanisms using protein-based prediction techniques, 2 of 14 variants influenced binding of SSADH to small molecules, whereas 3 of 14 variants led to instability. Besides, as the SSADH with variants in the oligomerization domain accumulates in the tetramer, the tetramer becomes increasingly unstable. Conclusion In this study, we illustrated that 14 ALDH5A1 variants affected the molecular structure and function by diverse mechanisms, and with varying degrees, which could help us to gain a deeper understanding of these variants by providing reasonable evidence based on the PS3/BS3 codes in the ACMG guidelines. Essentially, this pathogenic classification facilitates the diagnosis of SSADHD in future genetic testing processes.
Yan et al. (Sat,) studied this question.