Phenotypic variability in female individuals with the NAA10 missense variants p.(L126R), p.(L126V), or p.(F128L) leading to NAA10-related syndrome

NAA10-related syndrome is an exceptionally rare X-linked disorder caused by variants in the N-alpha-acetyltransferase 10 (NAA10) gene. Despite its role in acetylating nearly half of the human proteome, establishing genotype-phenotype correlations remains challenging due to the limited number of documented cases and the extremely broad phenotypic spectrum. We performed exome sequencing and clinical phenotyping of three female patients. To investigate the pathogenic mechanisms without interference from endogenous protein, we generated the first viable NAA10 knockout (ΔNAA10) cell line using CRISPR/Cas9 in the 8-MG-BA glioblastoma line. This null-background model allowed for the analysis of GFP-tagged patient variants, specifically focusing on colocalization with the auxiliary subunit NAA15. Our study expands the global landscape of NAA10-related diseases—now totaling 145 individuals with 46 pathogenic variants—by describing three females with de novo NAA10 variants clustering closely within the N-acetyltransferase domain: p.(L126R), p.(L126V), and p.(F128L). The first patient exhibits severe global developmental delay, neuroimaging anomalies, and congenital cardiac defects and remains non-verbal. The second patient experiences developmental delays, particularly in motor skills and language. The third patient also presents with severe global developmental delay with significant motor impairments and remains non-verbal. Localization studies in the ΔNAA10 cells revealed that while the p.L126V variant maintained near-wild-type protein stability and colocalization with NAA15, the bulky p.L126R and disruptive p.F128L substitutions severely impaired NatA complex formation and altered cellular distribution. This study expands the known clinical landscape by detailing the phenotypic spectrum of three female patients, including two entirely novel cases described here for the first time. We aimed to explore how specific variants in the catalytic domain affect protein stability and NatA complex formation, helping to explain the diverse clinical manifestations observed in affected females. This study highlights the broad phenotypic spectrum of NAA10-related syndrome and demonstrates that clinical severity is driven by the specific amino acid substitution rather than the position alone. With 145 cases now identified globally, the need for precision modeling is critical. Our novel ΔNAA10 cell line proves to be a robust tool for linking specific biochemical defects to clinical phenotypes, potentially offering new insights into this complex syndrome.