The Role of ATP9A (c.1091G>C; p.(Arg364Thr)) Variant in Cognitive Impairment: Diagnostic Insight from Whole Exome Sequencing

Background: The ATP9A gene encodes a P4-type ATPase involved in phospholipid translocation, essential for vesicular trafficking and neuronal development. Pathogenic ATP9A variants cause autosomal recessive neurodevelopmental disorders characterized by intellectual disability and microcephaly, yet the impact of missense variants remains poorly understood. Methods: A 7-year-old female patient with cognitive impairment, microcephaly, and developmental delay was admitted to Başakşehir Çam and Sakura City Hospital. Whole exome sequencing (WES) using Illumina technology identified a novel homozygous ATP9A variant, confirmed by Sanger sequencing and segregation analysis. In silico tools (RosettaFold, DynaMut, mCSM, SDM, DUET, AggreScan3D) assessed its structural impact. Quantitative real-time PCR (qPCR) was conducted to evaluate the relative expression levels of ATP9A . Results: WES revealed a homozygous missense variant, ATP9A (NM_006045.3):c.1091G > C p.(Arg364Thr), classified as variant of uncertain significance (ACMG: PP2, PM2, PM3). Protein modeling demonstrated reduced stability (ΔΔG = − 1.51 to − 0.26 kcal/mol), increased flexibility, and a 2.4-fold decrease in solvent accessibility. The mutation altered polar and hydrophobic interactions within the P-type ATPase IV domain, enhancing aggregation propensity. Expression analysis showed elevated ATP9A mRNA levels, suggesting a compensatory response. Conclusion: This novel ATP9A variant broadens the mutational spectrum of ATP9A -related neurodevelopmental disorders. Structural destabilization of the p.(Arg364Thr) protein may contribute to the patient’s cognitive impairment and microcephaly, warranting further functional studies.