Clinical and functional evidence supporting the pathogenicity of the novel <i>PSEN1</i> p.R358P variant in early-onset Alzheimer's disease

BackgroundPathogenic variants in <i>PSEN1</i>, <i>PSEN2</i>, or <i>AβPP</i> cause early-onset Alzheimer's disease (EOAD). Several novel variants remain of uncertain significance (VUS) due to limited evidence. The <i>PSEN1</i> p.R358P variant has not been previously characterized or reported in EOAD cases.ObjectiveTo determine the pathogenicity of the <i>PSEN1</i> p.R358P variant in a patient with EOAD and assess its effect on amyloid-β (Aβ) processing using a human cellular model.MethodsWe present the case of a 62-year-old female of Western European descent with memory impairment starting at 59 and a positive family history of Alzheimer's disease (AD). To evaluate the variant, a <i>PSEN1</i> knockout HEK293T line was generated using CRISPR/Cas9. Cells were co-transfected with <i>AβPP</i> and either wild-type or mutant <i>PSEN1,</i> and Aβ₄₂/Aβ₄₀ levels were measured by ELISA in culture supernatants.ResultsThe proband exhibited multidomain cognitive impairment and imaging biomarkers (PiB-PET and FDG-PET) consistent with AD. Whole-exome sequencing revealed a <i>PSEN1</i> (NM_000021.4:c.1073G > C:p.Arg358Pro) variant, classified as VUS by ACMG guidelines, together with a <i>SORL1</i> p.G1536D variant and <i>APOE</i> ε4/ε4 genotype. Cells expressing <i>PSEN1</i> p.R358P showed an increased Aβ₄₂/Aβ₄₀ ratio compared to wild-type, mainly due to reduced Aβ₄₀ levels. This profile partially mimicked the pathogenic <i>PSEN1</i> p.A246E variant. <i>In silico</i> analyses predicted deleterious effects for <i>PSEN1</i> p.R358P.ConclusionsOur results support a likely pathogenic role for the <i>PSEN1</i> p.R358P variant in EOAD. Nonetheless, in the absence of segregation data, the variant should be considered a hot VUS.