APOE ε4 variant interpretation and protein numbering discrepancy: a case report

Alzheimer's disease (AD) is the leading cause of dementia worldwide, and the apolipoprotein E (APOE) ε4 allele is the strongest genetic risk factor for late-onset form. Differences in protein numbering conventions may complicate recognition of clinically important variants during genomic interpretation.

We report a 57-year-old man with early-onset AD who underwent next-generation sequencing (NGS). Genetic findings were interpreted using transcript, protein, and dbSNP annotations to assess the clinical significance of the identified variant.

NGS identified a homozygous APOE variant annotated as p.Cys130Arg. This annotation corresponds to the APOE ε4-defining rs429358 variant, commonly reported as Cys112Arg in the mature protein sequence. The variant was initially classified as a variant of uncertain significance (VUS) in the clinical genetic report. Subsequent review demonstrated that p.Cys130Arg and Cys112Arg represent equivalent annotations of the same rs429358 allele.

This case highlights how alternative protein numbering conventions may complicate variant interpretation and underscores the importance of integrating genomic, transcript, protein, and dbSNP-level information during clinical genomic analysis.