Using structural analysis to assess the impact of missense variants in MEN1

Purpose: Thermodynamic analysis of protein structure in silico has been shown to be effective in discriminating between the effects of benign and pathogenic variation in the MSH2 protein. The aim of this study was to determine whether similar analysis of variants in MEN1 could help assess the impact of novel missense variants in the setting of a diagnostic laboratory. Methods: 338 previously-reported missense variants in MEN1 were analysed for their predicted effects on thermodynamic stability and position within the Menin protein. This analysis then was repeated on 7 novel missense variants identified through clinical testing. Results: Analysis of thermodynamic stability provided strong discrimination between groups of pathogenic and benign variants, with the majority of pathogenic variants also being buried within the protein interior. A threshold of >4 kcal/mol for the predicted change in stability, ΔΔG, yielded a positive predictive value for pathogenicity of 90.6% with 95% specificity. All seven novel variants had ΔΔG values >4 kcal/mol, giving a strong probability for pathogenicity. Conclusion: An integrated approach combining analysis of protein stability and positional effects of missense variants with existing sequence- and conservation-based approaches can provide increased specificity in assessing the impact of missense variants in MEN1 in a clinical setting.