MKRN3 Variants in Central Precocious Puberty as an Example of the Complexity to Classify Missense Variants in Imprinted Genes as Pathogenic

Abstract Introduction Makorin ring-finger protein 3 (MKRN3) is a maternally imprinted gene, and variants of this gene have been associated with central precocious puberty (CPP). To date, the biochemical function of MKRN3 is still uncertain. The aim of this study was to assess American College of Medical Genetics and Genomics (ACMG) criteria for pathogenic classification of missense variants of MKRN3 and to propose specific ACMG criteria for this gene. Methods MKRN3 missense variants from our cohort of CPP or the HGMD (considered pathogenic) and gnomAD (considered benign) databases were annotated by diverse in silico analysis tools. Performance of these tools was assessed by determining sensitivity, specificity, and positive and negative predictive values. We then assessed the relevance of using amino acid conservation between MKRN family proteins and the population constraint as additional criteria to annotate missense variants. Results Usual in silico tools showed limited ability to distinguish the deleterious effect of pathogenic from benign variants. Analyses of amino acid conservation between MKRN family proteins and population constraints facilitated characterization of the damaging effect of MKRN3 missense variants. Revised ACMG criteria expanding familial segregation, conservation within the MKRN protein family, and population constraint allowed reclassification of several uncertain significant variants to likely pathogenic. Conclusion This study highlights the challenge involved in the classification of missense variants of a maternally imprinted gene. Expanding familial segregation over three generations, protein-family conservation, and population constraint improve the accuracy of MKRN3 variant annotation in CPP.