Evaluation of rare NR1D2 variants in MODY-X: clinical, genetic, and in silico insights

The objective of this study was to investigate the protein-coding regions of the NR1D2 gene in patients clinically diagnosed with maturity-onset diabetes of the young (MODY), including those without pathogenic variants in known MODY genes (MODY-X), and to characterize the potential functional relevance of detected variants. The variants present in the exons and adjacent intronic regions of the NR1D2 gene in patients with MODY were subjected to comparative analysis with those observed in healthy individuals and patients with type 2 diabetes mellitus. The maximum credible allele frequency was set to be 0.0001. The potential impact of rare variants was evaluated using variety in silico prediction tools, including PolyPhen-2, SIFT, MutationTaster2025, FATHMM-XF, REVEL, CADD, and DynaMut2. Two extremely rare NR1D2 missense variants were identified in three MODY-X patients: p.I148V (rs148928938) in exon 4 and p.R286W (rs768518229) in exon 5, with allele frequencies of 74 per million and 3 per million in gnomAD, respectively. In silico predictions indicated a more consistent deleterious profile for p.I148V, whereas p.R286W demonstrated heterogeneous and predominantly benign or borderline predictions. The clinical manifestations exhibited by the carriers were found to be variable, which is consistent with the metabolic heterogeneity that is characteristic of MODY. The findings suggest that these variants may function as metabolic modifiers contributing to phenotypic variability in MODY-X. Prospective family-based studies and functional assays are needed to clarify their biological significance.