Structural and dynamic characterization of a novel in-frame indel variant in glucokinase associated with MODY2

Human glucokinase (GCK) catalyzes the rate-limiting step of β-cell glycolysis and serves as a critical glucose sensor in the regulation of glucose homeostasis. Variants in GCK are a leading cause of maturity-onset diabetes of the young (MODY), accounting for 30-50% of MODY cases depending on the population studied. Clinical management of GCK-MODY during pregnancy poses particular challenges, as the fetal genotype, which influences fetal insulin secretion and growth, is typically unknown in utero. In this report, we present a case of GCK-MODY identified during pregnancy and provide a mechanistic assessment of the functional impact of a variant of uncertain significance (VUS). We identified a novel heterozygous in-frame indel VUS (NM_000162.5:c.311_325delinsTCCCCGAGGACG - p.(Lys104_Ser109delinsIleProGluAspAla) in GCK in a patient initially managed as type 2 diabetes. The affected region lies within a β-strand of the small domain that undergoes a major conformational transition during enzyme activation and is known to be intolerant of sequence variation. Structural modeling and molecular dynamics simulations reveal that this variant disrupts normal movement of the small domain, alters coordinated residue fluctuations, and impairs inter-domain communication during the activation process. These perturbations are accompanied by pronounced protein destabilization and a trend toward weaker ATP interaction, consistent with a loss-of-function mechanism. These findings provide a mechanistic framework for interpreting this novel variant, expanding the known genotypic spectrum of GCK-MODY, and may inform future structure-guided strategies for GCK-targeted therapeutics.