ClinVar Genomic variation as it relates to human health

Reported in association with MODY in published literature (Osbak et al., 2009); however, no patient clinical information was provided; Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 19790256)

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 223 of the GCK protein (p.Gly223Arg). This variant is present in population databases (no rsID available, gnomAD 0.01%). This missense change has been observed in individuals with clinical features of autosomal dominant maturity onset diabetes of the young (PMID: 19790256; Invitae). ClinVar contains an entry for this variant (Variation ID: 2578075). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GCK protein function with a positive predictive value of 80%. This variant disrupts the p.Gly223 amino acid residue in GCK. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 21437567, 31216263, 32041611, 33294763, 33565752). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.