ClinVar

Description

The c.437T>C variant in the glucokinase gene, GCK causes an amino acid change of leucine to proline at codon 146 (p.(Leu146Pro)) of NM_000162.5. GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2). This variant is also predicted to be deleterious by computational evidence, with a REVEL score of 0.983, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in 4 unrelated individuals with diabetes/hyperglycemia (PS4_Moderate; PMID: 25015100, 31441606, internal lab contributors). This variant segregated with diabetes/hyperglycemia with 3 informative meioses in 1 family (PP1; internal lab contributors). This variant has been detected in the homozygous state in at least 3 individuals with permanent neonatal diabetes (PP4 and PM3; PMIDs: 25015100, 31441606, internal lab contributor). A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, the wild-type ATP Km is between 0.4-0.65, and the p.Leu146Pro variant has a relative activity index (RAI) <0.50 (PS3_Moderate; PMID: 25015100). In summary, the c.437T>C variant meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.3.0, approved 8/11/2023): PS4_Moderate, PM3, PP4, PP1, PM2_Supporting, PP2, PP3, PS3_Moderate.