GCK p.Pro153His

The c.458C>A variant in the glucokinase gene, GCK, causes an amino acid change of proline to histidine at codon 153 (p.(Pro153His)) 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 predicted to be deleterious by computational evidence, with a REVEL score of 0.985, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant resides in an amino acid that directly binds glucose, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1). This variant is absent from gnomAD 4.1.0 (PM2_Supporting). This variant was identified in five unrelated individuals with hyperglycemia; however PP4 was unable to be evaluated due to insufficient clinical information (PS4_Moderate; internal lab contributors). This variant was segregated with hyperglycemia, with seven informative meioses in five families (PP1_Strong; internal lab contributors). Another missense variant at the same residue, c.457C>T (p.Pro153Ser), has been interpreted as pathogenic by the ClinGen MDEP, and p.Pro153His has a greater Grantham distance (PM5). In summary, c.458C>A meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 3.1.0., approved 10/10/2025): PP1_Strong, PS4_Moderate, PM1, PM5, PM2_Supporting, PP2, PP3.