ClinVar Miner

Submissions for variant NM_000162.5(GCK):c.766G>C (p.Glu256Gln)

dbSNP: rs769268803
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000485821 SCV000570149 likely pathogenic not provided 2016-05-09 criteria provided, single submitter clinical testing The E256Q variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. E256Q is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. The residue E256 is part of a glucose binding site and is crucial for GCK protein activity (Kamata et al., 2004). Missense variants in the same codon (E256K/D) and in nearby residues (V253L/F/A, N254H, Thr255A/S/I, W257R, G258R/S/C/D, A259T/V) have been reported in the Human Gene Mutation Database in association with diabetes (Stenson et al., 2014), supporting the functional importance of this region of the protein. Therefore, this variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000485821 SCV004565146 likely pathogenic not provided 2023-06-12 criteria provided, single submitter clinical testing The GCK c.766G>C; p.Glu256Gln variant (rs769268803), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 421063). This variant is also absent from the Genome Aggregation Database, indicating it is not a common polymorphism. The Glu256 residue is part of the glucose binding domain and is critical for GCK protein activity (Kamata 2004). Additionally, other amino acid substitutions at this codon (Ala, Asp, Gly, Lys) have been reported in individuals with MODY and are considered pathogenic (Campos Franco 2022, Garin 2008, Xu 2020, Zmyslowska 2022). Computational analyses predict that this variant is deleterious (REVEL: 0.951). Based on available information, this variant is considered to be likely pathogenic. References: Campos Franco P et al. Clinical and genetic characterization and long-term evaluation of individuals with maturity-onset diabetes of the young (MODY): The journey towards appropriate treatment. Diabetes Res Clin Pract. 2022 May;187:109875. PMID: 35472491. Garin I et al. Haploinsufficiency at GCK gene is not a frequent event in MODY2 patients. Clin Endocrinol (Oxf). 2008 Jun;68(6):873-8. PMID: 18248649. Kamata K et al. Structural basis for allosteric regulation of the monomeric allosteric enzyme human glucokinase. Structure. 2004 Mar;12(3):429-38. PMID: 15016359. Xu A et al. Molecular diagnosis of maturity-onset diabetes of the young in a cohort of Chinese children. Pediatr Diabetes. 2020 May;21(3):431-440. PMID: 31957151. Zmyslowska A et al. Next- generation sequencing is an effective method for diagnosing patients with different forms of monogenic diabetes. Diabetes Res Clin Pract. 2022 Jan;183:109154. PMID: 34826540.

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