Submissions for variant NM_000162.5(GCK):c.760A>C (p.Asn254His)

dbSNP: rs193922327

Total submissions: 4

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000029917	SCV000052572	likely pathogenic	Maturity-onset diabetes of the young type 2	2011-08-18	criteria provided, single submitter	curation	Converted during submission to Likely pathogenic.
GeneDx	RCV001562130	SCV001784849	likely pathogenic	not provided	2021-05-03	criteria provided, single submitter	clinical testing	Not observed in large population cohorts (Lek et al., 2016); Missense variants in this gene are often considered pathogenic (Stenson et al., 2014); 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: 26587058, 24430320, 28012402, 19790256)
Labcorp Genetics (formerly Invitae), Labcorp	RCV001562130	SCV004295160	pathogenic	not provided	2025-01-13	criteria provided, single submitter	clinical testing	This sequence change replaces asparagine, which is neutral and polar, with histidine, which is basic and polar, at codon 254 of the GCK protein (p.Asn254His). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with maturity onset diabetes of the young, permanent neonatal diabetes mellitus and/or type 2 diabetes (PMID: 19790256, 26587058, 35112188). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 36254). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on GCK protein function. This variant disrupts the p.Asn254 amino acid residue in GCK. Other variant(s) that disrupt this residue have been determined to be pathogenic (internal data). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics	RCV004629143	SCV005126412	uncertain significance	Maturity onset diabetes mellitus in young	2024-05-13	criteria provided, single submitter	clinical testing	The p.N254H variant (also known as c.760A>C), located in coding exon 7 of the GCK gene, results from an A to C substitution at nucleotide position 760. The asparagine at codon 254 is replaced by histidine, an amino acid with similar properties. This variant was reported in multiple individuals with features consistent with maturity-onset diabetes of the young (Giuffrida FMA et al. Diabetes Res Clin Pract, 2017 Jan;123:134-142; Kleinberger JW et al. Genet Med, 2018 Jun;20:583-590; Mirshahi UL et al. Am J Hum Genet, 2022 Nov;109:2018-2028). This variant has been identified in conjunction with another GCK variant in am individual with features consistent with permanent neonatal diabetes mellitus; the variants were identified in trans (Esquiaveto-Aun AM et al. Diabetol Metab Syndr, 2015 Nov;7:101). In an assay testing GCK function, this variant showed a functionally abnormal result (Gersing S et al. Genome Biol, 2023 Apr;24:97). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear.