rs587780343
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PS4PP1_StrongPP4_ModeratePP2PP3PM2_Supporting
This summary comes from the ClinGen Evidence Repository: The c.1112G>T variant in the glucokinase gene, GCK, causes an amino acid change of cysteine to phenylalanine at codon 371 (p.(Cys371Phe)) of NM_000162.5. GCK is defined by the ClinGen MDEP VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.931, 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 hyperglycemia (PS4; PMID 24735133, internal lab contributors). This variant segregated with hyperglycemia with 12 informative meioses in 3 families with MODY (PP1_Strong; internal lab contributors). This variant was identified in at least two individuals with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% as well as either OGTT increment < 3 mmol/L or negative antibodies) (PP4_Moderate; internal lab contributors). In summary, this 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 1.2.0, approved 6/7/2023) : PP2, PP3, PM2_Supporting, PP1_Strong, PS4, PP4_Moderate . LINK:https://erepo.genome.network/evrepo/ui/classification/CA152950/MONDO:0015967/086
Frequency
Consequence
NM_000162.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GCK | NM_000162.5 | c.1112G>T | p.Cys371Phe | missense_variant | 9/10 | ENST00000403799.8 | NP_000153.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GCK | ENST00000403799.8 | c.1112G>T | p.Cys371Phe | missense_variant | 9/10 | 1 | NM_000162.5 | ENSP00000384247 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Monogenic diabetes Pathogenic:1
Pathogenic, reviewed by expert panel | curation | ClinGen Monogenic Diabetes Variant Curation Expert Panel | Aug 09, 2023 | The c.1112G>T variant in the glucokinase gene, GCK, causes an amino acid change of cysteine to phenylalanine at codon 371 (p.(Cys371Phe)) of NM_000162.5. GCK is defined by the ClinGen MDEP VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.931, 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 hyperglycemia (PS4; PMID 24735133, internal lab contributors). This variant segregated with hyperglycemia with 12 informative meioses in 3 families with MODY (PP1_Strong; internal lab contributors). This variant was identified in at least two individuals with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% as well as either OGTT increment < 3 mmol/L or negative antibodies) (PP4_Moderate; internal lab contributors). In summary, this 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 1.2.0, approved 6/7/2023) : PP2, PP3, PM2_Supporting, PP1_Strong, PS4, PP4_Moderate . - |
Gestational diabetes Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 23, 2020 | DNA sequence analysis of the GCK gene demonstrated a sequence change, c.1112G>T, in exon 9 that results in an amino acid change, p.Cys371Phe. The p.Cys371Phe change affects a highly conserved amino acid residue located in a Hexokinase domain of the GCK protein that is known to be functional. The p.Cys371Phe substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). This particular amino acid change has been described in the literature in two families with MODY (PMID: 19790256). This sequence change is absent from the large population databases such as ExAC and gnomAD (dbSNP rs587780343). Different sequence changes affecting the same amino acid residue (p.Cys371Arg, p.Cys371Trp, p.Cys371Trp) have also been described in patients with GCK-related MODY (PMID: 19790256) - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 03, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. 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) has been performed at Invitae 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. ClinVar contains an entry for this variant (Variation ID: 129140). This missense change has been observed in individual(s) with clinical features of autosomal dominant maturity-onset diabetes of the young (PMID: 19790256, 24735133; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with phenylalanine, which is neutral and non-polar, at codon 371 of the GCK protein (p.Cys371Phe). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at