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Variant: NM_000162.5(GCK):c.676G>A (p.Val226Met)

CA213827

36243 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: a3bc2935-1bf2-4171-b759-ca1cfb249eb6
Approved on: 2023-08-13
Published on: 2023-08-13

HGVS expressions

NM_000162.5:c.676G>A
NM_000162.5(GCK):c.676G>A (p.Val226Met)
NC_000007.14:g.44149763C>T
CM000669.2:g.44149763C>T
NC_000007.13:g.44189362C>T
CM000669.1:g.44189362C>T
NC_000007.12:g.44155887C>T
NG_008847.1:g.44661G>A
NG_008847.2:g.53408G>A
ENST00000395796.8:c.*674G>A
ENST00000616242.5:c.676G>A
ENST00000682635.1:n.1162G>A
ENST00000345378.7:c.679G>A
ENST00000403799.8:c.676G>A
ENST00000671824.1:c.676G>A
ENST00000673284.1:c.676G>A
ENST00000345378.6:c.679G>A
ENST00000395796.7:c.673G>A
ENST00000403799.7:c.676G>A
ENST00000437084.1:c.625G>A
ENST00000616242.4:n.673G>A
NM_000162.3:c.676G>A
NM_033507.1:c.679G>A
NM_033508.1:c.673G>A
NM_000162.4:c.676G>A
NM_001354800.1:c.676G>A
NM_033507.2:c.679G>A
NM_033508.2:c.673G>A
NM_033507.3:c.679G>A
NM_033508.3:c.673G>A

Pathogenic

Met criteria codes 8
PP4_Moderate PS3_Moderate PM2_Supporting PS4 PP3 PP2 PP1_Strong PM1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GCK Version 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.676G>A variant in the glucokinase gene, GCK, causes an amino acid change of valine to methionine at codon 261 (p.(Val226Met)) 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 0.789, which is greater than the MDEP threshold of 0.70 (PP3). This variant has a gnomAD v2.1.1 Popmax filtering allele frequency of 0.000002920 (below the MDEP threshold of 0.000003) and ≤ 2 copies observed in the European non-Finnish population and ≤ 1 copy in any other subpopulation, thereby meeting the ClinGen MDEP criteria for PM2_Supporting (PM2_Supporting). This variant was identified in more than 70 unrelated individuals with hyperglycemia (PS4; internal lab contributors). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antibodies) (PP4_Moderate; internal lab contributors). This variant segregated with diabetes/hyperglycemia with more than 20 informative meioses in more than 30 families (PP1_Strong; internal lab contributors). 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). 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.Val226Met variant has a relative activity index (RAI) of 0.009 to 0.198, which is less than the MDEP VCEP threshold of 0.50 (PS3_Moderate; PMID: 10525657, 25015100, https://doi.org/10.1159/isbn.978-3-318-01080-0​). 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 1.3.0, approved 8/11/2023): PS4, PP1_Strong, PS3_Moderate, PM2_Supporting, PP2, PP4_Moderate, PP3, PM1.
Met criteria codes
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antibodies) (PP4_Moderate; internal lab contributors).
PS3_Moderate
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.Val226Met variant has a relative activity index (RAI) of 0.009 to 0.198, which is less than the MDEP VCEP threshold of 0.50 (PS3_Moderate; PMID: 10525657, 25015100, https://doi.org/10.1159/isbn.978-3-318-01080-0​).
PM2_Supporting
This variant has a gnomAD v2.1.1 Popmax filtering allele frequency of 0.000002920 (below the MDEP threshold of 0.000003) and ≤ 2 copies observed in the European non-Finnish population and ≤ 1 copy in any other subpopulation, thereby meeting the ClinGen MDEP criteria for PM2_Supporting (PM2_Supporting).
PS4
This variant was identified in more than 70 unrelated individuals with diabetes (PS4; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.789, which is greater than the MDEP threshold of 0.70 (PP3).
PP2
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).
PP1_Strong
This variant segregated with diabetes/hyperglycemia with more than 20 informative meioses in more than 30 families (PP1_Strong; internal lab contributors).
PM1
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).
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