The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_033508.3:c.167T>G

CA367403318

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 80810179-5dcf-4d2d-a313-2582a98bd120
Approved on: 2024-10-31
Published on: 2025-02-28

HGVS expressions

NM_033508.3:c.167T>G
NC_000007.14:g.44153339A>C
CM000669.2:g.44153339A>C
NC_000007.13:g.44192938A>C
CM000669.1:g.44192938A>C
NC_000007.12:g.44159463A>C
NG_008847.1:g.41085T>G
NG_008847.2:g.49832T>G
ENST00000395796.8:c.*168T>G
ENST00000616242.5:c.170T>G
ENST00000682635.1:n.656T>G
ENST00000345378.7:c.173T>G
ENST00000403799.8:c.170T>G
ENST00000671824.1:c.170T>G
ENST00000673284.1:c.170T>G
ENST00000345378.6:c.173T>G
ENST00000395796.7:c.167T>G
ENST00000403799.7:c.170T>G
ENST00000437084.1:c.170T>G
ENST00000616242.4:c.167T>G
NM_000162.3:c.170T>G
NM_033507.1:c.173T>G
NM_033508.1:c.167T>G
NM_000162.4:c.170T>G
NM_001354800.1:c.170T>G
NM_033507.2:c.173T>G
NM_033508.2:c.167T>G
NM_000162.5:c.170T>G
NM_033507.3:c.173T>G
More

Likely Pathogenic

Met criteria codes 6
PM3_Supporting PM2_Supporting PM5 PP4 PP3 PP2

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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.170T>G variant in the glucokinase gene, GCK, causes an amino acid change of methionine to arginine at codon 57 (p.(Met57Arg)) of NM_000162.5. This variant is absent from gnomAD v2.1.1 and v4.1 (PM2_Supporting). 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 0.979, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in an individual with a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4; internal lab contributors). Additionally, it has been detected in the homozygous state in one individual with neonatal diabetes (PM3_Supporting, PMID: 38970407). Another missense variant at the same codon, c.171G>A, p.(Met57Ile), has been interpreted as pathogenic by the ClinGen MDEP, and p.(Met57Arg) has a greater Grantham distance (PM5). In summary, c.170T>G meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PM2_Supporting, PP2, PP3, PP4, PM3_Supporting, PM5).
Met criteria codes
PM3_Supporting
This variant has been detected in the homozygous state in one individual with neonatal diabetes (PM3_Supporting, PMID: 38970407).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 and v4.1 (PM2_Supporting).
PM5
Another missense variant at the same codon, c.171G>A, p.(Met57Ile), has been interpreted as pathogenic by the ClinGen MDEP, and p.(Met57Arg) has a greater Grantham distance (PM5).
PP4
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%) (PP4; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.979, which is greater than the MDEP VCEP 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).
Curation History
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