The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000162.5(GCK):c.499T>C (p.Trp167Arg)

CA367401768

447408 (ClinVar)

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 8baf769d-4142-48b1-9144-f9044b76b177
Approved on: 2026-09-02
Published on: 2026-09-02

HGVS expressions

NM_000162.5:c.499T>C
NM_000162.5(GCK):c.499T>C (p.Trp167Arg)
NC_000007.14:g.44150049A>G
CM000669.2:g.44150049A>G
NC_000007.13:g.44189648A>G
CM000669.1:g.44189648A>G
NC_000007.12:g.44156173A>G
NG_008847.1:g.44375T>C
NG_008847.2:g.53122T>C
ENST00000395796.8:c.*497T>C
ENST00000616242.5:c.499T>C
ENST00000682635.1:n.985T>C
ENST00000345378.7:c.502T>C
ENST00000403799.8:c.499T>C
ENST00000671824.1:c.499T>C
ENST00000673284.1:c.499T>C
ENST00000345378.6:c.502T>C
ENST00000395796.7:c.496T>C
ENST00000403799.7:c.499T>C
ENST00000437084.1:c.448T>C
ENST00000616242.4:c.496T>C
NM_000162.3:c.499T>C
NM_033507.1:c.502T>C
NM_033508.1:c.496T>C
NM_000162.4:c.499T>C
NM_001354800.1:c.499T>C
NM_033507.2:c.502T>C
NM_033508.2:c.496T>C
NM_033507.3:c.502T>C
NM_033508.3:c.496T>C
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Likely Pathogenic

Met criteria codes 5
PS4 PP3 PP2 PM2_Supporting PP4_Moderate
Not Met criteria codes 1
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 3.1

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.499T>C variant in the glucokinase gene, GCK, causes an amino acid change of tryptophan to arginine at codon 167 (p.(Trp167Arg)) 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 0.923, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant has an incomputable gnomAD v4.1.1 Grpmax filtering allele frequency due to no more than one copy in any non-founder subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (Grpmax FAF <= 0.000003) (PM2_Supporting). This variant was identified in eight unrelated individuals with hyperglycemia (PS4; PMID: 21978167, 36257325, ClinVar, internal lab contributors). Additionally, at least one of these individuals had a clinical history highly specific for GCK-hyperglycemia (fasting glucose 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antibodies) (PP4_Moderate; internal lab contributors). Another missense variant at the same residue, c.501G>C (p.Trp167Cys), has been classified as pathogenic; however, PM5_Supporting was not applied to avoid circularity as p.Trp167Ser contributed to the classification of the other variant at this residue. In summary, c.499T>C meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 3.1.0, approved 10/10/2025): PS4, PP4_Moderate, PM2_Supporting, PP2, PP3.
Met criteria codes
PS4
This variant was identified in eight unrelated individuals with hyperglycemia (PS4; PMID: 36257325, ClinVar, internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.923, 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).
PM2_Supporting
This variant has an incomputable gnomAD v4.1.1 Grpmax filtering allele frequency due to no more than one copy in any non-founder subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (Grpmax FAF <= 0.000003) (PM2_Supporting).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (fasting glucose 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antibodies) (PP4_Moderate; internal lab contributors).
Not Met criteria codes
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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