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.763A>G (p.Thr255Ala)

CA367400608

2735005 (ClinVar)

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: e4a05779-2d01-41ee-96a5-b471b87e9671
Approved on: 2025-11-24
Published on: 2025-11-26

HGVS expressions

NM_000162.5:c.763A>G
NM_000162.5(GCK):c.763A>G (p.Thr255Ala)
NC_000007.14:g.44147750T>C
CM000669.2:g.44147750T>C
NC_000007.13:g.44187349T>C
CM000669.1:g.44187349T>C
NC_000007.12:g.44153874T>C
NG_008847.1:g.46674A>G
NG_008847.2:g.55421A>G
ENST00000395796.8:c.*761A>G
ENST00000616242.5:c.763A>G
ENST00000345378.7:c.766A>G
ENST00000403799.8:c.763A>G
ENST00000671824.1:c.763A>G
ENST00000673284.1:c.763A>G
ENST00000345378.6:c.766A>G
ENST00000395796.7:c.760A>G
ENST00000403799.7:c.763A>G
ENST00000437084.1:c.712A>G
ENST00000616242.4:c.760A>G
NM_000162.3:c.763A>G
NM_033507.1:c.766A>G
NM_033508.1:c.760A>G
NM_000162.4:c.763A>G
NM_001354800.1:c.763A>G
NM_033507.2:c.766A>G
NM_033508.2:c.760A>G
NM_033507.3:c.766A>G
NM_033508.3:c.760A>G
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Pathogenic

Met criteria codes 8
PM5 PM1 PP4_Moderate PP1_Strong PS4 PP3 PP2 PM2_Supporting

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 3.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.763A>G variant in the glucokinase gene, GCK, causes an amino acid change of threonine to alanine at codon 255 (p.(Thr255Ala)) of transcript 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 0.832, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 and v4.1 (PM2_Supporting). This variant was identified in nine unrelated individuals with hyperglycemia (PS4; PMID 39504571, 25953829, 30259503, 17573900; 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; PMID: 25953829). This variant segregated with hyperglycemia with four informative meioses in three families (PP1_Strong; PMID: 17573900, 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). Another missense variant at the same residue, c.764C>G (p.Thr255Ser) has been interpreted as pathogenic by the ClinGen MDEP, and p.Thr255Ala has the same Grantham distance (PM5). In summary, c.763A>G meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 3.1.0, approved 10/10/2025): PS4, PP1_Strong, PM1, PM5, PM2_Supporting, PP2, PP3, PP4_Moderate.
Met criteria codes
PM5
Another missense variant at the same residue, c.764C>G (p.Thr255Ser) has been interpreted as pathogenic by the ClinGen MDEP, and p.Thr255Ala the same Grantham distance (PM5).
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).
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; PMID: 25953829).
PP1_Strong
This variant segregated with hyperglycemia with four informative meioses in three families (PP1_Strong; PMID: 17573900, internal lab contributors).
PS4
This variant was identified in nine unrelated individuals with hyperglycemia (PS4; PMID 39504571, 25953829, 30259503, 17573900; internal lab contributors)
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.832, 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 is absent from gnomAD v2.1.1 and v4.1 (PM2_Supporting).
Curation History
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