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.764C>T (p.Thr255Ile)

CA367400604

3720739 (ClinVar)

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 934f956a-ad7e-482e-b2ec-53721b097062
Approved on: 2025-11-24
Published on: 2025-11-26

HGVS expressions

NM_000162.5(GCK):c.764C>T (p.Thr255Ile)
NM_000162.5:c.764C>T
NC_000007.14:g.44147749G>A
CM000669.2:g.44147749G>A
NC_000007.13:g.44187348G>A
CM000669.1:g.44187348G>A
NC_000007.12:g.44153873G>A
NG_008847.1:g.46675C>T
NG_008847.2:g.55422C>T
ENST00000395796.8:c.*762C>T
ENST00000616242.5:c.764C>T
ENST00000345378.7:c.767C>T
ENST00000403799.8:c.764C>T
ENST00000671824.1:c.764C>T
ENST00000673284.1:c.764C>T
ENST00000345378.6:c.767C>T
ENST00000395796.7:c.761C>T
ENST00000403799.7:c.764C>T
ENST00000437084.1:c.713C>T
ENST00000616242.4:c.761C>T
NM_000162.3:c.764C>T
NM_033507.1:c.767C>T
NM_033508.1:c.761C>T
NM_000162.4:c.764C>T
NM_001354800.1:c.764C>T
NM_033507.2:c.767C>T
NM_033508.2:c.761C>T
NM_033507.3:c.767C>T
NM_033508.3:c.761C>T
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Pathogenic

Met criteria codes 8
PM5_Strong PM3_Supporting PP4_Moderate PS4_Moderate PP3 PP2 PM1 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.764C>T variant in the glucokinase gene, GCK, causes an amino acid change of threonine to isoleucine at codon 255 (p.(Thr255Ile)) 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 0.795, which is greater than the MDEP VCEP threshold of 0.70 (PP3). 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). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). This variant was identified in five unrelated individuals with hyperglycemia (PS4_Moderate, PMID: 28170077; 19410318; 35472491). Additionally, at least two of these individuals had a linical history highly specific for GCK-hyperglycemia (fasting glucose 5.5-8 mmol/L, HbA1c 5.6 - 7.6% and detectable C-peptide in pediatric patients after 3 years) (PP4_Moderate; PMID: 28170077). This variant was also detected in the homozygous state in one individual with neonatal diabetes (PM3_Supporting; PMID: 36510364). Other missense variants at the same residue, c.764C>G (p.Thr255Ser) and c.763A>G (p.Thr255Ala), have been interpreted as pathogenic by the ClinGen MDEP, and p.Thr255Ile has a greater Grantham distance (PM5_Strong). In summary, c.764C>T 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): PM1, PM2_Supporting, PM3_Supporting, PM5_Strong, PP2, PP3, PP4_Moderate, PS4_Moderate.
Met criteria codes
PM5_Strong
Other missense variants at the same residue, c.764C>G (p.Thr255Ser) and c.763A>G (p.Thr255Ala), have been interpreted as pathogenic by the ClinGen MDEP, and p.Thr255Ile has a greater Grantham distance (PM5_Strong).
PM3_Supporting
This variant has been detected in one individual with neonatal diabetes who was homozygous for this variant (PM3_Supporting; PMID: 3651036).
PP4_Moderate
This variant was identified in two individuals with a clinical history highly specific for GCK-hyperglycemia (fasting glucose 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and positive C-peptide three years post-diagnosis in a pediatric patient) (PP4_Moderate; PMID: 28170077).
PS4_Moderate
This variant was identified in five unrelated individuals with hyperglycemia (PS4_Moderate, PMID: 28170077; 19410318; 35472491).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.795, 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).
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).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 and v4.1 (PM2_Supporting).
Curation History
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