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.822C>A (p.Asp274Glu)

CA367400482

994611 (ClinVar)

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 878639da-2681-4ca3-968e-76c232e46fac
Approved on: 2025-09-08
Published on: 2025-09-08

HGVS expressions

NM_000162.5(GCK):c.822C>A (p.Asp274Glu)
NM_000162.5:c.822C>A
NC_000007.14:g.44147691G>T
CM000669.2:g.44147691G>T
NC_000007.13:g.44187290G>T
CM000669.1:g.44187290G>T
NC_000007.12:g.44153815G>T
NG_008847.1:g.46733C>A
NG_008847.2:g.55480C>A
ENST00000395796.8:c.*820C>A
ENST00000616242.5:c.822C>A
ENST00000345378.7:c.825C>A
ENST00000403799.8:c.822C>A
ENST00000671824.1:c.822C>A
ENST00000673284.1:c.822C>A
ENST00000345378.6:c.825C>A
ENST00000395796.7:c.819C>A
ENST00000403799.7:c.822C>A
ENST00000437084.1:c.771C>A
ENST00000616242.4:c.819C>A
NM_000162.3:c.822C>A
NM_033507.1:c.825C>A
NM_033508.1:c.819C>A
NM_000162.4:c.822C>A
NM_001354800.1:c.822C>A
NM_033507.2:c.825C>A
NM_033508.2:c.819C>A
NM_033507.3:c.825C>A
NM_033508.3:c.819C>A
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Likely Pathogenic

Met criteria codes 6
PP4_Moderate PP3 PP2 PM5_Supporting PS4_Moderate PM2_Supporting
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 3.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.822C>A variant in the glucokinase gene, GCK, is a missense variant resulting in an amino acid change of aspartic acid to glutamic acid at codon 274 (p.(Asp274Glu)) of NM_000162.5. This variant has an incomputable gnomAD v4.1.0 Grpmax filtering allele frequency due to the presence of only 1 copy in any subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (Grpmax FAF less than or equal to 0.000003) (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). Additionally, it is predicted to be deleterious by computational evidence, with a REVEL score of 0.929, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in five unrelated individuals with hyperglycemia (PS4_Moderate; PMIDs: 19790256, 34440516, 36178555; internal lab contributors). Additionally, one of these individuals had 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; PMID: 36178555, internal lab contributors). Another missense variant, c.821A>C p.(Asp274Ala), has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.(Asp274Glu) (PM5_Supporting). In summary, c.822C>A variant meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 3.0.0, approved 7/23/2025): PM2_Supporting, PM5_Supporting, PP2, PP3, PP4_Moderate, PS4_Moderate.
Met criteria codes
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: 36178555, internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.929, 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).
PM5_Supporting
Another missense variant, c.821A>C p.(Asp274Ala), has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.(Asp274Glu) (PM5_Supporting).
PS4_Moderate
This variant was identified in five unrelated individuals with hyperglycemia (PS4_Moderate; PMIDs: 19790256, 34440516, 36178555; internal lab contributors).
PM2_Supporting
This variant has an incomputable gnomAD v4.1.0 Grpmax filtering allele frequency due to the presence of only 1 copy in any subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (Grpmax FAF less than or equal to 0.000003) (PM2_Supporting).
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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