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 label mismatch: GCK vs undefined
  • 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.410A>G (p.His137Arg)

CA367402077

2136527 (ClinVar)

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 1f10f058-0d0a-4ae8-b1c8-902f00adc777
Approved on: 2025-04-17
Published on: 2025-04-17

HGVS expressions

NM_000162.5:c.410A>G
NM_000162.5(GCK):c.410A>G (p.His137Arg)
NC_000007.14:g.44151029T>C
CM000669.2:g.44151029T>C
NC_000007.13:g.44190628T>C
CM000669.1:g.44190628T>C
NC_000007.12:g.44157153T>C
NG_008847.1:g.43395A>G
NG_008847.2:g.52142A>G
ENST00000395796.8:c.*408A>G
ENST00000616242.5:c.410A>G
ENST00000682635.1:n.896A>G
ENST00000345378.7:c.413A>G
ENST00000403799.8:c.410A>G
ENST00000671824.1:c.410A>G
ENST00000673284.1:c.410A>G
ENST00000345378.6:c.413A>G
ENST00000395796.7:c.407A>G
ENST00000403799.7:c.410A>G
ENST00000437084.1:c.364-5A>G
ENST00000616242.4:c.407A>G
NM_000162.3:c.410A>G
NM_033507.1:c.413A>G
NM_033508.1:c.407A>G
NM_000162.4:c.410A>G
NM_001354800.1:c.410A>G
NM_033507.2:c.413A>G
NM_033508.2:c.407A>G
NM_033507.3:c.413A>G
NM_033508.3:c.407A>G
More

Likely Pathogenic

Met criteria codes 4
PP2 PP4_Moderate PM2_Supporting PP1_Strong
Not Met criteria codes 4
PS3 PS4 PP3 BP4

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 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.410A>G variant in the glucokinase gene, GCK, causes an amino acid change of histidine to arginine at codon 137 (p.(His137Arg)) 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). The variant is absent in gnomAD v2.1 and v4.1 (PM2_Supporting). It has a REVEL score of 0.598, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on GCK function. While studies exploring the effect of this variant on protein function have been performed, these studies do not meet the criteria set forth by the MDEP for the application of PS3 or BS3 (PMID: 10525657, 14517946). This variant was identified in two unrelated cases with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID: 904948, internal lab contributors). 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; internal lab contributor). Additionally, this variant segregated with hyperglycemia, with nine informative meioses in a single family (PP1_Strong; PMID: 9049484). In summary, c.410A>G meets the criteria to be classified as a likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.0.0, approved 8/11/2023): PP1_Strong, PP4_Moderate, PM2_Supporting, PP2.
Met criteria codes
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).
PP4_Moderate
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% and negative antibodies) (PP4_Moderate; Internal lab contributor).
PM2_Supporting
Absent in gnomAD v2.1 and v4.1 (PM2_Supporting).
PP1_Strong
This variant segregated with hyperglycemia, with nine informative meioses in one family (PP1_Strong; PMID: 9049484).
Not Met criteria codes
PS3
While studies exploring the effect of this variant on protein function have been performed, these studies do not meet the criteria set forth by the MDEP for the application of PS3 or BS3 (PMID: 10525657, 14517946).
PS4
This variant was identified in two unrelated cases with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID: 904948, Internal lab contributors).
PP3
This variant has a REVEL score of 0.598, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on GCK function.
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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