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.170T>A (p.Met57Lys)

CA367403317

2684202 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 4c1913c6-13c2-4f68-838d-dacb38248dcb
Approved on: 2025-06-17
Published on: 2025-06-17

HGVS expressions

NM_000162.5:c.170T>A
NM_000162.5(GCK):c.170T>A (p.Met57Lys)
NC_000007.14:g.44153339A>T
CM000669.2:g.44153339A>T
NC_000007.13:g.44192938A>T
CM000669.1:g.44192938A>T
NC_000007.12:g.44159463A>T
NG_008847.1:g.41085T>A
NG_008847.2:g.49832T>A
ENST00000395796.8:c.*168T>A
ENST00000616242.5:c.170T>A
ENST00000682635.1:n.656T>A
ENST00000345378.7:c.173T>A
ENST00000403799.8:c.170T>A
ENST00000671824.1:c.170T>A
ENST00000673284.1:c.170T>A
ENST00000345378.6:c.173T>A
ENST00000395796.7:c.167T>A
ENST00000403799.7:c.170T>A
ENST00000437084.1:c.170T>A
ENST00000616242.4:c.167T>A
NM_000162.3:c.170T>A
NM_033507.1:c.173T>A
NM_033508.1:c.167T>A
NM_000162.4:c.170T>A
NM_001354800.1:c.170T>A
NM_033507.2:c.173T>A
NM_033508.2:c.167T>A
NM_033507.3:c.173T>A
NM_033508.3:c.167T>A
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Likely Pathogenic

Met criteria codes 6
PM2_Supporting PP1 PP2 PP3 PM5 PP4_Moderate
Not Met criteria codes 1
PS4

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.170T>A variant in the glucokinase gene, GCK, causes an amino acid change of methionine to lysine at codon 57 (p.(Met57Lys)) of NM_000162.5. This variant is absent from gnomAD v4.1.0 (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). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.98, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in three unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID: 39859454, ClinVar ID: 2684202, internal lab contributors). At least one of these individuals had a clinical history highly specific for GCK-hyperglycemia (multiple instances of fasting glucose 5.5-8 mmol/L and HbA1c 5.6 - 7.6%, and negative antibodies) (PP4_Moderate; internal lab contributors). This variant segregated with hyperglycemia with at least 3 meioses in a single family (PP1; internal lab contributors). Another missense variant at the same codon, c.171G>A, p.(Met57Ile), has been interpreted as pathogenic by the ClinGen MDEP, and p.(Met57Lys) has a greater Grantham distance (PM5). In summary, c.170T>A meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.0.0, approved 2/17/2025): PM2_Supporting, PP1, PP2, PP3, PP4_Moderate, PM5.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting)
PP1
This variant segregated with hyperglycemia with at least 3 meioses in a single family (PP1; internal lab contributors).
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).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.98, which is greater than the MDEP VCEP threshold of 0.70 (PP3).
PM5
Another missense variant at the same codon, c.171G>A, p.(Met57Ile), has been interpreted as pathogenic by the ClinGen MDEP, and p.(Met57Lys) has a greater Grantham distance (PM5).
PP4_Moderate
This variant was identified in at least two individuals with a clinical history highly specific for GCK-hyperglycemia (multiple instances of both 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
PS4
This variant was identified in three unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID: 39859454, ClinVar ID: 2684202, internal lab contributors).
Curation History
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