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


Variant: NM_000162.5(GCK):c.171G>T (p.Met57Ile)

CA16603236

377026 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 6ef90ebe-8dcc-4008-ba71-a117dcb69619
Approved on: 2024-10-31
Published on: 2025-02-28

HGVS expressions

NM_000162.5:c.171G>T
NM_000162.5(GCK):c.171G>T (p.Met57Ile)
NC_000007.14:g.44153338C>A
CM000669.2:g.44153338C>A
NC_000007.13:g.44192937C>A
CM000669.1:g.44192937C>A
NC_000007.12:g.44159462C>A
NG_008847.1:g.41086G>T
NG_008847.2:g.49833G>T
ENST00000395796.8:c.*169G>T
ENST00000616242.5:c.171G>T
ENST00000682635.1:n.657G>T
ENST00000345378.7:c.174G>T
ENST00000403799.8:c.171G>T
ENST00000671824.1:c.171G>T
ENST00000673284.1:c.171G>T
ENST00000345378.6:c.174G>T
ENST00000395796.7:c.168G>T
ENST00000403799.7:c.171G>T
ENST00000437084.1:c.171G>T
ENST00000616242.4:c.168G>T
NM_000162.3:c.171G>T
NM_033507.1:c.174G>T
NM_033508.1:c.168G>T
NM_000162.4:c.171G>T
NM_001354800.1:c.171G>T
NM_033507.2:c.174G>T
NM_033508.2:c.168G>T
NM_033507.3:c.174G>T
NM_033508.3:c.168G>T
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Likely Pathogenic

Met criteria codes 6
PS1 PP4 PP3 PP2 PM2_Supporting PM5_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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.171G>T variant in the glucokinase gene, GCK, causes an amino acid change of methionine to isoleucine at codon 57 (p.(Met57Ile)) of NM_000162.5. This variant is absent from gnomAD v2.1.1 and v4.1 (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 0.987, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in an individual with a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4; PMID: 34440516). The nucleotide change c.171G>A, which results in the same amino acid change, has been classified as pathogenic for GCK-hyperglycemia by the ClinGen MDEP (PS1). Another missense variant at the same codon, c.170T>G (p.Met57Arg), has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting). In summary, c.171G>T p.(Met57Ile) meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PM2_Supporting, PM5_Supporting, PP2, PP3, PP4, PS1).
Met criteria codes
PS1
The nucleotide change c.171G>A, which causes the same amino acid change, has been classified as pathogenic for GCK-hyperglycemia by the ClinGen MDEP (PS1).
PP4
This variant was reported in an individual with a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4, PMID: 34440516).
PP3
This variant is predicted to be deleterious by computational evidence with a REVEL score of 0.987, which is greater than the MDEP VCEP threshold of 0.70 (PP3).
PP2
GCK, in which the variant was identified, is definted by the ClinGen Monogenic Diabetes Expert Panel as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2).
PM2_Supporting
This variant is absent from gnomAD v2.1 and v4.1 (PM2_Supporting).
PM5_Supporting
Another missense variant at the same codon, c.170T>G (p.Met57Arg), has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting).
Not Met criteria codes
PM1
Variant does occur in the glucose- or ATP-binding sites.
Curation History
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