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.532G>A (p.Gly178Arg)

CA213798

36227 (ClinVar)

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: e0c3c48e-9f0e-4d36-ab1c-010c4fe4aa9a
Approved on: 2026-03-22
Published on: 2026-03-26

HGVS expressions

NM_000162.5(GCK):c.532G>A (p.Gly178Arg)
NM_000162.5:c.532G>A
NC_000007.14:g.44150016C>T
CM000669.2:g.44150016C>T
NC_000007.13:g.44189615C>T
CM000669.1:g.44189615C>T
NC_000007.12:g.44156140C>T
NG_008847.1:g.44408G>A
NG_008847.2:g.53155G>A
ENST00000395796.8:c.*530G>A
ENST00000616242.5:c.532G>A
ENST00000682635.1:n.1018G>A
ENST00000345378.7:c.535G>A
ENST00000403799.8:c.532G>A
ENST00000671824.1:c.532G>A
ENST00000673284.1:c.532G>A
ENST00000345378.6:c.535G>A
ENST00000395796.7:c.529G>A
ENST00000403799.7:c.532G>A
ENST00000437084.1:c.481G>A
ENST00000616242.4:c.529G>A
NM_000162.3:c.532G>A
NM_033507.1:c.535G>A
NM_033508.1:c.529G>A
NM_000162.4:c.532G>A
NM_001354800.1:c.532G>A
NM_033507.2:c.535G>A
NM_033508.2:c.529G>A
NM_033507.3:c.535G>A
NM_033508.3:c.529G>A
More

Likely Pathogenic

Met criteria codes 6
PP3 PP2 PM5 PP4_Moderate PM2_Supporting PS4_Moderate
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 3.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.532G>A variant in the glucokinase gene, GCK, causes an amino acid change of glycine to arginine at codon 178 (p.(Gly178Arg)) 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). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.979, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant has an incomputable gnomAD v4.1 Grpmax filtering allele frequency due to 1 copy in the European non-Finnish subpopulation and no copies in any other subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (Grpmax FAF <= 0.000003) (PM2_Supporting). This variant was identified in five unrelated individuals with hyperglycemia (PS4_Moderate; PMID: 36257325,11508276; internal lab contributors). At least 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 OGTT with minimal increment (<3mmol/l) (PP4_Moderate; internal lab contributors). Another missense variant at the same residue, c.533G>A p.Gly178Glu, has been interpreted as pathogenic by the ClinGen MDEP, and p.Gly178Arg has a greater Grantham distance (PM5). In summary, c.532G>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 3.1.0, approved 10/10/2025): PP2, PP3, PM2_Supporting, PM5, PP4_Moderate, PS4_Moderate.
Met criteria codes
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.979, 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
Another missense variant at the same residue, c.533G>A p.Gly178Glu, has been interpreted as pathogenic by the ClinGen MDEP, and p.Gly178Arg has a greater Grantham distance (PM5).
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 OGTT with minimal increment (<3mmol/l) (PP4_Moderate; internal lab contributors)
PM2_Supporting
This variant has an incomputable gnomAD v4.1. Grpmax filtering allele frequency due to 1 copy in the European non-Finnish subpopulation and no copies in any other subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (Grpmax FAF <= 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting).
PS4_Moderate
This variant was identified in four unrelated individuals with hyperglycemia (PS4_Moderate; PMIDs: 36257325,11508276; internal lab contributors).
Not Met criteria codes
PM1
This variant does not reside in an amino acid that directly binds glucose or ATP, which are defined as critical for the GCK protein's function by the ClinGen MDEP.
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
ClinGen Terms of Use.
¤ Powered by BCM's Genboree.