The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000162.5(GCK):c.1265G>T (p.Arg422Leu)

CA157911892

1800884 (ClinVar)

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: e5079dda-99ad-4583-a42d-e93dbd143710
Approved on: 2026-10-22
Published on: 2026-10-22

HGVS expressions

NM_000162.5(GCK):c.1265G>T (p.Arg422Leu)
NM_000162.5:c.1265G>T
NC_000007.14:g.44145269C>A
CM000669.2:g.44145269C>A
NC_000007.13:g.44184868C>A
CM000669.1:g.44184868C>A
NC_000007.12:g.44151393C>A
NG_008847.1:g.49155G>T
NG_008847.2:g.57902G>T
ENST00000395796.8:c.*1263G>T
ENST00000616242.5:c.*385G>T
ENST00000683378.1:n.491G>T
ENST00000336642.9:c.299G>T
ENST00000345378.7:c.1268G>T
ENST00000403799.8:c.1265G>T
ENST00000671824.1:c.1328G>T
ENST00000672743.1:n.277G>T
ENST00000673284.1:c.1265G>T
ENST00000336642.8:c.317G>T
ENST00000345378.6:c.1268G>T
ENST00000395796.7:c.1262G>T
ENST00000403799.7:c.1265G>T
ENST00000437084.1:c.1214G>T
ENST00000459642.1:n.645G>T
ENST00000616242.4:c.1262G>T
NM_000162.3:c.1265G>T
NM_033507.1:c.1268G>T
NM_033508.1:c.1262G>T
NM_000162.4:c.1265G>T
NM_001354800.1:c.1265G>T
NM_001354801.1:c.254G>T
NM_001354802.1:c.125G>T
NM_001354803.1:c.299G>T
NM_033507.2:c.1268G>T
NM_033508.2:c.1262G>T
NM_033507.3:c.1268G>T
NM_033508.3:c.1262G>T
NM_001354803.2:c.299G>T
More

Likely Pathogenic

Met criteria codes 5
PS4_Moderate PP2 PP4_Moderate PM2_Supporting PM5_Supporting
Not Met criteria codes 2
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 3.1

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1265G>T variant in the glucokinase, GCK, causes an amino acid change of arginine to leucine at codon 422 (p.Arg422Leu) 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 has an incomputable gnomAD v4.1.2 Grpmax filtering allele frequency due to no more than one copy in any non-founder subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (Grpmax FAF <= 0.000003) (PM2_Supporting). This variant was identified in four unrelated individuals with hyperglycemia (PS4_Moderate; PMID: 23771925, 33218273, internal lab contributors). At least one of these individuals had a phenotype highly consistent for GCK-related hyperglycemia (persistent elevated fasting glucose 5.5-8 mmol/L (3x) and HbA1c 5.6 - 7.6% (4x)) (PP4_Moderate; PMID: 33218273). Another missense variant at the same residue, c.1265G>C (p.Arg422Pro), has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting). This variant has a REVEL score of 0.635, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on GCK function. In summary, c.1265G>T 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, approved 10/10/2025): PS4_Moderate, PP4_Moderate, PM2_Supporting, PM5_Supporting, PP2.
Met criteria codes
PS4_Moderate
This variant was identified in four unrelated individuals with hyperglycemia (PS4_Moderate; PMID: 23771925, 33218273, 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).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (persistent fasting glucose 5.5-8 mmol/L (3x) and HbA1c 5.6 - 7.6% (4x)) (PP4_Moderate; PMID: 33218273).
PM2_Supporting
This variant has an incomputable gnomAD v4.1.1 Grpmax filtering allele frequency due to no more than one copy in any non-founder subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (Grpmax FAF <= 0.000003) (PM2_Supporting).
PM5_Supporting
Another missense variant at the same residue, c.1265G>C (p.Arg422Pro), has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting).
Not Met criteria codes
PP3
This variant has a REVEL score of 0.635, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on HNF1A function.
BP4
This variant has a REVEL score of 0.635, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on HNF1A function.
Curation History
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