The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000162.5(GCK):c.824G>T (p.Arg275Leu)

CA367400477

435310 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 764f4360-61f7-488c-b85f-5a14e0738c32

HGVS expressions

NM_000162.5:c.824G>T
NM_000162.5(GCK):c.824G>T (p.Arg275Leu)
NC_000007.14:g.44147689C>A
CM000669.2:g.44147689C>A
NC_000007.13:g.44187288C>A
CM000669.1:g.44187288C>A
NC_000007.12:g.44153813C>A
NG_008847.1:g.46735G>T
NG_008847.2:g.55482G>T
ENST00000395796.8:c.*822G>T
ENST00000616242.5:c.824G>T
ENST00000345378.7:c.827G>T
ENST00000403799.8:c.824G>T
ENST00000671824.1:c.824G>T
ENST00000673284.1:c.824G>T
ENST00000345378.6:c.827G>T
ENST00000395796.7:c.821G>T
ENST00000403799.7:c.824G>T
ENST00000437084.1:c.773G>T
ENST00000616242.4:c.821G>T
NM_000162.3:c.824G>T
NM_033507.1:c.827G>T
NM_033508.1:c.821G>T
NM_000162.4:c.824G>T
NM_001354800.1:c.824G>T
NM_033507.2:c.827G>T
NM_033508.2:c.821G>T
NM_033507.3:c.827G>T
NM_033508.3:c.821G>T

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP3 PP2 PM5_Supporting PP4_Moderate

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.824G>T variant in the glucokinase gene, GCK, causes an amino acid change of arginine to leucine at codon 275 (p.(Arg275Leu)) of NM_000162.5. 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 contributors). 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 0.702, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). Another missense variant, c.823C>T p.Arg275Cys, has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Arg275Leu (PM5_Supporting). In summary, c.824G>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 1.3.0, approved 8/11/2023): PP4_Moderate, PP2, PP3, PM2_Supporting, PM5_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.702, 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_Supporting
Another missense variant, c.823C>T p.Arg275Cys, has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Arg275Leu (PM5_Supporting).
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 contributors).
Approved on: 2023-09-20
Published on: 2023-09-20
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