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.823C>T (p.Arg275Cys)

CA4239519

585927 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 10a41ed2-a058-4df3-b3ec-335ec9c2b90e

HGVS expressions

NM_000162.5:c.823C>T
NM_000162.5(GCK):c.823C>T (p.Arg275Cys)
NC_000007.14:g.44147690G>A
CM000669.2:g.44147690G>A
NC_000007.13:g.44187289G>A
CM000669.1:g.44187289G>A
NC_000007.12:g.44153814G>A
NG_008847.1:g.46734C>T
NG_008847.2:g.55481C>T
ENST00000395796.8:c.*821C>T
ENST00000616242.5:c.823C>T
ENST00000345378.7:c.826C>T
ENST00000403799.8:c.823C>T
ENST00000671824.1:c.823C>T
ENST00000673284.1:c.823C>T
ENST00000345378.6:c.826C>T
ENST00000395796.7:c.820C>T
ENST00000403799.7:c.823C>T
ENST00000437084.1:c.772C>T
ENST00000616242.4:c.820C>T
NM_000162.3:c.823C>T
NM_033507.1:c.826C>T
NM_033508.1:c.820C>T
NM_000162.4:c.823C>T
NM_001354800.1:c.823C>T
NM_033507.2:c.826C>T
NM_033508.2:c.820C>T
NM_033507.3:c.826C>T
NM_033508.3:c.820C>T

Pathogenic

Met criteria codes 6
PS4 PP1 PP3 PP2 PM2_Supporting PP4_Moderate
Not Met criteria codes 1
PS3

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.823C>T variant in the glucokinase gene, GCK, causes an amino acid change of arginine to cysteine at codon 275 (p.(Arg275Cys)) of NM_000162.5. This variant was identified in 7 unrelated individuals with hyperglycemia (PS4; PMID: 24001579, internal lab contributors). This variant was identified in two individuals with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT increment < 3 mmol/L) (internal lab contributors). This variant segregated with diabetes/hyperglycemia, with 3 informative meioses in 1 family (PP1; PMID: 24001579). 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 0.901, which is greater than the MDEP VCEP threshold of 0.70 (PP3). While a study exploring the effect of this variant on protein function has been performed and suggests a possible impact on stability and dimerization, the study does not meet the criteria set forth by the MDEP for the application of PS3 or BS3 (PMID: 24001579). This variant has an incomputable gnomAD v2.1.1 Popmax minor filtering allele frequency due to 1 copy in the European non-Finnish subpopulation, 1 copy in the African/African American subpopulation, and 1 copy in the South Asian subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Popmax FAF less than or equal to 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting). In summary, 823C>T meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PS4, PP4_Moderate, PP1, PP2, PP3, PM2_Supporting.
Met criteria codes
PS4
This variant was identified in 7 unrelated individuals with hyperglycemia (PS4; PMIDs: 24001579, internal lab contributors).
PP1
This variant segregated with diabetes, with 3 informative meioses in 1 family with MODY (PP1; PMID: 24001579).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.901, 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).
PM2_Supporting
This variant has an incomputable gnomAD v2.1.1 Popmax minor filtering allele frequency due to 1 copy in the European non-Finnish subpopulation, 1 copy in the African/African American subpopulation, and 1 copy in the South Asian subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Popmax FAF less than or equal to 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting).
PP4_Moderate
This variant was identified in two individuals with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT increment < 3 mmol/L) (internal lab contributors).
Not Met criteria codes
PS3
While a study exploring the effect of this variant on protein function has been performed and suggests a possible impact on stability and dimerization, the study does not meet the criteria set forth by the MDEP for the application of PS3 or BS3 (PMID: 24001579).
Approved on: 2023-09-20
Published on: 2023-09-20
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.
¤ Powered by BCM's Genboree.