The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document


Variant: NM_033508.3:c.779G>A

CA367400569

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 9ff98b1f-698d-45f3-a3d8-f835ad13f5a5
Approved on: 2023-08-12
Published on: 2023-08-12

HGVS expressions

NM_033508.3:c.779G>A
NC_000007.14:g.44147731C>T
CM000669.2:g.44147731C>T
NC_000007.13:g.44187330C>T
CM000669.1:g.44187330C>T
NC_000007.12:g.44153855C>T
NG_008847.1:g.46693G>A
NG_008847.2:g.55440G>A
ENST00000395796.8:c.*780G>A
ENST00000616242.5:c.782G>A
ENST00000345378.7:c.785G>A
ENST00000403799.8:c.782G>A
ENST00000671824.1:c.782G>A
ENST00000673284.1:c.782G>A
ENST00000345378.6:c.785G>A
ENST00000395796.7:c.779G>A
ENST00000403799.7:c.782G>A
ENST00000437084.1:c.731G>A
ENST00000616242.4:n.779G>A
NM_000162.3:c.782G>A
NM_033507.1:c.785G>A
NM_033508.1:c.779G>A
NM_000162.4:c.782G>A
NM_001354800.1:c.782G>A
NM_033507.2:c.785G>A
NM_033508.2:c.779G>A
NM_000162.5:c.782G>A
NM_033507.3:c.785G>A
More

Pathogenic

Met criteria codes 7
PP1_Strong PS4 PS3_Moderate PP3 PP2 PM5_Supporting PM2_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 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.782G>A variant in the glucokinase gene, GCK, causes an amino acid change of glycine to glutamic acid at codon 261 (p.(Gly261Glu)) 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 0.989, which is greater than the MDEP threshold of 0.70 (PP3). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). This variant was identified in more than 11 unrelated individuals with diabetes/hyperglycemia (PS4; PMID 19358091, 8168652 , internal lab contributors). This variant segregated with diabetes/hyperglycemia with 11 informative meioses in 4 families (PP1_Strong; internal lab contributors). A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, the wild-type ATP Km is between 0.4-0.65, and the p.Gly261Glu variant has a relative activity index (RAI) of 0, which is less than the MDEP VCEP threshold of 0.50 (PMID: 19903754). Another missense variant, c.781G>A, (p.Gly261Arg), has been classified as pathogenic by the ClinGen MDEP VCEP but has a greater Grantham distance than p.Gly261Glu​(PM5_Supporting). In summary, this variant meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.3.0, approved 8/11/2023): PM2_Supporting, PP2, PP3, PM5_Supporting, PS4, PP1_Strong, PS3_Moderate.
Met criteria codes
PP1_Strong
This variant segregated with diabetes/hyperglycemia with 11 informative meioses in 4 families (PP1_Strong; internal lab contributors).
PS4
This variant was identified in more than 11 unrelated individuals with diabetes (PS4; PMID 19358091, 8168652 , internal lab contributors).
PS3_Moderate
A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, the wild-type ATP Km is between 0.4-0.65, and the p.Gly261Glu variant has a relative activity index (RAI) of 0, which is less than the MDEP VCEP threshold of 0.50 (PMID: 19903754).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.989, which is greater than the MDEP 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.781G>A, (p.Gly261Arg), has been classified as pathogenic by the ClinGen MDEP VCEP but has a greater Grantham distance than p.(Gly261Glu)​. (PM5_Supporting)
PM2_Supporting
This variant is absent in the gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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.