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.434T>G

CA367401977

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: f3af0549-8683-41bb-8ef4-acf01bd35c38
Approved on: 2023-08-13
Published on: 2023-08-13

HGVS expressions

NM_033508.3:c.434T>G
NC_000007.14:g.44151002A>C
CM000669.2:g.44151002A>C
NC_000007.13:g.44190601A>C
CM000669.1:g.44190601A>C
NC_000007.12:g.44157126A>C
NG_008847.1:g.43422T>G
NG_008847.2:g.52169T>G
ENST00000395796.8:c.*435T>G
ENST00000616242.5:c.437T>G
ENST00000682635.1:n.923T>G
ENST00000345378.7:c.440T>G
ENST00000403799.8:c.437T>G
ENST00000671824.1:c.437T>G
ENST00000673284.1:c.437T>G
ENST00000345378.6:c.440T>G
ENST00000395796.7:c.434T>G
ENST00000403799.7:c.437T>G
ENST00000437084.1:c.386T>G
ENST00000616242.4:n.434T>G
NM_000162.3:c.437T>G
NM_033507.1:c.440T>G
NM_033508.1:c.434T>G
NM_000162.4:c.437T>G
NM_001354800.1:c.437T>G
NM_033507.2:c.440T>G
NM_033508.2:c.434T>G
NM_000162.5:c.437T>G
NM_033507.3:c.440T>G

Likely Pathogenic

Met criteria codes 6
PM5 PM2_Supporting PS3_Moderate PP4 PP3 PP2
Not Met criteria codes 2
PM1 PS4

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.437T>G variant in the glucokinase gene, GCK causes an amino acid change of leucine to arginine at codon 210 (p.(Leu146Arg)) 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 also predicted to be deleterious by computational evidence, with a REVEL score of 0.981, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). 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%) (PP4; PMIDs: 24804978, 29927023). 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.Leu146Arg variant has a relative activity index (RAI) <0.50 (PS3_Moderate; PMID: 16731834). Another missense variant, c.437T>C p.Leu146Pro, has been interpreted as pathogenic by the ClinGen MDEP VCEP and p.Leu146Arg has a greater Grantham distance. (PM5). This variant was identified in three unrelated individuals with a clinical picture consistent with monogenic diabetes; however, PS4_Moderate cannot be applied because this number is below the MDEP threshold (PMID 18399931, 24804978, 29927023, internal lab contributors). In summary, this variant meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.3.0, approved 8/13/2023): PS3_Moderate, PP2, PM2_Supporting, PP3, PP4, PM5.
Met criteria codes
PM5
Another missense variant, c.437T>C, p.Leu146Pro, has been interpreted as pathogenic by the ClinGen MDEP VCEP and p.Leu146Arg has a greater Grantham distance. (PM5).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
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.Leu146Arg variant has a relative activity index (RAI) <0.50 (PS3_Moderate; PMID: 16731834).
PP4
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%) (PP4; PMIDs: 24804978, 29927023).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.981, 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).
Not Met criteria codes
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
This variant was identified in three unrelated individuals with a clinical picture consistent with monogenic diabetes, however PS4_Moderate cannot be applied because this number is below the MDEP threshold (PMID 18399931, 24804978, 29927023, internal lab contributors).
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