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Variant: NM_000162.5(GCK):c.749G>A (p.Arg250His)

CA4239531

435311 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 168bac84-6ec4-49d4-a604-a4b470a9b4e8
Approved on: 2023-10-25
Published on: 2023-10-25

HGVS expressions

NM_000162.5:c.749G>A
NM_000162.5(GCK):c.749G>A (p.Arg250His)
NC_000007.14:g.44147764C>T
CM000669.2:g.44147764C>T
NC_000007.13:g.44187363C>T
CM000669.1:g.44187363C>T
NC_000007.12:g.44153888C>T
NG_008847.1:g.46660G>A
NG_008847.2:g.55407G>A
ENST00000395796.8:c.*747G>A
ENST00000616242.5:c.749G>A
ENST00000345378.7:c.752G>A
ENST00000403799.8:c.749G>A
ENST00000671824.1:c.749G>A
ENST00000673284.1:c.749G>A
ENST00000345378.6:c.752G>A
ENST00000395796.7:c.746G>A
ENST00000403799.7:c.749G>A
ENST00000437084.1:c.698G>A
ENST00000616242.4:c.746G>A
NM_000162.3:c.749G>A
NM_033507.1:c.752G>A
NM_033508.1:c.746G>A
NM_000162.4:c.749G>A
NM_001354800.1:c.749G>A
NM_033507.2:c.752G>A
NM_033508.2:c.746G>A
NM_033507.3:c.752G>A
NM_033508.3:c.746G>A

Likely Pathogenic

Met criteria codes 5
PM5_Supporting PP4_Moderate PM2_Supporting PP3 PP2
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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.749G>A variant in the glucokinase gene, GCK, causes an amino acid change of arginine to histidine at codon 250 (p.(Arg250His)) of NM_000162.5. This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (pediatric patient with incidental diagnosis with FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% persistently and negative antibodies (PP4_Moderate; PMID: 28170077, 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). 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 v2.1.1 Popmax minor filtering allele frequency due to 0 copies in the European non-Finnish subpopulation and 1 copy in the African/African American subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Popmax FAF <= 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting). Another missense variant, c.748C>T p.Arg250Cys, has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Arg250His (PM5_Supporting). The relative activity index (RAI) of this variant was above the MDEP cutoff of 0.5, and thermostability was not evaluated, and neither PS3 nor BS3 could be applied (PMID: 30592380). In summary, c.749G>A 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, approved 8/11/2023): PP4_Moderate, PP2, PP3, PM2_Supporting, PM5_Supporting.
Met criteria codes
PM5_Supporting
Another missense variant, c.748C>T p.Arg250Cys, has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Arg250His (PM5_Supporting).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (pediatric patient with incidental diagnosis with FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% persistently and negative antibodies (PP4_Moderate; PMID: 28170077, internal lab contributors).
PM2_Supporting
This variant has an incomputable gnomAD v2.1.1 Popmax minor filtering allele frequency due to 0 copies in the European non-Finnish subpopulation and 1 copy in the African/African American subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Popmax FAF <= 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.871, 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
PS3
The relative activity index (RAI) of this variant was above the MDEP cutoff of 0.5, and thermostability was not evaluated, and neither PS3 nor BS3 could be applied (PMID: 30592380).
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