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Variant: NM_000162.5(GCK):c.524G>A (p.Gly175Glu)

CA367401680

1746350 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 36b00893-c831-4ba0-921b-d83058abea63

HGVS expressions

NM_000162.5:c.524G>A
NM_000162.5(GCK):c.524G>A (p.Gly175Glu)
NC_000007.14:g.44150024C>T
CM000669.2:g.44150024C>T
NC_000007.13:g.44189623C>T
CM000669.1:g.44189623C>T
NC_000007.12:g.44156148C>T
NG_008847.1:g.44400G>A
NG_008847.2:g.53147G>A
ENST00000395796.8:c.*522G>A
ENST00000616242.5:c.524G>A
ENST00000682635.1:n.1010G>A
ENST00000345378.7:c.527G>A
ENST00000403799.8:c.524G>A
ENST00000671824.1:c.524G>A
ENST00000673284.1:c.524G>A
ENST00000345378.6:c.527G>A
ENST00000395796.7:c.521G>A
ENST00000403799.7:c.524G>A
ENST00000437084.1:c.473G>A
ENST00000616242.4:c.521G>A
NM_000162.3:c.524G>A
NM_033507.1:c.527G>A
NM_033508.1:c.521G>A
NM_000162.4:c.524G>A
NM_001354800.1:c.524G>A
NM_033507.2:c.527G>A
NM_033508.2:c.521G>A
NM_033507.3:c.527G>A
NM_033508.3:c.521G>A

Likely Pathogenic

Met criteria codes 7
PM5_Supporting PS2_Moderate PP4 PP3 PP2 PM2_Supporting PS4_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.524G>A variant in the glucokinase gene, GCK, causes an amino acid change of glycine to glutamate at codon 175 (p.(Gly175Glu)) 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 0.914, 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 four unrelated individuals with hyperglycemia (PS4_Moderate; PMID: 11508276, internal lab contributors). This variant was identified as a de novo occurrence with unconfirmed parental relationships in one individual with a clinical picture consistent with GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6-7.6) (PS2_Moderate; internal lab contributors). 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; internal lab contributors). Another missense variant, c.523G>A p.Gly175Arg, has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Gly175Glu (PM5_Supporting). In summary, c.524G>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 1.3.0, approved 8/11/2023): PS4_Moderate, PS2_Moderate, PP4, PM2_Supporting, PP2, PP3, PM5_Supporting.
Met criteria codes
PM5_Supporting
Another missense variant, c.523G>A p.Gly175Arg, has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Gly175Glu (PM5_Supporting).
PS2_Moderate
This variant was identified as a de novo occurrence with unconfirmed parental relationships in one individual with a clinical picture consistent with GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6-7.6) (PS2_Moderate; internal lab contributors).
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; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.914, 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 is absent from gnomAD v2.1.1 (PM2_Supporting).
PS4_Moderate
This variant was identified in four unrelated individuals with hyperglycemia (PS4_Moderate; PMID: 11508276, internal lab contributors).
Approved on: 2024-02-23
Published on: 2024-02-23
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