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Variant: NM_000162.5(GCK):c.737G>C (p.Gly246Ala)

CA367400661

804856 (ClinVar)

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 25a49c8d-f7da-4631-8407-5b2887f3fef3
Approved on: 2023-12-02
Published on: 2023-12-02

HGVS expressions

NM_000162.5:c.737G>C
NM_000162.5(GCK):c.737G>C (p.Gly246Ala)
NC_000007.14:g.44147776C>G
CM000669.2:g.44147776C>G
NC_000007.13:g.44187375C>G
CM000669.1:g.44187375C>G
NC_000007.12:g.44153900C>G
NG_008847.1:g.46648G>C
NG_008847.2:g.55395G>C
ENST00000395796.8:c.*735G>C
ENST00000616242.5:c.737G>C
ENST00000345378.7:c.740G>C
ENST00000403799.8:c.737G>C
ENST00000671824.1:c.737G>C
ENST00000673284.1:c.737G>C
ENST00000345378.6:c.740G>C
ENST00000395796.7:c.734G>C
ENST00000403799.7:c.737G>C
ENST00000437084.1:c.686G>C
ENST00000616242.4:c.734G>C
NM_000162.3:c.737G>C
NM_033507.1:c.740G>C
NM_033508.1:c.734G>C
NM_000162.4:c.737G>C
NM_001354800.1:c.737G>C
NM_033507.2:c.740G>C
NM_033508.2:c.734G>C
NM_033507.3:c.740G>C
NM_033508.3:c.734G>C
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Likely Pathogenic

Met criteria codes 7
PM2_Supporting PM5_Supporting PS4_Moderate PP4_Moderate PP3 PP2 PP1_Moderate
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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.737G>C variant in the glucokinase gene, GCK, causes an amino acid change of glycine to alanine at codon 246 (p.(Gly246Ala)) 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 0.839, 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 4 unrelated individuals with hyperglycemia (PS4_Moderate; PMID:27256595, internal lab contributors). One of these individuals had 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) (PP4_Moderate, PMID:27256595). This variant segregated with hyperglycemia, with 3 informative meioses in 2 families (PP1_Moderate; internal lab contributors). Another missense variant, c.736G>A p.Gly246Arg, has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Gly246Ala (PM5_Supporting). In summary, c.737G>C 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): PP4_Moderate, PS4_Moderate, PP1_Moderate, PP2, PP3, PM2_Supporting, PM5_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PM5_Supporting
p.Gly246Arg GD = 125 p.Gly246Ala GD = 60 Another missense variant, c.736G>A p.Gly246Arg, has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Gly246Ala (PM5_Supporting).
PS4_Moderate
This variant was identified in 4 unrelated individuals with hyperglycemia (PS4_Moderate; PMID:27256595, internal lab contributors)
PP4_Moderate
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% and OGTT increment < 3 mmol/L) (PP4_Moderate, PMID:27256595).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.839, 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).
PP1_Moderate
This variant segregated with hyperglycemia, with 3 informative meioses in 2 families (PP1_Moderate; internal lab contributors).
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
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