The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data


Variant: NM_000162.5(GCK):c.737G>A (p.Gly246Glu)

CA367400662

995373 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 7ada4a7b-94ed-491c-a1b9-4fc02afb251e
Approved on: 2024-01-22
Published on: 2024-01-22

HGVS expressions

NM_000162.5:c.737G>A
NM_000162.5(GCK):c.737G>A (p.Gly246Glu)
NC_000007.14:g.44147776C>T
CM000669.2:g.44147776C>T
NC_000007.13:g.44187375C>T
CM000669.1:g.44187375C>T
NC_000007.12:g.44153900C>T
NG_008847.1:g.46648G>A
NG_008847.2:g.55395G>A
ENST00000395796.8:c.*735G>A
ENST00000616242.5:c.737G>A
ENST00000345378.7:c.740G>A
ENST00000403799.8:c.737G>A
ENST00000671824.1:c.737G>A
ENST00000673284.1:c.737G>A
ENST00000345378.6:c.740G>A
ENST00000395796.7:c.734G>A
ENST00000403799.7:c.737G>A
ENST00000437084.1:c.686G>A
ENST00000616242.4:c.734G>A
NM_000162.3:c.737G>A
NM_033507.1:c.740G>A
NM_033508.1:c.734G>A
NM_000162.4:c.737G>A
NM_001354800.1:c.737G>A
NM_033507.2:c.740G>A
NM_033508.2:c.734G>A
NM_033507.3:c.740G>A
NM_033508.3:c.734G>A
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Likely Pathogenic

Met criteria codes 6
PM2_Supporting PP2 PP3 PP4_Moderate PM5_Supporting PS4_Moderate
Not Met criteria codes 2
PP1 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>A variant in the glucokinase gene, GCK, causes an amino acid change of glycine to glutamic acid at codon 246 (p.(Gly246Glu)) 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 0.882, 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 5 unrelated individuals with hyperglycemia (PMIDs: 30663027, 18248649, internal lab contributors). This variant was identified in 2 unrelated individuals and one related individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%, and negative antibodies) (PP4_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. In addition c.737C>G p.Gly246Ala has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting). In summary, c.737G>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): PP4_Moderate, PS4_Moderate, PP2, PP3, PM2_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
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).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.882, which is greater than the MDEP VCEP threshold of 0.70 (PP3).
PP4_Moderate
This variant was identified in 2 unrelated individuals and one related individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%, and negative antibodies) (PP4_Moderate, internal lab contributors).
PM5_Supporting
p.Gly246Arg pathogenic, GD = 125 p.Gly246Glu GD = 98 Another missense variant, c.736G>A p.Gly246Arg, has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance. In addition c.737C>G p.Gly246Ala has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting).
PS4_Moderate
This variant was identified in 5 unrelated individuals with hyperglycemia (PMIDs: 30663027, 18248649, internal lab contributors).
Not Met criteria codes
PP1
This variant segregated with diabetes with 1 informative meiosis in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (internal lab contributors).
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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