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Variant: NM_000162.5(GCK):c.1136C>G (p.Ala379Gly)

CA367398793

447382 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 0f794d08-1d2f-4df8-af21-c0c17c576764

HGVS expressions

NM_000162.5:c.1136C>G
NM_000162.5(GCK):c.1136C>G (p.Ala379Gly)
NC_000007.14:g.44145614G>C
CM000669.2:g.44145614G>C
NC_000007.13:g.44185213G>C
CM000669.1:g.44185213G>C
NC_000007.12:g.44151738G>C
NG_008847.1:g.48810C>G
NG_008847.2:g.57557C>G
ENST00000395796.8:c.*1134C>G
ENST00000616242.5:c.*256C>G
ENST00000683378.1:n.362C>G
ENST00000336642.9:c.170C>G
ENST00000345378.7:c.1139C>G
ENST00000403799.8:c.1136C>G
ENST00000671824.1:c.1199C>G
ENST00000672743.1:n.148C>G
ENST00000673284.1:c.1136C>G
ENST00000336642.8:c.188C>G
ENST00000345378.6:c.1139C>G
ENST00000395796.7:c.1133C>G
ENST00000403799.7:c.1136C>G
ENST00000437084.1:c.1085C>G
ENST00000459642.1:n.516C>G
ENST00000616242.4:c.1133C>G
NM_000162.3:c.1136C>G
NM_033507.1:c.1139C>G
NM_033508.1:c.1133C>G
NM_000162.4:c.1136C>G
NM_001354800.1:c.1136C>G
NM_001354801.1:c.125C>G
NM_001354802.1:c.-5C>G
NM_001354803.1:c.170C>G
NM_033507.2:c.1139C>G
NM_033508.2:c.1133C>G
NM_033507.3:c.1139C>G
NM_033508.3:c.1133C>G
NM_001354803.2:c.170C>G

Likely Pathogenic

Met criteria codes 5
PP4_Moderate PM5_Supporting PM2_Supporting PP3 PP2

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 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1136C>G variant in the glucokinase gene, GCK, causes an amino acid change of alanine to glycine at codon 379 (p.(Ala379Gly)) of NM_000162.5. GCK is defined by the ClinGen MDEP VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0 0.922, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). Two other missense variants, c.1136C>A p.Ala379Glu and c.1136C>T p.Ala379Val, have been classified as likely pathogenic by the ClinGen MDEP VCEP (PM5_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% and negative antibodies) (PP4_Moderate, 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 8/11/2023): PP4_Moderate, PP2, PP3, PM2_Supporting, PM5_supporting.
Met criteria codes
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 negative antibodies) (PP4_Moderate, internal lab contributors).
PM5_Supporting
Another missense variant, c.1136C>A p.Ala379Glu, has been classified as likely pathogenic by the ClinGen MDEP VCEP (PM5_Supporting).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.922, 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).
Approved on: 2024-03-31
Published on: 2024-03-31
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