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Variant: NM_000162.5(GCK):c.1136C>T (p.Ala379Val)

CA367398790

804834 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: faeecf67-a17e-4c56-b8d5-d7eabea68354

HGVS expressions

NM_000162.5:c.1136C>T
NM_000162.5(GCK):c.1136C>T (p.Ala379Val)
NC_000007.14:g.44145614G>A
CM000669.2:g.44145614G>A
NC_000007.13:g.44185213G>A
CM000669.1:g.44185213G>A
NC_000007.12:g.44151738G>A
NG_008847.1:g.48810C>T
NG_008847.2:g.57557C>T
ENST00000395796.8:c.*1134C>T
ENST00000616242.5:c.*256C>T
ENST00000683378.1:n.362C>T
ENST00000336642.9:c.170C>T
ENST00000345378.7:c.1139C>T
ENST00000403799.8:c.1136C>T
ENST00000671824.1:c.1199C>T
ENST00000672743.1:n.148C>T
ENST00000673284.1:c.1136C>T
ENST00000336642.8:n.188C>T
ENST00000345378.6:c.1139C>T
ENST00000395796.7:c.1133C>T
ENST00000403799.7:c.1136C>T
ENST00000437084.1:c.1085C>T
ENST00000459642.1:n.516C>T
ENST00000616242.4:n.1133C>T
NM_000162.3:c.1136C>T
NM_033507.1:c.1139C>T
NM_033508.1:c.1133C>T
NM_000162.4:c.1136C>T
NM_001354800.1:c.1136C>T
NM_001354801.1:c.125C>T
NM_001354802.1:c.-5C>T
NM_001354803.1:c.170C>T
NM_033507.2:c.1139C>T
NM_033508.2:c.1133C>T
NM_033507.3:c.1139C>T
NM_033508.3:c.1133C>T
NM_001354803.2:c.170C>T

Likely Pathogenic

Met criteria codes 7
PM5_Supporting PP3 PP2 PM2_Supporting PS4_Moderate PP1_Moderate PP4_Moderate
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 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1136C>T variant in the glucokinase gene, GCK, causes an amino acid change of alanine to proline at codon 379 (p.(Ala379Val)) 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 0.968, 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 five unrelated individuals with hyperglycemia (PS4_Moderate; PMID 18322640, 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% and negative antibodies) (PP4_Moderate; PMIDs: 18322640, 17573900). This variant segregated with diabetes, with three informative meioses in two families with MODY (PP1_Moderate; PMID 18322640). Another missense variant, c.1136C>A p.Ala379Glu, has been classified as pathogenic by the ClinGen MDEP VCEP but has a greater Grantham distance than p.Ala379Val (PM5_supporting). While studies exploring the effect of this variant on protein function have been performed, these studies do not meet the criteria set forth by the MDEP for the application of PS3 or BS3 (PMID: 18322640). 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 1.2.0, approved 6/7/2023): PP2, PP3, PM2_Supporting, PS4_Moderate, PP4_Moderate, PP1_Moderate, PM5_Supporting.
Met criteria codes
PM5_Supporting
Another missense variant, c.1136C>A p.Ala379Glu, has been classified as pathogenic by the ClinGen MDEP VCEP but has a greater Grantham distance than p.Ala379Val.
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.968, 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 five unrelated individuals with hyperglycemia (PS4_Moderate; PMID 18322640, internal lab contributors).
PP1_Moderate
This variant was segregated with diabetes, with three informative meioses in two families with MODY (PP1_Moderate; PMID 18322640).
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; PMIDs: 18322640, 17573900).
Not Met criteria codes
PS3
While studies exploring the effect of this variant on protein function have been performed, these studies do not meet the criteria set forth by the MDEP for the application of PS3 or BS3 (PMID: 18322640).
Approved on: 2023-08-01
Published on: 2023-08-01
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