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Variant: NM_000162.5(GCK):c.503C>T (p.Thr168Ile)

CA367401750

1490297 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 013ccb72-f009-4e24-af55-2fef3fc8abde

HGVS expressions

NM_000162.5:c.503C>T
NM_000162.5(GCK):c.503C>T (p.Thr168Ile)
NC_000007.14:g.44150045G>A
CM000669.2:g.44150045G>A
NC_000007.13:g.44189644G>A
CM000669.1:g.44189644G>A
NC_000007.12:g.44156169G>A
NG_008847.1:g.44379C>T
NG_008847.2:g.53126C>T
ENST00000395796.8:c.*501C>T
ENST00000616242.5:c.503C>T
ENST00000682635.1:n.989C>T
ENST00000345378.7:c.506C>T
ENST00000403799.8:c.503C>T
ENST00000671824.1:c.503C>T
ENST00000673284.1:c.503C>T
ENST00000345378.6:c.506C>T
ENST00000395796.7:c.500C>T
ENST00000403799.7:c.503C>T
ENST00000437084.1:c.452C>T
ENST00000616242.4:c.500C>T
NM_000162.3:c.503C>T
NM_033507.1:c.506C>T
NM_033508.1:c.500C>T
NM_000162.4:c.503C>T
NM_001354800.1:c.503C>T
NM_033507.2:c.506C>T
NM_033508.2:c.500C>T
NM_033507.3:c.506C>T
NM_033508.3:c.500C>T

Pathogenic

Met criteria codes 7
PM2_Supporting PS4_Moderate PP4 PP3 PP2 PM1 PM5_Strong

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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.503C>T variant in the glucokinase gene, GCK, causes an amino acid change of threonine to isoleucine at codon 168 (p.(Thr168Ile)) of NM_000162.5. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). 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 0.997 which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant resides in an amino acid that directly binds glucose, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1). 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). This variant was identified in 4 unrelated individuals with hyperglycemia (PS4_Moderate; internal lab contributors). Two other missense variants, c.502A>G p.Thr168Ala and c.503C>A p.Thr168Asn, have been interpreted as pathogenic by the ClinGen MDEP, and p.Thr168Ile has a greater Grantham distance than p.Thr168Ala and p.Thr168Asn (PM5_Strong). In summary, c.503C>T meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PM2_Supporting, PP2, PP3, PM1, PP4, PS4_Moderate, PM5_Strong.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PS4_Moderate
This variant was identified in 4 unrelated individuals with hyperglycemia (PS4_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 0.997 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).
PM1
This variant resides in an amino acid that directly binds glucose, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1).
PM5_Strong
Two other missense variants, c.502A>G p.Thr168Ala and c.503C>A p.Thr168Asn, have been interpreted as pathogenic by the ClinGen MDEP, and p.Thr168Ile has a greater Grantham distance than p.Thr168Ala and p.Thr168Asn (PM5_Strong).
Approved on: 2023-12-01
Published on: 2023-12-01
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