The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000162.5(GCK):c.167A>C (p.Lys56Thr)

CA367403326

1807279 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: cccc4ddd-e40e-445c-8837-961ca3441918

HGVS expressions

NM_000162.5:c.167A>C
NM_000162.5(GCK):c.167A>C (p.Lys56Thr)
NC_000007.14:g.44153342T>G
CM000669.2:g.44153342T>G
NC_000007.13:g.44192941T>G
CM000669.1:g.44192941T>G
NC_000007.12:g.44159466T>G
NG_008847.1:g.41082A>C
NG_008847.2:g.49829A>C
ENST00000395796.8:c.*165A>C
ENST00000616242.5:c.167A>C
ENST00000682635.1:n.653A>C
ENST00000345378.7:c.170A>C
ENST00000403799.8:c.167A>C
ENST00000671824.1:c.167A>C
ENST00000673284.1:c.167A>C
ENST00000345378.6:c.170A>C
ENST00000395796.7:c.164A>C
ENST00000403799.7:c.167A>C
ENST00000437084.1:c.167A>C
ENST00000616242.4:c.164A>C
NM_000162.3:c.167A>C
NM_033507.1:c.170A>C
NM_033508.1:c.164A>C
NM_000162.4:c.167A>C
NM_001354800.1:c.167A>C
NM_033507.2:c.170A>C
NM_033508.2:c.164A>C
NM_033507.3:c.170A>C
NM_033508.3:c.164A>C

Likely Pathogenic

Met criteria codes 6
PM2_Supporting PS4_Moderate PP3 PP2 PP1_Moderate PP4_Moderate
Not Met criteria codes 2
BP4 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 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.167A>C variant in the glucokinase gene, GCK, causes an amino acid change of lysine to threonine at codon 56 (p.(Lys56Thr)) 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 0.957, 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 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). This variant segregated with diabetes, with 3 informative meioses in 2 families (PP1_Moderate; internal lab contributors). This variant was identified in 4 unrelated individuals with hyperglycemia (PS4_Moderate; PMID: 33852230, ClinVar VCV001807279.3, Internal lab contributors). In summary, c.167A>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, approved 8/11/2023): PP4_Moderate, PP2, PP3, PP1_Moderate, PM2_Supporting, PS4_Moderate.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PS4_Moderate
This variant was identified in four unrelated individuals with hyperglycemia (PS4_Moderate; PMID: 33852230, ClinVar VCV001807279.3, Internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.957, 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 diabetes, with 3 informative meioses in 2 families (PP1_Moderate; 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 negative antibodies) (PP4_Moderate; internal lab contributors).
Not Met criteria codes
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2024-01-22
Published on: 2024-01-22
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