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.661G>A (p.Glu221Lys)

CA213824

36241 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: bcac1d6c-8f3c-4870-ae6e-44213e7b972a

HGVS expressions

NM_000162.5:c.661G>A
NM_000162.5(GCK):c.661G>A (p.Glu221Lys)
NC_000007.14:g.44149778C>T
CM000669.2:g.44149778C>T
NC_000007.13:g.44189377C>T
CM000669.1:g.44189377C>T
NC_000007.12:g.44155902C>T
NG_008847.1:g.44646G>A
NG_008847.2:g.53393G>A
ENST00000395796.8:c.*659G>A
ENST00000616242.5:c.661G>A
ENST00000682635.1:n.1147G>A
ENST00000345378.7:c.664G>A
ENST00000403799.8:c.661G>A
ENST00000671824.1:c.661G>A
ENST00000673284.1:c.661G>A
ENST00000345378.6:c.664G>A
ENST00000395796.7:c.658G>A
ENST00000403799.7:c.661G>A
ENST00000437084.1:c.610G>A
ENST00000616242.4:c.658G>A
NM_000162.3:c.661G>A
NM_033507.1:c.664G>A
NM_033508.1:c.658G>A
NM_000162.4:c.661G>A
NM_001354800.1:c.661G>A
NM_033507.2:c.664G>A
NM_033508.2:c.658G>A
NM_033507.3:c.664G>A
NM_033508.3:c.658G>A

Pathogenic

Met criteria codes 6
PP4_Moderate PS4 PP3 PP2 PP1_Strong PM2_Supporting
Not Met criteria codes 2
PS3 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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.661A>G variant in the glucokinase gene, GCK, causes an amino acid change of glutamic acid to lysine at codon 221 (p.(Glu221Lys)) 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 0.789, 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 is located in the larger hexokinase domain of the GCK gene (PMID: 31638168) but this variant does not reside in an amino acid that directly binds glucose or ATP, which is defined as critical for the protein’s function by the ClinGen MDEP. This variant was identified in 4 unelated individuals with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antibodies or 2 hour OGTT glucose increment < 3 mmol/L) (PP4_Moderate; PMID: 23295292, internal lab contributors). This variant has been identified in 25 unrelated individuals with hyperglycemia and segregated with the phenotype, with 17 informative meioses in at least 7 families (PS4, PP1_Strong; PMIDs: 10694920, 12955723, 31658956, 34462253, 35592779, 35733065, 23295292, and 30592380). A relative activity index (RAI) was calculated for this variant but the wild type parameters are outside of MDEP's recommendations; therefore, this data cannot be used towards PS3 (PMID: 30592380). In summary, c.661A>G 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, approved 8/11/2023): PS4, PP1_Strong, PP4_Moderate, PP2, PP3, PM2_Supporting.
Met criteria codes
PP4_Moderate
This variant was identified in 4 unrelated individuals with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antibodies or 2 hour OGTT increment < 3 mmol/L) (PP4_Moderate; PMID: 23295292, internal lab contributors).
PS4
This variant was identified in 25 unrelated individuals with hyperglycemia (PS4; PMIDs: 10694920, 12955723, 31658956, 34462253, 35592779, 35733065, 23295292, and 30592380, internal lab contributors)
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.789, 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_Strong
This variant segregated with hyperglycemia, with 17 informative meioses in at least 7 families (PP1_Strong; PMIDs: 23295292, 30592380, 35733065, 10694920, internal lab contributors).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PS3
A relative activity index (RAI) was calculated for this variant but the wild type parameters are outside of MDEP's recommendations; therefore, this data cannot be used towards PS3.
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2024-02-28
Published on: 2024-02-28
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