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.781G>A (p.Gly261Arg)

CA126211

16135 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 30f3b683-bd18-46bf-808d-e9059fa45ccb

HGVS expressions

NM_000162.5:c.781G>A
NM_000162.5(GCK):c.781G>A (p.Gly261Arg)
NC_000007.14:g.44147732C>T
CM000669.2:g.44147732C>T
NC_000007.13:g.44187331C>T
CM000669.1:g.44187331C>T
NC_000007.12:g.44153856C>T
NG_008847.1:g.46692G>A
NG_008847.2:g.55439G>A
ENST00000395796.8:c.*779G>A
ENST00000616242.5:c.781G>A
ENST00000345378.7:c.784G>A
ENST00000403799.8:c.781G>A
ENST00000671824.1:c.781G>A
ENST00000673284.1:c.781G>A
ENST00000345378.6:c.784G>A
ENST00000395796.7:c.778G>A
ENST00000403799.7:c.781G>A
ENST00000437084.1:c.730G>A
ENST00000616242.4:n.778G>A
NM_000162.3:c.781G>A
NM_033507.1:c.784G>A
NM_033508.1:c.778G>A
NM_000162.4:c.781G>A
NM_001354800.1:c.781G>A
NM_033507.2:c.784G>A
NM_033508.2:c.778G>A
NM_033507.3:c.784G>A
NM_033508.3:c.778G>A

Pathogenic

Met criteria codes 9
PS2 PS4 PP3 PP2 PP4_Moderate PM3 PS3_Moderate PM2_Supporting PP1_Strong
Not Met criteria codes 1
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.781G>A variant in the glucokinase gene, GCK, causes an amino acid change of glycine to arginine at codon 261 (p.(Gly261Arg)) 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 0.914, which is greater than the MDEP threshold of 0.70 (PP3). This variant has an incomputable gnomAD v2.1.1 Popmax minor filtering allele frequency due to 0 copies in the European non-Finnish subpopulation and 1 copy in the "Other" subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Popmax FAF less than or equal to 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting). This variant was identified in more than 38 unrelated individuals with diabetes (PS4; PMIDs: 29417725, 33324081, 21518409, 25015100, 22611063, 17573900, internal lab contributors). This variant was identified in at least two 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) (PP4_Moderate, internal lab contributors). This variant segregated with diabetes/hyperglycemia with 30 informative meioses in 18 families (PP1_Strong; PMID 33324081, 21518409, internal lab contributors). This variant was identified as a de novo occurrence with confirmed parental relationships in one individual with a clinical picture consistent with GCK-hyperglycemia (PS2; internal lab contributors). This variant has been detected in at least 2 individuals with neonatal diabetes who were both homozygous for the variant, confirmed in trans (PM3: PMID 33324081, 25015100, internal lab contributors). A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, the wild-type ATP Km is between 0.4-0.65, and the p.Gly261Arg variant has a relative activity index (RAI) of 0.02, which is less than the MDEP VCEP threshold of 0.50 (PMID: 19903754). In summary, this variant meets the criteria to be classified as pathogenic for monogenic diabetews. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.3.0, approved 8/11/2023): PM2_Supporting, PP2, PP3, PP4_Moderate, PS3_Moderate, PM3, PP1_Strong, PS4, PS2.
Met criteria codes
PS2
This variant was identified as a de novo occurrence with confirmed parental relationships in one individual with a clinical picture consistent with GCK-hyperglycemia (PS2; internal lab contributors).
PS4
This variant was identified in more than 38 unrelated individuals with diabetes /hyperglycemia (PS4; PMIDs: 29417725, 33324081, 21518409, 25015100, 22611063, 17573900, internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.914, which is greater than the MDEP 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).
PP4_Moderate
This variant was identified in at least two 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) (PP4_Moderate, internal lab contributors).
PM3
This variant has been detected in at least 2 individuals with neonatal diabetes who were both homozygous for the variant, confirmed in trans (PM3: PMID 33324081, 25015100, internal lab contributors).
PS3_Moderate
A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, the wild-type ATP Km is between 0.4-0.65, and the p.Leu304Pro variant has a relative activity index (RAI) of 0.02, which is less than the MDEP VCEP threshold of 0.50 (PMID: 19903754).
PM2_Supporting
This variant has an incomputable gnomAD v2.1.1 Popmax minor filtering allele frequency due to 0 copies in the European non-Finnish subpopulation and 1 copy in the "Other" subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Popmax FAF less than or equal to 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting).
PP1_Strong
This variant segregated with diabetes/hyperglycemia with 30 informative meioses in 18 families (PP1_Strong; PMID 33324081, 21518409, internal lab contributors).
Not Met criteria codes
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-08-12
Published on: 2023-08-12
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