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Variant: NM_000162.5(GCK):c.629T>C (p.Met210Thr)

CA367401300

804852 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 36ad32f3-6b33-4dae-8175-4a5daf06b61c

HGVS expressions

NM_000162.5:c.629T>C
NM_000162.5(GCK):c.629T>C (p.Met210Thr)
NC_000007.14:g.44149810A>G
CM000669.2:g.44149810A>G
NC_000007.13:g.44189409A>G
CM000669.1:g.44189409A>G
NC_000007.12:g.44155934A>G
NG_008847.1:g.44614T>C
NG_008847.2:g.53361T>C
ENST00000395796.8:c.*627T>C
ENST00000616242.5:c.629T>C
ENST00000682635.1:n.1115T>C
ENST00000345378.7:c.632T>C
ENST00000403799.8:c.629T>C
ENST00000671824.1:c.629T>C
ENST00000673284.1:c.629T>C
ENST00000345378.6:c.632T>C
ENST00000395796.7:c.626T>C
ENST00000403799.7:c.629T>C
ENST00000437084.1:c.578T>C
ENST00000616242.4:c.626T>C
NM_000162.3:c.629T>C
NM_033507.1:c.632T>C
NM_033508.1:c.626T>C
NM_000162.4:c.629T>C
NM_001354800.1:c.629T>C
NM_033507.2:c.632T>C
NM_033508.2:c.626T>C
NM_033507.3:c.632T>C
NM_033508.3:c.626T>C

Pathogenic

Met criteria codes 6
PS3_Supporting PP1_Strong PS4 PP3 PP2 PM2_Supporting
Not Met criteria codes 1
PP4

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.629T>C variant in the glucokinase gene, GCK, causes an amino acid change of methionine to threonine at codon 210 (p.(Met210Thr)) 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 0.982, which is greater than the MDEP threshold of 0.70 (PP3). A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, but the wild-type ATP Km is not between 0.4-0.65, and the p.Met210Thr has Kcat/S0.5<0.5 (PS3_Supporting; PMID: 14517946, DOI:10.1007/s001250051289). This variant has an incomputable gnomAD v2.1.1 Popmax filtering allele frequency of due to 0 copies observed in the European non-Finnish population and only 1 copy in another subpopulation (Latino/admixed), thereby meeting the ClinGen MDEP criteria for PM2_Supporting (PM2_Supporting). This variant was identified in 11 unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; PMIDs: 25555642, 9049484, ClinVar ID: 804852, internal lab contributor). This variant was identified in an individual with a phenotype suggestive of GCK-hyperglycemia; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributor). This variant segregated with diabetes, with 5 informative meioses in 2 families with MODY (PP1_Strong; internal lab contributors). Taken together, the evidence supports the classification of c.629T>C as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.2.0, approved 6/7/2023): PP1_Strong, PS4, PS3_Moderate, PP2, PP3, PM2_Supporting.
Met criteria codes
PS3_Supporting
A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, but the wild-type ATP Km is not between 0.4-0.65, and the p.Met210Thr has Kcat/S0.5<0.5 (PS3_Supporting; PMID: 14517946, DOI:10.1007/s001250051289).
PP1_Strong
This variant segregated with diabetes, with 5 informative meioses in 2 families with MODY (PP1_Strong; internal lab contributors).
PS4
This variant was identified in 11 unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; PMIDs: 25555642, 9049484, ClinVar ID: 804852, internal lab contributor).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.982, 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).
PM2_Supporting
This variant has an incomputable gnomAD v2.1.1 Popmax filtering allele frequency of due to 0 copies observed in the European non-Finnish population and only 1 copy in another subpopulation (Latino/admixed), thereby meeting the ClinGen MDEP criteria for PM2_Supporting (PM2_Supporting).
Not Met criteria codes
PP4
This variant was identified in an individual with a phenotype suggestive of GCK-hyperglycemia; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributor).
Approved on: 2024-01-18
Published on: 2024-01-18
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