The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: GCK vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000162.5(GCK):c.952G>T (p.Gly318Trp)

CA213870

36268 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: a9cc5a29-b599-4add-8c84-95d3c315cf99
Approved on: 2025-06-02
Published on: 2025-06-02

HGVS expressions

NM_000162.5:c.952G>T
NM_000162.5(GCK):c.952G>T (p.Gly318Trp)
NC_000007.14:g.44146530C>A
CM000669.2:g.44146530C>A
NC_000007.13:g.44186129C>A
CM000669.1:g.44186129C>A
NC_000007.12:g.44152654C>A
NG_008847.1:g.47894G>T
NG_008847.2:g.56641G>T
ENST00000395796.8:c.*950G>T
ENST00000616242.5:c.*72G>T
ENST00000683378.1:n.178G>T
ENST00000345378.7:c.955G>T
ENST00000403799.8:c.952G>T
ENST00000671824.1:c.1015G>T
ENST00000673284.1:c.952G>T
ENST00000345378.6:c.955G>T
ENST00000395796.7:c.949G>T
ENST00000403799.7:c.952G>T
ENST00000437084.1:c.901G>T
ENST00000473353.1:n.250G>T
ENST00000616242.4:c.949G>T
NM_000162.3:c.952G>T
NM_033507.1:c.955G>T
NM_033508.1:c.949G>T
NM_000162.4:c.952G>T
NM_001354800.1:c.952G>T
NM_001354801.1:c.8+89G>T
NM_033507.2:c.955G>T
NM_033508.2:c.949G>T
NM_033507.3:c.955G>T
NM_033508.3:c.949G>T
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Uncertain Significance

Met criteria codes 4
PM2_Supporting PP3 PP2 PM5
Not Met criteria codes 2
PS4 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 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.952G>T variant in the glucokinase gene, GCK, causes an amino acid change of glycine to tryptophan at codon 318 (p.(Gly318Trp)) 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 has an incomputable gnomAD v4.1.0 Grpmax filtering allele frequency due to zero copies in the European non-Finnish subpopulation and 1 copy in any other subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Grpmax FAF <= 0.000003) (PM2_Supporting). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.9, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in a single individual with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold and PP4 cannot be evaluated due to insufficient clinical data (internal lab contributors). Another missense variant, c.952G>A, p.(Gly318Arg) has been interpreted as pathogenic by the ClinGen MDEP, and p.(Gly318Trp) has a greater Grantham distance (PM5). In summary, c.952G>T meets the criteria to be classified as a variant of uncertain significance for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/23): PM5, PM2_Supporting, PP2, PP3.
Met criteria codes
PM2_Supporting
This variant has an incomputable gnomAD v4.1.0 Grpmax filtering allele frequency due to zero copies in the European non-Finnish subpopulation and 1 copy in any other subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Grpmax FAF <= 0.000003) (PM2_Supporting).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.9, 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).
PM5
Another missense variant, c.952G>A, p.(Gly318Arg) has been interpreted as pathogenic by the ClinGen MDEP, and p.(Gly318Trp) has a greater Grantham distance (PM5).
Not Met criteria codes
PS4
This variant was identified in a single individual with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors).
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 contributors).
Curation History
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