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.322T>G (p.Tyr108Asp)

CA213777

36212 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: ade76523-de50-4ccc-bb02-e619516ccd1e
Approved on: 2024-01-18
Published on: 2024-01-18

HGVS expressions

NM_000162.5:c.322T>G
NM_000162.5(GCK):c.322T>G (p.Tyr108Asp)
NC_000007.14:g.44152312A>C
CM000669.2:g.44152312A>C
NC_000007.13:g.44191911A>C
CM000669.1:g.44191911A>C
NC_000007.12:g.44158436A>C
NG_008847.1:g.42112T>G
NG_008847.2:g.50859T>G
ENST00000395796.8:c.*320T>G
ENST00000616242.5:c.322T>G
ENST00000682635.1:n.808T>G
ENST00000345378.7:c.325T>G
ENST00000403799.8:c.322T>G
ENST00000671824.1:c.322T>G
ENST00000673284.1:c.322T>G
ENST00000345378.6:c.325T>G
ENST00000395796.7:c.319T>G
ENST00000403799.7:c.322T>G
ENST00000437084.1:c.322T>G
ENST00000616242.4:c.319T>G
NM_000162.3:c.322T>G
NM_033507.1:c.325T>G
NM_033508.1:c.319T>G
NM_000162.4:c.322T>G
NM_001354800.1:c.322T>G
NM_033507.2:c.325T>G
NM_033508.2:c.319T>G
NM_033507.3:c.325T>G
NM_033508.3:c.319T>G
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Uncertain Significance

Met criteria codes 4
PP3 PP2 PM5 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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.322T>G variant in the glucokinase gene,GCK, causes an amino acid change of tyrosine to aspartic acid at codon 108 (p.(Tyr108Asp)) 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 0.967, 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 has been reported as likely pathogenic in ClinVar; however, no clinical information was provided (ClinVar ID: 36212). Another missense variant, c.322T>C p.Tyr108His,has been interpreted as pathogenic by the ClinGen MDEP, and p.Tyr108Asp has a greater Grantham distance (PM5). In summary, c.322T>G 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 8/11/2023): PM5, PP2, PP3, PM2_Supporting.
Met criteria codes
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.967, 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.322T>C p.Tyr108His, has been interpreted as pathogenic by the ClinGen MDEP, and p.Tyr108Asp has an equal or greater Grantham distance (PM5).
PM2_Supporting
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
PP4
This variant has been reported as likely pathogenic in ClinVar; however, no clinical information was provided (ClinVar ID: 36212).
Curation History
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