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.1113C>G (p.Cys371Trp)

CA367398928

447379 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: afd68dc6-fb48-483f-9a46-594d8059fb70

HGVS expressions

NM_000162.5:c.1113C>G
NM_000162.5(GCK):c.1113C>G (p.Cys371Trp)
NC_000007.14:g.44145637G>C
CM000669.2:g.44145637G>C
NC_000007.13:g.44185236G>C
CM000669.1:g.44185236G>C
NC_000007.12:g.44151761G>C
NG_008847.1:g.48787C>G
NG_008847.2:g.57534C>G
ENST00000395796.8:c.*1111C>G
ENST00000616242.5:c.*233C>G
ENST00000683378.1:n.339C>G
ENST00000336642.9:c.147C>G
ENST00000345378.7:c.1116C>G
ENST00000403799.8:c.1113C>G
ENST00000671824.1:c.1176C>G
ENST00000672743.1:n.125C>G
ENST00000673284.1:c.1113C>G
ENST00000336642.8:n.165C>G
ENST00000345378.6:c.1116C>G
ENST00000395796.7:c.1110C>G
ENST00000403799.7:c.1113C>G
ENST00000437084.1:c.1062C>G
ENST00000459642.1:n.493C>G
ENST00000616242.4:n.1110C>G
NM_000162.3:c.1113C>G
NM_033507.1:c.1116C>G
NM_033508.1:c.1110C>G
NM_000162.4:c.1113C>G
NM_001354800.1:c.1113C>G
NM_001354801.1:c.102C>G
NM_001354802.1:c.-28C>G
NM_001354803.1:c.147C>G
NM_033507.2:c.1116C>G
NM_033508.2:c.1110C>G
NM_033507.3:c.1116C>G
NM_033508.3:c.1110C>G
NM_001354803.2:c.147C>G

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP3 PP2 PM5 PP4_Moderate
Not Met criteria codes 2
PS4 PP1

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 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1113C>G variant in the glucokinase gene, GCK, causes an amino acid change of cysteine to tryptophan at codon 371 (p.(Cys371Trp)) of NM_000162.5. GCK is defined by the ClinGen MDEP VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.891, 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 was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT increment < 3 mmol/L and a 3-generation family history of diabetes) (PP4_Moderate; internal lab contributors). This variant was identified in three unrelated individuals with a clinical picture consistent with monogenic diabetes; however, PS4_Moderate cannot be applied because this number is below the MDEP threshold (internal lab contributors). This variant segregated with diabetes with one informative meiosis in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918; internal lab contributors). Another missense variant, c.1112G>T p.(Cys371Phe), has been interpreted as pathogenic by the ClinGen MDEP VCEP and p.Cys371Trp has a greater Grantham distance. (PM5). In summary, this variant meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.2.0 approved 6/7/2023): PP2, PP3, PM2_Supporting, PP4_Moderate, PM5 .
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.891, which is greater than the MDEP VCEP threshold of 0.70 (PP3).
PP2
GCK is defined by the ClinGen MDEP VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2).
PM5
Another missense variant, c.1112G>T p.(Cys371Phe) has been interpreted as pathogenic by the ClinGen MDEP VCEP and p.Cys371Trp has a greater Grantham distance. (PM5).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT increment < 3 mmol/L and a 3-generation family history of diabetes) (PP4_Moderate; internal lab contributors).
Not Met criteria codes
PS4
This variant was identified in three unrelated individuals with a clinical picture consistent with monogenic diabetes, however PS4_Moderate cannot be applied because this number is below the MDEP threshold (internal lab contributors).
PP1
This variant segregated with diabetes with one informative meiosis in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918; internal lab contributors).
Approved on: 2023-08-09
Published on: 2023-08-10
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