The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document


Variant: NM_001354803.2:c.178T>G

CA367398753

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 9c1ac4ec-a0c9-46a5-80e8-dffed2481ddc

HGVS expressions

NM_001354803.2:c.178T>G
NC_000007.14:g.44145606A>C
CM000669.2:g.44145606A>C
NC_000007.13:g.44185205A>C
CM000669.1:g.44185205A>C
NC_000007.12:g.44151730A>C
NG_008847.1:g.48818T>G
NG_008847.2:g.57565T>G
ENST00000395796.8:c.*1142T>G
ENST00000616242.5:c.*264T>G
ENST00000683378.1:n.370T>G
ENST00000336642.9:c.178T>G
ENST00000345378.7:c.1147T>G
ENST00000403799.8:c.1144T>G
ENST00000671824.1:c.1207T>G
ENST00000672743.1:n.156T>G
ENST00000673284.1:c.1144T>G
ENST00000336642.8:c.196T>G
ENST00000345378.6:c.1147T>G
ENST00000395796.7:c.1141T>G
ENST00000403799.7:c.1144T>G
ENST00000437084.1:c.1093T>G
ENST00000459642.1:n.524T>G
ENST00000616242.4:c.1141T>G
NM_000162.3:c.1144T>G
NM_033507.1:c.1147T>G
NM_033508.1:c.1141T>G
NM_000162.4:c.1144T>G
NM_001354800.1:c.1144T>G
NM_001354801.1:c.133T>G
NM_001354802.1:c.4T>G
NM_001354803.1:c.178T>G
NM_033507.2:c.1147T>G
NM_033508.2:c.1141T>G
NM_000162.5:c.1144T>G
NM_033507.3:c.1147T>G
NM_033508.3:c.1141T>G

Likely Pathogenic

Met criteria codes 7
PP4_Moderate PS4_Moderate PM5_Supporting PM2_Supporting PP1_Moderate PP3 PP2

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.1144T>G variant in the glucokinase gene, GCK, causes an amino acid change of alanine to proline at codon 382 (p.(Cys382Gly)) 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 0.912, 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 segregated with diabetes, with 4 informative meioses in a family with MODY (PP1_Moderate; internal lab contributors). This variant was identified in 4 unrelated individuals with hyperglycemia (PS4_Moderate; internal lab contributors). Two of these individuals had a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antibodies and 3 generation family history of diabetes) (PP4_Moderate; internal lab contributors). Another missense variant, c.1144T>C (p.Cys382Arg), has been classified as pathogenic by the ClinGen MDEP VCEP but has a greater Grantham distance than p.(Cys382Gly)(PM5_Supporting). 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 1.3.0, approved 8/11/2023): PP2, PP3, PM2_Supporting, PP1_Moderate, PS4_Moderate, PP4_Moderate, PM5_Supporting.
Met criteria codes
PP4_Moderate
This variant was identified in 2 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 and 3 generation family history of diabetes) (PP4_Moderate; internal lab contributors).
PS4_Moderate
This variant was identified in 4 unrelated individuals with hyperglycemia (PS4_Moderate; internal lab contributors)
PM5_Supporting
Another missense variant, c.1144T>C (p.Cys382Arg), has been classified as pathogenic by the ClinGen MDEP VCEP but has a greater Grantham distance than p.(Cys382Gly). (PM5_Supporting)
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP1_Moderate
This variant was segregated with diabetes, with 4 informative meioses in a family with MODY (PP1_Moderate; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.912, 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).
Approved on: 2023-11-24
Published on: 2023-11-24
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