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.223C>G

CA367398536

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 5196b25c-61aa-49ee-9505-ba8e4e4a0b36

HGVS expressions

NM_001354803.2:c.223C>G
NC_000007.14:g.44145561G>C
CM000669.2:g.44145561G>C
NC_000007.13:g.44185160G>C
CM000669.1:g.44185160G>C
NC_000007.12:g.44151685G>C
NG_008847.1:g.48863C>G
NG_008847.2:g.57610C>G
ENST00000395796.8:c.*1187C>G
ENST00000616242.5:c.*309C>G
ENST00000683378.1:n.415C>G
ENST00000336642.9:c.223C>G
ENST00000345378.7:c.1192C>G
ENST00000403799.8:c.1189C>G
ENST00000671824.1:c.1252C>G
ENST00000672743.1:n.201C>G
ENST00000673284.1:c.1189C>G
ENST00000336642.8:c.241C>G
ENST00000345378.6:c.1192C>G
ENST00000395796.7:c.1186C>G
ENST00000403799.7:c.1189C>G
ENST00000437084.1:c.1138C>G
ENST00000459642.1:n.569C>G
ENST00000616242.4:c.1186C>G
NM_000162.3:c.1189C>G
NM_033507.1:c.1192C>G
NM_033508.1:c.1186C>G
NM_000162.4:c.1189C>G
NM_001354800.1:c.1189C>G
NM_001354801.1:c.178C>G
NM_001354802.1:c.49C>G
NM_001354803.1:c.223C>G
NM_033507.2:c.1192C>G
NM_033508.2:c.1186C>G
NM_000162.5:c.1189C>G
NM_033507.3:c.1192C>G
NM_033508.3:c.1186C>G

Likely Pathogenic

Met criteria codes 5
PP4 PP3 PP2 PM5 PM2_Supporting
Not Met criteria codes 1
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.1189C>G variant in the glucokinase gene, GCK, causes an amino acid change of arginine to glycine at codon 397 (p.(Arg397Glyr)) 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 0.817, which is greater than or equal to the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in two related individuals with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4; internal lab contributors). This variant segregated with diabetes with two informative meioses in a single family, however this does not meet the thresholds for PP1 set by the ClinGen MDEP VCEP (PMID: 27236918, internal lab contributor). Another missense variant, c.1190G>T p.Arg397Leu, has been interpreted as pathogenic by the ClinGen MDEP VCEP and p.Arg397Gly has a greater Grantham distance(PM5). In summary, c.1189C>G 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): PM5, PP2, PP3, PP4, PM2_Supporting.
Met criteria codes
PP4
This variant was identified in two related individuals with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.817, which is greater than or equal to 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.1190G>T p.Arg397Leu has been interpreted as pathogenic by the ClinGen MDEP VCEP and p.Arg397Gly has a greater Grantham distance (PM5).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PP1
This variant segregated with disease with two informative meioses in a single family with diabetes, however this does not meet the thresholds for PP1 set by the ClinGen MDEP VCEP (PMID: 27236918, ) (internal lab contributor).
Approved on: 2023-11-23
Published on: 2023-11-23
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