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
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_033508.3:c.231C>G

CA367403035

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 48329529-1db9-488b-b8e4-2eba2e46ab2d
Approved on: 2024-12-02
Published on: 2024-12-02

HGVS expressions

NM_033508.3:c.231C>G
NC_000007.14:g.44152400G>C
CM000669.2:g.44152400G>C
NC_000007.13:g.44191999G>C
CM000669.1:g.44191999G>C
NC_000007.12:g.44158524G>C
NG_008847.1:g.42024C>G
NG_008847.2:g.50771C>G
ENST00000395796.8:c.*232C>G
ENST00000616242.5:c.234C>G
ENST00000682635.1:n.720C>G
ENST00000345378.7:c.237C>G
ENST00000403799.8:c.234C>G
ENST00000671824.1:c.234C>G
ENST00000673284.1:c.234C>G
ENST00000345378.6:c.237C>G
ENST00000395796.7:c.231C>G
ENST00000403799.7:c.234C>G
ENST00000437084.1:c.234C>G
ENST00000616242.4:c.231C>G
NM_000162.3:c.234C>G
NM_033507.1:c.237C>G
NM_033508.1:c.231C>G
NM_000162.4:c.234C>G
NM_001354800.1:c.234C>G
NM_033507.2:c.237C>G
NM_033508.2:c.231C>G
NM_000162.5:c.234C>G
NM_033507.3:c.237C>G
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Pathogenic

Met criteria codes 7
PM2_Supporting PP1_Strong PS4 PP4_Moderate PP3 PP2 PM1

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.234C>G variant in the glucokinase gene, GCK, causes an amino acid change of aspartic acid to glutamic acid at codon 78 (p.(Asp78Glu)) of NM_000162.5. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). 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 0.90, which is greater than the MDEP VCEP threshold of 0.70 (PP3). Furthermore, this variant resides in an amino acid that directly binds ATP, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1). This variant was identified in seven unrelated individuals with hyperglycemia (PS4; PMID: 17573900, 30663027, 36504295, 14517956, internal lab contributors). Furthermore, one of these reported individuals had a clinical history highly specific for GCK-hyperglycemia (fasting glucose 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative autoantibodies) (PP4_Moderate; PMID: 22060211). Additonally, this variant segregated with hyperglycemia, with 4 informative meioses in three families with hyperglycemia (PP1_Strong; internal lab contributors). In summary, c.234C>G meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PM2_Supporting, PP2, PP3, PM1, PS4, PP4_Moderate, PP1_Strong).
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP1_Strong
This variant segregated with hyperglycemia, with 4 informative meioses in three families with hyperglycemia (PP1_Strong; internal lab contributors).
PS4
This variant was identified in seven unrelated individuals with hyperglycemia (PS4; PMID: 17573900, 30663027, 36504295, 14517956, internal lab contributors).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (fasting glucose 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative autoantibodies) (PP4_Moderate; PMID: 22060211).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.90, 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).
PM1
This variant resides in an amino acid that directly binds ATP, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1).
Curation History
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