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.817G>T

CA367400486

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 79e886d4-de41-4cb2-ab9a-80243c31a34e
Approved on: 2024-11-04
Published on: 2024-11-05

HGVS expressions

NM_033508.3:c.817G>T
NC_000007.14:g.44147693C>A
CM000669.2:g.44147693C>A
NC_000007.13:g.44187292C>A
CM000669.1:g.44187292C>A
NC_000007.12:g.44153817C>A
NG_008847.1:g.46731G>T
NG_008847.2:g.55478G>T
ENST00000395796.8:c.*818G>T
ENST00000616242.5:c.820G>T
ENST00000345378.7:c.823G>T
ENST00000403799.8:c.820G>T
ENST00000671824.1:c.820G>T
ENST00000673284.1:c.820G>T
ENST00000345378.6:c.823G>T
ENST00000395796.7:c.817G>T
ENST00000403799.7:c.820G>T
ENST00000437084.1:c.769G>T
ENST00000616242.4:c.817G>T
NM_000162.3:c.820G>T
NM_033507.1:c.823G>T
NM_033508.1:c.817G>T
NM_000162.4:c.820G>T
NM_001354800.1:c.820G>T
NM_033507.2:c.823G>T
NM_033508.2:c.817G>T
NM_000162.5:c.820G>T
NM_033507.3:c.823G>T
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Likely Pathogenic

Met criteria codes 6
PM2_Supporting PP4_Moderate PP3 PP2 PM5 PP1_Moderate

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.820G>T variant in the glucokinase gene, GCK, is a missense variant resulting in an amino acid change of aspartic acid to tyrosine at codon 274 (p.(Asp274Tyr)) 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). Additionally, it is predicted to be deleterious by computational evidence, with a REVEL score of 0.99, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant segregated with hyperglycemia with four informative meioses in a single family (PP1_Moderate, internal lab contributors). 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 antibodies). (PP4_Moderate; internal lab contributors). Another missense variant at the same amino acid, c.820G>A p.(Asp274Ala), has been classified as pathogenic by the ClinGen MDEP and p.Asp274Tyr has a larger Grantham distance (PM5). In summary, c.820G>T 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, PP1_Moderate, PP4_Moderate, PM2_Supporting, PM5.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
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 antibodies. (PP4_Moderate; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.99, 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 at the same amino acid, c.820G>A p.(Asp274Ala), has been classified as pathogenic by the ClinGen MDEP and p.Asp274Tyr has a larger Grantham distance (PM5).
PP1_Moderate
This variant segregated with hyperglycemia with four informative meioses in a single family (PP1_Moderate, internal lab contributors).
Curation History
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