The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000162.5(GCK):c.232G>T (p.Asp78Tyr)

CA367403044

2500039 (ClinVar)

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 88f48350-ea18-4c3e-b5ba-ded690174d89
Approved on: 2024-12-02
Published on: 2024-12-02

HGVS expressions

NM_000162.5(GCK):c.232G>T (p.Asp78Tyr)
NM_000162.5:c.232G>T
NC_000007.14:g.44152402C>A
CM000669.2:g.44152402C>A
NC_000007.13:g.44192001C>A
CM000669.1:g.44192001C>A
NC_000007.12:g.44158526C>A
NG_008847.1:g.42022G>T
NG_008847.2:g.50769G>T
ENST00000395796.8:c.*230G>T
ENST00000616242.5:c.232G>T
ENST00000682635.1:n.718G>T
ENST00000345378.7:c.235G>T
ENST00000403799.8:c.232G>T
ENST00000671824.1:c.232G>T
ENST00000673284.1:c.232G>T
ENST00000345378.6:c.235G>T
ENST00000395796.7:c.229G>T
ENST00000403799.7:c.232G>T
ENST00000437084.1:c.232G>T
ENST00000616242.4:c.229G>T
NM_000162.3:c.232G>T
NM_033507.1:c.235G>T
NM_033508.1:c.229G>T
NM_000162.4:c.232G>T
NM_001354800.1:c.232G>T
NM_033507.2:c.235G>T
NM_033508.2:c.229G>T
NM_033507.3:c.235G>T
NM_033508.3:c.229G>T
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Pathogenic

Met criteria codes 6
PP4_Moderate PM5_Strong PP3 PP2 PM1 PM2_Supporting
Not Met criteria codes 2
PP1 PS4

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.232G>T variant in the glucokinase gene, GCK, causes an amino acid change of aspartic acid to tyrosine at codon 78 (p.(Asp78Tyr)) 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 0.993, 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 two unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors). One of the individuals harboring this variant had a clinical history highly specific for GCK-hyperglycemia (fasting glucose 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antiboides) (PP4_Moderate; internal lab contributors). While this variant segregated with diabetes with two informative meioses in a single family; this does not meet the thresholds for PP1 set by the ClinGen MDEP (internal lab contributors). Two other missense variants, c.234C>G (p.Asp78Glu) and c.232G>C (p.Asp78His) have been interpreted as pathogenic by the ClinGen MDEP (PM5_Strong). In summary, c.232G>T 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, PP4_Moderate, PM5_Strong).
Met criteria codes
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 negative antiboides) (PP4_Moderate; internal lab contributors).
PM5_Strong
Two other missense variants, c.234C>G (p.Asp78Glu) and c.232G>C (p.Asp78His) have been interpreted as pathogenic by the ClinGen MDEP (PM5_Strong).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.993, 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).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 and v4.1 (PM2_Supporting).
Not Met criteria codes
PP1
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 (PMID: 27236918, internal lab contributors).
PS4
This variant was identified in two unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold ( internal lab contributors).
Curation History
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