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.179C>T (p.Thr60Ile)

CA4239709

1343440 (ClinVar)

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: f4c31328-fdd2-4333-bd20-df37547edd03
Approved on: 2025-07-29
Published on: 2025-07-29

HGVS expressions

NM_000162.5:c.179C>T
NM_000162.5(GCK):c.179C>T (p.Thr60Ile)
NC_000007.14:g.44153330G>A
CM000669.2:g.44153330G>A
NC_000007.13:g.44192929G>A
CM000669.1:g.44192929G>A
NC_000007.12:g.44159454G>A
NG_008847.1:g.41094C>T
NG_008847.2:g.49841C>T
ENST00000395796.8:c.*177C>T
ENST00000616242.5:c.179C>T
ENST00000682635.1:n.665C>T
ENST00000345378.7:c.182C>T
ENST00000403799.8:c.179C>T
ENST00000671824.1:c.179C>T
ENST00000673284.1:c.179C>T
ENST00000345378.6:c.182C>T
ENST00000395796.7:c.176C>T
ENST00000403799.7:c.179C>T
ENST00000437084.1:c.179C>T
ENST00000616242.4:c.176C>T
NM_000162.3:c.179C>T
NM_033507.1:c.182C>T
NM_033508.1:c.176C>T
NM_000162.4:c.179C>T
NM_001354800.1:c.179C>T
NM_033507.2:c.182C>T
NM_033508.2:c.176C>T
NM_033507.3:c.182C>T
NM_033508.3:c.176C>T
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Pathogenic

Met criteria codes 7
PP1_Strong PS4 PP4 PP3 PP2 PM2_Supporting PS3_Supporting
Not Met criteria codes 1
PM1

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GCK Version 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.179C>T variant in the glucokinase gene, GCK causes an amino acid change of threonine to isoleucine at codon 60 (p.(Thr60Ile)) of NM_000162.5. 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 0.979, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant has an incomputable gnomAD v4.1.0 Grpmax filtering allele frequency due to a single copy present in the South Asian population and 0 copies in any other subpopulation thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (gnomAD v4.1 Grpmax FAF ≤ 0.000003) (PM2_Supporting). This variant was identified in at least 11 unrelated individuals with hyperglycemia (PS4; PMID: 18248649, 34746319, internal lab contributors). At least one of these individuals had a clinical history highly specific for GCK-hyperglycemia (fasting glucose 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4; internal lab contributors). Additionally, this variant segregated with hyperglycemia with eight meioses in six families (PP1_Strong; PMID: 34746319, internal lab contributors). Functional studies of this variant demonstrate that it disrupts normal GK-GKRP binding (PS3_Supporting; PMID: 33273586). In summary, c.179C>T meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.0.0, approved 2/17/2025): PS4, PP1_Strong, PP2, PP3, PP4 PM2_Supporting, PS3_Supporting.
Met criteria codes
PP1_Strong
This variant segregated with hyperglycemia with eight meioses in six families (PP1_Strong; PMID: 34746319, internal lab contributors).
PS4
This variant was identified in at least 11 unrelated individuals with hyperglycemia (PS4; PMID: 18248649, 34746319, internal lab contributors).
PP4
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%) (PP4; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.979, 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).
PM2_Supporting
This variant has an incomputable gnomAD v4.1.0 Grpmax filtering allele frequency due to a single copy present in the South Asian population and 0 copies in any other subpopulation thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (gnomAD v4.1 Grpmax FAF ≤ 0.000003) (PM2_Supporting).
PS3_Supporting
Functional studies of this variant demonstrate that it disrupts normal GK-GKRP binding (PS3_Supporting; PMID: 33273586).

Not Met criteria codes
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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