The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000162.5(GCK):c.389T>C (p.Ile130Thr)

CA157918200

1704126 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: e9744df7-5d66-4ddf-8ddf-eca9fab38ecc
Approved on: 2024-02-28
Published on: 2024-02-28

HGVS expressions

NM_000162.5:c.389T>C
NM_000162.5(GCK):c.389T>C (p.Ile130Thr)
NC_000007.14:g.44151050A>G
CM000669.2:g.44151050A>G
NC_000007.13:g.44190649A>G
CM000669.1:g.44190649A>G
NC_000007.12:g.44157174A>G
NG_008847.1:g.43374T>C
NG_008847.2:g.52121T>C
ENST00000395796.8:c.*387T>C
ENST00000616242.5:c.389T>C
ENST00000682635.1:n.875T>C
ENST00000345378.7:c.392T>C
ENST00000403799.8:c.389T>C
ENST00000671824.1:c.389T>C
ENST00000673284.1:c.389T>C
ENST00000345378.6:c.392T>C
ENST00000395796.7:c.386T>C
ENST00000403799.7:c.389T>C
ENST00000437084.1:c.364-26T>C
ENST00000616242.4:c.386T>C
NM_000162.3:c.389T>C
NM_033507.1:c.392T>C
NM_033508.1:c.386T>C
NM_000162.4:c.389T>C
NM_001354800.1:c.389T>C
NM_033507.2:c.392T>C
NM_033508.2:c.386T>C
NM_033507.3:c.392T>C
NM_033508.3:c.386T>C

Likely Pathogenic

Met criteria codes 6
PP3 PP2 PP4_Moderate PS4_Moderate PM2_Supporting PS3_Moderate
Not Met criteria codes 2
PP1 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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.389T>CT variant in the glucokinase gene, GCK, causes an amino acid change of isoleucine to threonine at codon 130 (p.(Ile130Thr)) 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 0.932, which is greater than the MDEP VCEP threshold of 0.70 (PP3). MDEP wild type quality control measures were met, and the relative activity Index (RAI) of this variant was found to be 0.17, which is below the MDEP cutoff (<0.5) (PMID: 22291974). This variant has an incomputable gnomAD v2.1.1 Popmax filtering allele frequency due to 1 copy in the European non-Finnish subpopulation and 0 copies in any other subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Popmax FAF <= 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting). This variant was identified in at least 6 unrelated individuals with hyperglycemia (PS4_Moderate; PMIDs: 36257325, 19790256, 14517956, 22291974, 34362814, internal lab contributor). One of these individuals had a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT increment < 3 mmol/L) (PP4_Moderate; PMID: 22291974). In summary, c.389T>C meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3, approved 8/11/2023): PP4_Moderate, PS3_Moderate, PS4_Moderate, PP2, PP3, PM2_Supporting.
Met criteria codes
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.932, 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).
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 OGTT increment < 3 mmol/L) (PP4_Moderate; PMID: 22291974).
PS4_Moderate
This variant was identified in at least 6 unrelated individuals with hyperglycemia (PS4_Moderate; PMIDs: 36257325, 19790256, 14517956, 22291974, 34362814, internal lab contributor).
PM2_Supporting
This variant has an incomputable gnomAD v2.1.1 Popmax filtering allele frequency due to 1 copy in the European non-Finnish subpopulation and 0 copies in any other subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Popmax FAF <= 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting).
PS3_Moderate
MDEP wild type quality control measures were met, and the relative activity Index (RAI) of this variant was found to be 0.17, which is below the MDEP cutoff (<0.5) (PMID: 22291974).
Not Met criteria codes
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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