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.776C>T (p.Ala259Val)

CA367400579

447417 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 82a2ea94-5ac2-4707-9095-99789b4b0229

HGVS expressions

NM_000162.5:c.776C>T
NM_000162.5(GCK):c.776C>T (p.Ala259Val)
NC_000007.14:g.44147737G>A
CM000669.2:g.44147737G>A
NC_000007.13:g.44187336G>A
CM000669.1:g.44187336G>A
NC_000007.12:g.44153861G>A
NG_008847.1:g.46687C>T
NG_008847.2:g.55434C>T
ENST00000395796.8:c.*774C>T
ENST00000616242.5:c.776C>T
ENST00000345378.7:c.779C>T
ENST00000403799.8:c.776C>T
ENST00000671824.1:c.776C>T
ENST00000673284.1:c.776C>T
ENST00000345378.6:c.779C>T
ENST00000395796.7:c.773C>T
ENST00000403799.7:c.776C>T
ENST00000437084.1:c.725C>T
ENST00000616242.4:n.773C>T
NM_000162.3:c.776C>T
NM_033507.1:c.779C>T
NM_033508.1:c.773C>T
NM_000162.4:c.776C>T
NM_001354800.1:c.776C>T
NM_033507.2:c.779C>T
NM_033508.2:c.773C>T
NM_033507.3:c.779C>T
NM_033508.3:c.773C>T

Pathogenic

Met criteria codes 7
PS4 PP3 PP2 PP4_Moderate PM5 PM2_Supporting PP1_Strong

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.776C>T variant in the glucokinase gene, GCK, causes an amino acid change of alanine to valine at codon 259 (p.(Ala259Val)) of NM_000162.5. This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.948, which is greater than the MDEP VCEP threshold of 0.70 (PP3) and is absent from gnomAD v2.1.1 (PM2_Supporting). Additionally, this variant was identified in 15 unrelated individuals with hyperglycemia (PS4; PMID:22035297, internal lab contributors). This variant segregated with diabetes/hyperglycemia, with 16 informative meioses in 5 families (PP1_Strong; PMID: 22035297, internal lab contributors). 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). Another missense variant, c.775G>A, p.Ala259Thr has been interpreted as pathogenic by the ClinGen MDEP, and p.Ala259Val has a greater Grantham distance (PM5). Lastly, this variant was identified in two individuals 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; internal lab contributors). In summary, c. 776C>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): PP3, PM2_Supporting, PS4, PP1_Strong, PP2, PM5, PP4_Moderate.
Met criteria codes
PS4
This variant was identified in 15 unrelated individuals with hyperglycemia (PS4; PMID: 22035297, internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.948, 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 two individuals 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; internal lab contributors).
PM5
Another missense variant, c.775G>A p.Ala259Thr, has been interpreted as pathogenic by the ClinGen MDEP, and p.Ala259Val has a greater Grantham distance (PM5).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP1_Strong
This variant segregated with diabetes/hyperglycemia, with 16 informative meioses in 5 families (PP1_Strong; PMID: 22035297, internal lab contributors).
Approved on: 2023-08-12
Published on: 2023-08-12
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