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


Variant: NM_033508.3:c.772G>T

CA367400582

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 0ba69fad-66dd-47dd-990b-138e4e43da99

HGVS expressions

NM_033508.3:c.772G>T
NC_000007.14:g.44147738C>A
CM000669.2:g.44147738C>A
NC_000007.13:g.44187337C>A
CM000669.1:g.44187337C>A
NC_000007.12:g.44153862C>A
NG_008847.1:g.46686G>T
NG_008847.2:g.55433G>T
ENST00000395796.8:c.*773G>T
ENST00000616242.5:c.775G>T
ENST00000345378.7:c.778G>T
ENST00000403799.8:c.775G>T
ENST00000671824.1:c.775G>T
ENST00000673284.1:c.775G>T
ENST00000345378.6:c.778G>T
ENST00000395796.7:c.772G>T
ENST00000403799.7:c.775G>T
ENST00000437084.1:c.724G>T
ENST00000616242.4:n.772G>T
NM_000162.3:c.775G>T
NM_033507.1:c.778G>T
NM_033508.1:c.772G>T
NM_000162.4:c.775G>T
NM_001354800.1:c.775G>T
NM_033507.2:c.778G>T
NM_033508.2:c.772G>T
NM_000162.5:c.775G>T
NM_033507.3:c.778G>T

Likely Pathogenic

Met criteria codes 4
PP4 PP3 PP2 PM5_Strong
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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.775G>T variant in the glucokinase gene, GCK, causes an amino acid change of alanine to serine at codon 259 (p.(Ala259Ser)) of NM_000162.5. This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.744, which is greater than the MDEP VCEP threshold of 0.70 (PP3). 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). Two other missense variants, c.776C>T p.Ala259Val and c.775G>A p.Ala259Thr, have been interpreted as pathogenic by the ClinGen MDEP, and p.Ala259Ser has a greater Grantham distance than p.Ala259Val and p.Ala259Thr (PM5_Strong). 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%) (PP4; PMID: 30245511). This variant segregated with hyperglycemia/diabetes with one informative meiosis in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMIDs: 27236918, 30245511). In summary, c.775G>T meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PP3, PP2, PM5_Strong, PP4.
Met criteria codes
PP4
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%) (PP4; PMID: 30245511).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.744, 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_Strong
Two other missense variants, c.776C>T p.Ala259Val and c.775G>A p.Ala259Thr, have been interpreted as pathogenic by the ClinGen MDEP, and p.Ala259Ser has a greater Grantham distance than p.Ala259Val and p.Ala259Thr (PM5_Strong).
Not Met criteria codes
PP1
This variant segregated with hyperglycemia/diabetes with one informative meiosis in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMIDs: 27236918, 30245511).
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-08-12
Published on: 2023-08-12
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