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.1322C>G (p.Ser441Trp)

CA367397017

1320655 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 5a5a400f-b924-4261-a797-30b4d0f80434

HGVS expressions

NM_000162.5:c.1322C>G
NM_000162.5(GCK):c.1322C>G (p.Ser441Trp)
NC_000007.14:g.44145212G>C
CM000669.2:g.44145212G>C
NC_000007.13:g.44184811G>C
CM000669.1:g.44184811G>C
NC_000007.12:g.44151336G>C
NG_008847.1:g.49212C>G
NG_008847.2:g.57959C>G
ENST00000395796.8:c.*1320C>G
ENST00000616242.5:c.*442C>G
ENST00000683378.1:n.548C>G
ENST00000336642.9:c.356C>G
ENST00000345378.7:c.1325C>G
ENST00000403799.8:c.1322C>G
ENST00000671824.1:c.1385C>G
ENST00000672743.1:n.334C>G
ENST00000673284.1:c.1322C>G
ENST00000336642.8:n.374C>G
ENST00000345378.6:c.1325C>G
ENST00000395796.7:c.1319C>G
ENST00000403799.7:c.1322C>G
ENST00000437084.1:c.1271C>G
ENST00000459642.1:n.702C>G
ENST00000616242.4:n.1319C>G
NM_000162.3:c.1322C>G
NM_033507.1:c.1325C>G
NM_033508.1:c.1319C>G
NM_000162.4:c.1322C>G
NM_001354800.1:c.1322C>G
NM_001354801.1:c.311C>G
NM_001354802.1:c.182C>G
NM_001354803.1:c.356C>G
NM_033507.2:c.1325C>G
NM_033508.2:c.1319C>G
NM_033507.3:c.1325C>G
NM_033508.3:c.1319C>G
NM_001354803.2:c.356C>G

Pathogenic

Met criteria codes 6
PS3_Moderate PP4_Moderate PS4 PP3 PP2 PM2_Supporting

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 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1322C>G variant in the glucokinase gene, GCK, causes an amino acid change of glycine to asparagine at codon 441 (p.(Ser441Trp)) 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 0.967, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in an individual with a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT increment < 3.0 mmol/L) (PP4_Moderate; PMID: 25665835). A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, the wild-type ATP Km is between 0.4-0.65, and the p.Ser441Trp has RAI=0.11, which is less than the MDEP VCEP threshold of 0.50 (PS3_Moderate; PMID 19884385). This variant was identified in 8 unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; PMID: 27420379, 25665835, 19884385, 17573900, 16965331, 11508276, internal lab contributors). In summary, 1322C>G meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.2.0, approved 6/7/2023): PM2_Supporting, PP2, PP3, PP4_Moderate, PS3, PS4.
Met criteria codes
PS3_Moderate
A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, the wild-type ATP Km is between 0.4-0.65, and the p.Ser441Trp has RAI=0.11, which is less than or equal to the MDEP VCEP threshold of 0.50 (PS3_Moderate; PMID 19884385).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT increment < 3.0 mmol/L) (PP4_Moderate; PMID: 25665835)
PS4
This variant was identified in 8 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; PMID: 27420379, 25665835, 19884385, 17573900, 16965331, 11508276, internal lab contributors).
PP3
Variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.967, which is greater than the MDEP VCEP threshold of 0.70.
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.
PM2_Supporting
This variant is absent from gnomAD v2.1.1.
Approved on: 2023-06-25
Published on: 2023-06-25
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