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.1142T>G (p.Met381Arg)

CA213719

36178 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 54862117-14b2-4c5d-8e05-9ac0d6c61ee2

HGVS expressions

NM_000162.5:c.1142T>G
NM_000162.5(GCK):c.1142T>G (p.Met381Arg)
NC_000007.14:g.44145608A>C
CM000669.2:g.44145608A>C
NC_000007.13:g.44185207A>C
CM000669.1:g.44185207A>C
NC_000007.12:g.44151732A>C
NG_008847.1:g.48816T>G
NG_008847.2:g.57563T>G
ENST00000395796.8:c.*1140T>G
ENST00000616242.5:c.*262T>G
ENST00000683378.1:n.368T>G
ENST00000336642.9:c.176T>G
ENST00000345378.7:c.1145T>G
ENST00000403799.8:c.1142T>G
ENST00000671824.1:c.1205T>G
ENST00000672743.1:n.154T>G
ENST00000673284.1:c.1142T>G
ENST00000336642.8:n.194T>G
ENST00000345378.6:c.1145T>G
ENST00000395796.7:c.1139T>G
ENST00000403799.7:c.1142T>G
ENST00000437084.1:c.1091T>G
ENST00000459642.1:n.522T>G
ENST00000616242.4:n.1139T>G
NM_000162.3:c.1142T>G
NM_033507.1:c.1145T>G
NM_033508.1:c.1139T>G
NM_000162.4:c.1142T>G
NM_001354800.1:c.1142T>G
NM_001354801.1:c.131T>G
NM_001354802.1:c.2T>G
NM_001354803.1:c.176T>G
NM_033507.2:c.1145T>G
NM_033508.2:c.1139T>G
NM_033507.3:c.1145T>G
NM_033508.3:c.1139T>G
NM_001354803.2:c.176T>G

Likely Pathogenic

Met criteria codes 6
PS4_Moderate PP3 PP2 PP4_Moderate PM5 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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1142T>G variant in the glucokinase gene, GCK, causes an amino acid change of methionine to arginine at codon 381 (p.(Met381Arg)) 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 0.9629, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting), and was identified in 5 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; PMID 22060211 (likely same cases as PMID 29927023, PMID 32375122, PMID 2555642, and PMID 24804978 (Kawakita et al 2014)), PMID 24804978, internal lab contributors). At least one of these individuals has a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antibodies) (PP4_Moderate; internal lab contributors). Another missense variant, c.1142T>C (p.Met381Thr, has been interpreted as pathogenic by the ClinGen MDEP, and p.Met381Arg has a greater Grantham distance (PM5). In summary, the c.1142T>G variant 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): PP4_Moderate, PM5, PS4_Moderate, PP2, PP3, PM2_Supporting.
Met criteria codes
PS4_Moderate
This variant was identified in 5 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; PMID 22060211 (likely same cases as PMID 29927023, PMID 32375122, PMID 2555642, and PMID 24804978 (Kawakita et al 2014)), PMID 24804978, internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.9629, 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-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and negative antibodies) (PP4_Moderate; internal lab contributors).
PM5
Another missense variant, c.1142T>C (p.Met381Thr, has been interpreted as pathogenic by the ClinGen MDEP, and p.Met381Arg has a greater Grantham distance (PM5). (GD for p.Met381Thr = 81, GD for p.Met381Arg = 101).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Approved on: 2023-07-17
Published on: 2023-07-17
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