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Variant: NM_000162.5(GCK):c.1112G>T (p.Cys371Phe)

CA152950

129140 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 9eb4e0f9-20ec-4efb-bf65-c18791943812

HGVS expressions

NM_000162.5:c.1112G>T
NM_000162.5(GCK):c.1112G>T (p.Cys371Phe)
NC_000007.14:g.44145638C>A
CM000669.2:g.44145638C>A
NC_000007.13:g.44185237C>A
CM000669.1:g.44185237C>A
NC_000007.12:g.44151762C>A
NG_008847.1:g.48786G>T
NG_008847.2:g.57533G>T
ENST00000395796.8:c.*1110G>T
ENST00000616242.5:c.*232G>T
ENST00000683378.1:n.338G>T
ENST00000336642.9:c.146G>T
ENST00000345378.7:c.1115G>T
ENST00000403799.8:c.1112G>T
ENST00000671824.1:c.1175G>T
ENST00000672743.1:n.124G>T
ENST00000673284.1:c.1112G>T
ENST00000336642.8:n.164G>T
ENST00000345378.6:c.1115G>T
ENST00000395796.7:c.1109G>T
ENST00000403799.7:c.1112G>T
ENST00000437084.1:c.1061G>T
ENST00000459642.1:n.492G>T
ENST00000616242.4:n.1109G>T
NM_000162.3:c.1112G>T
NM_033507.1:c.1115G>T
NM_033508.1:c.1109G>T
NM_000162.4:c.1112G>T
NM_001354800.1:c.1112G>T
NM_001354801.1:c.101G>T
NM_001354802.1:c.-29G>T
NM_001354803.1:c.146G>T
NM_033507.2:c.1115G>T
NM_033508.2:c.1109G>T
NM_033507.3:c.1115G>T
NM_033508.3:c.1109G>T
NM_001354803.2:c.146G>T

Pathogenic

Met criteria codes 6
PP4_Moderate PP1_Strong PM2_Supporting PS4 PP3 PP2

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.1112G>T variant in the glucokinase gene, GCK, causes an amino acid change of cysteine to phenylalanine at codon 371 (p.(Cys371Phe)) of NM_000162.5. GCK is defined by the ClinGen MDEP VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.931, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was hyperglycemia (PS4; PMID 24735133, internal lab contributors). This variant segregated with hyperglycemia with 12 informative meioses in 3 families with MODY (PP1_Strong; internal lab contributors). This variant was identified in at least two individuals with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% as well as either OGTT increment < 3 mmol/L or negative antibodies) (PP4_Moderate; internal lab contributors). In summary, this variant meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.2.0, approved 6/7/2023) : PP2, PP3, PM2_Supporting, PP1_Strong, PS4, PP4_Moderate .
Met criteria codes
PP4_Moderate
This variant was identified in at least two individuals with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% as well as either OGTT increment < 3 mmol/L or negative antibodies) (PP4_Moderate; internal lab contributors).
PP1_Strong
This variant segregated with diabetes with 12 informative meioses in 3 families with MODY (PP1_Strong; internal lab contributors).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PS4
This variant was identified in 9 unrelated individuals with hyperglycemia (PS4; PMID 24735133, internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.931, which is [greater than/equal to] 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).
Approved on: 2023-08-09
Published on: 2023-08-10
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