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Variant: NM_001354803.2:c.146G>A

CA367398935

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: b1d7557e-5fd6-45dd-86a1-c5c03cf413b9
Approved on: 2023-08-09
Published on: 2023-08-10

HGVS expressions

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

Likely Pathogenic

Met criteria codes 5
PP1_Strong PP3 PP2 PM5_Supporting PM2
Not Met criteria codes 1
PP4

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>A variant in the glucokinase gene, GCK, causes an amino acid change of cysteine to tyrosine at codon 371 (p.(Cys371Tyr)) 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 0.956, 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 segregated with diabetes with 5 informative meioses in a family with diabetes/hyperglycemia (PP1_Strong; internal lab contributors). This variant was identified in an individual with a phenotype suggestive of GCK-hyperglycemia; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributors). Another missense variant, c.1112G>T p.(Cys371Phe)​, has been classified as pathogenic by the ClinGen MDEP VCEP but has a greater Grantham distance than p.(Cys371Tyr)(PM5_Supporting). In summary, this variant meets the criteria to be classified as likely pathogenic for GENE-MODY. 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, PM5_Supporting.
Met criteria codes
PP1_Strong
This variant segregated with diabetes with 5 informative meioses in a family with diabetes/hyperglycemia (PP1_Strong; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.956, 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_Supporting
Another missense variant, c.1112G>T p.(Cys371Phe) ​, has been classified as pathogenic by the ClinGen MDEP VCEP but has a greater Grantham distance than p.(Cys371Tyr)(PM5_Supporting).
PM2
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PP4
This variant was identified in an individual with a phenotype suggestive of GCK-hyperglycemia; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributors).
Curation History
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