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_001354803.2:c.289T>G

CA367397313

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 8cc69ce5-3d1d-4cd9-9bd7-6b5cc6853539

HGVS expressions

NM_001354803.2:c.289T>G
NC_000007.14:g.44145279A>C
CM000669.2:g.44145279A>C
NC_000007.13:g.44184878A>C
CM000669.1:g.44184878A>C
NC_000007.12:g.44151403A>C
NG_008847.1:g.49145T>G
NG_008847.2:g.57892T>G
ENST00000395796.8:c.*1253T>G
ENST00000616242.5:c.*375T>G
ENST00000683378.1:n.481T>G
ENST00000336642.9:c.289T>G
ENST00000345378.7:c.1258T>G
ENST00000403799.8:c.1255T>G
ENST00000671824.1:c.1318T>G
ENST00000672743.1:n.267T>G
ENST00000673284.1:c.1255T>G
ENST00000336642.8:n.307T>G
ENST00000345378.6:c.1258T>G
ENST00000395796.7:c.1252T>G
ENST00000403799.7:c.1255T>G
ENST00000437084.1:c.1204T>G
ENST00000459642.1:n.635T>G
ENST00000616242.4:n.1252T>G
NM_000162.3:c.1255T>G
NM_033507.1:c.1258T>G
NM_033508.1:c.1252T>G
NM_000162.4:c.1255T>G
NM_001354800.1:c.1255T>G
NM_001354801.1:c.244T>G
NM_001354802.1:c.115T>G
NM_001354803.1:c.289T>G
NM_033507.2:c.1258T>G
NM_033508.2:c.1252T>G
NM_000162.5:c.1255T>G
NM_033507.3:c.1258T>G
NM_033508.3:c.1252T>G

Uncertain Significance

Met criteria codes 4
PP3 PP2 PM2_Supporting PM5_Supporting
Not Met criteria codes 2
PP4 PP1

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.1255T>G variant in the glucokinase gene, GCK, causes an amino acid change of alanine to proline at codon 419 (p.(Phe419Val)) 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 0.991, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). Another missense variant, c.1256T>C (p.Phe419Ser), has been classified as likely pathogenic by the ClinGen MDEP VCEP (PM5_Supporting). This variant segregated with the disease with two informative meioses in a single family with diabetes, however, this does not meet the thresholds for PP1 set by the ClinGen MDEP VCEP (PMID: 27236918, internal lab contributors). This variant was identified in an individual with diabetes, however, PP4 is unable to be evaluated due to incomplete clinical information. In summary, this variant meets the criteria to be classified as uncertain significance for GCK-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, PM5_Supporting.
Met criteria codes
PP3
REVEL = 0.991
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).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PM5_Supporting
Another missense variant, c.1256T>C (p.Phe419Ser), has been classified as likely pathogenic by the ClinGen MDEP VCEP (PM5_Supporting).
Not Met criteria codes
PP4
This variant was identified in an individual with diabetes, however, PP4 is unable to be evaluated due to incomplete clinical information.
PP1
This variant segregated with the disease with two informative meioses in a single family with diabetes, however, this does not meet the thresholds for PP1 set by the ClinGen MDEP VCEP (PMID: 27236918, ) (internal lab contributors).
Approved on: 2023-06-26
Published on: 2023-06-26
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