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.209G>C

CA367398617

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 23de61da-8a13-4720-89af-873cf375a486

HGVS expressions

NM_001354803.2:c.209G>C
NC_000007.14:g.44145575C>G
CM000669.2:g.44145575C>G
NC_000007.13:g.44185174C>G
CM000669.1:g.44185174C>G
NC_000007.12:g.44151699C>G
NG_008847.1:g.48849G>C
NG_008847.2:g.57596G>C
ENST00000395796.8:c.*1173G>C
ENST00000616242.5:c.*295G>C
ENST00000683378.1:n.401G>C
ENST00000336642.9:c.209G>C
ENST00000345378.7:c.1178G>C
ENST00000403799.8:c.1175G>C
ENST00000671824.1:c.1238G>C
ENST00000672743.1:n.187G>C
ENST00000673284.1:c.1175G>C
ENST00000336642.8:n.227G>C
ENST00000345378.6:c.1178G>C
ENST00000395796.7:c.1172G>C
ENST00000403799.7:c.1175G>C
ENST00000437084.1:c.1124G>C
ENST00000459642.1:n.555G>C
ENST00000616242.4:n.1172G>C
NM_000162.3:c.1175G>C
NM_033507.1:c.1178G>C
NM_033508.1:c.1172G>C
NM_000162.4:c.1175G>C
NM_001354800.1:c.1175G>C
NM_001354801.1:c.164G>C
NM_001354802.1:c.35G>C
NM_001354803.1:c.209G>C
NM_033507.2:c.1178G>C
NM_033508.2:c.1172G>C
NM_000162.5:c.1175G>C
NM_033507.3:c.1178G>C
NM_033508.3:c.1172G>C

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PM5_Supporting PP3 PP2 PP4_Moderate
Not Met criteria codes 1
PS4

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.1175G>C variant in the glucokinase gene, GCK, causes an amino acid change of alanine to proline at codon 392 (p.(Arg392Pro)) 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 0.909, 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.1174C>T p.Arg392Cys, has been classified as pathogenic by the ClinGen MDEP VCEP but has a greater Grantham distance than p.Arg392Pro (PM5_Supporting). This variant was identified in an individual with a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L, HbA1c 5.6 - 7.6%, OGTT increment < 3 mmol/L, and 3 generation family history of diabetes/hyperglycemia)(PP4_Moderate; internal lab contributors). This variant was identified in two unrelated individuals with a clinical picture consistent with monogenic diabetes; however, PS4_Moderate cannot be applied because this number is below the MDEP threshold (PMID 23624530, internal lab contributors). In summary, this variant meets the criteria to be classified as likely 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, PP4_Moderate, PM5_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PM5_Supporting
Another missense variant, c.1174C>T p.Arg392Cys, has been classified as pathogenic by the ClinGen MDEP VCEP but has a greater Grantham distance than p.Arg392Pro.
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.909, which is greater than or equal to the MDEP VCEP threshold of 0.70 (PP3).
PP2
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).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L, HbA1c 5.6 - 7.6%, OGTT increment < 3 mmol/L, and 3 generation family history of diabetes/hyperglycemia) (PP4_Moderate; internal lab contributors).
Not Met criteria codes
PS4
This variant was identified in two unrelated individuals with a clinical picture consistent with monogenic diabetes, however PS4_Moderate cannot be applied because this number is below the MDEP threshold (PMID 23624530, internal lab contributors)
Approved on: 2023-07-16
Published on: 2023-07-16
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