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.182C>G

CA367398735

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: d4bc58a6-cf17-49c5-97ce-635f8988c4b9
Approved on: 2024-02-28
Published on: 2024-02-28

HGVS expressions

NM_001354803.2:c.182C>G
NC_000007.14:g.44145602G>C
CM000669.2:g.44145602G>C
NC_000007.13:g.44185201G>C
CM000669.1:g.44185201G>C
NC_000007.12:g.44151726G>C
NG_008847.1:g.48822C>G
NG_008847.2:g.57569C>G
ENST00000395796.8:c.*1146C>G
ENST00000616242.5:c.*268C>G
ENST00000683378.1:n.374C>G
ENST00000336642.9:c.182C>G
ENST00000345378.7:c.1151C>G
ENST00000403799.8:c.1148C>G
ENST00000671824.1:c.1211C>G
ENST00000672743.1:n.160C>G
ENST00000673284.1:c.1148C>G
ENST00000336642.8:c.200C>G
ENST00000345378.6:c.1151C>G
ENST00000395796.7:c.1145C>G
ENST00000403799.7:c.1148C>G
ENST00000437084.1:c.1097C>G
ENST00000459642.1:n.528C>G
ENST00000616242.4:c.1145C>G
NM_000162.3:c.1148C>G
NM_033507.1:c.1151C>G
NM_033508.1:c.1145C>G
NM_000162.4:c.1148C>G
NM_001354800.1:c.1148C>G
NM_001354801.1:c.137C>G
NM_001354802.1:c.8C>G
NM_001354803.1:c.182C>G
NM_033507.2:c.1151C>G
NM_033508.2:c.1145C>G
NM_000162.5:c.1148C>G
NM_033507.3:c.1151C>G
NM_033508.3:c.1145C>G

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP3 PP2 PM5 PP1_Moderate

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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1148C>G variant in the glucokinase gene, GCK, causes an amino acid change of serine to tryptophan at codon 383 (p. (Ser383Trp)) of NM_000162.5. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). 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 located in the larger hexokinase domain of the GCK gene (PMID: 31638168) but this variant does not reside in an amino acid that directly binds glucose or ATP, which is defined as critical for the protein’s function by the ClinGen MDEP, so it does not meet PM1. This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.85 which is greater than the MDEP VCEP threshold of 0.70 (PP3). Another missense variant, c.1148C>T (p.Ser383Leu), has been interpreted as pathogenic by the ClinGen MDEP, and p.Ser383Trp has an equal or greater Grantham distance (PM5). This variant was found in one family, and segregated with hyperglycemia, with four informative meioses (PP1_Moderate; PMID: 3385223). In summary, c.1148C>G meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (VCEP specifications version v1.3.0; approved 8/11/2023): PP3, PP2, PP1_Moderate, PM5, PM2_Supporting
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP3
REVEL 0.85
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
Another missense variant, c.1148C>T (p.Ser383Leu), has been interpreted as pathogenic by the ClinGen MDEP, and p.Ser383Trp has an equal or greater Grantham distance (PM5).
PP1_Moderate
This variant segregated with hyperglycemia, with four informative meioses in one family (PP1_Moderate; PMID: 3385223).
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