The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000162.5(GCK):c.1133C>G (p.Ala378Gly)

CA367398802

972776 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: e241b715-2524-4df2-8eca-9f8e1b9d8ff6

HGVS expressions

NM_000162.5:c.1133C>G
NM_000162.5(GCK):c.1133C>G (p.Ala378Gly)
NC_000007.14:g.44145617G>C
CM000669.2:g.44145617G>C
NC_000007.13:g.44185216G>C
CM000669.1:g.44185216G>C
NC_000007.12:g.44151741G>C
NG_008847.1:g.48807C>G
NG_008847.2:g.57554C>G
ENST00000395796.8:c.*1131C>G
ENST00000616242.5:c.*253C>G
ENST00000683378.1:n.359C>G
ENST00000336642.9:c.167C>G
ENST00000345378.7:c.1136C>G
ENST00000403799.8:c.1133C>G
ENST00000671824.1:c.1196C>G
ENST00000672743.1:n.145C>G
ENST00000673284.1:c.1133C>G
ENST00000336642.8:c.185C>G
ENST00000345378.6:c.1136C>G
ENST00000395796.7:c.1130C>G
ENST00000403799.7:c.1133C>G
ENST00000437084.1:c.1082C>G
ENST00000459642.1:n.513C>G
ENST00000616242.4:c.1130C>G
NM_000162.3:c.1133C>G
NM_033507.1:c.1136C>G
NM_033508.1:c.1130C>G
NM_000162.4:c.1133C>G
NM_001354800.1:c.1133C>G
NM_001354801.1:c.122C>G
NM_001354802.1:c.-8C>G
NM_001354803.1:c.167C>G
NM_033507.2:c.1136C>G
NM_033508.2:c.1130C>G
NM_033507.3:c.1136C>G
NM_033508.3:c.1130C>G
NM_001354803.2:c.167C>G

Likely Pathogenic

Met criteria codes 4
PM5_Strong PP3 PP2 PM2_Supporting
Not Met criteria codes 3
PS4 PP4 PM1

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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1133C>G variant in the glucokinase gene, GCK, causes an amino acid change of alanine to glycine at codon 378 (p.(Ala378Gly)) of NM_000162.5. This variant has an incomputable Popmax filtering allele frequency in gnomAD 2.1.1 due to only one copy being present, below the PM2_Supporting threshold of Popmax filtering allele frequency ≤ 0.000003 in European Non-Finnish population AND ≤ 2 copies observed in ENF AND ≤ 1 copy in any other founder or non-founder population (PM2_Supporting). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.901, which is greater than the MDEP VCEP threshold of 0.70 (PP3). Additionally, 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). The c.1133C>T, p.(Ala378Val) and c.1132G>A, p.(Ala378Thr) variants have been interpreted as pathogenic by the ClinGen MDEP (PM5_Strong). This variant was identified in two unrelated individuals with a diabetes; however, this number does not meet the MDEP cutoff for PS4_Moderate (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). In summary, c.1133C>G meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.2.0, approved 6/7/2023): PM2_Supporting, PP2, PP3, PM5_Strong.
Met criteria codes
PM5_Strong
The c.1133C>T, p.(Ala378Val) and c.1132G>A, p.(Ala378Thr) variants have been interpreted as pathogenic by the ClinGen MDEP (PM5_Strong).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.901 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).
PM2_Supporting
This variant has an incomputable Popmax filtering allele frequency in gnomAD 2.1.1 due to only one copy being present, below the PM2_Supporting threshold of Popmax filtering allele frequency ≤ 0.000003 in European Non-Finnish population AND ≤ 2 copies observed in ENF AND ≤ 1 copy in any other founder or non-founder population (PM2_Supporting).
Not Met criteria codes
PS4
This variant was identified in two unrelated individuals with a diabetes; however this number does not meet the MDEP cutoff for PS4_Moderate (internal lab contributors).
PP4
This variant was identified in an individual with diabetes, however the MODY probability is unable to be calculated due to age of diagnosis over 35.
PM1
Variant is not within a glucose or Mg2+/ATP binding site.
Approved on: 2023-08-07
Published on: 2023-08-07
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