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Variant: NM_000162.5(GCK):c.1129C>A (p.Arg377Ser)

CA367398819

1727652 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 3fd09c5a-7334-4761-a861-775841b44fdb

HGVS expressions

NM_000162.5:c.1129C>A
NM_000162.5(GCK):c.1129C>A (p.Arg377Ser)
NC_000007.14:g.44145621G>T
CM000669.2:g.44145621G>T
NC_000007.13:g.44185220G>T
CM000669.1:g.44185220G>T
NC_000007.12:g.44151745G>T
NG_008847.1:g.48803C>A
NG_008847.2:g.57550C>A
ENST00000395796.8:c.*1127C>A
ENST00000616242.5:c.*249C>A
ENST00000683378.1:n.355C>A
ENST00000336642.9:c.163C>A
ENST00000345378.7:c.1132C>A
ENST00000403799.8:c.1129C>A
ENST00000671824.1:c.1192C>A
ENST00000672743.1:n.141C>A
ENST00000673284.1:c.1129C>A
ENST00000336642.8:c.181C>A
ENST00000345378.6:c.1132C>A
ENST00000395796.7:c.1126C>A
ENST00000403799.7:c.1129C>A
ENST00000437084.1:c.1078C>A
ENST00000459642.1:n.509C>A
ENST00000616242.4:c.1126C>A
NM_000162.3:c.1129C>A
NM_033507.1:c.1132C>A
NM_033508.1:c.1126C>A
NM_000162.4:c.1129C>A
NM_001354800.1:c.1129C>A
NM_001354801.1:c.118C>A
NM_001354802.1:c.-12C>A
NM_001354803.1:c.163C>A
NM_033507.2:c.1132C>A
NM_033508.2:c.1126C>A
NM_033507.3:c.1132C>A
NM_033508.3:c.1126C>A
NM_001354803.2:c.163C>A

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP3 PP2 PM5_Supporting PP1_Moderate
Not Met criteria codes 2
PS4 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.1129C>A variant in the glucokinase gene, GCK, causes an amino acid change of alanine to proline at codon 377 (p.(Arg377Ser)) 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 0.988, 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 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). This variant segregated with diabetes, with 4 informative meioses in a family with MODY (PP1_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 (internal lab contributors). Another missense variant, c.1129C>T p.Arg377Cys), has been classified as pathogenic by the ClinGen MDEP VCEP but has a greater Grantham distance than p.Arg377Ser) (PM5_Supporting). 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 1.3.0, approved 8/11/2023): PP2, PP3, PM2_Supporting, PP1_Moderate, PM5_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.988, 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.1129C>T p.Arg377Cys), has been classified as pathogenic by the ClinGen MDEP VCEP but has a greater Grantham distance than p.Arg377Ser) (PM5_Supporting).
PP1_Moderate
This variant was segregated with diabetes, with 4 informative meioses in a family with MODY (PP1_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 (internal lab contributors)
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).
Approved on: 2023-09-20
Published on: 2023-09-20
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