The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_000162.5(GCK):c.1229G>A (p.Gly410Asp)

CA367398309

447386 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: d064c5c8-3236-4805-ad04-ceb6948d456d
Approved on: 2024-06-22
Published on: 2024-06-22

HGVS expressions

NM_000162.5:c.1229G>A
NM_000162.5(GCK):c.1229G>A (p.Gly410Asp)
NC_000007.14:g.44145521C>T
CM000669.2:g.44145521C>T
NC_000007.13:g.44185120C>T
CM000669.1:g.44185120C>T
NC_000007.12:g.44151645C>T
NG_008847.1:g.48903G>A
NG_008847.2:g.57650G>A
ENST00000395796.8:c.*1227G>A
ENST00000616242.5:c.*349G>A
ENST00000683378.1:n.455G>A
ENST00000336642.9:c.263G>A
ENST00000345378.7:c.1232G>A
ENST00000403799.8:c.1229G>A
ENST00000671824.1:c.1292G>A
ENST00000672743.1:n.241G>A
ENST00000673284.1:c.1229G>A
ENST00000336642.8:c.281G>A
ENST00000345378.6:c.1232G>A
ENST00000395796.7:c.1226G>A
ENST00000403799.7:c.1229G>A
ENST00000437084.1:c.1178G>A
ENST00000459642.1:n.609G>A
ENST00000616242.4:c.1226G>A
NM_000162.3:c.1229G>A
NM_033507.1:c.1232G>A
NM_033508.1:c.1226G>A
NM_000162.4:c.1229G>A
NM_001354800.1:c.1229G>A
NM_001354801.1:c.218G>A
NM_001354802.1:c.89G>A
NM_001354803.1:c.263G>A
NM_033507.2:c.1232G>A
NM_033508.2:c.1226G>A
NM_033507.3:c.1232G>A
NM_033508.3:c.1226G>A
NM_001354803.2:c.263G>A

Pathogenic

Met criteria codes 7
PP4_Moderate PM5 PM1 PM2_Supporting PP1 PP3 PP2
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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1229G>A variant in the glucokinase gene, GCK, causes an amino acid change of glycine to aspartate at codon 410 (p.(Gly410Asp)) of NM_000162.5. 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 resides in an amino acid that directly binds ATP, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1). 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). This variant segregated with hyperglycemia, with 2 informative meioses in 2 families (PP1; internal lab contributors). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and antibody negative) (PP4_Moderate; internal lab contributors). This variant was identified in three unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors). Another missense variant, c.1228G>A p.Gly410Ser, has been interpreted as pathogenic by the ClinGen MDEP, and p.Gly410Asp has a greater Grantham distance (PM5). In summary, c.1229G>A meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PM1, PP2, PP3, PM2_Supporting, PM5, PP1, PP4_moderate.
Met criteria codes
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and antibody negative) (PP4_Moderate; internal lab contributors).
PM5
Another missense variant, c.1228G>A p.Gly410Ser, has been interpreted as pathogenic by the ClinGen MDEP, and p.Gly410Asp has a greater Grantham distance (PM5).
PM1
This variant resides in an amino acid that directly binds ATP, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting). 0 copies in gnomAD v4.1.0
PP1
This variant segregated with hyperglycemia, with 2 informative meioses in two families (PP1; internal lab contributors).
PP3
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).
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).
Not Met criteria codes
PS4
This variant was identified in three unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors).
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