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 computed assertion could be determined for this classification!


Variant: NM_033508.3:c.455C>A

CA367401917

2567920 (ClinVar)

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: dc0a8035-6e5a-4c6f-9c2e-bdda0a027ad3
Approved on: 2026-06-24
Published on: 2026-06-24

HGVS expressions

NM_033508.3:c.455C>A
NC_000007.14:g.44150981G>T
CM000669.2:g.44150981G>T
NC_000007.13:g.44190580G>T
CM000669.1:g.44190580G>T
NC_000007.12:g.44157105G>T
NG_008847.1:g.43443C>A
NG_008847.2:g.52190C>A
ENST00000395796.8:c.*456C>A
ENST00000616242.5:c.458C>A
ENST00000682635.1:n.944C>A
ENST00000345378.7:c.461C>A
ENST00000403799.8:c.458C>A
ENST00000671824.1:c.458C>A
ENST00000673284.1:c.458C>A
ENST00000345378.6:c.461C>A
ENST00000395796.7:c.455C>A
ENST00000403799.7:c.458C>A
ENST00000437084.1:c.407C>A
ENST00000616242.4:c.455C>A
NM_000162.3:c.458C>A
NM_033507.1:c.461C>A
NM_033508.1:c.455C>A
NM_000162.4:c.458C>A
NM_001354800.1:c.458C>A
NM_033507.2:c.461C>A
NM_033508.2:c.455C>A
NM_000162.5:c.458C>A
NM_033507.3:c.461C>A
More

Pathogenic

Met criteria codes 7
PM2_Supporting PS4_Moderate PP1_Strong PP3 PP2 PM1 PM5
Not Met criteria codes 1
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 3.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.458C>A variant in the glucokinase gene, GCK, causes an amino acid change of proline to histidine at codon 153 (p.(Pro153His)) 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 is predicted to be deleterious by computational evidence, with a REVEL score of 0.985, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant resides in an amino acid that directly binds glucose, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1). This variant is absent from gnomAD 4.1.0 (PM2_Supporting). This variant was identified in five unrelated individuals with hyperglycemia; however PP4 was unable to be evaluated due to insufficient clinical information (PS4_Moderate; internal lab contributors). This variant was segregated with hyperglycemia, with seven informative meioses in five families (PP1_Strong; internal lab contributors). Another missense variant at the same residue, c.457C>T (p.Pro153Ser), has been interpreted as pathogenic by the ClinGen MDEP, and p.Pro153His has a greater Grantham distance (PM5). In summary, c.458C>A meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 3.1.0., approved 10/10/2025): PP1_Strong, PS4_Moderate, PM1, PM5, PM2_Supporting, PP2, PP3.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PS4_Moderate
This variant was identified in five unrelated individuals with hyperglycemia (PS4_Moderate; internal lab contributors).
PP1_Strong
This variant was segregated with hyperglycemia, with seven informative meioses in five families (PP1_Strong; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.985, 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).
PM1
This variant resides in an amino acid that directly binds glucose, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1).
PM5
Another missense variant at the same residue, c.457C>T (p.Pro153Ser), has been interpreted as pathogenic by the ClinGen MDEP, and p.Pro153His has a greater Grantham distance (PM5).
Not Met criteria codes
PP4
This variant was identified in 5 unrelated individuals with a phenotype suggestive of GCK-hyperglycemia; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributors).
Curation History
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