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
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_033508.3:c.530G>T

CA367401649

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 2ba25ad4-e805-47e6-8995-9f8ad30d368a
Approved on: 2026-03-22
Published on: 2026-03-26

HGVS expressions

NM_033508.3:c.530G>T
NC_000007.14:g.44150015C>A
CM000669.2:g.44150015C>A
NC_000007.13:g.44189614C>A
CM000669.1:g.44189614C>A
NC_000007.12:g.44156139C>A
NG_008847.1:g.44409G>T
NG_008847.2:g.53156G>T
ENST00000395796.8:c.*531G>T
ENST00000616242.5:c.533G>T
ENST00000682635.1:n.1019G>T
ENST00000345378.7:c.536G>T
ENST00000403799.8:c.533G>T
ENST00000671824.1:c.533G>T
ENST00000673284.1:c.533G>T
ENST00000345378.6:c.536G>T
ENST00000395796.7:c.530G>T
ENST00000403799.7:c.533G>T
ENST00000437084.1:c.482G>T
ENST00000616242.4:c.530G>T
NM_000162.3:c.533G>T
NM_033507.1:c.536G>T
NM_033508.1:c.530G>T
NM_000162.4:c.533G>T
NM_001354800.1:c.533G>T
NM_033507.2:c.536G>T
NM_033508.2:c.530G>T
NM_000162.5:c.533G>T
NM_033507.3:c.536G>T
More

Likely Pathogenic

Met criteria codes 5
PP3 PP2 PM5 PP4_Moderate PM2_Supporting
Not Met criteria codes 3
PP1 PM1 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 3.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.533G>T variant in the glucokinase gene, GCK, causes an amino acid change of glycine to valine at codon 178 (p.(Gly178Val)) 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 0.987, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent in gnomAD v4.1 (PM2_Supporting). This variant was identified in three unrelated probands with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID: 36257325, internal lab contributors). At least one of these individuals did have a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT with minimal increment <3mmol/L) (PP4_Moderate; Internal lab contributor). This variant segregated with hyperglycemia with two informative meioses in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (Internal lab contributor). Another missense variant at the same residue, c.533G>A p.Gly178Glu, has been interpreted as pathogenic by the ClinGen MDEP, and p.Gly178Val has a greater Grantham distance (PM5). In summary, c.533G>T meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 3.1.0, approved 10/10/2025): PP2, PP3, PM2_Supporting, PM5, PP4_Moderate.
Met criteria codes
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.987, 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
Another missense variant at the same residue, c.533G>A p.Gly178Glu, has been interpreted as pathogenic by the ClinGen MDEP, and p.Gly178Val has a greater Grantham distance (PM5).
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 OGTT with minimal increment <3mmol/L) (PP4_Moderate; Internal lab contributor).
PM2_Supporting
This variant is absent in gnomAD v4.1 (PM2_Supporting).
Not Met criteria codes
PP1
This variant segregated with hyperglycemia with two informative meioses in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (Internal lab contributor).
PM1
This variant does not reside in an amino acid that directly binds glucose or ATP, which are defined as critical for the GCK protein's function by the ClinGen MDEP.
PS4
This variant was identified in three unrelated probands with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID: 36257325, internal lab contributors).
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
ClinGen Terms of Use.
¤ Powered by BCM's Genboree.