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.477T>A

CA367401841

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 5ef647b2-9826-4493-a4bf-8bd943827046
Approved on: 2026-01-22
Published on: 2026-01-28

HGVS expressions

NM_033508.3:c.477T>A
NC_000007.14:g.44150959A>T
CM000669.2:g.44150959A>T
NC_000007.13:g.44190558A>T
CM000669.1:g.44190558A>T
NC_000007.12:g.44157083A>T
NG_008847.1:g.43465T>A
NG_008847.2:g.52212T>A
ENST00000395796.8:c.*478T>A
ENST00000616242.5:c.480T>A
ENST00000682635.1:n.966T>A
ENST00000345378.7:c.483T>A
ENST00000403799.8:c.480T>A
ENST00000671824.1:c.480T>A
ENST00000673284.1:c.480T>A
ENST00000345378.6:c.483T>A
ENST00000395796.7:c.477T>A
ENST00000403799.7:c.480T>A
ENST00000437084.1:c.429T>A
ENST00000616242.4:c.477T>A
NM_000162.3:c.480T>A
NM_033507.1:c.483T>A
NM_033508.1:c.477T>A
NM_000162.4:c.480T>A
NM_001354800.1:c.480T>A
NM_033507.2:c.483T>A
NM_033508.2:c.477T>A
NM_000162.5:c.480T>A
NM_033507.3:c.483T>A
More

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PM5_Strong PP4_Moderate PP3 PP2
Not Met criteria codes 3
PS1 PS4 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 3.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.480T>A variant in the glucokinase gene, GCK, causes an amino acid change of aspartate to glutamine at codon 160 (p.(Asp160Glu)) 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 absent from gnomAD v2.1.1 (PM2_Supporting). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.893, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG fasting glucose 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and three-generation, dominant family history of diabetes or hyperglycemia) (PP4_Moderate; internal lab contributors). This variant was identified in two unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors). Two other missense variants at the same residue, c.478G>A (p.Asp160Asn) and c.478G>C (p.Asp160His), have been interpreted as pathogenic by the ClinGen MDEP (PM5_Strong). The nucleotide change c.480T>G, which causes the same amino acid change, has been classified as likely pathogenic for monogenic diabetes by the ClinGen MDEP; however, PS1_Moderate was not applied to avoid circularity. In summary, c.480T>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 3.1.0, approved 10/10/2025): PP4_moderate, PM5_strong, PP2, PP3, PM2_supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PM5_Strong
Two other missense variants at the same residue, c.478G>A (p.Asp160Asn) and c.478G>C (p.Asp160His), have been interpreted as pathogenic by the ClinGen MDEP (PM5_Strong).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG fasting glucose 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and three-generation, dominant family history of diabetes or hyperglycemia) (PP4_Moderate; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.893, 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
PS1
The nucleotide change c.480T>G, which causes the same amino acid change, has been classified as likely pathogenic for monogenic diabetes by the ClinGen MDEP; however, PS1_Moderate was not applied to avoid circularity.
PS4
This variant was identified in two unrelated individuals with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors).
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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