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.701T>G

CA367400741

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 7dcbe174-95cc-49ef-92a3-d9d3bdac4f6b
Approved on: 2026-01-22
Published on: 2026-01-28

HGVS expressions

NM_033508.3:c.701T>G
NC_000007.14:g.44147809A>C
CM000669.2:g.44147809A>C
NC_000007.13:g.44187408A>C
CM000669.1:g.44187408A>C
NC_000007.12:g.44153933A>C
NG_008847.1:g.46615T>G
NG_008847.2:g.55362T>G
ENST00000395796.8:c.*702T>G
ENST00000616242.5:c.704T>G
ENST00000345378.7:c.707T>G
ENST00000403799.8:c.704T>G
ENST00000671824.1:c.704T>G
ENST00000673284.1:c.704T>G
ENST00000345378.6:c.707T>G
ENST00000395796.7:c.701T>G
ENST00000403799.7:c.704T>G
ENST00000437084.1:c.653T>G
ENST00000616242.4:c.701T>G
NM_000162.3:c.704T>G
NM_033507.1:c.707T>G
NM_033508.1:c.701T>G
NM_000162.4:c.704T>G
NM_001354800.1:c.704T>G
NM_033507.2:c.707T>G
NM_033508.2:c.701T>G
NM_000162.5:c.704T>G
NM_033507.3:c.707T>G
More

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP3 PP2 PM5_Strong
Not Met criteria codes 3
PP4 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.704T>G variant in the glucokinase gene, GCK, causes an amino acid change of methionine to arginine at codon 235 (p.(Met235Arg)) 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 0.934, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). Two other missense variants at the same residue, c.704T>C (p.Met235Thr) and c.703A>G (p.Met235Val), have been interpreted as pathogenic by the ClinGen MDEP, and p.Met235Arg has a greater Grantham distance than both of these variants (PM5_Strong). 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). In summary, c.704T>G 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): PM5_Strong, PM2_Supporting, PP2, PP3.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.934, 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_Strong
Two other missense variants at the same residue, c.704T>C (p.Met235Thr) and c.703A>G (p.Met235Val), have been interpreted as pathogenic by the ClinGen MDEP, and p.Met235Arg has a greater Grantham distance than both variants (PM5_Strong).
Not Met criteria codes
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).
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
This variant was identified in one individual with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors).
Curation History
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