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 label mismatch: GCK vs undefined
  • 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_000162.5(GCK):c.1181G>T (p.Arg394Leu)

CA367398578

1522625 (ClinVar)

Gene: GCK (HGNC:2645)
Condition: monogenic diabetes (MONDO:0015967)
Inheritance Mode: Semidominant inheritance
UUID: 7b717baa-5df4-4bbc-8132-edfcceb7b495
Approved on: 2025-04-25
Published on: 2025-04-25

HGVS expressions

NM_000162.5:c.1181G>T
NM_000162.5(GCK):c.1181G>T (p.Arg394Leu)
NC_000007.14:g.44145569C>A
CM000669.2:g.44145569C>A
NC_000007.13:g.44185168C>A
CM000669.1:g.44185168C>A
NC_000007.12:g.44151693C>A
NG_008847.1:g.48855G>T
NG_008847.2:g.57602G>T
ENST00000395796.8:c.*1179G>T
ENST00000616242.5:c.*301G>T
ENST00000683378.1:n.407G>T
ENST00000336642.9:c.215G>T
ENST00000345378.7:c.1184G>T
ENST00000403799.8:c.1181G>T
ENST00000671824.1:c.1244G>T
ENST00000672743.1:n.193G>T
ENST00000673284.1:c.1181G>T
ENST00000336642.8:c.233G>T
ENST00000345378.6:c.1184G>T
ENST00000395796.7:c.1178G>T
ENST00000403799.7:c.1181G>T
ENST00000437084.1:c.1130G>T
ENST00000459642.1:n.561G>T
ENST00000616242.4:c.1178G>T
NM_000162.3:c.1181G>T
NM_033507.1:c.1184G>T
NM_033508.1:c.1178G>T
NM_000162.4:c.1181G>T
NM_001354800.1:c.1181G>T
NM_001354801.1:c.170G>T
NM_001354802.1:c.41G>T
NM_001354803.1:c.215G>T
NM_033507.2:c.1184G>T
NM_033508.2:c.1178G>T
NM_033507.3:c.1184G>T
NM_033508.3:c.1178G>T
NM_001354803.2:c.215G>T
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Likely Pathogenic

Met criteria codes 6
PM2_Supporting PP3 PP2 PS3_Supporting PP4_Moderate PM5_Supporting

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 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1181G>T variant in the glucokinase gene, GCK, causes an amino acid change of arginine to leucine at codon 394 (p.(Arg394Leu)) of transcript NM_000162.5. This variant is absent from gnomAD v4.1 (PM2_Supporting). 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 0.925 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-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and three generation family history of diabetes/hyperglycemia) (PP4_Moderate; internal lab contributors). While the relative activity index (RAI) of this variant was above the MDEP cutoff of 0.5, the relative stability index was below the MDEP cutoff of 0.5 (PS3_Supporting; internal lab contributors). Another missense variant at the same amino acid position, c.1181G>C p.Arg394Pro has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting). In summary, c.1181G>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 2.0.0, approved 2/17/2025): PM2_Supporting, PP2, PP3, PP4_Moderate, PS3_Supporting, PM5_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v4.1 (PM2_Supporting).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.801, which is greater than or equal to 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).
PS3_Supporting
While the relative activity index (RAI) of this variant was above the MDEP cutoff of 0.5, the relative stability index was below the MDEP cutoff of 0.5 (PS3_Supporting; internal lab contributors).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L, HbA1c 5.6 - 7.6%, and three generation family history of diabetes/hyperglycemia) (PP4_Moderate; internal lab contributors).
PM5_Supporting
Another missense variant at the same amino acid position, c.1181G>C p.Arg394Pro has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting).
Curation History
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