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


Variant: NM_001354803.2:c.412del

CA2573102978

Gene: GCK
Condition: maturity-onset diabetes of the young type 2
Inheritance Mode: Semidominant inheritance
UUID: 44ebdc11-ff37-4204-814b-b927afcb97ea

HGVS expressions

NM_001354803.2:c.412del
NC_000007.14:g.44145157del
CM000669.2:g.44145157del
NC_000007.13:g.44184756del
CM000669.1:g.44184756del
NC_000007.12:g.44151281del
NG_008847.1:g.49268del
NG_008847.2:g.58015del
ENST00000395796.8:c.*1376del
ENST00000616242.5:c.*498del
ENST00000683378.1:n.604del
ENST00000336642.9:c.412del
ENST00000345378.7:c.1381del
ENST00000403799.8:c.1378del
ENST00000671824.1:c.1441del
ENST00000672743.1:n.381+9del
ENST00000673284.1:c.1369+9del
ENST00000336642.8:n.430del
ENST00000345378.6:c.1381del
ENST00000395796.7:c.1375del
ENST00000403799.7:c.1378del
ENST00000437084.1:c.1327del
ENST00000459642.1:n.758del
ENST00000616242.4:n.1375del
NM_000162.3:c.1378del
NM_033507.1:c.1381del
NM_033508.1:c.1375del
NM_000162.4:c.1378del
NM_001354800.1:c.1369+9del
NM_001354801.1:c.367del
NM_001354802.1:c.229+9del
NM_001354803.1:c.412del
NM_033507.2:c.1381del
NM_033508.2:c.1375del
NM_000162.5:c.1378del
NM_033507.3:c.1381del
NM_033508.3:c.1375del

Pathogenic

Met criteria codes 3
PVS1 PM2_Supporting PP4_Moderate

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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1378del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 460 (NM_000162.5), adding 154 novel amino acids before encountering a stop codon (p.(Ala460ProfsTer154)). This variant, located in exon 10 of 10, is predicted to cause loss of a stop codon and result in an elongated protein. The additional residues are expected to cause improper folding, resulting in loss-of-function in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID 19790256). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). 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 antibody negative) (PP4_Moderate; PMID: 15841481). In summary, c.1378del meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.2.0, approved 6/7/2023): PVS1, PM2_supporting, PP4_Moderate.
Met criteria codes
PVS1
This variant, located in exon 10 of 10, is predicted to cause loss of a stop codon and result in an elongated protein. The additional residues are expected to cause improper folding, resulting in loss of function in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID 19790256).
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
PP4_Moderate
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 antibody negative) (PP4_Moderate; PMID: 15841481).
Approved on: 2023-06-18
Published on: 2023-06-18
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