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  • No ClinVar Id was directly found from the curated document


Variant: NM_001354803.2:c.425del

CA2573102976

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 97f80ba0-8d66-4523-8a8c-7d7e1d266044

HGVS expressions

NM_001354803.2:c.425del
NC_000007.14:g.44145145del
CM000669.2:g.44145145del
NC_000007.13:g.44184744del
CM000669.1:g.44184744del
NC_000007.12:g.44151269del
NG_008847.1:g.49281del
NG_008847.2:g.58028del
ENST00000395796.8:c.*1389del
ENST00000616242.5:c.*511del
ENST00000683378.1:n.617del
ENST00000336642.9:c.425del
ENST00000345378.7:c.1394del
ENST00000403799.8:c.1391del
ENST00000671824.1:c.1454del
ENST00000672743.1:n.381+22del
ENST00000673284.1:c.1369+22del
ENST00000336642.8:n.443del
ENST00000345378.6:c.1394del
ENST00000395796.7:c.1388del
ENST00000403799.7:c.1391del
ENST00000437084.1:c.1340del
ENST00000459642.1:n.771del
ENST00000616242.4:n.1388del
NM_000162.3:c.1391del
NM_033507.1:c.1394del
NM_033508.1:c.1388del
NM_000162.4:c.1391del
NM_001354800.1:c.1369+22del
NM_001354801.1:c.380del
NM_001354802.1:c.229+22del
NM_001354803.1:c.425del
NM_033507.2:c.1394del
NM_033508.2:c.1388del
NM_000162.5:c.1391del
NM_033507.3:c.1394del
NM_033508.3:c.1388del

Likely Pathogenic

Met criteria codes 2
PVS1 PM2_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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1391del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 464 (NM_000162.5), adding 150 novel amino acids before encountering a stop codon (p.(Gly464AlafsTer150)). 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 from gnomAD v2.1.1 (PM2_Supporting). In summary, c.1391del meets the criteria to be classified as likely 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
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
Absent in gnomAD v2.1.1 (PM2_Supporting).
Approved on: 2023-06-18
Published on: 2023-06-18
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