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.382del

CA2017997777

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 9ca2ade5-65cc-44cf-bb7b-f657f956b84f

HGVS expressions

NM_001354803.2:c.382del
NC_000007.14:g.44145187del
CM000669.2:g.44145187del
NC_000007.13:g.44184786del
CM000669.1:g.44184786del
NC_000007.12:g.44151311del
NG_008847.1:g.49238del
NG_008847.2:g.57985del
ENST00000395796.8:c.*1346del
ENST00000616242.5:c.*468del
ENST00000683378.1:n.574del
ENST00000336642.9:c.382del
ENST00000345378.7:c.1351del
ENST00000403799.8:c.1348del
ENST00000671824.1:c.1411del
ENST00000672743.1:n.360del
ENST00000673284.1:c.1348del
ENST00000336642.8:n.400del
ENST00000345378.6:c.1351del
ENST00000395796.7:c.1345del
ENST00000403799.7:c.1348del
ENST00000437084.1:c.1297del
ENST00000459642.1:n.728del
ENST00000616242.4:n.1345del
NM_000162.3:c.1348del
NM_033507.1:c.1351del
NM_033508.1:c.1345del
NM_000162.4:c.1348del
NM_001354800.1:c.1348del
NM_001354801.1:c.337del
NM_001354802.1:c.208del
NM_001354803.1:c.382del
NM_033507.2:c.1351del
NM_033508.2:c.1345del
NM_000162.5:c.1348del
NM_033507.3:c.1351del
NM_033508.3:c.1345del

Likely Pathogenic

Met criteria codes 2
PM2_Supporting PVS1
Not Met criteria codes 2
PS4 PP4

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.1348del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 450 (NM_000162.5), adding 164 novel amino acids before encountering a stop codon (p.(Ala450ProfsTer164)). 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 consistent with GCK-MODY; however, there was insufficient clinical information to evaluate for PP4. In summary, the c.1348del variant meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PVS1, PP4, PM2_Supporting.
Met criteria codes
PM2_Supporting
Absent in gnomAD v2.1.1 (PM2_Supporting).
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).
Not Met criteria codes
PS4
One case in internal contributor
PP4
This variant was identified in an individual with a clinical history highly consistent with GCK-MODY; however, there was insufficient clinical information to evaluate for PP4.
Approved on: 2023-09-01
Published on: 2023-09-01
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