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.407_410del

CA2573102979

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 39663460-688a-4c9c-aa98-1e094fc640fe

HGVS expressions

NM_001354803.2:c.407_410del
NC_000007.14:g.44145159_44145162del
CM000669.2:g.44145159_44145162del
NC_000007.13:g.44184758_44184761del
CM000669.1:g.44184758_44184761del
NC_000007.12:g.44151283_44151286del
NG_008847.1:g.49263_49266del
NG_008847.2:g.58010_58013del
ENST00000395796.8:c.*1371_*1374del
ENST00000616242.5:c.*493_*496del
ENST00000683378.1:n.599_602del
ENST00000336642.9:c.407_410del
ENST00000345378.7:c.1376_1379del
ENST00000403799.8:c.1373_1376del
ENST00000671824.1:c.1436_1439del
ENST00000672743.1:n.381+4_381+7del
ENST00000673284.1:c.1369+4_1369+7del
ENST00000336642.8:n.425_428del
ENST00000345378.6:c.1376_1379del
ENST00000395796.7:c.1370_1373del
ENST00000403799.7:c.1373_1376del
ENST00000437084.1:c.1322_1325del
ENST00000459642.1:n.753_756del
ENST00000616242.4:n.1370_1373del
NM_000162.3:c.1373_1376del
NM_033507.1:c.1376_1379del
NM_033508.1:c.1370_1373del
NM_000162.4:c.1373_1376del
NM_001354800.1:c.1369+4_1369+7del
NM_001354801.1:c.362_365del
NM_001354802.1:c.229+4_229+7del
NM_001354803.1:c.407_410del
NM_033507.2:c.1376_1379del
NM_033508.2:c.1370_1373del
NM_000162.5:c.1373_1376del
NM_033507.3:c.1376_1379del
NM_033508.3:c.1370_1373del

Pathogenic

Met criteria codes 4
PVS1 PP4 PP1 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.1373_1376del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 458 (NM_000162.5), adding 155 novel amino acids before encountering a stop codon (p.(Lys458ArgfsTer155)). 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). 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%) (PP4; internal lab contributors). This variant segregated with disease with 3 informative meioses in 1 family with MODY (PP1; internal lab contributors). In summary, the c.1373_1376del variant meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.2.0, approved 6/7/2023): PVS1, PM2_Supporting, PP4, PP1.
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).
PP4
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%) (PP4_Moderate; internal lab contributors).
PP1
This variant segregated with disease with 3 informative meioses in 1 family with MODY (PP1; internal lab contributors).
PM2_Supporting
Absent in gnomAD v2.1.1 (PM2_Supporting).
Approved on: 2023-07-29
Published on: 2023-07-29
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