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.432A>T

CA367396714

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 0fe65c06-f06d-4a08-8901-3ce48e53e3f8

HGVS expressions

NM_001354803.2:c.432A>T
NC_000007.14:g.44145136T>A
CM000669.2:g.44145136T>A
NC_000007.13:g.44184735T>A
CM000669.1:g.44184735T>A
NC_000007.12:g.44151260T>A
NG_008847.1:g.49288A>T
NG_008847.2:g.58035A>T
ENST00000395796.8:c.*1396A>T
ENST00000616242.5:c.*518A>T
ENST00000683378.1:n.624A>T
ENST00000336642.9:c.432A>T
ENST00000345378.7:c.1401A>T
ENST00000403799.8:c.1398A>T
ENST00000671824.1:c.1461A>T
ENST00000672743.1:n.381+29A>T
ENST00000673284.1:c.1369+29A>T
ENST00000336642.8:c.450A>T
ENST00000345378.6:c.1401A>T
ENST00000395796.7:c.1395A>T
ENST00000403799.7:c.1398A>T
ENST00000437084.1:c.1347A>T
ENST00000459642.1:n.778A>T
ENST00000616242.4:c.1395A>T
NM_000162.3:c.1398A>T
NM_033507.1:c.1401A>T
NM_033508.1:c.1395A>T
NM_000162.4:c.1398A>T
NM_001354800.1:c.1369+29A>T
NM_001354801.1:c.387A>T
NM_001354802.1:c.229+29A>T
NM_001354803.1:c.432A>T
NM_033507.2:c.1401A>T
NM_033508.2:c.1395A>T
NM_000162.5:c.1398A>T
NM_033507.3:c.1401A>T
NM_033508.3:c.1395A>T

Pathogenic

Met criteria codes 3
PM2_Supporting PVS1 PP4_Moderate
Not Met criteria codes 1
PP1

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.1398A>T variant in the glucokinase gene, GCK, causes a change from the stop codon to cysteine in the final exon (10/10), resulting in the addition of 144 amino acids at the end of the protein (p.(Ter466CysextTer144)). 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 was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT increment < 3 mmol/L and negative antibodies) (PP4_Moderate; internal lab contributors). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant segregated with hyperglycemia with two informative meioses in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918, internal lab contributors). In summary, c.1398A>T 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, PP4_Moderate, PM2_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from 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).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT increment < 3 mmol/L and negative antibodies) (PP4_Moderate; internal lab contributors).
Not Met criteria codes
PP1
This variant segregated with diabetes with two informative meioses in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918, internal lab contributors).
Approved on: 2024-01-02
Published on: 2024-01-02
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