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.64_73del

CA2580612102

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 8d9dc2d8-17dd-4a69-b89a-4672b1301428

HGVS expressions

NM_001354803.2:c.64_73del
NC_000007.14:g.44145713_44145722del
CM000669.2:g.44145713_44145722del
NC_000007.13:g.44185312_44185321del
CM000669.1:g.44185312_44185321del
NC_000007.12:g.44151837_44151846del
NG_008847.1:g.48704_48713del
NG_008847.2:g.57451_57460del
ENST00000395796.8:c.*1028_*1037del
ENST00000616242.5:c.*150_*159del
ENST00000683378.1:n.256_265del
ENST00000336642.9:c.64_73del
ENST00000345378.7:c.1033_1042del
ENST00000403799.8:c.1030_1039del
ENST00000671824.1:c.1093_1102del
ENST00000672743.1:n.42_51del
ENST00000673284.1:c.1030_1039del
ENST00000336642.8:c.82_91del
ENST00000345378.6:c.1033_1042del
ENST00000395796.7:c.1027_1036del
ENST00000403799.7:c.1030_1039del
ENST00000437084.1:c.979_988del
ENST00000459642.1:n.410_419del
ENST00000473353.1:n.328_337del
ENST00000616242.4:c.1027_1036del
NM_000162.3:c.1030_1039del
NM_033507.1:c.1033_1042del
NM_033508.1:c.1027_1036del
NM_000162.4:c.1030_1039del
NM_001354800.1:c.1030_1039del
NM_001354801.1:c.19_28del
NM_001354802.1:c.-111_-102del
NM_001354803.1:c.64_73del
NM_033507.2:c.1033_1042del
NM_033508.2:c.1027_1036del
NM_000162.5:c.1030_1039del
NM_033507.3:c.1033_1042del
NM_033508.3:c.1027_1036del

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 1.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1030_1039del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 344 (NM_000162.5), adding six novel amino acids before encountering a stop codon (p.(Asp344Argfs*6)). While this variant, located in exon 9 of 10, is predicted to cause a premature stop codon and to escape nonsense mediated decay, it is in a functionally important region of a gene where 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-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6-7.6% and antibody negative) (PP4_Moderate; internal lab contributor). In summary, c.1030_1039del meets 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, PM2_Supporting, PP4_Moderate.
Met criteria codes
PVS1
While this variant, located in exon 9 of 10, is predicted to cause a premature stop codon and to escape nonsense mediated decay, it is in a functionally important region of a gene where loss-of-function is an established disease mechanism (PVS1; PMID: 19790256).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
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 antibody negative) (PP4_Moderate; internal lab contributor).
Approved on: 2024-01-27
Published on: 2024-01-27
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