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.290del

CA1139771322

Gene: GCK
Condition: maturity-onset diabetes of the young type 2
Inheritance Mode: Semidominant inheritance
UUID: 5222dbb8-c9b7-4403-b77d-3bb564f07a5e

HGVS expressions

NM_001354803.2:c.290del
NC_000007.14:g.44145279del
CM000669.2:g.44145279del
NC_000007.13:g.44184878del
CM000669.1:g.44184878del
NC_000007.12:g.44151403del
NG_008847.1:g.49146del
NG_008847.2:g.57893del
ENST00000395796.8:c.*1254del
ENST00000616242.5:c.*376del
ENST00000683378.1:n.482del
ENST00000336642.9:c.290del
ENST00000345378.7:c.1259del
ENST00000403799.8:c.1256del
ENST00000671824.1:c.1319del
ENST00000672743.1:n.268del
ENST00000673284.1:c.1256del
ENST00000336642.8:n.308del
ENST00000345378.6:c.1259del
ENST00000395796.7:c.1253del
ENST00000403799.7:c.1256del
ENST00000437084.1:c.1205del
ENST00000459642.1:n.636del
ENST00000616242.4:n.1253del
NM_000162.3:c.1256del
NM_033507.1:c.1259del
NM_033508.1:c.1253del
NM_000162.4:c.1256del
NM_001354800.1:c.1256del
NM_001354801.1:c.245del
NM_001354802.1:c.116del
NM_001354803.1:c.290del
NM_033507.2:c.1259del
NM_033508.2:c.1253del
NM_000162.5:c.1256del
NM_033507.3:c.1259del
NM_033508.3:c.1253del

Pathogenic

Met criteria codes 5
PM3 PVS1_Strong PM2_Supporting PP4_Moderate PS4_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.1256del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 419 (NM_000162.5), adding 12 novel amino acids before encountering a stop codon (p.(Phe419SerfsTer12)). While this variant, located in exon 10 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). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). This variant was identified in 4 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; PMID: 25015100, PMID: 29056535, PMID: 33414663 and internal lab contributors). This variant has been detected in at least two individuals with neonatal diabetes. Of those individuals, two were homozygous. (PM3; PMID: 25015100, PMID: 29056535, internal lab contributors). 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%, antibody negative, and 3 generation dominant family history of diabetes) (PP4_Moderate; internal lab contributors). 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 (internal lab contributors). In summary, c.1256del 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, PS4_Moderate, PM3, PP4_moderate.
Met criteria codes
PM3
This variant has been detected in at least two individuals with neonatal diabetes. Of those individuals, two were homozygous. (PMID: 25015100, PMID: 29056535, internal lab contributors) (PM3).
PVS1_Strong
While this variant, located in exon 10 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).
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
PP4_Moderate
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% and antibody negative, 3 generation dominant family history of diabetes) (PP4_Moderate; internal lab contributors).
PS4_Moderate
This variant was identified in 4 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; PMIDs: 25015100, 29056535, 33414663, and 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 (internal lab contributors).
Approved on: 2023-06-26
Published on: 2023-06-26
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