The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000162.5(GCK):c.1360del (p.Ala454fs)

CA915944915

804844 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: ac4dff08-1dfe-4dd5-a88a-bbc30a9f7fae

HGVS expressions

NM_000162.5:c.1360del
NM_000162.5(GCK):c.1360del (p.Ala454fs)
NC_000007.14:g.44145175del
CM000669.2:g.44145175del
NC_000007.13:g.44184774del
CM000669.1:g.44184774del
NC_000007.12:g.44151299del
NG_008847.1:g.49250del
NG_008847.2:g.57997del
ENST00000395796.8:c.*1358del
ENST00000616242.5:c.*480del
ENST00000683378.1:n.586del
ENST00000336642.9:c.394del
ENST00000345378.7:c.1363del
ENST00000403799.8:c.1360del
ENST00000671824.1:c.1423del
ENST00000672743.1:n.372del
ENST00000673284.1:c.1360del
ENST00000336642.8:n.412del
ENST00000345378.6:c.1363del
ENST00000395796.7:c.1357del
ENST00000403799.7:c.1360del
ENST00000437084.1:c.1309del
ENST00000459642.1:n.740del
ENST00000616242.4:n.1357del
NM_000162.3:c.1360del
NM_033507.1:c.1363del
NM_033508.1:c.1357del
NM_000162.4:c.1360del
NM_001354800.1:c.1360del
NM_001354801.1:c.349del
NM_001354802.1:c.220del
NM_001354803.1:c.394del
NM_033507.2:c.1363del
NM_033508.2:c.1357del
NM_033507.3:c.1363del
NM_033508.3:c.1357del
NM_001354803.2:c.394del

Pathogenic

Met criteria codes 5
PP4_Moderate PVS1 PP1_Strong PM2_Supporting PS4_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 1.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1360del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 454 (NM_000162.5), adding 160 novel amino acids before encountering a stop codon (p.(Ala454ArgfsTer160)). 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 4 unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; 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% and negative antibodies) (PP4_Moderate; internal lab contributors). This variant segregated with diabetes, with 4 informative meioses in 2 families with MODY (PP1_Strong; internal lab contributors). In summary, the c.1360del 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, PS4_Moderate, PP4_Moderate, PP1_Strong.
Met criteria codes
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 negative antibodies) (PP4_Moderate; internal lab contributors).
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).
PP1_Strong
This variant segregated with diabetes, with 4 informative meioses in 2 families with MODY (PP1_Strong; internal lab contributors).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PS4_Moderate
This variant was identified in 4 unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; internal lab contributors).
Approved on: 2023-06-22
Published on: 2023-06-22
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