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.1344del (p.Ala449fs)

CA16609265

393448 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: fbe6afe4-7e88-4f73-aeae-8dee5e88c151

HGVS expressions

NM_000162.5:c.1344del
NM_000162.5(GCK):c.1344del (p.Ala449fs)
NC_000007.14:g.44145190del
CM000669.2:g.44145190del
NC_000007.13:g.44184789del
CM000669.1:g.44184789del
NC_000007.12:g.44151314del
NG_008847.1:g.49234del
NG_008847.2:g.57981del
ENST00000395796.8:c.*1342del
ENST00000616242.5:c.*464del
ENST00000683378.1:n.570del
ENST00000336642.9:c.378del
ENST00000345378.7:c.1347del
ENST00000403799.8:c.1344del
ENST00000671824.1:c.1407del
ENST00000672743.1:n.356del
ENST00000673284.1:c.1344del
ENST00000336642.8:n.396del
ENST00000345378.6:c.1347del
ENST00000395796.7:c.1341del
ENST00000403799.7:c.1344del
ENST00000437084.1:c.1293del
ENST00000459642.1:n.724del
ENST00000616242.4:n.1341del
NM_000162.3:c.1344del
NM_033507.1:c.1347del
NM_033508.1:c.1341del
NM_000162.4:c.1344del
NM_001354800.1:c.1344del
NM_001354801.1:c.333del
NM_001354802.1:c.204del
NM_001354803.1:c.378del
NM_033507.2:c.1347del
NM_033508.2:c.1341del
NM_033507.3:c.1347del
NM_033508.3:c.1341del
NM_001354803.2:c.378del

Pathogenic

Met criteria codes 5
PP4_Moderate PM2_Supporting PS4_Moderate PP1_Moderate PVS1

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.1344del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 449 (NM_000162.5), adding 165 novel amino acids before encountering a stop codon (p.(p.Ala449ArgfsTer165)). 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 five unrelated individuals with a clinical picture consistent with non-autoimmune/insulin-deficient diabetes (PS4_Moderate; ClinVar ID 393448, internal lab contributors). This variant segregated with disease, with 3 informative meioses in 2 families with MODY (PP1_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 contributor). In summary, the c.1344del 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, PP1_Moderate, PP4_Moderate, PS4_Moderate, PM2_Supporting).
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 contributor).
PM2_Supporting
Absent in gnomAD v2.1.1 (PM2_Supporting).
PS4_Moderate
This variant was identified in five unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; ClinVar ID 393448, internal lab contributors).
PP1_Moderate
This variant segregated with diabetes, with three informative meioses in two families with MODY (PP1_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).
Approved on: 2023-06-24
Published on: 2023-06-24
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