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.1148del (p.Ser383fs)

CA1139660056

973191 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 7f10321d-0fbe-42bc-8ce5-0d98a2b57100

HGVS expressions

NM_000162.5:c.1148del
NM_000162.5(GCK):c.1148del (p.Ser383fs)
NC_000007.14:g.44145602del
CM000669.2:g.44145602del
NC_000007.13:g.44185201del
CM000669.1:g.44185201del
NC_000007.12:g.44151726del
NG_008847.1:g.48822del
NG_008847.2:g.57569del
ENST00000395796.8:c.*1146del
ENST00000616242.5:c.*268del
ENST00000683378.1:n.374del
ENST00000336642.9:c.182del
ENST00000345378.7:c.1151del
ENST00000403799.8:c.1148del
ENST00000671824.1:c.1211del
ENST00000672743.1:n.160del
ENST00000673284.1:c.1148del
ENST00000336642.8:c.200del
ENST00000345378.6:c.1151del
ENST00000395796.7:c.1145del
ENST00000403799.7:c.1148del
ENST00000437084.1:c.1097del
ENST00000459642.1:n.528del
ENST00000616242.4:c.1145del
NM_000162.3:c.1148del
NM_033507.1:c.1151del
NM_033508.1:c.1145del
NM_000162.4:c.1148del
NM_001354800.1:c.1148del
NM_001354801.1:c.137del
NM_001354802.1:c.8del
NM_001354803.1:c.182del
NM_033507.2:c.1151del
NM_033508.2:c.1145del
NM_033507.3:c.1151del
NM_033508.3:c.1145del
NM_001354803.2:c.182del

Pathogenic

Met criteria codes 4
PM3_Supporting PP4 PVS1 PM2_Supporting
Not Met criteria codes 1
PS4

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.1148del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 383 (NM_000162.5), adding 19 novel amino acids before encountering a stop codon (p. (Ser383Trpfs*19)). This variant, located in biologically-relevant exon 9 of 10, is predicted to lead to nonsense mediated decay 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), but has been detected in two unrelated probands with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (Internal lab contributors). One proband, along with his sister, was diagnosed with neonatal diabetes; they have this variant in the homozygous state (PP4, PM3_Supporting; internal lab contributor). In summary, c.1148del meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (VCEP specifications version v 1.3.0; approved 8/11/2023): PVS1, PM2_Supporting, PM3_Supporting, PP4.
Met criteria codes
PM3_Supporting
This variant has been detected in two siblings with neonatal diabetes in the homozygous state (PM3_Supporting; internal cases contributor).
PP4
neonatal case
PVS1
This variant, located in biologically-relevant exon 9 of 10, is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID: 19790256)
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting)
Not Met criteria codes
PS4
It has been detected in two unrelated probands with hyperglycemia; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (Internal lab contributors).
Approved on: 2024-03-12
Published on: 2024-03-12
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