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.380_396del

CA2017997776

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: bd3084d6-9dc3-41fd-aa91-9835ae812ea8

HGVS expressions

NM_001354803.2:c.380_396del
NC_000007.14:g.44145176_44145192del
CM000669.2:g.44145176_44145192del
NC_000007.13:g.44184775_44184791del
CM000669.1:g.44184775_44184791del
NC_000007.12:g.44151300_44151316del
NG_008847.1:g.49236_49252del
NG_008847.2:g.57983_57999del
ENST00000395796.8:c.*1344_*1360del
ENST00000616242.5:c.*466_*482del
ENST00000683378.1:n.572_588del
ENST00000336642.9:c.380_396del
ENST00000345378.7:c.1349_1365del
ENST00000403799.8:c.1346_1362del
ENST00000671824.1:c.1409_1425del
ENST00000672743.1:n.358_374del
ENST00000673284.1:c.1346_1362del
ENST00000336642.8:n.398_414del
ENST00000345378.6:c.1349_1365del
ENST00000395796.7:c.1343_1359del
ENST00000403799.7:c.1346_1362del
ENST00000437084.1:c.1295_1311del
ENST00000459642.1:n.726_742del
ENST00000616242.4:n.1343_1359del
NM_000162.3:c.1346_1362del
NM_033507.1:c.1349_1365del
NM_033508.1:c.1343_1359del
NM_000162.4:c.1346_1362del
NM_001354800.1:c.1346_1362del
NM_001354801.1:c.335_351del
NM_001354802.1:c.206_222del
NM_001354803.1:c.380_396del
NM_033507.2:c.1349_1365del
NM_033508.2:c.1343_1359del
NM_000162.5:c.1346_1362del
NM_033507.3:c.1349_1365del
NM_033508.3:c.1343_1359del

Pathogenic

Met criteria codes 5
PM2_Supporting PVS1 PS4_Moderate PP1 PP4

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.1346_1362del variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 449 (NM_000162.5), adding 4 novel amino acids before encountering a stop codon (p.(Ala449GlyfsTer4)). 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; PMID: 19790256). This variant is absent in gnomAD (PM2_Supporting). This variant was identified in 5 unrelated individuals with a clinical picture consistent with non-autoimmune/insulin-deficient diabetes (PS4_Moderate; internal lab contributors). This variant was identified in at least two individuals with a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4_Moderate, internal lab contributors). This variant segregated with disease with 2 informative meioses in 2 families with MODY (PP1; internal lab contributors). In summary, the c.1346_1362del 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, PP4, PS4_Moderate, PP1, PM2_Supporting.
Met criteria codes
PM2_Supporting
Absent in gnomAD v2.1.1 (PM2_Supporting).
PVS1
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; PMID: 19790256).
PS4_Moderate
This variant was identified in 5 unrelated individuals with a clinical picture consistent with non-autoimmune/insulin-deficient diabetes (PS4_Moderate; internal lab contributors)
PP1
This variant segregated with disease with 2 informative meioses in 2 families with MODY (PP1; internal lab contributors).
PP4
This variant was identified in at least two individuals with a clinical history highly specific for GCK-MODY (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4_Moderate, internal lab contributors).
Approved on: 2023-06-24
Published on: 2023-06-24
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