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.425_426del

CA2573102977

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 913cc38d-3c81-4b2f-89c6-ad67dff5e319

HGVS expressions

NM_001354803.2:c.425_426del
NC_000007.14:g.44145142_44145143del
CM000669.2:g.44145142_44145143del
NC_000007.13:g.44184741_44184742del
CM000669.1:g.44184741_44184742del
NC_000007.12:g.44151266_44151267del
NG_008847.1:g.49281_49282del
NG_008847.2:g.58028_58029del
ENST00000395796.8:c.*1389_*1390del
ENST00000616242.5:c.*511_*512del
ENST00000683378.1:n.617_618del
ENST00000336642.9:c.425_426del
ENST00000345378.7:c.1394_1395del
ENST00000403799.8:c.1391_1392del
ENST00000671824.1:c.1454_1455del
ENST00000672743.1:n.381+22_381+23del
ENST00000673284.1:c.1369+22_1369+23del
ENST00000336642.8:n.443_444del
ENST00000345378.6:c.1394_1395del
ENST00000395796.7:c.1388_1389del
ENST00000403799.7:c.1391_1392del
ENST00000437084.1:c.1340_1341del
ENST00000459642.1:n.771_772del
ENST00000616242.4:n.1388_1389del
NM_000162.3:c.1391_1392del
NM_033507.1:c.1394_1395del
NM_033508.1:c.1388_1389del
NM_000162.4:c.1391_1392del
NM_001354800.1:c.1369+22_1369+23del
NM_001354801.1:c.380_381del
NM_001354802.1:c.229+22_229+23del
NM_001354803.1:c.425_426del
NM_033507.2:c.1394_1395del
NM_033508.2:c.1388_1389del
NM_000162.5:c.1391_1392del
NM_033507.3:c.1394_1395del
NM_033508.3:c.1388_1389del

Likely Pathogenic

Met criteria codes 2
PVS1 PM2_Supporting
Not Met criteria codes 2
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 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1391_1392delGC variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 464 (NM_000162.5), adding 69 novel amino acids before encountering a stop codon (p.(p.Gly464AlafsTer69)). 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 from gnomAD v2.1.1 (PM2_Supporting). The variant was reported in an individual with MODY, autosomal dominant family history of diabetes, antibody negativity, non-insulin dependence, and segregation with diabetes, but there was insufficient information given to apply PP4 or PP1 (PMID: 29056535). In summary, c.1391_1392delGC meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.1.0, approved 3/23/2023): PVS1, PM2_Supporting.
Met criteria codes
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2_Supporting
Absent from gnomAD 2.1.1
Not Met criteria codes
PP1
The variant was stated to segregate with diabetes in a family, but there was insufficient information to apply PP1 (PMID: 29056535).
PP4
Identified in an individual with a diagnosis of MODY, AD family history, antibody negativity, not treated with insulin, and segregation with diabetes, but there was insufficient information to assign PP4 (PMID: 29056535).
Approved on: 2023-03-24
Published on: 2023-05-26
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