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.397dup

CA2573102980

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 579e8430-0352-48b7-ae69-a21548395c33

HGVS expressions

NM_001354803.2:c.397dup
NC_000007.14:g.44145172dup
CM000669.2:g.44145172dup
NC_000007.13:g.44184771dup
CM000669.1:g.44184771dup
NC_000007.12:g.44151296dup
NG_008847.1:g.49253dup
NG_008847.2:g.58000dup
ENST00000395796.8:c.*1361dup
ENST00000616242.5:c.*483dup
ENST00000683378.1:n.589dup
ENST00000336642.9:c.397dup
ENST00000345378.7:c.1366dup
ENST00000403799.8:c.1363dup
ENST00000671824.1:c.1426dup
ENST00000672743.1:n.375dup
ENST00000673284.1:c.1363dup
ENST00000336642.8:n.415dup
ENST00000345378.6:c.1366dup
ENST00000395796.7:c.1360dup
ENST00000403799.7:c.1363dup
ENST00000437084.1:c.1312dup
ENST00000459642.1:n.743dup
ENST00000616242.4:n.1360dup
NM_000162.3:c.1363dup
NM_033507.1:c.1366dup
NM_033508.1:c.1360dup
NM_000162.4:c.1363dup
NM_001354800.1:c.1363dup
NM_001354801.1:c.352dup
NM_001354802.1:c.223dup
NM_001354803.1:c.397dup
NM_033507.2:c.1366dup
NM_033508.2:c.1360dup
NM_000162.5:c.1363dup
NM_033507.3:c.1366dup
NM_033508.3:c.1360dup

Likely Pathogenic

Met criteria codes 2
PM2_Supporting PVS1
Not Met criteria codes 1
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.1363dup variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 455 of NM_000162.5, adding 4 novel amino acids before encountering a stop codon (p.(Val455GlyfsTer4)). 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). This variant was identified in an individual with a phenotype suggestive of GCK-hyperglycemia; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributors). In summary, c.1363dup meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.3.0, approved 8/11/2023): PVS1, PM2_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from 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).
Not Met criteria codes
PP4
This variant was identified in an individual with a phenotype suggestive of GCK-hyperglycemia; however, PP4 is unable to be evaluated due to insufficient clinical information (internal lab contributors).
Approved on: 2023-09-01
Published on: 2023-09-01
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