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.339dup

CA2573106065

Gene: GCK
Condition: maturity-onset diabetes of the young type 2
Inheritance Mode: Semidominant inheritance
UUID: 1519820c-2ab9-49c6-b5b8-2fa2370155e0

HGVS expressions

NM_001354803.2:c.339dup
NC_000007.14:g.44145229dup
CM000669.2:g.44145229dup
NC_000007.13:g.44184828dup
CM000669.1:g.44184828dup
NC_000007.12:g.44151353dup
NG_008847.1:g.49195dup
NG_008847.2:g.57942dup
ENST00000395796.8:c.*1303dup
ENST00000616242.5:c.*425dup
ENST00000683378.1:n.531dup
ENST00000336642.9:c.339dup
ENST00000345378.7:c.1308dup
ENST00000403799.8:c.1305dup
ENST00000671824.1:c.1368dup
ENST00000672743.1:n.317dup
ENST00000673284.1:c.1305dup
ENST00000336642.8:c.357dup
ENST00000345378.6:c.1308dup
ENST00000395796.7:c.1302dup
ENST00000403799.7:c.1305dup
ENST00000437084.1:c.1254dup
ENST00000459642.1:n.685dup
ENST00000616242.4:c.1302dup
NM_000162.3:c.1305dup
NM_033507.1:c.1308dup
NM_033508.1:c.1302dup
NM_000162.4:c.1305dup
NM_001354800.1:c.1305dup
NM_001354801.1:c.294dup
NM_001354802.1:c.165dup
NM_001354803.1:c.339dup
NM_033507.2:c.1308dup
NM_033508.2:c.1302dup
NM_000162.5:c.1305dup
NM_033507.3:c.1308dup
NM_033508.3:c.1302dup

Likely Pathogenic

Met criteria codes 2
PVS1 PM2_Supporting
Not Met criteria codes 2
PS4 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.1305dup variant in the glucokinase gene, GCK, causes a frameshift in the protein at codon 436 (NM_000162.5), adding 23 novel amino acids before encountering a stop codon (p.(Ile436AspfsTer23)). 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). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). This variant was identified in an individual with a clinical history consistent with GCK-MODY, but there was insufficient clinical information to evaluate for PP4. This variant was identified in two unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID: 31704690​, internal lab contributors). In summary, c.1305dup 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
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).
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PS4
This variant was identified in two unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID: 31704690​, internal lab contributors).
PP4
This variant was identified in an individual with a clinical history consistent with GCK-MODY, but there was insufficient clinical information to evaluate for PP4.
Approved on: 2023-11-03
Published on: 2023-11-03
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