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
  • No CSPEC related information was provided by the message!

  • No Criteria Specification was provided in the publication event for the variant classifaction.
  • The Criteria Specification shown below is a best-estimate based on the VCEP, gene, disease, and publication date.

Variant: NM_000419.5:c.2338del

CA915940686

Gene: ITGA2B (HGNC:3674)
Condition: Glanzmann thrombasthenia (MONDO:0100326)
Inheritance Mode: Autosomal recessive inheritance
UUID: f28f1fac-9f0c-4f6c-b95c-6e7711948e9b
Approved on: 2022-05-17
Published on: 2022-06-12

HGVS expressions

NM_000419.5:c.2338del
NC_000017.11:g.44376319del
CM000679.2:g.44376319del
NC_000017.10:g.42453687del
CM000679.1:g.42453687del
NC_000017.9:g.39809213del
NG_008331.1:g.18188del
ENST00000262407.6:c.2338del
ENST00000648408.1:n.1769del
ENST00000262407.5:c.2338del
ENST00000592462.5:n.1133del
NM_000419.3:c.2338del
NM_000419.4:c.2338del
More

Pathogenic

Met criteria codes 3
PM2_Supporting PVS1 PP4_Moderate
Not Met criteria codes 1
PM3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The NM_000419.5:c.2338del (p.Glu780SerfsTer46) variant in ITGA2B exon 23 is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 25/30 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). This variant has been detected in at least one proband with Glanzmann thrombasthenia. However, it is unclear if the reported proband (GT38, PMID: 19691478) was homozygous for this variant or if a second ITGA2B variant was identified. At least one patient (Patient GT38 in PMID: 19691478) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_Moderate). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). In summary, this variant meets the criteria to be classified as pathogenic for autosomal recessive Glanzmann Thrombasthenia based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: PVS1, PM2_Supporting, PP4_Moderate. (VCEP specifications version 2; date of approval 05/17/2022)
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PVS1
The c.2338del (p.Glu780SerfsTer46) variant in exon 23 is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 25/30 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
PP4_Moderate
At least one patient (Patient GT38 in PMID: 19691478) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_Moderate).
Not Met criteria codes
PM3
This variant has been detected in at least one proband with Glanzmann thrombasthenia. However, it is unclear if the reported proband (GT38, PMID: 19691478) was homozygous for this variant or if a second ITGA2B variant was identified (0 points).
Curation History
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