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.2374del

CA915940267

Gene: ITGA2B (HGNC:3674)
Condition: Glanzmann thrombasthenia (MONDO:0100326)
Inheritance Mode: Autosomal recessive inheritance
UUID: b77bdc24-e8dd-45ca-b3c9-461c30d877ee
Approved on: 2022-04-07
Published on: 2022-12-07

HGVS expressions

NM_000419.5:c.2374del
NC_000017.11:g.44376160del
CM000679.2:g.44376160del
NC_000017.10:g.42453528del
CM000679.1:g.42453528del
NC_000017.9:g.39809054del
NG_008331.1:g.18347del
ENST00000262407.6:c.2374del
ENST00000648408.1:n.1805del
ENST00000262407.5:c.2374del
ENST00000587295.5:n.26del
ENST00000592462.5:n.1169del
NM_000419.3:c.2374del
NM_000419.4:c.2374del
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Pathogenic

Met criteria codes 4
PM2_Supporting PM3_Supporting PP4_Strong PVS1

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(ITGA2B):c.2374del (p.Val792TrpfsTer34) frameshift variant leads to to 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). At least one patient (Patient GT1 in PMID:25373348) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia. Additionally, αIIbβ3 surface expression was severly reduced, as measured by flow cytometry while αIIb was absent on Western blot and β3 was decreased. ITGA2B and ITGB3 were sequenced across all exons and intron/exon boundaries (PP4_strong). GT1 of PMID: 25373348 is homozygous for c.2374del (PM3_supporting). 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, PP4_strong, PM2_supporting, PM3_supporting. (VCEP specifications version 2; date of approval 01/18/2022)
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PM3_Supporting
GT1 of PMID: 25373348 is homozygous for c.2374del (parents confirmed carriers). 0.5pt
PP4_Strong
At least one patient (Patient GT1 in PMID:25373348) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia. Additionally, αIIbβ3 surface expression was severly reduced, as measured by flow cytometry while αIIb was absent on Western blot and β3 was decreased. ITGA2B and ITGB3 were sequenced across all exons and intron/exon boundaries. (PP4_strong)
PVS1
The c.2374del variant in exon 24 causes the p.Val792TrpfsTer34 frameshift variant leading to 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).
Curation History
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