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Variant: NM_000419.5:c.2902del

CA915940332

Gene: ITGA2B
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: bfcc13de-e293-4938-baa3-f88a6876f682
Approved on: 2022-04-15
Published on: 2022-06-12

HGVS expressions

NM_000419.5:c.2902del
NC_000017.11:g.44374700del
CM000679.2:g.44374700del
NC_000017.10:g.42452068del
CM000679.1:g.42452068del
NC_000017.9:g.39807594del
NG_008331.1:g.19806del
ENST00000262407.6:c.2902del
ENST00000648408.1:n.2333del
ENST00000262407.5:c.2902del
ENST00000587295.5:n.253+1133del
ENST00000592462.5:n.2413del
NM_000419.3:c.2902del
NM_000419.4:c.2902del
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Pathogenic

Met criteria codes 3
PVS1_Strong PM2_Supporting PP4_Strong
Not Met criteria codes 1
PM3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Platelet Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2.1

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The NM_000419.5(ITGA2B):c.2902del (p.Tyr968MetfsTer?) frameshift variant in exon 28 of 30 is predicted to alter the remaining 72 amino acids followed by a stop loss and the addition of 90 amino acids to the ITGA2B protein. This alters the transmembrane domain of the protein which is considered a critical region for protein function by the Platelet Disorders VCEP (PVS1_Strong). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). It has been reported in at least one patient (GT14 in PMID: 25728920), whom displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia. Additionally, αIIbβ3 surface expression was reduced to<5%, as measured by flow cytometry (PP4_strong). In summary this variant meets 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_strong, PP4_strong, PM2_supporting. (VCEP specifications version 2.1)
Met criteria codes
PVS1_Strong
This frameshift variant in exon 28 of 30 is predicted to alter the remaining 72 amino acids followed by a stop loss and the addition of 90 amino acids to the ITGA2B protein. This alters the transmembrane domain of the protein which is considered a critical region for protein function by the Platelet Disorders VCEP (PVS1_Strong).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP4_Strong
At least one patient (GT14 in PMID: 25728920) 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 reduced to<5%, as measured by flow cytometry. ITGA2B and ITGB3 were sequenced across all exons and intron/exon boundaries. (PP4_strong)
Not Met criteria codes
PM3
GT14 of PMID: 25728920 is compound heterozygous for Trp141Cys (classified as Likely Pathogenic by the PD-EP) and c.2902del, confirmation of trans phase was not reported. Not considered here to avoid circularity.
Curation History
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