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CA8622991

Gene: ITGB3
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: a90a149d-36d4-418d-b5ec-21892e80b517
Approved on: 2023-01-17
Published on: 2023-02-15

HGVS expressions

NM_000212.3:c.602del
NC_000017.11:g.47284683del
CM000679.2:g.47284683del
NC_000017.10:g.45362049del
CM000679.1:g.45362049del
NC_000017.9:g.42717048del
NG_008332.2:g.35842del
ENST00000559488.7:c.602del
ENST00000559488.5:c.602del
ENST00000560629.1:n.567del
ENST00000571680.1:c.602del
NM_000212.2:c.602del

Pathogenic

Met criteria codes 3
PM2_Supporting PP4_Moderate PVS1
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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The c.602del (p.Asn201ThrfsTer6) variant in exon 4 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 5 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 GTa in PMID:11722423) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_moderate). This individuals was compound heterozygous for this variant (reported by the authors as "a deletion at the 3' end of exon 3 resulting in a premature stop codon," but confirmed as c.602del from entry 57 in the GT database) and a likely pathogenic variant (NM_000212.3:c.655G>A (p.Val219Met)). This variant is also 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_Moderate, and PM2_Supporting (VCEP specifications version 2.1).
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP4_Moderate
At least one patient (Patient GTa in PMID:11722423) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia. However, ITGA2B and ITGB3 were not reported to be sequenced across all exons and intron/exon boundaries.(PP4_moderate).
PVS1
The c.602del (p.Asn201ThrfsTer6) variant in exon 4 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 5 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
Not Met criteria codes
PM3
This variant has been detected in at least 1 proband with Glanzmann thrombasthenia. This individuals was compound heterozygous for this variant and a likely pathogenic variant (NM_000212.3:c.655G>A (p.Val219Met)), confirmed in trans by cloning and sequencing of PCR amplified cDNA (PMID:11722423). Not considered here to avoid a circular argument.
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