ClinVar Miner

Submissions for variant NM_000419.5(ITGA2B):c.1600+1G>A

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Platelet Disorders Variant Curation Expert Panel, ClinGen RCV002511564 SCV002820963 pathogenic Glanzmann thrombasthenia 2022-12-01 reviewed by expert panel curation The c.1600+1G>A variant in ITGA2B occurs within the canonical splice donor site of intron 16. It is predicted to cause skipping of biologically-relevant-exon 16, resulting in a frameshift with a premature stop codon in exon 18, leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). This prediction is supported by a SpliceAI Donor Loss score of 0.98. At least two patients (Patients 11 and 12 in PMID: 19172520) 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 <10% (from GT database), as measured by flow cytometry. However, ITGA2B and ITGB3 were not reported to be sequenced across all exons and intron/exon boundaries. (PP4_moderate). This variant has been reported to segregate with Glanzmann thrombasthenia (confirmed by bleeding phenotype and platelet aggregometry) in the proband plus one affected family member, both with the homozygous genotype with the NM_000419.5(ITGA2B):c.1600+1G>A variant. (PP1; PMID: 19172520). This variant has been detected in the homozygous state in at least 2 probands with Glanzmann thrombasthenia. However, these two individuals are related (PMID: 19172520) and only one affected individual per family can be counted towards PM3. Total points: 0.5 (PM3_Supporting). This variant is also absent from gnomAD v2.1.1 (PM2_Supporting). This variant is not registered in ClinVar. 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, PP1, PM3_Supporting and PM2_Supporting (VCEP specifications version 2).

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