ClinVar Miner

Submissions for variant NM_000419.5(ITGA2B):c.475G>A (p.Gly159Ser)

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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 RCV002511534 SCV002820928 likely pathogenic Glanzmann thrombasthenia 2022-08-05 reviewed by expert panel curation The missense variant NM_000419.5(ITGA2B):c.475G>A (p.Gly159Ser has been identified in at least one patient UPN 2 (PMID: 16359515; PMID: 16359515) reported to have GT. The patient is homozygous for Gly159Ser (PM3_supporting). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.735, which is above the ClinGen PD VCEP threshold of >0.7 and predicts a damaging effect on function (PP3).The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003267 (1/30606 alleles) in the South Asian population, which is lower than the ClinGen PD VCEP threshold (<0.0001; PM2_Supporting). In HEK 293 cells there was expression on 52% of cells transfected with normal αIIb and β3 and 0% of cells with Gly159Ser were positive. Furthermore, immunoblotting from cell lysates found mature αIIb was seen in the normal αIIbβ3 cells, but there was no detectable mature αIIb in the G159S mutant (PMID: 16359515; PS3). In summary this variant meets criteria to be classified as Likely Pathogenic for autosomal recessive Glanzmann Thrombasthenia based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: PP3, PM2_supporting, PM3_supporting, PS3 (VCEP specifications version 2.1).

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