ClinVar Miner

Submissions for variant NM_000212.3(ITGB3):c.1690G>C (p.Gly564Arg)

dbSNP: rs2143114313
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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 RCV001803444 SCV002047596 uncertain significance Glanzmann thrombasthenia 2024-10-15 reviewed by expert panel curation The NM_000212.3(ITGB3):c.1690G>C (p.Gly564Arg) missense variant has been reported in one patient, GT3 (of PMID: 32237906) with mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_moderate). Additionally, β3 surface expression was reduced to 0.61%, as measured by flow cytometry. GT3 of PMID: 32237906 is compound heterozygous for this variant and a pathogenic variant (c.361+1G>A) (PM3_Supporting). The highest population minor allele frequency in gnomAD v4.1 is 8.475e-7 (1/1179884 alleles) in the European Non-Finnish population, which is lower than the ClinGen PD VCEP threshold (<0.0001; PM2_Supporting). The computational predictor REVEL gives a score of 0.749, which is above the ClinGen PD VCEP threshold of >0.7 and predicts a damaging effect on ITGB3 function (PP3). In summary, this variant meets the criteria to be classified as uncertain significance for autosomal recessive Glanzmann Thrombasthenia based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: PP4_moderate, PM3_supporting, PM2_supporitng, PP3. (VCEP specifications version 2).

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