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Variant: NM_000419.5:c.605T>G

CA399805605

Gene: ITGA2B (HGNC:3674)
Condition: Glanzmann thrombasthenia (MONDO:0100326)
Inheritance Mode: Autosomal recessive inheritance
UUID: d0ec0d32-e549-4ba4-97cb-8de97b73ac2d
Approved on: 2024-03-07
Published on: 2024-03-08

HGVS expressions

NM_000419.5:c.605T>G
NC_000017.11:g.44385305A>C
CM000679.2:g.44385305A>C
NC_000017.10:g.42462673A>C
CM000679.1:g.42462673A>C
NC_000017.9:g.39818199A>C
NG_008331.1:g.9201T>G
ENST00000262407.6:c.605T>G
ENST00000648408.1:c.36T>G
ENST00000262407.5:c.605T>G
ENST00000589645.5:n.59T>G
ENST00000592253.5:n.37T>G
ENST00000592944.1:n.290T>G
NM_000419.3:c.605T>G
NM_000419.4:c.605T>G
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Pathogenic

Met criteria codes 5
PP1_Moderate PM2_Supporting PP4_Moderate PS3 PP3

Evidence Links 1

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 c.605T>G variant in ITGA2B is a missense variant predicted to cause substitution of phenylalanine by cystine at amino acid 202. At least one patient (Proband in PMID:15219201) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_moderate). The variant has been reported to segregate with Glanzmann thrombasthenia in the proband (confirmed by bleeding phenotype and platelet aggregometry) plus two affected family members, all with the homozygous genotype with the c.605T>G variant. (PP1_moderate; PMID:15219201). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). Surface expression of αIIbβ3 measured by flow cytometry in CHO cells transiently co-transfected with p.Phe202Cys αIIb and wild type β3 showed absent expression (<5%) WT levels, indicating that this variant impacts protein function (PMID:15219201)(PS3). The computational predictor REVEL gives a score of 0.781, which is above the ClinGen PD VCEP threshold of >0.7 and predicts a damaging effect on function (PP3). 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: PS3, PP1_moderate, PP4_moderate, PP3, PM2_supporting. (VCEP specifications version 2; date of approval 03/07/2024)
Met criteria codes
PP1_Moderate
The variant has been reported to segregate with Glanzmann thrombasthenia in the proband (confirmed by bleeding phenotype and platelet aggregometry) plus two affected family members, all with the homozygous genotype with the c.605T>G variant. (PP1_moderate; PMID:c.605T>G).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP4_Moderate
At least one patient (Proband in PMID:15219201) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_moderate).
PS3
Surface expression of αIIbβ3 measured by flow cytometry in CHO cells transiently co-transfected with p.Phe202Cys αIIb and wild type β3 showed decreased expression at absent (<5%) WT levels, indicating that this variant impacts protein function (PMID:15219201)(PS3).

PP3
The computational predictor REVEL gives a score of 0.781, which is above the ClinGen PD VCEP threshold of >0.7 and predicts a damaging effect on function (PP3).
Curation History
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