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Variant: NM_000212.3(ITGB3):c.749A>G (p.Asp250Gly)

CA16043530

374016 (ClinVar)

Gene: ITGB3
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: 5cfe055c-97a2-4530-9287-d69b13220702

HGVS expressions

NM_000212.3:c.749A>G
NM_000212.3(ITGB3):c.749A>G (p.Asp250Gly)
NC_000017.11:g.47286394A>G
CM000679.2:g.47286394A>G
NC_000017.10:g.45363760A>G
CM000679.1:g.45363760A>G
NC_000017.9:g.42718759A>G
NG_008332.2:g.37553A>G
ENST00000559488.7:c.749A>G
ENST00000559488.5:c.749A>G
ENST00000560629.1:n.714A>G
ENST00000571680.1:c.749A>G
NM_000212.2:c.749A>G

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 4
PM3 PP4_Moderate PM2_Supporting PP3

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.749A>G variant in ITGB3 is a missense variant predicted to cause substitution of aspartic acid by glycine at amino acid 250. The variant has been reported in at least one patient (Glanzmann Patient, "HEMOSTAZA SKOZI KLINIČNE PRIMERE" August 2022) who displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_moderate). This individual is compound heterozygous for this variant and pathogenic variant c.1699C>T (p.Gln567Ter) (PM3). The variant is absent from gnomAD (PM2_supporting). The computational predictor REVEL gives a score of 0.988, which is above the ClinGen PD VCEP PP3 threshold of >0.7 and predicts a damaging effect on ITGB3 function. In summary, this variant meets the 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: PM2_Supporting, PP3, PP4_moderate, and PM3. (VCEP specifications version 2)
Met criteria codes
PM3
This variant has been detected in at least 1 proband with Glanzmann thrombasthenia. For 1 of those individuals, 1 was compound heterozygous for this variant and a pathogenic variant c.1699C>T (p.Gln567Ter), confirmed in trans by parental testing ("HEMOSTAZA SKOZI KLINIČNE PRIMERE").
PP4_Moderate
At least one patient (Glanzmann Patient Patient from "HEMOSTAZA SKOZI KLINIČNE PRIMERE") with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_moderate). Additionally, αIIbβ3 surface expression was reduced to 0% (<25%), as measured by flow cytometry/Western blot. However, ITGA2B and ITGB3 were not reported to be sequenced across all exons and intron/exon boundaries.
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP3
The computational predictor REVEL gives a score of .988, which is above the ClinGen PD VCEP threshold of >0.7 and predicts a damaging effect on function (PP3).
Approved on: 2023-04-06
Published on: 2023-04-07
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