The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000212.2:c.448A>G

CA8622961

953053 (ClinVar)

Gene: ITGB3
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: 61faa416-bb84-4ca5-b091-b1cb2ab8bea3
Approved on: 2022-08-05
Published on: 2022-12-07

HGVS expressions

NM_000212.2:c.448A>G
NC_000017.11:g.47284529A>G
CM000679.2:g.47284529A>G
NC_000017.10:g.45361895A>G
CM000679.1:g.45361895A>G
NC_000017.9:g.42716894A>G
NG_008332.2:g.35688A>G
ENST00000559488.7:c.448A>G
ENST00000559488.5:c.448A>G
ENST00000560629.1:n.413A>G
ENST00000571680.1:c.448A>G
NM_000212.3:c.448A>G
NM_000212.3(ITGB3):c.448A>G (p.Met150Val)

Likely Pathogenic

Met criteria codes 4
PM3_Strong PP3 PM2_Supporting PP4_Moderate
Not Met criteria codes 1
PS3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The NM_000419.5:c.448A>G variant in ITGB3 is a missense variant predicted to cause substitution of methionine by valine at amino acid 150 (p.Met150Val). This variant has been detected in at least 3 probands with Glanzmann thrombasthenia. Two of these individuals were compound heterozygous for this variant and a pathogenic variant and one of those was confirmed to carry the variants in trans by parental testing (c.774_775del (phase not confirmed) and p.Asp145Tyr (phase confirmed)). An additional proband was reported to be homozygous for the variant (personal communication with Dr. Jose Rivera (Servicio de Hematologıa y Oncologıa Medica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonacion, Universidad de Murcia)) (PM3_Strong). At least one patient (Patient GT-1, PMID: 25539746) 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 <25%), as measured by flow cytometry. However, ITGA2B and ITGB3 were not reported to be sequenced across all exons and intron/exon boundaries. The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003266 (1/30616 alleles) in the South Asian population, which is lower than the ClinGen Platelet Disorders VCEP threshold (<0.0001) (PM2_Supporting). Furthermore, the computational predictor REVEL gives a score of 0.968, which is above the ClinGen Platelet Disorders VCEP threshold of >0.7 and predicts a damaging effect on function (PP3). 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: PM2_Supporting, PM3_Strong, PP3, PP4_Moderate. (VCEP specifications version 2; date of approval 08/04/2022)
Met criteria codes
PM3_Strong
This variant has been detected in at least 3 probands with Glanzmann thrombasthenia. Two of these individuals were compound heterozygous for this variant and a pathogenic variant and one of those was confirmed to carry the variants in trans by parental testing (c.774_775del, GT-1 in PMID: 25539746, phase not confirmed, 0.5 points) and p.Asp145Tyr (PMID: 15583747, phase confirmed, 1.0 point). An additional proband was reported to be homozygous for the variant (personal communication with Dr. Jose Rivera (Servicio de Hematologıa y Oncologıa Medica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonacion, Universidad de Murcia), 0.5 points). Total points: 2.0 (PM3_Strong).
PP3
The computational predictor REVEL gives a score of 0.968, which is above the ClinGen Platelet Disorders VCEP threshold of >0.7 and predicts a damaging effect on function (PP3).
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003266 (1/30616 alleles) in the South Asian population, which is lower than the ClinGen Platelet Disorders VCEP threshold (<0.0001; PM2_Supporting).
PP4_Moderate
At least two patients (PMID: 25539746 and Patient GT-1, PMID: 15583747) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_moderate).
Not Met criteria codes
PS3
CHO cell lines were transfected with normal αIIb and either normal β3 or the Met150Val mutant. Cells transfected with the mutant form had a reduced amount of the αIIbβ3 complex, however the reduction was not quantified from the Western blot. Binding to Fibrinogen and PAC-1 were not disrupted.
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