The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000212.2:c.448A>G

CA8622961

953053 (ClinVar)

Gene: ITGB3 (HGNC:3690)
Condition: Glanzmann thrombasthenia (MONDO:0100326)
Inheritance Mode: Autosomal recessive inheritance
UUID: 61faa416-bb84-4ca5-b091-b1cb2ab8bea3
Approved on: 2025-06-19
Published on: 2025-06-19

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
ENST00000696963.1:c.448A>G
ENST00000559488.7:c.448A>G
ENST00000559488.5:c.448A>G
ENST00000560629.1:c.413A>G
ENST00000571680.1:c.448A>G
NM_000212.3:c.448A>G
More

Likely Pathogenic

Met criteria codes 4
PP4_Moderate PM2_Supporting PM3_Strong PP3
Not Met criteria codes 2
PS3 PM5

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

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Criteria Specification Approval History
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 v4.1 is 0.00001098 (1/91082 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)
Met criteria codes
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).
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1 is 0.00001098 (1/91082 alleles) in the South Asian population, which is lower than the ClinGen Platelet Disorders VCEP threshold (<0.0001; PM2_Supporting).
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).
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.
PM5
NM_000212.3(ITGB3):c.450G>A (p.Met150Ile) is not considered here to avoid circularity.
Curation History
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