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Variant: NM_000212.3(ITGB3):c.1699C>T (p.Gln567Ter)

CA16043531

374015 (ClinVar)

Gene: ITGB3
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: a0e24b71-1387-43a2-8143-51c44b659d9e

HGVS expressions

NM_000212.3:c.1699C>T
NM_000212.3(ITGB3):c.1699C>T (p.Gln567Ter)
NC_000017.11:g.47299316C>T
CM000679.2:g.47299316C>T
NC_000017.10:g.45376682C>T
CM000679.1:g.45376682C>T
NC_000017.9:g.42731681C>T
NG_008332.2:g.50475C>T
ENST00000559488.7:c.1699C>T
ENST00000559488.5:c.1699C>T
ENST00000560629.1:n.1664C>T
NM_000212.2:c.1699C>T

Pathogenic

Met criteria codes 3
PM2_Supporting PVS1 PP4_Moderate
Not Met criteria codes 1
PM3

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.1699C>T (p.Gln567Ter) variant in exon 11 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 11/15 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). At least one patient (Glanzmann Patient, "HEMOSTAZA SKOZI KLINIČNE PRIMERE", August 2022) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia. Additionally, αIIbβ3 surface expression was reduced to 0% (<25%), as measured by flow cytometry (PP4_moderate). This individual is compound heterozygous for this variant and likely pathogenic variant c.749A>G (p.Asp250Gly). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). 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: PVS1, PP4_Moderate and PM2_Supporting (VCEP specifications version 2).
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PVS1
The c.1699C>T (p.Gln567Ter) variant in exon 11 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 11/15 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established mechanism (PVS1).
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.
Not 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 likely pathogenic variant c.749A>G (p.Asp250Gly), confirmed in trans by parental testing ("HEMOSTAZA SKOZI KLINIČNE PRIMERE"). PM3 was not applied to avoid circularity.
Approved on: 2023-04-06
Published on: 2023-04-07
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