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_000212.3(ITGB3):c.325del (p.Val109fs)

CA913190317

623142 (ClinVar)

Gene: ITGB3
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: 238fb771-9622-4285-872d-53217b890cfe

HGVS expressions

NM_000212.3:c.325del
NM_000212.3(ITGB3):c.325del (p.Val109fs)
NC_000017.11:g.47283513del
CM000679.2:g.47283513del
NC_000017.10:g.45360879del
CM000679.1:g.45360879del
NC_000017.9:g.42715878del
NG_008332.2:g.34672del
ENST00000696963.1:c.325del
ENST00000559488.7:c.325del
ENST00000559488.5:c.325del
ENST00000560629.1:c.290del
ENST00000571680.1:c.325del
NM_000212.2:c.325del

Likely Pathogenic

Met criteria codes 2
PVS1 PM2_Supporting
Not Met criteria codes 2
PP4 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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The frameshift variant NM_000212.3(ITGB3):c.325del (p.Val109SerfsTer?) is predicted to cause a premature stop codon in biologically-relevant-exon 4/15 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established mechanism (PVS1). The variant is absent from gnomADv4.0.0 (PM2_supporting). The variant has been found in at least one individual with GT, ClinVar entry (SCV000891200.1) by the Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota. The patient is compound heterozygous with variant of uncertain significance NM_000212.3(ITGB3):c.778-2A>G, phasing not confirmed. The patient had bleeding since childhood, abnormal aggregation, and flow cytometry low levels of GPIIb/IIIa. Patient information is consistent with GT but insufficient for PP4. 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: PVS1 and PM2_supporting (VCEP specifications version 2.1.0).
Met criteria codes
PVS1
The c.325del (p.Val109SerfsTer?) variant frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 4/15 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established mechanism (PVS1).
PM2_Supporting
Variant is absent from gnomADv4.0.0
Not Met criteria codes
PP4
At least one patient has been reported bleeding since childhood, abnormal aggregation, and flow cytometry GPIIb/IIIa Monoclonal antibody binding was abnormal (low levels present). Patient information is consistent with GT but insufficient for PP4.
PM3
Patient is compound heterozygous with NM_000212.3(ITGB3):c.778-2A>G of unknown significance, confirmed by communication with submitter, phasing was unknown.
Approved on: 2024-05-02
Published on: 2024-05-03
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