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Variant: NM_000173.7:c.1039G>T

CA397319701

Gene: GP1BA (HGNC:2811)
Condition: Bernard-Soulier syndrome (MONDO:0009276)
Inheritance Mode: Autosomal recessive inheritance
UUID: a93d0f40-ca46-471c-b340-f0c9f3ce5eff
Approved on: 2025-02-11
Published on: 2025-02-12

HGVS expressions

NM_000173.7:c.1039G>T
NC_000017.11:g.4933643G>T
CM000679.2:g.4933643G>T
NC_000017.10:g.4836938G>T
CM000679.1:g.4836938G>T
NC_000017.9:g.4777718G>T
NG_008767.2:g.6349G>T
ENST00000329125.6:c.1039G>T
ENST00000649830.1:c.-888+699C>A
ENST00000329125.5:c.1039G>T
ENST00000611961.1:c.1039G>T
NM_000173.6:c.1039G>T
More

Likely Pathogenic

Met criteria codes 3
PP4 PVS1_Strong PM2_Supporting
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 for GP1BA Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The NM_000173.7(GP1BA):c.1039G>T (p.Glu347Ter) variant is a nonsense variant in exon 2 of 2, that may cause loss of function of the protein; it is predicted to escape nonsense mediated decay and truncate 47% of the protein (PVS1_Strong). One patient has been reported with this variant (Case I, of PMID: 23414566) and had no aggregation response to ristocetin and decreased thrombin-induced aggregation but normal aggregation with ADP and collagen, additionally GPIbα expression was completely absent on patient platelets, which is highly specific to Bernard-Soulier syndrome (PP4). Additionally, the patient had excessive mucocutaneous bleeding and macrothrombocytopenia which are consistent with BSS. This variant is absent from gnomAD v4.1 (PM2_Supporting). In summary, this variant meets the criteria to be classified as Likely Pathogenic for autosomal recessive Bernard-Soulier syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: PVS1_strong, PP4, PM2_supporting.
Met criteria codes
PP4
Case I, of PMID: 23414566, had no aggregation response to ristocetin and decreased thrombin-induced aggregation but normal aggregation with ADP and collagen, additionally GPIbα expression was completely absent on patient platelets, which is highly specific to Bernard-Soulier syndrome. Additionally, the patient had excessive mucocutaneous bleeding and macrothrombocytopenia which are consistent with BSS.
PVS1_Strong
The NM_000173.7(GP1BA):c.1039G>T (p.Glu347Ter) variant is a nonsense variant in exon 2 of 2, that may cause loss of function of the protein; it is predicted to escape nonsense mediated decay and truncate 47% of the protein (PVS1_Strong). The expected truncation product was observed in case 1 of PMID: 23414566.
PM2_Supporting
This variant is absent from gnomAD v4.1 (PM2_Supporting).
Not Met criteria codes
PM3
Case I is compound heterozygous for the paternal Glu347Ter (reported as Glu331Ter) and maternal c.1480del (reported as c.1444del, classified Pathogenic by the PD VCEP) variants. Not considered here to avoid circularity.
Curation History
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