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  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data


Variant: NM_000173.7(GP1BA):c.1480del (p.Thr494fs)

CA8315005

1691251 (ClinVar)

Gene: GP1BA
Condition: Bernard-Soulier syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 22733719-1f61-4201-84cf-ff86daf0a041
Approved on: 2025-02-11
Published on: 2025-02-13

HGVS expressions

NM_000173.7:c.1474delA
NM_000173.7:c.1480del
NM_000173.7(GP1BA):c.1480del (p.Thr494fs)
NC_000017.11:g.4934084del
CM000679.2:g.4934084del
NC_000017.10:g.4837379del
CM000679.1:g.4837379del
NC_000017.9:g.4778120del
NG_008767.2:g.6790del
ENST00000329125.6:c.1480del
ENST00000649830.1:c.-888+264del
ENST00000329125.5:c.1480del
ENST00000611961.1:c.1402del
NM_000173.6:c.1480del
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Pathogenic

Met criteria codes 4
PVS1_Strong PM3_Strong PP4 PM2
Not Met criteria codes 1
PP1

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 c.1480del (p.Thr494ProfsTer59) variant in GP1BA is a frameshift variant in exon 2 of 2, that may cause loss of function of the protein; it is predicted to escape nonsense mediated decay and remove 15% of the protein (PVS1_Strong). At least four Bernard-Soulier syndrome patients have been reported with this variant (PM3_Strong); two are homozygous (PMIDs: 9628437, 8772211; 1pt) and two are compound heterozygous with Glu347Ter and c.1454dup variants respectively (PMID: 23414566, 9241731). 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 (PP4). Additionally, the patient had excessive mucocutaneous bleeding and macrothrombocytopenia which are consistent with BSS. The Grpmax filtering allele frequency in gnomAD v4.1 is 0.00004345 (5/44886 alleles) in the East Asian population and is below the <0.0001114 threshold for PM2_Supporting. In summary, this variant meets the criteria to be classified as Pathogenic for autosomal recessive Bernard-Soulier syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: PP4, PM3_Strong, PVS1_Strong, PM2_Supporting (ClinGen Platelet Disorders VCEP specifications version 1).
Met criteria codes
PVS1_Strong
The c.1480del (p.Thr494ProfsTer59) variant in GP1BA is a frameshift variant in exon 2 of 2, that may cause loss of function of the protein; it is predicted to escape nonsense mediated decay and remove 15% of the protein (PVS1_Strong). The frame shift occurs at Thr452, just before the transmembrane region, and would predictably synthesize a new non-transmembrane 58 amino acid sequence prior to the premature termination.
PM3_Strong
At least four Bernard-Soulier syndrome patients have been reported with this variant; two are homozygous (PMIDs: 9628437, 8772211; 1pt) and two are compound heterozygous. Case I (PMID: 23414566) is compound heterozygous for the paternal Glu347Ter and maternal c.1480del variants (1pt) and Case 2 (PMID: 9241731) is compound heterozygous for the maternal c.1480del and paternal c.1454dup variants (not considered here to avoid circularity). Total 2p (PM3_Strong)
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.
PM2
The Grpmax filtering allele frequency in gnomAD v4.1 is 0.00004345 (5/44886 alleles) in the East Asian population and is below the <0.0001114 threshold for PM2_supporting.
Not Met criteria codes
PP1
Insufficient information to confirm segregation.
Curation History
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