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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.1601_1602del (p.Tyr534fs)

CA8315034

872581 (ClinVar)

Gene: GP1BA
Condition: Bernard-Soulier syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: d55a711f-0eeb-4654-9703-ade562cace1e
Approved on: 2025-02-11
Published on: 2025-02-17

HGVS expressions

NM_000173.7:c.1601_1602del
NM_000173.7(GP1BA):c.1601_1602del (p.Tyr534fs)
NC_000017.11:g.4934205_4934206del
CM000679.2:g.4934205_4934206del
NC_000017.10:g.4837500_4837501del
CM000679.1:g.4837500_4837501del
NC_000017.9:g.4778241_4778242del
NG_008767.2:g.6911_6912del
ENST00000329125.6:c.1601_1602del
ENST00000649830.1:c.-888+137_-888+138del
ENST00000329125.5:c.1601_1602del
ENST00000611961.1:c.1523_1524del
NM_000173.6:c.1601_1602del
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Pathogenic

Met criteria codes 5
PS3_Supporting PP4 PVS1_Strong PM2_Supporting PM3_Strong

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.1601_1602del (p.Tyr534CysfsTer82) variant in GP1BA is a frameshift variant that may cause a premature stop codon that is predicted to escape nonsense mediated decay, however it alters a functionally important region, the transmembrane domain (amino acids 532-553), in a gene where loss-of-function is an established disease mechanism (PVS1_Strong). At least one patient (Patient 1 in PMID: 9326230) with this variant had less than 10% expression of GPIba measured by Western blot, which is highly specific for Bernard-Soulier syndrome. The patient also had a severe defect in ristocetin agglutination and a life-long history of excessive bleeding (PP4). This variant has been detected in at least three probands with Bernard-Soulier syndrome. Two of these individuals were homozygous for the variant (PMIDs: 9326229 and 9326230) and one individual was compound heterozygous (confirmed in trans by parental testing) for this variant and the c.165_168del (p.Ser55ArgfsTer12) which was classified as Likely Pathogenic by the VCEP (PMID: 11054083) (PM3_Strong). Surface expression of GP1a measured by flow cytometry in CHO βIX cells transiently co-transfected with the c.1601_1602del variant GP1 and wild type GP1a showed decreased expression at 20% (<25%) WT levels, indicating that this variant impacts protein function (PMID: 9326230)(PS3_supporting). The Grpmax Filtering allele frequency in gnomAD v4.1.0 is 0.00002394 (based on 38/1179788 alleles) in the European non-Finnish population, which is lower than the ClinGen PD VCEP threshold (<0.0001114; 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: PVS1_Strong, PM3_Strong, PP4, PM2_Supporting and PS3_Supporting (VCEP specifications version 1).
Met criteria codes
PS3_Supporting
Surface expression of GP1a measured by flow cytometry in CHO βIX cells transiently co-transfected with the c.1601_1602del variant GP1 and wild type GP1a showed decreased expression at 10% WT levels above sham, indicating that this variant impacts protein function (PMID: 9326230)(PS3_supporting).
PP4
At least one patient (Patient 1 in PMID: 9326230) with this variant had less than 10% expression of GPIba measured by Western blot, which is highly specific for Bernard-Soulier syndrome. The patient also had a severe defect in ristocetin agglutination and a life-long history of excessive bleeding (PP4). All three BSS genes were sequenced, however, del/dup analysis is not mentioned for this patient.
PVS1_Strong
The c.1601_1602del (p.Tyr534CysfsTer82) variant in GP1BA is a frameshift variant that may cause a premature stop codon that is predicted to escape nonsense mediated decay, it removes <10% of the protein however it alters a functionally important region, the transmembrane domain (amino acids 532-553), in a gene where loss-of-function is an established disease mechanism (PVS1_Strong).
PM2_Supporting
The Grpmax Filtering allele frequency in gnomAD v4.1.0 is 0.00002394 (based on 38/1179788 alleles) in the European non-Finnish population, which is lower than the ClinGen PD VCEP threshold (<0.0001114; PM2_Supporting).
PM3_Strong
This variant has been detected in at least three probands with Bernard-Soulier syndrome. Two of these individuals were homozygous for the variant (1 PM3 point, PMIDs: 9326229 and 9326230). One individual was compound heterozygous (confirmed in trans by parental testing) for this variant and the c.165_168del (p.Ser55ArgfsTer12) which was classified as Likely Pathogenic by the VCEP (1 PM3 point, PMID: 11054083). Total points: 2 (PM3_Strong).
Curation History
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