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


Variant: NM_000407.5(GP1BB):c.406G>T (p.Glu136Ter)

CA322080037

1679210 (ClinVar)

Gene: GP1BB (HGNC:2812)
Condition: Bernard-Soulier syndrome (MONDO:0009276)
Inheritance Mode: Autosomal recessive inheritance
UUID: 8ea2064e-3b97-47af-aef1-194ab06ebdf3
Approved on: 2025-02-11
Published on: 2025-02-14

HGVS expressions

NM_000407.5(GP1BB):c.406G>T (p.Glu136Ter)
NM_000407.5:c.406G>T
NC_000022.11:g.19724249G>T
CM000684.2:g.19724249G>T
NC_000022.10:g.19711772G>T
CM000684.1:g.19711772G>T
NC_000022.9:g.18091772G>T
NG_007974.1:g.5707G>T
ENST00000366425.4:c.406G>T
ENST00000366425.3:c.406G>T
ENST00000431044.5:c.*1491G>T
NM_000407.4:c.406G>T
NR_037611.1:n.4146G>T
NR_037612.1:n.2650G>T
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Likely Pathogenic

Met criteria codes 4
PM2_Supporting PM3_Supporting PVS1_Strong PP4
Not Met criteria codes 1
PS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Platelet Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GP1BB Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The c.406G>T (p.Glu136Ter) variant in GP1BB is a nonsense variant that may cause loss of function of the protein, however it is predicted to escape nonsense mediated decay and remove 34% (>10%) of the protein (PVS1_Strong). At least one patient (Patient 2 in PMID: 33217855) with this variant had impaired aggregation for ristocetin (aggregation in response to other agonists is not specifically mentioned). Additionally, this patient showed less than 10% expression of GPIba (0%) measured by flow cytometry, which is highly specific for Bernard-Soulier syndrome (PP4). Full gene sequencing of all BSS genes was also performed for this patient by WES. Additionally, the patient had excessive mucocutaneous bleeding and macrothrombocytopenia which are consistent with Bernard-Soulier syndrome. The patient is homozygous for the variant (PM3_Supporting). The Grpmax filtering allele frequency in gnomaDv4.1 is 0.000002920 (based on 7/997364 alleles) in the European (non-Finnish) population, which is below the <0.0000651678 threshold for 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, PM3_Supporting and PM2_Supporting (VCEP specifications version 1).
Met criteria codes
PM2_Supporting
The Grpmax filtering allele frequency in gnomaDv4.1 is 0.000002920 (based on 7/997364 alleles) in the European (non-Finnish) population, which is below the <0.0000651678 threshold for PM2_supporting.
PM3_Supporting
This variant has been detected in at least 1 proband with Bernard-Soulier syndrome (Patient 2 in PMID: 33217855) who was homozygous for the variant (0.5 PM3 points, PM3_Supporting).
PVS1_Strong
The c.406G>T (p.Glu136Ter) variant in GP1BB is a nonsense variant that may cause loss of function of the protein, however it is predicted to escape nonsense mediated decay and remove 34% (>10%) of the protein (PVS1_Strong).
PP4
At least one patient (Patient 2 in PMID: 33217855) with this variant had impaired aggregation for ristocetin (aggregation in response to other agonists is not specifically mentioned). Additionally, this patient showed less than 10% expression of GPIba (0%) measured by flow cytometry, which is highly specific for Bernard-Soulier syndrome. Full gene sequencing of all BSS genes was also performed for this patient by WES but analysis for structural variants was not performed. Additionally, the patient had excessive mucocutaneous bleeding and macrothrombocytopenia which are consistent with Bernard-Soulier syndrome (PP4).
Not Met criteria codes
PS4
One patient heterozygous for Glu136Ter variant was reported (PMID: 36430862) with Thrombocytopenia (platelet count <150 × 109/L), platelet size = macro (MPV >12.8fl), 0.25pt
Curation History
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