The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000174.5(GP9):c.167T>C (p.Leu56Pro)

CA123179

13532 (ClinVar)

Gene: GP9 (HGNC:2815)
Condition: Bernard-Soulier syndrome (MONDO:0009276)
Inheritance Mode: Autosomal recessive inheritance
UUID: 9d1e9b08-a988-4354-89da-b849db863249
Approved on: 2025-12-17
Published on: 2025-12-17

HGVS expressions

NM_000174.5(GP9):c.167T>C (p.Leu56Pro)
NM_000174.5:c.167T>C
NC_000003.12:g.129061906T>C
CM000665.2:g.129061906T>C
NC_000003.11:g.128780749T>C
CM000665.1:g.128780749T>C
NC_000003.10:g.130263439T>C
NG_008715.1:g.6105T>C
ENST00000307395.5:c.167T>C
ENST00000307395.4:c.167T>C
NM_000174.4:c.167T>C
More

Likely Pathogenic

Met criteria codes 5
PM3_Supporting PP1 PP4 PP3_Moderate PM2_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Platelet Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GP9 Version 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The c.167T>C variant in GP9 is a missense variant predicted to cause substitution of Leucine by Proline at amino acid 56 (p.Leu56Pro). At least one patient (Patient II-2 in PMID: 9886312) with this variant had aggregation absent for ristocetin and present for all other agonists as well as less than 10% expression of GP9 measured by flow cytometry, which is highly specific for Bernard-Soulier syndrome. Additionally, the patient had excessive mucocutaneous bleeding and macrothrombocytopenia which are consistent with Bernard-Soulier syndrome (PP4). This individual was homozygous for the variant (0.5 PM3 points, PM3_Supporting). The variant has been reported to segregate in the proband plus 1 additional homozygous BSS affected family member (1 PP1 point, PP1). The computational predictor REVEL gives a score of 0.849, which is above the ClinGen PD VCEP threshold of >0.773 and predicts a damaging effect on function (PP3_Moderate). The largest MAF allele frequency in gnomAD v4.1.0 is 0.000001695 (based on 2/1179872 alleles) in the European (non-Finnish) population, which is lower than the ClinGen PD VCEP threshold (<0.0000329; 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: PP4, PM3_Supporting, PP1, PP3_Moderate and PM2_Supporting (VCEP specifications version 1.1).
Met criteria codes
PM3_Supporting
This variant has been detected in at least 1 proband with Bernard-Soulier syndrome (Patient II-2 in PMID: 9886312). This individual was homozygous for the variant (0.5 PM3 points, PM3_Supporting).
PP1
The variant has been reported to segregate in the proband plus 1 additional homozygous BSS affected family member (1 PP1 point, PP1).
PP4
At least one patient (Patient II-2 in PMID: 9886312) with this variant had aggregation absent for ristocetin and present for all other agonists as well as less than 10% expression of GP9 measured by flow cytometry, which is highly specific for Bernard-Soulier syndrome. Additionally, the patient had excessive mucocutaneous bleeding and macrothrombocytopenia which are consistent with Bernard-Soulier syndrome (PP4).
PP3_Moderate
The computational predictor REVEL gives a score of 0.849, which is above the ClinGen PD VCEP threshold of >0.644 and predicts a damaging effect on function (PP3_Moderate).
PM2_Supporting
The largest MAF allele frequency in gnomAD v4.1.0 is 0.000001695 (based on 2/1179872 alleles) in the European (non-Finnish) population, which is lower than the ClinGen PD VCEP threshold (<0.0000329; PM2_Supporting).
Curation History
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