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Variant: NM_000174.5:c.72T>G

CA354446617

Gene: GP9
Condition: Bernard-Soulier syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: e8e78b7a-0fd4-43f9-adbd-8e5e4480faad
Approved on: 2025-02-11
Published on: 2025-02-17

HGVS expressions

NM_000174.5:c.72T>G
NC_000003.12:g.129061811T>G
CM000665.2:g.129061811T>G
NC_000003.11:g.128780654T>G
CM000665.1:g.128780654T>G
NC_000003.10:g.130263344T>G
NG_008715.1:g.6010T>G
ENST00000307395.5:c.72T>G
ENST00000307395.4:c.72T>G
NM_000174.4:c.72T>G
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Uncertain Significance

Met criteria codes 5
PM3_Supporting PP4 PP1 PM5_Supporting PM2_Supporting
Not Met criteria codes 2
PP3 BP4

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 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The NM_000174.5(GP9):c.72T>G (p.Cys24Trp) missense variant is absent from gnomAD v4.1 (PM2_Supporting). Another missense variant in the same codon has been reported in a patient with Bernard-Soulier syndrome [c.70T>C (p.Cys24Arg)] (PMID:21173099) and classified Likely Pathogenic by the PD-VCEP (PM5_supporting). At least one patient (Patient P7 in PMID:21173099) with this variant had less than 10% expression of GPIba and GP9 measured by flow cytometry, which is highly specific for Bernard-Soulier syndrome (PP4). Additionally, the patient had excessive mucocutaneous bleeding and macrothrombocytopenia which are consistent with Bernard-Soulier syndrome. This individual was homozygous for the variant (PM3_supporting) and one affected first degree relative was also homozygous (PP1). In summary, this variant meets the criteria to be classified as uncertain significance for autosomal recessive Bernard-Soulier syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: PM2_supporting, PM5_supporting, PP4, PM3_supporting, PP1.
Met criteria codes
PM3_Supporting
This variant has been detected in 1 proband with Bernard-Soulier syndrome. This individual was homozygous for the variant (0.5 PM3 points, PMID:21173099). Total points: 0.5 (PM3_supporting).
PP4
At least one patient (Patient P7 in PMID:21173099) with this variant had less than 10% expression of GPIba and GP9 measured by flow cytometry, which is highly specific for Bernard-Soulier syndrome (PP4). Additionally, the patient had excessive mucocutaneous bleeding and macrothrombocytopenia which are consistent with Bernard-Soulier syndrome.
PP1
The variant has been reported to segregate with Bernard-Soulier syndrome in the proband (meeting PP4) plus one affected family member, both with the homozygous genotype. (PP1; PMID:21173099).
PM5_Supporting
Another missense variant in the same codon has been reported in a patient with Bernard-Soulier syndrome [c.70T>C (p.Cys24Arg)] (PMID:21173099) and classified Likely Pathogenic by the PD-VCEP (PM5_supporting).
PM2_Supporting
This variant is absent from gnomAD v4.1 (PM2_Supporting).
Not Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.619, which is below the ClinGen PD VCEP PP3 threshold of >0.644 and does not predict a damaging effect on GP9 function. And the computational splicing predictor SpliceAI indicated that the variant has no predicted impact on splicing.
BP4
The computational predictor REVEL gives a score of 0.619, which is above the ClinGen PD VCEP PP3 threshold of <0.290.
Curation History
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