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Variant: NM_000552.5:c.4225G>T

CA383503778

Gene: VWF (HGNC:7450)
Condition: von Willebrand disease type 2M (MONDO:0015630)
Inheritance Mode: Autosomal dominant inheritance
UUID: 2af4a425-9cc1-4fdf-b9c8-e03d528eaedf
Approved on: 2024-08-13
Published on: 2024-08-13

HGVS expressions

NM_000552.5:c.4225G>T
NC_000012.12:g.6019193C>A
CM000674.2:g.6019193C>A
NC_000012.11:g.6128359C>A
CM000674.1:g.6128359C>A
NC_000012.10:g.5998620C>A
NG_009072.1:g.110478G>T
NG_009072.2:g.110478G>T
ENST00000261405.10:c.4225G>T
ENST00000261405.9:c.4225G>T
ENST00000538635.5:n.421-25259G>T
NM_000552.3:c.4225G>T
NM_000552.4:c.4225G>T
More

Likely Pathogenic

Met criteria codes 5
PP4_Moderate PS4_Moderate PP3 PM2_Supporting PP1_Moderate

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen von Willebrand Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for VWF Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
von Willebrand Disease VCEP
The NM_000552.5(VWF):c.4225G>T variant in VWF is a missense variant predicted to cause substitution of valine by phenylalanine at amino acid 1409. This variant has been reported in at least 3 apparently unrelated probands exhibiting a VWD Type 2M phenotype (PMID: 28971901 and PMID: 19404524, PS4_Moderate). The two probands of PMID: 28971901, exhibit excessive mucocutaneous bleeding as well as a laboratory phenotype of normal multimers, low VWF:RCo/VWF:Ag ratio and low collagen binding, which together are specific for VWD type 2M (PP4_Moderate). Low FVIII activity, an inconsistent phenotype, was also reported in these patients. The variant has been reported to segregate with VWD type 2M through at least 2 affected meioses from 2 different families (PP1_Moderate; PMID: 28971901). This variant is absent from gnomAD v4.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.722, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). The computational splicing predictor SpliceAI indicates that the variant has no impact on splicing. In summary, this variant meets the criteria to be classified as Likely Pathogenic for von Willebrand disease type 2A. ACMG/AMP criteria applied as specified by the ClinGen von Willebrand disease Variant Curation Expert Panel: PP1_Moderate, PP3, PM2_Supporting, PS4_Moderate, PP4_Moderate.
Met criteria codes
PP4_Moderate
At least 2 patients with this variant displayed excessive mucocutaneous bleeding as well as a laboratory phenotype of low VWF:RCo/VWF:Ag ratio and low collagen binding, as well as normal multimer distribution, which together are specific for VWD type 2M. (PP4_Moderate, PMID: 28971901). Low FVIII activity, an inconsistent phenotype, was also reported in these patients . The D1472H variant was ruled out in these patients (PMID: 28971901). An additional proband is described in PMID: 19277422, but it is likely that this individual has also been reported in PMID: 28971901 and is a family member of one of the previously scored probands.
PS4_Moderate
This variant has been reported in 2 additional probands meeting at least the laboratory criteria of PP4 (PMID: 28971901 and PMID: 19404524, PS4_Moderate). An additional proband is described in PMID: 19277422, but it is not clear whether this individual is unrelated to the others.
PP3
The computational predictor REVEL gives a score of 0.722, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). The computational splicing predictor SpliceAI gives a score of 0.00 for all splicing types, indicating that the variant has no impact on splicing.
PM2_Supporting
This variant is absent from gnomAD v4.1 (PM2_Supporting).
PP1_Moderate
The variant has been reported to segregate with VWD type 2M through >2 affected meioses in 2 different families (PP1_moderate; PMID: 28971901).
Curation History
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