The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000552.5(VWF):c.3686T>G (p.Val1229Gly)

CA228433

100274 (ClinVar)

Gene: VWF
Condition: hereditary von Willebrand disease
Inheritance Mode: Undetermined mode of inheritance
UUID: d7460be9-5a18-4bda-b812-59f4ccae5c0d
Approved on: 2024-08-12
Published on: 2024-08-12

HGVS expressions

NM_000552.5:c.3686T>G
NM_000552.5(VWF):c.3686T>G (p.Val1229Gly)
NC_000012.12:g.6019732A>C
CM000674.2:g.6019732A>C
NC_000012.11:g.6128898A>C
CM000674.1:g.6128898A>C
NC_000012.10:g.5999159A>C
NG_009072.1:g.109939T>G
NG_009072.2:g.109939T>G
ENST00000261405.10:c.3686T>G
ENST00000261405.9:c.3686T>G
ENST00000538635.5:n.421-25798T>G
ENST00000539641.1:n.484T>G
NM_000552.3:c.3686T>G
NM_000552.4:c.3686T>G

Likely Benign

Met criteria codes 3
BS1 BP5 BP4
Not Met criteria codes 7
BS2 BS3 PS4 BP2 PP1 PP4 BA1

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
NM_000552.5(VWF):c.3686T>G is a missense variant encoding a substitution of valine by glycine at position 1229. It has been reported in at least seven probands, two of whom have a phenotype specific for VWD Type 2B and one of whom has a phenotype specific for VWD Type 2M (PMID: 8134377, PMID: 17190853, PMID: 31064749, PMID: 16115133). However, the phenotypes are not consistent, and other variants present in cis or in trans are suspected to be disease-causing. At least one patient with this variant displayed excessive mucocutaneous bleeding as well as a laboratory phenotypes of loss of high molecular weight multimers and increased ristocetin-induced platelet aggregation showing gain of function, which together are highly specific for VWD type 2B (PMID: 8134377, PMID: 2657729). Although three other genotype-positive family members were similarly affected with a VWD Type 2B phenotype, the patients harbored other variants in cis, including p.Arg1306Trp, which has been classified as Pathogenic by the ClinGen VWD VCEP (BP5). The variant has also been observed in at least three control individuals (PMID: 22197721). The computational predictor REVEL gives a score of 0.149, which is below the ClinGen VWD VCEP threshold of <0.290 and does not predict a damaging effect on VWF function (BP4). Additionally, the computational splicing predictor SpliceAI indicated that the variant has no impact on splicing. RIPA studies indicate that this variant does not contribute to enhanced ristocetin-induced platelet aggregation and that another variant found in the same patient was responsible instead (PMID: 16115133). The Grpmax filtering allele frequency in gnomAD v4.1 is 0.01529 (based on 1200/74796 alleles, with 10 homozygotes) in the African/African-American population, which is above the ClinGen VWD VCEP threshold (>0.01) for BS1. In summary, the variant meets the criteria to be classified as likely benign based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: BS1, BP5, BP4.
Met criteria codes
BS1
The Grpmax filtering allele frequency in gnomAD v4.1 is 0.01529 (based on 1200/74796 alleles, with 10 homozygotes) in the African/African-American population, which is above the ClinGen VWD VCEP threshold (>0.01) for BS1.
BP5
This variant has been observed in an individual with VWD Type 2B who also harbors the NM_000552.5(VWF):c.3916C>T (p.Arg1306Trp) variant in cis (PMID: 8134377), with the phase of the variants confirmed by family member genotyping. This second variant has been classified as Pathogenic for VWD 2B by the ClinGen VWD VCEP (BP5).
BP4
The computational predictor REVEL gives a score of 0.149, which is below the ClinGen VWD VCEP threshold of <0.290 and does not predict a damaging effect on VWF function (BP4). The computational splicing predictor SpliceAI gives a score of 0.00 for all splicing types, indicating that the variant has no impact on splicing.
Not Met criteria codes
BS2
This variant has been observed in at least three control individuals (PMID: 22197721), however, this criterion is considered not applicable to the gene-disease relationship due to incomplete penetrance.
BS3
Although functional evidence on this variant is available, the evidence is relevant only to VWD Type 2B (PMID: 16115133). In addition, this criterion is considered not applicable to the gene-disease relationship.
PS4
This variant has been reported in at least seven probands, two of whom have met PP4 for VWD Type 2B and one of whom has met PP4 for VWD Type 2M (PMID: 8134377, PMID: 17190853, PMID: 31064749, PMID: 16115133). However, PS4 cannot be applied because the phenotypes are not consistent, and other variants present in cis or in trans are suspected to be disease-causing.
BP2
This variant has been observed in an individual with VWD Type 2B who also harbors the NM_000552.5(VWF):c.3797C>T (p.Pro1266Leu) variant in cis (PMID: 16115133), with the phase of the variants confirmed by parental genotyping. This second variant has not yet been classified by the ClinGen VWD VCEP and this criterion is considered not applicable to this gene-disease relationship.
PP1
At least 1 family with this variant included four genotype-positive members (PMID: 8134377) affected with excessive mucocutaneous bleeding as well as a laboratory phenotypes of loss of high molecular weight multimers and increased ristocetin-induced platelet aggregation showing gain of function, which together are highly specific for VWD type 2B (PMID: 2657729). The family has not been counted for this criterion because of other variants harbored in cis, including p.Arg1306Trp.
PP4
At least 1 patient with this variant displayed excessive mucocutaneous bleeding as well as a laboratory phenotypes of loss of high molecular weight multimers and increased ristocetin-induced platelet aggregation showing gain of function, which together are highly specific for VWD type 2B. The patient was also reported to have thrombocytopenia and a VWF antigen/activity ratio <0.3, consistent with type 2B (PMID: 8134377, PMID: 2657729). The patient has not been counted for this criterion because of other variants harbored in cis, including p.Arg1306Trp.
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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