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 label mismatch: VWF vs undefined
  • 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_000552.5(VWF):c.3569G>A (p.Cys1190Tyr)

CA383510975

626960 (ClinVar)

Gene: VWF (HGNC:7450)
Condition: von Willebrand disease type 2A (MONDO:0015628)
Inheritance Mode: Autosomal dominant inheritance
UUID: 7451c2f1-7e09-46f1-be83-ab46032458b5
Approved on: 2025-05-06
Published on: 2025-05-09

HGVS expressions

NM_000552.5:c.3569G>A
NM_000552.5(VWF):c.3569G>A (p.Cys1190Tyr)
NC_000012.12:g.6022005C>T
CM000674.2:g.6022005C>T
NC_000012.11:g.6131171C>T
CM000674.1:g.6131171C>T
NC_000012.10:g.6001432C>T
NG_009072.1:g.107666G>A
NG_009072.2:g.107666G>A
ENST00000261405.10:c.3569G>A
ENST00000261405.9:c.3569G>A
ENST00000538635.5:n.421-28071G>A
NM_000552.3:c.3569G>A
NM_000552.4:c.3569G>A
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Pathogenic

Met criteria codes 5
PM2_Supporting PP3 PM5 PP4_Moderate PS4

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:c.3569G>A variant in VWF is a missense variant predicted to cause substitution of cysteine by tyrosine at amino acid 1190 (p.Cys1190Tyr). At least 1 patient with this variant displayed excessive mucocutaneous bleeding as well as laboratory phenotypes of very low VWF activity, low activity/VWF:Ag ratio, and loss of high molecular weight multimers, which together are highly specific for VWD type 2A. (PP4_moderate, PMID 34532631). Additional consistent phenotypes were also reported in the patient, specifically, FVIII activity consistent with VWF antigen. This variant has been reported in 5 additional probands meeting PP4 laboratory phenotype criteria (PS4; PMID 20351307, 32864553, 32803740, 34355501). Another missense variant NM_000552.5:c.3568T>C (p.Cys1190Arg) in the same codon has been classified as pathogenic for VWD type 2A by the ClinGen VWD VCEP (PM5). The Grpmax filtering allele frequency in gnomAD v4.1 is 0.0000006195 (1/1180046 European non-Finnish population), which is lower than the ClinGen VWD VCEP threshold of <0.0001 for type 2A (PM2_Supporting). The computational predictor REVEL gives a score of 0.947, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). In summary, this variant meets the criteria to be classified as pathogenic for autosomal dominant VWF type 2A based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: PP4_Moderate, PS4, PM5, PM2_Supporting, PP3. (ClinGen von Willebrand Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for VWF Version 1.0.0)
Met criteria codes
PM2_Supporting
The Grpmax filtering allele frequency in gnomAD v4.1 is 0.0000006195 (1/1180046 European non-Finnish population), which is lower than the ClinGen VWD VCEP threshold of <0.0001 for type 2A (PM2_Supporting).
PP3
The computational predictor REVEL gives a score of 0.947, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3).
PM5
Another missense variant NM_000552.5:c.3568T>C (p.Cys1190Arg) in the same codon has been classified as pathogenic for VWD type 2A by the ClinGen VWD VCEP (PM5).
PP4_Moderate
At least 1 patient with this variant displayed excessive mucocutaneous bleeding as well as laboratory phenotypes of very low VWF activity, low activity/VWF:Ag ratio, and loss of high molecular weight multimers, which together are highly specific for VWD type 2A. (PP4_moderate, PMID 34532631). Additional consistent phenotypes were also reported in the patient, specifically, FVIII activity consistent with VWF antigen.
PS4
This variant has been reported in 6 additional probands meeting PP4 laboratory phenotype criteria (PS4; PMID 20351307, 32864553, 32803740, 34355501, 36696193, GoldVariantDatabase PersonalCommunication).
Curation History
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