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_000552.5(VWF):c.2278C>T (p.Arg760Cys)

CA228314

100208 (ClinVar)

Gene: VWF (HGNC:7450)
Condition: von Willebrand disease type 2N (MONDO:0015631)
Inheritance Mode: Autosomal recessive inheritance
UUID: d000f4f9-fefb-4a45-9939-a12016651e14
Approved on: 2025-01-07
Published on: 2025-01-08

HGVS expressions

NM_000552.5(VWF):c.2278C>T (p.Arg760Cys)
NM_000552.5:c.2278C>T
NC_000012.12:g.6046726G>A
CM000674.2:g.6046726G>A
NC_000012.11:g.6155892G>A
CM000674.1:g.6155892G>A
NC_000012.10:g.6026153G>A
NG_009072.1:g.82945C>T
NG_009072.2:g.82945C>T
ENST00000261405.10:c.2278C>T
ENST00000261405.9:c.2278C>T
ENST00000538635.5:n.421-52792C>T
NM_000552.3:c.2278C>T
NM_000552.4:c.2278C>T
More

Likely Pathogenic

Met criteria codes 5
BP4 PP4_Moderate PM3 PS3 PM2_Supporting
Not Met criteria codes 2
PP1 PM5

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 c.2278C>T variant in VWF is a missense variant predicted to cause substitution of Arginine by Cysteine at amino acid 760 (p.Arg760Cys). This variant lies 4 amino acids before the cleavage site for pro-VWF. At least 1 patient with this variant displayed excessive mucocutaneous bleeding as well as low FVIII activity and decreased VWF:FVIII binding 0f 0.23, which is highly specific for VWD type 2N. (PP4_moderate, PMID: 12393698). This individual was compound heterozygous (confirmed in trans by parental testing) for this variant and the p.R854Q variant which was classified as pathogenic by the VCEP (1 PM3 points, PM3). Factor VIII binding assay performed with the p.Arg760Cys recombinant mutant and wt vWF expressed by FUR4BHK cells showed absent binding indicating that this variant has a damaging effect on protein function (PMID: 12393698 )(PS3). The Grpmax filtering allele frequency in gnomAD v4.1 is 0.000007410 (based on 2/60034 alleles in the Admixed American population), which is lower than the ClinGen VWD VCEP threshold of <0.005 for type 2N VWD (PM2_Supporting). The computational predictor REVEL gives a score of 0.219, which is below the ClinGen VWD VCEP threshold of <0.290 and does not predict a damaging effect on VWF function. Additionally, the computational splicing predictor SpliceAI indicated that the variant has no impact on splicing (BP4). In summary, this variant meets the criteria to be classified as Likely Pathogenic for autosomal recessive von Willebrand disease type 2N based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: PP4_Moderate, PM2_Supporting, PM3, PS3, and BP4 (VCEP specifications version 1.0.0; date of approval).
Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.219, which is below the ClinGen VWD VCEP threshold of <0.290 and does not predict a damaging effect on VWF function. Additionally, the computational splicing predictor SpliceAI indicated that the variant has no impact on splicing (BP4).
PP4_Moderate
At least 1 patient with this variant displayed excessive mucocutaneous bleeding as well as low FVIII activity and decreased VWF:FVIII binding, which is highly specific for VWD type 2N. (PP4_moderate, PMID: 12393698). The binding capacity of VWF:FVIIIB was found to be decreased both as an absolute value (11.9 U/dL versus normal range, 70-140 U/dL) and a ratio (0.23 versus normal > 0.75).
PM3
This variant has been detected in at least 1 individual with VWF Type 2N (PMID: 12393698) This individual was compound heterozygous (confirmed in trans by parental testing) for this variant and the p.R854Q variant which was classified as pathogenic by the VCEP (1 PM3 points, PM3).
PS3
Factor VIII binding assay performed with the p.Arg760Cys recombinant mutant and wt vWF expressed by FUR4BHK cells showed absent binding indicating that this variant has a damaging effect on protein function (PMID: 12393698 )(PS3).
PM2_Supporting
The Grpmax filtering allele frequency in gnomAD v4.1 is 0.000007410 (based on 2/60034 alleles in the Admixed American population), which is lower than the ClinGen VWD VCEP threshold of <0.005 for type 2N VWD (PM2_Supporting).
Not Met criteria codes
PP1
PMID: 12393698 Father carries variant, but has VWF:FVIIIB/VWF:Ag of 0.45. * Addition of PP1 would not change classification
PM5
Another missense variant NM_000552.5(VWF):c.2279G>A (p.Arg760His) (ClinVar 31011, Pathogenic) in the same codon has not yet been classified by the ClinGen VWD VCEP. However, this variant is consistently associated with type 1 VWD.
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
ClinGen Terms of Use.
¤ Powered by BCM's Genboree.