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.2384A>G (p.Tyr795Cys)

CA114166

312 (ClinVar)

Gene: VWF
Condition: von Willebrand disease type 2N
Inheritance Mode: Autosomal recessive inheritance
UUID: 51a932c7-ed92-419d-a693-6c18a63a3911
Approved on: 2025-01-07
Published on: 2025-01-08

HGVS expressions

NM_000552.5:c.2384A>G
NM_000552.5(VWF):c.2384A>G (p.Tyr795Cys)
NC_000012.12:g.6044349T>C
CM000674.2:g.6044349T>C
NC_000012.11:g.6153515T>C
CM000674.1:g.6153515T>C
NC_000012.10:g.6023776T>C
NG_009072.1:g.85322A>G
NG_009072.2:g.85322A>G
ENST00000261405.10:c.2384A>G
ENST00000261405.9:c.2384A>G
ENST00000538635.5:n.421-50415A>G
NM_000552.3:c.2384A>G
NM_000552.4:c.2384A>G
More

Pathogenic

Met criteria codes 5
PS3 PP3 PM3 PM2_Supporting PP4_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.2384A>G (p.Tyr795Cys) missense variant has a Grpmax filtering allele frequency in gnomAD v4.1 of 2.800e-7 (based on 2/1180036 alleles in the European non-Finnish population), which is lower than the ClinGen VWD VCEP threshold of <0.005 for type 2N (PM2_Supporting). The computational predictor REVEL gives a score of 0.688, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). At least three compound heterozygous VWD type 2N patients have been reported with this variant; two (PMIDs: 33807613, 15461624; PM3) compound heterozygous with R854Q (classified Pathogenic by the VWD VCEP), and one (PMID: 15213842) compound heterozygous with R1566X (not yet been evaluated by the VWD VCEP). At least 1 patient with this variant displayed excessive mucocutaneous bleeding as well as low FVIII activity (0.13 IU/ml) and decreased VWF:FVIII binding (<1.5%), which is highly specific for VWD type 2N. (PP4_moderate, PMID:15213842). Factor VIII binding assay performed with theY795C recombinant mutant showed severely impaired binding indicating that this variant has a damaging effect on protein function (PMID: 15213842, 15461624; PS3). In summary, this variant meets the criteria to be classified as Pathogenic for von Willebrand disease type 2N. ACMG/AMP criteria applied as specified by the ClinGen von Willebrand disease Variant Curation Expert Panel: PM2_supporting, PP3, PM3, PP4_moderate, PS3.
Met criteria codes
PS3
Factor VIII binding assay performed with the Y795C recombinant mutant showed severely impaired binding indicating that this variant has a damaging effect on protein function (PMID: 15213842, 15461624; PS3).
PP3
The computational predictor REVEL gives a score of 0.688, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3).
PM3
At least three compound heterozygous VWD type 2N patients have been reported with this variant; two (PMIDs: 33807613 1pt, 15461624 0.5pt) compound heterozygous with R854Q (classified Pathogenic by the VWD VCEP), and one (PMID: 15213842 0pt) compound heterozygous with R1566X (not yet been evaluated by the VWD VCEP). Total 1.5pt (PM3)
PM2_Supporting
The Grpmax filtering allele frequency in gnomAD v4.1 is 2.800e-7 (based on 2/1180036 alleles in the European non-Finnish population), which is lower than the ClinGen VWD VCEP threshold of <0.005 for type 2N (PM2_Supporting).
PP4_Moderate
At least 1 patient with this variant displayed excessive mucocutaneous bleeding as well as low FVIII activity (0.13 IU/ml) and decreased VWF:FVIII binding (<1.5%), which is highly specific for VWD type 2N. (PP4_moderate, PMID:15213842). Additionally a consistent phenotype of normal VWF:Ag (0.91 IU/ml) was reported however, there were aberrant multimers (i) relatively reduced concentration of large multimers in ii) the presence of ‘supranormal’ multimers and iii) a lack of a defined triplet structure of individual multimers which had a smeary appearance rather than displaying sharp bands.
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.
¤ Powered by BCM's Genboree.