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
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Variant: NM_000552.5(VWF):c.8318G>C (p.Cys2773Ser)

CA228847

100503 (ClinVar)

Gene: VWF
Condition: von Willebrand disease type 2A
Inheritance Mode: Autosomal dominant inheritance
UUID: 7f9772d1-c9d1-448a-855d-4e2b353a4d44
Approved on: 2024-08-12
Published on: 2024-08-12

HGVS expressions

NM_000552.5:c.8318G>C
NM_000552.5(VWF):c.8318G>C (p.Cys2773Ser)
NC_000012.12:g.5949139C>G
CM000674.2:g.5949139C>G
NC_000012.11:g.6058305C>G
CM000674.1:g.6058305C>G
NC_000012.10:g.5928566C>G
NG_009072.1:g.180532G>C
NG_009072.2:g.180532G>C
ENST00000261405.10:c.8318G>C
ENST00000261405.9:c.8318G>C
NM_000552.3:c.8318G>C
NM_000552.4:c.8318G>C
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Pathogenic

Met criteria codes 6
PS4_Moderate PS2_Moderate PP4_Moderate PS3 PP3 PM2_Supporting
Not Met criteria codes 5
BS1 BP4 PP1 BA1 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 NM_000552.5(VWF):c.8318G>C variant in VWF is a missense variant predicted to cause substitution of cysteine by serine at amino acid 2773. This variant is absent from gnomAD v4.1 (PM2_Supporting). At least one patients with this variant displayed laboratory phenotypes of excessive mucocutaneous bleeding, very low VWF activity (measured by VWF:RCo assay), low VWF:RCo/VWF:Ag ratio, and loss of high molecular weight multimers, which together are highly specific for VWD Type 2A (PP4_moderate, PMID: 17139364). This variant has been reported in 3 additional probands meeting type 2A laboratory criteria for PP4 (PS4_moderate; PMID: 21979291, 32664776, 28971901), and one was a de novo occurrence with unconfirmed parental relationships (PS2_Moderate; PMID: 32664776). Multimerization assay performed with the p.Cys2773Ser recombinant mutant and wild-type vWF co-expressed by HEK293 cells showed abnormal multimers (PMID: 17139364 Fig. 2) that were counteracted by an allele-specific siRNA targeting the mutant transgene, indicating that this variant has a damaging effect on protein function (PMID: 29734512)(PS3_supporting). The computational predictor REVEL gives a score of 0.876, 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 von Willebrand disease type 2A. ACMG/AMP criteria applied as specified by the ClinGen von Willebrand disease Variant Curation Expert Panel: PP4_Moderate, PS2_Moderate, PS4_Moderate, PS3, PP3, PM2_Supporting.
Met criteria codes
PS4_Moderate
This variant has been reported in 3 additional probands meeting type 2A laboratory criteria for PP4 (PS4_supporting; PMID: 21979291, 32664776, 28971901).
PS2_Moderate
This variant has been identified as a de novo occurrence with unconfirmed parental relationships in 1 individual with VWD Type 2A meeting PP4_Moderate (PM6; PMID: 32664776).
PP4_Moderate
At least one patients with this variant displayed laboratory phenotypes of excessive mucocutaneous bleeding, very low VWF activity (measured by VWF:RCo assay), low VWF:RCo/VWF:Ag ratio, and loss of high molecular weight multimers, which together are highly specific for VWD Type 2A (PP4_moderate, PMID: 17139364).
PS3
Multimerization assay performed with the p.Cys2773Ser recombinant mutant and wild-type vWF co-expressed by HEK293 cells showed abnormal multimers (PMID: 17139364 Fig. 2) that were counteracted by an allele-specific siRNA targeting the mutant transgene, indicating that this variant has a damaging effect on protein function (PMID: 29734512)(PS3).
PP3
The computational predictor REVEL gives a score of 0.876, 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).
Not Met criteria codes
BS1
This variant is absent from gnomAD v2.1.1 and v3.1.2. The criterion is not met.
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
The variant has been reported to segregate with VWD type 2A through only 1 affected meiosis from 1 family, so that the standard for this criterion of 2 segregations in one family is not met (PMID: 17139364).
BA1
This variant is absent from gnomAD v2.1.1 and v3.1.2. The criterion is not met.
PM5
Another missense variant in the same codon has been reported in a patient with VWD Type 2A (NM_000552.5(VWF):c.8317T>C (p.Cys2773Arg) but is not considered here to avoid circularity.
Curation History
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