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_000552.4(VWF):c.3922C>T (p.Arg1308Cys)

CA114125

289 (ClinVar)

Gene: VWF
Condition: von Willebrand disease type 2B
Inheritance Mode: Autosomal dominant inheritance
UUID: 37af012b-577e-4203-9623-1f3de52c5fec
Approved on: 2024-08-13
Published on: 2024-08-19

HGVS expressions

NM_000552.4:c.3922C>T
NM_000552.4(VWF):c.3922C>T (p.Arg1308Cys)
NC_000012.12:g.6019496G>A
CM000674.2:g.6019496G>A
NC_000012.11:g.6128662G>A
CM000674.1:g.6128662G>A
NC_000012.10:g.5998923G>A
NG_009072.1:g.110175C>T
NG_009072.2:g.110175C>T
ENST00000261405.10:c.3922C>T
ENST00000261405.9:c.3922C>T
ENST00000538635.5:n.421-25562C>T
NM_000552.3:c.3922C>T
NM_000552.5:c.3922C>T
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Pathogenic

Met criteria codes 7
PS3 PS4_Very Strong PP1 PP3 PS2_Supporting PP4_Moderate PM2_Supporting
Not Met criteria codes 1
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
NM_000552.4(VWF):c.3922C>T (p.Arg1308Cys) missense variant is predicted to cause substitution of arginine by cysteine at amino acid 1308. This variant has been reported in at least 30 probands, of which at least 19 reported sufficient phenotypic information to confirm type 2B VWD. (PS4; PMIDs: 18805962, 22077376, 1419803, 2010538, 16246252). Patient 9 of PMID: 2010538, has sufficient information to meet PP4_moerate: lacked HMWM in plasma and had a moderately heightened RIPA (0.6–0.7), as well as low VWF:RCo/VWF:Ag ratio (<0.45), with Platelet-type VWD excluded by mixing experiments to confirm that the defect was in the patient plasma and not in the patient platelets. The variant has been reported to segregate with VWD type 2B through at least 2 affected meioses from 1 family (PP1; PMID: 2010538). This variant has been identified as a de novo occurrence with unconfirmed parental relationships in 1 individual with VWD type 2B (PPS2_supporting; PMID: 2010538). This variant is absent from gnomAD v4.1 (PM2_Supporting). GP1bα binding assay in COS-7 cells expressing recombinant VWF, variant alone or together with WT, showed increased binding at low doses of ristocetin, indicating that this variant has a gain of function effect on the protein (PMID: 16246252) (PS3). Similar results have been reported in multiple studies (PMIDs: 26345337, 8630394). The computational predictor REVEL gives a score of 0.673, 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 VWD type 2B based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: PS3_supporting, PS4_VeryStrong, PM2_supporting, PS2_supporting, PP1, PP3, PP4_moderate.
Met criteria codes
PS3
GP1bα binding assay in COS-7 cells expressing recombinant VWF, variant alone or together with WT, showed increased binding at low doses of ristocetin, indicating that this variant has a gain of function effect on the protein (PMID: 16246252) (PS3). Similar results have been reported in multiple studies (PMIDs: 26345337, 8630394).
PS4_Very Strong
This variant has been reported in at least 30 probands, of which at least 19 reported sufficient phenotypic information to confirm type 2B VWD. (PS4_VeryStrong; PMIDs: 18805962, 22077376, 1419803, 2010538, 16246252).
PP1
The variant has been reported to segregate with VWD type 2B through at least 2 affected meioses from 1 family (PP1; PMID: 2010538).
PP3
The computational predictor REVEL gives a score of 0.673, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3).
PS2_Supporting
This variant has been identified as a de novo occurrence with unconfirmed parental relationships in 1 individual with VWD type 2B (PS2_supporting; PMID: 2010538)
PP4_Moderate
Patient 9 of PMID: 2010538, has sufficient information to meet PP4_moderate: lacked HMWM in plasma and had a moderately heightened RIPA (0.6–0.7), as well as low VWF:RCo/VWF:Ag ratio (<0.45). Additional consistent information was reduced VWF:Ag and low VWF:RCo. Platelet-type VWD was excluded by mixing experiments to confirm that the defect was in the patient plasma and not in the patient platelets.
PM2_Supporting
This variant is absent from gnomAD v4.1 (PM2_Supporting).
Not Met criteria codes
PM5
At least 3 different missense variants in the same codon (p.Arg1308Pro; ClinVar 100304, p.Arg1308Ser; PMID: 26278967, p.Arg1308Leu; PMID: 16246252) have been reported in patients with VWD type 2B, As well as p.Arg1308His (ClinVar 100303) with VWD type unknown. However, these variants have not yet been evaluated for criteria to be classified as pathogenic by the ClinGen VWD VCEP.
Curation History
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