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.4883T>C (p.Ile1628Thr)

CA114115

284 (ClinVar)

Gene: VWF
Condition: von Willebrand disease type 2A
Inheritance Mode: Autosomal dominant inheritance
UUID: a9a196dd-5934-4059-b7b5-a4b56727c325
Approved on: 2024-08-13
Published on: 2024-08-13

HGVS expressions

NM_000552.5:c.4883T>C
NM_000552.5(VWF):c.4883T>C (p.Ile1628Thr)
NC_000012.12:g.6018535A>G
CM000674.2:g.6018535A>G
NC_000012.11:g.6127701A>G
CM000674.1:g.6127701A>G
NC_000012.10:g.5997962A>G
NG_009072.1:g.111136T>C
NG_009072.2:g.111136T>C
ENST00000261405.10:c.4883T>C
ENST00000261405.9:c.4883T>C
ENST00000538635.5:n.421-24601T>C
NM_000552.3:c.4883T>C
NM_000552.4:c.4883T>C

Pathogenic

Met criteria codes 6
PS3_Supporting PP4_Moderate PM2_Supporting PP1_Moderate PS4 PP3
Not Met criteria codes 3
BA1 BS1 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_000552.5(VWF):c.4883T>C is a missense variant in VWF predicted to cause substitution of isoleucine by threonine at amino acid 1628. The Grpmax filtering allele frequency in gnomAD v4.1 is 2.800e-7 (based on 2/1179884 alleles in the European non-Finnish population), which is lower than the ClinGen VWD VCEP threshold of <0.0001 for (PM2_Supporting). The computational predictor REVEL gives a score of 0.703, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). At least sixteen patients with this variant have been diagnosed with VWD Type 2A, of whom nine are documented to have displayed excessive mucocutaneous bleeding as well as laboratory phenotypes of very low VWF activity (measured by VWF:RCo) low VWF:RCo/ VWF:Ag ratio, and absence of high-molecular weight VWF multimers, which together are highly specific for VWD type 2A (PP4_Moderate, PMID: 28536718, VCEP member-provided data). Thirteen total probands have been described in sufficient detail to establish a phenotype specific to VWD type 2A (PS4_VeryStrong, PMID: 28536718, VCEP member-provided data, PMID: 28971901). The variant has been reported to segregate with VWD type 2A through 6 affected meioses from 1 family and 3 affected meioses in another (PP1_Moderate; PMID: 1673047, PMID: 28971901). Proteolysis assays of an exogenously expressed VWF fragment showed higher susceptibility of the variant protein to ADAMTS13 proteolysis under non-denaturing conditions (PMID: 16221672, PMID: 16322474, PMID: 23110044), indicating that this variant has a damaging effect on protein function (PS3_Supporting). The variant protein exhibited normal multimer distribution (PMID: 16322474) and secretion rate (PMID: 8123844) in vitro. 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: PS3_supporting, PS4, PP1_Moderate, PM2_Supporting, PP3, PP4_Moderate.
Met criteria codes
PS3_Supporting
Proteolysis assays of an exogenously expressed VWF fragment showed a comparable rate of proteolysis by ADAMTS13 between the variant and wild-type proteins under denaturing conditions (PMID: 16221672, PMID: 16322474, PMID: 23110044). However, performing this assay under non-denaturing conditions revealed higher susceptibility of the variant protein to ADAMTS13 proteolysis (PMID: 16322474, PMID: 23110044, PS3_Supporting). On the other hand, the observed multimer distribution in vitro (PMID: 16322474) and rate of secretion (PMID: 8123844) appeared normal.
PP4_Moderate
At least 9 probands with this variant displayed excessive mucocutaneous bleeding as well as the laboratory phenotypes of very low VWF activity (measured by VWF:RCo), low activity/VWF:Ag ratio (VWF:RCo/ VWF:Ag of 0.4), and absence of VWF high-molecular weight multimers, along with impaired von Willebrand factor collagen binding activity and abnormal GPIbM, which together are highly specific for VWD type 2A (PP4_Moderate, VCEP member-provided data, PMID: 28971901). 4 additional probands with this variant met PP4 by displaying excessive mucocutaneous bleeding as well as a laboratory phenotypes of very low VWF activity (measured by VWF:RCo) and low activity/VWF:Ag ratio (VWF:RCo/ VWF:Ag of 0.4), despite the absence of data on high molecular weight multimers (PMID: 28536718, VCEP member-provided data). At least 3 other patients with this variant were diagnosed with VWD Type 2A but did not meet the requirements for PP4 (PMID: 17681836, PMID: 1673047, PMID: 28980759).
PM2_Supporting
The Grpmax filtering allele frequency in gnomAD v4.1 is 2.800e-7 (based on 2/1179884 alleles in the European non-Finnish population), which is lower than the ClinGen VWD VCEP threshold of <0.0001 for (PM2_Supporting).
PP1_Moderate
The variant has been reported to segregate with VWD type 2A through 6 affected meioses from 1 family and 3 affected meiosis from another (PP1_Moderate; PMID: 1673047, PMID: 28971901).
PS4
This variant has been reported in at least 7 additional probands (not including the one used to apply PP4) meeting PP4 or PP4_Moderate (PMID: 28536718, VCEP member-provided data, PS4). At least 3 additional probands could not be counted for this criterion due to not having met PP4 (PMID: 17681836, PMID: 1673047, PMID: 28980759).
PP3
The computational predictor REVEL gives a score of 0.703, 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.
Not Met criteria codes
BA1
This variant is absent from gnomAD v2.1.1 and v3.1.2. The criterion is not met.
BS1
This variant is absent from gnomAD v2.1.1 and v3.1.2. The criterion is not met.
PM5
NM_000552.5(VWF):c.4883T>A (p.Ile1628Asn) is reported Pathogenic in ClinVar but is not yet evaluated by the VWD VCEP.
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