NM_000552.5:c.4196G>A
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 7P and 5B. BP5BS1PM5_SupportingPP3PP4PS3
This summary comes from the ClinGen Evidence Repository: The NM_000552.5:c.4196G>A variant in VWF is a missense variant predicted to cause substitution of arginine by histidine at amino acid 1399. The Arg1399His variant has a relatively high Grpmax filtering allele frequency in gnomAD v4.1 of 0.01289 (based on 15410/1179858 alleles in the European non-Finnish population), which is higher than the ClinGen VWD VCEP threshold (>0.01; BS1). At least 4 patients with this variant displayed excessive mucocutaneous bleeding as well as the laboratory phenotype of an abnormal collagen binding assay, which together are consistent with VWD Type 2M (PP4, PS4_Moderate), however, all patients exhibited a VWF:RCo/VWF:Ag ratio between 0.7 and 1.5 (PMID:22507569, PMID:28083987, PMID:28971901). This variant has also been observed in at least 2 patients with an alternate molecular basis for disease, one of whom exhibited VWD Type 2B phenotypes and harbored the c.3916C>T (p.Arg1306Trp) variant in cis (PMID:1672694), which is classified as pathogenic for VWD Type 2B by the ClinGen VWD VCEP. The second patient exhibited a VWD Type 2M phenotype and harbored this variant as well as the c.4225G>T (p.Val1409Phe) variant, which is classified as likely pathogenic for VWD Type 2M by the ClinGen VWD VCEP (PMID:28971901). The computational predictor REVEL gives a score of 0.698, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). Another missense variant in the same codon, NM_000552.5(VWF):c.4195C>T (p.Arg1399Cys), has been reported in multiple patients with VWD Type 2M (PMID:17000885, PMID:26988807, PMID:28083987). This variant has been classified as likely pathogenic by the ClinGen VWD VCEP (PM5_supporting). Multiple functional studies show a deleterious effect on protein function, including a hydrodynamic mouse model showing >75% loss of both collagen 4 binding and platelet adhesion PMID:25662333) and a knock-in mouse model showing decreased VWF binding to collagen IV but not collagen III, decreased platelet adhesion, and increased bleeding, indicating a hypomorphic effect (PMID:30565388). Exogenous expression of the p.Arg1399His mutant in 293 cells identified undetectable binding to type VI (PMID:22507569) and type IV collagen (PMID:25662333) (PS3). In summary, this variant meets the criteria to be classified as a Variant of Unknown Significance for von Willebrand disease type 2M based on the ACMG/AMP criteria applied, as specified by the ClinGen von Willebrand disease Variant Curation Expert Panel: PS3, PM5_supporting, PP3, PP4, BP5, BS1. (VCEP Rule specifications for von Willebrand disease type 2A, 2B and 2M v1.0.0; date of approval 08/13/2024) LINK:https://erepo.genome.network/evrepo/ui/classification/CA114133/MONDO:0019565/090
Frequency
Consequence
NM_000552.5 missense
Scores
Clinical Significance
Conservation
Publications
- hereditary von Willebrand diseaseInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- von Willebrand disease type 2BInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
- von Willebrand disease 2Inheritance: AR, AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine
- von Willebrand disease 1Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
- von Willebrand disease type 2AInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- von Willebrand disease type 2MInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- von Willebrand disease 3Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- von Willebrand disease type 2NInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000552.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| VWF | NM_000552.5 | MANE Select | c.4196G>A | p.Arg1399His | missense | Exon 28 of 52 | NP_000543.3 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| VWF | ENST00000261405.10 | TSL:1 MANE Select | c.4196G>A | p.Arg1399His | missense | Exon 28 of 52 | ENSP00000261405.5 | ||
| VWF | ENST00000538635.5 | TSL:4 | n.421-25288G>A | intron | N/A |
Frequencies
GnomAD3 genomes 0.00877 AC: 1334AN: 152120Hom.: 11 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.00858 AC: 2152AN: 250796 AF XY: 0.00921 show subpopulations
GnomAD4 exome AF: 0.0114 AC: 16651AN: 1461652Hom.: 147 Cov.: 98 AF XY: 0.0112 AC XY: 8149AN XY: 727138 show subpopulations
Age Distribution
GnomAD4 genome 0.00876 AC: 1334AN: 152238Hom.: 11 Cov.: 31 AF XY: 0.00875 AC XY: 651AN XY: 74426 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Pathogenic:1Uncertain:3Benign:2
The VWF c.4196G>A (p.Arg1399His) variant has been reported in the published literature in individuals with Type 1 (PMIDs: 25662333 (2015), 22507569 (2012)), Type 2 (PMID: 33556167 (2021)), Type 2B (PMID: 1672694 (1991)), and Type 2M von Willebrand disease (PMID: 28971901 (2017)). It has also been observed in individuals with hemophilia (PMID: 34708896 (2021)) and thrombotic/platelet disorders (PMID: 31064749 (2019)). In addition, this variant has been identified in reportedly healthy individuals (PMIDs: 33556167 (2021), 25662333 (2015), 22507569 (2012), 1672694 (1991)). Functional studies indicate this variant causes reduced platelet adhesion and binding to type IV and VI collagen, however binding to type I and type III collagen is unaffected (PMIDs: 30565388 (2019), 25662333 (2015), 22507569 (2012)). The frequency of this variant in the general population, 0.017 (173/10360 chromosomes in Ashkenazi Jewish subpopulation (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is higher than would generally be expected for pathogenic variants in this gene. Analysis of this variant using bioinformatics tools (i.e., MutationTaster and PolyPhen-2) for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is benign or damaging. Based on the available information, we are unable to determine the clinical significance of this variant.
Published in vitro functional studies demonstrate a damaging effect with disrupted type VI collagen binding but no significant effect on type I or type III collagen binding (PMID: 22507569); Published in vivo functional studies in mice demonstrate a damaging effect with reduced binding and adhesion of platelets to collagen IV leading to increased bleeding times (PMID: 25662333, 30565388); Identified in the heterozygous state in multiple unrelated individuals with features of von Willebrand disease but also observed in healthy control individuals (PMID: 22507569, 1672694, 31064749); In silico analysis suggests that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 37872709, 1672694, 29924855, 34136746, 30565388, 31935285, 30690834, 28916584, 31064749, 28083987, 28971901, 23406206, 20409624, 34708896, 33556167, 24338593, 36754679, 22507569, 25662333, 37762110, 40577417, 37845247)
VWF: PM5, BP4, BS1, BS2
PP5, PM5, PS3
Hereditary von Willebrand disease Pathogenic:1Uncertain:1
The NM_000552.5:c.4196G>A variant in VWF is a missense variant predicted to cause substitution of arginine by histidine at amino acid 1399. The Arg1399His variant has a relatively high Grpmax filtering allele frequency in gnomAD v4.1 of 0.01289 (based on 15410/1179858 alleles in the European non-Finnish population), which is higher than the ClinGen VWD VCEP threshold (>0.01; BS1). At least 4 patients with this variant displayed excessive mucocutaneous bleeding as well as the laboratory phenotype of an abnormal collagen binding assay, which together are consistent with VWD Type 2M (PP4, PS4_Moderate), however, all patients exhibited a VWF:RCo/VWF:Ag ratio between 0.7 and 1.5 (PMID: 22507569, PMID: 28083987, PMID: 28971901). This variant has also been observed in at least 2 patients with an alternate molecular basis for disease, one of whom exhibited VWD Type 2B phenotypes and harbored the c.3916C>T (p.Arg1306Trp) variant in cis (PMID: 1672694), which is classified as pathogenic for VWD Type 2B by the ClinGen VWD VCEP. The second patient exhibited a VWD Type 2M phenotype and harbored this variant as well as the c.4225G>T (p.Val1409Phe) variant, which is classified as likely pathogenic for VWD Type 2M by the ClinGen VWD VCEP (PMID: 28971901). The computational predictor REVEL gives a score of 0.698, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). Another missense variant in the same codon, NM_000552.5(VWF):c.4195C>T (p.Arg1399Cys), has been reported in multiple patients with VWD Type 2M (PMID: 17000885, PMID: 26988807, PMID: 28083987). This variant has been classified as likely pathogenic by the ClinGen VWD VCEP (PM5_supporting). Multiple functional studies show a deleterious effect on protein function, including a hydrodynamic mouse model showing >75% loss of both collagen 4 binding and platelet adhesion PMID: 25662333) and a knock-in mouse model showing decreased VWF binding to collagen IV but not collagen III, decreased platelet adhesion, and increased bleeding, indicating a hypomorphic effect (PMID: 30565388). Exogenous expression of the p.Arg1399His mutant in 293 cells identified undetectable binding to type VI (PMID: 22507569) and type IV collagen (PMID: 25662333) (PS3). In summary, this variant meets the criteria to be classified as a Variant of Unknown Significance for von Willebrand disease type 2M based on the ACMG/AMP criteria applied, as specified by the ClinGen von Willebrand disease Variant Curation Expert Panel: PS3, PM5_supporting, PP3, PP4, BP5, BS1. (VCEP Rule specifications for von Willebrand disease type 2A, 2B and 2M v1.0.0; date of approval 08/13/2024)
von Willebrand disease type 2 Uncertain:1Benign:1
von Willebrand disease type 1 Uncertain:1Benign:1
ACMG Criteria: BS1, BS2, PS3, PM5, PP3, PP5; Variant found in a heterozygous state
Abnormality of coagulation Pathogenic:1
not specified Uncertain:1
Variant summary: VWF c.4196G>A (p.Arg1399His) results in a non-conservative amino acid change located in the von Willebrand factor, type A domain (IPR002035) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0086 in 250796 control chromosomes in the gnomAD database, including 21 homozygotes. c.4196G>A has been reported in the literature in both heterozygous and compound heterozygous individuals affected with Von Willebrand Disease (e.g., Flood_2012, Flood_2015, Nava_2019, Borras_2017, Sadler_2021). However, co-occurrences with other pathogenic variants have been reported, providing supporting evidence for either a benign role or a role in recessive disease (e.g., Flood_2012, Borras_2017). Several publications report experimental evidence evaluating an impact on protein function showing a complete disruption of binding to type VI collagen but no significant effect on type III collagen in vitro (Flood_2015, Flood_2012) as well as decreased collagen binding, decreased platelet adhesion, and increased bleeding times in a mouse model (e.g., Slobodianuk_2019). The following publications have been ascertained in the context of this evaluation (PMID: 28971901, 25662333, 22507569, 30690834, 33556167, 30565388). A different missense variant at this same amino acid position (c.4195C>T; p.Arg1399Cys) has been classified as pathogenic by our laboratory, suggesting this codon could be critical for normal function of the protein. ClinVar contains an entry for this variant (Variation ID: 293). Based on the evidence outlined above, the variant was classified as uncertain significance.
VWF-related disorder Uncertain:1
The VWF c.4196G>A variant is predicted to result in the amino acid substitution p.Arg1399His. This variant was reported in healthy controls and in VWD type 1 and type 2 patients, some of whom had other likely pathogenic VWF gene variants (Borràs et al. 2017. PubMed ID: 28971901; Flood et al. 2015. PubMed ID: 25662333; Perez-Rodriquez et al. 2018. PubMed ID: 29924855). Amino acid residue p.Arg1399 resides in the VWF A1 collagen binding domain. Data in Flood et al. and in another report, Slobodianuk et al. 2018. PubMed ID: 30565388, indicate that the p.Arg1399His substitution decreases type IV and VI collagen binding. A similar variant, c.4195C>T (p.Arg1399Cys) was also reported in a patient with VWF 2m (Gadisseur et al. 2009. PubMed ID: 19506359). However, the p.Arg1399His substitution occurs frequently in several populations, including in the homozygous state, and is reported at frequencies ranging from ~ 0.2 -1.6%. Although we suspect that the c.4196G>A (p.Arg1399His) variant may be benign, at this time, the clinical significance is uncertain due to the absence of conclusive functional and genetic information.
von Willebrand disease type 1;C1264041:von Willebrand disease type 3 Uncertain:1
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at