12-6019474-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PP4_ModeratePP3PM2_SupportingPS4_Moderate
This summary comes from the ClinGen Evidence Repository: The missense variant NM_000552.5(VWF):c.3944G>A (p.Arg1315His) is a rare variant which occurs at a Grpmax filtering allele frequency in gnomAD v4.1 is 0.00002255 (based on 4/60004 alleles in the Admixed American population), which is lower than the ClinGen VWD VCEP threshold of <0.0001 (PM2_supporting). The computational predictor REVEL gives a score of 0.815, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). Portuguese patient P30, with this variant, (PMID:26988807) displayed excessive mucocutaneous bleeding (bleeding score 7) as well as a laboratory phenotype of normal multimers, low VWF:RCo/VWF:Ag ratio (VWF:RCo 11%, VWF:Ag 16%, ratio 0.69) and an abnormal collagen binding assay (VWF:CB 19%), which together are highly specific for VWD type 2M (PP4_moderate). At least 3 additional probands have been reported with this variant and VWD reported as type 1 (but with VWF:RCo/VWF:Ag ratio <0.7) or type 2M (PMID:26986123, 25689060, 16985174; PS4_moderate). In summary, the variant meets the criteria to be classified as Likely Pathogenic for von Willebrand disease type 2M based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: PM2_supporting, PP3, PP4_moderate, PS4_moderate. LINK:https://erepo.genome.network/evrepo/ui/classification/CA228504/MONDO:0015630/081
Frequency
Consequence
NM_000552.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VWF | NM_000552.5 | c.3944G>A | p.Arg1315His | missense_variant | 28/52 | ENST00000261405.10 | NP_000543.3 | |
VWF | XM_047429501.1 | c.3944G>A | p.Arg1315His | missense_variant | 28/52 | XP_047285457.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VWF | ENST00000261405.10 | c.3944G>A | p.Arg1315His | missense_variant | 28/52 | 1 | NM_000552.5 | ENSP00000261405.5 | ||
VWF | ENST00000538635.5 | n.421-25540G>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250994Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135700
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461606Hom.: 0 Cov.: 38 AF XY: 0.0000193 AC XY: 14AN XY: 727108
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not provided Pathogenic:2Uncertain:1Other:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Jul 31, 2024 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jun 28, 2023 | The VWF c.3944G>A; p.Arg1315His variant (rs61749396) is reported in the literature in multiple individuals affected with Von Willebrand disease types 1, 2m and 3 (Elayaperumal 2018, Goodeve 2007, Veyradier 2016). This variant is also reported in ClinVar (Variation ID: 100311) and is found in the general population with an overall allele frequency of 0.002% (6/250,994 alleles) in the Genome Aggregation Database. Additionally, other amino acid substitutions at this codon (Cys, Gly, Leu, Pro) have been reported in individuals with VWF and are considered disease causative (Elayaperumal 2018, Goodeve 2007, Veyradier 2016). Computational analyses predict that this variant is deleterious (REVEL: 0.815). Based on available information, this variant is considered to be likely pathogenic. References: Elayaperumal S et al. Type-3 von Willebrand disease in India-Clinical spectrum and molecular profile. Haemophilia. 2018 Nov;24(6):930-940. PMID: 29984440. Goodeve A et al. Phenotype and genotype of a cohort of families historically diagnosed with type 1 von Willebrand disease in the European study, Molecular and Clinical Markers for the Diagnosis and Management of Type 1 von Willebrand Disease (MCMDM-1VWD). Blood. 2007 Jan 1;109(1):112-21. PMID: 16985174. Veyradier A et al. A Laboratory Phenotype/Genotype Correlation of 1167 French Patients From 670 Families With von Willebrand Disease: A New Epidemiologic Picture. Medicine (Baltimore). 2016 Mar;95(11):e3038. PMID: 26986123. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Sep 12, 2022 | The frequency of this variant in the general population, 0.000087 (3/34586 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals affected with Type 1 von Willebrand disease (vWD) (PMID: 16985174 (2007)), Type 2 vWD with a collagen binding defect (PMID: 26986123 (2016), 28083987 (2017)), and Type 3 vWD (PMID: 29984440 (2018)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant. - |
not provided, no classification provided | literature only | Academic Unit of Haematology, University of Sheffield | - | - - |
von Willebrand disease type 2 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Genetics and Molecular Pathology, SA Pathology | Jul 26, 2019 | - - |
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 14, 2024 | The c.3944G>A (p.R1315H) alteration is located in exon 28 (coding exon 27) of the VWF gene. This alteration results from a G to A substitution at nucleotide position 3944, causing the arginine (R) at amino acid position 1315 to be replaced by a histidine (H). for autosomal dominant, autosomal recessive Von Willebrand disease; however, its clinical significance for autosomal dominant von Willebrand disease Type 2B is uncertain Based on data from gnomAD, the A allele has an overall frequency of 0.002% (6/250994) total alleles studied. The highest observed frequency was 0.016% (1/6124) of Other alleles. This variant has been identified in the heterozygous state or in conjunction with other VWF variants in individuals with features consistent with various forms of von Willebrand disease; in at least one instance, the variants were identified in trans (Álvarez-Laderas, 2015; Fidalgo, 2017; Elayaperumal, 2018). Two other alterations at the same codon, c.3943C>T (p.R1315C) and c.3944G>T (p.R1315L), have been detected in multiple individuals with autosomal dominant/autosomal recessive loss of function von Willebrand disease forms (Baronciani, 2006; Elayaperumal, 2018). This amino acid position is well conserved in available vertebrate species. Based on internal structural analysis, R1315H is deleterious. The variant is moderately destabilizing to the local structure. The variant is not on an interface. The variant has no nearby pathogenic variants and has no nearby benign variants (Ribba, 2001; Ambry internal data). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. - |
von Willebrand disease type 1 Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Zotz-Klimas Genetics Lab, MVZ Zotz Klimas | Oct 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at