rs61750603
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4_StrongBS2_Supporting
The ENST00000261405.10(VWF):c.5191T>A(p.Ser1731Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00116 in 1,614,210 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S1731L) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000261405.10 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VWF | NM_000552.5 | c.5191T>A | p.Ser1731Thr | missense_variant | 30/52 | ENST00000261405.10 | NP_000543.3 | |
VWF | XM_047429501.1 | c.5191T>A | p.Ser1731Thr | missense_variant | 30/52 | XP_047285457.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VWF | ENST00000261405.10 | c.5191T>A | p.Ser1731Thr | missense_variant | 30/52 | 1 | NM_000552.5 | ENSP00000261405 | P1 | |
VWF | ENST00000538635.5 | n.421-22702T>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000992 AC: 151AN: 152198Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00157 AC: 394AN: 251490Hom.: 1 AF XY: 0.00162 AC XY: 220AN XY: 135920
GnomAD4 exome AF: 0.00118 AC: 1719AN: 1461894Hom.: 3 Cov.: 32 AF XY: 0.00122 AC XY: 887AN XY: 727248
GnomAD4 genome AF: 0.000991 AC: 151AN: 152316Hom.: 2 Cov.: 32 AF XY: 0.000886 AC XY: 66AN XY: 74492
ClinVar
Submissions by phenotype
not provided Pathogenic:1Uncertain:2Benign:1Other:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Oct 25, 2024 | Published functional studies including in vitro collagen binding assays showed a reduction in binding to both type I and type III collagen (PMID: 20345715, 25051961); In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 21967679, 25662333, 25051961, 19506356, 19687512, 26986123, 16870550, 30046704, 31605304, 32394456, 24385719, 23406206, 18036186, 23216583, 32998182, 19630771, 34426522, 30792900, 29924855, 34758185, 34708896, 37163579, 20345715, 11583318, 38762018, 38968155) - |
not provided, no classification provided | literature only | Academic Unit of Haematology, University of Sheffield | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Mar 20, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 23, 2022 | The p.Ser1731Thr variant in VWF has been reported in at least 3 individuals with clinical features of Von Willebrand disease and 1 homozygous individual with Glanzmann thrombasthenia, and segregated with disease in 2 affected relatives from 2 families. However, it was also identified in 1 individual with an alternate molecular cause of disease and 4 asymptomatic relatives (Ribba 2001 PMID: 11583318, Riddell 2009 PMID: 19687512, Veyradier 2016 PMID: 26986123, Owaidah 2019 PMID: 30792900, Al-Doory 2020). This variant has been identified in 2.1% (217/10370) of Ashkenazi Jewish chromosomes and 0.11% (136/129190) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org) and is reported in ClinVar (Variation ID: 100420). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In vitro functional studies provide some evidence that the p.Ser1731Thr variant may have a partial impact to protein function (Flood 2009 PMID: 20345715, Riddell 2009 PMID: 19687512, Flood 2015 PMID: 25662333); however, these in vitro results may not be biologically relevant. In summary, while the clinical significance of this variant is uncertain, its frequency suggests that it is more likely to be benign. ACMG/AMP Criteria applied: PS3_Supporting, BS1. - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | VWF: PS3:Supporting, BS1 - |
not specified Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 18, 2021 | DNA sequence analysis of the VWF gene demonstrated a sequence change, c.5191T>A, in exon 30 that results in an amino acid change, p.Ser1731Thr. This sequence change has been described in the gnomAD database with a frequency of 2.1% in Ashkenazi Jewish subpopulation (dbSNP rs61750603). This sequence change has been previously described in the heterozygous states in individuals and families with von Willebrand disease (PMIDs: 11583318, 26986123, 19687512, 28971901). The p.Ser1731Thr change affects a highly conserved amino acid residue located in the A3 domain of the VWF protein. Functional studies show p.Ser1731Thr disrupts the binding of VWF to collagen (PMIDs: 11583318, 19687512, 20345715). Due to the lack of sufficient evidence, the clinical significance of the p.Ser1731Thr change remains unknown at this time. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Sep 16, 2024 | Variant summary: VWF c.5191T>A (p.Ser1731Thr) results in a conservative amino acid change located in the third VWF type A (A3) domain (IPR002035), which is the main binding site for collagens type I and III (UniProt) 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 0.0012 in 1614210 control chromosomes in the gnomAD database, including 5 homozygotes. However, in certain subpopulations, e.g. in the Ashkenazi Jewish the variant was found at a much higher allele frequency. The observed relatively high frequency, together with the homozygous occurrences, might indicate a benign nature for the variant, or alternatively the variant might represent a hypomorphic allele associated with a milder phenotype / reduced penetrance.The variant, c.5191T>A, has been reported in the literature in multiple heterozygous individuals affected with Von Willebrand Disease (e.g. Ribba_2001, Riddell_2009, Veyradier_2016, Borras_2017, Maas_2022), and in a homozygous individual with Glanzmann thrombasthenia (Owaidah 2019). However, in at least one family the variant was also observed in asymptomatic younger family members (Riddell_2009), although they also displayed the biochemical phenotype (i.e. decresed VWF binding to type I collagen; see below). Furthermore, in one of these reported cases a co-occurring pathogenic variant could explain the phenotype (Borras_2017). Several publications reported experimental evidence evaluating an impact on protein function, and in general demonstrated reduced binding to collagen type I, with mostly unaffected binding to collagen type III (e.g. Ribba_2001, Riddell_2009, Flood_2010, Shida_2014, Posch_2018). This finding was confirmed by utilizing a knock-in mouse model (Shida_2014), however authors of the study concluded that mice were still able to initiate platelet adhesion and thrombus formation in their model, demonstrating an important role for collagen-independent pathway(s) of primary hemostasis that likely contribute to the mild bleeding phenotype in patients with VWF collagen-binding mutations. The following publications have been ascertained in the context of this evaluation (PMID: 11583318, 19687512, 26986123, 28971901, 30792900, 20345715, 25051961, 29604837, 34758185, 34708896). ClinVar contains an entry for this variant (Variation ID: 100420). Based on the evidence outlined above, the variant was classified as uncertain significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Feb 06, 2024 | - - |
VWF-related disorder Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 23, 2024 | The VWF c.5191T>A variant is predicted to result in the amino acid substitution p.Ser1731Thr. This variant has been reported previously to reduce binding between VWF protein and different collagen types (including collagen I and III) and has been reported, with variable expressivity, in several patients with von Willebrand Disease (Ribba et al. 2001. PubMed ID: 11583318; Flood et al. 2010. PubMed ID: 20345715; Riddell et al. 2009. PubMed ID: 19687512; Veyradier et al. 2016. PubMed ID: 26986123, see figure 6). However, several unaffected family members, who displayed only mildly altered biochemical findings, also harbored this variant, suggesting incomplete penetrance (see, for example, Riddell et al. 2009. PubMed ID: 19687512). This variant was also reported in the homozygous state in an individual with suspected Glanzmann thrombasthenia (Owaidah et al. 2019. PubMed ID: 30792900). This variant is reported in 2.1% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. A different missense change impacting the same amino acid (p.Ser1731Leu) was reported in two siblings with significantly reduced values for von Willebrand factor collagen-binding activity (Fels et al. 2022. PubMed ID: 35104900). Taken together, the VWF c.5191T>A (p.Ser1731Thr) variant is interpreted as likely pathogenic with reduced penetrance and variable expressivity. - |
Hereditary von Willebrand disease Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | The c.5191T>A (p.Ser1731Thr) variant has been reported in three studies in which it is found in at least four patients in a heterozygous state (Ribba et al. 2001, Riddell et al. 2009, Veyradier et al. 2016). Control data are unavailable for this variant, which is reported at a frequency of 0.00205 in the European (Non-Finnish) population from the Exome Sequencing Project. This frequency is high in comparison to disease prevalence, but may be explained by a milder phenotype or reduced penetrance. Functional studies including expression of the variant in COS-7 cells demonstrated significantly decreased binding of the variant protein to collagen. Analysis in HEK293T cells showed the p.Ser1731Thr variant affects binding to collagen type I but not type III. Additional functional studies utilizing mouse models, HEK293T cell constructs, flow chamber analysis, and collagen thin films in flow assays support normal expression but reduced collagen binding of the p.Ser1731Thr variant (Flood et al. 2010; Shida et al. 2014; Hansen et al. 2011). Based on the limited number of cases but with supporting functional data, the p.Ser1731Thr variant is classified as a variant of unknown significance but suspicious for pathogenicity for von Willebrand disease. - |
von Willebrand disease type 2 Benign:1
Benign, no assertion criteria provided | clinical testing | Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico | Apr 26, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at