rs61750081
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1PP2PP3_ModeratePP5_Very_Strong
The NM_000552.5(VWF):c.4247T>C(p.Ile1416Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,672 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_000552.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251152Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135736
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461672Hom.: 0 Cov.: 99 AF XY: 0.00000413 AC XY: 3AN XY: 727146
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not provided Pathogenic:3
PP1_strong, PP5, PM2, PS3, PS4_moderate -
The VWF c.4247T>C; p.Ile1416Thr variant (rs61750081, ClinVar Variation ID: 439338) is reported in the literature in multiple individuals affected with VWF type 2M and shown to segregate with disease (McKinnon 2012, Starke 2013). This variant is only found on one allele in the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.724). In support of these predictions, functional analyses show the variant has an impact on the normal protein function (McKinnon 2012, Starke 2013). Based on available information, this variant is considered to be pathogenic. References: McKinnon TA et al. Characterisation of von Willebrand factor A1 domain mutants I1416N and I1416T: correlation of clinical phenotype with flow-based platelet adhesion. J Thromb Haemost. 2012 Jul;10(7):1409-16. PMID: 22537243. Starke RD et al. Cellular and molecular basis of von Willebrand disease: studies on blood outgrowth endothelial cells. Blood. 2013 Apr 4;121(14):2773-84. PMID: 23355534. -
The VWF c.4247T>C (p.Ile1416Thr) variant has been reported in the published literature in families with Type 2M von Willebrand disease (vWD) (PMID: 22537243 (2012), 23355534 (2013)). Published functional studies show that this variant significantly reduced glycoproteinIb (GPIb) binding (PMID: 22537243 (2012), 23355534 (2013)). The frequency of this variant in the general population, 0.000004 (1/251152 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Based on the available information, this variant is classified as pathogenic. -
Hereditary von Willebrand disease Pathogenic:2
Variant summary: VWF c.4247T>C (p.Ile1416Thr) results in a non-conservative amino acid change located in the type A1 domain (IPR002035), affecting the binding site for platelet glycoprotein Ib (amino acids 1277 -1453; UniProt) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 251152 control chromosomes (gnomAD). c.4247T>C has been reported in the literature in multiple individuals in a family, who were affected with Von Willebrand Disease (McKinnon_2012). These data indicate that the variant is very likely to be associated with disease. This publication also reported experimental evidence evaluating an impact on protein function, and demonstrated significantly reduced glycoprotein Ib binding (McKinnon_2012). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 , and both of them classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
The VWF c.4247T>C (p.Ile1416Thr) variant is a missense variant that has been reported in two studies, in which it is found in a heterozygous state in 11 individuals from two families with von Willebrand disease type 2 (McKinnon et al. 2012; Starke et al. 2013). The large family reported in McKinnon et al. (2012) includes nine affected individuals across three generations. The p.Ile1416Thr variant was absent from nine control subjects. It is reported at a frequency of 0.000009 in the European (non-Finnish) population of the Genome Aggregation Database though this is based on one allele in a region of good sequence coverage so the variant is presumed to be rare. The variant is in the A1 domain of the protein, and transient transfection in HEK293T cells reduced expression by ~40% and significantly reduced GPIb-a (McKinnon et al. 2012). Another pathogenic variant, p.Ile1416Asn, is located at the same amino acid residue (McKinnon et al. 2012). Based on the collective evidence and application of the ACMG criteria, the p.Ile1416Thr variant is classified as pathogenic for von Willebrand disease. -
von Willebrand disease type 2 Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at