PB0833 - VWF Expression Mostly Confirms Genetic Prediction Algorithms in Type 1 VWD Variants

Background: Decreased level or abnormal function of von Willebrand factor (VWF) causes von Willebrand disease (VWD). Variants in the VWF gene are often identified in VWD patients and may or may not be causative.

Aims: To correlate pathogenicity of VWF variants predicted by in silico methods to variant VWF expression studies.

Methods: Nineteen variants identified in type 1 VWD patients were expressed in HEK293T cells and VWF:Ag, VWF:GPIbM, VWF:CBIII and VWF multimers analyzed on the expressed recombinant VWF. Pathogenicity of variants was predicted using popular in silico tools: Combined Annotation Dependent Depletion (CADD), Sorting Intolerant From Tolerant (SIFT), Polymorphism Phenotyping v2 (PolyPhen-2) and Mutation Taster. To assess the frequency of the variant in population databases and obtain control allele frequencies (Popmax AF), ANNOVAR annotations of the Genome Aggregation Database (gnomAD) was utilized.

Results: All of the variants analyzed were rare (Popmax AF 0.0000234-0.0006) or not present (-) in gnomAD. Variants p.M947V, p.R1763Q, p.T2282I, and p.A2569E were predicted to be benign, consistent with the observed normal expression studies. Stop codon variants p.W199X, p.Q1353X and p.E1660X were automatically assigned to be disease causing, also consistent with expression study results. Variants p.V86M, p.C524Y, p.R960P, p.G994D, p.C996W, p.C2199Y, p,Q2256H, p.C2693F, p.C2701Y and p.C2754Y were predicted to be deleterious and likely disease causing. Abnormal expression study data confirm the deleterious nature of these variants, except for variants p.V86M and p.Q2256H that had normal expression studies. Variants p.R1204W (predicted as possibly damaging) and p.P2524L(predicted as benign) had normal expression studies, indicating no deleterious effect.

Conclusion(s): Predicted pathogenicity by population frequency and prediction tools, correlated well with expression studies for ~80% of the VWF variants, although expression studies do not take into account VWF clearance or other potential functional defects.