Algorithmic Assessment of Missense Mutation Severity in the Von-Hippel Lindau Protein

Abstract

21Von Hippel-Lindau disease (VHL) is an autosomal dominant rare disease that causes the 22 formation of angiogenic tumors. When functional, pVHL acts as an E3 ubiquitin ligase that 23 negatively regulates hypoxia inducible factor (HIF). Genetic mutations that perturb the structure 24 of pVHL result in dysregulation of HIF, causing a wide array of tumor pathologies including 25 retinal angioma, pheochromocytoma, central nervous system hemangioblastoma, and clear cell 26 renal carcinoma. These VHL-related cancers occur throughout the lifetime of the patient, 27 requiring frequent intervention procedures, such as surgery, to remove the tumors. Although 28 VHL is classified as a rare disease (1 in 39,000 to 1 in 91,000 affected) there is a large 29 heterogeneity in genetic mutations listed for observed pathologies. Understanding how these 30 specific mutations correlate with the myriad of observed pathologies for VHL could provide 31 clinicians insight into the potential severity and onset of disease. Using a set of 285 ClinVar 32 mutations in VHL, we developed a multiparametric scoring algorithm to evaluate the overall 33 clinical severity of missense mutations in pVHL. The mutations were assessed according to eight 34 weighted parameters as a comprehensive evaluation of protein misfolding and malfunction.35 Higher mutation scores were strongly associated with pathogenicity. Our approach establishes a 36 novel in silico method by which VHL-specific mutations can be assessed for their severity and 37 effect on the biophysical functions of the VHL protein. 38 Introduction 39 Von Hippel-Lindau (VHL) disease is an autosomal-dominant hereditary disease 40 associated with the development of multiple angiogenic tumor types. This includes clear cell 41 renal carcinoma (ccRCC), retinal angioma (RA), central nervous system hemangioblastoma 42 (CHB), and pheochromocytoma (PCC)(1,2). The presence or absence of PCC divides VHL 3 43 disease into type 1 or type 2. Type 2 VHL is further subdivided into three subtypes depending on 44 the appearance of other cancers: type 2A, PCCs but no ccRCCs, type 2B, PCCs and ccRCCs, or 45 type 2C, PCCs only(1). While this allows for some preliminary genotype-phenotype 46 associations, a patient's association with a specific subtype alternates as different cancers arise 47 throughout their lifetime(1). 48 Patients with VHL disease have a single mutation in one allele of the VHL gene(3). Upon 49 spontaneous inactivation of the second allele, tumor development can initiate, making the loss of 50 heterozygosity (LOH) a crucial step in the development of VHL disease(1,4,5). The VHL gene 51 encodes two protein products, both of which exhibit equivalent activity: the 30kDa isoform 52 (pVHL 30 ) and the more common 19kDa isoform (pVHL 19 ) found in most tissues (6,7). pVHL 53 forms a complex with elongin B (EloB) and elongin C (EloC) for the VCB complex(8-10). This 54 stabilizes EloB, EloC, and pVHL, making them resistant to proteosomal degradation; however, 55 upon mutation of pVHL, contacts with EloB ...