In-silico Analysis of NF1 Missense Variants in ClinVar: Translating Variant Predictions into Variant Interpretation and Classification

Abstract

Background: With the advent of next-generation sequencing in genetic testing, predicting the pathogenicity of missense variants represents a major challenge potentially leading to misdiagnoses in the clinical setting. In neurofibromatosis type 1 (NF1), where clinical criteria for diagnosis may not be fully present until late infancy, correct assessment of variant pathogenicity is fundamental for appropriate patients’ management. Methods: Here, we analyzed three different computational methods, VEST3, REVEL and ClinPred, and after extracting predictions scores for 1585 NF1 missense variants listed in ClinVar, evaluated their performances and the score distribution throughout the neurofibromin protein. Results: For all the three methods, no significant differences were present between the scores of “likely benign”, “benign”, and “likely pathogenic”, “pathogenic” variants that were consequently collapsed into a single category. The cutoff values for pathogenicity were significantly different for the three methods and among benign and pathogenic variants for all methods. After training five different models with a subset of benign and pathogenic variants, we could reclassify variants in three sharply separated categories. Conclusions: The recently developed metapredictors, which integrate information from multiple components, after gene-specific fine-tuning, could represent useful tools for variant interpretation, particularly in genetic diseases where a clinical diagnosis can be difficult.

Clinical presentation and genetic analyses of neurofibromatosis type 1 in independent patients with monoallelic double de novo closely spaced mutations in the NF1 gene

“…Furthermore, it is not present in gnomAD (ACMG_AMP rule PM2), and is predicted to be pathogenic by 9 of 12 variant predictions (ACMG/AMP rule PP3). Also, the c.2548G>A variant had scores equal to or above the cutoff values for pathogenicity, as previously defined (Accetturo et al, 2020), for 5/5 of cutoff performance indicators (ClinPred), and for 3/5 (REVEL and VEST4).…”

“…NF1 pathogenic variants (PVs) can occur across the entire coding region and include virtually the full range of various types from multiexons deletion/duplication, including whole gene deletions, to missense mutations (Messiaen, 2020). In addition, most missense variants are still classified as variants of uncertain clinical significance (VUS), and little has been reported on the correlation between variants’ position and their pathogenic effects (Accetturo et al, 2020; Koczkowska et al, 2020, 2018).…”

Prevalence of Germline Variants in a Large Cohort of Japanese Patients with Pheochromocytoma and/or Paraganglioma

“…Recently, several in silico meta-prediction tools have been developed based on the analysis of multiple individual scores. Among them, Rare Exome Variant Ensemble Learner (REVEL) has been confirmed to be an excellent predictive tool for assessing the pathogenicity of missense variants [42][43][44]. We used this reliable in silico tool and the latest disease and population databases to facilitate the identification of disease-causing variants.…”

Identification of Germinal Neurofibromin Hotspots

“…This suggests that mutations that fall into areas of greater structural disorder in neurofibromin must have a greater functional impact on the protein (such as frame shifts vs missense mutations) for a clinical phenotype to occur. This relationship could be interesting in the categorization of variants of uncertain meaning considering the structural region and its protein impact [ 58 ]. However, more deep studies based in broad groups of genes must be done to corroborate this relationship.…”