Example data included in the package containing MAVE-derived functional scores and class labels for missense variants in BRCA1 and TP53. Functional scores are from high-throughput assays (Findlay et al., 2018; Giacomelli et al., 2018), and class labels are P/LP and B/LB from ClinVar.
data(variant_data)A dataframe with 459 observations and 4 variables:
Gene symbol in which the variant occurs (e.g., BRCA1).
Missense variant, represented in single-letter amino acid
notation (e.g., L3F).
Binary class label indicating pathogenicity:
P: Pathogenic
B: Benign
Functional assay score, typically representing the degree of functional disruption (numeric).
Giacomelli et al., 2018. Mutational processes shape the landscape of TP53 mutations in human cancer. Nature Genetics, 50(10), 1381–1387. tools:::Rd_expr_doi("10.1038/s41588-018-0204-y")
Findlay et al., 2018. Accurate classification of BRCA1 variants with saturation genome editing. Nature, 562(7726), 217–222. tools:::Rd_expr_doi("10.1038/s41586-018-0461-z")
Landrum et al., 2020. ClinVar: improvements to accessing data. Nucleic Acids Research, 48(D1), D835–D844. tools:::Rd_expr_doi("10.1093/nar/gkz972")