Interpreting variants of uncertain significance (VUS) is a central challenge in medical genetics. One approach is to experimentally measure the functional consequences of VUS, but to date this approach has been post hoc and low throughput. Here we use massively parallel assays to measure the effects of nearly 2000 missense substitutions in the RING domain of BRCA1 on its E3 ubiquitin ligase activity and its binding to the BARD1 RING domain. From the resulting scores, we generate a model to predict the capacities of full-length BRCA1 variants to support homology-directed DNA repair, the essential role of BRCA1 in tumor suppression, and show that it outperforms widely used biological-effect prediction algorithms. We envision that massively parallel functional assays may facilitate the prospective interpretation of variants observed in clinical sequencing.
Submitter: Shu-Ching Ou
Submission Date: July 19, 2018, 4:56 p.m.
|Number of data points||8367|
|Proteins||Breast cancer type 1 susceptibility protein|
|Assays/Quantities/Protocols||Experimental Assay: Yeast-Two-Hybrid (Y2H) selection ; Experimental Assay: E3 ligase activity ; Computational Protocol: Homology-Directed DNA Rescue (HDR) score prediction|
|Libraries||Normalized HDR Prediction ; Normalized E3 functional score ; Normalized BARD1 binding functional score|
|Percent Identity||Matching Chains||Protein||Accession||Entry Name|
|100.0||Breast cancer type 1 susceptibility protein||P38398||BRCA1_HUMAN|
|98.5||Breast cancer type 1 susceptibility protein||Q9GKK8||BRCA1_PANTR|
|98.1||Breast cancer type 1 susceptibility protein||Q6J6I8||BRCA1_GORGO|
|96.9||Breast cancer type 1 susceptibility protein||Q6J6J0||BRCA1_PONPY|
|93.0||Breast cancer type 1 susceptibility protein||Q6J6I9||BRCA1_MACMU|