Massively Parallel Functional Analysis of BRCA1 RING Domain Variants.


Abstract

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.

Submission Details

ID: BZrWSn9q

Submitter: Shu-Ching Ou

Submission Date: July 19, 2018, 4:56 p.m.

Version: 1

Publication Details
Starita LM;Young DL;Islam M;Kitzman JO;Gullingsrud J;Hause RJ;Fowler DM;Parvin JD;Shendure J;Fields S,Genetics (2015) Massively Parallel Functional Analysis of BRCA1 RING Domain Variants. PMID:25823446
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
3PXC 2010-12-09T00:00:00+0000 2.8 Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1699Q
3PXB 2010-12-09T00:00:00+0000 2.5 Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: T1700A
3PXA 2010-12-09T00:00:00+0000 2.55 Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: G1656D
3PXD 2010-12-09T00:00:00+0000 2.8 Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1835P
3PXE 2010-12-09T00:00:00+0000 2.85 Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K
4Y18 2015-02-06T00:00:00+0000 3.5 Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide
7LYB 2021-03-06T00:00:00+0000 3.28 Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c
4Y2G 2015-02-09T00:00:00+0000 2.5 Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide
1N5O 2002-11-06T00:00:00+0000 2.8 Structural consequences of a cancer-causing BRCA1-BRCT missense mutation
4IFI 2012-12-14T00:00:00+0000 2.2 Structure of human BRCA1 BRCT in complex with BAAT peptide

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
93.0 Breast cancer type 1 susceptibility protein Q6J6I9 BRCA1_MACMU
96.9 Breast cancer type 1 susceptibility protein Q6J6J0 BRCA1_PONPY
98.1 Breast cancer type 1 susceptibility protein Q6J6I8 BRCA1_GORGO
98.5 Breast cancer type 1 susceptibility protein Q9GKK8 BRCA1_PANTR
100.0 Breast cancer type 1 susceptibility protein P38398 BRCA1_HUMAN