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
1JM7 2001-10-03 Solution structure of the BRCA1/BARD1 RING-domain heterodimer
1OQA 2004-06-15 Solution structure of the BRCT-c domain from human BRCA1
4IGK 2013-10-30 1.75 Structure of human BRCA1 BRCT in complex with ATRIP peptide
1T15 2004-05-11 1.85 Crystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase
4IFI 2013-10-30 2.2 Structure of human BRCA1 BRCT in complex with BAAT peptide
1T29 2004-05-11 2.3 Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide
3PXB 2011-04-20 2.5 Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: T1700A
4Y2G 2016-01-27 2.5 Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide
1JNX 2001-09-21 2.5 Crystal structure of the BRCT repeat region from the breast cancer associated protein, BRCA1
1Y98 2005-08-30 2.5 Structure of the BRCT repeats of BRCA1 bound to a CtIP phosphopeptide.
3PXA 2011-04-20 2.55 Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: G1656D
3K0H 2010-03-02 2.7 The crystal structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with an amidated C-terminus
3K0K 2010-03-02 2.7 Crystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus.
3PXC 2011-04-20 2.8 Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1699Q
1T2U 2004-05-11 2.8 Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1: structure of BRCA1 missense variant V1809F
3PXD 2011-04-20 2.8 Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1835P
1N5O 2002-12-25 2.8 Structural consequences of a cancer-causing BRCA1-BRCT missense mutation
3K15 2010-03-02 2.8 Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with an amidated C-terminus
3PXE 2011-04-20 2.85 Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K
3K16 2010-03-02 3.0 Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus
4OFB 2015-04-15 3.05 Crystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor
3COJ 2008-05-27 3.21 Crystal Structure of the BRCT Domains of Human BRCA1 in Complex with a Phosphorylated Peptide from Human Acetyl-CoA Carboxylase 1
1T2V 2004-05-11 3.3 Structural basis of phospho-peptide recognition by the BRCT domain of BRCA1, structure with phosphopeptide
4Y18 2016-01-27 3.5 Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide
4JLU 2014-09-10 3.5 Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas
4U4A 2015-08-26 3.51 Complex Structure of BRCA1 BRCT with singly phospho Abraxas
2ING 2007-09-04 3.6 X-ray Structure of the BRCA1 BRCT mutant M1775K
6G2I 2018-06-13 5.9 Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) at 5.9 A resolution

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