Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

No abstract is available for this paper.

• Publication year

  2015

• Venue

  Genetics

• Publication date

  2015-03-30

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1534/genetics.115.175802PMID 25823446PMCID PMC4492368
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

  2017cited by this paper
• Functional Assays for Analysis of Variants of Uncertain Significance in BRCA2

  2014influential reference
• Multifactorial Likelihood Assessment of BRCA1 and BRCA2 Missense Variants Confirms That BRCA1:c.122A>G(p.His41Arg) Is a Pathogenic Mutation

  2014cited by this paper
• Massively Parallel Single Amino Acid Mutagenesis

  2014influential reference
• Deep mutational scanning: a new style of protein science

  2014cited by this paper
• A general framework for estimating the relative pathogenicity of human genetic variants

  2014cited by this paper
• Analysis of BRCA1 Variants in Double‐Strand Break Repair by Homologous Recombination and Single‐Strand Annealing

  2013influential reference
• Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein

  2013influential reference
• Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis

  2013influential reference
• A high-throughput functional complementation assay for classification of BRCA1 missense variants.

  2013cited by this paper
• A review of a multifactorial probability‐based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS)

  2012cited by this paper
• Massively parallel functional dissection of mammalian enhancers in vivo

  2012cited by this paper
• A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

  2012cited by this paper
• BRCA1 RING function is essential for tumor suppression but dispensable for therapy resistance.

  2011cited by this paper
• BRCA1 R71K missense mutation contributes to cancer predisposition by increasing alternative transcript levels

  2011cited by this paper
• BRCA1 Tumor Suppression Depends on BRCT Phosphoprotein Binding, But Not Its E3 Ligase Activity

  2011influential reference
• Enrich: software for analysis of protein function by enrichment and depletion of variants

  2011influential reference
• High Resolution Mapping of Protein Sequence–Function Relationships

  2010cited by this paper
• HERC2 is an E3 ligase that targets BRCA1 for degradation.

  2010cited by this paper
• On Over-fitting in Model Selection and Subsequent Selection Bias in Performance Evaluation

  2010cited by this paper
• Identification of breast tumor mutations in BRCA1 that abolish its function in homologous DNA recombination.

  2010influential reference
• COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

  2010cited by this paper
• A method and server for predicting damaging missense mutations

  2010cited by this paper
• Characterization of BRCA1 ring finger variants of uncertain significance

  2010cited by this paper
• Parallel, tag-directed assembly of locally derived short sequence reads

  2010cited by this paper
• Clinically applicable models to characterize BRCA1 and BRCA2 variants of uncertain significance.

  2008cited by this paper
• Building Predictive Models in R Using the caret Package

  2008cited by this paper
• E3 ligase activity of BRCA1 is not essential for mammalian cell viability or homology-directed repair of double-strand DNA breaks

  2008influential reference
• A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes.

  2007cited by this paper
• E2–BRCA1 RING interactions dictate synthesis of mono- or specific polyubiquitin chain linkages

  2007cited by this paper
• Genetic analysis of BRCA1 ubiquitin ligase activity and its relationship to breast cancer susceptibility.

  2006influential reference
• Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral

  2005influential reference
• Distribution and intensity of constraint in mammalian genomic sequence.

  2005cited by this paper
• Binding and recognition in the assembly of an active BRCA1/BARD1 ubiquitin-ligase complex

  2003influential reference
• SIFT: predicting amino acid changes that affect protein function

  2003cited by this paper
• Redistribution of BRCA1 among Four Different Protein Complexes following Replication Blockage*

  2001cited by this paper
• Structure of a BRCA1–BARD1 heterodimeric RING–RING complex

  2001influential reference
• The R71G BRCA1 is a founder Spanish mutation and leads to aberrant splicing of the transcript

  2001influential reference
• Ku DNA end-binding protein modulates homologous repair of double-strand breaks in mammalian cells.

  2001cited by this paper
• The RING Heterodimer BRCA1-BARD1 Is a Ubiquitin Ligase Inactivated by a Breast Cancer-derived Mutation*

  2001cited by this paper
• Preparation and analysis of the common urinary forms of human chorionic gonadotropin.

  2000cited by this paper
• High-throughput screening for protein-protein interactions using two-hybrid assay.

  2000cited by this paper
• Brca1 controls homology-directed DNA repair.

  1999influential reference
• Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast.

  1996influential reference
• Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds.

  1995cited by this paper
• A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1.

  1994cited by this paper
• Amino Acid Difference Formula to Help Explain Protein Evolution

  1974cited by this paper

• New methods drive new biology

  2026cites this paper
• Higher Throughput Assays for Understanding the Pathogenicity of Variants of Unknown Significance in the RPE65 Gene

  2025cites this paper
• Predicting the structure-altering mechanisms of disease variants.

  2025cites this paper
• DTreePred: an online viewer based on machine learning for pathogenicity prediction of genomic variants

  2025cites this paper
• Functional characterization of BRCA1 variants of unknown significance using homologous recombination repair assays

  2025cites this paper
• Deep Mutational Scanning in Immunology: Techniques and Applications

  2025cites this paper
• A comprehensive map of missense trafficking variants in rhodopsin and their response to pharmacologic correction

  2025cites this paper
• MMRT: MultiMut Recursive Tree for predicting functional effects of high-order protein variants from low-order variants

  2025cites this paper
• Higher throughput assays for understanding the pathogenicity of variants of unknown significance (VUS) in the RPE65 gene

  2025cites this paper
• Variant scoring tools for deep mutational scanning

  2025cites this paper
• Characterizing Variants of Uncertain Drug Resistance (VUDRs) Using Quantitative Measurements at Clinical Exposures

  2025cites this paper
• The functional landscape of coding variation in the familial hypercholesterolemia gene LDLR.

  2025cites this paper
• BRCA1 and BRCA2 in DNA damage and replication stress response: Insights into their functions, mechanisms, and implications for cancer treatment.

  2025cites this paper
• Deep Evolutionary Fitness Inference for Variant Nomination from Directed Evolution

  2025cites this paper
• Advancing protein evolution with inverse folding models integrating structural and evolutionary constraints.

  2025cites this paper
• HSP90 buffers deleterious genetic variations in BRCA1.

  2025cites this paper
• Ultrahigh-Throughput Multiplexed Screening of Purified Protein from Cell-Free Expression Using Droplet Microfluidics.

  2025cites this paper
• Multiplexed assays of variant effect for clinical variant interpretation

  2025cites this paper
• Optimal sequencing depth for measuring the concentrations of molecular barcodes

  2025cites this paper
• popDMS infers mutation effects from deep mutational scanning data

  2024cites this paper
• popDMS infers mutation effects from deep mutational scanning data

  2024cites this paper
• Interface-guided phenotyping of coding variants in the transcription factor RUNX1

  2024cites this paper
• Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression

  2024cites this paper
• Protein-folding chaperones predict structure-function relationships and cancer risk in BRCA1 mutation carriers

  2024cites this paper
• Predicting functionally important breast cancer SNPs using pleiotropy, conservation, and protein structure

  2024cites this paper
• Deep neural networks for predicting the affinity landscape of protein-protein interactions

  2024cites this paper
• Scalable approaches for generating, validating and incorporating data from high-throughput functional assays to improve clinical variant classification

  2024cites this paper
• Functional effects of mutations in proteins can be predicted and interpreted by guided selection of sequence covariation information

  2024cites this paper
• Deciphering the impact of genomic variation on function

  2024cites this paper
• Functional assessment of protein variants in structured domains by fluorescence cross-correlation spectroscopy

  2024influential citation
• Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort

  2024cites this paper
• PHACTboost: A Phylogeny-Aware Pathogenicity Predictor for Missense Mutations via Boosting

  2024cites this paper
• Are Next-Generation Pathogenicity Predictors Applicable to Cancer?

  2024cites this paper
• Are the Next-Generation Pathogenicity Predictors Applicable to Cancer?

  2024cites this paper
• Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation

  2023cites this paper
• Optimization of a deep mutational scanning workflow to improve quantification of mutation effects on protein–protein interactions

  2023cites this paper
• The Impact of Genomic Variation on Function (IGVF) Consortium

  2023cites this paper
• Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data

  2023cites this paper
• Mutational scanning pinpoints distinct binding sites of key ATGL regulators in lipolysis

  2023cites this paper
• Inference of annealed protein fitness landscapes with AnnealDCA

  2023cites this paper
• Refinement of the assignment to the ACMG/AMP BS3 and PS3 criteria of eight BRCA1 variants of uncertain significance by integrating available functional data with protein interaction assays

  2023cites this paper
• The landscape of tolerated genetic variation in humans and primates.

  2023cites this paper
• The landscape of tolerated genetic variation in humans and primates

  2023cites this paper
• Integrated multiplexed assays of variant effect reveal cis-regulatory determinants of catechol-O-methyltransferase gene expression

  2023cites this paper
• ACIDES: on-line monitoring of forward genetic screens for protein engineering

  2023cites this paper
• Identifying Promising Sequences For Protein Engineering Using A Deep Transformer Protein Language Model

  2023cites this paper
• Deep mutational scanning of proteins in mammalian cells

  2023cites this paper
• Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage

  2023cites this paper
• Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data

  2023cites this paper
• Multiplexed assay of variant effect reveals residues of functional importance in the BRCA1 coiled-coil and serine cluster domains

  2023cites this paper
• Mutational fitness landscape and drug resistance.

  2023cites this paper
• Quantitative determination of SLC2A1 variant functional effects in GLUT1 deficiency syndrome

  2023cites this paper
• Deep mutational scanning: A versatile tool in systematically mapping genotypes to phenotypes

  2023cites this paper
• Accurate prediction of functional effect of single amino acid variants with deep learning

  2023cites this paper
• Minimal epistatic networks from integrated sequence and mutational protein data

  2023cites this paper
• DNA repair function scores for 2172 variants in the BRCA1 amino-terminus

  2023cites this paper
• Finding significance: New perspectives in variant classification of the RAD51 regulators, BRCA2 and beyond.

  2023cites this paper
• Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS

  2023cites this paper
• Crucial roles of the BRCA1-BARD1 E3 ubiquitin ligase activity in homology-directed DNA repair.

  2023cites this paper
• DNA Repair Function Scores for 2172 Variants in the BRCA1 Amino-Terminus

  2023cites this paper
• Protein-Folding Chaperones Predict Structure-Function Relationships and Cancer Risk in BRCA1 Mutation Carriers

  2023cites this paper
• Functional Analyses of Rare Germline Missense BRCA1 Variants Located within and outside Protein Domains with Known Functions

  2023cites this paper
• BRCA1/2 variants of unknown significance in hereditary breast and ovarian cancer (HBOC) syndrome: looking for the hidden meaning.

  2022cites this paper
• Current and Future Approaches to Classify VUSs in LGMD-Related Genes

  2022cites this paper
• The functional impact of BRCA1 BRCT domain variants using multiplexed DNA double-strand break repair assays.

  2022cites this paper
• Predicting the pathogenicity of missense variants using features derived from AlphaFold2

  2022influential citation
• Missense variant interaction scanning reveals a critical role of the FERM domain for tumor suppressor protein NF2 conformation and function

  2022cites this paper
• Intragenic compensation through the lens of deep mutational scanning

  2022influential citation
• Infer global, predict local: quantity-quality trade-off in protein fitness predictions from sequence data

  2022cites this paper
• Scalable Functional Assays for the Interpretation of Human Genetic Variation.

  2022cites this paper
• Interpreting protein variant effects with computational predictors and deep mutational scanning

  2022cites this paper
• Differential requirement for BRCA1-BARD1 E3 ubiquitin ligase activity in DNA damage repair and meiosis in the Caenorhabditis elegans germ line

  2022cites this paper
• Comprehensive evaluation and efficient classification of BRCA1 RING domain missense substitutions.

  2022cites this paper
• Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants

  2022cites this paper
• satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect

  2022cites this paper
• mutscan—a flexible R package for efficient end-to-end analysis of multiplexed assays of variant effect data

  2022cites this paper
• Defining the Sensitivity Landscape of EGFR Variants to Tyrosine Kinase Inhibitors.

  2022cites this paper
• Updated benchmarking of variant effect predictors using deep mutational scanning

  2022cites this paper
• D R A F T In-silico monitoring of directed evolution convergence to unveil best performing variants with credibility score

  2022cites this paper
• Integration of Protein Structure and Population-Scale DNA Sequence Data for Disease Gene Discovery and Variant Interpretation.

  2022cites this paper
• Decoding the cellular effects of genetic variation through interaction proteomics.

  2021cites this paper
• BRCA1/ATF1-Mediated Transactivation is Involved in Resistance to PARP Inhibitors and Cisplatin

  2021cites this paper
• ELASPIC2 (EL2): Combining contextualized language models and graph neural networks to predict effects of mutations.

  2021cites this paper
• PacRAT: A program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment

  2021cites this paper
• Insulin’s Discovery: New Insights on Its Hundredth Birthday: From Insulin Action and Clearance to Sweet Networks

  2021influential citation
• Interpretable pairwise distillations for generative protein sequence models

  2021cites this paper
• Integrating thousands of PTEN variant activity and abundance measurements reveals variant subgroups and new dominant negatives in cancers

  2021cites this paper
• Maintenance of Genetic Information in the First Ribocell

  2021cites this paper
• The BRCA1/BARD1 ubiquitin ligase and its substrates.

  2021cites this paper
• Personalized Medicine Through GPCR Pharmacogenomics

  2021cites this paper
• Improving sequence-based modeling of protein families using secondary-structure quality assessment

  2021cites this paper
• Aktualisierte Kriterien des Deutschen Konsortiums Familiärer Brust- und Eierstockkrebs zur Klassifizierung von Keimbahn-Sequenzvarianten in Risikogenen für familiären Brust- und Eierstockkrebs

  2021cites this paper
• Improved pathogenicity prediction for rare human missense variants

  2021cites this paper
• AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape

  2021cites this paper
• Defining the Sensitivity Landscape of 74,389 EGFR Variants to Tyrosine Kinase Inhibitors

  2021cites this paper
• The Use of Whole Genome and Exome Sequencing for Newborn Screening: Challenges and Opportunities for Population Health

  2021cites this paper
• Massively parallel DNA target capture using long adapter single stranded oligonucleotide (LASSO) probes assembled through a novel DNA recombinase mediated methodology

  2021cites this paper
• Predicting and interpreting large scale mutagenesis data using analyses of protein stability and conservation

  2021cites this paper
• Exploring absent protein function in yeast: assaying post translational modification and human genetic variation

  2021cites this paper
• Towards a New, Endophenotype-Based Strategy for Pathogenicity Prediction in BRCA1 and BRCA2: In Silico Modeling of the Outcome of HDR/SGE Assays for Missense Variants

  2021influential citation