ArticleNature communications2017
Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Article
- Detection of germline variants in human population chronically exposed to high level natural background radiation in Kerala coast.Genes and environment : the official journal of the Japanese Environmental Mutagen Society · 2026Article
- The emergence of genetic variants linked to brain and cognitive traits in human evolution.Cerebral cortex (New York, N.Y. : 1991) · 2025Article
- CommonGenome research · 2025Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- Contradiction in Star-Allele Nomenclature of Pharmacogenes between Common Haplotypes and Rare Variants.Genes · 2024Article
- Article
- Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma.Cancer research communications · 2023Article
- Cardiac Genetic Investigation of Sudden Infant and Early Childhood Death: A Study From Victims to Families.Journal of the American Heart Association · 2023Article
- aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants.Bioinformatics (Oxford, England) · 2023Article
- The mutational landscape of a US Midwestern breast cancer cohort reveals subtype-specific cancer drivers and prognostic markers.Human genomics · 2023Article
- Deep structured learning for variant prioritization in Mendelian diseases.Nature communications · 2023Article
- Human subsistence and signatures of selection on chemosensory genes.Communications biology · 2023Article
- Unified views on variant impact across many diseases.Trends in genetics : TIG · 2023Review
- LoFTK: a framework for fully automated calculation of predicted Loss-of-Function variants and genes.BioData mining · 2023Article
- FAVOR: functional annotation of variants online resource and annotator for variation across the human genome.Nucleic acids research · 2023Article
- X-CAP improves pathogenicity prediction of stopgain variants.Genome medicine · 2022Article
- Identification of putative genetic variants in major depressive disorder patients in Pakistan.Molecular biology reports · 2022Article
- Computational Resources for the Interpretation of Variations in Cancer.Advances in experimental medicine and biology · 2022Article
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9 authors.
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Abstract
Variants predicted to result in the loss of function of human genes have attracted interest because of their clinical impact and surprising prevalence in healthy individuals. Here, we present ALoFT (annotation of loss-of-function transcripts), a method to annotate and predict the disease-causing potential of loss-of-function variants. Using data from Mendelian disease-gene discovery projects, we show that ALoFT can distinguish between loss-of-function variants that are deleterious as heterozygotes and those causing disease only in the homozygous state. Investigation of variants discovered in healthy populations suggests that each individual carries at least two heterozygous premature stop alleles that could potentially lead to disease if present as homozygotes. When applied to de novo putative loss-of-function variants in autism-affected families, ALoFT distinguishes between deleterious variants in patients and benign variants in unaffected siblings. Finally, analysis of somatic variants in >6500 cancer exomes shows that putative loss-of-function variants predicted to be deleterious by ALoFT are enriched in known driver genes.Variants causing loss of function (LoF) of human genes have clinical implications. Here, the authors present a method to predict disease-causing potential of LoF variants, ALoFT (annotation of Loss-of-Function Transcripts) and show its application to interpreting LoF variants in different contexts.
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