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Protocols

REVEL specifications

Information


Unique identifier OMICS_13231
Name REVEL
Alternative name Rare Exome Variant Ensemble Learner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Weiva Sieh

Publication for Rare Exome Variant Ensemble Learner

REVEL citations

 (10)
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Fanconi anemia and homologous recombination gene variants are associated with functional DNA repair defects in vitro and poor outcome in patients with advanced head and neck squamous cell carcinoma

2018
Oncotarget
PMCID: 5915066
PMID: 29719599
DOI: 10.18632/oncotarget.24797
call_split See protocol

[…] arScan 2.3.9 using Samtools mpileup 0.1.19 []. Next, we annotated these variants with the RefSeq and 1000 Genomes august 2015 databases using Annovar version date 11-05-2016 []. CADD [], PolyPhen [], REVEL [] and SIFT [] were used for in silico variant effect predictions. describes the filtering steps of the variant selection protocol that was designed to enrich for variants with a functional imp […]

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Evaluating the breast cancer predisposition role of rare variants in genes associated with low penetrance breast cancer risk SNPs

2018
PMCID: 5761188
PMID: 29316957
DOI: 10.1186/s13058-017-0929-z
call_split See protocol

[…] shift or essential splice site mutations. The in silico assessment tools Condel [], Polymorphism Phenotyping version 2 (PolyPhen-2) [], SIFT [], Combined Annotation Dependent Depletion (CADD) [] and rare exome variant ensemble learner (REVEL) [] were used to examine the likely pathogenicity of missense variants. Variant were defined as “likely deleterious” when predicted deleterious or damaging b […]

library_books

A recurrent de novo missense mutation in UBTF causes developmental neuroregression

2018
Hum Mol Genet
PMCID: 5886272
PMID: 29300972
DOI: 10.1093/hmg/ddx435

[…] NSFPv3.3 (Database for Nonsynonymous SNP’s Functional Predictions), UBTF E210K was predicted to be highly deleterious to protein function with a MetaLR_rankscore of 0.982, CADD_phred score of 32, and REVEL score of 0.683 (). In addition, UBTF has an ExAC missense Z-score of 5.61 (highly intolerant of variation) and pLI (probability of loss-of-function intolerance) of 1.00. […]

library_books

Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines

2017
Genome Biol
PMCID: 5704597
PMID: 29179779
DOI: 10.1186/s13059-017-1353-5

[…] LL FIELDS] OR METALR[ALL FIELDS] OR CONDEL[ALL FIELDS] OR CADD[ALL FIELDS] OR MUTATIONASSESSOR[ALL FIELDS] OR PROVEAN[ALL FIELDS] OR FATHMM[ALL FIELDS] OR EIGEN[ALL FIELDS] OR MUTPRED[ALL FIELDS] OR “REVEL”[ALL FIELDS] OR DANN[All Fields] OR LRT[All Fields] OR MUTATIONTASTER[All Fields] OR GERP[All Fields] OR VEST3[All Fields] OR Genocanyon[All Fields] OR fitcons[All Fields] OR phastcons[All Field […]

library_books

Exome Pool Seq in neurodevelopmental disorders

2017
Eur J Hum Genet
PMCID: 5865117
PMID: 29158550
DOI: 10.1038/s41431-017-0022-1

[…] n our experience, stricter filtering and prediction criteria than used in this study might also reduce the number of benign variants and thus follow-up time and costs. For example, the combination of REVEL and M-CAP currently seems to have the highest prediction rate for missense variants.In contrast to trio exome sequencing where segregation criteria such as de novo occurrence enormously reduce t […]

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Comprehensive investigation of CASK mutations and other genetic etiologies in 41 patients with intellectual disability and microcephaly with pontine and cerebellar hypoplasia (MICPCH)

2017
PLoS One
PMCID: 5546575
PMID: 28783747
DOI: 10.1371/journal.pone.0181791
call_split See protocol

[…] ools: Polymorphism Phenotyping v2 (PolyPhen-2) (http://genetics.bwh.harvard.edu/pph2), Sorting Intolerant from Tolerant (SIFT) (http://sift.jcvi.org/), SNPs&GO (http://snps.biofold.org/snps-and-go/), REVEL [], CADD (http://cadd.gs.washington.edu/home), and HOPE (http://www.cmbi.ru.nl/hope/). The STRING database (http://string-db.org/) was used to assess the presence of functional interactions betw […]

Citations

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REVEL institution(s)
Department of Genetics, Stanford University, Stanford, CA, USA; Department of Health Research and Policy, Stanford University, Stanford, CA, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Health Sciences Research, Mayo Clinic, Chinahester, MN, USA; Computational and Statistical Genomics Branch, National Human Genome Research Institute, Baltimore, MD, USA; Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA; Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Brady Urological Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; NorthShore University HealthSystem Research Institute, Evanston, IL, USA; Departments of Internal Medicine and Urology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland; Department of Medical Genetics, Tyks Microbiology and Genetics, Turku University Hospital, Turku, Finland; Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA; Department of Urology, Wayne State University, Detroit, MI, USA; Centre de Recherche sur les Pathologies Prostatiques et Urologiques, Universite Paris, Paris, France; Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC, Australia; Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC, Australia; Institute of Human Genetics, University Hospital of Ulm, Ulm, Germany; Department of Urology, University Hospital of Ulm, Ulm, Germany; Department of Urology, University of Southern California, Los Angeles, CA, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Departments of Oncology and Human Genetics, Montreal General Hospital, Montreal, QC, Canada; Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, USA; Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA; Department of Statistics, Stanford University, Stanford, CA, USA; Department of Laboratory Medicine and Pathology, Mayo Clinic, Chinahester, MN, USA
REVEL funding source(s)
This research was funded by NIH grants U01CA089600, R01CA094069, R01LM009722, R01MH105524, K07CA143047, and F32HG008330 and by the Intramural Research Program of the National Human Genome Research Institute, NIH.

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