ArticlePeerJ2015
VaRank: a simple and powerful tool for ranking genetic variants.
Article in PeerJ, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
52 citing papers in PubMed, 1 synthesis or guideline pooled it, 79 citations in OpenAlex.
- Intragenic FMR1 disease-causing variants: a significant mutational mechanism leading to Fragile-X syndrome.European journal of human genetics : EJHG · 2017Pooled it
- A recurrent North African ZP1 variant and a literature review of genotype-phenotype correlations in ZP-related infertility.Journal of assisted reproduction and genetics · 2026Review
- Disruption of meiotic double-strand break dynamics provokes germline human infertility in both sexes.Journal of assisted reproduction and genetics · 2026Article
- Autism-associated ARHGEF9 variants impair GABAergic synapses and ultrasonic communication by reducing gephyrin phosphorylation.Molecular psychiatry · 2026Article
- Evaluation of the contribution of trio-exome sequencing in selected prenatal indications.Frontiers in genetics · 2026Article
- Syndromic gingival fibromatosis associated with pathogenic variation in the voltage-gated potassium channel gene KCNH1: a case report and proposed treatment protocol.BMC oral health · 2025Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Evaluation of an Updated Gene Panel as a Diagnostic Tool for Both Male and Female Infertility.Reproductive sciences (Thousand Oaks, Calif.) · 2024Article
- Exome sequencing in undiagnosed congenital myopathy reveals new genes and refines genes-phenotypes correlations.Genome medicine · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- Pathogenic missense variation in PABPC1L/EPAB causes female infertility due to oocyte maturation arrest at the germinal vesicle stage.Journal of assisted reproduction and genetics · 2024Article
- WGS Revealed NovelInternational journal of molecular sciences · 2023Article
- Telomere Length as a New Risk Marker of Early-Onset Colorectal Cancer.International journal of molecular sciences · 2023Article
- Unexpected Inheritance Patterns in a Large Cohort of Patients with a Suspected Ciliopathy.Human mutation · 2023Article
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- De novo variants in genes regulating stress granule assembly associate with neurodevelopmental disorders.Science advances · 2022Article
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- Evaluation of a Custom Design Gene Panel as a Diagnostic Tool for Human Non-Syndromic Infertility.Genes · 2021Article
- X-linked partial corpus callosum agenesis with mild intellectual disability: identification of a novel L1CAM pathogenic variant.Neurogenetics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background. Most genetic disorders are caused by single nucleotide variations (SNVs) or small insertion/deletions (indels). High throughput sequencing has broadened the catalogue of human variation, including common polymorphisms, rare variations or disease causing mutations. However, identifying one variation among hundreds or thousands of others is still a complex task for biologists, geneticists and clinicians. Results. We have developed VaRank, a command-line tool for the ranking of genetic variants detected by high-throughput sequencing. VaRank scores and prioritizes variants annotated either by Alamut Batch or SnpEff. A barcode allows users to quickly view the presence/absence of variants (with homozygote/heterozygote status) in analyzed samples. VaRank supports the commonly used VCF input format for variants analysis thus allowing it to be easily integrated into NGS bioinformatics analysis pipelines. VaRank has been successfully applied to disease-gene identification as well as to molecular diagnostics setup for several hundred patients. Conclusions. VaRank is implemented in Tcl/Tk, a scripting language which is platform-independent but has been tested only on Unix environment. The source code is available under the GNU GPL, and together with sample data and detailed documentation can be downloaded from http://www.lbgi.fr/VaRank/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.