ArticleNucleic acids research2017
PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
116 citing papers in PubMed, 1 synthesis or guideline pooled it, 253 citations in OpenAlex.
- The Clinical Pharmacogenetics Implementation Consortium's consensus-based framework for assigning allele function.American journal of human genetics · 2025Guideline
- Integrated Structural and Dynamic Analysis Reveals Destabilizing Effects of KRAS Missense Variants Associated with Lung Cancer.The protein journal · 2026Article
- Computational identification and characterization of high-risk human KRAS nsSNPs: Impacting structure, ligand binding, and cancer prognosis.Journal, genetic engineering & biotechnology · 2026Article
- Genome-Wide Characterization of the TGF-β Gene Family in Donkey (Animals : an open access journal from MDPI · 2026Article
- Association of MUC3A P258S mutation with advanced phase CML structural and in silico insights.Functional & integrative genomics · 2026Article
- Identification of non-synonymous SNPs affecting structure and function of MLH1 and NBN proteins: a computational approach.Journal of applied genetics · 2026Article
- CDsyn: A comprehensive database for deleterious human synonymous variation prediction.iScience · 2026Article
- Article
- Cancer-associated TRF1 mutations alter PARP1 interaction dynamics: an in silico study.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Computational analysis of the structural and functional impact of the deleterious nsSNPs in the humanBiochemistry and biophysics reports · 2026Article
- In silico prioritisation of EDN1 missense variants identifies mature endothelin-1 substitutions with predicted receptor-binding effects.BMC genomics · 2026Article
- Computational analysis of MYC gene variants: structural and functional impact of non-synonymous SNPs.Journal of applied genetics · 2026Article
- Computational analysis and validation of UGT1A1/4 missense variants impacting tecovirimat metabolism in monkeypox patients.Frontiers in systems biology · 2026Article
- Computational Characterization of Pathogenic LMNA Missense Variants: Structural Instability, Altered Binding, and Conformational Dynamics.Human mutation · 2026Article
- Exploring Deleterious Nonsynonymous SNPs in theGenetics research · 2026Article
- In silico functional, structural, and pathogenicity assessment of single nucleotide polymorphisms in the human SOX9 gene.Scientific reports · 2025Article
- Identification of deleterious non-synonymous single nucleotide polymorphisms in the mRNA decay activator ZFP36L2.RNA biology · 2025Article
- Functional synonymous mutations and their evolutionary consequences.Nature reviews. Genetics · 2025Review
- Comprehensive computational analysis of PKCδ non-synonymous variants identifies rs1703863535 as a potential breast cancer biomarker.BMC cancer · 2025Article
- DRP-PSM: Multi-Level Feature Integration Reveals Hierarchical Contributions to Pathogenic Synonymous Mutation Prediction.ACS omega · 2025Article
56 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the major challenges in human genetics is to identify functional effects of coding and non-coding single nucleotide variants (SNVs). In the past, several methods have been developed to identify disease-related single amino acid changes but only few tools are able to score the impact of non-coding variants. Among the most popular algorithms, CADD and FATHMM predict the effect of SNVs in non-coding regions combining sequence conservation with several functional features derived from the ENCODE project data. Thus, to run CADD or FATHMM locally, the installation process requires to download a large set of pre-calculated information. To facilitate the process of variant annotation we develop PhD-SNPg, a new easy-to-install and lightweight machine learning method that depends only on sequence-based features. Despite this, PhD-SNPg performs similarly or better than more complex methods. This makes PhD-SNPg ideal for quick SNV interpretation, and as benchmark for tool development. AVAILABILITY: PhD-SNPg is accessible at http://snps.biofold.org/phd-snpg.
Indexed as
Identifiers
What OpenQuestion holds
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 OpenQuestion graph.