ArticleNucleic acids research2023
PhD-SNPg: updating a webserver and lightweight tool for scoring nucleotide variants.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it, 24 citations in OpenAlex.
- The Clinical Pharmacogenetics Implementation Consortium's consensus-based framework for assigning allele function.American journal of human genetics · 2025Guideline
- Clinical Function Assignment of NAT2 Alleles by the Clinical Pharmacogenetics Implementation Consortium Pharmacogene Curation Expert Panel.Clinical pharmacology and therapeutics · 2026Article
- Clinical and molecular characterization of giant axonal neuropathy due to a homozygous c.851 + 1G>A variant inGlobal medical genetics · 2026Article
- An inherited SLC25A12-related recessive form of congenital porencephaly in Limousin cattle.Genetics, selection, evolution : GSE · 2026Article
- NovelVeterinary and animal science · 2026Article
- Pathogenicity prediction for noncanonical splice-altering variants based on multimodal feature fusion.Briefings in bioinformatics · 2026Article
- A CACNA2D2-Related Recessive Form of Cerebellar Abiotrophy in Angus Cattle.Animal genetics · 2026Article
- Computational identification of rare pathogenic genomic variants in esophageal cancer markers: Transcript-level analysis, sequence-based insights, and structural-functional impacts of non-synonymous SNPs.Biochemistry and biophysics reports · 2026Article
- Comprehensive In Silico Analysis of the CXCL12, C55Y Mutation Reveals Structural and Functional Disruption in CXCR4/CXCR7 Signaling.Evolutionary bioinformatics online · 2026Article
- Computational screening of oncogenic genetic variations in tumor suppressor proteins driving gastric cancer pathogenesis.PloS one · 2026Article
- Article
- Predictive Analysis and Validation of Critical Missense SNPs of theInternational journal of molecular sciences · 2025Review
- Intratumoral Microbiota Correlates with AP-2 Expression: A Pan-Cancer Map with Cohort-Specific Prognostic and Molecular Footprints.International journal of molecular sciences · 2025Article
- Federated learning for the pathogenicity annotation of genetic variants in multi-site clinical settings.Bioinformatics (Oxford, England) · 2025Article
- Rare phenotypes of white coat color in Simmental calves: genetic causes of syndromic forms of albinism and depigmentation.Molecular genetics and genomics : MGG · 2025Article
- Prediction of human pathogenic start loss variants based on self-supervised contrastive learning.BMC biology · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Assessing predictions on fitness effects of missense variants in HMBS in CAGI6.Human genetics · 2025Article
- AFFIPred: AlphaFold2 structure-based Functional Impact Prediction of missense variations.Protein science : a publication of the Protein Society · 2025Article
- Impact of nonsynonymous single nucleotide polymorphisms inFrontiers in genetics · 2025Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the primary challenges in human genetics is determining the functional impact of single nucleotide variants (SNVs) and insertion and deletions (InDels), whether coding or noncoding. In the past, methods have been created to detect disease-related single amino acid changes, but only some can assess the influence of noncoding variations. CADD is the most commonly used and advanced algorithm for predicting the diverse effects of genome variations. It employs a combination of sequence conservation and functional features derived from the ENCODE project data. To use CADD, a large set of pre-calculated information must be downloaded during the installation process. To streamline the variant annotation process, we developed PhD-SNPg, a machine-learning tool that is easy to install and lightweight, relying solely on sequence-based features. Here we present an updated version, trained on a larger dataset, that can also predict the impact of the InDel variations. Despite its simplicity, PhD-SNPg performs similarly to CADD, making it ideal for rapid genome interpretation and as a benchmark for tool development.
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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 OpenQuestion graph.