What is a SNP (Single Nucleotide Polymorphism)?
Definition
A single nucleotide polymorphism (SNP, pronounced 'snip') is a variation at a single position in a DNA sequence among individuals. SNPs are the most common type of genetic variation in humans, with approximately 4-5 million SNPs per individual genome and over 660 million cataloged in the dbSNP database.
Detailed Explanation
SNPs occur roughly once every 300 base pairs in the human genome. Most are located in non-coding regions and have no functional impact, but those within or near genes can alter protein structure, gene expression, or mRNA splicing. A SNP in a coding region that changes an amino acid is called a missense variant — for example, rs429358 in the APOE gene changes cysteine to arginine at position 112, creating the APOE4 allele associated with Alzheimer's disease risk. SNPs in regulatory regions can increase or decrease gene expression without changing the protein sequence.
In pharmacogenomics, SNPs are the primary unit of analysis. Each pharmacogenomically relevant SNP is assigned an rsID (reference SNP identifier) by the dbSNP database. Clinicians and researchers use rsIDs to look up variant annotations in databases like ClinVar, PharmGKB, and CPIC. For example, rs3892097 identifies the CYP2D6*4 allele, the most common cause of poor metabolizer status in European populations. Knowing a patient's SNP genotype at key pharmacogenes allows clinicians to adjust drug selection and dosing before prescribing.
PepFold uses SNPs as the primary input for its pharmacogenomic peptide design pipeline. When a user submits one or more rsIDs, the system queries ClinVar for clinical annotations, maps the variant to its host protein via UniProt, identifies the affected functional domain, and generates peptide candidates that account for the structural change introduced by the SNP. This SNP-to-peptide workflow bridges the gap between genomic data and actionable therapeutic design.
Related Terms
An rsID (reference SNP cluster ID) is a unique identifier assigned by the NCBI dbSNP database to a specific genetic variant, typically a single nucleotide polymorphism (SNP). The format is 'rs' followed by a number — for example, rs429358 identifies the APOE4-defining variant. rsIDs serve as the universal language for referencing genetic variants across research, clinical testing, and bioinformatics tools.
What is Pharmacogenomics?Pharmacogenomics (PGx) is the study of how an individual's genetic makeup influences their response to medications. It combines pharmacology (the science of drugs) and genomics (the study of genes and their functions) to develop effective, personalized drug therapies based on a patient's DNA.
What is ClinVar?ClinVar is a freely accessible public database maintained by the National Center for Biotechnology Information (NCBI) that aggregates information about the relationships between human genetic variants and observed health conditions (phenotypes). Submitters — including clinical laboratories, research groups, and expert panels — classify variants using a standardized five-tier system: pathogenic, likely pathogenic, uncertain significance (VUS), likely benign, and benign.
What is Personalized Medicine?Personalized medicine (also called precision medicine) is a medical model that uses an individual's genetic, environmental, and lifestyle information to guide clinical decisions. Rather than prescribing the same drug at the same dose to every patient with a given condition, personalized medicine selects therapies and dosages based on the patient's unique biological profile — particularly their genomic data.
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