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Single Nucleotide Polymorphisms-SNPs

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

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Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase.

Yum L Yip¹, Maria Famiglietti, Arnaud Gos

¹Swiss-Prot Group, Swiss Institute of Bioinformatics, Centre Médical Universitaire, Geneva, Switzerland. lina.yip@isb-sib.ch

|January 5, 2008

Summary

UniProtKB/Swiss-Prot manually curates single amino acid polymorphisms (SAPs) impacting human proteins. This database details SAP effects on protein function and disease links, enhancing genomic and phenotypic data integration.

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Area of Science:

Biochemistry
Genetics
Bioinformatics

Background:

UniProtKB/Swiss-Prot is a manually curated protein knowledgebase.
It is part of the Universal Protein Resource (UniProt).
The database contains extensive information on protein sequences and functional annotation.

Purpose of the Study:

To summarize the content and utility of UniProtKB/Swiss-Prot for single amino acid polymorphism (SAP) data.
To highlight the value of SAP information for understanding protein function and disease.
To emphasize the integration of SAP data with genomic and phenotypic databases.

Main Methods:

Manual curation of literature reports for single amino acid polymorphisms (SAPs).
Inclusion of data on mutation position, amino acid change, and functional effects.
Cross-referencing with human disease and gene-specific databases, including OMIM.

Main Results:

UniProtKB/Swiss-Prot records 32,282 SAPs affecting 6,086 human proteins.
Includes 16,043 disease-related SAPs, 14,266 polymorphisms, and 1,973 unclassified variants.
Provides data on protein sequencing, post-translational modifications, and links to disease databases.

Conclusions:

UniProtKB/Swiss-Prot offers a comprehensive resource for SAP information, including functional and disease-related aspects.
The database integrates protein-level data with genomic and phenotypic information, aiding disease research.
Swiss-Prot variant pages provide a concise view of SAPs, complementing other mutation databases.