Short Report
Interpreting missense mutations in Human TRIM5alpha by computational methods
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Correspondence: Philip A Chan pchan@lifespan.org
Department of Internal Medicine, Rhode Island Hospital, Providence, RI 02903, USA
BMC Research Notes 2008, 1:116 doi:10.1186/1756-0500-1-116
Published: 24 November 2008Abstract
Background
The human restriction factor TRIM5α may play an important role in regulation of the human immunodeficiency virus (HIV). It is unclear whether non-synonymous single nucleotide polymorphisms (nsSNP) in TRIM5α affect the clinical course of HIV infection.
Findings
We surveyed the literature for TRIM5α nsSNPs and used comparative sequence analysis to predict the effect of each polymorphism on protein function. Twenty-eight nsSNPs were identified with available functional data, clinical data, or both. The four comparative method programs assessed included SIFT, PolyPhen, A-GVGD, and average BLOSUM62 pairwise score. Two common polymorphisms, H43Y and R136Q, were predicted to be benign based on comparative sequence analysis. The nsSNPs P323R, K324N, I328M, G330Q, R332P, I348V, and T369S were all predicted to affect protein function.
Conclusion
Comparative sequence analysis offers a functional tool to analyze unknown nsSNPs in TRIM5α.