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Interpreting missense mutations in Human TRIM5alpha by computational methods
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...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2611994/ https://www.ncbi.nlm.nih.gov/pubmed/19025647 http://dx.doi.org/10.1186/1756-0500-1-116 |
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author | Chan, Philip A |
author_facet | Chan, Philip A |
author_sort | Chan, Philip A |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-2611994 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26119942008-12-30 Interpreting missense mutations in Human TRIM5alpha by computational methods Chan, Philip A BMC Res Notes Short Report 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. BioMed Central 2008-11-24 /pmc/articles/PMC2611994/ /pubmed/19025647 http://dx.doi.org/10.1186/1756-0500-1-116 Text en Copyright © 2008 Chan et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Short Report Chan, Philip A Interpreting missense mutations in Human TRIM5alpha by computational methods |
title | Interpreting missense mutations in Human TRIM5alpha by computational methods |
title_full | Interpreting missense mutations in Human TRIM5alpha by computational methods |
title_fullStr | Interpreting missense mutations in Human TRIM5alpha by computational methods |
title_full_unstemmed | Interpreting missense mutations in Human TRIM5alpha by computational methods |
title_short | Interpreting missense mutations in Human TRIM5alpha by computational methods |
title_sort | interpreting missense mutations in human trim5alpha by computational methods |
topic | Short Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2611994/ https://www.ncbi.nlm.nih.gov/pubmed/19025647 http://dx.doi.org/10.1186/1756-0500-1-116 |
work_keys_str_mv | AT chanphilipa interpretingmissensemutationsinhumantrim5alphabycomputationalmethods |