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基于计算机的 CD-209 基因相关疾病的错义 SNP 筛选、鉴定及其对 CD-209 基因的影响

In silico screening and identification of deleterious missense SNPs along with their effects on CD-209 gene: An insight to CD-209 related-diseases.

机构信息

Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology (BIT), Beijing, PR China.

Department of Biomedical Engineering, National University of Science and Technology (NUST), Islamabad, Pakistan.

出版信息

PLoS One. 2021 Feb 26;16(2):e0247249. doi: 10.1371/journal.pone.0247249. eCollection 2021.

DOI:10.1371/journal.pone.0247249
PMID:33635927
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7909662/
Abstract

DC-SIGN receptor articulated by macrophages and dendritic cells is encoded by CD209 gene and plays a role to activate and proliferate the T-lymphocytes in response of virus attack. The dysfunctional activity of DC-SIGN receptor because of missense SNPs can lead to cause dengue haemorrhage fever, HIV-1 infection etc. Out of 11 transcripts of CD209, all missense SNPs of canonical transcript were retrieved from Ensembl database and evaluated by their deleteriousness by using Polyphen-2, PMut, SIFT, MutPred, PROVEAN and PhD-SNP together with stimulation of its complete 3D structure. 10 nsSNPs were chosen depending on both the significance value of nsSNP and their prediction among SNPs evaluating servers which are based on different algorithms. Moreover, the position and native role of 10 nsSNPs in wild 3D model has been described which assist to acknowledge their importance. This study urges the researcher's community to experimentally validate these SNPs and their association in causing the diseases like dengue fever, Tuberculosis etc.

摘要

树突状细胞特异性细胞间黏附分子-3 结合非整合素由巨噬细胞和树突状细胞表达，其编码基因为 CD209 基因，在病毒攻击时发挥作用，激活并增殖 T 淋巴细胞。由于错义 SNPs 导致 DC-SIGN 受体功能障碍，可能导致登革出血热、HIV-1 感染等疾病。在 CD209 的 11 种转录本中，从 Ensembl 数据库中检索到了规范转录本的所有错义 SNPs，并使用 Polyphen-2、PMut、SIFT、MutPred、PROVEAN 和 PhD-SNP 及其完整 3D 结构的刺激来评估其有害性。根据 nsSNP 的显著性值及其在基于不同算法的 SNP 评估服务器中的预测，选择了 10 个 nsSNP。此外，还描述了野生 3D 模型中 10 个 nsSNP 的位置和固有作用，有助于了解它们的重要性。这项研究敦促研究人员社区对这些 SNP 及其与登革热、结核病等疾病的关联进行实验验证。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/82aed1ef9a80/pone.0247249.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/b4beb2a3b636/pone.0247249.g001.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/a70c1bd81cb0/pone.0247249.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/a452b0a901f6/pone.0247249.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/9ef3af9d18eb/pone.0247249.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/4ecc29683ccc/pone.0247249.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/82aed1ef9a80/pone.0247249.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/b4beb2a3b636/pone.0247249.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/d1e59fe07eb6/pone.0247249.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/a70c1bd81cb0/pone.0247249.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/a452b0a901f6/pone.0247249.g004.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/4ecc29683ccc/pone.0247249.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/87a9/7909662/82aed1ef9a80/pone.0247249.g007.jpg

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