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Title

Identification and analysis of pathogenic nsSNPs in human LSP1 gene

 

Authors

Hani Mohammed Ali*

 

Affiliation

Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia

 

Email

Email: hmohammedali@kau.edu.sa; haniolfat@hotmail.com; *Corresponding author

 

Article Type

Research Article

 

Date

Received September 11, 2019; Revised September 20, 2019; Accepted September 19, 2019; Published September 30, 2019

 

Abstract

LSP1 (Lymphocyte-specific protein 1) protein plays an important role in neutrophil motility, fibrinogen matrix proteins adhesion, and trans-endothelial migration. Variation in the LSP1 gene is associated with leukemia and lymphomas in tumor cells of Hodgkin's disease and breast cancer. Despite extensive study on the human LSP1, a comprehensive analysis on the Single Nucleotide Polymorphism (SNPs) of the gene is not available. Therefore, it is of interest to identify, collect, store and analyze the SNPs of the LSP1 gene in relation to several known diseases. Hence, the SNP data (398 rsids) from dbSNP database was downloaded and mapped to the genomic coordinate of 'NM_002339.2' transcript expressed by LSP1 (P33241). There were 300 nsSNPs with missense mutation in the dataset. Tools such as SIFT, PROVEAN, Condel, and PolyPhen-2 were further used to identify 29 highly deleterious or damaging on synonymous SNP (nsSNPs) for LSP1. These high confident damaging nsSNPs were further analyzed for disease association using SNPs & GO tool. SNPs of the gene such as nsSNPs C283R, G234R, Y328D and H325P showed disease association with high prevalence.

 

Keywords

SNP; Lymphocyte-specific protein; computational analysis; F-actin binding protein; neutrophil actin dysfunction

 

Citation

Ali, Bioinformation 15(9): 621-626 (2019)

 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.