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 and GO tool. SNPs of the gene such as nsSNPs C283R, G234R, Y328D and H325P showed disease association with high prevalence.
Highlights
Human LSP1 gene encodes an intracellular F-actin binding protein, recently renamed as leukocyte specific protein
LSP1 is found in plasma membrane internal surface of the, the cytoplasm, and is thought to mediate cytoskeleton-driven responses in activated leukocytes that involve receptor capping, cell-cell interactions and cell motility [3]
398rsIDof nsSNPs mapped in human LSP1 gene was downloaded from dbSNP database of NCBI(Table 3), after filtering variation class SNV and function class missense, there were 9590 Single nucleotide polymorphism (SNPs) mapped to intron, while 457SNPs mapped to 5’UTR, 134SNPs mapped to 3’UTR and 10815 mapped to total SNPs of different variation class (Figure 2)
Summary
Human LSP1 (lymphocyte specific protein 1) gene encodes an intracellular F-actin binding protein, recently renamed as leukocyte specific protein. Due to alternative splicing there are multiple transcript variants which encodes different isoforms. Highest expression of this gene in spleen (RPKM 60.6), appendix (RPKM 43.3) and other tissues [1, 2] is known. Lymphocyte specific protein 1 modulates leukocyte populations in resting and inflamed peritoneum [2]. SNPs can alter the functional consequences of proteins. In the coding region of gene, SNPs may be synonymous, non-synonymous (nsSNPs) or nonsense. Synonymous SNPs changes the nucleotide base residue but does not change the amino acid residue in protein sequence due to degeneracy of genetic code.
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