A comprehensive in silico analysis of non-synonymous and regulatory SNPs of human MBL2 gene

Namarta Kalia; Aarti Sharma; Manpreet Kaur; Sukhdev Singh Kamboj; Jatinder Singh

doi:10.1186/s40064-016-2543-4

A comprehensive in silico analysis of non-synonymous and regulatory SNPs of human MBL2 gene

Springerplus. 2016 Jun 21;5(1):811. doi: 10.1186/s40064-016-2543-4. eCollection 2016.

Authors

Namarta Kalia¹, Aarti Sharma², Manpreet Kaur², Sukhdev Singh Kamboj¹, Jatinder Singh¹

Affiliations

¹ Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, 143005 India.
² Department of Human Genetics, Guru Nanak Dev University, Amritsar, India.

Abstract

Mannose binding lectin (MBL) is a liver derived protein which plays an important role in innate immunity. Mannose binding lectin gene 2 (MBL2) polymorphisms are reported to be associated with various diseases. In spite of being exhaustively studied molecule, no attempt has been made till date to comprehensively and systematically analyze the SNPs of MBL2 gene. The present study was carried out to identify and prioritize the SNPs of MBL2 gene for further genotyping and functional studies. To predict the possible impact of SNPs on MBL structure and function SNP data obtained from dbSNP database were analyzed using various bioinformatics tools. Out of total 661 SNPs, only 37 validated SNPs having minor allele frequency ≥0.10 were considered for the present study. These 37 SNPs includes one in 3' near gene, nine in 3' UTR, one non-synonymous SNP (nsSNP), thirteen intronic SNPs and thirteen in 5' near gene. From these 37 SNPs, 11 non-coding SNPs were identified to be of functional significance and evolutionary conserved. Out of these, 4 SNPs from 3' UTR were found to play role in miRNA binding, 7 SNPs from 5' near and intronic region were predicted to involve in transcription factor binding and expression of MBL2 gene. One nsSNP Gly54Asp (rs1800450) was found to be deleterious and damaging by both SIFT and Polyphen-2 servers and thus affecting MBL2 protein stability and expression. Protein structural analysis with this amino acid variant was performed by using I-TASSER, RAMPAGE, Swiss-PdbViewer, Chimera and I-mutant. Information regarding solvent accessibility, molecular dynamics and energy minimization calculations showed that this variant causes clashes with neighboring amino acids residues that must interfere in the normal triple helix formation of trimeric subunit and further with the normal assembly of MBL oligomeric form, hence decrease in stability. Thus, findings of the present study indicated 12 SNPs of MBL2 gene to be functionally important. Exploration of these variants may provide novel remedial markers for various diseases.

Keywords: Candidate gene studies; Computational analysis; Mannose binding lectin gene 2; Non-coding SNPs; Non-synonymous SNPs; Single nucleotide polymorphism (SNP).