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

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About: A comprehensive in silico analysis of non-synonymous and regulatory SNPs of human MBL2 gene Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	A comprehensive in silico analysis of non-synonymous and regulatory SNPs of human MBL2 gene
Creator	Kaur, Manpreet Singh, Jatinder Kalia, Namarta Sharma, Aarti Kamboj, Sukhdev
Source	Medline; PMC
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.
has issue date	2016-06-21(xsd:dateTime)
bibo:doi	10.1186/s40064-016-2543-4
bibo:pmid	27390651
has license	cc-by
sha1sum (hex)	1af8d169cf2d572b46f2b94b1e83c66686973297
schema:url	https://doi.org/10.1186/s40064-016-2543-4
resource representing a document's title	A comprehensive in silico analysis of non-synonymous and regulatory SNPs of human MBL2 gene
has PubMed Central identifier	PMC4916122
has PubMed identifier	27390651
schema:publication	Springerplus
resource representing a document's body	covid:1af8d169cf2d572b46f2b94b1e83c66686973297#body_text
is schema:about of	named entity 'NON-' named entity 'studies' named entity 'acid' named entity 'stability' named entity 'calculations' named entity 'normal' named entity 'energy minimization' named entity 'Information' named entity 'SNPs' named entity 'SNPS' named entity 'COMPREHENSIVE' named entity 'MINOR ALLELE FREQUENCY' named entity 'MBL2' named entity 'VARIOUS' named entity 'ENERGY' named entity 'DAMAGING' named entity 'PROTEIN STRUCTURAL ANALYSIS' named entity 'MOLECULE' named entity 'MINIMIZATION' named entity 'CAUSES' named entity 'EXPRESSION' named entity 'NEAR' named entity 'INTERFERE' named entity 'PRESENT' named entity 'CARRIED' named entity 'NOVEL' named entity 'TRIPLE HELIX' named entity 'DBSNP' named entity 'INNATE IMMUNITY' named entity 'AMINO ACID' named entity 'SIFT' named entity 'STUDIES' named entity 'VALIDATED' named entity 'DATE' named entity 'ASSEMBLY' named entity 'SERVERS' named entity 'FUNCTIONAL' named entity 'ANALYZED' named entity 'IMPACT' named entity 'PERFORMED BY' named entity 'SNP DATA' named entity 'STUDY' named entity 'MBL2 GENE' named entity 'TO IDENTIFY' named entity 'DISEASES' named entity 'CONSERVED' named entity 'NON-' named entity 'USING' named entity 'FINDINGS' named entity 'SOLVENT' named entity 'DATABASE' named entity 'PLAY ROLE' named entity 'TOTAL' named entity 'INTRONIC' named entity 'DECREASE' named entity 'EXPLORATION' named entity 'TILL' named entity 'THIRTEEN' named entity 'LIVER' named entity 'RAMPAGE' named entity 'DERIVED' named entity 'NORMAL' named entity 'PROTEIN STABILITY' named entity 'MARKERS' named entity 'ACCESSIBILITY' named entity 'BEING' named entity 'MBL2 GENE' named entity 'REGULATORY' named entity 'TRANSCRIPTION FACTOR BINDING' named entity 'MUTANT' named entity 'TOOLS' named entity 'REPORTED' named entity 'MIRNA BINDING' named entity 'FUNCTION' named entity 'AFFECTING' named entity 'MOLECULAR DYNAMICS' named entity 'SIGNIFICANCE'

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