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In-Silico analysis of missense SNPs in Human HPPD gene associated with Tyrosinemia type III and Hawkinsinuria.
Comput Biol Chem 2019; 80:284-291CB

Abstract

HPPD gene codes a dioxygenase enzyme involved in catalysis of different molecules such as tyrosine and phenylalanine by oxidizing them to produce energy. A single change in protein can trigger serious genetic disorders like Tyrosinemia type III and Hawkinsinuria. This study aims to identify the functional missense SNPs of the HPPD gene by using multiple computational tools. All deleterious missense SNPs retrieved from Ensembl and OMIM database were evaluated through six different software. Ultimately, out of 148 missense SNPs, only 27 were confirmed as diseasecausing SNPs by developing a consensus approach. These damaging SNPs were further examined to evaluate their impact on protein stability and energy including their evolutionary conservation. Native and mutated proteins structures were also designed and superimposed by I-TASSER and PyMol respectively. This work results in narrowing down missense SNPs which are still not confirmed experimentally and demands the confirmation by GWAS data. Thus, these missense SNPs could directly or indirectly destabilize the amino acid interactions causing functional deviations of protein.

Authors+Show Affiliations

Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, 54000, Pakistan. Electronic address: naveed.quaidian@gmail.com.Department of Biochemistry and Biotechnology, University of Gujrat, 50700, Pakistan.Department of Biochemistry and Biotechnology, University of Gujrat, 50700, Pakistan.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31054541

Citation

Naveed, Muhammad, et al. "In-Silico Analysis of Missense SNPs in Human HPPD Gene Associated With Tyrosinemia Type III and Hawkinsinuria." Computational Biology and Chemistry, vol. 80, 2019, pp. 284-291.
Naveed M, Tehreem S, Mehboob MZ. In-Silico analysis of missense SNPs in Human HPPD gene associated with Tyrosinemia type III and Hawkinsinuria. Comput Biol Chem. 2019;80:284-291.
Naveed, M., Tehreem, S., & Mehboob, M. Z. (2019). In-Silico analysis of missense SNPs in Human HPPD gene associated with Tyrosinemia type III and Hawkinsinuria. Computational Biology and Chemistry, 80, pp. 284-291. doi:10.1016/j.compbiolchem.2019.04.007.
Naveed M, Tehreem S, Mehboob MZ. In-Silico Analysis of Missense SNPs in Human HPPD Gene Associated With Tyrosinemia Type III and Hawkinsinuria. Comput Biol Chem. 2019;80:284-291. PubMed PMID: 31054541.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - In-Silico analysis of missense SNPs in Human HPPD gene associated with Tyrosinemia type III and Hawkinsinuria. AU - Naveed,Muhammad, AU - Tehreem,Sana, AU - Mehboob,Muhammad Zubair, Y1 - 2019/04/25/ PY - 2018/03/24/received PY - 2019/04/14/revised PY - 2019/04/18/accepted PY - 2019/5/6/pubmed PY - 2019/8/6/medline PY - 2019/5/5/entrez KW - GWAS studies KW - Hawkinsinuria KW - Missense SNPs KW - Tyrosinemia type III SP - 284 EP - 291 JF - Computational biology and chemistry JO - Comput Biol Chem VL - 80 N2 - HPPD gene codes a dioxygenase enzyme involved in catalysis of different molecules such as tyrosine and phenylalanine by oxidizing them to produce energy. A single change in protein can trigger serious genetic disorders like Tyrosinemia type III and Hawkinsinuria. This study aims to identify the functional missense SNPs of the HPPD gene by using multiple computational tools. All deleterious missense SNPs retrieved from Ensembl and OMIM database were evaluated through six different software. Ultimately, out of 148 missense SNPs, only 27 were confirmed as diseasecausing SNPs by developing a consensus approach. These damaging SNPs were further examined to evaluate their impact on protein stability and energy including their evolutionary conservation. Native and mutated proteins structures were also designed and superimposed by I-TASSER and PyMol respectively. This work results in narrowing down missense SNPs which are still not confirmed experimentally and demands the confirmation by GWAS data. Thus, these missense SNPs could directly or indirectly destabilize the amino acid interactions causing functional deviations of protein. SN - 1476-928X UR - https://www.unboundmedicine.com/medline/citation/31054541/In-Silico_analysis_of_missense_SNPs_in_Human_HPPD_gene_associated_with_Tyrosinemia_type_III_and_Hawkinsinuria L2 - https://linkinghub.elsevier.com/retrieve/pii/S1476-9271(18)30212-3 DB - PRIME DP - Unbound Medicine ER -