Volume 8, Issue 1, March 2020, Page: 41-47
Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome
Sahar Mohamed Ali Mohamed Babiker, Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bari, Khartoum, Sudan
Afra Mohamed Al Bkrye, Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bari, Khartoum, Sudan
Hind Abdelaziz Elnasri, Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bari, Khartoum, Sudan
Mona Abdelrahman Mohamed Khaier, Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bari, Khartoum, Sudan
Received: Dec. 20, 2019;       Accepted: Jan. 13, 2020;       Published: Jan. 31, 2020
DOI: 10.11648/j.ijgg.20200801.15      View  351      Downloads  103
Abstract
Roberts’s syndrome is a genetic disorder characterized by limb and facial abnormalities. Affected individuals also grow slowly before and after birth. This syndrome is associated with ESCO2 (Establishment of Sister Chromatid cohesion N- acetyltransferase 2) gene mutations. SNPs in the coding region (exonal SNPs) that are non-synonymous (nsSNPs), the SNPs and related ensembles protein (ESNP) were obtained from the SNPs database (dbSNP) for computational analysis. Bioinformatics analysis of ESCO2 exonal non-synonymous SNPs initiated by GeneMANIA, SIFT, Polyphen-2, PHD, SNP&GO, Provean and ProjctHope. There were 85 nsSNPs, they had been submitted to SIFT software to predict the tolerant and intolerant SNPs, they had been sorted to 65 Tolerated SNPs and 20 Deleterious SNPs. SIFT deleterious SNPs had been tested by polyphen-2 software and the result was 3 benign SNPs, 3 possibly damaging and 14 probably damaging SNPs. The same 20 SNPs were tested using SNP&GO software and gave the same result for PHD and SNP&GO (4 diseased and 16 neutral) and the result obtained when using Provean software was 12 SNPs were neutral while only 8 SNPs were deleterious. The total nsSNPs affecting the structure, function and causing disease in the tested software were 4 nsSNPs (rs80359868, rs146312522, rs200548692, rs373708669) Protein structural analysis was done using all of CPH server, Raptor X, Project HOPE and chimera for the 4 pathological SNPs (W539, C392Y, R427C and D403V) resulted in all function prediction software. and, these results are at use for further researches and studies on this gene and it`s mutations.
Keywords
ESCO2 Gene, Roberts’s Syndrome, SIFT, Polyphen-2, PHD, SNP&GO and Provean
To cite this article
Sahar Mohamed Ali Mohamed Babiker, Afra Mohamed Al Bkrye, Hind Abdelaziz Elnasri, Mona Abdelrahman Mohamed Khaier, Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome, International Journal of Genetics and Genomics. Vol. 8, No. 1, 2020, pp. 41-47. doi: 10.11648/j.ijgg.20200801.15
Copyright
Copyright © 2020 Authors retain the copyright of this article.
This article is an open access article distributed under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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