Data Mining Analysis of &amp;lt;i&amp;gt;ESCO2&amp;lt;/i&amp;gt; Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome

Sahar Mohamed Ali Mohamed Babiker,Mona Abdelrahman Mohamed Khaier,Afra Mohamed Al Bkrye,Hind Abdelaziz Elnasri

doi:10.11648/j.ijgg.20200801.15

Data Mining Analysis of &lt;i&gt;ESCO2&lt;/i&gt; Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome

Sahar Mohamed Ali Mohamed Babiker, Mona Abdelrahman Mohamed Khaier + Show 2 more

Open Access

https://doi.org/10.11648/j.ijgg.20200801.15

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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 <i>ESCO2</i> (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 <i>ESCO2</i> 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.

Highlights

Roberts’s syndrome (RBS), (SC phocomelia syndrome or Roberts’s tetraphocomelia syndrome) is a genetic disorder characterized by limb and facial abnormalities
SIFT (Sorting Intolerant From Tolerant) Predict whether an amino acid substitution affects protein function based on sequence homology and physical properties of amino acids [4]
ESCO2 gene single nucleotide polymorphisms and ensembles protein were obtained from the SNPs database for computational analysis and UniprotKB database are 308 SNPs, which had been filtered to 241 SNPs for only ESCO2 gene in Homo sapiens, filtered to 114 for the isoform ENSP00000306999, which filtered for only 85 SNPs representing exonal non-synonymous single nucleotide polymorphism

Summary

Introduction

Roberts’s syndrome (RBS), (SC phocomelia syndrome or Roberts’s tetraphocomelia syndrome) is a genetic disorder characterized by limb and facial abnormalities. Affected individuals grow slowly before and after birth [1]. Roberts’s syndrome is known by limbs abnormalities, hypomelia; in forearms and lower legs. People with Roberts syndrome may have abnormal or missing fingers and toes, and joint deformities commonly occur at the elbows and knees [2]. Individuals with Roberts’s syndrome typically have numerous facial abnormalities, including cleft lip with or without cleft palate, micrognathia, ear abnormalities, hypertelorism, small nostrils, they may have microcephalic head and in severe cases affected individuals have encephalocele. Infants with severe form of Roberts’s syndrome are often stillborn or die shortly after birth. Affected individuals may live up to adulthood [1]

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