Global Journal of Medical Research, F: Diseases, Volume 22 Issue 4

22 Year 2022 Global Journal of Medical Research Volume XXII Issue IV Version I ( DD ) F © 2022 Global Journals Computational Analysis of Possibly Pathogenic Non-Synonymous Single Nucleotide Polymorphisms Variants in HGD Gene D iscussion AKU is normally characterized through genetic changes in the HGD gene but the identification of variants likely affecting structure is not always straightforward. Evolutionary conservation (Shannon entropy) and population conservation (MTR) scores indicated that AKU variants were located at more conserved residue positions. This could provide insight into novel missense variants that have a high probability of being deleterious (Ascher et al., 2019). In this study a total of 11 SNPs were shown to be damaging, disease related and affecting the protein stability using 6 different software. Seven of them were novel not reported in ClinVar database. Namely, rs370453859 (G11K), rs199536408 (A41D), rs143267384 (W60V), rs199536408 (G198D), rs199927284 (V316F), rs139501220 (M339I), rs138558042 (P373L). The effect of the mutation on the protein function was due to the location if it is in a conserved region the protein will be highly affected. Most of these mutations were in a conserved region. Also the difference in size between the wild and mutant residue affects the protein function, if the mutant residue is bigger in size (G11K, A41D, G198D, V316F and P373L) it cannot fit and might lead to bumps, if it is smaller (W60V and M339I) this will cause an empty space in the core of the protein. The difference in hydrophobicity will leads to loss of hydrophobic interactions with other molecules on the surface of the protein. The physical properties between the wild and mutant amino acid also affects the protein function (the flexibility of Glycine and the rigidity of Proline). Compromising the Homogentisate oxidase enzyme function Nemethova et al., 2016 showed that the missense variants are predicted to affect the activity of the enzyme by three molecular mechanisms: decrease of stability of individual protomers, disruption of protomer–protomer interactions or modification of residues in the active site region. In agreement with our results fournsSNPs namely rs373921680 (E42A), rs200808744 (R53Q), rs375283568 (E168K), and rs368717991 (G360R), have already been previously reported as mutation in HDG gene in patients with AKU through direct DNA sequencing (de Bernabe et al., 1998; Nemethova et al, 2016; Ascher et al., 2019; Vilboux et al., 2009; Higashino, 1998; and Porfirio et al., 2000). According to, de Bernabe et al., 1998,who mentioned that rs373921680 (E42A) is pathogenic and clustered within exon 03, the variant remarks is missense, predicted mutation resulting in the amino acid substitutions affect the protomer destabilization, hexamer disruptionis crucial for the enzymatic activity of HGD. In the study by, Nemethova et al, 2015, they recorded that, SNPsrs200808744 (R53Q) was remarkably changing the amino acid residues and found to be pathogenic, and this mutation has recently been reported as one of the important mutations in this HDG gene, predicted the mutation to be highly destabilize the formation of the hexamer, because of the loss of the interactions made by the arginine. Higashino et al., 1998 approved that, rs375283568 (E168K) as a pathogenic mutation and changed a glutamic acid residue at position 168 to a lysine residue. Predicted mutation affect substitution hexamer disruption. Porfirio et al., 2000, found that, rs368717991 (G360R) affect the protomer destabilization and hexamer disruption due to substitution of wide amino Glycine into an Arginine at position 360. The mutated residue is located in a domain that is important for the main activity of the protein. Mutation of the residue might disturb this function. These nsSNPs, rs375396766 (P158L) and rs143556739 (R307C) were predicted by other researchers to be pathogenic, in this study they were predicted to be damaging but not disease related. The structural analysis of the identified variants allowed their classification based on the predicted effects into three classes: (i) those that alter the active site, reducing activity; (ii) those that destabilize the protein, reducing activity; and (iii) those that prevent formation of the homohexamer, disrupting activity (Nemethova et al, 2016). Stabilizing amino acids can be predicted based on long-range interactions in protein structures and hydrophobicity and conservation of amino acid residues. Mutations found at stability centers were considered by us to be destabilizing and thus deleterious. SRide combines several methods to identify residues expected to play key roles in stabilization. It analyzes tertiary structures, rather than primary structures, and the evolutionary conserved residues contained within. A residue is predicted to be stabilizing if it is surrounded by hydrophobic residues, exhibits long-range order, has a high conservation score, and is part of a stability center (Magyar et al., 2005). C onclusion The data presented in this study represent extensive computational account of AKU nsSNPs, to filter out deleterious substitutions that are unlikely to a ff ect protein function and can o ff er a more feasible means for phenotype prediction based on the biochemical severity of the amino acid substitution and the protein sequence and structural information. A total of 423 SNPs were found to be associated with mutations in HGD gene and we identified 7 novel HGD gene variants and associated intragenic polymorphisms, and they provide a general understanding of the variability at the HGD gene locus in both AKU and normal individuals, population genetics and clinical studies are important to confirm the outcomes of such study. IV. V.