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

Computational Analysis of Possibly Pathogenic Non-Synonymous Single Nucleotide Polymorphisms Variants in HGD Gene Nabaa Kamal Alshafei α , Intisar Hassan Saeed σ & Mona Abdelrahman Mohamed Khaier ρ Abstract- Alkaptonuria (AKU) is an autosomal recessive disorder caused by mutations in the homogentisate-1,2- dioxygenase (HGD) gene leading to the deficiency of HGD enzyme activity. The aim of this study was to use some computational bioinformatics tools to predict the most pathogenic non-synonymous mutations in the HGD gene. The data was retrieved from the SNPs database of the National Center for Biotechnology Information (dbSNPs) (Oct. 2021). The primary sequence of the protein was obtained from the UniProt database (Oct. 2021). The pathogenic effect on the protein structure and function was predicted by GeneMANIA, SIFT, Provean, Polyphen-2, I-Mutant, and Project Hope software. The human HGD gene comprises a total of 423SNPs out of that 348 were found to be synonymous, 75 were missense SNPs (nsSNPs). Analysis of the nsSNPs by SIFT predicts 35 as deleterious and 40 as tolerated ones. Using Provean only 30 were deleterious while 5 SNPs were neutral. Taking the deleterious nsSNPSs to Polyphen-2, 25 nsSNPs were damaging (22 were probably damaging and 3 were possibly damaging), while 5 were benign. Using SNPs&GO 11 nsSNPs were predicted as disease-related while 14 were predicted to be neutral. Project Hope analysis the mutations according to their size, charge, hydrophobicity, and conservancy. In conclusion, 7 of the predicted mutations were not reported before according to the ClinVar database while the remaining 4 were reported from patients through DNA sequencing. More research is needed to confirm these new mutations in patients. Keywords: Alkaptonuria (AKU); homogentisate-1,2- dioxygenase (HGD) gene; I-Mutant; Non-synonymous Single Nucleotide Polymorphisms (nsSNPs); Project Hope, and SIFT. I. I ntroduction he HGD gene provides instructions for making Homogentisate oxidase enzyme, which is active mainly in the liver and kidneys. This enzyme participates in a stepwise process that breaks down two amino acids, phenylalanine and tyrosine when they are no longer needed or are present in excess. These two amino acids also play a role in making certain Author α : Department of Biochemistry, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan. Author σ : Department of Physiology, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan. Corresponding Author ρ : Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan. e-mail: munakhaier@gmail.com hormones, pigments, and brain chemicals called neurotransmitters (Aliu et al., 2018). Homogentisate oxidase is responsible for a specific step in the breakdown of phenylalanine and tyrosine. Previous steps convert the two amino acids into a molecule called homogentisic acid. Homogentisate oxidase adds two oxygen atoms to homogentisic acid, converting it to another molecule called maleylacetoacetate. Other enzymes break down maleylacetoacetate into smaller molecules that are later used for energy or to make other products that can be used by the body (Berniniet al., 2021). Mutations in the HGD gene inactivate Homogentisate oxidase by changing its structure. Without a functional version of this enzyme, phenylalanine and tyrosine are not broken down properly and homogentisic acid builds up in the body. Excess homogentisic acid and related compounds are deposited in connective tissues such as cartilage and skin, which causes them to darken. Over time, a buildup of this substance in the joints leads to arthritis. Homogentisic acid is also excreted in the urine, making the urine turn dark when exposed to air(Wilson et al., 2021). Single Nucleotides Polymorphisms (SNPs) responsible for the maximum communal type of hereditary change in humans. Regarding throughout a coding areas of mammalian genomes, 500,000 SNPs fell into it (Shameem et al., 2021).The HGD protein protomer is composed of 445 amino acids (NP_000178.2) and is expressed in the prostate, small intestine, colon, kidney, and liver (Fernández et al., 1996), as well as in osteoarticular compartment cells (chondrocytes, synoviocytes, and osteoblasts) (Laschiet al., 2012).The enzymatic defect in AKU is caused by recessive mutations within the HGD gene (HGNC:4892), a single-copy gene that spans 54363bp of genomic sequence (3q13.33) and is split into 14 exons and codes for the HGD protomer (Zatkova and Nemethova, 2015.). The active form of the HGD protein is organized as a hexamer comprising two disc-like trimers. An intricate network of non-covalent interactions is required to maintain the spatial structure of the protomer, of the trimer andfinally of the hexamer, which can be easily disrupted by variants leading to effects on enzyme function (Titus et al., 2000). Compromising enzyme function, the missense variants are predicted to affect T 15 Year 2022 Global Journal of Medical Research Volume XXII Issue IV Version I ( D ) F © 2022 Global Journals