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Computational Analysis of Single Nucleotide Polymorphism (SNPs) in HumanSLC5A1 Gene

Received: 15 August 2019     Accepted: 8 November 2019     Published: 23 December 2019
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Abstract

Glucose galactose malabsorption (GGM) is an autosomal recessive disease manifesting within the first weeks of life. It is characterized by a selective failure to absorb dietary glucose and galactose from the intestine leading to severe life threatening diarrhea and dehydration. Mutations in the Na+/glucose co-transporter gene (SLC5A1 gene) have been determined to be associated with congenital GGM. In this study different computational tools were used to investigate the nsSNPs (Single nucleotide polymorphisms) in the SLC5A1 gene and to determine their effects on the protein function and structure. SLC5A1 gene was investigated in NCBI database and SNPs were analyzed using seven computational software (SIFT, Polyphen-2, PROVEAN, SNPs and GO, PHD-SNPs, I-mutant and MU Pro). The protein structural analysis was done by modeling using Project Hope and Chimera after homology modeling by CPH models 3.2. In addition Gene MANIA software was used to study the association between this gene and related ones. A total of 166 nsSNPs were obtained from the SNPs database in NCBI during 2019. A total of 37 SNP were predicted to be deleterious using SIFT software, while 25 SNPs were predicted to be probably damaging by PolyPhen-2 and 30 SNPs were predicted to be deleterious by PROVEAN. The results of SIFT, PolyPhen-2, PROVEAN, SNPs&GO, PHD-SNP collectively revealed that 16 SNPs were predicted to be highly damaging.

Published in International Journal of Biomedical Science and Engineering (Volume 7, Issue 4)
DOI 10.11648/j.ijbse.20190704.12
Page(s) 85-91
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2019. Published by Science Publishing Group

Keywords

Computational Analysis, Glucose–Galactose Malabsorption, SLC5A1 Gene

References
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[2] Xin B, Wang H. (2011). Multiple sequence variations in SLC5A1 gene are associated with glucose–galactose malabsorption in a large cohort of Old Order Amish. Clin Genet. 79: 86–91.
[3] Lindquist B, Meeuwisse GW. (1962) Chronic diarrhea caused by monosaccharide malabsorption. Acta Paediatr. 51: 674–685.
[4] Wright EM, Turk E, Martin MG. (2002). Molecular basis for glucose galactose malabsorption. Cell Biochem Biophys. 36: 115–121.
[5] Assiri A, Saeed A, Alnimri A, et al. (2013). Five Arab children with glucose-galactose malabsorption. Paediatr Intern Child Health. 33: 108-10.
[6] Al- Suyufi Y, Al Saleem K, Al- Mehaidib A. et al. (2018). SLC5A1 mutations in Saudi Arabian patients with congential glucose- galactose malabsorption. J Pediatr Gastronterol Nutr. 66: 250-2.
[7] Hediger MA, Coady MJ, Ikeda TS, et al. (1987). Expression cloning and cDNA sequencing of the Na+/glucose co-transporter. Nature. 330: 379-81.
[8] Turk E, Martin MG, Wright EM. (1994). Structure of the human Na+/glucose cotransporter gene SGLT1. The Journal of biological chemistry. 269: 15204-9.
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[10] Chasman D, Adams RM (2001) Predicting the functional consequences of non-synonymous single nucleotide polymorphisms:structure-based assessment of amino acid variation. J Mol Biol 307: 683–706.
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[16] Capriotti E, Altman RB, Bromberg Y. (2013) Collective judgment predicts disease-associated single nucleotide variants. BMC Genomics. 14 Suppl 3:S2.
[17] Capriotti E, Fariselli P, Casadio R. (2005) I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res., 33 (Web Server issue): W306-W310.
[18] Cheng J., Randall A., and Baldi P. (2005). Prediction of Protein Stability Changes for Single Site Mutations Using Support Vector Machines. Proteins: Structure, Function, vol. 62, no. 4, pp. 1125-1132.
[19] Venselaar H, TeBeek TA, Kuipers RK, Hekkelman ML, Vriend G. (2010). Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics. 8; 11: 548.
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    Rashid Abualamah Albasheer Abbas, Afra Mohamed Suliman Albakry, Mona Abdelrahman Mohamed Khaier, Hind Abdelaziz Elnasri. (2019). Computational Analysis of Single Nucleotide Polymorphism (SNPs) in HumanSLC5A1 Gene. International Journal of Biomedical Science and Engineering, 7(4), 85-91. https://doi.org/10.11648/j.ijbse.20190704.12

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    ACS Style

    Rashid Abualamah Albasheer Abbas; Afra Mohamed Suliman Albakry; Mona Abdelrahman Mohamed Khaier; Hind Abdelaziz Elnasri. Computational Analysis of Single Nucleotide Polymorphism (SNPs) in HumanSLC5A1 Gene. Int. J. Biomed. Sci. Eng. 2019, 7(4), 85-91. doi: 10.11648/j.ijbse.20190704.12

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    AMA Style

    Rashid Abualamah Albasheer Abbas, Afra Mohamed Suliman Albakry, Mona Abdelrahman Mohamed Khaier, Hind Abdelaziz Elnasri. Computational Analysis of Single Nucleotide Polymorphism (SNPs) in HumanSLC5A1 Gene. Int J Biomed Sci Eng. 2019;7(4):85-91. doi: 10.11648/j.ijbse.20190704.12

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  • @article{10.11648/j.ijbse.20190704.12,
      author = {Rashid Abualamah Albasheer Abbas and Afra Mohamed Suliman Albakry and Mona Abdelrahman Mohamed Khaier and Hind Abdelaziz Elnasri},
      title = {Computational Analysis of Single Nucleotide Polymorphism (SNPs) in HumanSLC5A1 Gene},
      journal = {International Journal of Biomedical Science and Engineering},
      volume = {7},
      number = {4},
      pages = {85-91},
      doi = {10.11648/j.ijbse.20190704.12},
      url = {https://doi.org/10.11648/j.ijbse.20190704.12},
      eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijbse.20190704.12},
      abstract = {Glucose galactose malabsorption (GGM) is an autosomal recessive disease manifesting within the first weeks of life. It is characterized by a selective failure to absorb dietary glucose and galactose from the intestine leading to severe life threatening diarrhea and dehydration. Mutations in the Na+/glucose co-transporter gene (SLC5A1 gene) have been determined to be associated with congenital GGM. In this study different computational tools were used to investigate the nsSNPs (Single nucleotide polymorphisms) in the SLC5A1 gene and to determine their effects on the protein function and structure. SLC5A1 gene was investigated in NCBI database and SNPs were analyzed using seven computational software (SIFT, Polyphen-2, PROVEAN, SNPs and GO, PHD-SNPs, I-mutant and MU Pro). The protein structural analysis was done by modeling using Project Hope and Chimera after homology modeling by CPH models 3.2. In addition Gene MANIA software was used to study the association between this gene and related ones. A total of 166 nsSNPs were obtained from the SNPs database in NCBI during 2019. A total of 37 SNP were predicted to be deleterious using SIFT software, while 25 SNPs were predicted to be probably damaging by PolyPhen-2 and 30 SNPs were predicted to be deleterious by PROVEAN. The results of SIFT, PolyPhen-2, PROVEAN, SNPs&GO, PHD-SNP collectively revealed that 16 SNPs were predicted to be highly damaging.},
     year = {2019}
    }
    

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  • TY  - JOUR
    T1  - Computational Analysis of Single Nucleotide Polymorphism (SNPs) in HumanSLC5A1 Gene
    AU  - Rashid Abualamah Albasheer Abbas
    AU  - Afra Mohamed Suliman Albakry
    AU  - Mona Abdelrahman Mohamed Khaier
    AU  - Hind Abdelaziz Elnasri
    Y1  - 2019/12/23
    PY  - 2019
    N1  - https://doi.org/10.11648/j.ijbse.20190704.12
    DO  - 10.11648/j.ijbse.20190704.12
    T2  - International Journal of Biomedical Science and Engineering
    JF  - International Journal of Biomedical Science and Engineering
    JO  - International Journal of Biomedical Science and Engineering
    SP  - 85
    EP  - 91
    PB  - Science Publishing Group
    SN  - 2376-7235
    UR  - https://doi.org/10.11648/j.ijbse.20190704.12
    AB  - Glucose galactose malabsorption (GGM) is an autosomal recessive disease manifesting within the first weeks of life. It is characterized by a selective failure to absorb dietary glucose and galactose from the intestine leading to severe life threatening diarrhea and dehydration. Mutations in the Na+/glucose co-transporter gene (SLC5A1 gene) have been determined to be associated with congenital GGM. In this study different computational tools were used to investigate the nsSNPs (Single nucleotide polymorphisms) in the SLC5A1 gene and to determine their effects on the protein function and structure. SLC5A1 gene was investigated in NCBI database and SNPs were analyzed using seven computational software (SIFT, Polyphen-2, PROVEAN, SNPs and GO, PHD-SNPs, I-mutant and MU Pro). The protein structural analysis was done by modeling using Project Hope and Chimera after homology modeling by CPH models 3.2. In addition Gene MANIA software was used to study the association between this gene and related ones. A total of 166 nsSNPs were obtained from the SNPs database in NCBI during 2019. A total of 37 SNP were predicted to be deleterious using SIFT software, while 25 SNPs were predicted to be probably damaging by PolyPhen-2 and 30 SNPs were predicted to be deleterious by PROVEAN. The results of SIFT, PolyPhen-2, PROVEAN, SNPs&GO, PHD-SNP collectively revealed that 16 SNPs were predicted to be highly damaging.
    VL  - 7
    IS  - 4
    ER  - 

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Author Information
  • Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan

  • Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan

  • Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan

  • Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan

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