Computational Analysis of Single Nucleotide Polymorphism (SNPs) in Human<i>SLC5A1</i> Gene

Rashid Abualamah Albasheer Abbas; Afra Mohamed Suliman Albakry; Mona Abdelrahman Mohamed Khaier; Hind Abdelaziz Elnasri

doi:doi:10.11648/j.ijbse.20190704.12

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

Rashid Abualamah Albasheer Abbas, Afra Mohamed Suliman Albakry, Mona Abdelrahman Mohamed Khaier, Hind Abdelaziz Elnasri

Published in International Journal of Biomedical Science and Engineering (Volume 7, Issue 4)

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), 2024. Published by Science Publishing Group

Keywords

Computational Analysis, Glucose–Galactose Malabsorption, SLC5A1 Gene

References

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[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.
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[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.
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[20]	Nielsen M., Lundegaard C., Lund O., Petersen TN. (2010) CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles. Nucleic Acids Research, Vol. 38.
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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

Rashid Abualamah Albasheer Abbas

Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan
Afra Mohamed Suliman Albakry

Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan
Mona Abdelrahman Mohamed Khaier

Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum, Sudan
Hind Abdelaziz Elnasri

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

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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}
}

Copy | Download

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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