Scrutinizing Deleterious Nonsynonymous SNPs and Their Effect on Human POLD1 Gene
POLD1 (DNA polymerase delta 1, catalytic subunit) is a protein-coding gene that encodes the large catalytic subunit (POLD1/p125) of the DNA polymerase delta (Polδ) complex. The consequence of missense or nonsynonymous SNPs (nsSNPs), which occur in the coding region of a specific gene, is the replace...
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| Format: | Article |
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Wiley
2022-01-01
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| Series: | Genetics Research |
| Online Access: | http://dx.doi.org/10.1155/2022/1740768 |
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| author | Md. Nazmul Islam Bappy Anindita Roy Md Gulam Rabbany Rabbi Nusrat Jahan Fahmida Akther Chowdhury Syeda Farjana Hoque Emran Hossain Sajib Parvez Khan Ferdaus Mohd Altaf Hossain Kazi Md. Ali Zinnah |
| author_facet | Md. Nazmul Islam Bappy Anindita Roy Md Gulam Rabbany Rabbi Nusrat Jahan Fahmida Akther Chowdhury Syeda Farjana Hoque Emran Hossain Sajib Parvez Khan Ferdaus Mohd Altaf Hossain Kazi Md. Ali Zinnah |
| author_sort | Md. Nazmul Islam Bappy |
| collection | DOAJ |
| description | POLD1 (DNA polymerase delta 1, catalytic subunit) is a protein-coding gene that encodes the large catalytic subunit (POLD1/p125) of the DNA polymerase delta (Polδ) complex. The consequence of missense or nonsynonymous SNPs (nsSNPs), which occur in the coding region of a specific gene, is the replacement of single amino acid. It may also change the structure, stability, and/or functions of the protein. Mutation in the POLD1 gene is associated with autosomal dominant predisposition to colonic adenomatous polyps, colon cancer, endometrial cancer (EDMC), breast cancer, and brain tumors. These de novo mutations in the POLD1 gene also result in autosomal dominant MDPL syndrome (mandibular hypoplasia, deafness, progeroid features, and lipodystrophy). In this study, genetic variations of POLD1 which may affect the structure and/or function were analyzed using different types of bioinformatics tools. A total of 17038 nsSNPs for POLD1 were collected from the NCBI database, among which 1317 were missense variants. Out of all missense nsSNPs, 28 were found to be deleterious functionally and structurally. Among these deleterious nsSNPs, 23 showed a conservation scale of >5, 2 were predicted to be associated with binding site formation, and one acted as a posttranslational modification site. All of them were involved in coil, extracellular structures, or helix formation, and some cause the change in size, charge, and hydrophobicity. |
| format | Article |
| id | doaj-art-4e18f22601c648bdbbfa2dbeb6f47ce4 |
| institution | Kabale University |
| issn | 1469-5073 |
| language | English |
| publishDate | 2022-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Genetics Research |
| spelling | doaj-art-4e18f22601c648bdbbfa2dbeb6f47ce42025-08-20T03:36:41ZengWileyGenetics Research1469-50732022-01-01202210.1155/2022/1740768Scrutinizing Deleterious Nonsynonymous SNPs and Their Effect on Human POLD1 GeneMd. Nazmul Islam Bappy0Anindita Roy1Md Gulam Rabbany Rabbi2Nusrat Jahan3Fahmida Akther Chowdhury4Syeda Farjana Hoque5Emran Hossain Sajib6Parvez Khan7Ferdaus Mohd Altaf Hossain8Kazi Md. Ali Zinnah9Faculty of Biotechnology and Genetic EngineeringFaculty of Biotechnology and Genetic EngineeringFaculty of Biotechnology and Genetic EngineeringFaculty of Biotechnology and Genetic EngineeringFaculty of Biotechnology and Genetic EngineeringFaculty of Biotechnology and Genetic EngineeringFaculty of Biotechnology and Genetic EngineeringDept. of Biochemistry & Molecular BiologyFaculty of VeterinaryFaculty of Biotechnology and Genetic EngineeringPOLD1 (DNA polymerase delta 1, catalytic subunit) is a protein-coding gene that encodes the large catalytic subunit (POLD1/p125) of the DNA polymerase delta (Polδ) complex. The consequence of missense or nonsynonymous SNPs (nsSNPs), which occur in the coding region of a specific gene, is the replacement of single amino acid. It may also change the structure, stability, and/or functions of the protein. Mutation in the POLD1 gene is associated with autosomal dominant predisposition to colonic adenomatous polyps, colon cancer, endometrial cancer (EDMC), breast cancer, and brain tumors. These de novo mutations in the POLD1 gene also result in autosomal dominant MDPL syndrome (mandibular hypoplasia, deafness, progeroid features, and lipodystrophy). In this study, genetic variations of POLD1 which may affect the structure and/or function were analyzed using different types of bioinformatics tools. A total of 17038 nsSNPs for POLD1 were collected from the NCBI database, among which 1317 were missense variants. Out of all missense nsSNPs, 28 were found to be deleterious functionally and structurally. Among these deleterious nsSNPs, 23 showed a conservation scale of >5, 2 were predicted to be associated with binding site formation, and one acted as a posttranslational modification site. All of them were involved in coil, extracellular structures, or helix formation, and some cause the change in size, charge, and hydrophobicity.http://dx.doi.org/10.1155/2022/1740768 |
| spellingShingle | Md. Nazmul Islam Bappy Anindita Roy Md Gulam Rabbany Rabbi Nusrat Jahan Fahmida Akther Chowdhury Syeda Farjana Hoque Emran Hossain Sajib Parvez Khan Ferdaus Mohd Altaf Hossain Kazi Md. Ali Zinnah Scrutinizing Deleterious Nonsynonymous SNPs and Their Effect on Human POLD1 Gene Genetics Research |
| title | Scrutinizing Deleterious Nonsynonymous SNPs and Their Effect on Human POLD1 Gene |
| title_full | Scrutinizing Deleterious Nonsynonymous SNPs and Their Effect on Human POLD1 Gene |
| title_fullStr | Scrutinizing Deleterious Nonsynonymous SNPs and Their Effect on Human POLD1 Gene |
| title_full_unstemmed | Scrutinizing Deleterious Nonsynonymous SNPs and Their Effect on Human POLD1 Gene |
| title_short | Scrutinizing Deleterious Nonsynonymous SNPs and Their Effect on Human POLD1 Gene |
| title_sort | scrutinizing deleterious nonsynonymous snps and their effect on human pold1 gene |
| url | http://dx.doi.org/10.1155/2022/1740768 |
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