اخبار و اعلانات

 آمار

تعداد نشریات24
تعداد شماره‌ها850
تعداد مقالات7,548
تعداد مشاهده مقاله13,324,207
تعداد دریافت فایل اصل مقاله11,541,399
Shivani, Narendra, Smiline-Girija, Aseervatham Selvi, Paramasivam, Arumugam, Vijayashree-Priyadharsini, Jayaseelan. (1399). Computational approach towards identification of pathogenic missense mutations in AMELX gene and their possible association with amelogenesis imperfecta. , 9(2), 63-69. doi: 10.22099/mbrc.2020.35413.1456
Narendra Shivani; Aseervatham Selvi Smiline-Girija; Arumugam Paramasivam; Jayaseelan Vijayashree-Priyadharsini. "Computational approach towards identification of pathogenic missense mutations in AMELX gene and their possible association with amelogenesis imperfecta". , 9, 2, 1399, 63-69. doi: 10.22099/mbrc.2020.35413.1456
Shivani, Narendra, Smiline-Girija, Aseervatham Selvi, Paramasivam, Arumugam, Vijayashree-Priyadharsini, Jayaseelan. (1399). 'Computational approach towards identification of pathogenic missense mutations in AMELX gene and their possible association with amelogenesis imperfecta', , 9(2), pp. 63-69. doi: 10.22099/mbrc.2020.35413.1456
Shivani, Narendra, Smiline-Girija, Aseervatham Selvi, Paramasivam, Arumugam, Vijayashree-Priyadharsini, Jayaseelan. Computational approach towards identification of pathogenic missense mutations in AMELX gene and their possible association with amelogenesis imperfecta. , 1399; 9(2): 63-69. doi: 10.22099/mbrc.2020.35413.1456

Computational approach towards identification of pathogenic missense mutations in AMELX gene and their possible association with amelogenesis imperfecta

Molecular Biology Research Communications
مقاله 4، دوره 9، شماره 2، 2020، صفحه 63-69    اصل مقاله (250.9 K)
نوع مقاله: Original article
شناسه دیجیتال (DOI): 10.22099/mbrc.2020.35413.1456
نویسندگان
Narendra Shivani1؛ Aseervatham Selvi Smiline-Girija2؛ Arumugam Paramasivam3؛ Jayaseelan Vijayashree-Priyadharsini* 3
1Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
2Department of Microbiology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, 162, Poonamallee High Road, Chennai 600077, Tamil Nadu, India
3Biomedical Research Unit and Laboratory Animal Centre-Dental Research Cell, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai 600077, India
چکیده
Amelogenin gene (AMEL-X) encodes an enamel protein called amelogenin, which plays a vital role in tooth development. Any mutations in this gene or the associated pathway lead to developmental abnormalities of the tooth. The present study aims to analyze functional missense mutations in AMEL-X genes and derive an association with amelogenesis imperfecta. The information on missense mutations of human AMEL-X gene was collected from Ensembl database (https://asia.ensembl.org). Three different computational tools viz., SIFT, PolyPhen and PROVEAN were used to identify the deleterious or pathogenic forms of mutations in the gene studied. I-Mutant Suit was used to identify the stability of the proteins identified as deleterious by the three tools. Further, MutPred analysis revealed the pathogenicity of these mutations. Among 96 missense variants reported in AMEL-X gene, 18 were found to be deleterious using the three prediction tools (SIFT, PolyPhen and PROVEAN). When these variants were subjected to protein stability analysis, about 14 missense variants showed decreased stability whereas the other 8 variants showed increased stability. Further, these variants were analyzed using MutPred which identified 9 variants to be highly pathogenic. ExAC database revealed that all the pathogenic mutations had a minor allele frequency less than 0.01. The in silico analysis revealed highly pathogenic mutations in amelogenin gene which could have a putative association with amelogenesis imperfecta. These mutations should be screened in patients for early diagnosis of susceptibility to AI.
کلیدواژه‌ها
Mutation؛ AMELX gene؛ Enamel؛ Amelogenesis imperfecta؛ In silico
مراجع

1. Nowwarote N, Theerapanon T, Osathanon T, Pavasant P, Porntaveetus T, Shotelersuk V. Amelogenesis imperfecta: A novel FAM83H mutation and characteristics of periodontal ligament cells. Oral Dis 2018;24:1522-1531.

2. Bandaru BK, Thankappan P, Kumar Nandan SR, Amudala R, Annem SK, Rajendra Santosh AB. The prevalence of developmental anomalies among school children in Southern district of Andhra Pradesh, India. J Oral Maxillofac Pathol 2019;23:160.

3. Gadhia K, McDonald S, Arkutu N, Malik K. Amelogenesis Imperfecta: An introduction. Br Dent J 2012;212:377-379.

4. Smith CEL, Poulter JA, Antanaviciute A, Kirkham J, Brookes SJ, Inglehearn CF, Mighell AJ. Amelogenesis Imperfecta; Genes, Proteins, and Pathways. Front Physiol. 2017;8:435.

5. Gibson CW, Yuan ZA, Hall B, Longenecker G, Chen E, Thyagarajan T, Sreenath T,Wright JT, Decker S, Piddington R, Harrison G, Kulkarni AB. Amelogenin-deficient mice display an amelogenesis imperfecta phenotype. J  Biol Chem 2001;276:31871-31875.

6. Mardh CK, Backman B, Holmgren G, Hu JC, Simmer JP, Forsman-Semb K. A nonsense mutation in the enamelin gene causes local hypoplastic autosomal dominant amelogenesis imperfecta (AIH2) Hum Mol Genet 2002;11:1069-1074.

7. Hart TC, Hart  PS, Gorry MC, Michalec MD, Ryu OH, Uygur C, Ozdemir D, Firatli S, Aren G, Firatli E. Novel ENAM mutation responsible for autosomal recessive Amelogenesis imperfecta and localised enamel defects. J  Med Genet. 2003;40:900-906.

8. Kim JW, Zhang H, Seymen F, Koruyucu M, Hu Y, Kang J, Kim YJ,  Ikeda A, Kasimoglu Y, Bayram M, Zhang C, Kawasaki K, Bartlett JD, Saunders TL, Simmer JP, Hu JC. Mutations in RELT cause autosomal recessive  amelogenesis imperfecta. Clin Genet 2019;95;375-383. 

9. Wright JT, Hart PS, Aldred MJ, Seow K, Crawford PJ, Hong SP, Gibson CW, Hart TC. Relationship of phenotype and genotype in X-linked amelogenesis imperfecta. Connect Tissue Res 2003;44:72-78.

10. Crawford PJ, Aldred M, Bloch-Zupan A. Amelogenesis imperfecta. Orphanet J Rare Dis 2007;4:17.

11. Sarah EH, McLaren W, Laurent G, Anja T, Helen S, Dan S, Andrew P, Irina MA, Stephen JT, Paul F, Fiona C. Ensembl variation resources. Database 2018;2018:119.

12. Vaser R, Adusumalli S, Leng SN, Sikic M, Ng PC. SIFT missense predictions for genomes. Nat Protco 2016;11:1-9.

13. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods 2010;7:248-249.

14. Choi Y, Chan AP. PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics 2015; 31:2745-2747.

15. Capriotti E, Fariselli P, Casadio R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res 2005;33:W306-310.

16. Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, Mooney SD, Radivojac P. Automated inference of molecular mechanisms of disease from amino acid substitutions.   Bioinformatics 2009;25:2744-2750.

17. Pejaver V, Urresti J, Lugo-Martinez J, Pagel KA, Lin GN, Nam H, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. MutPred2: inferring the molecular and phenotypic impact of amino acid variants. bioRxiv 2017; 134981; doi: https://doi.org/10.1101/134981.

18. Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T,O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J,Cooper DN, Deflaux N, DePristo M, Do R, Flannick J, Fromer M, Gauthier L,Goldstein J, Gupta N, Howrigan D, Kiezun A, Kurki MI, Moonshine AL, Natarajan P, Orozco L, Peloso GM, Poplin R, Rivas MA, Ruano-Rubio V, Rose SA, Ruderfer DM, Shakir K, Stenson PD, Stevens C, Thomas BP, Tiao G, Tusie-Luna MT, Weisburd B,Won HH, Yu D, Altshuler DM, Ardissino D, Boehnke M, Danesh J, Donnelly S, Elosua R, Florez JC, Gabriel SB, Getz G, Glatt SJ, Hultman CM, Kathiresan S, Laakso M,McCarroll S, McCarthy MI, McGovern D, McPherson R, Neale BM, Palotie A, Purcell SM, Saleheen D, Scharf JM, Sklar P, Sullivan PF, Tuomilehto J, Tsuang MT, Watkins HC, Wilson JG, Daly MJ, MacArthur DG; Exome Aggregation Consortium. Analysis of protein-coding genetic variation in 60,706 humans. Nature 2016;536:285-291.

19. Witkop CJ Jr.Amelogenesis imperfecta, dentinogenesis imperfecta and dentin dysplasia revisited: problems in classification. J Oral Pathol 1988;17:547-553.

20. El-Sayed W, Shore RC, Parry DA, Inglehearn CF, Mighell AJ. Hypomaturation amelogenesis imperfecta due to WDR72 mutations: a novel mutation and ultrastructural analyses of deciduous teeth. Cells Tissues Organs 2011; 194:60-66.

22.Kim  YJ, Kang  J, Shin  TJ, Hyun  HK, Lee  SH, Lee  ZH, Kim  JW. A novel AMELX mutation causes hypoplastic amelogenesis imperfecta. Arch Oral Biol 2017;76,61-65.

22. Cho ES, Kim KJ, Lee KE, Lee EJ, Yun CY, Lee MJ, Shin TJ, Hyun HK, Kim YJ, Lee SH, Jung HS, Lee ZH, Kim JW. Alteration of conserved alternative splicing in AMELX causes enamel defects. J Dent Res 2014;93:980-987.

23. Snead ML, Zhu DH, Lei Y, Luo W, Bringas PO Jr, Sucov HM, Rauth RJ, Paine ML, White SN. A simplified genetic design for mammalian enamel. Biomaterials 2011;32:3151-3157.

24. Hart  PS, Aldred  MJ, Crawford  PJ, Wright  NJ, Hart  TC, Wright  JT. Amelogenesis imperfecta phenotype-genotype correlations with two amelogenin gene mutations. Arch Oral Biol 2002;47:261-265.

25. Bidlack FB, Xia Y, Pugach MK. Dose-dependent rescue of KO amelogenin enamel by transgenes in vivo. Front Physiol 2017;8:932.

26. Duan X, Yang S, Zhang H, Wu J, Zhang Y, Ji D, Tie L, Boerkoel CF. A Novel AMELX  mutation, its phenotypic features, and skewed X inactivation. J Dent Res 2019;98:870-878.

آمار
تعداد مشاهده مقاله: 1,146
تعداد دریافت فایل اصل مقاله: 827


سامانه مدیریت نشریات علمی. قدرت گرفته از سیناوب