Identification of Deleterious Missense Single Nucleotide Polymorphisms in Human Gene: An In Silico Study

Paul MK, Mukhopadhyay AK. Tyrosine kinase—role and significance in Cancer. Int J Med Sci. 2004;1(2):101–1152. https://doi.org/10.7150/ijms.1.101.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Azevedo A, Silva S, Rueff J. Non-receptor tyrosine kinases role and significance in hematological malignancies. In: Ren H, editor. Tyrosine kinases as druggable targets in cancer. London: IntechOpen; 2019. pp. 1–33.

Google Scholar 

Du Z, Lovly CM. Mechanisms of receptor tyrosine kinase activation in cancer. Mol Cancer. 2018;17(1):58. https://doi.org/10.1186/s12943-018-0782-4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gocek E, Moulas AN, Studzinski GP. Non-receptor protein tyrosine kinases signaling pathways in normal and cancer cells. Crit Rev Clin Lab Sci. 2014;51(3):125–37. https://doi.org/10.3109/10408363.2013.874403.

Article  CAS  PubMed  Google Scholar 

Lechner KS, Neurath MF, Weigmann B. Role of the IL-2 inducible tyrosine kinase ITK and its inhibitors in disease pathogenesis. J Mol Med. 2020;98:1385–95. https://doi.org/10.1007/s00109-020-01958-z.

Article  CAS  PubMed  Google Scholar 

Zhong Y, Johnson AJ, Byrd JC, Dubovsky JA. Targeting interleukin-2-inducible T-cell kinase (ITK) in T-cell related diseases. Postdoc J. 2014;2(6):1–11. https://doi.org/10.14304/surya.jpr.v2n6.1.

Article  PubMed  PubMed Central  Google Scholar 

Huang L, Ye K, McGee MC, Nidetz NF, Elmore JP, Limper CB, et al. Interleukin-2-inducible T-cell kinase deficiency impairs early pulmonary protection against Mycobacterium tuberculosis infection. Front Immunol. 2020;10:3103. https://doi.org/10.3389/fimmu.2019.03103.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ghosh S, Drexler I, Bhatia S, Gennery AR, Borkhardt A. Interleukin-2-inducible T-cell kinase deficiency—new patients, new insight? Front Immunol. 2018;9:979. https://doi.org/10.3389/fimmu.2018.00979.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huck K, Feyen O, Niehues T, Rüschendorf F, Hübner N, Laws H, et al. Girls homozygous for an IL-2–inducible T cell kinase mutation that leads to protein deficiency develop fatal EBV-associated lymphoproliferation. J Clin Invest. 2009;119(5):1350–8. https://doi.org/10.1172/jci37901.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Linka RM, Risse SL, Bienemann K, Werner M, Linka Y, Krux F, et al. Loss-of-function mutations within the IL-2 inducible kinase ITK in patients with EBV-associated lymphoproliferative diseases. Leukemia. 2012;26:963–71. https://doi.org/10.1038/leu.2011.371.

Article  CAS  PubMed  Google Scholar 

Dowdell KC, Howe M, Roy A, Niemela J, Wilson W, McElwee J, et al. A missense mutation impairs ITK function in a patient with severe Epstein-Barr virus disease. J Immunol. 2018;200(1Supplement):1665. https://doi.org/10.4049/jimmunol.200.Supp.166.5.

Article  Google Scholar 

Wallace JG, Alosaimi M, Khayat CD, Jaber F, Almutairi A, Beaussant-Cohen S, et al. ITK deficiency presenting as autoimmune lymphoproliferative syndrome. J Allergy Clin Immunol. 2020;147(2):743–5. https://doi.org/10.1016/j.jaci.2020.06.019.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Youssefian L, Vahidnezhad H, Yousefi M, Saeidian AH, Azizpour A, Touati A, et al. Inherited Interleukin 2–inducible T-cell kinase deficiency in siblings with epidermodysplasia verruciformis and hodgkin lymphoma. Clin Infect Dis. 2019;68(11):1983–1941. https://doi.org/10.1093/cid/ciy942.

Article  CAS  Google Scholar 

Ogishi M, Yang R, Rodriguez R, Golec DP, Martin E, Philippot Q, et al. Inherited human ITK deficiency impairs IFN-γ immunity and underlies tuberculosis. J Exp Med. 2023;220(1):e20220484. https://doi.org/10.1084/jem.20220484.

Article  CAS  PubMed  Google Scholar 

Farrokh P. Bioinformatics analysis of non-synonymous single nucleotide polymorphisms in human Adk gene. Russ J Genet. 2024;60(6):828–37. https://doi.org/10.1134/S1022795424700273.

Article  CAS  Google Scholar 

Pal LR, Moult J. Genetic basis of common human disease: insight into the role of missense SNPs from genome wide association studies. J Mol Biol. 2015;427(13):2271–89. https://doi.org/10.1016/j.jmb.2015.04.014.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31(13):3812–4. https://doi.org/10.1093/nar/gkg509.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Capriotti E, Calabrese R, Casadio R. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics. 2006;22(22):2729–34. https://doi.org/10.1093/bioinformatics/btl423.

Article  CAS  PubMed  Google Scholar 

Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R. WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. BMC Genomics. 2013;14(Suppl 3):S6. https://doi.org/10.1186/1471-2164-14-S3-S6.

Article  PubMed  PubMed Central  Google Scholar 

Yates CM, Filippis I, Kelley LA, Sternberg MJE. SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features. J Mol Biol. 2014;426(14):2692–701. https://doi.org/10.1016/j.jmb.2014.04.026.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GLA, Edwards KJ, et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat. 2013;34(1):57–65. https://doi.org/10.1002/humu.22225.

Article  CAS  PubMed  Google Scholar 

Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet. 2013. https://doi.org/10.1002/0471142905.hg0720s76.

Schubach M, Maass T, Nazaretyan L, Röner S, Kircher M. CADD v1.7: using protein Language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions. Nucleic Acids Res. 2024;52:D1143–54. https://doi.org/10.1093/nar/gkad989.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tang H, Thomas PD. PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation. Bioinformatics. 2016;32(14):2230–2. https://doi.org/10.1093/bioinformatics/btw222.

Article  CAS  PubMed  Google Scholar 

Capriotti E, Altman RB, Bromberg Y. Collective judgment predicts disease-associated single nucleotide variants. BMC Genomics. 2013;14(Suppl 3):S2. https://doi.org/10.1186/1471-2164-14-S3-S2.

Article  PubMed  PubMed Central  Google Scholar 

Pejaver V, Urresti J, Lugo-Martinez J, Pagel KA, Lin GN, Nam H, et al. Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. Nat Commun. 2020;11:5918. https://doi.org/10.1038/s41467-020-19669-x.

Article  CAS  PubMed  PubMed Central  Google Scholar 

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:W306–10. https://doi.org/10.1093/nar/gki375.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cheng J, Randall A, Baldi P. Prediction of protein stability changes for single-site mutations using support vector machines. Proteins. 2006;62(4):1125–32. 1002/prot.20810.

CAS  PubMed  Google Scholar 

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