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Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance

The effects of synonymous single nucleotide variants (sSNVs) are often neglected because they do not alter protein primary structure. Nevertheless, there is growing evidence that synonymous variations may affect messenger RNA (mRNA) expression and protein conformation and activity, which may lead to...

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Autores principales: Jankowska, Katarzyna I., Meyer, Douglas, Holcomb, David D., Kames, Jacob, Hamasaki-Katagiri, Nobuko, Katneni, Upendra K., Hunt, Ryan C., Ibla, Juan C., Kimchi-Sarfaty, Chava
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society of Hematology 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9631689/
https://www.ncbi.nlm.nih.gov/pubmed/35667091
http://dx.doi.org/10.1182/bloodadvances.2022007065
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author Jankowska, Katarzyna I.
Meyer, Douglas
Holcomb, David D.
Kames, Jacob
Hamasaki-Katagiri, Nobuko
Katneni, Upendra K.
Hunt, Ryan C.
Ibla, Juan C.
Kimchi-Sarfaty, Chava
author_facet Jankowska, Katarzyna I.
Meyer, Douglas
Holcomb, David D.
Kames, Jacob
Hamasaki-Katagiri, Nobuko
Katneni, Upendra K.
Hunt, Ryan C.
Ibla, Juan C.
Kimchi-Sarfaty, Chava
author_sort Jankowska, Katarzyna I.
collection PubMed
description The effects of synonymous single nucleotide variants (sSNVs) are often neglected because they do not alter protein primary structure. Nevertheless, there is growing evidence that synonymous variations may affect messenger RNA (mRNA) expression and protein conformation and activity, which may lead to protein deficiency and disease manifestations. Because there are >21 million possible sSNVs affecting the human genome, it is not feasible to experimentally validate the effect of each sSNV. Here, we report a comprehensive series of in silico analyses assessing sSNV impact on a specific gene. ADAMTS13 was chosen as a model for its large size, many previously reported sSNVs, and associated coagulopathy thrombotic thrombocytopenic purpura. Using various prediction tools of biomolecular characteristics, we evaluated all ADAMTS13 sSNVs registered in the National Center for Biotechnology Information database of single nucleotide polymorphisms, including 357 neutral sSNVs and 19 sSNVs identified in patients with thrombotic thrombocytopenic purpura. We showed that some sSNVs change mRNA-folding energy/stability, disrupt mRNA splicing, disturb microRNA-binding sites, and alter synonymous codon or codon pair usage. Our findings highlight the importance of considering sSNVs when assessing the complex effects of ADAMTS13 alleles, and our approach provides a generalizable framework to characterize sSNV impact in other genes and diseases.
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spelling pubmed-96316892022-11-04 Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance Jankowska, Katarzyna I. Meyer, Douglas Holcomb, David D. Kames, Jacob Hamasaki-Katagiri, Nobuko Katneni, Upendra K. Hunt, Ryan C. Ibla, Juan C. Kimchi-Sarfaty, Chava Blood Adv Thrombosis and Hemostasis The effects of synonymous single nucleotide variants (sSNVs) are often neglected because they do not alter protein primary structure. Nevertheless, there is growing evidence that synonymous variations may affect messenger RNA (mRNA) expression and protein conformation and activity, which may lead to protein deficiency and disease manifestations. Because there are >21 million possible sSNVs affecting the human genome, it is not feasible to experimentally validate the effect of each sSNV. Here, we report a comprehensive series of in silico analyses assessing sSNV impact on a specific gene. ADAMTS13 was chosen as a model for its large size, many previously reported sSNVs, and associated coagulopathy thrombotic thrombocytopenic purpura. Using various prediction tools of biomolecular characteristics, we evaluated all ADAMTS13 sSNVs registered in the National Center for Biotechnology Information database of single nucleotide polymorphisms, including 357 neutral sSNVs and 19 sSNVs identified in patients with thrombotic thrombocytopenic purpura. We showed that some sSNVs change mRNA-folding energy/stability, disrupt mRNA splicing, disturb microRNA-binding sites, and alter synonymous codon or codon pair usage. Our findings highlight the importance of considering sSNVs when assessing the complex effects of ADAMTS13 alleles, and our approach provides a generalizable framework to characterize sSNV impact in other genes and diseases. American Society of Hematology 2022-09-21 /pmc/articles/PMC9631689/ /pubmed/35667091 http://dx.doi.org/10.1182/bloodadvances.2022007065 Text en Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved.
spellingShingle Thrombosis and Hemostasis
Jankowska, Katarzyna I.
Meyer, Douglas
Holcomb, David D.
Kames, Jacob
Hamasaki-Katagiri, Nobuko
Katneni, Upendra K.
Hunt, Ryan C.
Ibla, Juan C.
Kimchi-Sarfaty, Chava
Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance
title Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance
title_full Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance
title_fullStr Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance
title_full_unstemmed Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance
title_short Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance
title_sort synonymous adamts13 variants impact molecular characteristics and contribute to variability in active protein abundance
topic Thrombosis and Hemostasis
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9631689/
https://www.ncbi.nlm.nih.gov/pubmed/35667091
http://dx.doi.org/10.1182/bloodadvances.2022007065
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