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Molecular Origins of the Mendelian Rare Diseases Reviewed by Orpha.net: A Structural Bioinformatics Investigation
Open accessPreprint — published as 10.3390/ijms25136953 · Paper page
Abstract
The study of rare diseases is important not only for the individuals affected but also for the advancement of medical knowledge and a deeper understanding of human biology and genetics. The wide repertoire of structural information now available from reliable and accurate prediction methods provides the opportunity to investigate the molecular origins of most of the rare diseases reviewed in the Orpha.net database. Thus, it has been possible to analyze the topology of the missense mutations found in the 2,535 proteins involved in Mendelian rare diseases (MRD), which form the database for our structural bioinformatics study. The amino acid substitutions responsible for MRD show different mutation site distributions at different three-dimensional protein depths. We then predicted the depth-dependent effects of mutations for the 20,248 pathogenic variants that are present in our database. The results of this structural bioinformatics investigation are relevant, as they provide additional clues to mitigate the damage caused by MRD.
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![Figure 3 The sterical distribution of mutation sites in MRD proteins of our dataset. Structural data are clustered according to the POPS algorithm [4], and the Q(SASA) parameter categorizes the 20.248 mutation sites as follows: (i) fully buried < 0.15; (ii) internal > 0.15 and <0.24; (iii) intermediate > 0.24 and <0.60; (iv) external > 0.60 and <0.80; and (v) fully solvent-exposed > 0.8.](/paper-figures/c35b12a41abb4ecf9134a351718b974d/molecular-origins-of-the-mendelian-rare-diseases-reviewed-by-orpha-net-a-figure-3.jpg)
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Metadata
- Authors
- Visibelli, A., Finetti, R., Niccolai, N., Spiga, O., & Santucci, A.
- Affiliations
- University of Siena (IT)
- Corresponding author
- Niccolai, Neri
- Venue
- International Journal of Molecular Sciences
- Publisher
- MDPI AG
- Published
- 2024-04-02
- Volume
- 25
- Issue
- 13
- Pages
- 6953-6953
- ISSN
- 1422-0067 (ISSN-L)
- PMC
- PMC11241713
- OpenAlex
- W4400092293
- Cited by
- 1
- References
- 1
- Citations by year
- 2025: 1
- FWCI
- 0.27
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- International Journal of Molecular Sciences (publishedVersion, cc-by)
- Preprints.org (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Use Siena air (University of Siena) (submittedVersion, cc-by)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- protein structure, amino acid substitutions, structural bioinformatics
- MeSH terms
- Humans, Models, Molecular, Protein Conformation, Proteins, Computational Biology, Amino Acid Substitution, Mutation, Missense, Databases, Genetic, Rare Diseases
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- CoChat. (2026). Citation check: Molecular Origins of the Mendelian Rare Diseases Reviewed by Orpha.net: A Structural Bioinformatics Investigation. https://app.cochat.ai/papers/10.20944/preprints202404.0156.v1
- The paper
- Visibelli, A., Finetti, R., Niccolai, N., Spiga, O., & Santucci, A. (2024). Molecular Origins of the Mendelian Rare Diseases Reviewed by Orpha.net: A Structural Bioinformatics Investigation. International Journal of Molecular Sciences. https://doi.org/10.20944/preprints202404.0156.v1
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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