ArticleHuman genetics2021
Missense3D-DB web catalogue: an atom-based analysis and repository of 4M human protein-coding genetic variants.
Article in Human genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 68 citations in OpenAlex.
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- Clinical Discovery and Molecular Analysis of Two Novel MSH2 Gene Mutations (p.Ala771Gly and p.Val797Gly) in Saudi Colorectal Cancer Patients: Potential Implications for Tumorigenesis.Health science reports · 2026Article
- Biallelic variants in COX18 cause a mitochondrial disorder primarily manifesting as peripheral neuropathy.Brain : a journal of neurology · 2026Article
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- Prognostic Modeling of Deleterious IDUA Mutations L238Q and P385R in Hurler Syndrome Through Molecular Dynamics Simulations.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Identification of a binding pocket of letermovir in the terminase subunit pUL56 of human cytomegalovirus.Scientific reports · 2025Article
- Challenges in bridging the gap between protein structure prediction and functional interpretation.Proteins · 2025Article
- Functional Screen of Wilson Disease ATP7B Variants Reveals Residual Transport Activities.Human mutation · 2025Article
- A systematic in-silico functional and structural analysis reveals deleterious missense nsSNPs in the humanMolecular biology research communications · 2025Article
- Identification of a novel, pathogenicFrontiers in genetics · 2025Article
- Comprehensive computational analysis of deleterious nsSNPs inMolecular biology research communications · 2025Article
- LTβR deficiency causes lymph node aplasia and impaired B cell differentiation.Science immunology · 2024Article
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- Unveiling New Genetic Variants Associated with Age at Onset in Alzheimer's Disease and Frontotemporal Lobar Degeneration Due toInternational journal of molecular sciences · 2024Article
- ProtVar: mapping and contextualizing human missense variation.Nucleic acids research · 2024Article
- The natural history and genotype-phenotype correlations of TMPRSS3 hearing loss: an international, multi-center, cohort analysis.Human genetics · 2024Article
- A rare inherited homozygous missense variant inTranslational pediatrics · 2024Article
- Landscape of FLT3 Variations Associated with Structural and Functional Impact on Acute Myeloid Leukemia: A Computational Study.International journal of molecular sciences · 2024Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The interpretation of human genetic variation is one of the greatest challenges of modern genetics. New approaches are urgently needed to prioritize variants, especially those that are rare or lack a definitive clinical interpretation. We examined 10,136,597 human missense genetic variants from GnomAD, ClinVar and UniProt. We were able to perform large-scale atom-based mapping and phenotype interpretation of 3,960,015 of these variants onto 18,874 experimental and 84,818 in house predicted three-dimensional coordinates of the human proteome. We demonstrate that 14% of amino acid substitutions from the GnomAD database that could be structurally analysed are predicted to affect protein structure (n = 568,548, of which 566,439 rare or extremely rare) and may, therefore, have a yet unknown disease-causing effect. The same is true for 19.0% (n = 6266) of variants of unknown clinical significance or conflicting interpretation reported in the ClinVar database. The results of the structural analysis are available in the dedicated web catalogue Missense3D-DB ( http://missense3d.bc.ic.ac.uk/ ). For each of the 4 M variants, the results of the structural analysis are presented in a friendly concise format that can be included in clinical genetic reports. A detailed report of the structural analysis is also available for the non-experts in structural biology. Population frequency and predictions from SIFT and PolyPhen are included for a more comprehensive variant interpretation. This is the first large-scale atom-based structural interpretation of human genetic variation and offers geneticists and the biomedical community a new approach to genetic variant interpretation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.