Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

Full name:
Description: The Missense3D portal hosts resources developed to characterise and prioritise missense variants (amino acid substitutions) using protein three-dimensional structural information from models or experimental coordinates.
Year founded: 2020
Last update:
Real time : Checking...
Country/Region: United Kingdom
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Contact information

University/Institution: Centre for Integrative System Biology and Bioinformatics
Address: Department of Life Sciences, Centre for Integrative System Biology and Bioinformatics, Imperial College London, London, SW7 2AZ, UK.
Province/State: London
Country/Region: United Kingdom
Contact name (PI/Team): Alessia David
Contact email (PI/Helpdesk):


Missense3D-DB web catalogue: an atom-based analysis and repository of 4M human protein-coding genetic variants. [PMID: 33502607]
Tarun Khanna, Gordon Hanna, Michael J E Sternberg, Alessia David

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 ( ). 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.

Hum Genet. 2021:() | 0 Citations (from Europe PMC, 2021-05-01)



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Created on: 2021-03-10
Curated by:
lin liu [2021-03-25]
Dong Zou [2021-03-10]