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All rights reserved. Background image by Spencer Phillips</div> </aside> <aside id="eu_cookie_law_widget-2" class="widget widget_eu_cookie_law_widget"> <div class="hide-on-button" data-hide-timeout="30" data-consent-expiration="365" id="eu-cookie-law" > <form method="post"> <input type="submit" value="Close and accept" class="accept" /> </form> This website requires cookies, and the limited processing of your personal data in order to function. By using the site you are agreeing to this as outlined in our <a href="https://www.ebi.ac.uk/data-protection/ensembl/privacy-notice" rel=""> Privacy Policy </a> </div> </aside> </div> </div> </div> <div id="primary" class="content-area col-lg-9" itemprop="mainContentOfPage"> <div id="content" class="site-content" role="main" itemscope itemtype="http://schema.org/Article"> <article id="post-15474" class="post-15474 post type-post status-publish format-standard hentry category-02-updates tag-alphafold tag-alphamissense tag-ensembl tag-ensembl-vep tag-variation tag-vep"> <header class="entry-header"> <h1 class="entry-title" itemprop="name">Integration of AlphaMissense scores into Ensembl</h1> <div class="entry-meta"><span class="entry-date"><a href="https://www.ensembl.info/2024/05/24/integration-of-alphamissense-scores-into-ensembl/" rel="bookmark"><time class="entry-date published" datetime="2024-05-24T11:30:27+01:00" itemprop="datepublished">24th May 2024</time></a></span> by <span class="author vcard" itemscope itemprop="author" itemtype="http://schema.org/Person"><a class="url fn n" href="https://www.ensembl.info/author/lpmirabueno/" rel="author" itemprop="url"><span itemprop="name">Louisse Paola Mirabueno</span></a></span><span class="sep">·</span><span class="comments-link"><span>Comments Off<span class="screen-reader-text"> on Integration of AlphaMissense scores into Ensembl</span></span></span></div> </header> <div class="entry-content" itemprop="articleBody"> <p>We’re excited to announce the integration of AlphaMissense pathogenicity scores into Ensembl! The display of AlphaMissense data in Ensembl and other EMBL-EBI resources aims to empower scientists to gain new insights, expand the exploration of genetic variation and the tolerance to change of different regions in proteins.</p> <span id="more-15474"></span> <p>AlphaMissense is an AI model developed by <a href="https://deepmind.google/" target="_blank" rel="noreferrer noopener">Google DeepMind</a> which classifies genetic variants, specifically missense variants, as more likely to be pathogenic or benign. This information is helpful when researching variant-disease associations and provides an indication of the most functionally important parts of a protein.</p> <p>AlphaMissense scores are now integrated into the Ensembl Variant Effect Predictor (VEP) tool, enabling easy annotation of variants via the web interface, REST API, or command-line interface. Average AlphaMissense pathogenicity scores for each amino acid can also be visualised on the AlphaFold predicted 3D protein structure, available from the associated Ensembl transcript page.</p> <div style="height:17px" aria-hidden="true" class="wp-block-spacer"></div> <h3 class="wp-block-heading">Ensembl VEP</h3> <p>You can enable AlphaMissense scores on Ensembl VEP as follows:</p> <h4 class="wp-block-heading">Web interface</h4> <p>Open <a href="https://www.ensembl.org/Multi/Tools/VEP?db=core" target="_blank" rel="noreferrer noopener">Ensembl VEP</a> on the browser, scroll down to ‘Additional configurations’ and expand the ‘Predictions’ tab where you can enable AlphaMissense scores.</p> <figure class="wp-block-image size-large"><img fetchpriority="high" decoding="async" width="1024" height="638" src="https://www.ensembl.info/wp-content/uploads/2024/05/image-1-1024x638.png" alt="A screenshot of the Ensembl VEP web interface input form highlighting how to retrieve AlphaMissense scores. Under 'Additional configurations', open the 'Predictions' tab and select 'AlphaMissense'." class="wp-image-15477" srcset="https://www.ensembl.info/wp-content/uploads/2024/05/image-1-1024x638.png 1024w, https://www.ensembl.info/wp-content/uploads/2024/05/image-1-300x187.png 300w, https://www.ensembl.info/wp-content/uploads/2024/05/image-1-768x479.png 768w, https://www.ensembl.info/wp-content/uploads/2024/05/image-1.png 1300w" sizes="(max-width: 1024px) 100vw, 1024px" /><figcaption class="wp-element-caption">A screenshot of how to enable AlphaMissense scores in the Ensembl VEP web interface input form.</figcaption></figure> <p>The AlphaMissense pathogenicity score and classification will be reported in separate fields in the Ensembl VEP output table:</p> <figure class="wp-block-image"><img decoding="async" src="https://lh7-us.googleusercontent.com/VffWKKRjJgY-axxwtN9_UKWL-Pr5VgK9dvBQ2Boqr37MZ8h_mJpoEsn1RLLYpuH2Q8f61vK5V0gHB67-1TAn98z8XwZUa4IPmwrj-DThYxxmaofuQYm5JjvSYCZnhk7w6b0mIOK8M5Ti9BcFxl5pDTE" alt="A screenshot of an example output table of an Ensembl VEP web interface query. AlphaMissense classification and scores can be found in separate columns in the output table." /><figcaption class="wp-element-caption">A screenshot of an example output table including ‘AlphaMissense classification’ and ‘AlphaMissense pathogenicity score’ in separate columns.</figcaption></figure> <h4 class="wp-block-heading">REST API</h4> <p>AlphaMissense scores and pathogenicity classifications can be enabled by adding the optional parameter <code>AlphaMissense=1</code> when querying any <a href="https://rest.ensembl.org/#:~:text=phased%20genotype%20data-,VEP,-Resource" target="_blank" rel="noreferrer noopener"><code>/vep/</code> endpoint</a>.</p> <h4 class="wp-block-heading">Command-line</h4> <p>On the command-line Ensembl VEP, you can use the <a href="https://github.com/Ensembl/VEP_plugins/blob/release/112/AlphaMissense.pm" target="_blank" rel="noreferrer noopener">AlphaMissense plug-in</a> to analyse your data locally. Read more about how to use plug-ins on the <a href="https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#plugins_use" target="_blank" rel="noreferrer noopener">Ensembl VEP documentation page</a>.</p> <div style="height:17px" aria-hidden="true" class="wp-block-spacer"></div> <h3 class="wp-block-heading">AlphaMissense scores in the Ensembl browser</h3> <p>Average AlphaMissense pathogenicity scores for each amino acid can also be visualised on the AlphaFold predicted 3D protein structure, available under ‘Transcript-based displays: Protein Information’ and selecting the ‘AlphaFold predicted model’ display.</p> <figure class="wp-block-image size-large"><img decoding="async" width="1024" height="561" src="https://www.ensembl.info/wp-content/uploads/2024/05/image-1024x561.png" alt="A screenshot of the 'Transcript' tab for the human CLINT1 gene. AlphaMissense scores can be visualised by opening the 'Protein Information: AlphaFold predicted model' display." class="wp-image-15476" srcset="https://www.ensembl.info/wp-content/uploads/2024/05/image-1024x561.png 1024w, https://www.ensembl.info/wp-content/uploads/2024/05/image-300x164.png 300w, https://www.ensembl.info/wp-content/uploads/2024/05/image-768x421.png 768w, https://www.ensembl.info/wp-content/uploads/2024/05/image.png 1478w" sizes="(max-width: 1024px) 100vw, 1024px" /><figcaption class="wp-element-caption">A screenshot of the ‘Transcript’ tab of the human CLINT1-201 transcript highlighting how to visualise AlphaMissense scores in the AlphaFold predicted protein structure.</figcaption></figure> <p>This interactive view allows users to switch between variants, domains, exons, and AlphaMissense results, supporting the interpretation of different regions of the protein and their sensitivity to change.</p> <figure class="wp-block-image size-large"><img decoding="async" width="1024" height="545" src="https://www.ensembl.info/wp-content/uploads/2024/05/image-2-1024x545.png" alt="A screenshot of the 'AlphaFold predicted model' for the human CLINT1-201 transcript. AlphaMissense scores can be visualised in the protein model by selecting 'AlphaMissense Pathogenicity' under 'Toggle' in the right-hand panel. Likely pathogenic regions are highlighted in red in the protein structure and likely benign regions are highlighted in blue." class="wp-image-15478" srcset="https://www.ensembl.info/wp-content/uploads/2024/05/image-2-1024x545.png 1024w, https://www.ensembl.info/wp-content/uploads/2024/05/image-2-300x160.png 300w, https://www.ensembl.info/wp-content/uploads/2024/05/image-2-768x409.png 768w, https://www.ensembl.info/wp-content/uploads/2024/05/image-2.png 1522w" sizes="(max-width: 1024px) 100vw, 1024px" /><figcaption class="wp-element-caption">A screenshot of the ‘AlphaFold predicted model’ for the human CLINT1-201 transcript, highlighting where to enable AlphaMissense scores. Likely pathogenic regions are highlighted in red in the protein structure and likely benign regions are highlighted in blue.</figcaption></figure> <div style="height:17px" aria-hidden="true" class="wp-block-spacer"></div> <p>AlphaMissense data are also available in other EMBL-EBI resources <a href="https://www.uniprot.org/" target="_blank" rel="noreferrer noopener">UniProt</a> and the <a href="https://alphafold.ebi.ac.uk/" target="_blank" rel="noreferrer noopener">AlphaFold Protein Structure Database</a>. You can read more about AlphaMissense in the <a href="https://europepmc.org/article/MED/37733863" target="_blank" rel="noreferrer noopener">2023 publication by Cheng, et al.</a> and its availability in EMBL-EBI resources in the blog post <a href="https://www.ebi.ac.uk/about/news/technology-and-innovation/alphamissense-data-integration/" target="_blank" rel="noreferrer noopener">‘AlphaMissense data integrated into Ensembl, UniProt and AlphaFold DB’</a>. </p> <div style="height:44px" aria-hidden="true" class="wp-block-spacer"></div> <p>Author: Louisse Paola Mirabueno<br>Editors: Sarah Hunt, Benjamin Moore, Roz Onions, Jamie Allen</p> </div> <div class="tags-links"><a href="https://www.ensembl.info/tag/alphafold/" rel="tag">alphafold</a> <a href="https://www.ensembl.info/tag/alphamissense/" rel="tag">AlphaMissense</a> <a href="https://www.ensembl.info/tag/ensembl/" rel="tag">Ensembl</a> <a href="https://www.ensembl.info/tag/ensembl-vep/" rel="tag">Ensembl VEP</a> <a href="https://www.ensembl.info/tag/variation/" rel="tag">variation</a> <a href="https://www.ensembl.info/tag/vep/" rel="tag">VEP</a></div></article> <nav class="navigation post-navigation" aria-label="Posts"> <h2 class="screen-reader-text">Post navigation</h2> <div class="nav-links"><div class="nav-previous"><a href="https://www.ensembl.info/2024/05/13/ensembl-112-has-been-released/" rel="prev"><span class="meta-nav" aria-hidden="true">Previous</span> <span class="screen-reader-text">Previous post:</span> <span class="post-title">Ensembl 112 has been released.</span></a></div><div class="nav-next"><a href="https://www.ensembl.info/2024/06/28/getting-to-know-us-ian-tsang-visiting-phd-student/" rel="next"><span class="meta-nav" aria-hidden="true">Next</span> <span class="screen-reader-text">Next post:</span> <span class="post-title">Getting to know us: Ian Tsang (visiting PhD student)</span></a></div></div> </nav> </div> <footer class="site-info" itemscope itemtype="http://schema.org/WPFooter"> <a href="http://wordpress.org/" title="Semantic Personal Publishing Platform">Proudly powered by WordPress</a>. 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