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Ensembl Variant Effect Predictor (VEP)
<!DOCTYPE html> <html lang="en-gb"> <head> <title>Ensembl Variant Effect Predictor (VEP)</title> <!--[if lte IE 7]><link rel="stylesheet" type="text/css" media="all" href="/minified/98adc89a8b4418c03a4c81d5bf76272d.ie7.css"/><![endif]--><!--[if gt IE 7]><link rel="stylesheet" type="text/css" media="all" href="/minified/98adc89a8b4418c03a4c81d5bf76272d.css"/><![endif]--><!--[if !IE]><!--><link rel="stylesheet" type="text/css" media="all" href="/minified/98adc89a8b4418c03a4c81d5bf76272d.css"/><!--<![endif]--><!--[if lte IE 7]><link rel="stylesheet" type="text/css" media="all" href="/minified/9bafd8bb591fb39bcb766b0160434c45.image.ie7.css"/><![endif]--><!--[if gt IE 7]><link rel="stylesheet" type="text/css" media="all" href="/minified/9bafd8bb591fb39bcb766b0160434c45.image.css"/><![endif]--><!--[if !IE]><!--><link rel="stylesheet" type="text/css" media="all" href="/minified/9bafd8bb591fb39bcb766b0160434c45.image.css"/><!--<![endif]--> <link type="image/png" rel="icon" 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title="API & Software">API & Software</a></li><li><a href="/info/docs/tools/" title="Ensembl Tools">Ensembl Tools</a></li><li class="last"><a href="/info/docs/tools/vep/" title="Ensembl Variant Effect Predictor (VEP)">Ensembl Variant Effect Predictor (VEP)</a></li></ul> <div id="content"><div id="static"><html> <head> <title>Ensembl Variant Effect Predictor (VEP)</title> <meta name="order" content="1" /> </head> <body> <style> img.opaque-hover:hover { opacity:0.6; filter:alpha(opacity=60); } img.opaque-hover { opacity:1.0; filter:alpha(opacity=100); } </style> <div style="float:right"><img src="/img/vep_logo.png"/></div> <h1 id="top"><span style="color:#006">Ensembl Variant Effect Predictor (VEP)</span></h1> <hr/> <p> <span style="color:#006;font-weight:bold">VEP determines the effect of your variants</span> (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. </p> <span>Simply input the coordinates of your variants and the nucleotide changes to find out the:</span> <ul> <li><b>Genes</b> and <b>Transcripts</b> affected by the variants</li> <li><b>Location</b> of the variants (e.g. upstream of a transcript, in coding sequence, in non-coding RNA, in regulatory regions)</li> <li><b>Consequence</b> of your variants on the protein sequence (e.g. stop gained, missense, stop lost, frameshift), see <a href="/info/genome/variation/prediction/predicted_data.html">variant consequences</a></li> <li><b>Known variants</b> that match yours, and associated minor allele frequencies from the <b>1000 Genomes Project</b></li> <li><b>SIFT</b> and <b>PolyPhen-2</b> scores for changes to protein sequence</li> <li>... And more! See <a href="/info/docs/tools/vep/online/input.html#ident">data types</a>, <a href="/info/docs/tools/vep/script/vep_cache.html#cache_content">versions</a>.</li> </ul> <h2><img src="/i/16/star.png"/> <a href="/info/docs/tools/vep/script/vep_download.html#new">What's new in release 113?</a></h2> <br /> <h2 id="vep_interfaces">VEP interfaces</h2> <div class="bottom-margin" style="display:table"> <!-- Web interface --> <div style="display:table-cell;padding-right:2em"> <div class="tinted-box" style="padding-bottom:16px;margin-bottom:-1px"> <div><h1 style="text-align:center;padding-top:0px;margin-bottom:16px">Web interface</h1></div> <div style="float:left;margin-right:15px"> <a href="/Tools/VEP" class="_ht" title="Launch the web interface"><img src="/img/vep_globe.png" style="border:2px solid #FFF;border-radius:5px;background:#336"/></a> </div> <div style="float:left;color:#333"> <ul style="padding-left:1.5em;margin-bottom:2em"> <li>Point-and-click interface</li> <li>Suits smaller volumes of data</li> </ul> <div style="font-weight:bold;margin-left:5px"> <img src="/i/16/documentation.png" style="vertical-align:bottom"/> <a href="/info/docs/tools/vep/online/index.html">Documentation</a> </div> </div> </div> <div class="tinted-box" style="padding-top:10px;text-align:center;background-color:#FFF;height:105px"> <a href="/Tools/VEP" class="_ht" title="Launch the web interface"><img src="/img/vep_launch_small.png" class="opaque-hover" style="width:200px"/></a> </div> </div> <!-- Perl script --> <div style="display:table-cell;padding-right:2em"> <div class="tinted-box" style="padding-bottom:16px;margin-bottom:-1px"> <div><h1 style="text-align:center;padding-top:0px;margin-bottom:16px">Command line tool</h1></div> <div style="float:left;margin-right:15px"> <a href="/info/docs/tools/vep/script/index.html" class="_ht" title="View VEP documentation"><img src="/img/vep_cmd.png" style="border:2px solid #FFF;border-radius:5px;background:white"/></a> </div> <div style="float:left;color:#333"> <ul style="padding-left:1.5em;margin-bottom:2em"> <li>More options and flexibility</li> <li>For large volumes of data</li> </ul> <div style="font-weight:bold;margin-left:5px"> <img src="/i/16/documentation.png" style="vertical-align:bottom"/> <a href="/info/docs/tools/vep/script/index.html">Documentation</a> </div> </div> </div> <div class="tinted-box" style="padding-top:10px;text-align:center;background-color:#FFF;height:105px"> <div style="padding-top:10px"> <h3><img src="/i/16/copy.png" style="vertical-align:bottom"/> <a href="https://github.com/Ensembl/ensembl-vep" rel="external">Clone from GitHub</a></h3> <h3><img src="/i/16/download.png" style="vertical-align:bottom"/> <a href="https://github.com/Ensembl/ensembl-vep/archive/release/113.zip" rel="external">Download (zip)</a></h3> <h3><img src="/i/16/copy.png" style="vertical-align:bottom"/> <a href="https://hub.docker.com/r/ensemblorg/ensembl-vep" rel="external">Pull Docker image from DockerHub</a></h3> </div> </div> </div> <!-- REST API --> <div style="display:table-cell"> <div class="tinted-box" style="padding-bottom:16px;margin-bottom:-1px"> <div><h1 style="text-align:center;padding-top:0px;margin-bottom:16px">REST API</h1></div> <div style="float:left;margin-right:5px"> <a href="https://rest.ensembl.org/#VEP" class="_ht" title="Go to REST documentation" rel="external"><img src="/img/restlogo_sq.png" style="padding:1px;border:1px solid #b0bbd8;border-radius:5px;background:white;text-decoration:none"/></a> </div> <div style="float:left;color:#333"> <ul style="padding-left:1.5em;margin-bottom:2em"> <li>Language-independent API</li> <li>Simple URL-based queries</li> </ul> <div style="font-weight:bold;margin-left:5px"> <img src="/i/16/documentation.png" style="vertical-align:bottom"/> <a href="https://rest.ensembl.org/#VEP" rel="external">Documentation</a> </div> </div> </div> <div class="tinted-box" style="padding-top:10px;text-align:center;background-color:#FFF;height:105px"> <div style="padding-top:40px"> <h3><img src="/i/16/globe.png" style="vertical-align:bottom"/> <a href="https://rest.ensembl.org/#VEP" title="VEP REST endpoint" rel="external">VEP REST API</a></h3> </div> </div> </div> </div> <br /> <hr /> <h2 id="publication">Publication</h2> <p>If you use VEP, please cite our UPDATED publication so we can continue to support VEP development:</p> <div> <div style="float:left;margin-bottom:20px" class="info"> <h3 id="cite_us">Cite us</h3> <div class="message-pad"> <p>McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F.<br /> <strong>The Ensembl Variant Effect Predictor.</strong><br /> <em>Genome Biology</em> Jun 6;17(1):122. (<strong>2016</strong>)<br /> <a rel="external" href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4" rel="external">doi:10.1186/s13059-016-0974-4 </a> </p> </div> </div> <div style="clear:both"></div> </div> <br /> <hr /> <h2 id="vep_tools"><img src="/i/16/tool.png" style="vertical-align:bottom;margin-right:5px"/>VEP related tools</h2> <div style="display:table;margin-top:10px"> <!-- Variant recoder --> <div style="display:table-cell;padding-right:2em"> <div class="tinted-box" style="padding-bottom:16px;margin-bottom:-1px"> <div><h1 style="text-align:center;padding-top:0px;margin-bottom:16px">Variant recoder</h1></div> <div style="color:#333"> <p>Translate a <b>variant identifier</b> or <b>HGVS notation</b> to all possible variant IDs and HGVS</p> <div><img src="/i/16/documentation.png" style="vertical-align:bottom"> <a href="/info/docs/tools/vep/recoder/index.html">Documentation</a></div> </div> </div> <div class="tinted-box" style="background-color:#FFF;padding-top:20px;padding-bottom:6px"> <table> <tr> <td><h3>Command line (VEP):</h3></td> <td> <h3><img src="/i/16/copy.png" style="vertical-align:bottom"/> <a href="https://github.com/Ensembl/ensembl-vep" rel="external">Clone from GitHub</a><span style="padding:0px 8px">|</span><img src="/i/16/download.png" style="vertical-align:bottom"/> <a href="https://github.com/Ensembl/ensembl-vep/archive/release/113.zip" rel="external">Download (zip)</a></h3> </td> </tr> <tr> <td><h3>REST API:</h3></td> <td> <h3><img src="/i/16/globe.png" style="vertical-align:bottom"/> <a href="http://rest.ensembl.org/documentation/info/variant_recoder" title="Variant Recoder REST endpoint" rel="external">Variant Recoder REST API</a></h3> </td> </tr> </table> </div> </div> <!-- Haplosaurus --> <div style="display:table-cell"> <div class="tinted-box" style="padding-bottom:16px;margin-bottom:-1px"> <div><h1 style="text-align:center;padding-top:0px;margin-bottom:16px">Haplosaurus</h1></div> <div style="color:#333"> <p>Computes observed transcript <b>haplotype</b> sequences based on <b>phased genotype</b> data</p> <div><img src="/i/16/documentation.png" style="vertical-align:bottom"> <a href="/info/docs/tools/vep/haplo/index.html">Documentation</a></div> </div> </div> <div class="tinted-box" style="background-color:#FFF;padding-top:20px;padding-bottom:6px"> <table> <tr> <td><h3>Command line (VEP):</h3></td> <td> <h3><img src="/i/16/copy.png" style="vertical-align:bottom"/> <a href="https://github.com/Ensembl/ensembl-vep" rel="external">Clone from GitHub</a><span style="padding:0px 8px">|</span><img src="/i/16/download.png" style="vertical-align:bottom"/> <a href="https://github.com/Ensembl/ensembl-vep/archive/release/113.zip" rel="external">Download (zip)</a></h3> </td> </tr> <tr> <td><h3>REST API:</h3></td> <td> <h3><img src="/i/16/globe.png" style="vertical-align:bottom"/> <a href="http://rest.ensembl.org/documentation/info/transcript_haplotypes_get" title="Haplosaurus REST endpoint" rel="external">Haplosaurus REST API</a></h3> </td> </tr> </table> </div> </div> </div> </div> </div></div> </div> <div id="footer"> <div class="column-wrapper"> <div class="column-two left"> <p>Ensembl release 113 - October 2024 © <span class="print_hide"><a href="http://www.ebi.ac.uk/" class="nowrap constant">EMBL-EBI</a></span> <span class="screen_hide_inline">EMBL-EBI<br />http://useast.ensembl.org</span> </p> </div> <div class="column-two right print_hide"><p> <a class="modal_link" id="p_link" href="/Help/Permalink?url=http%3A%2F%2FOct2024.archive.ensembl.org">Permanent link</a> </p></div> <p class="invisible">.</p> </div> <div class="column-wrapper"><hr /><div id="fat-footer"> <div class="column-four left"> <h3>About Us</h3> <p><a href="/info/about" rel="nofollow">About us</a></p> <p><a href="/info/about/contact/" rel="nofollow">Contact us</a></p> <p><a 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value=Otus_sunia|Oncorhynchus_tshawytscha|Tupaia_belangeri|Naja_naja|Seriola_lalandi_dorsalis|Myotis_lucifugus|Ursus_americanus|Periophthalmus_magnuspinnatus|Ovis_aries_polled_dorset|Vombatus_ursinus|Calidris_pygmaea|Sus_scrofa_usmarc|Fundulus_heteroclitus|Salmo_salar|Sorex_araneus|Moschus_moschiferus|Oncorhynchus_kisutch|Carlito_syrichta|Mus_musculus_WSB_EiJ|Hucho_hucho|Lepisosteus_oculatus|Mus_musculus_LP_J|Heterocephalus_glaber_male|Sander_lucioperca|Poecilia_mexicana|Sarcophilus_harrisii|Sus_scrofa_ningxiang|Ictalurus_punctatus|Mus_musculus_CAST_EiJ|Rhinopithecus_roxellana|Physeter_catodon|Callithrix_jacchus|Esox_lucius|Salvator_merianae|Cyclopterus_lumpus|Amphilophus_citrinellus|Erinaceus_europaeus|Manacus_vitellinus|Salmo_salar_european_origin_alta|Castor_canadensis|Mus_musculus_BALB_cJ|Canis_lupus_familiarisbasenji|Nomascus_leucogenys|Pan_troglodytes|Gasterosteus_aculeatus|Phocoena_sinus|Panthera_pardus|Mus_musculus|Pavo_cristatus|Suricata_suricatta|Capra_hircus|Oryctolagus_cuniculus|Peromyscus_maniculatus_bairdii|Mus_musculus_A_J|Pan_paniscus|Leptobrachium_leishanense|Gallus_gallus_GCA_000002315.5|Oryzias_latipes_hni|Echeneis_naucrates|Sus_scrofa_bama_miniature|Rattus_norvegicus_SHRSPBbbUtx|Sus_scrofa_hampshire|Anser_cygnoides|Ovis_aries_white_dorper|Salmo_trutta|Cricetulus_griseus_picr|Podarcis_muralis|Ficedula_albicollis|Ovis_aries_kermani|Lonchura_striata_domestica|Ovis_aries_chinese_merino|Apteryx_owenii|Sus_scrofa_ossabaw_miniature|Panthera_leo|Rattus_norvegicus_SHRUtx|Cyprinodon_variegatus|Carassius_auratus|Neovison_vison|Salarias_fasciatus|Poecilia_formosa|Caenorhabditis_elegans|Ciona_intestinalis|Oryzias_javanicus|Sus_scrofa_duroc|Mandrillus_leucophaeus|Pogona_vitticeps|Stegastes_partitus|Rhinopithecus_bieti|Spermophilus_dauricus|Phasianus_colchicus|Otolemur_garnettii|Cynoglossus_semilaevis|Mus_musculus_CBA_J|Mus_musculus_AKR_J|Takifugu_rubripes|Salmo_salar_north_american_origin_brian|Gasterosteus_aculeatus_marine_syl|Amazona_collaria|Mastacembelus_armatus|Sus_scrofa_nihs_2020|Gambusia_affinis|Amphiprion_percula|Ovis_aries_qiaoke|Electrophorus_electricus|Bos_mutus|Sus_scrofa_wuzhishan|Piliocolobus_tephrosceles|Lates_calcarifer|Strix_occidentalis_caurina|Felis_catus|Larimichthys_crocea|Buteo_japonicus|Chlorocebus_sabaeus|Ursus_maritimus|Monopterus_albus|Parus_major|Haplochromis_burtoni|Maylandia_zebra|Cyprinus_carpio_huanghe|Sus_scrofa_meishan|Sus_scrofa_bamei|Capra_hircus_xinong_saanen_dairy|Geospiza_fortis|Dromaius_novaehollandiae|Oreochromis_aureus|Serinus_canaria|Equus_asinus|Gallus_gallus_GCA_016700215.2|Bos_taurus|Rattus_norvegicus|Sus_scrofa|Pelusios_castaneus|Monodelphis_domestica|Vulpes_vulpes|Oryzias_melastigma|Cairina_moschata_domestica|Astatotilapia_calliptera|Betta_splendens|Cricetulus_griseus_chok1gshd|Pygocentrus_nattereri|Bison_bison_bison|Gorilla_gorilla|Anas_zonorhyncha|Pundamilia_nyererei|Ovis_aries_east_friesian|Falco_tinnunculus|Neolamprologus_brichardi|Camelus_dromedarius|Bos_grunniens|Tetraodon_nigroviridis|Sinocyclocheilus_rhinocerous|Theropithecus_gelada|Lynx_canadensis|Echinops_telfairi|Pelodiscus_sinensis|Octodon_degus|Drosophila_melanogaster|Equus_caballus|Parambassis_ranga|Oryzias_latipes|Sus_scrofa_pietrain|Oreochromis_niloticus|Xiphophorus_couchianus|Denticeps_clupeoides|Accipiter_nisus|Canis_lupus_familiarisboxer|Sus_scrofa_tibetan|Laticauda_laticaudata|Erpetoichthys_calabaricus|Ovis_aries_rambouillet|Saccharomyces_cerevisiae|Sus_scrofa_jinhua|Dicentrarchus_labrax|Notechis_scutatus|Macaca_nemestrina|Neogobius_melanostomus|Urocitellus_parryii|Papio_anubis|Aotus_nancymaae|Rhinolophus_ferrumequinum|Callorhinchus_milii|Myripristis_murdjan|Ochotona_princeps|Capra_hircus_saanen_dairy|Amphiprion_ocellaris|Strigops_habroptila|Erythrura_gouldiae|Zonotrichia_albicollis|Sus_scrofa_rongchang|Microtus_ochrogaster|Sinocyclocheilus_grahami|Oryzias_latipes_hsok|Seriola_dumerili|Vicugna_pacos|Bubo_bubo|Catharus_ustulatus|Heterocephalus_glaber_female|Aquila_chrysaetos_chrysaetos|Ailuropoda_melanoleuca|Eptatretus_burgeri|Chelydra_serpentina|Taeniopygia_guttata|Delphinapterus_leucas|Mustela_putorius_furo|Anas_platyrhynchos_platyrhynchos|Sus_scrofa_meishan_GCA_017957985.1|Cervus_hanglu_yarkandensis|Pseudonaja_textilis|Macaca_mulatta|Xiphophorus_maculatus|Sus_scrofa_pb115|Fukomys_damarensis|Ornithorhynchus_anatinus|Ursus_thibetanus_thibetanus|Marmota_marmota_marmota|Macaca_fascicularis|Mesocricetus_auratus|Jaculus_jaculus|Paramormyrops_kingsleyae|Lepidothrix_coronata|Mus_musculus_C3H_HeJ|Sus_scrofa_landrace|Balaenoptera_musculus|Prolemur_simus|Mus_musculus_NOD_ShiLtJ|Mola_mola|Salmo_salar_north_american_atlantic_salmon|Canis_lupus_familiaris|Mus_musculus_129S1_SvImJ|Mus_musculus_C57BL_6NJ|Sinocyclocheilus_anshuiensis|Cottoperca_gobio|Petromyzon_marinus|Chrysolophus_pictus|Canis_lupus_familiarisgreatdane|Struthio_camelus_australis|Zalophus_californianus|Choloepus_hoffmanni|Gouania_willdenowi|Mus_caroli|Mus_spretus|Numida_meleagris|Terrapene_carolina_triunguis|Nothobranchius_furzeri|M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