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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 href="/i/ensembl-favicon.png" type="image/png" 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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=Vombatus_ursinus|Sus_scrofa_pietrain|Gambusia_affinis|Castor_canadensis|Sus_scrofa_wuzhishan|Mus_spretus|Moschus_moschiferus|Oryzias_latipes|Propithecus_coquereli|Chrysemys_picta_bellii|Pelusios_castaneus|Dicentrarchus_labrax|Malurus_cyaneus_samueli|Sus_scrofa_meishan|Sphenodon_punctatus|Mus_musculus_CAST_EiJ|Salmo_salar_north_american_atlantic_salmon|Procavia_capensis|Rattus_norvegicus_SHRSPBbbUtx|Gasterosteus_aculeatus|Pygocentrus_nattereri|Cyprinodon_variegatus|Sus_scrofa_rongchang|Ciona_savignyi|Physeter_catodon|Chlorocebus_sabaeus|Haplochromis_burtoni|Cavia_aperea|Oryctolagus_cuniculus|Periophthalmus_magnuspinnatus|Saccharomyces_cerevisiae|Peromyscus_maniculatus_bairdii|Echeneis_naucrates|Mandrillus_leucophaeus|Sus_scrofa_ossabaw_miniature|Drosophila_melanogaster|Oryzias_latipes_hni|Ovis_aries_kermani|Amazona_collaria|Delphinapterus_leucas|Calidris_pygmaea|Geospiza_fortis|Spermophilus_dauricus|Gallus_gallus_GCA_000002315.5|Ornithorhynchus_anatinus|Mus_caroli|Myotis_lucifugus|Phascolarctos_cinereus|Salmo_trutta|Bos_grunniens|Macaca_fascicularis|Pongo_abelii|Maylandia_zebra|Ovis_aries_rambouillet|Anser_brachyrhynchus|Latimeria_chalumnae|Serinus_canaria|Mesocricetus_auratus|Gallus_gallus|Stegastes_partitus|Panthera_pardus|Oreochromis_aureus|Neogobius_melanostomus|Oryzias_javanicus|Gadus_morhua|Anolis_carolinensis|Mus_musculus_PWK_PhJ|Ficedula_albicollis|Urocitellus_parryii|Notamacropus_eugenii|Sus_scrofa_nihs_2020|Echinops_telfairi|Mola_mola|Mus_musculus_LP_J|Catharus_ustulatus|Pavo_cristatus|Strix_occidentalis_caurina|Sciurus_vulgaris|Gopherus_agassizii|Cairina_moschata_domestica|Manacus_vitellinus|Oryzias_sinensis|Cebus_imitator|Eptatretus_burgeri|Anas_platyrhynchos|Poecilia_mexicana|Struthio_camelus_australis|Erpetoichthys_calabaricus|Paramormyrops_kingsleyae|Sinocyclocheilus_grahami|Seriola_lalandi_dorsalis|Mus_musculus_C3H_HeJ|Rattus_norvegicus_WKYBbb|Sus_scrofa_berkshire|Meriones_unguiculatus|Monodelphis_domestica|Rhinolophus_ferrumequinum|Callorhinchus_milii|Clupea_harengus|Cyprinus_carpio_german_mirror|Taeniopygia_guttata|Mus_musculus_CBA_J|Xenopus_tropicalis|Capra_hircus_blackbengal|Crocodylus_porosus|Salmo_salar_north_american_origin_brian|Sus_scrofa_euw1|Seriola_dumerili|Neolamprologus_brichardi|Esox_lucius|Cricetulus_griseus_chok1gshd|Microtus_ochrogaster|Tursiops_truncatus|Salmo_salar|Sus_scrofa_landrace|Athene_cunicularia|Larimichthys_crocea|Canis_lupus_familiarisgermanshepherd|Sus_scrofa|Mastacembelus_armatus|Otolemur_garnettii|Poecilia_formosa|Melopsittacus_undulatus|Heterocephalus_glaber_male|Nannospalax_galili|Cricetulus_griseus_picr|Astyanax_mexicanus_pachon|Cyclopterus_lumpus|Sus_scrofa_largewhite|Parus_major|Lepidothrix_coronata|Betta_splendens|Hucho_hucho|Vicugna_pacos|Cricetulus_griseus_crigri|Petromyzon_marinus|Oncorhynchus_tshawytscha|Aotus_nancymaae|Sparus_aurata|Xiphophorus_couchianus|Chinchilla_lanigera|Leptobrachium_leishanense|Bubo_bubo|Lonchura_striata_domestica|Mus_spicilegus|Mus_musculus_BALB_cJ|Ictalurus_punctatus|Canis_lupus_dingo|Homo_sapiens|Varanus_komodoensis|Junco_hyemalis|Mus_pahari|Notechis_scutatus|Bos_indicus_hybrid|Phasianus_colchicus|Ciona_intestinalis|Rhinopithecus_bieti|Oryzias_melastigma|Microcebus_murinus|Acanthochromis_polyacanthus|Theropithecus_gelada|Salarias_fasciatus|Dipodomys_ordii|Oncorhynchus_kisutch|Gasterosteus_aculeatus_freshwater_bot|Sus_scrofa_bama_miniature|Dromaius_novaehollandiae|Cynoglossus_semilaevis|Ovis_aries_romanov|Gadus_morhua_celtic_sea|Sarcophilus_harrisii|Ovis_aries_qiaoke|Cercocebus_atys|Heterocephalus_glaber_female|Falco_tinnunculus|Phocoena_sinus|Poecilia_reticulata|Zonotrichia_albicollis|Cavia_porcellus|Otus_sunia|Pan_paniscus|Pteropus_vampyrus|Canis_lupus_familiaris|Sus_scrofa_ningxiang|Sphaeramia_orbicularis|Stachyris_ruficeps|Scleropages_formosus|Numida_meleagris|Catagonus_wagneri|Salvator_merianae|Corvus_moneduloides|Ursus_americanus|Nothobranchius_furzeri|Lates_calcarifer|Mus_musculus|Rattus_norvegicus_SHRUtx|Neovison_vison|Cyprinus_carpio_hebao_red|Tupaia_belangeri|Danio_rerio|Panthera_leo|Oncorhynchus_mykiss|Coturnix_japonica|Ursus_maritimus|Sus_scrofa_tibetan|Balaenoptera_musculus|Apteryx_haastii|Dasypus_novemcinctus|Sus_scrofa_meishan_GCA_017957985.1|Kryptolebias_marmoratus|Bos_mutus|Mustela_putorius_furo|Capra_hircus_xinong_saanen_dairy|Felis_catus|Oryzias_latipes_hsok|Denticeps_clupeoides|Loxodonta_africana|Erinaceus_europaeus|Gopherus_evgoodei|Parambassis_ranga|Oreochromis_niloticus|Amphiprion_ocellaris|Amphiprion_percula|Electrophorus_electricus|Cervus_hanglu_yarkandensis|Monopterus_albus|Sus_scrofa_duroc|Chelonoidis_abingdonii|Astyanax_mexicanus|Zosterops_lateralis_melanops|Myripristis_murdjan|Equus_asinus|Cyprinus_carpio_huanghe|Sander_lucioperca|Salmo_salar_european_origin_alta|Choloepus_hoffmanni|Cyprinus_carpio_carpio|Pelodiscus_sinensis|Strigops_habroptila|Piliocolobus_tephrosceles|Ovis_aries_polled_dorset|Anabas_testudineus|Nothoprocta_perdicaria|Gallus_gallus_GCA_016700215.2|Panthera_tigris_altaica|P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