Ensembl MCP Server

@cyanheads/ensembl-mcp-server Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross-database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP. 7 Tools • 4 Resources • 1 Prompt

Public Hosted Server: https://ensembl.caseyjhand.com/mcp

Overview

Gene, sequence, and variant data for vertebrates and other model organisms from the Ensembl REST API. Look up genes, fetch sequences, predict variant consequences, find orthologs, and cross-reference external databases.

Tools

Resources

The species resources return the first 50 species by internal name; the ensembl_list_species tool pages through the rest and filters by name.

Prompts

Capability reference

Ensembl's stable-ID endpoints answer a versioned ID (ENSG00000139618.19) as not found, so every tool and resource that takes an Ensembl stable ID drops a trailing .N from an ENS… ID before the request and returns the current version. HGVS input to ensembl_predict_variant (ENST00000380152.8:c.2T>A) keeps its version, and IDs from other sources (AT3G52430.1) are forwarded unchanged.

ensembl_list_species tool

• Optional division (EnsemblVertebrates, EnsemblPlants, EnsemblFungi, EnsemblMetazoa, EnsemblProtists; omitted, the endpoint default — vertebrates, ~356 species on GRCh38) and nameContains, a substring match against name, display name, and common name
• Returns the internal name every other tool expects (homo_sapiens), plus display name, common name, taxon ID, assembly, and division
• Sorted by internal name and paged by offset (default 0) and max_results (default 50, 0 uncapped); totalCount reports every match, and nextOffset is where the next page starts when more follow

ensembl_lookup_gene tool

• Exactly one of symbol (+ species, default homo_sapiens), id, ids, or symbols (up to 1,000 submitted items; first 20 distinct trimmed queries processed); expand_transcripts (default false) adds the transcript list with biotype and canonical flag
• canonicalTranscript identifies the canonical transcript without expansion; transcript-ID lookups also return parentGeneId. Expanded transcripts include maneSelect RefSeq accessions when available (BRCA2: ENST00000380152.8, NM_000059.4)
• A symbol that is not a current gene name falls back to synonyms and former symbols (HER2 → ERBB2), reported as matchedAlias; a name shared by several genes (MDR1) returns ambiguous with candidates to retry by id
• A single lookup returns gene (or ambiguous); a batch returns ordered succeeded items carrying the submitted query, failed items with query, reason (not_found, ambiguous with candidates, or unavailable), error, and recovery, and omitted queries past the processing cap. Omitted queries are never requested or reported as failed; resubmit them separately. Errors: not_found, invalid_species, no_input, conflicting_input

ensembl_get_sequence tool

• A stable ID (ENSG…/ENST…/ENSP…) or a region (species:chr:start-end, or chr:start-end with species; at most 10,000,000 bases); type is genomic (default), cdna, cds, or protein — cdna and cds from a transcript ID only, protein from a transcript or protein ID; expand_5prime/expand_3prime add flanking bases
• Regions take a :1/:-1 strand suffix (1:1000000-1000020:-1 returns the reverse complement); the mitochondrion is MT in vertebrates (mitochondrion_genome in Drosophila, MtDNA in C. elegans), and M/chrM are rejected as invalid_region where they would not resolve to it
• Returns a window set by offset (default 0) and max_length (default 10000, 0 uncapped); length is the full sequence length, and truncated/nextOffset say where to resume
• Errors: not_found, type_mismatch (also a protein ID asked for genomic/cdna/cds, or a non-coding transcript asked for protein/cds), invalid_species, missing_species, invalid_region (also an id with a colon that is not a valid region)

ensembl_query_region tool

• region as species:chr:start-end, or chr:start-end with species (at most 5,000,000 bases; reversed coordinates are rejected; mitochondrion naming as in ensembl_get_sequence); feature defaults to ["gene"] and also accepts transcript, variation, regulatory, exon; optional case-sensitive biotype filter (protein_coding, lncRNA). An empty filtered result suggests removing the filter without inferring the locus is intergenic
• max_results caps the list (default 100, 0 uncapped) while totalCount reports the true count; assemblyName names the coordinates' assembly, and exon rows carry parentId and rank. Errors: invalid_region, invalid_species, missing_species

ensembl_predict_variant tool

• variant as HGVS (transcript-relative or genomic), region+allele (chr:start:end:strand/allele), or a dbSNP rsID
• Returns the most severe consequence, per-transcript impact (HIGH/MODERATE/LOW/MODIFIER), and colocated known variants with clinical significance. Errors: invalid_notation, not_found, invalid_species
• Requests HGVS, canonical and MANE annotations on every input route. Consequences retain variantAllele, optional canonical/maneSelect, HGVS and available SIFT/PolyPhen prediction-score pairs; records retain alleleString
• Colocated clinicalSignificance is aggregate, not a classification of the submitted allele. clinicalSignificanceByAllele preserves explicit per-allele terms and clinicalSignificanceReferenceAllele identifies their reference allele; absent annotations remain omitted
• max_transcript_consequences and max_pubmed_ids_per_variant (default 10 each, 0 uncapped; include_all_colocated_pubmed lifts the PubMed cap) bound the result, while transcriptConsequencesTotal and pubmedTotal report the full counts

ensembl_get_homology tool

• Exactly one of symbol (+ species, default homo_sapiens) or id; type is orthologues (default), paralogues, or all; optional target_species filter
• A target_species outside the comparison Ensembl runs for the source species (a fly gene to homo_sapiens) is answered from Ensembl's pan-taxonomic comparison when it holds both species, with a notice saying so
• max_results caps the list (default 25, 0 uncapped) while totalCount reports the true count. Errors: not_found, invalid_species (unknown species or target_species), target_not_compared (a target outside the source species' comparison that the pan-taxonomic comparison cannot answer), no_input, conflicting_input
• Each row retains optional targetProteinId for ensembl_get_sequence with type:"protein". Optional targetSymbol comes from a lookup of the returned rows' distinct gene IDs, in chunks of at most 1,000, with one five-second budget bounded by the call's remaining deadline and no retries. Missing names or failed lookups retain every primary homolog with a notice; cancellation still aborts

ensembl_get_xrefs tool

• id (ENSG…/ENST…/ENSP…) required; optional dbname filter (e.g. HGNC, Uniprot_gn, Uniprot/SWISSPROT for the reviewed UniProt accession on the translation, EntrezGene, MIM_GENE, RefSeq_mRNA, Reactome_gene for gene pathways, Reactome for translation pathways, GO)
• Default all_levels:false queries the requested object's level. Set all_levels:true to include a gene's transcript and translation references, independently of dbname; for example, gene-level RefSeq_mRNA may need this or a transcript ID. Empty lists remain successful with totalCount:0. Errors: not_found
• Each reference carries how Ensembl assigned it (infoType: DIRECT, DEPENDENT, PROJECTION, …; infoText: its source, such as UniProt or the ortholog a projection came from) and its evidence codes (linkageTypes, GO evidence such as IDA or IEA) when su