ensembl_predict_variant
ActiveTool of io.github.cyanheads/ensembl-mcp-server
Predict the functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP). Accepts three input formats: HGVS notation (transcript-relative, e.g. ENST00000380152.8:c.2T>A, or genomic, e.g. 13:g.32316462T>A); region+allele (chr:start:end:strand/allele, e.g. 1:65568:65568:1/T); and a dbSNP rsID (e.g. rs334). Returns the most severe consequence term, affected transcripts and genes, impact level (HIGH/MODERATE/LOW/MODIFIER), and any colocated known variants with clinical significance. HGVS input: provide the full notation including transcript version for best results. Region+allele input: Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (a chr-prefixed name is also accepted). By default the response caps transcript consequences (max_transcript_consequences) and per-variant PubMed IDs (max_pubmed_ids_per_variant) to keep large VEP results compact — well-studied variants like rs334 otherwise carry 60+ consequences and 100+ citations. Truthful totals are always reported; set a cap to 0 (or include_all_colocated_pubmed=true) to retrieve the full set.
Parameters schema
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"required": [
"variant"
],
"properties": {
"species": {
"type": "string",
"default": "homo_sapiens",
"description": "Species in Ensembl internal format. Default is homo_sapiens. For non-human variants, set the appropriate species (e.g. mus_musculus for mouse). Use ensembl_list_species to discover valid values."
},
"variant": {
"type": "string",
"description": "Variant in one of three formats: (1) HGVS notation — transcript-relative: ENST00000380152.8:c.2T>A; genomic: 13:g.32316462T>A; (2) Region+allele: chr:start:end:strand/allele — e.g. 1:65568:65568:1/T (strand is 1 for forward or -1 for reverse); (3) dbSNP rsID — e.g. rs334. Ensembl normalizes chromosome names; canonical vertebrate output omits the \"chr\" prefix, though a chr-prefixed name is also accepted."
},
"max_pubmed_ids_per_variant": {
"type": "integer",
"default": 10,
"maximum": 9007199254740991,
"minimum": 0,
"description": "Maximum PubMed IDs to return per colocated known variant. Well-studied variants (e.g. rs334) cite 100+ papers; the default trims each list. Set to 0 to return every PubMed ID uncapped. pubmedTotal on each colocated variant reports the true pre-cap count. Ignored when include_all_colocated_pubmed is true."
},
"max_transcript_consequences": {
"type": "integer",
"default": 10,
"maximum": 9007199254740991,
"minimum": 0,
"description": "Maximum transcript consequences to return per VEP record. High-impact variants can affect 60+ transcripts; the default keeps the response focused on the top consequences. Set to 0 to return every transcript consequence uncapped. transcriptConsequencesTotal on each record always reports the true pre-cap count."
},
"include_all_colocated_pubmed": {
"type": "boolean",
"default": false,
"description": "When true, return every PubMed ID for each colocated variant, overriding max_pubmed_ids_per_variant. Default false to keep responses compact."
}
}
}Parent server
io.github.cyanheads/ensembl-mcp-server
https://github.com/cyanheads/ensembl-mcp-server
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