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).
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."
}
}
}Parent server
io.github.cyanheads/ensembl-mcp-server
https://github.com/cyanheads/ensembl-mcp-server
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