`vep`

Pack: ensembl · Endpoint: https://gateway.pipeworx.io/ensembl/mcp

“What’s the effect of [variant]” / “predict consequences of [genomic change]” / “VEP for [chrom:pos]” — Variant Effect Predictor for a specified region + allele. Returns consequences (missense, synonymous, splice, etc.), affected genes, transcript impacts, SIFT/PolyPhen predictions. Use for variant interpretation in clinical or research genomics.

Parameters

Name	Type	Required	Description
`species`	string	yes
`region`	string	yes	e.g. “9:22125504-22125504:1”
`allele`	string	yes	e.g. “C”

Example call

Arguments

{
  "species": "human",
  "region": "9:22125504-22125504:1",
  "allele": "C"
}

curl

curl -X POST https://gateway.pipeworx.io/ensembl/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"vep","arguments":{"species":"human","region":"9:22125504-22125504:1","allele":"C"}}}'

TypeScript (@pipeworx/sdk)

import { Pipeworx } from '@pipeworx/sdk';
const pipeworx = new Pipeworx();

const result = await pipeworx.call('vep', {
  "species": "human",
  "region": "9:22125504-22125504:1",
  "allele": "C"
});

Response shape

Always returns: items, count

Field	Type	Description
`items`	array	Variant Effect Predictor results
`count`	integer	Number of items returned.

Full JSON Schema

{
  "type": "object",
  "properties": {
    "items": {
      "type": "array",
      "description": "Variant Effect Predictor results",
      "items": {
        "type": "object",
        "properties": {
          "variant_id": {
            "type": "string",
            "description": "Variant identifier"
          },
          "allele_string": {
            "type": "string",
            "description": "Reference/alternate alleles"
          },
          "seq_region_name": {
            "type": "string",
            "description": "Chromosome"
          },
          "start": {
            "type": "integer",
            "description": "Start position"
          },
          "end": {
            "type": "integer",
            "description": "End position"
          },
          "strand": {
            "type": "integer",
            "description": "Strand"
          },
          "transcript_consequences": {
            "type": "array",
            "description": "Predicted consequences",
            "items": {
              "type": "object",
              "properties": {
                "consequence_terms": {
                  "type": "array",
                  "description": "Consequence term list",
                  "items": {
                    "type": "string"
                  }
                },
                "transcript_id": {
                  "type": "string",
                  "description": "Transcript ID"
                },
                "gene_id": {
                  "type": "string",
                  "description": "Gene ID"
                },
                "biotype": {
                  "type": "string",
                  "description": "Transcript biotype"
                },
                "impact": {
                  "type": "string",
                  "description": "Predicted impact"
                },
                "hgvsc": {
                  "type": "string",
                  "description": "HGVS cDNA notation"
                },
                "hgvsp": {
                  "type": "string",
                  "description": "HGVS protein notation"
                }
              }
            }
          }
        }
      }
    },
    "count": {
      "type": "integer",
      "description": "Number of items returned."
    }
  },
  "required": [
    "items",
    "count"
  ]
}

Connect

Add this to your MCP client config, or use one-click install buttons:

{
  "mcpServers": {
    "ensembl": {
      "url": "https://gateway.pipeworx.io/ensembl/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

vep