AI agents call get_variation_pmid to retrieve information from OrigeneMCP without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
This tool appears to query and retrieve bibliographic data (PMIDs) related to genomic variations—a read-only operation with no apparent capacity to modify, delete, or execute code. The medium severity reflects potential misuse in a research context (e.g., flooding literature databases with requests), but the core function is information retrieval.
From the tool's definition Tool name 'get_variation_pmid' indicates retrieval of PubMed IDs (PMIDs) associated with genetic variations. The sibling tools (clinvar_*, depmap_*) all perform biomedical data queries and retrievals.
Documented attack patterns abuse exactly the kind of access get_variation_pmid gives an agent:
PolicyLayer is an MCP gateway — it sits between your AI agents and OrigeneMCP, and nothing reaches the server without passing your rules. This is the rule we recommend for get_variation_pmid:
{
"version": "1",
"default": "deny",
"tools": {
"get_variation_pmid": {}
}
}get_variation_pmid is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.
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get_variation_pmid. It is categorised as a Read tool in the OrigeneMCP MCP Server, which means it retrieves data without modifying state.
Register the Origene MCP server in PolicyLayer and add a rule for get_variation_pmid: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches OrigeneMCP. Nothing to install.
get_variation_pmid is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the get_variation_pmid rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.
Set action: deny in the PolicyLayer policy for get_variation_pmid. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.
get_variation_pmid is provided by the Origene MCP server (gentel-lab/origenemcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Start from OrigeneMCP, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.
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439 OrigeneMCP tools catalogued and risk-classified — across an index of 43,000+ MCP servers.