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u9401066

pubmed-search-mcp

by u9401066
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

search_clinvar

Read-onlyIdempotent

Search ClinVar to look up clinical significance of genetic variants, find disease associations, and retrieve pathogenicity classifications for genes or conditions.

Instructions

Search ClinVar for clinical variants.

═══════════════════════════════════════════════════════════════ USE CASES: ═══════════════════════════════════════════════════════════════

  • Look up clinical significance of genetic variants

  • Find variants associated with diseases

  • Research gene-disease associations

  • Get variant pathogenicity classifications

Args: query: Gene name, variant, or disease condition limit: Maximum results (1-50)

Returns: JSON with variant records including significance and conditions

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo
queryYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed4 schema fields changedv0.7.7
    • addedInput schema / properties / limit / anyOf
      Added value: +[
+  {
+    "default": 10,
+    "maximum": 50,
+    "minimum": 1,
+    "title": "Limit",
+    "type": "integer"
+  },
+  {
+    "description": "ASCII decimal integer; the integer branch's bounds apply after conversion.",
+    "maxLength": 32,
+    "pattern": "^[ \\t\\r\\n]*-?(?:0|[1-9][0-9]*)[ \\t\\r\\n]*$",
+    "type": "string"
+  }
+]
    • removedInput schema / properties / limit / maximum
      Removed value: -50
    • removedInput schema / properties / limit / minimum
      Removed value: -1
    • removedInput schema / properties / limit / type
      Removed value: -"integer"
  2. Changed8 schema fields changedv0.7.2
    • addedInput schema / additionalProperties
      Added value: +false
    • removedInput schema / properties / limit / anyOf
      Removed value: -[
-  {
-    "type": "integer"
-  },
-  {
-    "type": "string"
-  }
-]
    • addedInput schema / properties / limit / maximum
      Added value: +50
    • addedInput schema / properties / limit / minimum
      Added value: +1
    • addedInput schema / properties / limit / type
      Added value: +"integer"
    • addedInput schema / properties / query / maxLength
      Added value: +500
    • addedInput schema / properties / query / minLength
      Added value: +1
    • changedOutput schema / (root)
      Previous value: -{
-  "properties": {
-    "result": {
-      "title": "Result",
-      "type": "string"
-    }
-  },
-  "required": [
-    "result"
-  ],
-  "title": "search_clinvarOutput",
-  "type": "object"
-}New value: +null
  3. First observedv0.5.16

TDQS

A4/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint, idempotentHint, openWorldHint, and destructiveHint=false, so the safety profile is fully covered. The description adds value beyond that by stating the return shape ('JSON with variant records including significance and conditions'), which is useful given there is no output schema.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The content is short and front-loaded: purpose first, then use cases, args, and returns. The heavy '═' divider lines are decorative noise, but they do not meaningfully bloat the semantic content.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a two-parameter read-only search with no output schema, the description covers purpose, invocation contexts, both parameters, and the general return shape. Pagination or ranking details are absent, but they are not essential for correct invocation.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description carries the full burden. It explains that 'query' accepts a gene name, variant, or disease condition, and that 'limit' is a 1–50 maximum-result count, which meaningfully supplements the bare schema constraints.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb and resource ('Search ClinVar for clinical variants') and the use cases make the domain explicit. It does not, however, distinguish itself from sibling tools such as search_gene, search_compound, or unified_search, so an agent cannot route between them from this text alone.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The USE CASES section gives clear contexts for when to call it (looking up clinical significance, disease associations, pathogenicity classifications). There are no explicit exclusions or alternatives named, but the positive guidance is strong enough to be actionable.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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