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PharmGKB Variant Lookup

pharmgkb.pharmacology.variant_lookup
Read-onlyIdempotent

Look up pharmacogenomic details for a genetic variant by dbSNP rsID (e.g. rs1799853 for CYP2C92, rs4244285 for CYP2C192, rs12248560 for CYP2C19*17). Returns variant ID, change classification (Missense/Synonymous/Intronic), clinical significance (drug-response/pathogenic), variant type (SNP/Indel), chromosomal position (GRCh38), associated genes, rarity flag, and ClinVar IDs. Focused on variants with known drug-response relevance. Source: PharmGKB, CC BY-SA 4.0.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
rsidYesdbSNP reference SNP ID for the variant (e.g. rs1799853, rs4244285, rs12248560). Must be prefixed with "rs" followed by digits. PharmGKB annotates variants with known pharmacogenomic relevance.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
errorNoPresent only when the call failed. Includes error code, message, request_id, and any provider-specific extras.
resultNoTool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.5/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, openWorldHint=true, idempotentHint=true, and destructiveHint=false, so the safety profile is fully covered. The description adds useful behavioral context: it returns GRCh38 positions specifically, focuses on drug-response-relevant variants, and cites the data source (PharmGKB, CC BY-SA 4.0). It does not mention pagination or error behavior, but for a single-rsID lookup with an output schema, this is adequate.

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

Conciseness5/5

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

The description is compact and information-dense. It front-loads the action ('Look up pharmacogenomic details'), provides examples, lists return fields, states the scope, and cites the source—all in three sentences with no filler.

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

Completeness5/5

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

For a single-parameter read-only lookup with a full output schema and complete annotations, the description covers everything an agent needs: input format, examples, return fields, scope, and data source. The output schema handles return value details, so no additional explanation is needed.

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 100%, so the schema already documents the rsid parameter thoroughly, including format and examples. The description reinforces the format with three concrete examples and clarifies the scope (variants with known pharmacogenomic relevance). This adds value beyond the schema by giving the agent realistic example values to use.

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

Purpose5/5

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

The description clearly states the tool looks up pharmacogenomic details for a genetic variant by dbSNP rsID, with concrete examples (rs1799853, rs4244285, rs12248560). It enumerates the specific fields returned (variant ID, change classification, clinical significance, variant type, chromosomal position, associated genes, rarity flag, ClinVar IDs), which distinguishes it from sibling tools like pharmgkb.pharmacology.drug_search and pharmgkb.pharmacology.gene_search.

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 description specifies the input format (dbSNP rsID) and gives examples, making it clear when to use this tool. It notes the focus on variants with known drug-response relevance, which implies a selection criterion. However, it does not explicitly state when NOT to use it or name alternative tools for non-pharmacogenomic variants, though the sibling list makes the domain clear.

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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