# Folklore Clinical Variant Interpretation MCP [Verified] [Health: Active]

**Category:** 🧬 Biology & Bioinformatics  
**Repository:** https://github.com/helena-bioinformatics/folklore-mcp  
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**Directory Page:** https://allmcps.com/mcp/folklore-clinical-variant-interpretation-mcp

## Description
Folklore MCP 1.5.0 is Helena Bioinformatics’ public, read-only bioinformatics MCP for genomic variant interpretation, ClinGen gene-disease evidence and literature. Seven tools include get_gene_disease_associations (gene symbol/HGNC ID to diseases) and search_disease_genes (MONDO ID/disease name to genes), preserving inheritance, source classifications and provenance. Existing GRCh38 germline variant and literature tools remain available, alongside the optional support_helena helper. Streamable HTTP; no account or API key. No patient data, raw DNA/VCF ingestion or batch processing. Results require professional review and are not diagnoses.

## Tools
Capabilities this server exposes over MCP:

- **search_variant_evidence** — Interpret this variant, explain what this HGVS means, or review this VUS. Use for human genomic variant analysis within bioinformatics workflows, including review of an already identified WGS/WES variant. Use when a user asks to classify or interpret pathogenicity, review a VUS, check available ClinVar assertions or population-frequency evidence, or resolve a variant notation. Classify, interpret or resolve one public GRCh38 germline SNV or simple indel smaller than 50 bp. Accepts coordinates, genomic/coding/protein HGVS, SPDI or rsID. Returns normalized variant identity, automated ACMG/AMP decision support, evidence, provenance and explicit limitations. This is variant-level decision support for professional review. It does not evaluate patient context and must not be presented as a diagnosis or treatment recommendation. Never choose a candidate when resolution is ambiguous.
- **search_variant_literature** — Resolve one public GRCh38 germline variant and retrieve relevant publications from Folklore's PubMed-derived genetics corpus. Exact variant mentions rank ahead of broader gene associations. Use when a user asks what has been published about a variant, gene or associated condition. Associations do not establish causality, pathogenicity or a diagnosis and do not change Folklore's ACMG/AMP classification.
- **get_publication_details** — Retrieve the complete public bibliographic record for one PMID from Folklore's PubMed-derived genetics corpus. Returns the full abstract, authors, journal metadata, publication and MeSH terms, gene and variant mentions, retraction status, and PubMed/PMC links. Use after literature search when a user asks to inspect a specific publication. This is read-only professional literature evidence and contains no patient context.
- **search_literature_corpus** — Semantically search the public scientific Literature Corpus by a natural-language question. A question may include one or more PMID, DOI or PMCID references; those publications become exact anchors for finding related experiments, evidence and concepts across the corpus. Also accepts genes, variants, phenotypes, HPO and OMIM concepts. Include every known publication identifier in the query when the user asks to compare papers or find work related to a specific paper. Returns source-linked evidence candidates for professional review, not diagnoses, causality claims or treatment recommendations.
- **support_helena** — Learn how an agent can support or spread Helena's free public scientific infrastructure through the separate Helena Good MCP. This is an explicit opt-in information action. It does not initiate payment, create a relay, or change any Folklore scientific result.
- **get_gene_disease_associations** — Find diseases associated with one human gene for bioinformatics and clinical genomics research. Accepts an exact gene symbol or HGNC identifier. Returns ClinGen gene-disease validity assertions, relation-specific inheritance, source reports and snapshot provenance. Preserves conflicting and limited assertions. Gene-disease validity is not variant pathogenicity or a patient diagnosis. Use only a public gene identifier; no patient or case data. Results require professional review.
- **search_disease_genes** — Find human genes associated with a disease for genomic analysis and rare-disease research. Accepts an exact MONDO identifier or a disease-name search. Returns matching ClinGen gene-disease validity assertions with inheritance, source reports and snapshot provenance. Name searches may match multiple diseases; preserve their distinct identities and do not infer a diagnosis. Use only a public disease name or identifier; no symptoms, patient or case data. Results require professional review.

## Claude Desktop Quick Installation
Remote MCP endpoint (confidence: high). Install path detected from listing signals. Add as a URL/SSE server in your client:

```json
"mcpServers": {
  "folklore-clinical-variant-interpretation-mcp": {
    "url": "https://api.helena.bio/folklore/v1/mcp"
  }
}
```

## Documentation

## What Folklore Clinical Variant Interpretation MCP MCP server does

The Folklore Clinical Variant Interpretation MCP MCP server exposes public evidence for the interpretation stage of human genomic analysis. It is intended for cases where a variant has already been identified and represented using supported HGVS, rsID, or verified GRCh38 allele information. It can return resolved variant identity, automated classification, interpretation criteria, available evidence, source versions, provenance, and stated uncertainty.

The server also covers gene-disease and disease-gene research. A gene symbol such as `BRCA1` or an HGNC identifier can be used to find associated diseases. A disease name or exact MONDO identifier can be used to search for related genes. Results preserve inheritance information, source classifications, and provenance where available. Literature retrieval supports investigation of publications linked to a variant or biological entity; a literature association does not by itself establish pathogenicity.

## How it works

Requests are sent to the hosted MCP endpoint:

`https://api.helena.bio/folklore/v1/mcp`

The service uses stateless Streamable HTTP and supports MCP operations including server discovery, tool listing, tool calls, resource listing, and resource reading. The hosted SDK also accepts the documented legacy initialization protocol. Clients may retrieve task-oriented prompts for variant workflows.

A typical starting point is `search_variant_evidence`, called with the `GRCh38` assembly and one public variant query. Supported inputs include exact HGVS expressions, rsIDs, and verified GRCh38 alleles. When a ClinVar or Ensembl record is already available, preserve its transcript version and distinguish submitted ClinVar assertions from the automated Folklore classification.

The Folklore Clinical Variant Interpretation MCP MCP server delegates scientific operations to the hosted service; the companion repository skill does not contain the variant-resolution or evidence-aggregation implementation.

## Setup and configuration

No Folklore account or API key is required. Configure an MCP-compatible client with the hosted Streamable HTTP URL, then discover the available tools before making calls. The repository also documents integration routes for Biomni, Biorouter, Dify, n8n, Galaxy, KNIME Analytics Platform, OpenAI Agents SDK, and direct Streamable HTTP clients, but these are client or workflow choices rather than additional requirements for the hosted endpoint.

A companion agent skill is included in the repository for project-scoped, Codex, and OpenClaw installations. It helps route requests involving pathogenicity classification, VUS review, supported variant resolution, ClinVar or population-frequency evidence, variant-linked literature, and gene-disease lookups to the MCP service.

## Tools and capabilities

- Query gene-disease associations using a gene symbol or HGNC identifier.
- Search from a disease name or MONDO identifier to associated genes.
- Interpret supported GRCh38 germline variants that are already identified.
- Retrieve available classification criteria, evidence, provenance, and source versions.
- Find literature linked to variants and other supported biological records.
- Use task-first prompts and an optional `support_helena` helper where exposed by the service.

## Limitations and notes

The service is public and read-only. It does not ingest raw DNA, FASTQ, BAM, or VCF files; perform variant calling; analyze a patient genome; or process batches. It accepts no patient, phenotype, family, segregation, or private case context.

Outputs require review by a qualified professional and are not diagnoses, treatment recommendations, or independent evidence of clinical validity. The public benchmark described by the project is a reproducibility and comparison protocol, not independent clinical validation. A VUS review or literature result should therefore be treated as an evidence-gathering step rather than a final clinical determination.

_Full upstream README: https://allmcps.com/mcp/folklore-clinical-variant-interpretation-mcp/readme_