Folklore Clinical Variant Interpretation MCP

Measured conclusion: Deep-tested. L2 outcome: tools_ok.

Bioinformatics MCP for genomic variant interpretation, gene-disease evidence and literature.

Add to your agent

Copy this into your MCP client config:

{
  "mcpServers": {
    "Folklore Clinical Variant Interpretation MCP": {
      "url": "https://api.helena.bio/folklore/v1/mcp",
      "transport": "streamable-http"
    }
  }
}

Measured tools (7)

• search_variant_evidence read-only

  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. Never invent or swap REF/ALT, guess a transcript accession, or relabel another assembly as GRCh38. For reference_mismatch, ask the user to verify the source assembly, position, reference and accession version; preserve the refusal. A bare protein consequence needs a gene or versioned protein accession. A report row may include matching genomic, coding and protein descriptions with a versioned transcript; submit the complete row without discarding conflicting parts. For not_found, preserve the missing exact mapping rather than back-translating a protein change.

  Parameters:

  • query (required) — string — One germline nuclear SNV or simple indel to resolve and interpret; accepted forms include coordinates, genomic/coding/protein HGVS, SPDI, rsID, or a returned Folklore canonical_key in GRCh38:chrN:position:REF:ALT form.
  • assembly — string — Reference genome assembly. Folklore currently accepts GRCh38 only.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• search_variant_literature read-only

  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.

  Parameters:

  • query (required) — string — One germline nuclear SNV or simple indel to resolve before retrieving its literature; this is a variant identifier, not a natural-language question. Accepts a returned Folklore canonical_key in GRCh38:chrN:position:REF:ALT form.
  • limit — integer — Maximum number of publications to return, from 1 to 25.
  • assembly — string — Reference genome assembly. Folklore currently accepts GRCh38 only.
  • question — Optional natural-language focus applied after the variant is resolved, such as a condition or evidence question; do not put the variant identifier here.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• get_publication_details read-only

  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.

  Parameters:

  • pmid (required) — string — One PubMed identifier to look up in Folklore's current corpus, as 1 to 12 digits without a PMID prefix.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• search_literature_corpus read-only

  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.

  Parameters:

  • query (required) — string — Natural-language literature question or exact PMID, DOI, PMCID, gene, variant, phenotype, HPO, or OMIM query. Include every known publication identifier when comparing or finding related papers.
  • sort — string — Result ordering: relevance-ranked, newest publication first, or oldest publication first.
  • limit — integer — Maximum number of publications to return, from 1 to 25.
  • cursor — Opaque continuation cursor from the preceding response for the same query and sort order; omit for the first page.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• support_helena read-only

  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.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• get_gene_disease_associations read-only

  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.

  Parameters:

  • gene (required) — string — One public human gene symbol or HGNC identifier, for example BRCA1 or HGNC:1100. No patient data.
  • limit — integer — Maximum number of source assertions per page, from 1 to 50.
  • offset — integer — Zero-based assertion offset; use the returned nextOffset when present.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

• search_disease_genes read-only

  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.

  Parameters:

  • disease (required) — string — One public disease name or exact MONDO identifier (MONDO: followed by seven digits). A name search may match multiple distinct diseases. No symptoms or patient narrative.
  • limit — integer — Maximum number of source assertions per page, from 1 to 50.
  • offset — integer — Zero-based assertion offset; use the returned nextOffset when present.

  Hints: read-only yes · destructive no · idempotent yes · open-world no

Publisher website Repository

Measured by MCPYP probing. Untested fields are omitted, never estimated. Listing is always free; MCPYP never proxies calls or stores user tokens.