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Annotate variant structure context

Use variant structure when you need the protein-structure context for one exact variant. The helper is opt-in because it joins several network sources.

biomcp variant structure "BRAF V600E"
biomcp --json variant structure "BRAF V600E"

The JSON response includes:

  • variant, gene, and input_kind
  • residue with the selected protein position, matched HGVSp aliases, other source positions, and confidence
  • protein with the UniProt accession and entry
  • overlapping InterPro domains with start and end
  • UniProt structures.pdb rows plus structures.alphafold.url
  • source-labelled cancerhotspots recurrence
  • warnings and _meta.next_commands

BioMCP selects the requested HGVSp position when MyVariant.info/dbNSFP returns multiple transcript or isoform positions. Ambiguous residue-only inputs are rejected with the same guidance as get variant; search first, then run this helper on the exact variant.

This helper does not run ΔΔG or stability prediction and does not change default get variant output.