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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
  • nullable, source-labelled cancerhotspots recurrence
  • top-level lookup_outcomes for domains and cancerhotspots
  • warnings and _meta.next_commands

A successful provider check with no overlap or hotspot match is empty and may name the checked source. If the selected residue or normalizable protein change is missing, the lookup is inapplicable; if the provider fails, it is unavailable. Those states do not claim a checked absence or provider source, and an inapplicable/unavailable Cancer Hotspots recurrence is JSON null.

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.