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### AlphaMissense DB Fetch (`alphamissense-db-fetch`) Retrieves the complete AlphaMissense prediction set for a single human UniProt accession and returns every per-substitution prediction, the prediction count, the mean pathogenicity score, and the source CSV URL. The `coordinate_system` configuration selects the protein-coordinate grid of every possible substitution or one of the genomic-coordinate tables, which are limited to substitutions reachable by a single-nucleotide change. The genomic tables additionally populate chromosome, position, reference allele, alternate allele, and transcript identifier on each prediction. #### API Reference

Source UniProt accession (must be a human protein covered by AlphaMissense; e.g. 'P04637').

Source Which AFDB CSV to fetch. `"uniprot"` (default) returns the full protein-coordinate saturation grid (\~7,500 rows for TP53). `"hg19"` / `"hg38"` return SNV-accessible substitutions in genomic coordinates (\~2,500 rows for TP53) and populate `chrom` / `pos` / `ref` / `alt` / `transcript_id` on each prediction; a protein variant reachable by multiple SNVs appears multiple times. Available options: `uniprot`, `hg19`, `hg38` Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source UniProt accession that was looked up. All per-substitution pathogenicity predictions in the source CSV (full saturation grid: `sequence_length * 19` for UniProt-coordinate fetches). 1-indexed residue position in the canonical UniProt sequence. Single-letter wild-type amino acid at this position. Single-letter alternate amino acid being scored. AlphaMissense pathogenicity score (0.0-1.0). Higher values indicate the variant is more likely to be pathogenic. AlphaMissense class label ('likely\_benign', 'ambiguous', or 'likely\_pathogenic'). Chromosome (e.g. 'chr17'); populated only for genomic-coordinate fetches. 1-indexed genomic position; populated only for genomic-coordinate fetches. Reference allele; populated only for genomic- coordinate fetches. Alternate allele; populated only for genomic- coordinate fetches. GENCODE transcript identifier; populated only for genomic-coordinate fetches. Number of predictions in the source CSV. Mean pathogenicity score across all predictions; None when `predictions` is empty. URL of the AlphaMissense CSV that was fetched.

#### Applications Use this to pull model-based missense pathogenicity into a pipeline: triage missense variants of uncertain significance from clinical sequencing, prioritize candidate disease-causing variants from case cohorts, avoid disruptive substitutions during sequence design or optimization, or apply a per-residue pathogenicity penalty in a generative-design loop. The accession can come from the [UniProt](https://bio-pro.mintlify.app/tools/database-retrieval/uniprot) tool, which resolves a gene symbol and organism to a canonical reviewed human accession. The same accession also drives the [AlphaFold DB](https://bio-pro.mintlify.app/tools/database-retrieval/alphafold-db) tool, aligning per-residue pathogenicity scores with predicted backbone coordinates. #### Usage Tips * **The tool always returns the entire prediction set.** There is no server-side filtering on the static CSV. Filter the returned `predictions` list in your own code by position, score, or classification. * **Cache the output once per accession.** A typical protein has roughly 7,000 to 20,000 substitution rows. Fetch once and reuse the result rather than refetching inside tight loops. * **Group by `position` for hotspot analysis.** `mean_pathogenicity` over a wide region is a coarse summary. Inspect predictions grouped by residue position to surface hotspots. * **Coverage is human canonical isoforms only.** Non-canonical isoforms and non-human accessions return a 404 and surface as a clear error. Resolve the accession with the UniProt tool first if the organism is uncertain.