AlphaGenome MCP Server

predict_tissue_specific

Predict the effect of a genetic variant in specific tissues, such as brain, liver, or heart, to compare impacts and prioritize research.

Instructions

The strongest predicted effect of a variant in each of several tissues: the same scores, filtered to the tracks of one tissue at a time.

Runs live inference (score_variant with the SDK's recommended variant scorers); works for single-nucleotide variants, indels and multi-nucleotide variants. The result states source: live.

Results are AlphaGenome model predictions for research prioritization, not clinical classifications: scores and calibrated quantiles are reported as returned, and no pathogenic/benign call is made.

Example: "Compare the predicted effect of chr19:44908684 T>C in brain, liver and heart"

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "chromosome": "<chromosome>",
      "position": "<position>",
      "ref": "<ref>",
      "alt": "<alt>"
    },
    "name": "predict_tissue_specific"
  }
}

Input Schema

Name	Required	Description
`alt`	Yes	Alternate allele (A, C, G, T; more than one base for an indel)
`ref`	Yes	Reference allele (A, C, G, T; more than one base for an indel)
`tissues`	No	Tissue names (brain, neuron, blood, liver, heart, lung, kidney) or ontology CURIEs. Default: brain, liver, heart
`position`	Yes	Genomic position (1-based, hg38)
`chromosome`	Yes	Chromosome (chr1-chr22, chrX, chrY)

Schema Changelog

Changes observed during successful MCP inspections.

Changed5 schema fields changedv0.3.0Sep 28, 2026

changedInput schema / properties / alt / description

Previous value: -"Alternate allele"New value: +"Alternate allele (A, C, G, T; more than one base for an indel)"

changedInput schema / properties / chromosome / description

Previous value: -"Chromosome"New value: +"Chromosome (chr1-chr22, chrX, chrY)"

changedInput schema / properties / position / description

Previous value: -"Genomic position"New value: +"Genomic position (1-based, hg38)"

changedInput schema / properties / ref / description

Previous value: -"Reference allele"New value: +"Reference allele (A, C, G, T; more than one base for an indel)"

changedInput schema / properties / tissues / description

Previous value: -"List of tissues to test (default: brain, liver, heart)"New value: +"Tissue names (brain, neuron, blood, liver, heart, lung, kidney) or ontology CURIEs. Default: brain, liver, heart"

First observedDec 29, 2025

TDQS

A3.7/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the burden well: it discloses that inference runs live (latency/cost implication), that results carry `source: live`, what is returned (scores and calibrated quantiles), and that no pathogenic/benign call is made. It omits auth/permission and rate-limit details, but otherwise adds meaningful behavioral context.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three short blocks with the core purpose front-loaded and no filler paragraphs; the live-inference and research-use notes each earn their place. The opening sentence 'the same scores' lacks an antecedent, which briefly obscures what it is being compared against.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

No output schema exists, and the description compensates by describing the return content (scores, calibrated quantiles, `source: live`) plus the research-only scope, and it covers supported variant classes. It is complete enough to call correctly, with only routing to sibling tools left implicit.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the baseline is 3. The description adds modest meaning by mapping a tissue entry to 'the tracks of one tissue at a time', but it gives no extra detail on the chromosome/position/ref/alt inputs beyond what the schema already documents.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb+resource ('predicted effect of a variant in each of several tissues') and clarifies the output shape (same scores filtered to one tissue's tracks at a time). It is distinguishable from siblings like batch_tissue_comparison and predict_variant_effect, though it never explicitly names which sibling it is not.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Usage is only implied via the example ('Compare the predicted effect of chr19:44908684 T>C in brain, liver and heart'). There is no explicit statement of when to prefer this over predict_variant_effect, compare_variants, or batch_tissue_comparison, so the agent must infer routing.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.