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get_meta_domain

Read-only

Retrieve Pfam domain annotations and per-residue missense tolerance at a specified position in a human transcript, helping identify affected functional domains.

Instructions

Signature: get_meta_domain(transcript_id, position, domains=, limit=, offset=, response_mode=).

Input Schema

TableJSON Schema

Name	Required	Description
`limit`	No	Limit.
`offset`	No	Offset.
`domains`	No	Pfam selector.
`position`	Yes	Pos.
`response_mode`	No	Mode.
`transcript_id`	Yes	ENST.

Output Schema

TableJSON Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

Changed17 schema fields changedv0.3.7Sep 4, 2026

changedInput schema / properties / domains / anyOf

Previous value: -[
-  {
-    "additionalProperties": {
-      "items": {
-        "type": "integer"
-      },
-      "type": "array"
-    },
-    "type": "object"
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "additionalProperties": {
+      "items": {
+        "maximum": 1000000000,
+        "minimum": 1,
+        "type": "integer"
+      },
+      "maxItems": 256,
+      "minItems": 1,
+      "type": "array"
+    },
+    "maxProperties": 32,
+    "propertyNames": {
+      "maxLength": 64,
+      "minLength": 1,
+      "type": "string"
+    },
+    "type": "object"
+  },
+  {
+    "type": "null"
+  }
+]

removedInput schema / properties / domains / default
```
Removed value: -null
```

changedInput schema / properties / domains / description

Previous value: -"Optional meta-domain selector {PfamID: [consensus_pos, ...]}. Omit to derive it from the residue's cached domain mapping."New value: +"Pfam selector."

removedInput schema / properties / domains / examples

Removed value: -[
-  {
-    "PF00870": [
-      81
-    ]
-  }
-]

removedInput schema / properties / limit / default
```
Removed value: -100
```

changedInput schema / properties / limit / description

Previous value: -"Maximum rows to return (1..1000; default 200)."New value: +"Limit."

removedInput schema / properties / offset / default
```
Removed value: -0
```

changedInput schema / properties / offset / description

Previous value: -"Zero-based offset into the result list (for paging)."New value: +"Offset."

changedInput schema / properties / position / description

Previous value: -"1-based protein residue position."New value: +"Pos."

changedInput schema / properties / position / examples

Previous value: -[
-  273
-]New value: +[
+  175
+]

addedInput schema / properties / position / maximum
```
Added value: +1000000
```
removedInput schema / properties / response_mode / default
```
Removed value: -"compact"
```

changedInput schema / properties / response_mode / description

Previous value: -"Verbosity: minimal|compact|standard|full (default compact)."New value: +"Mode."

removedInput schema / properties / response_mode / type
```
Removed value: -"string"
```

changedInput schema / properties / transcript_id / description

Previous value: -"A versioned Ensembl transcript id (the .N version suffix is required), e.g. ENST00000269305.4. Resolve a gene symbol with resolve_transcript first."New value: +"ENST."

changedInput schema / properties / transcript_id / examples

Previous value: -[
-  "ENST00000269305.4"
-]New value: +[
+  "ENST00000269305.9"
+]

changedOutput schema / (root)

Previous value: -nullNew value: +{
+  "$defs": {
+    "M": {
+      "additionalProperties": false,
+      "patternProperties": {
+        "^(tool|request_id|capabilities_version)$": {
+          "type": "string"
+        },
+        "^data_versions$": {
+          "additionalProperties": false,
+          "minProperties": 8,
+          "patternProperties": {
+            "^(assembly|gencode|uniprot|gnomad|clinvar|pfam|metadome_app|data_doi)$": {
+              "type": "string"
+            }
+          },
+          "type": "object"
+        },
+        "^elapsed_ms$": {
+          "type": "integer"
+        },
+        "^next_commands$": {
+          "items": {
+            "additionalProperties": false,
+            "minProperties": 2,
+            "properties": {
+              "arguments": {
+                "properties": {
+                  "domains": {
+                    "additionalProperties": {
+                      "items": {
+                        "type": "integer"
+                      },
+                      "type": "array"
+                    },
+                    "type": "object"
+                  }
+                },
+                "propertyNames": {
+                  "pattern": "^(transcript_id|position|limit|offset|domains)$"
+                },
+                "type": "object"
+              },
+              "tool": {
+                "type": "string"
+              }
+            },
+            "type": "object"
+          },
+          "type": "array"
+        },
+        "^unsafe_for_clinical_use$": {
+          "const": true
+        }
+      },
+      "required": [
+        "tool",
+        "request_id",
+        "data_versions",
+        "unsafe_for_clinical_use"
+      ],
+      "type": "object"
+    },
+    "v": {
+      "patternProperties": {
+        "^(alt|alt_aa|alt_aa_triplet|alt_codon|cdna_pos|chr|chr_positions|exon_numbers|gene_name|ref|ref_aa|ref_aa_triplet|ref_codon|strand|type)$": {
+          "type": "string"
+        },
+        "^(pos|protein_pos)$": {
+          "type": "integer"
+        }
+      },
+      "required": [
+        "alt",
+        "alt_aa",
+        "alt_aa_triplet",
+        "alt_codon",
+        "cdna_pos",
+        "chr",
+        "chr_positions",
+        "gene_name",
+        "pos",
+        "protein_pos",
+        "ref",
+        "ref_aa",
+        "ref_aa_triplet",
+        "ref_codon",
+        "strand",
+        "type"
+      ],
+      "type": "object"
+    }
+  },
+  "oneOf": [
+    {
+      "additionalProperties": false,
+      "patternProperties": {
+        "^(dropped_summary|transcript_id|recommended_citation|data_currency_caveat)$": {
+          "type": "string"
+        },
+        "^_meta$": {
+          "$ref": "#/$defs/M"
+        },
+        "^meta_domains$": {
+          "additionalProperties": {
+            "additionalProperties": false,
+            "minProperties": 4,
+            "properties": {
+              "alignment_depth": {
+                "type": "integer"
+              },
+              "normal_variants": {
+                "items": {
+                  "allOf": [
+                    {
+                      "$ref": "#/$defs/v"
+                    },
+                    {
+                      "patternProperties": {
+                        "^(allele_count|allele_number)$": {
+                          "type": "number"
+                        }
+                      },
+                      "required": [
+                        "allele_count",
+                        "allele_number"
+                      ],
+                      "type": "object"
+                    }
+                  ],
+                  "unevaluatedProperties": false
+                },
+                "type": "array"
+              },
+              "pagination": {
+                "additionalProperties": false,
+                "minProperties": 2,
+                "patternProperties": {
+                  "^(normal_variants|pathogenic_variants)$": {
+                    "additionalProperties": false,
+                    "minProperties": 6,
+                    "patternProperties": {
+                      "^(total|returned|limit|offset)$": {
+                        "type": "integer"
+                      },
+                      "^next_offset$": {
+                        "type": [
+                          "integer",
+                          "null"
+                        ]
+                      },
+                      "^truncated$": {
+                        "type": "boolean"
+                      }
+                    },
+                    "type": "object"
+                  }
+                },
+                "type": "object"
+              },
+              "pathogenic_variants": {
+                "items": {
+                  "allOf": [
+                    {
+                      "$ref": "#/$defs/v"
+                    },
+                    {
+                      "patternProperties": {
+                        "^(clinvar_ID|clinvar_clinsig)$": {
+                          "type": "string"
+                        }
+                      },
+                      "required": [
+                        "clinvar_ID"
+                      ],
+                      "type": "object"
+                    }
+                  ],
+                  "unevaluatedProperties": false
+                },
+                "type": "array"
+              }
+            },
+            "type": "object"
+          },
+          "type": "object"
+        },
+        "^protein_position$": {
+          "type": "integer"
+        },
+        "^requested_domains$": {
+          "additionalProperties": {
+            "items": {
+              "type": "integer"
+            },
+            "type": "array"
+          },
+          "type": "object"
+        },
+        "^success$": {
+          "const": true
+        }
+      },
+      "required": [
+        "success",
+        "_meta",
+        "transcript_id",
+        "protein_position",
+        "meta_domains",
+        "recommended_citation"
+      ]
+    },
+    {
+      "additionalProperties": false,
+      "patternProperties": {
+        "^(message|recovery_action|field|hint)$": {
+          "type": "string"
+        },
+        "^_meta$": {
+          "$ref": "#/$defs/M"
+        },
+        "^allowed_values$": {
+          "items": {
+            "type": "string"
+          },
+          "type": "array"
+        },
+        "^error_code$": {
+          "enum": [
+            "invalid_input",
+            "not_found",
+            "ambiguous_query",
+            "upstream_unavailable",
+            "rate_limited",
+            "internal"
+          ]
+        },
+        "^retryable$": {
+          "type": "boolean"
+        },
+        "^success$": {
+          "const": false
+        }
+      },
+      "required": [
+        "success",
+        "_meta",
+        "error_code",
+        "message",
+        "retryable",
+        "recovery_action"
+      ]
+    }
+  ],
+  "type": "object"
+}

Changed2 schema fields changedv0.3.1Jul 16, 2026

addedInput schema / properties / position / examples
```
Added value: +[
+  273
+]
```

changedOutput schema / (root)

Previous value: -{
-  "additionalProperties": true,
-  "properties": {
-    "_meta": {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    "candidates": {
-      "type": "array"
-    },
-    "data_versions": {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    "error_code": {
-      "type": "string"
-    },
-    "field": {
-      "type": "string"
-    },
-    "hint": {
-      "type": "string"
-    },
-    "message": {
-      "type": "string"
-    },
-    "meta_domains": {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    "protein_position": {
-      "type": "integer"
-    },
-    "recommended_citation": {
-      "type": "string"
-    },
-    "recovery_action": {
-      "type": "string"
-    },
-    "requested_domains": {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    "retryable": {
-      "type": "boolean"
-    },
-    "success": {
-      "type": "boolean"
-    },
-    "transcript_id": {
-      "type": "string"
-    }
-  },
-  "required": [
-    "success"
-  ],
-  "type": "object"
-}New value: +null

First observedv0.1.0Jun 20, 2026

TDQS

D1.8/5.0

Behavior2/5

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

The readOnlyHint annotation communicates that this is a read-only operation, but the description itself adds no behavioral context: no mention of output semantics, scope, or side effects. It neither contradicts nor enriches the annotation.

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

Conciseness2/5

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

The description is short, but this is under-specification rather than disciplined concision. A single signature line does not earn its place because it duplicates information already available in the input schema.

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

Completeness1/5

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

With six parameters, an output schema, and a large sibling set, a signature-only description leaves the agent without the information needed to invoke the tool correctly. It omits purpose, domain-selection semantics, and result interpretation.

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 even though the description adds no real meaning. The signature repeats parameter names, and the schema's own descriptions are mostly one-word placeholders, but no additional semantics are required by the high-coverage rule.

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

Purpose1/5

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

The description is only a signature line that restates the tool name and parameter names; it never says what a 'meta domain' is or what the tool returns. This is tautology-level description and provides no way to distinguish it from siblings like get_protein_domains.

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

Usage Guidelines2/5

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

There is no guidance about when to call this tool versus the 10 siblings. No context, prerequisites, or exclusions are given, so the agent must guess the appropriate scenario.

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

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