metadome-link

Overview Schema Source Related Servers Discussions Admin

summarize_intolerant_regions

Read-only

Summarize intolerant regions in a human transcript using MetaDome data, with configurable thresholds, run lengths, and response modes.

Instructions

Signature: summarize_intolerant_regions(transcript_id, threshold=, min_run=, top_n=, response_mode=).

Input Schema

TableJSON Schema

Name	Required	Description
`top_n`	No	Region count.
`min_run`	No	Run length.
`threshold`	No	Cutoff.
`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.

Changed12 schema fields changedv0.3.7Sep 4, 2026

removedInput schema / properties / min_run / default
```
Removed value: -3
```

changedInput schema / properties / min_run / description

Previous value: -"Minimum number of consecutive residues to form a region (default 3). Shorter stretches are discarded."New value: +"Run length."

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"
```
removedInput schema / properties / threshold / default
```
Removed value: -0.5
```

changedInput schema / properties / threshold / description

Previous value: -"sw_dn_ds threshold (exclusive upper bound) for intolerant residues (default 0.5). Lower values identify only the most constrained positions."New value: +"Cutoff."

removedInput schema / properties / top_n / default
```
Removed value: -15
```

changedInput schema / properties / top_n / description

Previous value: -"Maximum number of regions to return, ranked by mean_sw_dn_ds ascending (default 15)."New value: +"Region count."

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": {
+                "propertyNames": {
+                  "pattern": "^(transcript_id|position)$"
+                },
+                "type": "object"
+              },
+              "tool": {
+                "type": "string"
+              }
+            },
+            "type": "object"
+          },
+          "type": "array"
+        },
+        "^unsafe_for_clinical_use$": {
+          "const": true
+        }
+      },
+      "required": [
+        "tool",
+        "request_id",
+        "data_versions",
+        "unsafe_for_clinical_use"
+      ],
+      "type": "object"
+    }
+  },
+  "oneOf": [
+    {
+      "additionalProperties": false,
+      "patternProperties": {
+        "^(dropped_summary|transcript_id|recommended_citation|data_currency_caveat)$": {
+          "type": "string"
+        },
+        "^(min_run|top_n)$": {
+          "type": "integer"
+        },
+        "^_meta$": {
+          "$ref": "#/$defs/M"
+        },
+        "^gene_name$": {
+          "type": [
+            "string",
+            "null"
+          ]
+        },
+        "^regions$": {
+          "items": {
+            "additionalProperties": false,
+            "minProperties": 7,
+            "patternProperties": {
+              "^(mean_sw_dn_ds|min_sw_dn_ds)$": {
+                "type": "number"
+              },
+              "^(start|stop|length)$": {
+                "type": "integer"
+              },
+              "^domains$": {
+                "items": {
+                  "type": "string"
+                },
+                "type": "array"
+              },
+              "^variant_evidence$": {
+                "additionalProperties": false,
+                "minProperties": 2,
+                "properties": {
+                  "meta_domain_homolog_aggregate": {
+                    "additionalProperties": false,
+                    "patternProperties": {
+                      "^(gnomad|clinvar)$": {
+                        "additionalProperties": false,
+                        "minProperties": 2,
+                        "patternProperties": {
+                          "^(variant_count|missense_variant_count)$": {
+                            "type": "integer"
+                          }
+                        },
+                        "type": "object"
+                      },
+                      "^(provenance|scope|reason)$": {
+                        "type": "string"
+                      },
+                      "^available$": {
+                        "type": "boolean"
+                      }
+                    },
+                    "required": [
+                      "available",
+                      "provenance"
+                    ],
+                    "type": "object"
+                  },
+                  "residue_level": {
+                    "additionalProperties": false,
+                    "minProperties": 1,
+                    "properties": {
+                      "clinvar": {
+                        "additionalProperties": false,
+                        "minProperties": 4,
+                        "patternProperties": {
+                          "^(variant_count|missense_variant_count)$": {
+                            "type": "integer"
+                          },
+                          "^available$": {
+                            "const": true
+                          },
+                          "^provenance$": {
+                            "type": "string"
+                          }
+                        },
+                        "type": "object"
+                      },
+                      "gnomad": {
+                        "additionalProperties": false,
+                        "minProperties": 2,
+                        "properties": {
+                          "available": {
+                            "const": false
+                          },
+                          "reason": {
+                            "type": "string"
+                          }
+                        },
+                        "type": "object"
+                      }
+                    },
+                    "type": "object"
+                  }
+                },
+                "type": "object"
+              }
+            },
+            "type": "object"
+          },
+          "type": "array"
+        },
+        "^success$": {
+          "const": true
+        },
+        "^threshold$": {
+          "type": "number"
+        }
+      },
+      "required": [
+        "success",
+        "_meta",
+        "transcript_id",
+        "threshold",
+        "min_run",
+        "top_n",
+        "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"
+}

Changed1 schema field changedv0.3.1Jul 16, 2026

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"
-    },
-    "gene_name": {
-      "type": [
-        "string",
-        "null"
-      ]
-    },
-    "hint": {
-      "type": "string"
-    },
-    "message": {
-      "type": "string"
-    },
-    "min_run": {
-      "type": "integer"
-    },
-    "recommended_citation": {
-      "type": "string"
-    },
-    "recovery_action": {
-      "type": "string"
-    },
-    "region_count": {
-      "type": "integer"
-    },
-    "regions": {
-      "items": {
-        "additionalProperties": true,
-        "properties": {
-          "clinvar_variant_count": {
-            "type": "integer"
-          },
-          "domains": {
-            "type": "array"
-          },
-          "gnomad_variant_count": {
-            "type": "integer"
-          },
-          "length": {
-            "type": "integer"
-          },
-          "mean_sw_dn_ds": {
-            "type": [
-              "number",
-              "null"
-            ]
-          },
-          "min_sw_dn_ds": {
-            "type": [
-              "number",
-              "null"
-            ]
-          },
-          "start": {
-            "type": "integer"
-          },
-          "stop": {
-            "type": "integer"
-          }
-        },
-        "type": "object"
-      },
-      "type": "array"
-    },
-    "retryable": {
-      "type": "boolean"
-    },
-    "success": {
-      "type": "boolean"
-    },
-    "threshold": {
-      "type": "number"
-    },
-    "top_n": {
-      "type": "integer"
-    },
-    "transcript_id": {
-      "type": "string"
-    }
-  },
-  "required": [
-    "success"
-  ],
-  "type": "object"
-}New value: +null

First observedv0.1.0Jun 20, 2026

TDQS

D1.4/5.0

Behavior1/5

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

The description discloses no behavior at all. The readOnlyHint=true annotation is the only safety signal, and the description adds nothing beyond it — it doesn't say what is computed, what gets returned, or any side effects. With annotations present the bar is lower, but the description still contributes zero 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.

Conciseness2/5

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

The single-line signature is short but this is under-specification, not conciseness. It is redundant with the input schema, which already enumerates the parameters. No useful content is front-loaded because there is no content.

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?

Despite having an output schema and 5 parameters, the description gives no indication of what the tool computes or returns. An agent has no way to know what 'intolerant regions' means, what the output structure represents, or when to invoke this tool. Completely inadequate for a tool of this complexity.

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 with no param detail in the description. The signature merely lists parameter names already present in the schema and adds no meaning beyond it. The terse schema descriptions ('Region count', 'Cutoff', 'Mode') remain the only semantic source.

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 states what 'summarize_intolerant_regions' actually does — no verb, no resource semantics, no explanation of what 'intolerant regions' means or what gets summarized. This is a tautology of the name.

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

Usage Guidelines1/5

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

There is zero guidance on when to use this tool versus the sibling tools (get_tolerance_landscape, get_position_tolerance, get_variant_counts, compare_positions). No context, no exclusions, no alternatives are mentioned. An agent cannot distinguish when to pick this over a sibling.

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

Deploy Server