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get_tolerance_landscape

Read-only

Retrieve per-residue missense tolerance and Pfam domain annotations for a human transcript by providing its ENST ID and optional position range, enabling analysis of constrained regions.

Instructions

Signature: get_tolerance_landscape(transcript_id, position_start=, position_stop=, limit=, offset=, response_mode=).

Input Schema

TableJSON Schema

Name	Required	Description
`limit`	No	Limit.
`offset`	No	Offset.
`position_stop`	No	Pos.
`response_mode`	No	Mode.
`transcript_id`	Yes	ENST.
`position_start`	No	Pos.

Output Schema

TableJSON Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

Changed22 schema fields changedv0.3.7Sep 4, 2026

removedInput schema / properties / limit / default
```
Removed value: -200
```

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."

removedInput schema / properties / position_start / anyOf

Removed value: -[
-  {
-    "minimum": 1,
-    "type": "integer"
-  },
-  {
-    "type": "null"
-  }
-]

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

changedInput schema / properties / position_start / description

Previous value: -"1-based protein residue position (inclusive range bound)."New value: +"Pos."

addedInput schema / properties / position_start / maximum
```
Added value: +1000000
```
addedInput schema / properties / position_start / minimum
```
Added value: +1
```
addedInput schema / properties / position_start / type
```
Added value: +[
+  "integer",
+  "null"
+]
```

removedInput schema / properties / position_stop / anyOf

Removed value: -[
-  {
-    "minimum": 1,
-    "type": "integer"
-  },
-  {
-    "type": "null"
-  }
-]

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

changedInput schema / properties / position_stop / description

Previous value: -"1-based protein residue position (inclusive range bound)."New value: +"Pos."

addedInput schema / properties / position_stop / maximum
```
Added value: +1000000
```
addedInput schema / properties / position_stop / minimum
```
Added value: +1
```
addedInput schema / properties / position_stop / type
```
Added value: +[
+  "integer",
+  "null"
+]
```
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": {
+                "propertyNames": {
+                  "pattern": "^(transcript_id|position(_start|_stop)?|limit|offset)$"
+                },
+                "type": "object"
+              },
+              "tool": {
+                "type": "string"
+              }
+            },
+            "type": "object"
+          },
+          "type": "array"
+        },
+        "^unsafe_for_clinical_use$": {
+          "const": true
+        }
+      },
+      "required": [
+        "tool",
+        "request_id",
+        "data_versions",
+        "unsafe_for_clinical_use"
+      ],
+      "type": "object"
+    }
+  },
+  "oneOf": [
+    {
+      "additionalProperties": false,
+      "oneOf": [
+        {
+          "required": [
+            "status",
+            "poll_after_s",
+            "cold_build_warning"
+          ]
+        },
+        {
+          "required": [
+            "pagination"
+          ]
+        }
+      ],
+      "patternProperties": {
+        "^(dropped_summary|transcript_id|cold_build_warning|recommended_citation|data_currency_caveat)$": {
+          "type": "string"
+        },
+        "^(gene_name|protein_ac)$": {
+          "type": [
+            "string",
+            "null"
+          ]
+        },
+        "^_meta$": {
+          "$ref": "#/$defs/M"
+        },
+        "^domains$": {
+          "items": {
+            "additionalProperties": false,
+            "minProperties": 6,
+            "patternProperties": {
+              "^(ID|Name)$": {
+                "type": "string"
+              },
+              "^(start|stop|meta_domain_alignment_depth)$": {
+                "type": "integer"
+              },
+              "^metadomain$": {
+                "type": "boolean"
+              }
+            },
+            "type": "object"
+          },
+          "type": "array"
+        },
+        "^pagination$": {
+          "additionalProperties": false,
+          "minProperties": 6,
+          "patternProperties": {
+            "^(total|returned|limit|offset)$": {
+              "type": "integer"
+            },
+            "^next_offset$": {
+              "type": [
+                "integer",
+                "null"
+              ]
+            },
+            "^truncated$": {
+              "type": "boolean"
+            }
+          },
+          "type": "object"
+        },
+        "^poll_after_s$": {
+          "type": "number"
+        },
+        "^positional_annotation$": {
+          "items": {
+            "additionalProperties": false,
+            "patternProperties": {
+              "^(cdna_pos|chr(_positions)?|exon_numbers|ref_(aa(_triplet)?|codon)|strand)$": {
+                "type": "string"
+              },
+              "^(protein_pos|sw_size)$": {
+                "type": "integer"
+              },
+              "^ClinVar$": {
+                "items": {
+                  "additionalProperties": false,
+                  "patternProperties": {
+                    "^(alt(_aa(_triplet)?|_codon)?|clinvar_(ID|clinsig)|ref|type|url)$": {
+                      "type": "string"
+                    },
+                    "^pos$": {
+                      "type": "integer"
+                    }
+                  },
+                  "required": [
+                    "alt",
+                    "alt_aa",
+                    "alt_aa_triplet",
+                    "alt_codon",
+                    "clinvar_ID",
+                    "pos",
+                    "ref",
+                    "type"
+                  ],
+                  "type": "object"
+                },
+                "type": "array"
+              },
+              "^domains$": {
+                "additionalProperties": {
+                  "oneOf": [
+                    {
+                      "type": "null"
+                    },
+                    {
+                      "additionalProperties": false,
+                      "minProperties": 7,
+                      "patternProperties": {
+                        "^(normal|pathogenic)(_missense)?_variant_count$": {
+                          "type": "number"
+                        },
+                        "^consensus_pos$": {
+                          "items": {
+                            "type": "integer"
+                          },
+                          "type": "array"
+                        },
+                        "^pathogenic(_missense)?_variant_count_per_clinsig$": {
+                          "additionalProperties": {
+                            "type": "number"
+                          },
+                          "type": "object"
+                        }
+                      },
+                      "type": "object"
+                    }
+                  ]
+                },
+                "type": "object"
+              },
+              "^sw_coverage$": {
+                "type": "number"
+              },
+              "^sw_dn_ds$": {
+                "type": [
+                  "number",
+                  "null"
+                ]
+              }
+            },
+            "required": [
+              "cdna_pos",
+              "chr",
+              "chr_positions",
+              "protein_pos",
+              "ref_aa",
+              "ref_aa_triplet",
+              "ref_codon",
+              "strand",
+              "sw_dn_ds",
+              "sw_coverage",
+              "sw_size",
+              "domains"
+            ],
+            "type": "object"
+          },
+          "type": "array"
+        },
+        "^refseq_ids$": {
+          "items": {
+            "type": "string"
+          },
+          "type": "array"
+        },
+        "^status$": {
+          "const": "processing"
+        },
+        "^success$": {
+          "const": true
+        }
+      },
+      "required": [
+        "success",
+        "_meta",
+        "transcript_id",
+        "recommended_citation"
+      ]
+    },
+    {
+      "additionalProperties": false,
+      "patternProperties": {
+        "^(message|recovery_action|field|hint)$": {
+          "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"
+}

Changed5 schema fields changedv0.3.1Jul 16, 2026

changedInput schema / properties / position_start / anyOf

Previous value: -[
-  {
-    "description": "1-based protein residue position (inclusive range bound).",
-    "minimum": 1,
-    "type": "integer"
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "minimum": 1,
+    "type": "integer"
+  },
+  {
+    "type": "null"
+  }
+]

addedInput schema / properties / position_start / description

Added value: +"1-based protein residue position (inclusive range bound)."

changedInput schema / properties / position_stop / anyOf

Previous value: -[
-  {
-    "description": "1-based protein residue position (inclusive range bound).",
-    "minimum": 1,
-    "type": "integer"
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "minimum": 1,
+    "type": "integer"
+  },
+  {
+    "type": "null"
+  }
+]

addedInput schema / properties / position_stop / description

Added value: +"1-based protein residue position (inclusive range bound)."

changedOutput schema / (root)

Previous value: -{
-  "additionalProperties": true,
-  "properties": {
-    "_meta": {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    "candidates": {
-      "type": "array"
-    },
-    "data_versions": {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    "domains": {
-      "items": {
-        "additionalProperties": true,
-        "properties": {
-          "id": {
-            "type": "string"
-          },
-          "meta_domain_alignment_depth": {
-            "type": "integer"
-          },
-          "metadomain": {
-            "type": "boolean"
-          },
-          "name": {
-            "type": "string"
-          },
-          "start": {
-            "type": "integer"
-          },
-          "stop": {
-            "type": "integer"
-          }
-        },
-        "type": "object"
-      },
-      "type": "array"
-    },
-    "error_code": {
-      "type": "string"
-    },
-    "field": {
-      "type": "string"
-    },
-    "gene_name": {
-      "type": [
-        "string",
-        "null"
-      ]
-    },
-    "hint": {
-      "type": "string"
-    },
-    "message": {
-      "type": "string"
-    },
-    "pagination": {
-      "additionalProperties": true,
-      "properties": {
-        "limit": {
-          "type": "integer"
-        },
-        "next_offset": {
-          "type": [
-            "integer",
-            "null"
-          ]
-        },
-        "offset": {
-          "type": "integer"
-        },
-        "returned": {
-          "type": "integer"
-        },
-        "total": {
-          "type": "integer"
-        },
-        "truncated": {
-          "type": "boolean"
-        }
-      },
-      "type": "object"
-    },
-    "poll_after_s": {
-      "type": [
-        "number",
-        "null"
-      ]
-    },
-    "positional_annotation": {
-      "items": {
-        "additionalProperties": true,
-        "properties": {
-          "domain_ids": {
-            "type": "array"
-          },
-          "protein_pos": {
-            "type": "integer"
-          },
-          "ref_aa": {
-            "type": [
-              "string",
-              "null"
-            ]
-          },
-          "sw_coverage": {
-            "type": [
-              "number",
-              "null"
-            ]
-          },
-          "sw_dn_ds": {
-            "type": [
-              "number",
-              "null"
-            ]
-          },
-          "sw_size": {
-            "type": "integer"
-          },
-          "variant_count_total": {
-            "type": "integer"
-          }
-        },
-        "type": "object"
-      },
-      "type": "array"
-    },
-    "protein_ac": {
-      "type": [
-        "string",
-        "null"
-      ]
-    },
-    "recommended_citation": {
-      "type": "string"
-    },
-    "recovery_action": {
-      "type": "string"
-    },
-    "refseq_ids": {
-      "type": "array"
-    },
-    "retryable": {
-      "type": "boolean"
-    },
-    "status": {
-      "type": [
-        "string",
-        "null"
-      ]
-    },
-    "success": {
-      "type": "boolean"
-    },
-    "transcript_id": {
-      "type": "string"
-    }
-  },
-  "required": [
-    "success"
-  ],
-  "type": "object"
-}New value: +null

First observedv0.1.0Jun 20, 2026

TDQS

D1.3/5.0

Behavior1/5

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

The description discloses no behavioral traits at all. It only lists the signature, which adds nothing beyond the readOnlyHint annotation already provided. No information about side effects, output format, pagination, or error handling is given.

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

Conciseness1/5

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

The description is extremely short but this is under-specification, not conciseness. It lacks structure and fails to front-load a purpose statement. Every useful piece of information is missing.

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?

For a tool with six parameters and an output schema, the description is grossly incomplete. It does not explain the tool's purpose, usage context, or any behavior needed for correct invocation, making it inadequate for an agent to use it properly.

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 coverage is 100%, so the baseline is 3. However, the schema descriptions are trivial (e.g., 'Limit.', 'Pos.', 'Mode.'), and the description's signature merely repeats parameter names without adding any meaning. It does not compensate for the poor schema descriptions, so it stays at the baseline.

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 nothing more than a function signature, restating the tool name and parameters without explaining what a 'tolerance landscape' is or what the tool returns. It provides no verb or resource beyond the name, making it a tautology that fails to distinguish the tool from siblings like get_position_tolerance or request_tolerance_landscape.

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 no guidance on when to use this tool versus its alternatives. The description does not mention any context, prerequisites, or exclusions, leaving the agent to guess which of the many related tools to call.

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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