metadome-link

by berntpopp

Overview Schema Source Related Servers Discussions Admin

Python

Remote

get_variant_counts

Read-only

Retrieve variant counts for a human transcript, filtered by position range and source (gnomad, ClinVar, or both).

Instructions

Signature: get_variant_counts(transcript_id, position=, position_start=, position_stop=, source=, limit=, offset=, response_mode=).

Input Schema

TableJSON Schema

Name	Required	Description
`limit`	No	Limit.
`offset`	No	Offset.
`source`	No	Source.
`position`	No	Pos.
`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.

Changed29 schema fields changedv0.3.7Sep 4, 2026

changedInput schema / properties / limit / description

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

changedInput schema / properties / offset / description

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

removedInput schema / properties / position / anyOf

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

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

changedInput schema / properties / position / description

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

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

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: -"Inclusive start of a residue range."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: -"Inclusive stop of a residue range."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"
```
removedInput schema / properties / source / default
```
Removed value: -"both"
```

changedInput schema / properties / source / description

Previous value: -"Evidence source to report: both|gnomad|clinvar (default both)."New value: +"Source."

removedInput schema / properties / source / 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)?|source|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,
+      "patternProperties": {
+        "^(dropped_summary|transcript_id|recommended_citation|data_currency_caveat)$": {
+          "type": "string"
+        },
+        "^_meta$": {
+          "$ref": "#/$defs/M"
+        },
+        "^pagination$": {
+          "additionalProperties": false,
+          "minProperties": 6,
+          "patternProperties": {
+            "^(total|returned|limit|offset)$": {
+              "type": "integer"
+            },
+            "^next_offset$": {
+              "type": [
+                "integer",
+                "null"
+              ]
+            },
+            "^truncated$": {
+              "type": "boolean"
+            }
+          },
+          "type": "object"
+        },
+        "^positions$": {
+          "items": {
+            "additionalProperties": false,
+            "properties": {
+              "clinvar_variants": {
+                "items": {
+                  "additionalProperties": false,
+                  "patternProperties": {
+                    "^(alt(_aa(_triplet)?|_codon)?|clinvar_(ID|clinsig)|ref|type|url)$": {
+                      "type": "string"
+                    },
+                    "^pos$": {
+                      "type": "integer"
+                    }
+                  },
+                  "required": [
+                    "alt",
+                    "alt_aa",
+                    "alt_aa_triplet",
+                    "alt_codon",
+                    "clinvar_ID",
+                    "pos",
+                    "ref",
+                    "type"
+                  ],
+                  "type": "object"
+                },
+                "type": "array"
+              },
+              "protein_pos": {
+                "type": "integer"
+              },
+              "ref_aa": {
+                "type": "string"
+              },
+              "sw_dn_ds": {
+                "type": [
+                  "number",
+                  "null"
+                ]
+              },
+              "variant_evidence": {
+                "additionalProperties": false,
+                "minProperties": 2,
+                "properties": {
+                  "meta_domain_homolog_aggregate": {
+                    "additionalProperties": false,
+                    "patternProperties": {
+                      "^(gnomad|clinvar)$": {
+                        "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"
+              }
+            },
+            "required": [
+              "protein_pos",
+              "ref_aa",
+              "sw_dn_ds",
+              "variant_evidence"
+            ],
+            "type": "object"
+          },
+          "type": "array"
+        },
+        "^source$": {
+          "enum": [
+            "both",
+            "gnomad",
+            "clinvar"
+          ]
+        },
+        "^success$": {
+          "const": true
+        }
+      },
+      "required": [
+        "success",
+        "_meta",
+        "transcript_id",
+        "source",
+        "positions",
+        "pagination",
+        "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

changedInput schema / properties / source / description

Previous value: -"Variant source to report: both|gnomad|clinvar (default both)."New value: +"Evidence source to report: both|gnomad|clinvar (default both)."

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"
-    },
-    "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"
-    },
-    "positions": {
-      "items": {
-        "additionalProperties": true,
-        "type": "object"
-      },
-      "type": "array"
-    },
-    "recommended_citation": {
-      "type": "string"
-    },
-    "recovery_action": {
-      "type": "string"
-    },
-    "retryable": {
-      "type": "boolean"
-    },
-    "returned": {
-      "type": "integer"
-    },
-    "source": {
-      "type": "string"
-    },
-    "success": {
-      "type": "boolean"
-    },
-    "total": {
-      "type": "integer"
-    },
-    "transcript_id": {
-      "type": "string"
-    }
-  },
-  "required": [
-    "success"
-  ],
-  "type": "object"
-}New value: +null

Changed2 schema fields changedv0.1.5Jul 11, 2026

addedInput schema / properties / limit

Added value: +{
+  "default": 200,
+  "description": "Maximum rows to return (1..1000; default 200).",
+  "maximum": 1000,
+  "minimum": 1,
+  "type": "integer"
+}

addedInput schema / properties / offset

Added value: +{
+  "default": 0,
+  "description": "Zero-based offset into the result list (for paging).",
+  "minimum": 0,
+  "type": "integer"
+}

First observedv0.1.0Jun 20, 2026

TDQS

D1.6/5.0

Behavior2/5

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

The annotation readOnlyHint=true is present, and the description adds no behavioral context beyond the signature. It does not disclose return format, pagination behavior, source semantics, or any side effects. Since the description contributes nothing to the annotation, it fails to add value.

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 a single line, but it is under-specification rather than concise. It lacks any structure or front-loaded intent, providing only a bare function signature that omits all explanatory value.

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 8 parameters and an output schema, this description is grossly incomplete. It does not state what the tool returns, how to interpret the response, or any operational details. The agent cannot determine correctness or expected output without external knowledge.

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

Parameters1/5

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

Although schema description coverage is 100%, the schema descriptions are unhelpful (e.g., 'Limit.', 'Pos.', 'ENST.'). The description provides no additional parameter meaning, so it fails to compensate for the schema's lack of clarity. The signature alone does not explain how parameters interact or what values are valid.

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

Purpose2/5

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

The description only provides a signature line, restating the tool name and parameters without any verb, resource, or scope explanation. It does not distinguish this tool from siblings like get_tolerance_landscape or compare_positions, leaving the agent to guess what 'variant counts' means.

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 alternatives, no context for typical scenarios, and no mention of exclusions or prerequisites. The agent receives no directional help.

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

Deploy Server