Query per-residue missense tolerance for a given transcript position to evaluate variant pathogenicity.
Signature: get_position_tolerance(transcript_id, position, response_mode=).
| Name | Required | Description | Default |
|---|---|---|---|
| position | Yes | Pos. | |
| response_mode | No | Mode. | |
| transcript_id | Yes | ENST. |
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Changes observed during successful MCP inspections.
v0.3.7Input schema / properties / position / descriptionPrevious value: -"1-based protein residue position."New value: +"Pos."Input schema / properties / position / examplesPrevious value: -[
- 273
-]New value: +[
+ 175
+]Input schema / properties / position / maximumAdded value: +1000000Input schema / properties / response_mode / defaultRemoved value: -"compact"Input schema / properties / response_mode / descriptionPrevious value: -"Verbosity: minimal|compact|standard|full (default compact)."New value: +"Mode."Input schema / properties / response_mode / typeRemoved value: -"string"Input schema / properties / transcript_id / descriptionPrevious 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."Input schema / properties / transcript_id / examplesPrevious value: -[
- "ENST00000269305.4"
-]New value: +[
+ "ENST00000269305.9"
+]Output 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|positions?)$"
+ },
+ "type": "object"
+ },
+ "tool": {
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "^unsafe_for_clinical_use$": {
+ "const": true
+ }
+ },
+ "required": [
+ "tool",
+ "request_id",
+ "data_versions",
+ "unsafe_for_clinical_use"
+ ],
+ "type": "object"
+ }
+ },
+ "oneOf": [
+ {
+ "additionalProperties": false,
+ "patternProperties": {
+ "^(dropped_summary|transcript_id|cdna_pos|chr|chr_positions|exon_numbers|ref_aa|ref_aa_triplet|ref_codon|strand|recommended_citation)$": {
+ "type": "string"
+ },
+ "^(protein_pos|sw_size)$": {
+ "type": "integer"
+ },
+ "^_meta$": {
+ "$ref": "#/$defs/M"
+ },
+ "^domains$": {
+ "additionalProperties": {
+ "additionalProperties": false,
+ "minProperties": 1,
+ "properties": {
+ "meta_domain_homolog_aggregate_available": {
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "type": "object"
+ },
+ "^success$": {
+ "const": true
+ },
+ "^sw_coverage$": {
+ "type": "number"
+ },
+ "^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$": {
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "gnomad": {
+ "additionalProperties": false,
+ "minProperties": 2,
+ "properties": {
+ "available": {
+ "const": false
+ },
+ "reason": {
+ "type": "string"
+ }
+ },
+ "type": "object"
+ }
+ },
+ "type": "object"
+ }
+ },
+ "type": "object"
+ }
+ },
+ "required": [
+ "success",
+ "_meta",
+ "transcript_id",
+ "protein_pos",
+ "variant_evidence",
+ "recommended_citation"
+ ]
+ },
+ {
+ "additionalProperties": false,
+ "patternProperties": {
+ "^(message|recovery_action|field|hint)$": {
+ "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"
+}v0.3.1Input schema / properties / position / examplesAdded value: +[
+ 273
+]Output schema / (root)Previous value: -{
- "additionalProperties": true,
- "properties": {
- "_meta": {
- "additionalProperties": true,
- "type": "object"
- },
- "candidates": {
- "type": "array"
- },
- "data_versions": {
- "additionalProperties": true,
- "type": "object"
- },
- "domain_ids": {
- "type": "array"
- },
- "error_code": {
- "type": "string"
- },
- "field": {
- "type": "string"
- },
- "hint": {
- "type": "string"
- },
- "message": {
- "type": "string"
- },
- "protein_pos": {
- "type": "integer"
- },
- "recommended_citation": {
- "type": "string"
- },
- "recovery_action": {
- "type": "string"
- },
- "ref_aa": {
- "type": [
- "string",
- "null"
- ]
- },
- "retryable": {
- "type": "boolean"
- },
- "success": {
- "type": "boolean"
- },
- "sw_coverage": {
- "type": [
- "number",
- "null"
- ]
- },
- "sw_dn_ds": {
- "type": [
- "number",
- "null"
- ]
- },
- "sw_size": {
- "type": "integer"
- },
- "transcript_id": {
- "type": "string"
- },
- "variant_count_total": {
- "type": "integer"
- }
- },
- "required": [
- "success"
- ],
- "type": "object"
-}New value: +nullv0.1.0Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The readOnlyHint annotation already declares this a safe read operation, but the description adds zero behavioral context beyond that—no mention of response format, output granularity, or semantics. The signature line contributes nothing that the annotation doesn't already convey.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is extremely short, but this is under-specification rather than genuine conciseness. It front-loads a signature that an agent can already derive from the schema, wasting the only sentence on redundant information instead of meaningful guidance.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Even with an output schema present, this is a specialized genomics/transcript tool whose core concept (position tolerance) is never defined. With 3 parameters, an enum, and multiple closely related siblings, the description is far too thin to enable correct invocation.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
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 nearly empty ('Pos.', 'Mode.', 'ENST.'), and the description itself adds nothing beyond the parameter names. The 'response_mode' enum is defined in the schema, but the description gives no context on what each mode returns. The description fails to compensate for the low-quality schema text.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description is a bare function signature that restates the tool name ('get_position_tolerance(transcript_id, position, response_mode=)') without saying what a position tolerance is, what unit it returns, or how it relates to the sibling landscape/domain tools. It is nearly 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.
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 siblings like get_tolerance_landscape, request_tolerance_landscape, compare_positions, or get_protein_domains. An agent has no way to choose between these overlapping tolerance-related tools.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.