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gnomad-genetics-mcp-server

gnomad-genetics-mcp-server: get gene constraint

gnomad_get_gene_constraint
Read-onlyIdempotent

Fetch gnomAD loss-of-function constraint for a gene — pLI (probability of LoF intolerance; >0.9 intolerant), LOEUF (oe_lof_upper, the headline metric; <0.6 intolerant in v4, <0.35 in v2) plus its lower bound, observed/expected ratios for LoF, missense, and synonymous variation, and the three Z-scores. This is the orthogonal axis to allele frequency: a loss-of-function variant matters far more in a gene intolerant to being broken. Accepts an HGNC symbol (PCSK9) or an Ensembl gene ID (ENSG00000169174). Many genes have null constraint (sparse upstream) — null fields are reported as such, never fabricated. v4 constraint is flagged beta by the gnomAD team; constraint_flags surfaces any caveats. Echoes the effective dataset and reference build. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
geneYesGene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.
datasetNognomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.
reference_genomeNoReference build. Derived from dataset when omitted (v4/v3=GRCh38, v2.1/ExAC=GRCh37). If supplied it must match the dataset, or the call is rejected. Keep aligned with ensembl coordinates.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
pliNopLI — probability of LoF intolerance; >0.9 intolerant. Null when unavailable.
errorNoPresent when the call failed. Absent on success.
lof_zNoLoF constraint Z-score. Null when unavailable.
mis_zNoMissense constraint Z-score. Null when unavailable.
syn_zNoSynonymous constraint Z-score. Null when unavailable.
oe_lofNoNon-negative observed/expected LoF ratio. Null when unavailable.
oe_misNoObserved/expected missense ratio. Null when unavailable.
oe_synNoObserved/expected synonymous ratio. Null when unavailable.
symbolNoHGNC gene symbol.
datasetNoEffective gnomAD dataset.
exp_lofNoNon-negative expected LoF variant count. Null when unavailable.
exp_misNoNon-negative expected missense count. Null when unavailable.
exp_synNoNon-negative expected synonymous count. Null when unavailable.
gene_idNoEnsembl gene ID resolved for the gene.
obs_lofNoNon-negative observed LoF variant count. Null when unavailable.
obs_misNoNon-negative observed missense count. Null when unavailable.
obs_synNoNon-negative observed synonymous count. Null when unavailable.
oe_lof_lowerNoLOEUF confidence-interval lower bound. Null when unavailable.
oe_lof_upperNoLOEUF (oe_lof_upper) — the headline intolerance metric. Null when unavailable.
constraint_flagsNoConstraint caveat flags (e.g. beta/experimental notes for v4).
reference_genomeNoEffective reference build.

TDQS

A4.4/5.0
Behavior5/5

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

Annotations already provide readOnlyHint, openWorldHint, and idempotentHint, so the bar is lower. The description adds substantial behavioral context: it discloses that null constraint fields are reported as such and never fabricated, that v4 constraint is flagged beta, that constraint_flags surfaces caveats, and that the effective dataset and reference build are echoed. These details address output edge cases and data-source caveats beyond what annotations convey, without contradicting them.

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

Conciseness4/5

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

The description is information-dense and front-loaded with the core purpose, then systematically elaborates on metrics, version differences, null behavior, and data source. Every sentence serves a purpose, with no filler. It is somewhat long but justified by the tool's complexity. A 4 reflects strong structure with minor verbosity, not a flaw.

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

Completeness5/5

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

The output schema exists, so return-value explanation is not required. The description covers the core metrics, version-specific thresholds (pLI >0.9, LOEUF <0.6 v4 / <0.35 v2), null-field handling, beta status, covariance with reference genome, and the data source attribution. There are no obvious gaps that would prevent an agent from correctly invoking and interpreting the tool.

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. The description reiterates the accepted gene identifier types (HGNC symbol or Ensembl ID) and mentions echoing dataset/reference build, but it does not add new meaning beyond the schema for parameters. The threshold values (LOEUF <0.6 in v4) are interpretation aids, not parameter semantics. Credit is given for reinforcing schema details, but no substantive additions.

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

Purpose5/5

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

The description opens with a specific verb and resource: 'Fetch gnomAD loss-of-function constraint for a gene' and enumerates the exact metrics returned (pLI, LOEUF, observed/expected ratios, Z-scores). It explicitly differentiates itself from the allele-frequency axis, making clear it is the orthogonal tool for gene tolerance. This distinguishes it from sibling tools like gnomad_get_variant and gnomad_list_gene_variants without ambiguity.

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

Usage Guidelines4/5

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

The description provides strong contextual guidance on when this tool is relevant ('a loss-of-function variant matters far more in a gene intolerant to being broken') and notes the beta flag for v4 constraint. However, it does not explicitly name alternative tools or state when NOT to use this tool. The schema also covers required input types. This is clear context but lacks explicit exclusions or sibling routing, so a 4 is appropriate.

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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TDQS

A4.2/5.0
Disambiguation5/5

Every tool has a clearly distinct role: specific variant lookup, gene constraint, coverage, ClinVar search, and canvas SQL describe/query. The closest pair, gnomad_get_variant and gnomad_list_gene_variants, is separated by input type and the depth of data returned.

Naming Consistency4/5

Most tools follow a gnomad_<verb>_<object> pattern like get_coverage, get_variant, list_gene_variants, and search_clinvar. The two canvas helpers break this with gnomad_dataframe_describe and gnomad_dataframe_query, but they form a readable and internally consistent sub-pattern.

Tool Count5/5

Seven tools is well-scoped for a gnomAD/ClinVar genetics server. Each tool addresses a distinct query need, and the two dataframe utilities add real analytic value without bloating the API.

Completeness5/5

The surface covers the core read-only workflows: variant lookup, gene variant listing with filters, constraint, coverage, and ClinVar curation. The dataframe query path prevents dead ends when working with large staged result sets.