gnomad-genetics-mcp-server: get gene constraint
gnomad_get_gene_constraintFetch 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
| Name | Required | Description | Default |
|---|---|---|---|
| gene | Yes | Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. | |
| dataset | No | gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output. | |
| reference_genome | No | Reference 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
| Name | Required | Description | Default |
|---|---|---|---|
| pli | No | pLI — probability of LoF intolerance; >0.9 intolerant. Null when unavailable. | |
| error | No | Present when the call failed. Absent on success. | |
| lof_z | No | LoF constraint Z-score. Null when unavailable. | |
| mis_z | No | Missense constraint Z-score. Null when unavailable. | |
| syn_z | No | Synonymous constraint Z-score. Null when unavailable. | |
| oe_lof | No | Non-negative observed/expected LoF ratio. Null when unavailable. | |
| oe_mis | No | Observed/expected missense ratio. Null when unavailable. | |
| oe_syn | No | Observed/expected synonymous ratio. Null when unavailable. | |
| symbol | No | HGNC gene symbol. | |
| dataset | No | Effective gnomAD dataset. | |
| exp_lof | No | Non-negative expected LoF variant count. Null when unavailable. | |
| exp_mis | No | Non-negative expected missense count. Null when unavailable. | |
| exp_syn | No | Non-negative expected synonymous count. Null when unavailable. | |
| gene_id | No | Ensembl gene ID resolved for the gene. | |
| obs_lof | No | Non-negative observed LoF variant count. Null when unavailable. | |
| obs_mis | No | Non-negative observed missense count. Null when unavailable. | |
| obs_syn | No | Non-negative observed synonymous count. Null when unavailable. | |
| oe_lof_lower | No | LOEUF confidence-interval lower bound. Null when unavailable. | |
| oe_lof_upper | No | LOEUF (oe_lof_upper) — the headline intolerance metric. Null when unavailable. | |
| constraint_flags | No | Constraint caveat flags (e.g. beta/experimental notes for v4). | |
| reference_genome | No | Effective reference build. |