Gnomad Constraint Tools

Configuration File: gnomad_constraint_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the gnomad_constraint_tools.json configuration file.

Available Tools

gnomad_get_constraint (Type: GnomADConstraintTool)

Get gene-level constraint metrics from gnomAD (Genome Aggregation Database) for a single gene, gi…

gnomad_get_constraint tool specification

Tool Information:

  • Name: gnomad_get_constraint

  • Type: GnomADConstraintTool

  • Description: Get gene-level constraint metrics from gnomAD (Genome Aggregation Database) for a single gene, given a gene symbol (e.g. BRCA1) OR an Ensembl gene ID (e.g. ENSG00000012048). Returns a flat, curated summary: pLI (probability of loss-of-function intolerance), oe_lof (observed/expected LoF ratio) with its lower/upper confidence bounds, LOEUF (= oe_lof_upper, the recommended constraint metric; lower = more constrained), missense Z-score (mis_z), synonymous Z-score (syn_z), and expected/observed LoF counts (exp_lof, obs_lof). The dataset parameter selects the constraint release: gnomad_r4 (default) and gnomad_r3 use GRCh38 (gnomAD v4 constraint); gnomad_r2_1 and exac use GRCh37. Note: gnomAD uses current HGNC symbols (e.g. GBA1, not GBA). No API key required.

Parameters:

  • gene_symbol (string) (optional) HGNC gene symbol, e.g. ‘BRCA1’, ‘TP53’, ‘GBA1’. Provide this OR gene_id.

  • gene_id (string) (optional) Ensembl gene ID, e.g. ‘ENSG00000012048’ (BRCA1). Provide this OR gene_symbol.

  • dataset (string) (optional) gnomAD dataset release selecting the constraint table. ‘gnomad_r4’ (default) and ‘gnomad_r3’ -> GRCh38 / gnomAD v4 constraint; ‘gnomad_r2_1’ and ‘exac’ -> GRCh37 / gnomAD v2.1.1 era constraint.

Example Usage:

query = {
    "name": "gnomad_get_constraint",
    "arguments": {
    }
}
result = tu.run(query)