io.github.cyanheads/gnomad-genetics-mcp-server

Est-ce que io.github.cyanheads/gnomad-genetics-mcp-server est sûr ?

Au dernier audit MCP Hub, le serveur MCP « io.github.cyanheads/gnomad-genetics-mcp-server » est classé « Non encore testé ». Référencé dans l'annuaire. Seul le pentest comportemental fait foi, et il n'a pas encore été exécuté sur ce serveur. Le verdict est réévalué en continu ; consultez la fiche pour l'état à jour.

Méthode : MCP Hub analyse la description de chaque outil (couche 1) et, pour le verdict fort, exécute le serveur dans une micro-VM isolée avec leurres et réseau bloqué (couche 2). On publie des noms et des compteurs, jamais le contenu brut renvoyé par un outil.

Les 7 outils

• gnomad_dataframe_describe≈ 719 tokens

  List the tables staged on a canvas and their columns (name and type) so you can write correct SQL for gnomad_dataframe_query. Use the canvas_id returned by gnomad_list_gene_variants or gnomad_search_clinvar. Returns one entry per table with its row count and column schema.

  Paramètres, retour & exemple (1)

  Paramètres

  • canvas_id · string · requis
    Canvas ID returned by a prior staging call (gnomad_list_gene_variants or gnomad_search_clinvar).

  Exemple d'appel

  {"name": "gnomad_dataframe_describe", "arguments": {"canvas_id": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"error": {}, "tables": []}}

• gnomad_dataframe_query≈ 1168 tokens

  Run a read-only SQL SELECT against a canvas table staged by gnomad_list_gene_variants (table gene_variants) or gnomad_search_clinvar (table clinvar_variants) and return one page of the result. Use the canvas_id and table_name those tools returned to rank by allele frequency, group by consequence class, count loss-of-function variants, or filter the full set the inline preview only sampled. A page holds up to limit rows (default 100, max 500) and ends early once its rows reach 10,000 characters of JSON; continue from next_offset until it is null. Each page re-runs the SQL, so stable paging needs an ORDER BY over a unique key (such as variant_id) and an unchanged table. Paging reaches the server row cap: above it total is null and later rows are reachable only by filtering or aggregating in SQL. SELECT statements only — writes, DDL, and file/HTTP table functions are rejected by the canvas gate. Call gnomad_dataframe_describe first to discover staged table and column names.

  Paramètres, retour & exemple (4)

  Paramètres

  • sql · string · requis
    Read-only SQL SELECT. Reference tables by the names the staging tool returned (e.g. gene_variants). Add an ORDER BY over a unique key when paging.
  • limit · integer · optionnel
    Maximum rows on the page (1–500). A page also ends before its rows pass 10,000 characters of JSON.
  • offset · integer · optionnel
    Row offset of the page to return. Start at 0, then pass next_offset from the previous page.
  • canvas_id · string · requis
    Canvas ID returned by gnomad_list_gene_variants or gnomad_search_clinvar.

  Exemple d'appel

  {"name": "gnomad_dataframe_query", "arguments": {"sql": "texte", "canvas_id": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"rows": [], "error": {}, "total": 1, "offset": 1, "columns": [], "returned": 1, "truncated": true, "next_offset": 1}}

• gnomad_get_coverage≈ 2463 tokens

  Fetch gnomAD sequencing-coverage summary across a gene, transcript, or region — mean and median read depth, plus the mean fraction of samples covered at each depth threshold (1× through 100×), separated by exome and genome track. gnomAD reports coverage in buckets: 1 bp for a region spanning under 850 bp, wider for larger targets (bucket_size), and a gene or transcript is summarized over its exons ±75 bp, not its introns. Use this to disambiguate a true absent variant from an uncallable position: a variant missing from a well-covered region is informative, while one missing from a poorly-covered region is not. Supply exactly one of gene, transcript_id, or region. The optional coverage_source narrows to one track; by default both available tracks are returned. Echoes the effective dataset and build. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/

  Paramètres, retour & exemple (6)

  Paramètres

  • gene · ? · optionnel
    Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted.
  • region · ? · optionnel
    Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852): chromosome 1–22, X, or Y with an optional chr prefix (mitochondrial regions are not served) and a span (stop − start) under 2,500,000 bp. Mutually exclusive with gene and transcript_id.
  • dataset · string · optionnel · gnomad_r4 | gnomad_r3 | gnomad_r2_1 | exac
    gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.
  • transcript_id · string · optionnel
    Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted.
  • coverage_source · string · optionnel · exome | genome
    Restrict to one coverage track. Omit to return every available track.
  • reference_genome · string · optionnel · GRCh38 | GRCh37
    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.

  Exemple d'appel

  {"name": "gnomad_get_coverage", "arguments": {"gene": "texte", "region": "texte", "dataset": "gnomad_r4", "transcript_id": "texte", "coverage_source": "exome", "reference_genome": "GRCh38"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"error": {}, "notice": "texte", "target": "texte", "dataset": "texte", "summaries": [], "target_kind": "gene", "reference_genome": "texte"}}

• gnomad_get_gene_constraint≈ 1915 tokens

  Fetch gnomAD loss-of-function constraint for a gene — pLI (probability of LoF intolerance; >0.9 intolerant), LOEUF (oe_lof_upper, the headline metric) 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). constraint_release names the release the metrics come from: gnomAD v4.1.2 for gnomad_r4 and gnomad_r3 (gnomAD publishes no v3 constraint), gnomAD v2.1.1 for gnomad_r2_1, and ExAC r0.3 for exac. gnomAD recommends LOEUF < 0.45 to call a gene LoF-intolerant on v4.1.2 and LOEUF < 0.35 on v2.1.1. ExAC r0.3 publishes only pLI, the Z-scores, and observed/expected counts, so on exac the ratios and LOEUF are null, constraint_flags is empty, and pLI is the intolerance measure. Many genes have null constraint (sparse upstream) — null fields are reported as such, never fabricated. Echoes the effective dataset and reference build. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/

  Paramètres, retour & exemple (3)

  Paramètres

  • gene · string · requis
    Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene.
  • dataset · string · optionnel · gnomad_r4 | gnomad_r3 | gnomad_r2_1 | exac
    gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.
  • reference_genome · string · optionnel · GRCh38 | GRCh37
    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.

  Exemple d'appel

  {"name": "gnomad_get_gene_constraint", "arguments": {"gene": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"pli": "texte", "error": {}, "lof_z": 1, "mis_z": 1, "syn_z": 1, "oe_lof": "texte", "oe_mis": "texte", "oe_syn": "texte", "symbol": "texte", "dataset": "texte", "exp_lof": "texte", "exp_mis": "texte"}}

• gnomad_get_variant≈ 2871 tokens

  Fetch the full gnomAD population record for one or more variants — allele count/number/frequency overall and broken down per genetic-ancestry group, homozygote and hemizygote counts, quality flags, transcript consequence, in-silico predictor scores, and joined ClinVar clinical significance. The "how common, is it benign" answer in one call. Accepts a batch of up to 25 IDs (chrom-pos-ref-alt or rsID) with per-item partial success: a malformed or absent ID lands in failed[] — with its reason and a recovery hint — without failing the others. An empty found[] for a well-formed ID means the variant is not in the chosen dataset — pair with gnomad_get_coverage to confirm the position is callable before concluding true absence. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/

  Paramètres, retour & exemple (3)

  Paramètres

  • dataset · string · optionnel · gnomad_r4 | gnomad_r3 | gnomad_r2_1 | exac
    gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.
  • variants · array · requis
    1–25 variant IDs (chrom-pos-ref-alt or rsID) to look up in one batched call.
  • reference_genome · string · optionnel · GRCh38 | GRCh37
    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.

  Exemple d'appel

  {"name": "gnomad_get_variant", "arguments": {"variants": []}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"error": {}, "found": [], "failed": [], "notice": "texte", "dataset": "texte", "reference_genome": "texte"}}

• gnomad_list_gene_variants≈ 2193 tokens

  List every gnomAD variant in a gene, transcript, or region with allele frequencies and predicted consequences, optionally filtered to one consequence class (lof, missense, synonymous, other) and/or a maximum allele frequency. A result too large to inline is staged on a DataCanvas table named gene_variants, returned as canvas_id and table_name beside an inline preview — call gnomad_dataframe_describe for its columns, then gnomad_dataframe_query to rank by AF, count by consequence, or group across every row rather than the preview. A result that fits inline stages no table unless canvas_id is supplied. When the canvas is disabled (CANVAS_PROVIDER_TYPE != duckdb) the tool returns a capped inline preview and the SQL path is unavailable. Supply exactly one of gene, transcript_id, or region. Echoes the effective dataset and build. Data source: gnomAD (Broad Institute) — https://gnomad.broadinstitute.org/

  Paramètres, retour & exemple (8)

  Paramètres

  • gene · ? · optionnel
    Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted.
  • max_af · number · optionnel
    Keep only variants with allele frequency ≤ this value (0–1). Variants with null AF are always kept.
  • region · ? · optionnel
    Genomic region chrom-start-stop (1-based inclusive, e.g. 13-32315474-32400266): chromosome 1–22, X, or Y with an optional chr prefix (mitochondrial regions are not served), a span (stop − start) under 2,500,000 bp, and at most ~30,000 variants. Mutually exclusive with gene and transcript_id.
  • dataset · string · optionnel · gnomad_r4 | gnomad_r3 | gnomad_r2_1 | exac
    gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output.
  • canvas_id · string · optionnel
    Optional canvas ID from a prior call, to reuse the same canvas. When supplied, this call always writes its result to the gene_variants table on that canvas, replacing (not appending to) the previous one — even when the result fits inline; a result with no variants removes the table. Omit to stage on a fresh canvas only when the result is too large to inline.
  • transcript_id · string · optionnel
    Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted.
  • reference_genome · string · optionnel · GRCh38 | GRCh37
    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.
  • consequence_class · string · optionnel · lof | missense | synonymous | other
    Keep only variants in this consequence class. Omit to return all classes.

  Exemple d'appel

  {"name": "gnomad_list_gene_variants", "arguments": {"gene": "texte", "max_af": 1, "region": "texte", "dataset": "gnomad_r4", "canvas_id": "texte", "transcript_id": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"error": {}, "total": 1, "notice": "texte", "dataset": "texte", "preview": [], "spilled": true, "canvas_id": "texte", "table_name": "texte", "reference_genome": "texte"}}

• gnomad_search_clinvar≈ 2337 tokens

  Search ClinVar (NCBI E-utilities) for a gene and return its classified variants — clinical significance, review status with a 0–4 star rating, associated conditions, molecular consequences, submission counts, and gnomAD-compatible identifiers (canonical SPDI, rsIDs, GRCh38 variant ID for gnomad_get_variant) — turning the variant-level significance gnomAD joins into a gene-panel curation view. Optionally filter by clinical_significance (e.g. pathogenic) and a minimum star rating. Each call returns one window of up to 500 ClinVar records: total_found is the ClinVar candidate count for the search terms, taken before the significance and star filters narrow each window, and next_offset continues through the rest via offset. A window too large to inline is staged on a DataCanvas table named clinvar_variants, returned as canvas_id and table_name beside an inline preview — call gnomad_dataframe_describe for its columns, then gnomad_dataframe_query to rank or count across the window. A window that fits inline stages no table unless canvas_id is supplied. Keyless, but honors NCBI_API_KEY for a higher rate limit. When the canvas is disabled the tool returns a capped inline preview. Credit: ClinVar, NCBI.

  Paramètres, retour & exemple (6)

  Paramètres

  • gene · string · requis
    Gene HGNC symbol (e.g. PCSK9). ClinVar indexes HGNC symbols only — Ensembl gene IDs (ENSG…) are not resolved here, unlike the other gnomAD tools; resolve one to its symbol via ensembl_lookup_gene.
  • limit · integer · optionnel
    ClinVar records to fetch in this window (1–500). Counted before the clinical_significance and min_review_stars filters, so a window can return fewer rows.
  • offset · integer · optionnel
    Zero-based position of the first ClinVar record in this window. Pass next_offset from the previous call to continue.
  • canvas_id · string · optionnel
    Optional canvas ID from a prior call, to reuse the same canvas. When supplied, each search writes its window to the clinvar_variants table on that canvas, replacing (not appending to) the previous one — even when the window fits inline; a window with no rows removes the table. An Ensembl gene ID searches nothing and leaves the canvas as it was. Omit to stage on a fresh canvas only when the window is too large to inline.
  • min_review_stars · integer · optionnel
    Keep only variants with at least this gold-star review rating (0–4).
  • clinical_significance · string · optionnel
    Filter by ClinVar clinical significance term (e.g. pathogenic, likely_pathogenic, uncertain significance), matched as whole words; underscores read as spaces. Blank means no filter.

  Exemple d'appel

  {"name": "gnomad_search_clinvar", "arguments": {"gene": "texte"}}

  Exemple de retour

  {"content": [{"type": "text", "text": "…"}], "structuredContent": {"error": {}, "total": 1, "notice": "texte", "preview": [], "spilled": true, "canvas_id": "texte", "truncated": true, "table_name": "texte", "next_offset": 1, "total_found": 1, "unavailable_ids": []}}

C'est votre serveur ?

Revendiquez-le sur l'espace créateur (preuve GitHub, domaine ou npm) pour afficher le badge « propriétaire vérifié » et lancer un pentest comportemental à la demande afin d'obtenir le badge « Vérifié ».

Créer un compte / revendiquer →

Source

https://gnomad-genetics.caseyjhand.com/mcp