gnomad-genetics-mcp-server

endpoint

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

protocol

http-sse ·2025-06-18

authentication

none observed

public key

none — nobody has proven they own this listing · is it yours? claim it

karma

0 · newcomer

Is gnomad-genetics-mcp-server live?

Yes — it answered the hub's last check (checked 55m ago). It answered 100% of checks over the last 30 days.

Is gnomad-genetics-mcp-server free to use?

Yes — the hub reached it with no key and no payment.

What tools does gnomad-genetics-mcp-server have?

7 tools: gnomad_dataframe_describe, gnomad_list_gene_variants, gnomad_search_clinvar, gnomad_get_variant, gnomad_get_gene_constraint, gnomad_get_coverage, gnomad_dataframe_query.

Is gnomad-genetics-mcp-server safe to connect?

The hub found no text in its card or tool descriptions aimed at the agent reading them. It measures what the server answers, not its code — grant it only the access its tools need.

Price is per tool, not per server. An agent whose handshake is open can hold tools that demand a key or a payment, and one figure for the whole agent sends callers into a wall.

• gnomad_dataframe_describe reads unknown 4h ago

  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.

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "required": [
      "canvas_id"
    ],
    "properties": {
      "canvas_id": {
        "type": "string",
        "pattern": "^[A-Za-z0-9_-]{10}$",
        "description": "Canvas ID returned by a prior staging call (gnomad_list_gene_variants or gnomad_search_clinvar)."
      }
    },
    "additionalProperties": false
  }

  arguments 15 lines copy
• gnomad_list_gene_variants reads unknown 20h ago

  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/

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "properties": {
      "gene": {
        "anyOf": [
          {
            "type": "string",
            "minLength": 2,
            "description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene."
          },
          {
            "type": "string",
            "maxLength": 0,
            "description": "Blank — the gene is treated as omitted."
          }
        ],
        "description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted."
      },
      "max_af": {
        "type": "number",
        "maximum": 1,
        "minimum": 0,
        "description": "Keep only variants with allele frequency ≤ this value (0–1). Variants with null AF are always kept."
      },
      "region": {
        "anyOf": [
          {
            "type": "string",
            "const": ""
          },
          {
            "type": "string",
            "pattern": "^(?:chr)?[0-9A-Z]+-\\d+-\\d+$",
            "description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 13-32315474-32400266) on chromosome 1–22, X, or Y, optional chr prefix."
          }
        ],
        "description": "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": {
        "enum": [
          "gnomad_r4",
          "gnomad_r3",
          "gnomad_r2_1",
          "exac"
        ],
        "type": "string",
        "description": "gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output."
      },
      "canvas_id": {
        "type": "string",
        "pattern": "^[A-Za-z0-9_-]{10}$",
        "description": "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": {
        "type": "string",
        "description": "Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted."
      },
      "reference_genome": {
        "enum": [
          "GRCh38",
          "GRCh37"
        ],
        "type": "string",
        "description": "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": {
        "enum": [
          "lof",
          "missense",
          "synonymous",
          "other"
        ],
        "type": "string",
        "description": "Keep only variants in this consequence class. Omit to return all classes."
      }
    },
    "additionalProperties": false
  }

  arguments 79 lines copy
• gnomad_search_clinvar reads unknown 11h ago

  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.

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "required": [
      "gene"
    ],
    "properties": {
      "gene": {
        "type": "string",
        "minLength": 2,
        "description": "Gene HGNC symbol (e.g. PCSK9). ClinVar indexes HGNC symbols only — Ensembl gene IDs (ENSG…) are not resolved here, unlike the other gnomAD tools; resolve one to its symbol via ensembl_lookup_gene."
      },
      "limit": {
        "type": "integer",
        "default": 500,
        "maximum": 500,
        "minimum": 1,
        "description": "ClinVar records to fetch in this window (1–500). Counted before the clinical_significance and min_review_stars filters, so a window can return fewer rows."
      },
      "offset": {
        "type": "integer",
        "default": 0,
        "maximum": 2147483647,
        "minimum": 0,
        "description": "Zero-based position of the first ClinVar record in this window. Pass next_offset from the previous call to continue."
      },
      "canvas_id": {
        "type": "string",
        "pattern": "^[A-Za-z0-9_-]{10}$",
        "description": "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": {
        "type": "integer",
        "maximum": 4,
        "minimum": 0,
        "description": "Keep only variants with at least this gold-star review rating (0–4)."
      },
      "clinical_significance": {
        "type": "string",
        "description": "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."
      }
    },
    "additionalProperties": false
  }

  arguments 44 lines copy
• gnomad_get_variant reads unknown 11h ago

  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/

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "required": [
      "variants"
    ],
    "properties": {
      "dataset": {
        "enum": [
          "gnomad_r4",
          "gnomad_r3",
          "gnomad_r2_1",
          "exac"
        ],
        "type": "string",
        "description": "gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output."
      },
      "variants": {
        "type": "array",
        "items": {
          "type": "string",
          "minLength": 1,
          "description": "Variant ID — chrom-pos-ref-alt (1-based, e.g. 1-55051215-G-GA) on chromosome 1–22, X, or Y with an optional chr prefix, or an rsID (rs11591147). Mitochondrial IDs (M, MT, chrM) are not served. Obtain a variantId from ensembl_predict_variant or a VCF. Malformed IDs are reported per-item in failed[], not rejected wholesale."
        },
        "maxItems": 25,
        "minItems": 1,
        "description": "1–25 variant IDs (chrom-pos-ref-alt or rsID) to look up in one batched call."
      },
      "reference_genome": {
        "enum": [
          "GRCh38",
          "GRCh37"
        ],
        "type": "string",
        "description": "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."
      }
    },
    "additionalProperties": false
  }

  arguments 39 lines copy
• gnomad_get_gene_constraint reads unknown 11h ago

  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/

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "required": [
      "gene"
    ],
    "properties": {
      "gene": {
        "type": "string",
        "minLength": 2,
        "description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene."
      },
      "dataset": {
        "enum": [
          "gnomad_r4",
          "gnomad_r3",
          "gnomad_r2_1",
          "exac"
        ],
        "type": "string",
        "description": "gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output."
      },
      "reference_genome": {
        "enum": [
          "GRCh38",
          "GRCh37"
        ],
        "type": "string",
        "description": "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."
      }
    },
    "additionalProperties": false
  }

  arguments 33 lines copy
• gnomad_get_coverage reads unknown 20h ago

  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. 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/

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "properties": {
      "gene": {
        "anyOf": [
          {
            "type": "string",
            "minLength": 2,
            "description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene."
          },
          {
            "type": "string",
            "maxLength": 0,
            "description": "Blank — the gene is treated as omitted."
          }
        ],
        "description": "Gene — HGNC symbol (e.g. PCSK9) or Ensembl gene ID (e.g. ENSG00000169174). Obtain a stable ID from ensembl_lookup_gene. Mitochondrial genes (e.g. MT-TL1) are not served. Mutually exclusive with transcript_id and region; blank means omitted."
      },
      "region": {
        "anyOf": [
          {
            "type": "string",
            "const": ""
          },
          {
            "type": "string",
            "pattern": "^(?:chr)?[0-9A-Z]+-\\d+-\\d+$",
            "description": "Genomic region chrom-start-stop (1-based inclusive, e.g. 1-55039447-55064852) on chromosome 1–22, X, or Y, optional chr prefix."
          }
        ],
        "description": "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": {
        "enum": [
          "gnomad_r4",
          "gnomad_r3",
          "gnomad_r2_1",
          "exac"
        ],
        "type": "string",
        "description": "gnomAD dataset: gnomad_r4 (GRCh38, default), gnomad_r3 (GRCh38), gnomad_r2_1 (GRCh37), exac (GRCh37). Echoed in output."
      },
      "transcript_id": {
        "type": "string",
        "description": "Ensembl transcript ID (e.g. ENST00000302118). Mutually exclusive with gene and region; blank means omitted."
      },
      "coverage_source": {
        "enum": [
          "exome",
          "genome"
        ],
        "type": "string",
        "description": "Restrict to one coverage track. Omit to return every available track."
      },
      "reference_genome": {
        "enum": [
          "GRCh38",
          "GRCh37"
        ],
        "type": "string",
        "description": "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."
      }
    },
    "additionalProperties": false
  }

  arguments 66 lines copy
• gnomad_dataframe_query reads unknown 20h ago

  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.

  mcp-tool

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  {
    "type": "object",
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "required": [
      "canvas_id",
      "sql"
    ],
    "properties": {
      "sql": {
        "type": "string",
        "minLength": 1,
        "description": "Read-only SQL SELECT. Reference tables by the names the staging tool returned (e.g. gene_variants). Add an ORDER BY over a unique key when paging."
      },
      "limit": {
        "type": "integer",
        "default": 100,
        "maximum": 500,
        "minimum": 1,
        "description": "Maximum rows on the page (1–500). A page also ends before its rows pass 10,000 characters of JSON."
      },
      "offset": {
        "type": "integer",
        "default": 0,
        "maximum": 9007199254740991,
        "minimum": 0,
        "description": "Row offset of the page to return. Start at 0, then pass next_offset from the previous page."
      },
      "canvas_id": {
        "type": "string",
        "pattern": "^[A-Za-z0-9_-]{10}$",
        "description": "Canvas ID returned by gnomad_list_gene_variants or gnomad_search_clinvar."
      }
    },
    "additionalProperties": false
  }

  arguments 35 lines copy

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