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/shaip/gene2transcripts-v2

Purpose

Resolve gene identifiers into the set of transcripts available for downstream variant processing.

This endpoint is typically used to:

  • Identify valid transcripts for a gene prior to validation or formatting
  • Restrict variant analysis to clinically relevant transcript sets
  • Support workflows requiring controlled transcript selection
  • Build bedfiles for panels of genes
  • See our mapping data e.g. exon boundaries and CIGAR strings

Method

POST

Path

/shaip/gene2transcripts-v2

Input

Parameter Type Required
gene_query string or array Yes
genome_build string Yes
transcript_set string Yes
limit_transcripts string or array Yes (see transcript_selection.md)
show_exon_info boolean No

Parameter Notes

  • gene_query accepts:
  • HGNC symbols (e.g. COL1A1)
  • HGNC IDs (e.g. HGNC:2197)

  • Transcript IDs (RefSeq or Ensembl)

  • limit_transcripts controls which transcripts are returned
    (see ../transcript_selection.md)

  • show_exon_info:

  • true (default): includes exon structure and alignment data
  • false: returns transcript identifiers only (recommended for performance)

Example Request

[{
    "gene_query": "COL1A1",
    "genome_build": "GRCh38",
    "transcript_set": "refseq",
    "limit_transcripts": "mane_select",
    "show_exon_info": false
  }]

Example Response

[
  {
    "current_symbol": "COL1A1",
    "previous_symbol": "",
    "current_name": "collagen type I alpha 1 chain",
    "lovd_corrections": null,
    "lovd_messages": null,
    "hgnc": "HGNC:2197",
    "transcripts": [
      {
        "reference": "NM_000088.4",
        "description": "Homo sapiens collagen type I alpha 1 chain (COL1A1), mRNA",
        "annotations": {
          "db_xref": {
            "CCDS": "CCDS11561.1",
            "select": "MANE",
            "ncbigene": "1277",
            "ensemblgene": null,
            "hgnc": "HGNC:2197"
          },
          "chromosome": "17",
          "map": "17q21.33",
          "note": "collagen type I alpha 1 chain",
          "variant": "0",
          "refseq_select": true,
          "mane_select": true,
          "ensembl_select": false,
          "mane_plus_clinical": false
        },
        "translation": "NP_000079.2",
        "length": 5914,
        "coding_start": 119,
        "coding_end": 4513,
        "genomic_spans": {}
      }
    ],
    "requested_symbol": "COL1A1"
  }
]

Behaviour

  • Resolves the input gene or transcript identifier
  • Determines associated transcripts from the selected dataset
  • Applies transcript filtering using limit_transcripts
  • Returns transcript identifiers and, optionally, exon structures

Multiple inputs are supported via: - JSON arrays
- Pipe-delimited strings

When to Use

Use this endpoint when:

  • Preparing variant inputs for /VariantFormatter_v2 or /VariantValidator
  • Restricting analysis to MANE or canonical transcripts
  • Inspecting transcript availability for a given gene

Notes

  • Using mane_select or mane provides clinically curated transcript sets
  • Using all or raw can generate large outputs and impact performance
  • Setting "show_exon_info": false significantly reduces response size
  • Results are dependent on the selected transcript dataset (refseq vs ensembl)