Transcript NR_19979.1 not present in VV

[corbin-chris]

Describe the bug
Gene 'RNU2-2' (HGNC:10152) has a transcript NR_199791, which is of clinical relevance. However, the gene has no transcripts associated with it in VariantValidator:

The 'genes to transcripts' tool also returns no transcripts for RNU2-2 (or the previous symbol RNU2-2P):

I thought this was unusual behaviour, should the transcript be present?
Thank you in advance for any help you can provide - apologies if I've misunderstood and this is just a quirk of snRNAs.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'VariantValidator' validator tool
2. Enter any variant with the transcript NR_199791.1
3. Validator throws error because the transcript isn't in the database

Expected behavior
The variant should be visible in the database and variant validation should be attempted against it.

Screenshots
Please see above.

Desktop (please complete the following information):

• OS: Windows 11
• Browser: Chrome

Additional context
NA

[Peter-J-Freeman]

Hi @corbin-chris. Its possible that we may not have the transcript in our database currently but we are overdue a database update. We are working on this. Im a bit swamped with teaching at the moment, but if you run the genes2transcripts tool on the gui website and check to see if it comes up. That's the first clue. If it's not returned it's not in the database most likely.

Ill take a better look on Monday

[corbin-chris]

Hi @Peter-J-Freeman. No transcripts showed up for RNU2-2 in 'genes to transcripts' unfortunately, so as you say, maybe it's just not present at the moment.
Thanks for checking in!

[Peter-J-Freeman]

Ah. That explains it. I looked at the revision history for the transcript. It was created after our last database update. It will arrive soon as we can update.

[leicray]

Accession NR_199791 was first seen at NCBI on May 30, 2025 08:00 PM

[Peter-J-Freeman]

Yep. That's what I saw. That's after the last release or during the compiling of the database so was likely missed. Should be added soon

[vidboda]

Hi all,
I was about to post the same issue - no transcirpt for RNU2-2:

[
  {
    "current_name": "RNA, U2 small nuclear 2",
    "current_symbol": "RNU2-2",
    "hgnc": "HGNC:10152",
    "lovd_corrections": null,
    "lovd_messages": null,
    "previous_symbol": "RNU2B,RNU2-2P",
    "requested_symbol": "RNU2-2",
    "transcripts": []
  }
]

[Peter-J-Freeman]

Yep @vidboda, thanks and same issue https://www.ncbi.nlm.nih.gov/nuccore/NR_199791.1 was created May 2025.

Will be addedd soon

[vidboda]

Yep @vidboda, thanks and same issue https://www.ncbi.nlm.nih.gov/nuccore/NR_199791.1 was created May 2025.

Will be addedd soon

great plz let us know when it's done so that I can update the docker