Q (sonnet): <conversation_so_far>
<user>
I'm importing a study into my own cBioPortal instance and the validator says some genes are not known to cBioPortal. What does that mean?
</user>

<assistant>
The validator checks every Hugo_Symbol / Entrez_Gene_Id in your data files against the gene table loaded in your instance (built from HGNC/NCBI). "Gene not known" means the symbol or ID isn't in that table — usually an outdated symbol, an alias, or a typo.
</assistant>
</conversation_so_far>

Continue this conversation: reply to the user's new message.

<user>
what if the genes, like AC002511.1 or LOC100506271, just aren't in HGNC or NCBI at all?
</user>

═ answer (success)
That's a real gap, not a validator error — a small fraction of symbols in genomic data files (LOC placeholders, some readthrough/antisense transcripts like AC002511.1, and other provisional loci) genuinely aren't in the standard gene reference tables cBioPortal ships with, because they were never assigned a stable HGNC symbol or are Ensembl/RefSeq-only identifiers.

A few things worth knowing:

- **This is a known, common situation.** Genome annotations (Ensembl/RefSeq/GENCODE) contain tens of thousands of predicted or provisional loci that HGNC hasn't curated with an official symbol. LOC IDs are NCBI/Entrez placeholder names for exactly these cases.
- **cBioPortal's validator is strict by design** — it flags anything not in the local `gene` table rather than guessing, since silently dropping or mismapping genes would corrupt downstream analyses.
- **Your options for your own instance:**
  1. **Drop these genes from the file** if they're not central to your analysis — most are low-evidence/uncharacterized loci and won't affect typical mutation/CNA summaries.
  2. **Add them to your instance's gene table yourself.** Since you control your own cBioPortal deployment, you can insert custom gene records (symbol, Entrez ID if one exists, chromosome/coordinates) directly into the seed database before import, so the validator recognizes them going forward. This is a database administration step on your instance, not something done through the portal UI.
  3. **Map to an approved alias** if the gene actually does have a current HGNC symbol under a different name — check the symbol on the HGNC website (genenames.org) or NCBI Gene, since some "unknown" hits are just outdated aliases rather than truly absent genes.
  4. **Check the cBioPortal documentation/GitHub** for the gene table update scripts — the cBioPortal team periodically refreshes the reference gene set from NCBI, so it's worth confirming you're on a current gene table build before assuming a symbol is missing entirely.

This is a genuinely out-of-scope area for me to dig further into — I only have read access to the public cBioPortal database, not to your local instance's admin tooling or the gene-table update scripts. For the exact steps to add custom genes to a self-hosted instance, the cBioPortal GitHub repository/documentation or their Google Group/Slack support channel would be the right place to ask.