Hi,

I'm using R package biomaRt to map Ensembl gene IDs to HGNC symbols. I find some Ensembl IDs can be mapped to multiple symbols. For example,

mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
getBM(attributes = c("ensembl_gene_id", "hgnc_symbol"), filters = "ensembl_gene_id", values = c("ENSG00000187510", "ENSG00000230417", "ENSG00000276085"), mart = mart)     
  ensembl_gene_id hgnc_symbol
1 ENSG00000187510    C12orf74
2 ENSG00000187510     PLEKHG7
3 ENSG00000230417   LINC00595
4 ENSG00000230417   LINC00856
5 ENSG00000276085      CCL3L1
6 ENSG00000276085      CCL3L3

> packageVersion("biomaRt")
[1] ‘2.38.0’

This is unsurprising given that we don't expect 1:1 map. However, what is confusing is that, if I query those IDs with Ensembl website, I will get unambiguously one symbol. That is,

ENSG00000187510 -> C12orf74
ENSG00000230417 -> LINC00856
ENSG00000276085 -> CCL3L1

In theory, what is behind biomaRt is just SQL query against Ensembl database online, and we should expect same results given the same version of the database. So I want to know why we get this discrepancy.

Thanks,

When you map to the HGNC symbol, you are asking for an external reference. In other words, what symbols does the HUGO consortium say map to this Ensembl ID, which you can see here, and which include both of the symbols you get from the Biomart server.