[ensembl-dev] Possibly incorrect entrezgene ids for CCL3L1, CCL3L1, HLA-DQA2

[Gerhard Burger]

Hi ensemble-dev,

I'm trying to get entrizid for hgnc gene symbols, but I got some confusing
results for CCL3L1, CCL3L1, HLA-DQA1, HLA-DQA2. I am using the following R
code:

    library(biomaRt)
    ensembl <- useEnsembl(biomart = "genes", dataset =
"hsapiens_gene_ensembl")
    getBM(values = c("CCL3L1", "CCL3L3", "HLA-DQA1", "HLA-DQA2"),
               attributes = c("entrezgene_id", "hgnc_symbol"),
               filters = "hgnc_symbol", mart = ensembl)

which gives:

      entrezgene_id hgnc_symbol
    1            6349      CCL3L1
    2        414062      CCL3L1
    3            6349      CCL3L3
    4        414062      CCL3L3
    5            3117  HLA-DQA1
    6            3117   HLA-DQA2
    7            3118   HLA-DQA2

However, when I look up these hgnc symbols online I believe the result
should be:

        entrezgene_id hgnc_symbol
    1          6349      CCL3L1
    2      414062      CCL3L3
    3          3117  HLA-DQA1
    4          3118  HLA-DQA2

The online sources:

CCL3L1:
https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:10628
CCL3L3:
https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:30554
HLA-DQA1:
https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4942
HLA-DQA2:
https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4943

Also AnnotationDbi does give me the expected results:

    require(AnnotationDbi)
    require(org.Hs.eg.db)
    AnnotationDbi::mapIds(org.Hs.eg.db,
        keys=c("CCL3L1", "CCL3L3", "HLA-DQA1", "HLA-  DQA2"),
        column = "ENTREZID", keytype = "SYMBOL")

Am I doing something wrong or is this is bug?

(biomaRt version 2.44.4, ensemble version 101)

Kind regards,
Gerhard
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