<div dir="ltr">Hi ensemble-dev,<div><br></div><div>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:</div><div><br></div><div>    library(biomaRt)</div>    ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")<br>    getBM(values = c("CCL3L1", "CCL3L3", "HLA-DQA1", "HLA-DQA2"),<br>               attributes = c("entrezgene_id", "hgnc_symbol"),<br>               filters = "hgnc_symbol", mart = ensembl)<div><br></div><div>which gives:</div><div><br></div><div>      entrezgene_id hgnc_symbol<br>    1            6349      CCL3L1<br>    2        414062      CCL3L1<br>    3            6349      CCL3L3<br>    4        414062      CCL3L3<br>    5            3117  HLA-DQA1<br>    6            3117   HLA-DQA2<br>    7            3118   HLA-DQA2<br></div><div><br></div><div>However, when I look up these hgnc symbols online I believe the result should be:</div><div><br></div><div>        entrezgene_id hgnc_symbol<br>    1          6349      CCL3L1<br>    2      414062      CCL3L3<br>    3          3117  HLA-DQA1<br>    4          3118  HLA-DQA2  <br></div><div><br></div><div>The online sources:</div><div><br></div><div>CCL3L1:      <a href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:10628" target="_blank">https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:10628</a><br></div><div>CCL3L3:      <a href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:30554" target="_blank">https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:30554</a></div><div>HLA-DQA1: <a href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4942" target="_blank">https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4942</a><br></div><div>HLA-DQA2: <a href="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4943" target="_blank">https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4943</a><br></div><div><br></div><div>Also AnnotationDbi does give me the expected results:</div><div><br></div><div>    require(AnnotationDbi)<br>    require(org.Hs.eg.db)<br>    AnnotationDbi::mapIds(org.Hs.eg.db, </div><div>        keys=c("CCL3L1", "CCL3L3", "HLA-DQA1", "HLA-  DQA2"), </div><div>        column = "ENTREZID", keytype = "SYMBOL")<br></div><div><br></div><div>Am I doing something wrong or is this is bug?</div><div><br></div><div>(biomaRt version 2.44.4, ensemble version 101)</div><div><br></div><div>Kind regards,</div><div>Gerhard</div></div>