Variants for FAM86B2 map to two different chromosomes

[Matteo Tiberti]

Dear cBioPortal,

We have noticed that for the FAM86B2 gene, some variants are annotated on chromosome 16 rather than chromosome 8 (as I would expect) - see attached screenshot.

We didn't check all of them, but some of the corresponding genomic coordinates match to the locus of a related FAM86A (aka EEF2KMT) gene (e.g. 16:g.5140130C>T 16:g.5139227G>A 16:g.5141897C>A). The two genes share a very similar coding sequence.

Do you think this might be due to a misannotation?

Thanks in advance,

_____________________________

Matteo Tiberti, PhD

Staff Scientist at the Cancer Structural Biology group
Danish Cancer Society Research Center

Strandboulevarden 49

2100, Copenhagen, Denmark

[de Bruijn, Ino]

Hi Matteo,

Thanks for reaching out! This looks like a potential two-fold issue. It could be that some variant callers incorrectly called the mutation at the paralog gene. We usually don’t change the genomic coordinates themselves, but as you observed we also incorrectly annotate  the gene sometimes (FAM68A instead of EEF2KMT).

It looks like this is fixed in the latest version of Genome Nexus (the annotator we use) where it correctly gets annotated as EEF2KMT:

https://www.genomenexus.org/variant/16:g.5140515C%3ET

I’m looping in @Madupuri, Ramyasree and @Li, Xiang to reannotate the studies with this problem. You can find the full debug chat session here: https://chat.cbioportal.org/share/-2Z6pmVhe6EwVtdMOIvC2

Best

Ino

From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of Matteo Tiberti <matteo....@gmail.com>
Date: Wednesday, August 12, 2026 at 6:35 AM
To: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: [EXTERNAL] [cbioportal] Variants for FAM86B2 map to two different chromosomes

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