If you broadly accept the findings of our 2015 BALB/c mouse study, you will agree that there is major problem with the existing nomenclature for inbred mouse genes.
The details of the paper are: Collins AM, Wang Y, Roskin KM, Marquis CP, Jackson KJ. The mouse antibody heavy chain repertoire is germline-focused and highly variable between inbred strains. Philosophical transactions of the Royal Society of London Series B, Biological sciences 2015; 370:20140236.
The mouse nomenclature comes from the C57 genome reference sequence. It is a quasi-positional nomenclature. Unlike the human nomenclature, names do not point to the position of the genes within the genome, but rather it refers to positions within the genome of each family of IGHV genes. So IGHV2-1 is the first gene of the V2 family, within the genome, and IGHV3-2 is the second V3 family gene within the genome. Sequences from other strains have been named, I think, on the basis of similarity to C57 genes. Within the IMGT database, many BALB/c sequences are shown as mapped, but it is unclear what this means, and what data supports the mapped position. The BALB/c genome has just been released, so we may soon find out more. (It may be that mapping relates to the Retter 2007 study of the 3’ half of the 129S1 IGH locus, but that should be confirmed.
If there are something like 100 C57 IGHV genes and 160 BALB/c genes, it is almost impossible to imagine that correspondence can be found between sequences, so that BALB sequences can be given names according to the C57-based nomenclature. If that is the case, what is to be done?
Should a second quasi-positional nomenclature be defined for BALB/c genes? This would require tags being added to the existing names, giving something like c57IGHV1-101 and balbIGHV1-101. It might be easier to head down that road if we knew what other treats are in store for us as other inbred and wild strains of mice are investigated.
Should a non-positional nomenclature, like that of VBASE2, be adopted? If this was used to name BALB/c genes, would C57 names be left in place?
Should BALB/c sequences that presently have C57-based names be renamed?