***SEE UPDATES PAGE***

The research community is increasingly becoming aware that genes previously believed to be single copy, can be present in variable copy numbers in different individuals (PMID:15286789, 15273396 and 15918152). The nomenclature of these 'complex' loci has previously been dealt with on a case-by-case basis; however, as more such genes are identified, the HGNC would like to determine if a standard approach would be of benefit to the scientific community.

Examples of HGNC ‘case-by-case’ approved scenarios include:

1. The RNR1-5 loci, which contain arrays of ribosomal RNA at p12 of the acrocentric chromosomes 13, 14, 15, 21, and 22 respectively. There are 150-300 copies of ribosomal genes in the human genome that are homogenised by concerted evolution, recombination and gene conversion. The individual rRNA genes in each RNR# cluster are not approved by the HGNC.

2. DEFA1A3 (defensin, alpha 1 and alpha 3, variable copy number locus) at 8p23.1 comprises variable copy number tandem repeats that include the DEFA1, DEFA3 and DEFT1P genes, each present in the current human genome build. We also have three separate approved gene records for DEFA1, DEFA3 and DEFT1P, as they can be distinguished by sequence although some individuals do not possess any DEFA3 copies (PMID:15944200, 16039093 and 15588320).

3. The KIR2DL5A and KIR2DL5B variable copy number genes. Although there is only one of these genes in the current human genome build, and some individuals do not possess both, the KIR2DL5A and KIR2DL5B genes are not in tandem and can be distinguished by sequence. The NCBI creates separate gene records for different genes so they have also created two separate Entrez Gene records for these (PMID:12185535).

 

As illustrated above there is currently no consensus for naming variable copy number genes and, indeed, it may not be feasible to apply a standard nomenclature system to all cases. We would greatly appreciate your opinion and thoughts regarding the potential problems of the current nomenclature systems, benefits and pitfalls of a standard nomenclature, and ideas for an ideal new nomenclature scheme for variable copy number genes.

Please email hgnc@genenames.org with your view.