Certain gene deserts are heavy regulators, while others may be deleted without any effect. As a possible classification, gene deserts can be broken down into two subtypes: stable and variable. Stable gene deserts have fewer repeats and have relatively higher Guanine to Cytosine (GpC) content than observed in variable gene deserts.
Guanine and cytosine content is indicative of protein-coding functionality. For example, in a study on chromosomes 2 and 4, which have been linked to several genetic diseases, there were elevated GpC content in certain regions. Mutations in these GC-rich regions caused a variety of diseases, revealing the necessary integrity of these genes. High density CpG regions serve as regulatory regions for DNA methylation. Therefore, essential coding genes should be represented by high-CpG regions. In particular, regions with high GC content should tend to have high densities of genes that are devoted mainly to the essential housekeeping and tissue specific processes. These processes would require the most protein production to express functionality. Stable gene deserts, which have higher levels of GC content, should therefore contain the essential enhancer sequences. This could determine the conservatory functions of stable gene deserts.
On the other hand, approximately 80% of gene deserts have low GpC contents, indicating that they have very few essential genes. Thus, the majority of gene deserts are variable gene deserts, which may have alternate functions. One prevalent theory regarding the origins of gene deserts postulates that gene deserts are accumulations of essential genes that act as a distance. This may hold true, as given the low numbers of essential genes within them, these regions would have been less conserved. As a result, due to the prevalence of cytosine to thymine conversions, the [http://genome.sph.umich.edu/wiki/SNP_Call_Set_Properties most common SNP], would cause a gradual separation between the few essential genes within variable gene deserts. These essential sequences would have been maintained and conserved, leading to small regions of high density that regulate at a distance. GC content is therefore indication for the presence of coding or regulatory processes in DNA. 
While stable gene deserts have higher GC content, this relative value is only an average. Within stable gene deserts, although the ends contain very high levels of GC content, the main bulk of the DNA contains even less GC content than observed in variable gene deserts. This indicates that there are very few highly conserved regions in stable gene deserts that do not recombine, or do so at very low rates. Given that the ends of the stable gene deserts have particularly high levels of GC contents, these sequences must be extremely conserved. This conservation may in turn cause the flanking genes to also have higher conservation rates. Thus, stable genes should be directly linked to at least one of their flanking genes and cannot be separated from coding sequences by recombination events. Most gene deserts appear to cluster in pairs around a small number of genes. This clustering creates long loci that have very low gene density; small regions with high numbers of genes are surrounded by long stretches of gene deserts, creating a low gene average. Therefore, the minimized probability of recombination events in these long loci creates syntenic blocks that are inherited together over time. These syntenic blocks can be conserved for very long periods of time, preventing loss of essential material, even while the distance between essential genes may grow in time.
Although this effect should theoretically be amplified through the even lower GC-content in variable gene deserts (thereby truly minimalizing gene density), the gene conservation rates in variable gene deserts are even lower than observed in stable gene deserts—in fact, the rate is far lower than the rest of the genome. A possible explanation for this phenomenon is that variable gene deserts may be recently evolved regions that have not yet been fixed into stable gene deserts. Therefore, shuffling may still occur before stabilizing regions within the variable gene deserts begin to cluster as whole units. There are a few exceptions to this minimal rate of conservation, as a few GC gene deserts are subjected to hypermethylation, which greatly reduces the accessibility to the DNA, thus effectively protecting the region from recombination. However, these occur rarely in observation.
Although stable and variable gene deserts differ in content and function, both wield conservatory abilities. It is possible that since most variable gene deserts have regulatory elements that can act at a distance, conservation of the entire gene desert into a sytenic locus would not have been necessary, so long as these regulatory elements themselves were conserved as units. Given the particularly low levels of GC content, the regulatory elements would therefore be in a minimal gene density situation as observed similarly in flanking stable gene deserts, with the same effect. Thus, both types of gene deserts serve to retain essential genes within the genome.