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Autism Chromosome: A Look At Genome Studies on Autism

October 13, 2023

Science tells us that our genes contribute to deficits in communication, social cognition, and behavior. This might lead you to question: is there an autism chromosome? Well, a growing number of physiological and genetic studies are being conducted to determine the cause of autism and target the biological route of its symptoms, so let’s find out.

Autism Chromosome: A Look At Genome Studies on Autism

The core features of autism spectrum disorder (ASD) include persistent deficits in social communication and social interaction and restricted, repetitive patterns of behavior or interests. Other symptoms include intellectual disability, some experience developmental delay, delayed brain development, pervasive developmental symptoms etc. Due to all these anomalies, autism is generally considered a developmental disorder.

The core features of autism spectrum disorder (ASD) include persistent deficits in social communication and social interaction and restricted, repetitive patterns of behavior or interests.

According to Rylaarsdam, et al. (2019), other conditions that occur with autism include motor abnormalities, epilepsy, intellectual disability, sleep disorders, and gastrointestinal problems. 

Genetic studies that focus on autism related abnormalities suggest ASD is linked to the interaction between genes and the environment and the percentage of heritability is estimated to range between 40% to 80%.

What is a gene?

Within the entire DNA, there are several segments called genes that code for specific proteins and functions critical for cellular functioning. When the DNA coils around proteins, it forms chromosomes found in the cell nucleus, in other words the chromosome is the hyper store that contains hundreds of genes.

Let’s break that down:

  • DNA is a long fiber that contains segments called genes
  • When the DNA coils up around proteins, it forms a structure called chromosomes 
  • Chromosomes are found within the nucleus of cells and the genes found within the chromosomes serve specific functions. Gene regulation is therefore important as it determines which genes are turned on and which should be off in the cell

The human organism is designed through DNA information that makes up genes. When fertilization occurs, half the genetic information is drafted from the egg and the other half comes from the sperm; the information carried over is known as heredity. Therefore, the fertilization egg carries two copies of each gene; one inherited from each parent. In the average human body, there are 23 total pairs of chromosomes and the 23rd pair is the sex chromosomes where one set comes from the mother and the other comes from the father.

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Fun fact: The female always has XX chromosomes and the male has XY chromosomes. At fertilization, if the male’s Y chromosome fertilizes with the female’s X chromosome, the pair of XY yields a male offspring; or if the male’s X chromosome fertilizes with the female X chromosome, the XX pair yields a female offspring. Therefore the male sex chromosome informs the sex of the offspring.

Genetic studies on autism

Following extensive research on autism and genetic links, several genes have been found to potentially be connected to ASD. Rylaarsdam, et al. (2019) highlights various findings from genetic studies; these are highlighted below:

At the genesis of genome studies, genetic studies on heredity have been conducted through twin studies, namely monozygotic twins and dizygotic twins. Monozygotic (identical) twins are derived from one fertilized egg that has split into two; and dizygotic twins (also known as fraternal twins) are derived from two separate eggs released at the same time fertilized by two separate sperm. It has been found that monozygotic twins are more likely to share a diagnosis than dizygotic twins, therefore suggesting a genetic influence. 

Thanks to the growth of genetic research, genomic studies have increased with findings citing that the etiology of autism spectrum disorder is both multigenic (disease or disorder results from mutation occurring in multiple genes all of which lead to one phenotypic trait) and heterogeneous. 

Large scale genetic studies have been conducted on patients with ASD as well as their families. Through these studies, several risk genes have been identified. Of these, two broad classes of proteins have been found to be related, namely: synapse formation and transcriptional regulation and chromatin-remodeling pathways. In addition, several studies have found a variety of changes in chromosome structure and number in some samples of autistic children.

Let’s break down the two classes and why autism risk genes are found to be related with these classes:

1. Synapse-related risk genes

As discussed in The Pathophysiology of Autism Unpacked, a synapse is the endpoint on a nerve which transmits neural information flows from one neuron to the next. In order for neural information to be transmitted, certain proteins are involved for the process to occur smoothly. Remember that genes regulate and code for certain proteins, therefore, if the protein encoded is abnormal, it will affect the overall functioning of that cell. Hence, if a risk gene is present at the synaptic region, depending on the function of that gene, it can give rise to disorders. In this case, some risk genes have been implicated with the occurrence of autism.

Synapse-related risk genes involve those that encode cell adhesion protein. As defined in Ren, et al.(2011), adhesion proteins “play an important role in initiating and sustaining an effective immune response against foreign pathogens”. These processes “mediate the interaction between cells, or between cells and the extracellular matrix (ECM)”. Additionally, cell adhesion proteins work together to regulate signaling processes that detect and respond to any change in the surrounding. 

Genetic studies conducted through In Vivo (within the organism) have found abnormality in the synapse as well as abnormal neural network formation to have some implication in autism spectrum disorder.

2. Transcriptional regulation and chromatin-remodeling pathways

The processes that encompass transcriptional regulation and chromatin-remodeling are complex. In short, these two processes control which genes can be expressed to form the corresponding protein. 

Accurate follow-through of these processes is important as, if any of the steps involved during either transcriptional regulation or in the chromatin remodeling pathway are affected, it will bring rise to the formation of risk genes, some of which have been potentially linked to autism. 

For example, the process of transcriptional regulation converts (transcribes) DNA to RNA. Once RNA is transcribed, it goes through cellular processes to coordinate cellular activity. When RNA is transcribed, RNA editing or modification can occur whereby discrete changes can take place within the RNA molecule. In the study by Tran et al. (2019), it was found that mutations such as FMRP (fragile X mental retardation protein) and FXRP1 (fragile X related protein 1) can cause abnormal RNA modification activity.

According to Rylaarsdam, et al. (2019), the genes that impact transcription and chromatin-remodeling pathways include “MeCP2, UBE3A, chromodomain helicase DNA binding protein 8 (CHD8), activity dependent neuroprotector homeobox (ADNP), pogo transposable element derived with ZNF domain (POGZ), fragile X mental retardation protein (FMRP), and RNA binding forkhead box (RBFOX) genes”.

Is autism a chromosomal disorder?

According to El-Baz, et al. (2016) clinical genetic studies have conducted research on the genetic causes of autism and found autism genes in “5% with high resolution chromosomal abnormality, 5% with fragile x syndrome, 5% with Rett syndrome, 10% with other genetic syndromes (tuberous sclerosis) and 10% with structural genomic deletions or duplications…”

From a genetic standpoint, the chromosomal abnormality found in autism explains why there’s such a high number of varieties in the phenotypic expression of autism. Therefore, autism is considered to be polygenic (phenotypic expression (what we see) is influenced by more than one gene) and multifactorial (many factors are involved causing abnormality i.e. environmental and genetic). 

While it is believed that some genes on the X chromosome contribute to the development of autism, studies point to the fact there are genes across the human genome capable of epigenetic modulation that are found to be involved in the susceptibility of autism. Epigenetic changes are those which do not change your DNA sequence, but the manner in which that sequence is read.

There are genes that are involved in regulating the occurrence of an epigenetic change. If there’s any mutation in these genes, it can lead to other risk genes related to disorders such as autism. According to Rylaarsdam, et al. (2019) there are two key genes that increase an individual’s susceptibility or predisposition to autism if mutated, namely: MeCP2 and UBE3A.

  1. The MeCP2 gene is a “chromatin modifier” that is found to be implicated in ASD. This is because of its function in regulating genes involved in synaptic function, as well as many others. Additionally, this gene is also found to be reduced in the prefrontal cortex of individuals with ASD
  2. The UBE3A gene is a E3 ubiquitin protein ligase (a ligase is a class of enzyme that causes the binding of two molecules); in this case, UBE3A binds E3 ubiquitin proteins. UBE3A is also strongly implicated in the pathology of ASD because it is an epigenetic regulator; and is also modulated by MeCP2.
  • “UBE3A lies in the chromosomal region 15q11-13, which is commonly duplicated in autism” according to Rylaarsdam, et al. (2019)

From these two genes, we can see how mutation in one epigenetic regulator can impact the entire genome function of an individual which eventually leads to the development of disorders.

In summary

Genetic and epidemiological studies have made great progress to determine which environmental factors and genetic factors or predispositions contribute to the occurrence of autism spectrum disorder. Through genome studies, scientists have uncovered several mutations in genes, particularly regulatory genes, that are involved in the susceptibility of ASD development. 

The human genome is large and, although science has made great progress, there’s still much to be uncovered to determine which gene in particular is solely responsible for the occurrence of ASD. From a genetic standpoint, there’s no one size fits all approach to understand the etiology of autism. 

The study of genes requires analyzing and comparing how each gene functions and making comparisons between healthy gene function and abnormal gene function in a given population or sample population. This therefore helps scientists to study the occurrence of abnormality and how that impacts the physiology of the person to cause the pathology we observe. Essentially, studying the microscopic effect, as well as analyzing the cellular and molecular consequence to the phenotypic expression. 

Reading about these studies and understanding them can help parents understand the etiology of autism, and also grasp the reason why autism is such a complex heterogeneous condition. 


El-Baz, F., Zaghloul, M. S., El Sobky, E., Elhossiny, R. M., Salah, H., Abdelaziz, N. E.,  (2016). Chromosomal abnormalities and autism, Egyptian Journal of Medical Human Genetics, 17(1), 57-62, https://doi.org/10.1016/j.ejmhg.2015.05.002 

Finegold, D. N., (2021) Genes and Chromosomes, https://www.msdmanuals.com/home/fundamentals/genetics/genes-and-chromosomes

Ren, G., Roberts, A. I., & Shi, Y. (2011). Adhesion molecules: key players in Mesenchymal stem cell-mediated immunosuppression. Cell adhesion & migration, 5(1), 20–22. https://doi.org/10.4161/cam.5.1.13491

Rylaarsdam, L., & Guemez-Gamboa, A. (2019). Genetic Causes and Modifiers of Autism Spectrum Disorder. Frontiers in cellular neuroscience, 13, 385. https://doi.org/10.3389/fncel.2019.00385

Tran, S. S., Jun, H.-I., Bahn, J. H., Azghadi, A., Ramaswami, G., Van Nostrand, E. L., et al. (2019). Widespread RNA editing dysregulation in brains from autistic individuals. Nature Neuroscience, 22, 25–36. https://doi.org/10.1038/s41593-018-0287-x

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