Autism and genetics

Autism genetics, explained | Spectrum

Editor’s Note

This article was originally published in June 2017. It has been revised to reflect more recent research.

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Researchers have known that genes contribute to autism since the 1970s, when a team found that identical twins often share the condition. Since then, scientists have been racking up potential genetic culprits in autism, a process that DNA-decoding technologies have accelerated in the past decade.

As this work has progressed, scientists have unearthed a variety of types of genetic changes that can underlie autism. The more scientists dig into DNA, the more intricate its contribution to autism seems to be.

How do researchers know genes contribute to autism?
Since the first autism twin study in 1977, several teams have compared autism rates in twins and shown that autism is highly heritable. When one identical twin has autism, there is about an 80 percent chance that the other twin has it too. The corresponding rate for fraternal twins is around 40 percent.

However, genetics is not entirely responsible for a child’s chances of having autism. Environmental factors also contribute to the condition — although researchers disagree on the relative contributions of genes and environment. Some environmental influences, such as exposure to a maternal immune response in the womb or complications during birth, may work with genetic factors to produce autism or intensify its traits.

Genetics in motion: The secret to understanding autism lies largely in our DNA.

Is there such a thing as an autism gene?
Not really. There are several conditions associated with autism that stem from mutations in a single gene, including fragile X and Rett syndromes. But less than 1 percent of non-syndromic cases of autism stem from mutations in any single gene. So far, at least, there is no such thing as an ‘autism gene’ — meaning that no gene is consistently mutated in every person with autism. There also does not seem to be any gene that causes autism every time it is mutated.

Still, the list of genes implicated in autism is growing. Researchers have tallied about 100 genes they consider strongly linked to autism. Many of these genes are important for communication between neurons or control the expression of other genes.

How do these genes contribute to autism?
Changes, or mutations, in the DNA of these genes can lead to autism. Some mutations affect a single DNA base pair, or ‘letter.’ In fact, everyone has thousands of these genetic variants. A variant that is found in 1 percent or more of the population is considered ‘common’ and is called a single nucleotide polymorphism, or SNP.

Common variants typically have subtle effects and may work together to contribute to autism. ‘Rare’ variants, which are found in less than 1 percent of people, tend to have stronger effects. Many of the mutations linked to autism so far have been rare. It is significantly more difficult to find common variants associated with autism. The largest study to date, published in 2019 and involving more than 18,000 autistic and 27,000 non-autistic people, revealed 12 regions of the genome that harbor autism-linked common variants. Two additional regions turned up in a 2020 re-analysis of the 2019 data along with about 6,000 additional samples.

Other changes, known as copy number variations (CNVs), show up as deletions or duplications of long stretches of DNA and often include many genes.

But mutations that contribute to autism are probably not all in genes, which make up less than 2 percent of the genome. Researchers are trying to wade into the remaining 98 percent of the genome to look for irregularities associated with autism. So far, these regions are poorly understood, but some evidence links autism to mutations in stretches of noncoding DNA containing regulatory elements that control gene expression.

Are all mutations equally harmful?
No. At the molecular level, the effects of mutations may differ, even among SNPs. Mutations can be either harmful or benign, depending on many cells they affect in the body and how much they alter the corresponding protein’s function. A missense mutation, for example, swaps one amino acid in the protein for another. If the substitution doesn’t significantly change the protein, it is likely to be benign. A nonsense mutation, on the other hand, inserts a ‘stop’ sign within a gene, causing protein production to halt prematurely. The resulting protein is too short and functions poorly, if at all.

How do people acquire mutations?
Most mutations are inherited from parents, and they can be common or rare. Mutations can also arise spontaneously in an egg or sperm, and so are found only in the child and not in her parents. Researchers can find these rare ‘de novo’ mutations by comparing the DNA sequences of people who have autism with those of their unaffected family members. Spontaneous mutations that arise after conception are usually ‘mosaic,’ meaning they affect only some of the cells in the body. The fewer cells these mutations affect, the milder their contributions to autism traits.

Can genetics explain why boys are more likely than girls to have autism?
Perhaps. Girls with autism seem to have more mutations than do boys with the condition. And boys with autism sometimes inherit their mutations from unaffected mothers. Together, these results suggest that girls may be somehow resistant to mutations that contribute to autism and need a bigger genetic hit to have the condition.

Is there a way to test for mutations before a child is born?
Clinicians routinely screen the chromosomes of a developing baby to identify large chromosomal abnormalities, including CNVs. There are prenatal genetic tests for some syndromes associated with autism, such as fragile X syndrome. But even if a developing baby has these rare mutations, there is no way to know for sure whether he will later be diagnosed with autism.

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This article was republished in The Washington Post.


Autism spectrum disorder: MedlinePlus Genetics


Autism spectrum disorder (ASD) is a condition that appears very early in childhood development, varies in severity, and is characterized by impaired social skills, communication problems, and repetitive behaviors. These difficulties can interfere with affected individuals' ability to function in social, academic, and employment settings. People with ASD also have an increased risk of psychiatric problems such as anxiety, depression, obsessive-compulsive disorder, and eating disorders.

From as early as 1 to 2 years of age, people with ASD have an impaired ability to interact with other people; they are often more comfortable dealing with objects. Affected individuals have difficulty understanding and using non-verbal social cues such as eye contact, facial expressions, gestures, and body language. Inability to recognize and use these cues makes it hard for affected individuals to understand the feelings of others or communicate their own feelings appropriately. Behavioral signs of ASD, such as reduced eye contact and social interaction, can sometimes be detected before age 2. However, the condition is usually diagnosed between ages 2 and 4, when more advanced communication and social skills, such as learning to play with others, typically begin to develop.

Repetitive behaviors in ASD can include simple actions such as rocking, hand-flapping, or repetition of words or noises (echolalia). Affected individuals often dwell on or repeatedly express particular thoughts; this behavior is called perseveration. People with ASD tend to be rigid about their established routines and may strongly resist disruptions such as changes in schedule. They may also have difficulty tolerating sensory stimuli such as loud noises or bright lights.

While social and communication difficulties and unusual behaviors define ASD, affected individuals can have a wide range of intellectual abilities and language skills. A majority of people with ASD have mild to moderate intellectual disability, while others have average to above-average intelligence. Some have particular cognitive abilities that greatly surpass their overall level of functioning, often in areas such as music, mathematics, or memory.

Some people with ASD do not speak at all, while others use language fluently. However, fluent speakers with ASD often have problems associated with verbal communication. They might speak in a monotone voice, have unusual vocal mannerisms, or choose unusual topics of conversation.

Several diagnoses that used to be classified as separate conditions are now grouped together under the diagnosis of ASD. For example, autistic disorder was a term that was used when affected individuals had limited or absent verbal communication, often in combination with intellectual disability. By contrast, Asperger syndrome was a diagnosis formerly applied to affected individuals of average or above-average intelligence who were not delayed in their language development. The broader diagnosis of ASD was established because many affected individuals fall outside of the strict definitions of the narrower diagnoses, and their intellectual and communication abilities may change over time. However, some individuals who were previously diagnosed with one of the subtypes now do not meet all the criteria of the new umbrella diagnosis.


ASD is a common condition, and the number of children diagnosed with ASD has been increasing rapidly in the past few decades. In 2021, the prevalence of the disorder in the United States is estimated at 1 in 44 children. In the 1980s, before the term ASD was used, the prevalence of autism was reported to be about 1 in 2,000. However, it is unclear whether this represents a true increase in the prevalence of ASD or reflects changes in the way behaviors characteristic of the disorder have been diagnosed and categorized.

ASD is more than four times as common in boys than it is in girls.


Changes in over 1,000 genes have been reported to be associated with ASD, but a large number of these associations have not been confirmed. Many common gene variations are thought to affect the risk of developing ASD, but not all people with one or more of these gene variations will be affected. Individually, most of the gene variations have only a small effect. Genetic factors are estimated to contribute 40 to 80 percent of ASD risk.

The risk from gene variants combined with environmental risk factors, such as parental age, birth complications, and others that have not been identified,  determine an individual's risk of developing this complex condition.

By contrast, in about 2 to 4 percent of people with ASD, rare gene mutations or chromosome abnormalities are thought to be the cause of the condition, often as a feature of syndromes that also involve additional signs and symptoms affecting various parts of the body. For example, mutations in the ADNP gene cause a disorder called ADNP syndrome. In addition to ASD and intellectual disability, this condition involves distinctive facial features and a wide variety of other signs and symptoms. Some of the other genes in which rare mutations are associated with ASD, often with other signs and symptoms, are ARID1B, ASh2L, CHD2, CHD8, DYRK1A, POGZ, SHANK3, and SYNGAP1. In most individuals with ASD caused by rare gene mutations, the mutations occur in only a single gene.

Many of the genes associated with ASD are involved in the development of the brain. The proteins produced from these genes affect multiple aspects of brain development, including production, growth, and organization of nerve cells (neurons). Some affect the number of neurons that are produced, while others are involved in the development or function of the connections between neurons (synapses) where cell-to-cell communication takes place, or of the cell projections (dendrites) that carry signals received at the synapses to  the neuron. Many other genes associated with ASD  affect development by controlling (regulating) the activity of other genes or proteins.

The specific ways that changes in these and other genes relate to the development of ASD are unknown. However, studies indicate that during brain development, some people with ASD have more neurons than normal and overgrowth in parts of the outer surface of the brain (the cortex). In addition, there are often patchy areas where the normal structure of the cortex is disturbed. Normally the cortex has six layers, which are established during development before birth, and each layer has specialized neurons and different patterns of neural connection. The neuron and brain abnormalities occur in the frontal and temporal lobes of the cortex, which are involved in emotions, social behavior, and language. These abnormalities are thought to underlie the differences in socialization, communication, and cognitive functioning characteristic of ASD.


ASD has a tendency to run in families, but the inheritance pattern is usually unknown. People with gene changes associated with ASD generally inherit an increased risk of developing the condition, rather than the condition itself. When ASD is a feature of another genetic syndrome, it can be passed on according to the inheritance pattern of that syndrome.

Other Names for This Condition

  • ASD
  • Autistic continuum
  • Pervasive developmental disorder

Additional Information & Resources

Genetic Testing Information

  • Genetic Testing Registry: Autism spectrum disorder

Genetic and Rare Diseases Information Center

  • Autism spectrum disorder

Patient Support and Advocacy Resources

  • Disease InfoSearch
  • National Organization for Rare Disorders (NORD)

Research Studies from


Catalog of Genes and Diseases from OMIM


Scientific Articles on PubMed

  • PubMed


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  • Sanders SJ. First glimpses of the neurobiology of autism spectrum disorder. Curr Opin Genet Dev. 2015 Aug;33:80-92. doi: 10.1016/j.gde.2015.10.002. Epub 2015 Nov 9. Citation on PubMed
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  • Stoner R, Chow ML, Boyle MP, Sunkin SM, Mouton PR, Roy S, Wynshaw-Boris A, Colamarino SA, Lein ES, Courchesne E. Patches of disorganization in the neocortex of children with autism. N Engl J Med. 2014 Mar 27;370(13):1209-1219. doi: 10.1056/NEJMoa1307491. Citation on PubMed or Free article on PubMed Central
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Fundamentals of Autism Genetics | Foundation Exit, autism in Russia


Basic information about the latest data from genetic studies of autism

Source: Spectrum News

Researchers know that autism is related to genetic factors, more in the 1970s, when one team found that identical twins were more likely to have autism at the same time than non-identical twins. Since then, scientists have been trying to identify potential genetic causes of autism. Over the past ten years, thanks to new DNA decoding technologies, this process has accelerated significantly. nine0003

As these studies progress, scientists have identified many different genetic changes that can lead to autism. But the better scientists understand human DNA, the more difficult it becomes to influence the development of autism.

How do scientists determine which genes influence autism?

The first study of autism among twins was conducted in 1977. Several teams of scientists have compared levels of autism among twins, and they have found that there is a very high level of inheritance for autism. If one identical twin has autism, then there is an 80% chance that the other twin will also have it. For non-identical twins, this probability is 40%. nine0003

However, the development of autism cannot be explained by genetics alone. Obviously, this condition is also associated with various environmental factors, although there is disagreement among scientists about how much autism is determined by genes, and how much is environmental.

Many environmental factors are associated with autism risk, such as maternal infections during pregnancy and complications during childbirth. These factors may interact with genetic factors, resulting in the development of autism or may exacerbate its manifestations. nine0003

Is there an “autism gene”?

No, we can say that there is no such gene. There are syndromes associated with a mutation in a single gene that can lead to autism, such as fragile X syndrome and Rett syndrome. However, among non-syndrome cases of autism, less than 1% of cases are caused by a mutation in any one gene. So there is no one “autism gene”, that is, there is no one genetic mutation that every person with autism has. Also, there doesn't seem to be a gene that will always cause autism when mutated. nine0003

The list of genes associated with autism is constantly growing. So far, researchers have identified 65 genes that are most associated with autism, and another 200 genes that show a lesser association. Most of these genes play an important role in communication between neurons in the brain, or they control the expression of other genes.

How might these genes be linked to autism?

Changes, ie mutations, in these genes can lead to autism. Some mutations affect one DNA base pair, one "letter". In fact, each of us has thousands of genetic variations. If some variation occurs in 1% of the population or more, then it is considered "common" and is called a single nucleotide polymorphism or SNP. nine0003

Common variations usually affect development in subtle ways, but their combinations can lead to autism. "Rare" variations, which occur in less than 1% of the population, have a much stronger effect. Many known mutations associated with autism are rare. Finding risk factors among common variations is much more difficult, although such studies are underway.

Other changes, called copy number variations (CNCs), involve the deletion or duplication of DNA and often involve multiple genes. nine0003

Moreover, mutations that can contribute to autism are not necessarily found only in genes that make up only 2% of the genome. Scientists are trying to study the remaining 98% of the genome in order to notice abnormalities associated with autism. So far, these genetic features are very little studied.

Are all mutations harmful?

No. At the molecular level, the consequences of mutations are very different, even when it comes to SNPs. Mutations can be harmful or harmless depending on how much they affect the corresponding function of the protein. For example, some mutations replace one amino acid in a protein with another. If such a substitution does not change the action of the protein, then such a mutation is likely to be harmless. Other mutations can introduce a stop sign into the gene, causing protein production to stop too soon. As a result, the protein will be too short and will not function correctly, if at all. nine0003

How do people get mutations?

Most mutations are inherited from parents, and this applies to both common and rare mutations. They can also spontaneously arise in an egg or sperm cell, in which case the mutation will only be present in the child, but not in the parents. Researchers discover such de novo mutations when they compare the DNA of people with autism with that of their non-autistic family members. Spontaneous mutations after conception are usually "mosaic", meaning they only affect some cells in the body. nine0003

Can geneticists explain why autism is more common in boys than in girls?

Possibly. Girls with autism tend to have more autistic-associated mutations than boys. Sometimes boys with autism inherit these mutations from mothers who do not have autism. These data suggest that girls may be resistant to mutations associated with autism and need a stronger "genetic hit" to develop the disorder.

Can these mutations be detected before the baby is born?

During the routine examination during pregnancy, a test is made for possible chromosomal abnormalities, including SNPs. There are prenatal genetic tests for some syndromes that may be associated with autism, such as fragile X syndrome. However, the test will not be able to identify all possible variations that are potentially associated with autism. In addition, even if a child has these rare mutations, it is impossible to determine whether a child will be diagnosed with autism in the future, since genetic characteristics only speak about the likelihood of such a development. nine0003

How likely is it to have a second child with autism

Interview. Autism treatment - present and future

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Autism Biomedicine, Research

Genetic causes of autism

November 16, 2018

identify the genetic causes of the disease. nine0003

Approximately 1% of children are diagnosed with ASD today. Scientists believe that a significant contribution to the development of autism is made by the genetic component: heritability is about 70%, and a possible connection with autism has now been described for more than 700 genes.

Symptoms of ASD are accompanied by a large number of hereditary diseases, the risk of having a sick child depends on the age of the father. In families where there is already a child with ASD, the likelihood of having children with the same diagnosis increases - according to the medical literature, for boys born in a family where there is a girl diagnosed with autism, this risk is as much as 16.7%. However, this is a general risk, and the likelihood of recurrence of autism in a particular family is usually unknown. nine0094 Experts are sure that genetic testing for ASD is useful in order to determine the risk of recurrence of the disease in the family, not only in one couple, but also in parents in a new family, in future brothers, sisters, and in more distant relatives.
In 2017, the Genetico Center launched the Genetico.Autism program to study the genetic forms of autism among Russians and reduce the risk of having children with autism spectrum disorders (ASD).
As of September 2018, families from 98 children: 17 girls, 81 boys. So far, 56 children have been examined by all the methods provided for by the program, for the rest, the examination continues.
One of the objectives of the study was to evaluate the effectiveness of various laboratory methods in identifying the genetic causes of autism.
The data obtained showed that karyotyping (analysis of structural and quantitative chromosome anomalies) did not result in a single case of identifying the cause of ASD in the study sample. This may be due both to the low information content of the karyotype for this group of diseases, and to the characteristics of the sample. Probably, some children with the most severe syndromic forms of autism do not get examined under the Genetico.Autism program - for example, autism in Down syndrome is not uncommon, but it is often possible to make a diagnosis of Down syndrome even in the maternity hospital. nine0094 Whole-exome sequencing (NGS) is the most informative method in terms of the number of detected mutations and overtakes the XMA method (chromosomal microarray analysis).
In several cases, the identified mutation has been described in the scientific literature as the cause of epileptic encephalopathy. This is a logical result, since epilepsy and autism are often comorbid, i.e. meet together.
Also of interest are cases when autism in a child arose as a manifestation of autosomal recessive Cohen's syndrome (25% risk of recurrence) and an unbalanced translocation, which was the result of carriage by one of the parents of a balanced chromosomal rearrangement. In this family, the risk of recurrence of problems in the next child is also high. On the other hand, in several families, it was confirmed that the mutation that caused the disease arose de novo and is absent in DNA isolated from the blood of the parents - in such families, the risk of recurrence, on the contrary, is low, less than 4%. nine0094 Thus, in about a quarter of cases, genetic testing allows you to understand whether the risk of recurrence of autism in the family that has been examined is high or low. Moreover, if it is high, there are ways to conduct a timely diagnosis of the unborn child, due to the fact that a specific mutation responsible for the problem has been found.
Participation in the Genetico.Autism program is especially useful for families who already have a child with ASD and who are planning to have another child.
To reduce the risk of having a child with a hereditary disease, a family can undergo a PGT (pre-implantation genetic testing) procedure during IVF for a specific genetic variant that determines an increased risk of disease in the family. And choose an embryo for replanting the mother, free from mutations leading to the development of the disease. For such preimplantation testing of embryos, the “causal” genetic variant must be known in advance and an individual test system should be developed for each family.

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