CTCF-Related Syndrome

This guide is not meant to take the place of medical advice. Please consult with your doctor about your genetic results and health care choices. This Gene Guide was last updated on 2024. As new information comes to light with new research we will update this page. You may find it helpful to share this guide with friends and family members or doctors and teachers of the person who has CTCF-Related Syndrome.
a doctor sees a patient

CTCF-related syndrome happens when there are changes to the CTCF gene. These changes can keep the gene from working as it should.

Key Role

The CTCF gene plays a key role in the growth of the brain and the body. The CTCF gene helps to control other genes in the brain.


Because the CTCF gene is important in the development and function of brain cells, many people who have CTCF-related syndrome have:

  • Developmental delay
  • Intellectual disability
  • Autism and other behavior concerns

Our genes contain the instructions, or code, that tell our cells how to grow, develop, and work. Every child gets two copies of the CTCF gene: one copy from their mother, from the egg, and one copy from their father, from the sperm. In most cases, parents pass on exact copies of the gene to their child. But the process of copying genes is not perfect. A change in the genetic code can lead to physical issues, developmental issues, or both.

Sometimes a random change happens in the sperm or egg. This change to the genetic code is called a ‘de novo’, or new, change. The child can be the first in the family to have the gene change.

De novo changes can take place in any gene. We all have some de novo changes, most of which don’t affect our health. But because CTCF plays a key role in development, de novo changes in this gene can have a meaningful effect.

Research shows that CTCF-related syndrome is often the result of a de novo change in CTCF. Many parents who have had their genes tested do not have the CTCF gene change found in their child who has the syndrome. In some cases, CTCF-related syndrome happens because the gene change was passed down from a parent. This is called dominant inheritance.

Dominant Inheritance

Children have a 50% chance of inheriting the genetic change.


Child who has genetic change in CTCF gene

Genetic change occurs in egg or sperm after fertilization
Child with de novo genetic change in autism gene

Why does my child have a change in the CTCF gene?

No parent causes their child’s CTCF-related syndrome. We know this because no parent has any control over the gene changes that they do or do not pass on to their children. Please keep in mind that nothing a parent does before or during the pregnancy causes this to happen. The gene change takes place on its own and cannot be predicted or stopped.

Each family is different. A geneticist or genetic counselor can give you advice on the chance that this will happen again in your family.

The risk of having another child who has CTCF-related syndrome depends on the genes of both birth parents.

  • If neither birth parent has the same gene change found in their child, the chance of having another child who has the syndrome is on average 1 percent. This 1 percent chance is higher than the chance of the general population. The increase in risk is due to the very unlikely chance that more of the mother’s egg cells or the father’s sperm cells carry the same change in the gene.
  • If one birth parent has the same gene change found in their child, the chance of having another child who has the syndrome is 50 percent.

For a symptom-free sibling, a brother or sister, of someone who has CTCF-related syndrome, the risk of having a child who has the syndrome depends on the symptom-free sibling’s genes and their parents’ genes.

  • If neither parent has the same gene change found in their child who has the syndrome, the symptom-free sibling has a nearly 0 percent chance of having a child who has CTCF-related syndrome.
  • If one birth parent has the same gene change found in their child who has the syndrome, the symptom-free sibling has a small chance of also having the same gene change. If the symptom-free sibling has the same gene change as their sibling who has the syndrome, the symptom-free sibling’s chance of having a child who has CTCF-related syndrome is 50 percent.

For a person who has CTCF-related syndrome, the risk of having a child who has the syndrome is about 50 percent.

As of 2019, about 46 people in the world with changes in the CTCF gene had been described in the medical literature. The first case of CTCF-related syndrome was described in 2013. Scientists expect to find more people who have the syndrome as access to genetic testing improves.

About one-half of those who have CTCF-related syndrome have a small head. Otherwise, people who have CTCF-related syndrome do not look very different.

Scientists and doctors have only just begun to study CTCF-related syndrome. At this point, there are no medicines designed to treat the syndrome. A genetic diagnosis can help people decide on the best way to track the condition and manage therapies. Doctors can refer people to specialists for:

  • Physical exams and brain studies.
  • Genetics consults.
  • Development and behavior studies.
  • Other issues, as needed.

A developmental pediatrician, neurologist, or psychologist can follow progress over time and can help:

  • Suggest the right therapies. This can include physical, occupational, speech, or behavioral therapy.
  • Guide individualized education plans (IEPs).

Specialists advise that therapies for CTCF-related syndrome should begin as early as possible, ideally before a child begins school.

If seizures happen, consult a neurologist. There are many types of seizures, and not all types are easy to spot. To learn more, you can refer to resources such as the Epilepsy Foundation’s website:

This section includes a summary of information from major published articles. It highlights how many people have different symptoms. To learn more about the articles, see the Sources and references section of this guide.


About three-quarters of those who have the syndrome have behavior issues, including autism.

  • 3 out of 4 people had behavior issues.


Learning challenges vary widely in people who have the syndrome. Some have severe intellectual disability. Others have an average IQ.

3 out of 4 people had behavior issues. 

Feeding and digestion issues

More than three-quarters of those who have the syndrome have a hard time eating and may not gain enough weight, also called failure to thrive. Some people need a feeding tube.

  • 3 out of 4 people had a hard time eating.

Eyes and eyesight

More than 60 percent have issues with vision.

3 out of 4 people have a hard time eating.
6 out of 10 people have issues with their vision.

Where can I find support and resources?

CTCF Related Disorder Support Group Genetics for Families

Simons Searchlight is another research program sponsored and run by the Simons Foundation Autism Research Initiative, also known as SFARI. As part of the next step in your research journey, Simons Searchlight offers you the opportunity to partner with scientists and other families who have the same gene change. Simons Searchlight is a registry for more than 200 genetic changes that are associated with neurodevelopmental conditions, including autism spectrum disorder. Simons Searchlight makes it easier for researchers to access the information they need to advance research on a condition. To register for Simons Searchlight, go to the Simons Searchlight website at and click “Join Us Today”.

Learn more about Simons Searchlight

Simons Searchlight page on CTCF

Simons Searchlight CTCF Facebook community

Sources and References

The content in this guide comes from published studies about CTCF-related syndrome. Below you can find details about each study, as well as links to summaries or, in some cases, the full article.

  • Gregor A. et al. American Journal of Human Genetics, 93, 124-131, (2013). De novo mutations in the genome organizer CTCF cause intellectual disability
  • Bastaki F. et al. BMC Medical Genetics, 18, 68, (2017). Identification of a novel CTCF mutation responsible for syndromic intellectual disability – A case report
  • Chen F. et al. American Journal of Medical Genetics Part C, Seminars in Medical Genetics, 181, 218-225, (2019). Three additional de novo CTCF mutations in Chinese patients help to define an emerging neurodevelopmental disorder
  • Konrad EDH. et al. Genetics in Medicine: Official Journal of the American College of Medical Genetics, (2019). CTCF variants in 39 individuals with a variable neurodevelopmental disorder broaden the mutational and clinical spectrum

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