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PubMed This is a summary of 21 peer-reviewed journal articles Updated
Pediatric Neurology

Uncovering the Cause: Genetics and Imaging in EMA

At a Glance

EMA has no single known gene, so doctors may use a gene panel, chromosomal microarray, or whole-exome sequencing to look for a cause. MRI is often normal, but an epilepsy-protocol scan may be recommended when seizures show focal signs, development regresses, or medicines do not work.

When your child is diagnosed with Epilepsy with Myoclonic Absences (EMA), one of the most natural questions is “Why did this happen?” Understanding the cause is a puzzle that doctors and families piece together using genetic testing and advanced imaging. While we do not yet have a single “EMA gene,” we know that for many children, the answer involves their unique genetic blueprint.

There is No Single “EMA Gene”

It is important to understand that EMA is genetically heterogeneous, meaning it can be associated with many different genetic changes rather than just one [1][2]. Because EMA is so rare, researchers are still identifying which genes are most frequently involved.

Several genes have been linked to overlapping phenotypes or rare EMA-like presentations in medical reports:

  • SETD1B: Some children with changes in this gene have myoclonic absences along with broader developmental or learning challenges, though this represents a rare association [1][3].
  • SYNGAP1: While often associated with a more complex condition called a developmental and epileptic encephalopathy, SYNGAP1 can sometimes present with myoclonic absences and other “staring” seizures [4][5].
  • SLC2A1: This gene is responsible for GLUT1 deficiency syndrome, where the brain doesn’t get enough sugar (glucose) for energy. Identifying this is vital because it can be treated differently with a specific medical diet [2][6].
  • Other Associations: Researchers have also seen EMA-like symptoms in children with changes in genes like RORB, FOXP1, or a specific small missing piece of DNA known as a 15q11.2 microdeletion [7][8][9]. These are case-report level associations rather than defining features of all EMA.

Why Genetic Testing is Recommended

Because EMA often overlaps with other conditions and can be difficult to treat, genetic testing is often considered when epilepsy is early-onset, development is atypical, or seizures are drug-resistant [10][11]. In children with early-onset epilepsy, broad testing finds a definitive cause in roughly 25% to 33% of cases across mixed clinical cohorts [12][13].

Common tests your doctor may order include:

  1. Epilepsy Multi-Gene Panel: A test that looks at hundreds of genes known to cause seizures all at once [12].
  2. Chromosomal Microarray (CMA): This looks for extra or missing “chunks” of DNA (copy-number variants) [14].
  3. Whole-Exome Sequencing (WES): A more comprehensive test that “spells out” almost all of the protein-coding genes in the body, which can be effective for finding rare causes depending on guidelines [12][15].

Working with a Genetics Team

Genetic results are rarely a simple “positive” or “negative.” Sometimes a test finds a Variant of Uncertain Significance (VUS)—a change in the DNA that we don’t fully understand yet [16]. A VUS is not diagnostic by itself and should not be used alone to guide medication changes or family-planning decisions.

A genetic counselor or clinical geneticist is a vital part of your care team. They help interpret these complex results, explain if the genetic change was inherited from a parent or happened for the first time in the child (de novo), and discuss privacy, consent, and what it means for your child’s future [16][17].

The Role of Brain Imaging (MRI)

In most children with “classic” generalized epilepsy like EMA, a brain MRI (Magnetic Resonance Imaging) is typically normal [18]. However, structural and genetic causes are not mutually exclusive, and a normal MRI does not guarantee a genetic cause.

Your doctor may still order an epilepsy-protocol MRI—a high-resolution scan designed to find tiny structural changes—if:

  • The seizures seem to start in one specific spot or there are focal signs on examination [19].
  • Developmental progress slows down or starts to go backward (regression) [20][21].
  • The child does not respond to standard medications and the diagnosis is uncertain [19].

Finding a cause, whether genetic or structural, can be an emotional milestone. It provides a roadmap for what to expect and sometimes allows your doctors to refine treatments to your child’s needs.

Common questions in this guide

Is there one gene that causes epilepsy with myoclonic absences?
No. EMA is genetically heterogeneous, meaning different genetic changes may be involved, and researchers have not identified one gene that explains every case. Reported associations such as SETD1B, SYNGAP1, and SLC2A1 may occur in overlapping or rare presentations rather than in all children with EMA.
Which genetic tests may be used when a child has EMA?
Doctors may consider an epilepsy multi-gene panel, chromosomal microarray, or whole-exome sequencing. The best first test depends on your child’s seizure pattern, development, medical history, and the advice of a genetics team.
What does a VUS mean on an epilepsy genetic test?
A variant of uncertain significance, or VUS, is a DNA change whose medical meaning is not yet clear. It is not diagnostic by itself and should not alone determine medication changes or family-planning decisions; a genetic counselor or clinical geneticist can interpret it with the rest of your child’s information.
Does a child with generalized EMA still need a brain MRI?
Often, the MRI is normal in classic generalized EMA, but a normal scan does not prove that the cause is genetic. An epilepsy-protocol MRI may be recommended if seizures suggest a focal starting point, development regresses, medications do not control seizures, or the diagnosis is uncertain.
Could SLC2A1 testing identify a treatable cause of EMA?
Testing the SLC2A1 gene can help identify GLUT1 deficiency syndrome, in which the brain has difficulty getting enough glucose for energy. Finding this cause matters because a ketogenic or other specialized medical diet may be considered under medical supervision.
How can a genetic counselor help after my child’s testing?
A genetic counselor or clinical geneticist can explain what a result means, whether a change was inherited or arose for the first time in your child, and what is known about its health implications. They can also discuss privacy, consent, and possible implications for siblings or future family planning.

Questions For You

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Questions to Ask Your Doctor

Curated prompts to bring to your next appointment.

  1. 1.Given the diagnosis of EMA, which genetic test—an epilepsy panel, chromosomal microarray, or whole-exome sequencing—do you recommend as the first step?
  2. 2.If a 'variant of uncertain significance' (VUS) is found, what are the next steps to determine if it is actually causing my child's seizures?
  3. 3.Should we be testing specifically for the SLC2A1 gene to rule out GLUT1 deficiency, especially if the ketogenic diet might be a treatment option?
  4. 4.Does my child's developmental profile or the specific way their seizures look suggest we should look for genes like SETD1B or SYNGAP1?
  5. 5.Since EMA is a generalized epilepsy, is a brain MRI still necessary, and should it follow a specific 'epilepsy protocol'?
  6. 6.Can you refer us to a genetic counselor to help us understand how these results might affect our other children or future family planning?

References

References (21)
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    Dissecting the phenotypic and genetic spectrum of early childhood-onset generalized epilepsies.

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    Seizure 2019; (71()):222-228 doi:10.1016/j.seizure.2019.07.024.

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    SETD1B variants associated with absence seizures.

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    A Case of a Seven-Year-old boy with Epilepsy with Myoclonic Absence: Importance of Seizure Semiology, Genetic Etiology, and Electroencephalogram Correlation for Timely Intervention.

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This page explains genetic testing and MRI in epilepsy with myoclonic absences for informational purposes only; it does not replace professional medical advice. Your child’s neurologist and genetics team should interpret results and recommend care.