A guide for families, caregivers, and adults navigating SETD5 Syndrome.
SETD5 Syndrome is a rare genetic neurodevelopmental disorder caused by a disease-causing change that reduces the function of one copy of the SETD5 gene on chromosome 3. This gene regulates how other genes are switched on and off during development. When one copy doesn't function correctly, it can lead to a range of developmental, behavioral, medical, and physical features, though no two individuals are exactly alike.
The condition was first identified in published research in 2014 (see Sources & References), which means it is still relatively new to researchers and clinicians. See the Symptoms & Features tab for a full breakdown of common features.
You may see it listed under several names in medical records or research papers. All refer to the same condition, and you may encounter any of them in reports, research, or conversations with your care team:
There is no single official count, and the answer depends on what is being counted. Two figures are often cited, and they mean different things.
About 250 worldwide, identified in a clinic. Simons Searchlight, an international patient registry and research program for rare genetic conditions, estimates that about 250 people around the world have been identified with SETD5 Syndrome as of 2026. This is an estimate rather than an exact count, and it keeps growing as genetic testing becomes more widely available.
Described in published research. The exact number of unique individuals described in published research is not known. Across the studies summarized in our research guide, individuals with SETD5 Syndrome have been described in the medical literature starting with the first cases reported in 2014.
These numbers differ because being diagnosed in a clinic and being written up in a research paper are two separate things. Many people who have a diagnosis have never taken part in a published study, so the number identified worldwide is larger than the number found in the research.
Syndrome describes a recognizable pattern of features that tend to appear together, which is why "SETD5 Syndrome" has become the most widely used name among families.
Disorder refers to how the condition disrupts typical development and functioning. "Neurodevelopmental disorder" is the clinical category, alongside conditions like autism spectrum disorder.
Disease is a broad medical term for a condition that affects normal body structure or function. Many families use "syndrome" or "disorder" day-to-day, but you may encounter "disease" in research papers or insurance contexts.
In published case series, most reported SETD5 Syndrome cases have been de novo (meaning the genetic change arose spontaneously and was not passed down from either parent). Families may want to discuss inheritance with a genetic counselor, as each family's situation is different.
In a minority of families, however, one parent may carry the same genetic change and pass it on to their child. After a SETD5 Syndrome diagnosis, genetic testing of parents may be recommended to determine whether the variant is de novo or inherited, which can affect the recurrence risk for future pregnancies.
Recurrence risk depends on whether parents carry the variant. Your genetic counselor can explain specific risks for your family, including possibilities like germline mosaicism (where a genetic variant is present in some of a parent's egg or sperm cells, even if it is not detected in a routine blood test) that may affect future pregnancies.
Based on published research, SETD5 is believed to function as a chromatin regulator. Chromatin is the material that makes up chromosomes, a combination of DNA and proteins that keeps your genetic instructions organized. SETD5 helps regulate gene activity through its role in chromatin-related processes. Researchers are still studying exactly how it works.
Research suggests that when one copy of SETD5 doesn't function properly, the balance of gene expression during brain development may be disrupted. This is called haploinsufficiency: one working copy of the gene isn't enough to carry out its full function.
Think of SETD5 as a volume knob for development. It helps turn genes up or down at the right moments. Everyone has two copies of this knob. In SETD5 Syndrome, one knob is either missing or not working. The single working copy can't keep everything properly tuned, so changes in SETD5 function can disrupt normal patterns of gene activity during development. That's what haploinsufficiency means: one copy isn't enough.
SETD5 Syndrome is diagnosed through genetic testing. Many families receive the diagnosis after years of searching for answers, a process sometimes called a "diagnostic odyssey." If you are newly diagnosed, know that the testing has now given you a specific answer, which may help guide next steps and make it easier to seek out appropriate specialists and support.
We have a plain-language guide that walks you through what every section means: classifications, databases, variant types, and what to ask your genetics team.
To understand genetic variants, it can be helpful to think of human DNA as a massive instruction manual. Genes are the specific chapters within that manual that tell the body how to grow, develop, and function. Every person has two copies of most genes, one inherited from each parent. Sometimes, there is a change in the text of those instructions. In genetics, any change to the standard DNA sequence is called a variant. Variants can happen in a few different ways:
A mutation is like a spelling mistake within a word in the instruction manual. The chapter is still there, but one or more of the "letters" (the DNA sequence) is swapped out, altered, or scrambled. Depending on where this spelling mistake happens, it can make the instructions unreadable or change their meaning, preventing the gene from working properly.
A deletion is like having a paragraph, a page, or an entire chapter ripped out of the instruction manual. A piece of the DNA is completely missing. The deleted copy can no longer provide its normal instructions. For genes such as SETD5, one remaining working copy is not enough for normal function.
A duplication is like having an extra page or chapter accidentally printed and inserted into the manual. Instead of the standard two copies of a gene, there are three or more. A duplication involving SETD5 is interpreted separately. Increased SETD5 dosage is not an established cause of SETD5 Syndrome.
Most genes in the human body come in pairs, as we inherit one copy from each parent. For many genes, if one copy is missing or has a mutation that stops it from working, the second copy can pick up the slack. The body still makes enough of the necessary protein, and everything functions normally.
However, for some genes, one working copy is not enough. These genes require both working copies to develop and function correctly.
When a mutation or deletion causes one copy of such a gene to stop working, the single remaining copy is left to do all the work. For these specific genes, the remaining working copy is not enough for normal function.
This mechanism is called haploinsufficiency ("haplo" meaning half, and "insufficiency" meaning not enough).
Because SETD5 is a haploinsufficient gene, having only one working copy instead of two is believed to be the primary underlying cause of the developmental and physical features associated with SETD5 Syndrome. Research into the exact mechanisms is ongoing.
SETD5 Syndrome can result from a loss-of-function variant in SETD5 or from a deletion that removes one copy of the gene. Both disrupt the gene's function in a similar way, and both can result in a diagnosis of SETD5 Syndrome, though, as with all features of this condition, the experience varies from person to person. A deletion at chromosome 3p25.3 may include SETD5 along with other nearby genes. SETD5 loss may contribute to the person's features, while other deleted genes may also have an effect.
Some families have a larger chromosomal deletion in the 3p25 region that includes SETD5 along with several neighboring genes. In those cases, the full set of features your child experiences may be somewhat broader because more than one gene is affected. If this applies to your child, your genetics team can help you understand which features are related to SETD5 and which may be connected to the other genes in the deletion.
One neighboring gene worth noting is BRPF1, which sits close to SETD5 on chromosome 3p25. Deletions that span both SETD5 and BRPF1 have been reported in individuals with intellectual disability and additional features. Mattioli et al. (2017) described a series of individuals with BRPF1 mutations or deletions involving the 3p25 region, some of whom also had SETD5 involved. Notably, ptosis (drooping eyelid) and blepharophimosis (an unusually narrow eye opening) are features more specifically associated with loss of BRPF1 function, rather than SETD5 alone. If your child has a larger deletion that spans both genes and these particular eye features are present, they may be connected to BRPF1. If your child's report mentions a larger 3p25 deletion, your genetics team can help clarify which genes are included and what that may mean for your child's features.
In most reported cases, SETD5 Syndrome arises from a de novo variant, meaning the genetic change was not inherited from a parent and occurred for the first time in the affected individual. However, in a smaller number of families, a parent has been found to carry the same variant. This is called incomplete penetrance: a person can carry a disease-causing SETD5 variant without showing clear features of the condition.
One documented example comes from Powis et al. (2018), who described a mother with normal intelligence who carried the same SETD5 variant as her two sons, both of whom had developmental delays and intellectual disability. Cases like this are uncommon but they show that a SETD5 variant can sometimes be inherited from a parent who appears largely unaffected.
When a parent is found to carry the same SETD5 variant as their affected child but appears unaffected, it can raise complicated questions. It does not mean the variant is harmless. The reasons for this variability are not fully understood. A genetic counselor can help explain what this means for recurrence risk in future pregnancies.
Families sometimes ask whether the specific type of genetic change, such as a point mutation versus a deletion of the gene, will predict how their child is affected. Based on current research, genotype does not reliably predict phenotype in SETD5 Syndrome. Individuals with very similar genetic changes can have significantly different outcomes.
This variability has been reported across published studies. The reasons are not fully understood, and current research does not allow a person's development or medical features to be reliably predicted from their specific SETD5 variant. What this means practically is that no genetic report can tell you in advance exactly how your child will develop. Outcomes in SETD5 Syndrome span a wide range.
When a genetic test is performed, the laboratory analyzes a person's DNA to identify variants, which are differences from the standard reference sequence. For each variant, the laboratory evaluates whether there is enough evidence to determine its effect on health. When the available evidence is not sufficient to classify a variant as either disease-causing or harmless, it is designated a Variant of Uncertain Significance, or VUS.
Laboratories classify variants using standardized criteria, most commonly the guidelines published by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP). These criteria weigh several lines of evidence, including how frequently the variant occurs in the general population, whether it has been reported in other people with the condition, its predicted effect on the gene and its protein, and the results of laboratory functional studies. A variant is classified as a VUS when these lines of evidence are incomplete or conflicting, so a definitive classification cannot yet be made.
Genetic variation is common, and every person carries many variants that have no effect on health. A VUS classification does not mean a variant is harmful. It means that more data are needed before the variant can be classified as pathogenic (disease-causing) or benign (harmless).
A duplication involving SETD5 is interpreted separately. Increased SETD5 dosage is not an established cause of SETD5 Syndrome. Variant classifications are not permanent. As more individuals are tested and laboratories share evidence through public databases such as ClinVar, the data supporting a variant can grow, and a variant classified as a VUS today may later be reclassified as pathogenic or benign.
This list describes features found in published research. It is not a prediction of what your child or you will experience. Every person with SETD5 Syndrome is different, and no single feature shows up in everyone.
How much any feature affects daily life can vary a great deal, even between people with the same type of genetic change. Some individuals have very few challenges; others face more. This list covers features found in published research and may not include everything; researchers are still learning. Bring any specific questions to your care team.
Not sure what a term means? The Medical Terms Guide explains many of the words used on this page in plain language.
SETD5 Syndrome is a rare genetic condition caused by a disease-causing change that reduces the function of one copy of the SETD5 gene, or by a deletion of the region of chromosome 3 that contains it. It is a neurodevelopmental condition, meaning it affects how the brain develops. Common features include developmental delay, intellectual disability, and autism spectrum traits, though how it affects each person varies widely. You can read more on this Understanding SETD5 Syndrome page.
Reported features include developmental delay, intellectual disability, autism spectrum traits, speech and language delays, low muscle tone, feeding difficulties in infancy, and distinctive facial features. Some individuals also have heart, hearing, growth, or skeletal differences. Features and their impact differ from person to person, even among people with the same genetic change. See the full list on our At a Glance page.
SETD5 Syndrome is diagnosed through genetic testing that identifies a change in the SETD5 gene or a deletion of the 3p25 region of chromosome 3 that includes SETD5. Genetic testing may include exome sequencing, gene-panel testing, or chromosomal microarray, depending on the type of genetic change being evaluated. Genetic test results are typically interpreted with a genetics professional. Our Understanding Your Genetic Report page explains how to read these results.
In most reported cases the genetic change happens for the first time in the affected person (called a de novo variant) and was not inherited from a parent. In a smaller number of families, a variant can be passed down. A genetic counselor can explain what the specific change means for your family and any future pregnancies.
SETD5 (SET domain containing 5) is the name of the gene. Search terms such as "set5," "SETD 5," or "set d5" may appear as informal variations or misspellings, but they are not separate medical names for the condition. You may also see the condition called SETD5-related intellectual disability or SETD5 haploinsufficiency; these refer to the same underlying condition. If the diagnosis came from a small chromosome deletion at 3p25.3 rather than a variant within the SETD5 gene, you may also see it called 3p25.3 microdeletion syndrome or 3p25 microdeletion syndrome. A deletion involving SETD5 can cause SETD5 haploinsufficiency. If the deletion also includes other nearby genes, those genes may also contribute to the person's features. This is explained in Understanding Mutations and Deletions below.
A new diagnosis can feel overwhelming. A practical first step is to connect with others and gather information at your own pace. Our Family Toolkit brings together guides for medical appointments, school support, and everyday life.
Because SETD5 Syndrome was first identified around 2014, long-term data on aging and life expectancy in people with SETD5 Syndrome is still limited. The effect of SETD5 Syndrome on life expectancy has not been established.
This information is for general understanding and does not replace advice from your own care team.