Chromosome 3q13.31 deletion syndrome is a rare genetic condition where a small piece is missing (deleted) from the long arm of chromosome 3, in a region called 3q13.31. This missing piece removes one copy of several important genes that help the brain, body growth, and other organs develop in a normal way. Because these genes are partly “switched off,” children usually have developmental delay, learning problems, low muscle tone (they feel floppy), and special facial features.
Chromosome 3q13.31 deletion syndrome is a rare genetic condition where a small piece of DNA is missing from the long arm (q arm) of chromosome 3, around the 3q13.31 region. This loss affects genes that are important for brain and body development, so many children have developmental delay, low muscle tone, learning problems, and special facial features. [¹]
Doctors call this a “microdeletion” syndrome because the missing part is too small to see with a simple chromosome test, and usually needs a detailed test such as chromosomal microarray to find it. The condition is very rare, with an estimated frequency of fewer than 1 in 1,000,000 people worldwide, and the signs can be very different from one person to another, even in the same family.
Other names
Chromosome 3q13.31 deletion syndrome has several other names that mean almost the same thing. Common synonyms include 3q13 microdeletion syndrome, chromosome 3q13 microdeletion syndrome, del(3)(q13), and monosomy 3q13. All of these names describe a missing (deleted) segment in the 3q13 region on chromosome 3.
In medical databases and research articles, you may also see codes or labels such as OMIM 615433, ORPHA1621, or MONDO:0014185 attached to this syndrome. These codes help doctors and scientists find the same condition across different genetic and rare disease registries, even when the written name is slightly different.
Types
1. Isolated 3q13.31 microdeletion (classic form)
In the “classic” type, only the 3q13.31 region is deleted and the rest of the chromosomes look normal. These people usually show the most typical features: developmental delay, overgrowth after birth, low muscle tone, and distinctive facial appearance such as a broad forehead, short space between nose and upper lip, and protruding lips.
2. Larger 3q13 deletions including 3q13.31
Some patients have a bigger deletion that covers 3q13.31 and nearby regions (for example 3q13 to 3q21). These larger deletions may cause more severe or extra problems, such as more serious learning difficulties, brain structure changes like partial absence of the corpus callosum, or additional organ problems, because more genes are missing.
3. De novo (new) 3q13.31 deletion
In many families, the 3q13.31 deletion happens for the first time in the child and is not found in either parent. This is called a de novo deletion. It usually occurs by chance when the egg or sperm is formed, or just after conception, so the parents did nothing to cause it and could not have prevented it.
4. Inherited 3q13.31 deletion from a carrier parent
In some families, a parent carries the same deletion or a balanced chromosome change that can produce the deletion in children. When a parent has a balanced rearrangement (for example a balanced translocation involving 3q13.31), they may be healthy but can pass an unbalanced form to a child, leading to 3q13.31 deletion syndrome with clinical features.
5. Mosaic 3q13.31 deletion
Rarely, only some cells in the body have the deletion, while other cells are normal; this is called mosaicism. A person with mosaic 3q13.31 deletion may have milder signs or a more patchy pattern of symptoms, because not all tissues carry the missing piece of chromosome.
Causes
1. Random chromosomal error during egg or sperm formation
The most common cause is a random mistake when chromosomes are copied and divided to form eggs or sperm. A small piece of chromosome 3 at 3q13.31 can break off and be lost, so the child receives only one copy instead of two. This process is usually accidental and is not under anyone’s control.
2. Chromosomal error shortly after fertilization
Sometimes the deletion happens just after the egg and sperm join to form the first embryo cells. As the embryo grows, these cells divide and pass on the missing piece to many body cells. This early error can still cause the full syndrome, even if both the egg and sperm were normal.
3. De novo 3q13.31 microdeletion with no family history
In many reported patients, the deletion is de novo, meaning it appears for the first time in the affected child and is not seen in the parents’ blood tests. These cases help doctors understand that most 3q13.31 deletions are new events rather than inherited problems.
4. Inherited unbalanced translocation involving 3q13.31
If a parent carries a balanced translocation that involves the 3q13.31 region, a child may inherit an unbalanced form where part of 3q13.31 is missing. The child then develops 3q13.31 deletion syndrome because they have too little genetic material from that region, even though the parent may appear healthy.
5. Larger interstitial deletion of chromosome 3q including 3q13.31
Some deletions cover a broader area like 3q13.3–3q21.2. In these cases, the 3q13.31 region is included inside a bigger missing block. The clinical picture then reflects the loss of genes in 3q13.31 plus additional genes, often leading to a wider neurodevelopmental disorder.
6. Haploinsufficiency of the ZBTB20 gene
Research suggests that losing one copy of the ZBTB20 gene, which lies in 3q13.31, may be a key cause of developmental delay, distinctive facial features, and overgrowth in this syndrome. When only one working copy of ZBTB20 is present, the gene cannot fully perform its normal role in brain and body development.
7. Haploinsufficiency of the DRD3 gene
The DRD3 gene, also in the deleted region, codes for a dopamine receptor important in brain signaling. Deletion of one copy may contribute to movement problems, behavior changes, and psychiatric symptoms, such as those reported in some adults with 3q13.31 microdeletion.
8. Haploinsufficiency of the GAP43 gene
The GAP43 gene plays a role in nerve growth and wiring of the brain. Losing one copy in the 3q13.31 deletion may lead to problems with learning, speech, and autistic features in some patients, by disturbing normal connections between brain cells.
9. Haploinsufficiency of the LSAMP gene
The LSAMP gene encodes a protein involved in brain development and emotional behavior. Deletion of LSAMP inside the 3q13.31 region is thought to contribute to anxiety, behavioral problems, and possibly psychiatric illness in some affected individuals.
10. Combined loss of multiple 3q13.31 genes
Most patients lose a block of several genes together, not just one. The combined effect of losing multiple genes (for example ZBTB20, DRD3, GAP43, LSAMP and others) likely explains the wide range of developmental, growth, and facial features seen in this syndrome.
11. MicroRNA loss within the deleted region
Some 3q13.31 deletions also remove small regulatory RNA molecules (microRNAs). These microRNAs normally help control how other genes are turned on and off. Their loss may change brain signaling and contribute to neurodevelopmental and psychiatric features.
12. Parental germline mosaicism
In rare situations, a parent may have some egg or sperm cells with the 3q13.31 deletion, even if their blood test appears normal. This is called germline mosaicism and can cause more than one child in the family to have the syndrome, even though both parents test negative in standard blood studies.
13. Advanced parental age as a general risk factor
For many chromosomal microdeletions, older maternal or paternal age may slightly increase the chance of random chromosome errors, although data for 3q13.31 specifically are limited. This is a general risk factor for chromosomal changes, not a direct proven cause for every case.
14. Exposure of germ cells to radiation or toxins (theoretical)
High doses of radiation or certain toxic chemicals can damage DNA in egg or sperm cells and might increase the risk of chromosome breaks and deletions. However, for 3q13.31 deletion syndrome, most cases appear random, and such exposures are rarely identified in families.
15. Structural chromosome instability in a parent
Some people have a subtle structural rearrangement or fragile site in chromosome 3 that makes breaks more likely. This can predispose to the creation of the 3q13.31 deletion in their children, especially when chromosomes swap pieces during reproduction.
16. Complex chromosomal rearrangements involving chromosome 3
Occasionally, a child’s chromosomes show complex rearrangements like inversions or insertions that involve 3q13.31. In these complex cases, the deletion of 3q13.31 is one part of a larger chromosome pattern that leads to the clinical syndrome.
17. Larger genomic imbalance including duplications elsewhere
A few patients may have both a deletion at 3q13.31 and a duplication of material from another chromosome. The combined imbalance can worsen developmental problems and organ malformations beyond what the 3q13.31 deletion alone would cause.
18. Overlap with nearby chromosomal syndromes
When deletions extend beyond 3q13.31, features can overlap with other 3q syndromes, which may affect how the condition presents and is labelled. These overlapping deletions are still rooted in the primary cause of missing genetic material around 3q13.31.
19. Chance (sporadic) genetic event with unknown trigger
In many families, doctors cannot identify any clear environmental trigger, parental chromosome change, or specific risk factor. The deletion is then considered a sporadic event, meaning it happened by chance during normal cell division, which is unfortunately a part of nature.
20. Inherited autosomal dominant pattern in some families
When a parent has the same 3q13.31 deletion and also shows features, the condition can follow an autosomal dominant pattern: each child has a 50% chance of inheriting the deletion. However, the severity can be very different even within the same family.
Symptoms
1. Global developmental delay
Most children with 3q13.31 deletion syndrome have delays in sitting, standing, walking, and learning skills compared with other children of the same age. They may need extra help in school and therapy to reach their milestones.
2. Intellectual disability or learning difficulty
Many affected people have mild to moderate intellectual disability or specific learning problems. They often need special education support, but the degree of difficulty can vary widely, even between people with similar deletions.
3. Speech and language delay
Speech often develops late, and some children say their first words much later than expected. Expressive language (speaking) is often more affected than understanding, and speech therapy is commonly needed.
4. Low muscle tone (hypotonia)
Babies may feel floppy when held and can have trouble lifting their head, rolling over, or sitting without support. This low muscle tone can also affect feeding and later motor skills like running or climbing stairs.
5. Postnatal overgrowth or tall stature
Many children grow faster than expected after birth and can be taller or bigger than average for their age. This overgrowth is often seen together with a large head size and may be linked to the loss of growth-regulating genes in the 3q13.31 region.
6. Macrocephaly (large head)
Some patients have a larger than average head circumference. This feature can be part of the syndrome’s growth pattern and may accompany changes in brain structure seen on imaging.
7. Distinctive facial features
Typical facial features can include a broad and prominent forehead, wide-set eyes (hypertelorism), folds of skin at the inner corners of the eyes (epicanthic folds), down-slanting eye openings, droopy eyelids (ptosis), a short space between the nose and upper lip (short philtrum), and full or protruding lips with a full lower lip and high-arched palate.
8. Abnormal male genitalia
Boys may have small or underdeveloped genitalia, undescended testicles, or other genital differences. These findings reflect the role of the deleted genes in urogenital development.
9. Brain malformations such as corpus callosum anomalies
Some individuals show missing or underdeveloped corpus callosum (the band of nerve fibers connecting the two brain hemispheres) or other brain anomalies on MRI. These structural changes can contribute to developmental delay and movement or coordination problems.
10. Skeletal abnormalities
Skeletal differences may include spine curvature, unusual bone shapes, or limb anomalies. These changes vary but are reported in a significant number of patients and may need orthopedic evaluation.
11. Behavioral and psychiatric features
Some people with 3q13.31 deletion syndrome have behavioral differences like attention problems, anxiety, or mood disorders. A few adults have been reported with schizophrenia or nonverbal learning disability, suggesting that the deletion can affect mental health in later life.
12. Autism spectrum features
Autistic traits such as difficulties with social interaction, repetitive behaviors, or restricted interests have been described in several patients. The loss of brain-related genes like GAP43 is believed to contribute to these autism-like features.
13. Feeding difficulties in infancy
Babies may have weak sucking, poor coordination of sucking and swallowing, or reflux. These feeding problems are often linked to low muscle tone and can improve with time and feeding therapy.
14. Vision or eye movement problems
Strabismus (crossed or misaligned eyes), unusual eye slant, or other eye movement issues can occur. These may affect visual tracking and depth perception and often need review by an eye specialist.
15. Congenital organ anomalies (heart, kidneys, others) in some cases
A minority of patients have structural problems in the heart, kidneys, or other organs detected on imaging or during newborn checks. These anomalies are not present in everyone but can be part of the syndrome in some individuals.
Diagnostic tests
Physical examination tests
1. General pediatric physical examination
The doctor carefully looks at growth (weight, height, head size), body proportions, and general health. The combination of tall stature, large head, and certain facial features can raise suspicion for a chromosome 3q13.31 deletion and prompt genetic testing.
2. Dysmorphology (clinical genetics) examination
A clinical geneticist examines facial shape, eye position, ears, mouth, hands, feet, and body shape in detail. Recognizing a pattern—broad forehead, short philtrum, protruding lips, and hypotonia—helps the specialist consider 3q13.31 deletion syndrome among other microdeletion conditions.
3. Growth chart assessment
Height, weight, and head circumference are plotted on standardized charts over time. Many children with this syndrome show postnatal overgrowth and large head size compared with age-matched peers, which can be a clue that a growth-regulating genetic change is present.
4. Neurological physical examination
The neurologist checks muscle tone, reflexes, coordination, and movement patterns. Findings such as low muscle tone, delayed motor skills, or abnormal reflexes support the idea of an underlying neurodevelopmental syndrome like 3q13.31 deletion.
Manual and developmental tests
5. Standardized developmental assessment (e.g., Bayley or similar scales)
Psychologists or therapists use structured tests to measure cognitive, language, and motor development. The results help document the degree of delay and guide therapies, and when combined with physical signs, they point doctors toward genetic causes like 3q13.31 microdeletion.
6. Speech and language evaluation
Speech therapists assess understanding, expression, sound production, and communication skills. Marked speech delay with relatively better understanding, plus the typical physical signs, can support evaluation for this chromosome deletion.
7. Occupational therapy fine-motor assessment
Occupational therapists look at hand skills, daily living tasks, and sensory responses. Difficulties with fine motor tasks, such as using utensils or writing, together with hypotonia and developmental delay, are consistent with a global neurodevelopmental syndrome.
8. Behavioral and autism screening tools
Screening tools for autism or behavioral problems (for example, questionnaires used in clinics) help identify social communication issues and repetitive behaviors. Positive screens in a child with 3q13.31 features can guide further genetic testing and support services.
Laboratory and pathological tests
9. Chromosomal microarray analysis (CMA)
CMA is the key test for diagnosing 3q13.31 deletion syndrome. It scans all chromosomes to look for missing or extra DNA segments and can detect the small microdeletion at 3q13.31 that is too small to see on a standard karyotype. In most reported cases, this is how the diagnosis was confirmed.
10. Conventional karyotyping
A standard chromosome study can sometimes show large deletions or translocations involving chromosome 3, especially when the deleted segment is big. While it may miss small microdeletions, it is still useful to detect balanced rearrangements in parents that explain how the child inherited the unbalanced deletion.
11. FISH (fluorescence in situ hybridization) for 3q13.31 region
FISH uses fluorescent probes that attach to specific chromosome regions. Probes designed for 3q13.31 can confirm the deletion seen on microarray and are sometimes used for targeted testing of parents or other family members.
12. MLPA (multiplex ligation–dependent probe amplification)
MLPA can measure the copy number of selected genes in the 3q13.31 region. It is useful as a follow-up test to confirm the size and exact genes affected by the deletion or to screen relatives for the same deletion.
13. Targeted gene panel or exome sequencing
If symptoms suggest a complex neurodevelopmental disorder, doctors may order gene panel testing or exome sequencing. These tests can detect small sequence changes in genes and may identify other conditions or help rule out additional genetic causes alongside the 3q13.31 deletion.
14. Basic metabolic screening
Blood and urine tests for metabolic diseases (such as amino acid disorders or mitochondrial problems) may be done to rule out other treatable causes of developmental delay. Normal metabolic results with ongoing suspicion can push clinicians to look for chromosomal microdeletions like 3q13.31.
15. Endocrine and growth-hormone tests (when overgrowth or growth issues are present)
If a child shows very tall stature, unusual weight gain, or delayed puberty, doctors may check growth hormone and other hormone levels. These tests help rule out hormonal causes of growth problems and clarify that the pattern is linked to the chromosome deletion itself.
Electrodiagnostic tests
16. Electroencephalogram (EEG)
An EEG records the brain’s electrical activity. It may be used if there are suspected seizures, staring spells, or unusual movements. Some microdeletion syndromes are associated with seizures, and EEG helps detect abnormal electrical patterns even when seizures have not been clearly seen.
17. Nerve conduction studies and electromyography (EMG)
When there is significant hypotonia or weakness, doctors may use EMG and nerve conduction tests to see how well nerves and muscles work. In 3q13.31 deletion syndrome, these tests are often normal or show only mild changes, but they help rule out primary muscle or nerve diseases that could mimic the clinical picture.
Imaging tests
18. Brain MRI
Magnetic resonance imaging (MRI) can show detailed brain structures. In some patients with 3q13.31 deletion, MRI may reveal absence or underdevelopment of the corpus callosum and other brain malformations, which support the diagnosis and help explain the developmental and movement difficulties.
19. Echocardiogram (heart ultrasound)
If a heart murmur or other signs suggest a heart defect, an echocardiogram is done to examine heart chambers, valves, and blood flow. Some children with chromosome deletions, including 3q ones, can have congenital heart problems that need monitoring or treatment.
20. Abdominal and renal ultrasound; skeletal imaging
Ultrasound of the kidneys and abdomen can reveal structural abnormalities such as kidney malformations or other organ changes. X-rays or other skeletal imaging may be used to evaluate spine curvature, bone shape, or limb differences, which sometimes occur in this syndrome and can affect mobility and growth.
Non-Pharmacological Treatments
1. Early developmental intervention programs
This means starting help very early, often in infancy, with a team that may include physiotherapists, occupational therapists, and teachers. The purpose is to support sitting, walking, using the hands, and basic learning. The mechanism is simple: repeated, playful practice builds brain connections and helps the child slowly reach milestones, even if they come later than usual. [³]
2. Physiotherapy (physical therapy)
Physiotherapy uses exercises, stretching, and play to improve muscle strength, balance, and coordination. The purpose is to reduce low muscle tone (hypotonia), help the child move more safely, and prevent joint stiffness. The mechanism is repeated movement and muscle activation, which trains nerves and muscles to work together more effectively over time. [⁴]
3. Occupational therapy (OT)
OT focuses on daily skills such as holding objects, dressing, feeding, and writing. The purpose is to help the child become more independent at home and school. The mechanism is step-by-step training using adaptive tools, like special grips or splints, so the brain learns better ways to control the hands and body. [³]
4. Speech and language therapy
Many children with 3q13.31 deletion have delayed speech or unclear words. Speech therapy helps the child understand language and communicate using speech, signs, or pictures. The purpose is better communication and fewer frustrations. The mechanism is repeated practice of sounds, words, and social communication, which helps brain language centers develop. [³]
5. Feeding and swallowing therapy
Low muscle tone can cause weak sucking, slow feeding, or reflux. Feeding therapists show safe positions, special nipples, and thickened feeds if needed. The purpose is safe feeding, good weight gain, and less coughing or vomiting. The mechanism is changing posture, texture, and swallowing patterns to protect the airway and improve nutrition. [⁵]
6. Behavioral therapy (including autism-style support)
Some children show autism-like traits, attention problems, or meltdowns with change. Behavioral therapy teaches new coping skills and replaces unsafe behaviors with safer ones. The purpose is calmer daily life at home and school. The mechanism is structured routines, positive rewards, and teaching the child step-by-step what is expected in different situations. [³]
7. Special education and individualized learning plans (IEP)
Most children need extra help in school. A personalized plan sets small learning goals and includes extra time, visual supports, and flexible teaching methods. The purpose is to let the child learn at their own pace. The mechanism is breaking tasks into tiny steps and matching teaching style to the child’s strengths (for example, using pictures or hands-on tasks). [⁴]
8. Assistive communication devices (AAC)
If speech is very late or limited, devices like picture boards, tablets with communication apps, or simple symbol books can be used. The purpose is to give the child a “voice” even before speech improves. The mechanism is pairing symbols or buttons with words, so the child can tap or point to express needs, which reduces frustration and supports language development. [³]
9. Vision and hearing support
Some children may have eye movement problems or hearing loss. Glasses, patching, hearing aids, or surgery can be used. The purpose is to give the best possible sensory input for learning and safety. The mechanism is improving how clearly the brain receives sound and visual signals, which directly helps speech, school performance, and movement. [⁶]
10. Orthopedic and physiotherapy aids (braces, walkers, wheelchairs)
If walking is delayed or unstable, braces for ankles, standing frames, or walkers may be helpful. The purpose is safer movement and better posture. The mechanism is external support that holds joints in a stable position, reducing energy use and preventing deformities while the child grows. [⁵]
11. Behavioral and family counseling
Living with a rare disorder is stressful for the whole family. Counseling gives parents and siblings a space to talk about fears, stress, and plans for the future. The purpose is emotional support and better coping skills. The mechanism is guided discussion and problem-solving strategies that reduce anxiety and improve family communication. [³]
12. Sleep hygiene programs
Children with neurodevelopmental disorders often have sleep problems. A sleep program sets fixed bedtimes, screen limits, calm routines, and bedroom changes (light, noise). The purpose is better sleep for the child and parents. The mechanism is training the brain and body to link bedtime cues with sleep, which normalizes hormone patterns and mood. [⁷]
13. Nutritional counseling
Some children are underweight due to feeding issues. Others may gain too much due to low activity. Dietitians adjust calories, protein, fiber, and micronutrients. The purpose is healthy growth and energy. The mechanism is matching food type and amount to the child’s needs, reducing constipation, reflux, or obesity risk. [⁵]
14. Social skills groups
Older children and teens may struggle with social rules. Group sessions practice sharing, turn-taking, conversation, and coping with conflict. The purpose is better friendships and less isolation. The mechanism is repeated role-play in a safe setting, so the brain learns social patterns more clearly. [³]
15. Sensory integration therapy
Some children are very sensitive to noise, touch, or lights, while others seek strong sensory input. Sensory therapy uses swings, brushes, weighted blankets, and structured games. The purpose is to make daily sensations more tolerable. The mechanism is slowly exposing the nervous system to controlled input, teaching the brain to respond in a calmer way. [⁷]
16. Vocational and life-skills training (for adolescents and adults)
As the child grows, training moves to self-care, money handling, basic work tasks, and community skills. The purpose is maximum independence in adult life. The mechanism is step-by-step teaching with repetition and visual aids, allowing skills to become automatic over time. [⁸]
17. Genetic counseling for the family
Genetic counselors explain the cause of the deletion, recurrence risk in future pregnancies, and testing options for relatives. The purpose is informed family planning and reduced guilt or confusion. The mechanism is clear education using family trees and test results, turning complex science into understandable information. [¹]
18. Regular multidisciplinary follow-up clinics
Children benefit from review by a combined team (pediatrics, neurology, genetics, rehabilitation, and others). The purpose is early detection of new problems like seizures, spinal changes, or kidney issues. The mechanism is scheduled check-ups, tests, and coordinated care plans instead of crisis-based visits. [⁶]
19. Use of vision aids and low-vision training (if needed)
If there are structural brain or eye issues, low-vision specialists can teach larger print, high-contrast materials, and special lighting. The purpose is to use remaining vision as efficiently as possible. The mechanism is adapting the environment so the weak visual system can still gather enough clear information for reading and mobility. [⁶]
20. Surgery-linked rehabilitation (pre- and post-operative)
If the child needs heart, skeletal, or genital surgery, therapy before and after surgery helps recovery. The purpose is to maintain strength, breathing, and function through stressful procedures. The mechanism is targeted exercises and breathing work that prepare the body and then restore movement after hospital stays. [⁶]
Drug Treatments
Important: No medicine is currently approved specifically for “Chromosome 3q13.31 deletion syndrome.” Drugs below are used for common associated problems (such as seizures, ADHD, spasticity, sleep, or mood). Doses must always be chosen and adjusted by a specialist; families should never start or change these medicines on their own. [⁹]
For each drug: description (~100 words), class, general dosing concept, timing, purpose, mechanism, and major side-effects. Label information comes from FDA prescribing information on [accessdata.fda.gov]. [¹⁰]
1. Levetiracetam (Keppra®)
Levetiracetam is a modern antiepileptic drug used widely for focal and generalized seizures. It belongs to the “antiseizure medication” class. Usual pediatric doses are weight-based and divided twice daily, with slow increases guided by the neurologist. It is taken at the same times each day to keep blood levels steady. The purpose is to reduce or stop seizures that sometimes occur in chromosomal deletion syndromes. The exact mechanism is not fully known, but levetiracetam binds to the synaptic vesicle protein SV2A and calms overactive nerve firing. Common side-effects include irritability, sleepiness, and dizziness. [¹¹]
2. Valproic acid / Sodium valproate
Valproate is a broad-spectrum antiepileptic used for many seizure types and sometimes for mood stabilization. It is usually classed as a “broad-spectrum antiseizure drug.” Doses are calculated in mg/kg/day, divided two or three times daily, and adjusted based on blood levels and response. The purpose is seizure control when EEG shows generalized or mixed patterns. The mechanism includes increasing GABA (an inhibitory neurotransmitter) and stabilizing neuronal membranes. Side-effects can include weight gain, tremor, hair loss, liver toxicity, and, rarely, serious blood problems, so careful monitoring and avoidance in pregnancy are essential. [¹²]
3. Clonazepam
Clonazepam is a benzodiazepine used as an add-on drug for some seizure types and for severe anxiety. It is a “benzodiazepine antiepileptic and anxiolytic.” Doses are usually small and given once or twice daily, sometimes at bedtime. The purpose is short-term seizure suppression or calming severe agitation. The mechanism is boosting the effect of GABA at its receptors, making neurons less likely to fire excessively. Side-effects include sleepiness, drooling, poor coordination, and tolerance or dependence with long-term use, so doctors try to use the lowest effective dose and taper slowly if stopping. [¹³]
4. Baclofen (oral)
Baclofen is a muscle relaxant and antispastic agent used when a child has spasticity or painful muscle stiffness. It belongs to the “GABA-B agonist muscle relaxant” class. Doses start very low and are slowly increased, usually three times daily. The purpose is to make tight muscles more relaxed, improving comfort and range of motion. Mechanism: baclofen activates GABA-B receptors in the spinal cord and brain, reducing the release of excitatory neurotransmitters to muscles. Common side-effects are drowsiness, dizziness, weakness, and, with sudden stop, withdrawal symptoms, so tapering is required. [¹⁴]
5. Intrathecal baclofen (via pump, specialist use)
In severe spasticity that does not respond to tablets, baclofen can be delivered into the spinal fluid using a pump. This is still the same class of drug, but given directly to the central nervous system. Dosing is continuous and adjusted by the specialist team. The purpose is strong spasticity control with lower systemic doses. Mechanism is targeted GABA-B activation in the spinal cord. Side-effects can be life-threatening if the pump fails or the dose changes suddenly, including withdrawal or overdose, so close monitoring and emergency plans are needed. [¹⁴]
6. Risperidone (Risperdal®)
Risperidone is an atypical antipsychotic used in children for severe irritability and aggression associated with autism and other neurodevelopmental disorders. It belongs to the “second-generation antipsychotic” class. Pediatric doses start extremely low (for example 0.25–0.5 mg/day) and are carefully increased. The purpose is to reduce dangerous outbursts and intense self-injury. Mechanism: blocking dopamine D2 and serotonin 5-HT2 receptors, which stabilizes mood and behavior. Side-effects include weight gain, sedation, hormonal changes (prolactin rise), and movement disorders, so growth and metabolic markers need regular checks. [¹⁵]
7. Aripiprazole
Aripiprazole is another atypical antipsychotic approved for irritability in autism. It is considered a “dopamine D2 partial agonist antipsychotic.” Doses start low and are given once daily. The purpose is similar to risperidone: to calm severe aggression, mood swings, and self-harm behaviors. Mechanism: partial agonist activity at D2 receptors and serotonin modulation, which stabilizes dopamine signaling rather than simply blocking it. Side-effects include restlessness, weight gain, sleep problems, and rarely movement disorders; heart rhythm and metabolic health must be monitored. [¹⁶]
8. Atomoxetine (Strattera®)
Atomoxetine is a non-stimulant medicine for ADHD. It belongs to the “selective norepinephrine reuptake inhibitor” class. Doses are based on weight and taken once or twice daily, usually in the morning. The purpose is to improve attention, reduce impulsivity, and support school learning in children with strong attention problems. Mechanism: blocking norepinephrine reuptake in the brain, which increases its levels and improves focus. Side-effects include reduced appetite, stomach upset, sleep changes, and a small risk of suicidal thoughts, so close mood monitoring is essential. [¹⁷]
9. Methylphenidate
Methylphenidate is a stimulant commonly used for ADHD. It belongs to the “stimulant / dopamine-norepinephrine reuptake inhibitor” class. Doses are started low and adjusted in the morning and sometimes at midday. Purpose: improve attention and reduce hyperactivity to make learning and social behavior easier. Mechanism: blocking dopamine and norepinephrine reuptake in key brain areas, making signals clearer. Side-effects include decreased appetite, trouble sleeping, higher heart rate, and, rarely, mood changes or tics. Growth and heart health must be followed regularly. [¹⁸]
10. Melatonin
Melatonin is a hormone-based medicine used widely for sleep onset problems in children with neurodevelopmental disorders. It is often considered a “chronobiotic sleep aid.” Doses are usually small and given 30–60 minutes before bedtime. The purpose is to help the child fall asleep faster and develop a more regular sleep pattern. Mechanism: melatonin acts on brain receptors that set the body clock, aligning sleep with night-time. Side-effects are usually mild: morning drowsiness, vivid dreams, or headache, but long-term use should still be reviewed by a doctor. [¹⁹]
11. Proton-pump inhibitors (for reflux, e.g., omeprazole)
If reflux is severe, PPIs like omeprazole may be used. They are in the “proton-pump inhibitor” class. Doses are weight-based and given once daily, often before breakfast. Purpose: reduce stomach acid to relieve pain, vomiting, and feeding refusal. Mechanism: blocking the proton pump in stomach cells, which lowers acid production. Side-effects include diarrhea, constipation, headache, and, with long use, possible nutrient malabsorption or infection risk, so doctors aim to use the lowest effective dose for the shortest time. [²⁰]
12. Laxatives (e.g., polyethylene glycol)
Constipation is common with low muscle tone and low activity. Osmotic laxatives such as polyethylene glycol are often used. They are “osmotic agents.” Doses are based on weight and adjusted to achieve soft, painless stools. Purpose: prevent painful constipation, stool withholding, and poor appetite. Mechanism: drawing water into the bowel to soften stool and stimulate movement. Side-effects include bloating, cramps, or loose stools if the dose is too high. Adequate water intake is essential. [²⁰]
13. Selective serotonin reuptake inhibitors (SSRIs, e.g., sertraline)
In older children or adults, anxiety or depression may be significant. SSRIs like sertraline are “antidepressant / anxiolytic” drugs. Doses start very low and are increased slowly. Purpose: reduce persistent sadness, worry, and obsessive thoughts that limit daily functioning. Mechanism: blocking serotonin reuptake, increasing serotonin signaling in brain pathways for mood. Side-effects include stomach upset, sleep changes, activation (restlessness), or, rarely, suicidal thoughts early in treatment, so close supervision is needed. [²¹]
14. Antihypertensives like clonidine or guanfacine (for sleep / hyperactivity)
These medicines are originally blood pressure drugs but are also used for hyperactivity, impulsivity, and sleep in some children. They belong to the “alpha-2 adrenergic agonist” class. Doses are low and usually given in the evening and sometimes daytime. Purpose: calm hyperactivity, reduce tics, and support sleep. Mechanism: stimulating alpha-2 receptors in the brainstem to reduce sympathetic output. Side-effects include low blood pressure, dizziness, and daytime sleepiness, so blood pressure and heart rate must be checked. [²²]
15. Antiepileptic alternatives (e.g., lamotrigine, topiramate)
If first-line seizure drugs fail, others like lamotrigine or topiramate may be added. These are “antiepileptic drugs” with different mechanisms. Doses are carefully titrated over weeks. Purpose: better seizure control while balancing side-effects. Lamotrigine blocks sodium channels and stabilizes membranes; topiramate affects GABA and glutamate pathways. Side-effects may include rash (lamotrigine), cognitive slowing (topiramate), or weight changes. Skin and cognitive status must be watched closely. [¹¹]
16. Vitamin D and calcium (with AEDs or limited mobility)
Children taking certain antiepileptics or with low activity may have weaker bones. Vitamin D and calcium are “nutritional supplements.” Doses depend on age and blood levels. Purpose: protect bone mineral density and reduce fracture risk. Mechanism: vitamin D improves calcium absorption and bone formation. Side-effects are uncommon at proper doses but very high doses can cause high calcium and kidney problems, so monitoring is needed. [²³]
17. Multivitamin with iron (for poor intake)
Feeding problems can cause micronutrient deficits. A balanced multivitamin with iron is a “nutrient supplement.” Dose follows age instructions. Purpose: cover basic vitamin and iron needs when diet is limited. Mechanism: replacing missing vitamins and iron supports blood formation, immunity, and energy production. Side-effects include stomach upset or constipation if iron dose is high; stool may look darker but this is usually harmless. [²³]
18. Ketogenic diet (specialist-supervised)
Although not a “drug,” the ketogenic diet is used like a medical therapy for difficult seizures. It is a high-fat, very low-carb diet done under strict supervision. Purpose: reduce seizure frequency when medications are not enough. Mechanism: shifting metabolism to ketone bodies, which may stabilize neuronal activity. Side-effects include constipation, kidney stones, and nutrient gaps, so blood tests and dietitian input are essential. [²⁴]
19. Rescue seizure medicines (e.g., buccal or intranasal benzodiazepines)
For prolonged seizures, emergency benzodiazepines can be used. These are “short-acting benzodiazepine rescue medicines.” Dose is based on weight and given only as directed in a seizure plan. Purpose: stop long seizures quickly to prevent injury and hospital admission. Mechanism: strong activation of GABA receptors, rapidly calming electrical activity. Side-effects include drowsiness and slowed breathing, so caregivers must be trained and emergency services contacted if needed. [¹³]
20. Targeted treatments for associated organ problems
If the child has a heart defect, kidney anomaly, or endocrine issue, other drugs (like ACE inhibitors for blood pressure or hormone replacements) may be used. These belong to various classes, chosen by organ specialists. Purpose: protect organ function and prevent long-term damage. Mechanism and side-effects depend on the drug, so regular specialist follow-up is necessary. [⁶]
Dietary Molecular Supplements
(All supplements must be discussed with a doctor; some interact with medicines.)
Omega-3 fatty acids (DHA/EPA) – Support brain cell membranes, may help attention and mood. Usual pediatric doses are weight-based; mechanism is anti-inflammatory and membrane-stabilizing.
Vitamin D – Supports bones and immune function; mechanism is hormone-like action on calcium and immune cells.
Calcium – Needed for bones and nerve signals; works with vitamin D.
Iron – Prevents iron-deficiency anemia that can worsen fatigue and attention.
Zinc – Supports immune and enzyme function.
Magnesium – Helps nerve and muscle relaxation; low levels may worsen cramps or sleep problems.
B-complex vitamins (including B6, B12, folate) – Support energy, nerve function, and blood cells.
Probiotics – May improve gut health and constipation or diarrhea.
Fiber supplements (psyllium, inulin) – Help constipation when diet is low in fiber.
Specialized medical formulas – High-calorie, nutrient-dense drinks or feeds to support growth in children with poor oral intake. [²³]
Immunity-Booster, Regenerative and Stem-Cell–Related Drugs
At present, there are no approved stem cell or gene therapies specifically for 3q13.31 deletion syndrome. Supportive “immunity” and regenerative approaches focus on good nutrition, vaccines, and careful treatment of infections. Any experimental stem-cell trial must be done only in approved research centers. [²⁵]
Examples used in broader neuro or immune care (not specific to this syndrome):
Standard childhood vaccines and boosters – Protect against serious infections; mechanism is training the immune system to recognize germs.
Seasonal influenza and COVID-19 vaccines (where recommended) – Reduce risk of severe respiratory illness, especially important for children with developmental and feeding problems.
Immunoglobulin therapy (very selected cases) – Used only when there is proven antibody deficiency; provides ready-made antibodies.
Erythropoietin in anemia of chronic disease (specialist use) – Stimulates red blood cell production; used only in specific conditions.
Clinical-trial regenerative therapies – Research-only stem-cell or gene-directed therapies; families should ask about legitimate trials and avoid unregulated clinics.
Intensive nutritional and rehabilitation programs – Though not drugs, these act “regeneratively” by supporting plasticity of brain and muscles.
Surgeries
Heart defect repair – If congenital heart problems are present, cardiac surgery may close holes or repair valves. Purpose: improve blood flow and reduce heart failure risk. Procedure: done under general anesthesia with heart-lung bypass; recovery includes ICU care and long-term cardiology follow-up. [⁶]
Orthopedic surgery for skeletal abnormalities – Spinal curvature or hip dislocation may need correction. Purpose: improve posture, walking, and reduce pain. Procedure: bone cutting, reshaping, or fixation with plates or rods; physiotherapy follows to restore movement. [⁶]
Genital reconstruction in males with hypoplastic genitalia
Some boys have underdeveloped genitalia or undescended testes. Surgery aims to improve function, fertility potential, and appearance. Procedures may include orchiopexy (moving testes into the scrotum) or reconstructive steps; done by pediatric urologists. [¹]Ophthalmologic surgery (for strabismus or other eye issues)
If the eyes are misaligned, surgery can adjust eye muscles. Purpose: improve alignment, depth perception, and appearance. Procedure: tightening or loosening eye muscles under general anesthesia; often combined with glasses and vision therapy afterwards. [⁶]Gastrostomy tube placement (G-tube)
When feeding by mouth is unsafe or insufficient, a tube can be placed into the stomach. Purpose: provide reliable nutrition and medicine delivery. Procedure: endoscopic or surgical placement of a small tube; parents are trained to care for the site and use the tube at home. [⁵]
Preventions
Genetic counseling before future pregnancies – Understand recurrence risk and test options (like prenatal or pre-implantation testing).
Regular vaccinations and infection prevention – Protects lungs and general health.
Early therapy and school support – Prevents avoidable delays and secondary problems like contractures or severe learning gaps.
Safe feeding and reflux management – Lowers risk of aspiration pneumonia and malnutrition.
Monitoring for seizures and prompt treatment – Prevents injury and school setbacks.
Good dental and oral-motor care – Prevents pain and infections that worsen feeding.
Weight management and physical activity – Reduces obesity and joint strain.
Routine heart, kidney, and vision checks – Finds problems early when they are easier to manage.
Mental health and caregiver support – Prevents burnout and depression in the family.
Avoiding unproven “cure” clinics – Protects from risky, expensive, non-scientific treatments. [²⁶]
When to See Doctors
Parents should keep regular appointments with the child’s pediatrician, neurologist, geneticist, and therapists. You should seek urgent medical care if there are new or worsening seizures, severe feeding problems (choking, refusing all food, weight loss), high fever with breathing trouble, sudden change in behavior or consciousness, or signs of pain that the child cannot explain. Planned visits are also important when school difficulties increase, puberty begins, or major decisions (like surgery or transition to adult care) are coming. Early contact with the care team usually prevents small issues from becoming big crises. [²⁷]
What to Eat and What to Avoid
Eat: balanced meals with fruits, vegetables, whole grains, and protein to support growth and brain function.
Eat: enough protein (eggs, fish, beans, meat) to help muscles, especially when doing physiotherapy.
Eat: healthy fats (olive oil, nuts, seeds, fatty fish) which provide omega-3 and energy.
Eat: calcium- and vitamin-D–rich foods (milk, yogurt, fortified alternatives) for bones.
Eat: high-fiber foods (whole grains, lentils, vegetables) to reduce constipation.
Avoid: very sugary drinks and snacks that cause weight gain and dental problems.
Avoid: highly processed salty foods that can affect blood pressure and kidneys.
Avoid: choking-risk foods (hard nuts, large raw carrot pieces) if chewing and swallowing are weak.
Avoid: extreme diets or supplements without medical advice, especially in children.
Avoid: excess caffeine or energy drinks in teens, as they may worsen sleep and heart rate. [²³]
Frequently Asked Questions (FAQs)
1. Is there a cure for Chromosome 3q13.31 deletion syndrome?
No. The chromosome change is present in every cell and cannot currently be “fixed.” Treatment focuses on symptoms and on helping the child reach their best possible level of independence through therapy, education, and medical support. Research into gene-based and regenerative treatments is ongoing but is not yet routine care. [¹]
2. Will my child always be delayed?
Most children have lifelong learning and developmental differences, but many make steady progress with early and ongoing support. They may reach milestones later and may always need some help, but the exact outcome is highly variable. It depends on deletion size, other health issues, and the quality of therapy, school support, and family environment. [²]
3. Is this syndrome inherited?
Often the deletion happens “de novo,” which means it is a new change at conception and not inherited from either parent. In some families, a parent may carry a balanced rearrangement or mosaic change. Genetic testing of parents and counseling can clarify the pattern and the risk for future pregnancies. [¹]
4. How is the diagnosis made?
Doctors suspect the syndrome based on developmental delay, low muscle tone, and physical features. The diagnosis is confirmed using chromosome microarray or similar genetic testing, which can see small deletions around 3q13.31. Sometimes additional tests like MRI, heart ultrasound, or kidney imaging are done to look for associated findings. [³]
5. What specialists should follow my child?
A typical team includes a pediatrician or developmental pediatrician, neurologist, clinical geneticist, rehabilitation specialist, physiotherapist, occupational therapist, speech therapist, dietitian, and sometimes cardiologist, nephrologist, ophthalmologist, and child psychiatrist or psychologist. The exact mix depends on the child’s problems. [⁶]
6. Can my child go to regular school?
Some children may attend mainstream classes with support, while others do better in special education settings. Decisions are based on learning level, behavior, and local resources. Individualized education plans and classroom aides often make inclusion more successful. [⁴]
7. Does every child with this syndrome have seizures?
No. Seizures are reported in some patients with 3q13-region deletions and related conditions, but not all. If there are episodes of staring, jerking, or unusual movements, an EEG may be done. Medicines like levetiracetam or valproate are used if seizures are confirmed. [¹¹]
8. Are behavior problems part of the syndrome?
Behavior difficulties, autism-like traits, anxiety, or attention problems are common in many neurodevelopmental syndromes and have been reported in 3q13.31 deletions. Good structure, clear routines, behavioral therapy, and, in some cases, medicines can improve daily life a lot. [³]
9. Will my child’s condition get worse with age?
This is not a degenerative disease. Most problems are developmental, not progressive damage. However, challenges can change with age: school demands increase, puberty may bring new emotional or behavioral issues, and orthopedic or weight problems may appear. Regular follow-up helps catch and manage these changes early. [⁸]
10. Can anything be done before birth?
If a couple already knows they carry a structural rearrangement involving 3q13, prenatal testing or pre-implantation genetic testing may be possible. For most families, the deletion is only discovered after a child is born. Prenatal interventions cannot correct the deletion; care focuses on informed planning and postnatal support. [¹]
11. Are special diets needed?
There is no single “3q13.31 diet.” The focus is on balanced nutrition, preventing under- or overweight, and managing reflux or constipation. In difficult epilepsy, a ketogenic diet may be suggested by specialists. Any strong diet change should be supervised by a dietitian and doctor. [²⁴]
12. Is physical activity safe?
Yes, and it is usually very helpful. Gentle, regular activity such as swimming, walking, and adapted sports helps muscles, joints, weight control, and mood. Activities should be adjusted to the child’s abilities, with safety precautions for balance or seizure risk. [⁴]
13. What is the life expectancy?
Data are limited because the syndrome is rare, but published adult cases show that some people live into adulthood. Life expectancy depends mainly on the presence and severity of major organ problems (heart, lungs, kidneys) and seizures, and on access to good medical care and nutrition. [⁸]
14. How can families find support?
Support can come from rare-disease organizations, online parent groups for chromosome 3 disorders, local disability services, and hospital social workers. These groups share practical tips, school guidance, and emotional support, which often makes daily life easier. [²]
15. What is the most important thing parents can do?
The most important actions are: stay connected to a trusted medical team; start early therapies; keep vaccines and check-ups up to date; support good nutrition and sleep; and advocate for school and social services. Small, steady steps over many years are usually more powerful than any single treatment. [²]
Disclaimer: Each person’s journey is unique, treatment plan, life style, food habit, hormonal condition, immune system, chronic disease condition, geological location, weather and previous medical history is also unique. So always seek the best advice from a qualified medical professional or health care provider before trying any treatments to ensure to find out the best plan for you. This guide is for general information and educational purposes only. Regular check-ups and awareness can help to manage and prevent complications associated with these diseases conditions. If you or someone are suffering from this disease condition bookmark this website or share with someone who might find it useful! Boost your knowledge and stay ahead in your health journey. We always try to ensure that the content is regularly updated to reflect the latest medical research and treatment options. Thank you for giving your valuable time to read the article.
The article is written by Team RxHarun and reviewed by the Rx Editorial Board Members
Last Updated: January 16, 2026.
