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3q29 microdeletion syndrome is a recurrent subtelomeric deletion syndrome with variable clinical manifestations including intellectual deficit and dysmorphic features.
Features include: Gait ataxia, Failure to thrive, Aggressive behavior, and Autism and 21 more.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 6 | Gait ataxia, Aggressive behavior, Anxiety |
Head and neck | 4 | Thin upper lip vermilion, Narrow face, Microcephaly |
Arms and legs | 3 | Long fingers, Tapered finger, Clinodactyly of the 5th finger |
Growth and development | 1 | Failure to thrive |
Age of onset: infancy.
3q29 recurrent deletion is characterized by neurodevelopmental and/or psychiatric manifestations. Other common findings are failure to thrive, feeding problems, gastrointestinal disorders, ocular issues, dental anomalies, and congenital heart defects. To date more than 200 affected individuals have been identified. The summary below is based on the comprehensive review of all reported individuals in , the self-reported findings in 44 individuals from the 3q29 Deletion Registry , and deep phenotyping of 32 individuals . Table 2. 3q29 Recurrent Deletion: Frequency of Select Features
Feature | % of Personsw/Feature | Comment |
|---|---|---|
DD | 70%-90% | Speech delay (60%), motor delay |
ID | 30%-40% | Mild to moderate (34%), severe (5%) |
ADHD | 63% | — |
Anxiety disorders |
The 3q29 recurrent deletion should be considered in individuals with the following clinical findings :
Developmental delay typically including speech and motor delays
Intellectual disability; mild to moderate (34%), severe (5%)
Neuropsychiatric disorders including attention-deficit/hyperactivity disorder, anxiety disorders, and/or autism spectrum disorder (ASD)
Failure to thrive and/or feeding problems in infancy that persist into childhood
Gastrointestinal disorders including gastroesophageal reflux disease
Ocular issues
Dental anomalies
Congenital heart defects, especially patent ductus arteriosus
Subtle facial dysmorphology including a prominent forehead, prominent nasal tip, and thin vermilion of the upper lip
Source: GeneReviews — "3q29 Recurrent Deletion"
The differential diagnosis of the 3q29 recurrent deletion is broad due to the variable spectrum and presence of relatively common abnormal phenotypes that occur in affected individuals including developmental delay, learning problems, and neuropsychiatric disorders. All manifestations of the 3q29 recurrent deletion can also be seen in individuals with other genomic disorders.
Source: GeneReviews — "3q29 Recurrent Deletion"
Biomarker and diagnostic research for chromosome 3q29 microdeletion syndrome has been reported in the published literature.
No approved treatments are currently available for chromosome 3q29 microdeletion syndrome. The disease remains an area of unmet medical need.
To establish the extent of disease and needs in an individual diagnosed with the 3q29 recurrent deletion, the evaluations summarized (if not performed as part of the evaluation that led to diagnosis) are recommended.
Table 3.
Recommended Evaluations Following Initial Diagnosis in Individuals with 3q29 Recurrent Deletion
System | Evaluation | Comment
Neuro-
developmental | Eval by developmental pediatrician /or clinical psychologist | • Eval for developmental needs early intervention (e.g., PT, speech-language therapy, cognitive behavioral therapy for social skills training)
Eval of fine motor function (e.g., OT)
Eval for ASD, cognitive ability, for executive function deficits
| Eval by child/adult psychiatrist | Eval for anxiety disorders, ADHD, emerging features of prodrome/psychosis
| • Eval for seizures if indicated
Eval of muscle tone
Brain MRI to identify posterior fossa anomalies
| Referral to neurologist as needed
Musculo-
skeletal | Clinical exam for chest anomalies, flat feet, scoliosis | Referral to orthopedist as needed
| • Assess growth feeding
Assess for signs/symptoms of GER, constipation, /or chronic diarrhea
|
| Ophthalmology exam | To assess vision, evaluate for refractive errors, identify strabismus
| Dental eval for abnormal enamel tooth shape number | Initial pediatric dental eval by age 1 yr
| Eval by cardiologist echocardiogram for congenital heart disease |
Ears, nose
Source: GeneReviews — "3q29 Recurrent Deletion"
Search ClinicalTrials.gov in the US and EU Clinical Trials Register in Europe for access to information on clinical studies for a wide range of diseases and conditions. Note: There may not be clinical trials for this disorder.
Source: GeneReviews — "3q29 Recurrent Deletion"
1 trial found
Table 5. Recommended Surveillance for Individuals with 3q29 Recurrent Deletion
System/Concern | Evaluation | Frequency |
|---|---|---|
Development | Monitor developmental progress educational needs. | At each visit throughout early childhood Psychiatric/ |
Behavioral | Behavioral assessment for anxiety, attentional difficulties, emerging symptoms of schizophrenia prodrome or psychosis | Annual evals; more often if symptoms begin to emerge or medication is necessary Neurologic |
Scoliosis | Clinical exam for scoliosis | Annually throughout childhood Feeding |
Ocular issues | Ophthalmology exam vision screening for refractive errors strabismus | As recommended by ophthalmologist |
Dental anomalies | Eval w/pediatric dentist throughout childhood for abnormal enamel, tooth shape number | Every 6 mos or more frequently as recommended by pediatric dentist |
Ears, nose, throat | Assess for recurrent otitis epistasis. | At each visit Enuresis |
Source: GeneReviews — "3q29 Recurrent Deletion"
Estimated prevalence: Unknown (Unknown prevalence).
1 clinical trial registered. Interventions under study include other interventions. Research is primarily sponsored by academic and government institutions.
9 publications have been identified in PubMed for chromosome 3q29 microdeletion syndrome. Research spans Case Report / Case Series (56%), Diagnostic / Biomarker (11%), and Review / Meta-Analysis (11%).
Choi N (2026). [PMID: 41479269](https://pubmed.ncbi.nlm.nih.gov/41479269/). *J Clin Lab Anal*. [Diagnostic / Biomarker]
Pollak RM (2025). [PMID: 38216835](https://pubmed.ncbi.nlm.nih.gov/38216835/). *J Autism Dev Disord*. [Epidemiology / Natural History]
Lin R (2025). [PMID: 40747102](https://pubmed.ncbi.nlm.nih.gov/40747102/). *Front Genet*. [Case Report / Case Series]
Boyd BM (2025). [PMID: 39189835](https://pubmed.ncbi.nlm.nih.gov/39189835/). *Am J Med Genet A*. [Case Report / Case Series]
Zhao J (2024). [PMID: 38684312](https://pubmed.ncbi.nlm.nih.gov/38684312/). *Zhonghua Yi Xue Yi Chuan Xue Za Zhi*. [Case Report / Case Series]
Zhou B (2024). [PMID: 39042694](https://pubmed.ncbi.nlm.nih.gov/39042694/). *Proc Natl Acad Sci U S A*. [Basic Science / Preclinical]
Pollak RM (2024). [PMID: 37354284](https://pubmed.ncbi.nlm.nih.gov/37354284/). *J Autism Dev Disord*. [Case Report / Case Series]
Biswal SR (2024). [PMID: 39001960](https://pubmed.ncbi.nlm.nih.gov/39001960/). *Mol Biol Rep*. [Review / Meta-Analysis]
Belnekar M (2024). [PMID: 39412938](https://pubmed.ncbi.nlm.nih.gov/39412938/). *J Cancer Res Ther*. [Case Report / Case Series]
Data assembled from 7 of 12 sources · Last updated Sep 19, 2026, 1:12 PM UTC
Patient Advocacy Groups (PAGs) provide support, resources, and community for patients and caregivers.
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center
Common questions about chromosome 3q29 microdeletion syndrome
Generalized anxiety disorder, separation anxiety, social anxiety disorder, specific phobias |
ASD | 38% | Executive function |
deficits | 46% | Graphomotor |
weakness | 78% | Psychosis/ |
Schizophrenia | 20% | %s based on a small sample of young persons still at risk for these manifestations; prevalence is likely higher. Musculoskeletal |
concerns | 84% | Chest deformities (41%) GI issues / |
Nutrition feeding | 80% | Pediatric feeding disorder (60%), gastroesophageal reflux (50%), failure to thrive (44%), constipation (41%) |
Ocular phenotypes | 59% | Strabismus (28%) |
Dental anomalies | 41% | — |
Allergies | 28% | Congenital heart |
defects | 25% | Recurrent ear |
infections | 22% | — |
Epistaxis | 22% | May require surgical mgmt. Additional bleeding disorders have not been reported to date. |
Enuresis | 22% | Cause is unknown to date. |
Sleep disturbance | 31% | Reported in persons of all ages Posterior fossa abnormalities on |
brain MRI | 71% | Cerebellar vermis hypoplasia (33%), retrocerebellar arachnoid cyst (29%) ADHD = attention-deficit/hyperactivity disorder; ASD = autism spectrum disorder; DD = developmental delay; GI = gastrointestinal; ID = intellectual disability Speech delay is reported in 60% of individuals. |
Source: GeneReviews — "3q29 Recurrent Deletion"