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Features include always present findings: Generalized hypotonia, Micropenis, Weakness of facial musculature, and Difficulty swallowing (dysphagia) and others; and very common findings: Strabismus, Intellectual disability, Global developmental delay, and Motor delay and others. 67 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 12 | Seizure, Gait ataxia, Ataxia |
Head and neck | 8 | Microcephaly, Triangular face, Weakness of facial musculature |
Muscles | 5 | Generalized hypotonia, Shrinkage of the cerebellum (cerebellar atrophy), Weakness of facial musculature |
Digestive system | 2 | Gastroesophageal reflux, Difficulty swallowing (dysphagia) |
Eyes | 1 | Strabismus |
Growth and development | 1 | Short stature |
Arms and legs | 1 | Tapered finger |
Pregnancy and birth | 1 | Decreased fetal movement |
Age of onset: infancy, before birth.
EBF3 neurodevelopmental disorder (EBF3-NDD) is associated with developmental delay, intellectual disability, speech delay, gait or truncal ataxia, hypotonia, behavioral problems, and facial dysmorphism. Less common issues can include genitourinary abnormalities, gastrointestinal involvement, and/or musculoskeletal involvement. To date, 42 symptomatic individuals from 39 families have been reported [, , , , , , , , , , , , , ]. The following description of the phenotypic features associated with this condition is based on these reports (when information is available on these features). Developmental delay (DD) and intellectual disability (ID). All affected individuals have developmental delay noted in early infancy.
Source: GeneReviews — "EBF3 Neurodevelopmental Disorder"
EBF3 encodes EBF transcription factor 3 (596 aa). Transcriptional activator. Recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' Highest expression in Adipose Subcutaneous (37.0 TPM) and Nerve Tibial (25.6 TPM).
Hypotonia, ataxia, and delayed development syndrome is caused by mutations in the EBF3 gene on chromosome 10.
EBF3 is classified as a druggable target (Transcription Factor category) with score 0.0.
No genotype-phenotype correlations have been identified.
Source: GeneReviews — "EBF3 Neurodevelopmental Disorder"
No consensus clinical diagnostic criteria for EBF3 neurodevelopmental disorder have been published.
EBF3 neurodevelopmental disorder (EBF3-NDD) should be considered in individuals with the following clinical and brain MRI findings and family history. Clinical findings include developmental delay (DD) or intellectual disability (ID) AND any of the following features presenting in infancy or childhood:
Source: GeneReviews — "EBF3 Neurodevelopmental Disorder"
Because the phenotypic features associated with EBF3 neurodevelopmental disorder are not sufficient to diagnose this condition, all disorders with intellectual disability without other distinctive findings should be considered in the differential diagnosis. See OMIM Autosomal Dominant, Autosomal Recessive, Nonsyndromic X-Linked, and Syndromic X-Linked Intellectual Developmental Disorder Phenotypic Series. Note: Hereditary ataxia syndromes can also be considered in children presenting with developmental delay or intellectual disability in combination with ataxia (see Hereditary Ataxia Overview). In a cohort of 50 children with ataxia, genetic alterations involving EBF3 (including 1 multigene deletion) were identified in three children .
Source: GeneReviews — "EBF3 Neurodevelopmental Disorder"
Genetic testing for EBF3 is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for hypotonia, ataxia, and delayed development syndrome has been reported in the published literature.
No approved treatments are currently available for hypotonia, ataxia, and delayed development syndrome. The disease remains an area of unmet medical need.
No clinical practice guidelines for EBF3 neurodevelopmental disorder (EBF3-NDD) have been published. Evaluations Following Initial Diagnosis To establish the extent of disease and needs in an individual diagnosed with EBF3-NDD, the evaluations summarized (if not performed as part of the evaluation that led to diagnosis) are recommended. Table 2. Recommended Evaluations Following Initial Diagnosis in Individuals with EBF3 Neurodevelopmental Disorder
System/Concern | Evaluation | Comment |
|---|---|---|
Constitutional | Measure height, weight, head circumference. | Attention to possible feeding issues /or poor weight gain |
Neurologic | Neurologic eval | To incl brain MRI (if not performed at time of diagnosis) when there are specific neurologic findings of concern |
Dysarthria | Speech language eval | To determine need for speech language therapy /or alternate means of communication Developmental |
delay | Developmental assessment | To incl motor, adaptive, cognitive, speech/language eval; Eval for early intervention / special education Psychiatric/ |
Behavioral | Neuropsychiatric eval | Persons age 12 mos: screen for behavior concerns incl sleep disturbances, ADHD, anxiety, /or traits suggestive of ASD. Musculoskeletal / Activities of |
Source: GeneReviews — "EBF3 Neurodevelopmental Disorder"
Ataxia and intellectual disability could result in frequent falls in childhood; supervision of patient activity at home is recommended to limit the risk.
Source: GeneReviews — "EBF3 Neurodevelopmental Disorder"
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 — "EBF3 Neurodevelopmental Disorder"
View trials for hypotonia, ataxia, and delayed development syndrome
Table 4.
Recommended Surveillance for Individuals with EBF3 Neurodevelopmental Disorder
System/Concern | Evaluation | Frequency
| • Measurement of growth parameters
Eval of nutritional status safety of oral intake
| At each visit
| Monitor for constipation.
| Assess for new manifestations such as ataxia.
| Monitor developmental progress educational needs.
Psychiatric/
| Behavioral assessment for new manifestations incl anxiety, attention, aggressive or self-injurious behavior
| Physical medicine, OT/PT assessment of mobility, self-help skills
| Follow up of vesicoureteral reflux, renal dysplasia, cryptorchidism | Per treating urologist
Family/
| Assess family need for social work support (e.g., palliative/respite care, home nursing, other local resources) care coordination. | At each visit
OT = occupational therapy; PT = physical therapy
Source: GeneReviews — "EBF3 Neurodevelopmental Disorder"
Phenotype severity distribution: 5 always present features, 5 very common features, 31 common features.
Estimated prevalence: <1 in 1,000,000 (VERY_RARE).
No clinical trials have been registered for hypotonia, ataxia, and delayed development syndrome.
200 publications have been identified in PubMed for hypotonia, ataxia, and delayed development syndrome. Research spans Basic Science / Preclinical (28%), Review / Meta-Analysis (24%), and Case Report / Case Series (24%).
Research Type | Count | % of Total |
|---|---|---|
Laboratory research | 56 | 28% |
Research summaries | 48 | 24% |
Patient case studies | 48 | 24% |
Disease patterns and progression | 25 | 13% |
Testing and diagnosis research | 10 | 5% |
Other research | 6 | 3% |
Clinical study results | 4 | 2% |
New treatment approaches | 3 | 2% |
Vermeulen-Kalk K (2026). [PMID: 42378039](https://pubmed.ncbi.nlm.nih.gov/42378039/). *J Clin Invest*. [Other]
Nunes IS (2026). [PMID: 41087597](https://pubmed.ncbi.nlm.nih.gov/41087597/). *J Hum Genet*. [Case Report / Case Series]
Warmoeskerken T (2026). [PMID: 41821414](https://pubmed.ncbi.nlm.nih.gov/41821414/). *Am J Med Genet A*. [Diagnostic / Biomarker]
Yue SL (2026). [PMID: 41652658](https://pubmed.ncbi.nlm.nih.gov/41652658/). *Am J Med Genet A*. [Epidemiology / Natural History]
Doganli C (2026). [PMID: 42550797](https://pubmed.ncbi.nlm.nih.gov/42550797/). *PLoS Biol*. [Basic Science / Preclinical]
Ge Y (2026). [PMID: 41545737](https://pubmed.ncbi.nlm.nih.gov/41545737/). *Eur J Pediatr*. [Case Report / Case Series]
Chen N (2026). [PMID: 41233206](https://pubmed.ncbi.nlm.nih.gov/41233206/). *Journal of medical genetics*. [Basic Science / Preclinical]
Chattannavar G (2026). [PMID: 41486651](https://pubmed.ncbi.nlm.nih.gov/41486651/). *Ophthalmic Genet*. [Case Report / Case Series]
van der Laan L (2026). [PMID: 41028553](https://pubmed.ncbi.nlm.nih.gov/41028553/). *European journal of human genetics : EJHG*. [Diagnostic / Biomarker]
Lyu Q (2026). [PMID: 41370039](https://pubmed.ncbi.nlm.nih.gov/41370039/). *J Mol Cell Biol*. [Basic Science / Preclinical]
Data assembled from 8 of 12 sources · Last updated Sep 18, 2026, 11:51 PM UTC
Online Mendelian Inheritance in Man
European rare disease database
daily living | Orthopedics / physical medicine rehab / PT/OT eval | To incl assessment of:; Gross motor fine motor skills; Contractures, clubfoot, kyphoscoliosis; Ataxia; Mobility, activities of daily living, need for adaptive devices |
Gastrointestinal | Gastroenterology | If indicated, assessment for GERD, dysphagia, constipation |
Genitourinary | Kidney urinary tract eval | To assess for vesicoureteral reflux, cryptorchidism, neurogenic bladder, renal dysplasia; Ultrasound eval of kidney urinary bladder Genetic |
counseling | By genetics professionals1 | To inform affected persons their families re nature, MOI, implications of EBF3-NDD to facilitate medical personal decision making Family support/ resources |
Treatment of Manifestations in Individuals with EBF3 Neurodevelopmental Disorder Manifestation/Concern | Treatment | Considerations/Other Developmental delay / |
Intellectual disability | See . | Poor weight gain / |
Failure to thrive | Feeding therapy; gastrostomy tube placement may be required for persistent feeding issues. | Low threshold for clinical feeding eval /or radiographic swallowing study if clinical signs or symptoms of dysphagia |
Bowel dysfunction | Monitor for constipation. | Stool softeners, prokinetics, osmotic agents, or laxatives as needed Family/Community |