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Features include always present findings: Hypertonia, Thin vermilion border, Micrognathia, and Intellectual disability and others; and common findings: Strabismus, Microcephaly, Delayed speech and language development, and Low muscle tone (hypotonia) and others. 100 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 14 | Dystonia, Anxiety, Enlarged brain ventricles (ventriculomegaly) |
Arms and legs | 6 | Prominent fingertip pads, Tapered finger, Finger syndactyly |
Head and neck | 5 | Microcephaly, Thin upper lip vermilion, Coarse facial features |
Bones and joints | 5 | Sideways curvature of the spine (scoliosis), Excessive outward curvature of the upper spine (kyphosis), Joint hypermobility |
Digestive system | 3 | Gastroesophageal reflux, Chronic constipation, Feeding difficulties |
Eyes | 2 | Strabismus, Ptosis |
Growth and development | 2 | Short stature, Failure to thrive |
Muscles | 2 | Shrinkage of the cerebellum (cerebellar atrophy), Low muscle tone (hypotonia) |
Ears | 1 | Hearing loss (hearing impairment) |
Blood and immune system | 1 | Recurrent infections |
Heart and blood vessels | 1 | Ventricular septal defect |
To date, more than 100 individuals have been identified with a pathogenic variant in CTCF . Table 2. Select Features of CTCF-Related Disorder
Feature | % of Persons w/Feature | Comment |
|---|---|---|
Developmental delay/ intellectual disability | 91% | Both speech motor delays have been described. |
Feeding difficulties/ growth problems | 66% | Most typically poor growth in infancy |
Eye anomalies | 56% | Most commonly strabismus or refractive errors |
Musculoskeletal anomalies | 53% | Most commonly scoliosis |
Behavioral issues | 52% | — |
Hypotonia | 45% | Which may contribute to motor delay feeding difficulties |
Tooth anomalies | 39% | Most typically crowded teeth abnormal decay |
Sleep disturbance | 34% | — |
Gastrointestinal issues | 34% | Incl constipation /or GERD |
ASD or autistic features | 31% | — |
Low weight | 29% | — |
Microcephaly | 26% | — |
Recurrent infections | ~26% | No primary immune deficiency in affected persons has been reported, although 1 person had low IgA levels.1 |
Palatal anomalies | 25% | — |
Genitourinary anomalies | 25% | — |
Hearing loss | 24% | Both sensorineural conductive hearing loss have been reported. |
Short stature | 23% | — |
Congenital heart defects | 22% | — |
Seizures | 18% | No consistent type has been reported. Adapted from ASD = autism spectrum disorder; GERD = gastroesophageal reflux disease; IgA = immunoglobulin A 1. Developmental delay (DD) and intellectual disability (ID). |
Source: GeneReviews — "CTCF-Related Disorder"
CTCF encodes CCCTC-binding factor (727 aa). Chromatin binding factor that binds to DNA sequence specific sites and regulates the 3D structure of chromatin. Highest expression in Cells EBV-transformed lymphocytes (53.0 TPM) and Brain Cerebellar Hemisphere (51.4 TPM).
Intellectual disability-feeding difficulties-developmental delay-microcephaly syndrome is associated with mutations in the CTCF gene on chromosome 16.
The CTCF protein participates in CHD8 and CHD7 bind CTCF, CHD8:CTCF-dependent repression of maternal IGF2 gene expression, and HOXA3 chromatin is activated pathways.
CTCF is classified as a druggable target (Clinically Actionable and Transcription Factor categories) with score 0.0.
No consistent genotype-phenotype correlations have been identified .
Source: GeneReviews — "CTCF-Related Disorder"
No consensus clinical diagnostic criteria for CTCF-related disorder have been published.
CTCF-related disorder should be considered in probands with the following clinical findings and family history.
Clinical findings
Mild-to-profound developmental delay (DD) or intellectual disability (ID)
AND
Source: GeneReviews — "CTCF-Related Disorder"
The phenotypic features associated with CTCF-related disorder are not sufficient to diagnose this condition clinically; therefore, all conditions in which affected individuals have developmental delay and/or intellectual disability without other distinctive findings should be considered in the differential diagnosis, especially if the condition is also associated with feeding difficulties and growth deficiency. See OMIM Phenotypic Series for genes associated with:
• Autosomal dominant intellectual developmental disorder
• Autosomal recessive intellectual developmental disorder
• Nonsyndromic X-linked intellectual developmental disorders
• Syndromic X-linked intellectual developmental disorders
Source: GeneReviews — "CTCF-Related Disorder"
Genetic testing for CTCF is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for intellectual disability-feeding difficulties-developmental delay-microcephaly syndrome has been reported in the published literature.
No approved treatments are currently available for intellectual disability-feeding difficulties-developmental delay-microcephaly syndrome. The disease remains an area of unmet medical need.
No clinical practice guidelines for CTCF-related disorder have been published.
To establish the extent of disease and needs in an individual diagnosed with CTCF-related disorder, the evaluations summarized (if not performed as part of the evaluation that led to diagnosis) are recommended.
Table 3.
CTCF-Related Disorder: Recommended Evaluations Following Initial Diagnosis
System/Concern | Evaluation | Comment
| Measurement of growth parameters | To assess for poor growth, short stature, microcephaly
| Assessment for palatal anomalies /or dental anomalies | Consider referral to a craniofacial clinic.
Gastrointestinal/
| Gastroenterology/ nutrition/ feeding team eval | • To incl eval of aspiration risk, nutritional status, GERD, constipation
Consider eval for feeding therapy or gastrostomy tube placement in affected persons w/dysphagia /or aspiration risk.
Assess for intestinal malrotation GI anomalies prior to gastrostomy tube placement.
| Neurologic eval | • To incl brain MRI as clinically indicated
Consider EEG if seizures are a concern.
| Developmental assessment | • To incl motor, adaptive, cognitive, speech-language eval
Eval for early intervention/ special education
Neurobehavioral/
| Neuropsychiatric eval | For persons age 12 mos: screening for concerns incl sleep disturbances, ADHD, anxiety, /or findings suggestive of ASD
Source: GeneReviews — "CTCF-Related 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 — "CTCF-Related Disorder"
View trials for intellectual disability-feeding difficulties-developmental delay-microcephaly syndrome
To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, the evaluations summarized in are recommended. Table 5. CTCF-Related Disorder: Recommended Surveillance
System/Concern | Evaluation | Frequency |
|---|---|---|
Cardiovascular | Standard follow up w/cardiologist if anomalies are detected.1 | As clinically indicated |
Dental | Dental eval | At least annually or as clinically indicated |
Eyes | Ophthalmology eval | At least annually or as clinically indicated |
Hearing | Audiology eval | At least annually through childhood or as clinically indicated |
Source: GeneReviews — "CTCF-Related Disorder"
Phenotype severity distribution: 6 always present features, 8 common features.
Estimated prevalence: <1 in 1,000,000 (VERY_RARE).
No clinical trials have been registered for intellectual disability-feeding difficulties-developmental delay-microcephaly syndrome.
224 publications have been identified in PubMed for intellectual disability-feeding difficulties-developmental delay-microcephaly syndrome. Kisho has analyzed 161 by research type. Research spans Case Report / Case Series (30%), Review / Meta-Analysis (29%), and Basic Science / Preclinical (18%).
Research Type | Count | % of Total |
|---|---|---|
Patient case studies | 49 | 30% |
Research summaries | 46 | 29% |
Laboratory research | 29 | 18% |
Disease patterns and progression | 17 | 11% |
Testing and diagnosis research | 10 | 6% |
Other research | 5 | 3% |
New treatment approaches | 3 | 2% |
Clinical study results | 2 | 1% |
Shah M (2026). [PMID: 29083768](https://pubmed.ncbi.nlm.nih.gov/29083768/). *Unknown Journal*. [Other]
Winters R (2026). [PMID: 31334998](https://pubmed.ncbi.nlm.nih.gov/31334998/). *Unknown Journal*. [Other]
Pichon E (2026). [PMID: 41025404](https://pubmed.ncbi.nlm.nih.gov/41025404/). *Movement disorders clinical practice*. [Review / Meta-Analysis]
Anderson EN (2026). [PMID: 41468891](https://pubmed.ncbi.nlm.nih.gov/41468891/). *American journal of human genetics*. [Case Report / Case Series]
Zhao Y (2026). [PMID: 41705901](https://pubmed.ncbi.nlm.nih.gov/41705901/). *Prenat Diagn*. [Review / Meta-Analysis]
Hindermann M (2026). [PMID: 41729076](https://pubmed.ncbi.nlm.nih.gov/41729076/). *JCI Insight*. [Basic Science / Preclinical]
Xu X (2026). [PMID: 42138082](https://pubmed.ncbi.nlm.nih.gov/42138082/). *J Clin Invest*. [Basic Science / Preclinical]
Daley SF (2026). [PMID: 31985954](https://pubmed.ncbi.nlm.nih.gov/31985954/). *Unknown Journal*. [Other]
Liman MNP (2026). [PMID: 32644338](https://pubmed.ncbi.nlm.nih.gov/32644338/). *Unknown Journal*. [Other]
Tripathi M (2026). [PMID: 36256770](https://pubmed.ncbi.nlm.nih.gov/36256770/). *Unknown Journal*. [Other]
Data assembled from 7 of 12 sources · Last updated Sep 20, 2026, 3:06 PM UTC
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center