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Features include always present findings: Coarse facial features and Cryptorchidism; and very common findings: Short stature, Anteverted nares, Intellectual disability, and Global developmental delay and others. 89 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Lungs and breathing | 7 | Chronic lung disease, Aspiration pneumonia, Anomalous pulmonary venous return |
Head and neck | 7 | Coarse facial features, Round face, Microcephaly |
Digestive system | 5 | Gastroesophageal reflux, Constipation, Enlarged spleen (splenomegaly) |
Eyes | 5 | Cataract, Damage to the optic nerve (optic atrophy), Strabismus |
Heart and blood vessels | 5 | Ventricular septal defect, Abnormal heart morphology, Congestive heart failure |
Ears | 4 | Hearing loss (hearing impairment), Conductive hearing impairment, Inner ear hearing loss (sensorineural hearing impairment) |
Bones and joints | 4 | Cervical C2/C3 vertebral fusion, Abnormal skeletal morphology, Abnormal vertebral morphology |
Arms and legs | 4 | Abnormal fingernail morphology, Hypoplastic toenails, Abnormal toenail morphology |
Growth and development | 2 | Short stature, Decreased response to growth hormone stimulation test |
Brain and nerves | 2 | Intellectual disability, Global developmental delay |
Hormones | 2 | Hypothyroidism, Decreased response to growth hormone stimulation test |
Kidneys and urinary system | 1 | Horseshoe kidney |
Blood and immune system | 1 | Enlarged spleen (splenomegaly) |
Muscles | 1 | Damage to the optic nerve (optic atrophy) |
AFF4-related CHOPS syndrome is characterized by coarse facial features/ cognitive impairment, heart defects, obesity, pulmonary involvement, and short stature/ skeletal abnormalities. To date, 14 individuals with AFF4-related CHOPS syndrome have been reported in the literature [, , , , , ]. The following description of the phenotypic features associated with this condition is based on these reports. Table 2. AFF4-Related CHOPS Syndrome: Frequency of Select Features
Feature | % of Persons w/Feature | Comment |
|---|---|---|
Developmental delay | 100% (14/14) | Mild to moderate |
Characteristic craniofacial features | 100% (14/14) | Microcephaly, large anterior fontanel, coarse facial features, synophrys, highly arched eyebrows, long eyelashes, proptosis, anteverted nares |
AFF4 encodes ALF transcription elongation factor 4 (1,163 aa). Key component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. Highest expression in Artery Tibial (52.0 TPM) and Ovary (48.0 TPM).
Cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome is associated with mutations in the AFF4 gene on chromosome 5.
AFF4 is classified as a druggable target (Clinically Actionable and Transcription Factor categories) with score 0.0.
Penetrance is thought to be 100%, as all individuals with pathogenic AFF4 variants demonstrate clinical symptoms.
Source: GeneReviews — "AFF4-Related CHOPS Syndrome"
No consensus clinical diagnostic criteria for AFF4-related CHOPS syndrome have been published.
AFF4-related CHOPS syndrome should be considered in probands with the following clinical and imaging findings and family history.
Clinical findings
Source: GeneReviews — "AFF4-Related CHOPS Syndrome"
Genetic disorders with facial features overlapping those of AFF4-related CHOPS syndrome, developmental delay, and short stature of interest in the differential diagnosis of AFF4-related CHOPS syndrome are listed in .
Table 3.
AFF4-Related CHOPS Syndrome: Genetic Differential Diagnosis
Gene(s)/ GeneticMechanism | Disorder | MOI | Features Similar to AFF4-Related CHOPS Syndrome | Features Distinct from AFF4-Related CHOPS Syndrome
AFF3 | KINSSHIP syndrome (OMIM 619297) | AD | Short stature, characteristic facial features (incl coarse facial features), skeletal features, developmental delay | Not assoc w/obesity
ANKRD11 PV or16q24.3 deletionincl ANKRD11 | KBG syndrome | AD | Characteristic facial features, short stature, developmental delay | Macrodontia
| Bohring-Opitz syndrome | AD | Characte...
Source: GeneReviews — "AFF4-Related CHOPS Syndrome"
Genetic testing for AFF4 is available. Testing is considered confirmatory for diagnosis.
No approved treatments are currently available for cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome. The disease remains an area of unmet medical need.
No clinical practice guidelines for AFF4-related CHOPS syndrome have been published. In the absence of published guidelines, the following recommendations are based on the authors' personal experience managing individuals with this disorder.
To establish the extent of disease and needs in an individual diagnosed with AFF4-related CHOPS syndrome, the evaluations summarized (if not performed as part of the evaluation that led to diagnosis) are recommended.
Table 4.
AFF4-Related CHOPS Syndrome: Recommended Evaluations Following Initial Diagnosis
System/Concern | Evaluation | Comment
| 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 issues incl disruptive behaviors food-seeking behaviors
Constitutional
| Measurement of growth parameters |
| Eval of short stature/ obesity | Consider referral to endocrinologist.
| • Assessment for respiratory issues
Referral to pediatric pulmonologist otolaryngologist for those w/chronic lung disease, tracheomalacia, /or laryngomalacia
|
| Echocardiogram | To assess for congenital heart defects
| Orthopedics/ physical medicine rehab/ PT OT eval | To incl assessment of:
Source: GeneReviews — "AFF4-Related CHOPS Syndrome"
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 — "AFF4-Related CHOPS Syndrome"
View trials for cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia 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 6. AFF4-Related CHOPS Syndrome: Recommended Surveillance
System/Concern | Evaluation | Frequency |
|---|---|---|
Development | Monitor developmental progress educational needs. | At each visit Neurobehavioral/ Psychiatric |
Ophthalmologic involvement | Assess for myopia strabismus. | Frequency per treating ophthalmologist; at least annually |
Hearing | Audiology eval | Annually Feeding/ Gastrointestinal |
Source: GeneReviews — "AFF4-Related CHOPS Syndrome"
Phenotype severity distribution: 2 always present features, 10 very common features, 22 common features.
Estimated prevalence: <1 in 1,000,000 (VERY_RARE).
No clinical trials have been registered for cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome.
5 publications have been identified in PubMed for cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome. Research spans Case Report / Case Series (75%) and Basic Science / Preclinical (25%).
Gokdemir I (2026). [PMID: 42273204](https://pubmed.ncbi.nlm.nih.gov/42273204/). *Mol Syndromol*. [Case Report / Case Series]
Kerimoglu C (2026). [PMID: 42178648](https://pubmed.ncbi.nlm.nih.gov/42178648/). *Int J Paediatr Dent*. [Case Report / Case Series]
Sakata T (2025). [PMID: 39983729](https://pubmed.ncbi.nlm.nih.gov/39983729/). *Curr Biol*. [Basic Science / Preclinical]
Deng X (2025). [PMID: 40904637](https://pubmed.ncbi.nlm.nih.gov/40904637/). *Intractable Rare Dis Res*. [Case Report / Case Series]
Data assembled from 7 of 12 sources · Last updated Sep 20, 2026, 11:36 PM UTC
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center
Common questions about cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome
Obesity | 100% (14/14) | — |
Short stature | 92% (12/13) | — |
Pulmonary/respiratory involvement | 86% (12/14) | Chronic lung disease, tracheomalacia, laryngomalacia, subglottic stenosis, respiratory failure, apnea |
Heart defects | 79% (11/14) | Patent ductus arteriosus, ventricular septal defect |
Ocular abnormalities | 69% (9/13) | Cataracts, strabismus, astigmatism, myopia |
Hearing loss | 62% (8/13) | Sensorineural, conductive, or mixed |
Genitourinary abnormalities | 46% (6/13) | Horseshoe kidney, cryptorchidism, vesicoureteral reflux, kidney agenesis Developmental delay. All individuals with AFF4-related CHOPS syndrome have mild-to-moderate developmental delay. |
Source: GeneReviews — "AFF4-Related CHOPS Syndrome"