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Any Coffin-Siris syndrome in which the cause of the disease is a mutation in the ARID1A gene.
Features include always present findings: Delayed eruption of teeth, Strabismus, Coarse facial features, and Thick vermilion border and others; and common findings: Hearing loss (hearing impairment), Short stature, Seizure, and Low muscle tone (hypotonia) and others. 48 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 5 | Seizure, Intellectual disability, Global developmental delay |
Head and neck | 5 | Coarse facial features, Microcephaly, Cleft palate |
Eyes | 3 | Strabismus, Ptosis, Visual impairment |
Arms and legs | 3 | Absent fifth toenail, Absent fifth fingernail, Short distal phalanx of finger |
Growth and development | 2 | Short stature, Intrauterine growth retardation |
Ears | 1 | Hearing loss (hearing impairment) |
Muscles | 1 | Low muscle tone (hypotonia) |
Bones and joints | 1 | Delayed skeletal maturation |
Digestive system | 1 | Feeding difficulties |
Skin | 1 | Small nail |
Blood and immune system | 1 | Recurrent infections |
Heart and blood vessels | 1 | Abnormal heart morphology |
Age of onset: at birth.
The clinical manifestations of Coffin-Siris syndrome have expanded over the years as greater phenotypic variability has been recognized. Classically, the syndrome was first identified by the absence or underdevelopment of the fifth digit finger/toe or nail. Additional "classic" features have included sparse scalp hair, hypertrichosis, learning and developmental differences, and various organ system-related anomalies. As genetic technology has evolved, more individuals with subtle physical exam findings are being diagnosed with CSS. To date, at least 550 individuals have been identified with a diagnosis of Coffin-Siris syndrome, including those enrolled in the Coffin-Siris syndrome/ BAF complex registry [; ; ; ; ; ; S Schrier Vergano, unpublished data]. ARID1B has been reported in around 1% of cohorts of individuals with neurodevelopmental disorder . The following description of the phenotypic features associated with this condition is based on these reports. Table 2. Select Features of Coffin-Siris Syndrome
Feature | % of Persons w/Feature | Comment |
|---|---|---|
Developmental delay/ intellectual disability | 98% |
ARID1A encodes AT-rich interaction domain 1A (2,285 aa). Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Highest expression in Cells EBV-transformed lymphocytes (51.5 TPM) and Thyroid (42.8 TPM).
Intellectual disability, autosomal dominant 14 is associated with mutations in the ARID1A gene on chromosome 1.
The ARID1A protein participates in Formation of neuronal progenitor BAF (npBAF) pathway.
ARID1A is classified as a druggable target (Clinically Actionable category) with score 1.9.
No consensus clinical diagnostic criteria for Coffin-Siris syndrome (CCS) have been published.
CSS should be suspected in individuals with the following clinical findings and family history:
Clinical findings
Source: GeneReviews — "Coffin-Siris Syndrome"
Genes of interest in the differential diagnosis of Coffin-Siris syndrome (CSS) are listed in . Table 4. Genes of Interest in the Differential Diagnosis of Coffin-Siris Syndrome
Gene(s) | Disorder | MOI | Clinical Characteristics | Comment |
|---|---|---|---|---|
SMC3 | Cornelia de Lange syndrome (CdLS) | ADXL1 | Severe (classic) CdLS is characterized by distinctive facial features, growth restriction, hypertrichosis, upper limb reduction defects that range from subtle phalangeal abnormalities to oligodactyly (missing digits). | CdLS-related limb anomalies may incl 5th finger hypoplasia similar to CSS. |
PHF6 | Borjeson-Forssman-Lehmann syndrome (OMIM 301900) | XL | See . |
Genetic testing for ARID1A is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for intellectual disability, autosomal dominant 14 has been reported in the published literature.
No approved treatments are currently available for intellectual disability, autosomal dominant 14. The disease remains an area of unmet medical need.
Gene therapy approaches for intellectual disability, autosomal dominant 14 have been reported in the published literature.
Several publications have recommended various medical surveillance guidelines for individuals with Coffin-Siris syndrome (CSS) . However, as clinical variability between individuals is high, clinicians are encouraged to use their own clinical judgment when evaluating and managing these individuals.
To establish the extent of disease and needs in an individual diagnosed with CSS, the evaluations summarized (if not performed as part of the evaluation that led to diagnosis) are recommended.
Table 5:
Coffin-Siris Syndrome: Recommended Evaluations Following Initial Diagnosis
System/Concern | Evaluation | Comment
| Measurement of growth parameters | To assess for growth restriction or poor growth in younger persons obesity in adults
| Neurologic eval to incl assessment for signs symptoms of seizures/tics | • To incl brain MRI if 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 ADHD, aggression, /or findings suggestive of ASD
| Assessment for signs symptoms of sleep disturbance | Consider referral to sleep medicine clinic /or sleep study.
| Orthopedics/ physical medicine rehab/ PT OT eval | To incl assessment of:
Source: GeneReviews — "Coffin-Siris Syndrome"
View trials for intellectual disability, autosomal dominant 14
To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, the evaluations summarized in are recommended. Table 7. Coffin-Siris Syndrome: Recommended Surveillance
System/Concern | Evaluation | Frequency |
|---|---|---|
Eyes | Ophthalmology eval vision assessment | Annually or as clinically indicated Hearing |
Dental | Dental eval | At least every 6 mos in those w/teeth |
Oncology | Consider serum AFP level liver ultrasound in those who have a pathogenic variant in ARID1A1 | Every 3 mos until age 4 yrs ADHD = attention-deficit/hyperactivity disorder; AFP = alpha-fetoprotein; ASD = autism spectrum disorder; OT = occupational therapy; PT = physical therapy 1. Because of the rarity of tumors in CSS, the utility of tumor surveillance is unclear. |
Source: GeneReviews — "Coffin-Siris Syndrome"
Phenotype severity distribution: 26 always present features, 17 common features.
No clinical trials have been registered for intellectual disability, autosomal dominant 14.
40 publications have been identified in PubMed for intellectual disability, autosomal dominant 14. Research spans Case Report / Case Series (45%), Basic Science / Preclinical (20%), and Review / Meta-Analysis (18%).
Research Type | Count | % of Total |
|---|---|---|
Patient case studies | 18 | 45% |
Laboratory research | 8 | 20% |
Research summaries | 7 | 18% |
Testing and diagnosis research | 4 | 10% |
Disease patterns and progression | 2 | 5% |
New treatment approaches | 1 | 3% |
Schuhmann S (2026). [PMID: 42173440](https://pubmed.ncbi.nlm.nih.gov/42173440/). *Eur J Med Genet*. [Case Report / Case Series]
van der Leij M (2026). [PMID: 41680088](https://pubmed.ncbi.nlm.nih.gov/41680088/). *American journal of medical genetics. Part A*. [Review / Meta-Analysis]
Schumaier NP (2026). [PMID: 39531587](https://pubmed.ncbi.nlm.nih.gov/39531587/). *Retinal cases & brief reports*. [Basic Science / Preclinical]
Murthy H (2026). [PMID: 40717498](https://pubmed.ncbi.nlm.nih.gov/40717498/). *Brain : a journal of neurology*. [Case Report / Case Series]
Pan X (2026). [PMID: 41764152](https://pubmed.ncbi.nlm.nih.gov/41764152/). *Journal of molecular medicine (Berlin, Germany)*. [Epidemiology / Natural History]
Ou S (2026). [PMID: 41532374](https://pubmed.ncbi.nlm.nih.gov/41532374/). *Molecular genetics & genomic medicine*. [Basic Science / Preclinical]
Somayyeh Heidargholizadeh G (2026). [PMID: 41454640](https://pubmed.ncbi.nlm.nih.gov/41454640/). *Pediatrics international : official journal of the Japan Pediatric Society*. [Case Report / Case Series]
Barakat N (2026). [PMID: 41358577](https://pubmed.ncbi.nlm.nih.gov/41358577/). *American journal of medical genetics. Part A*. [Case Report / Case Series]
Sokolova T (2026). [PMID: 41718288](https://pubmed.ncbi.nlm.nih.gov/41718288/). *Reports (MDPI)*. [Case Report / Case Series]
Li M (2026). [PMID: 41710014](https://pubmed.ncbi.nlm.nih.gov/41710014/). *Frontiers in pediatrics*. [Case Report / Case Series]
Data assembled from 6 of 12 sources · Last updated Sep 19, 2026, 9:40 PM UTC
Online Mendelian Inheritance in Man
Genetic and Rare Diseases Info Center
Typically in the moderate-to-severe range
Feeding problems | 90% | — |
Hypotonia | 75% | — |
Hypoplasia of the fifth digits/nails1 | 65%-80% | Some individuals with a molecularly confirmed diagnosis of CSS have little or no fifth digit involvement. |
Dysmorphic facial features | 65% | ~30% at birth. Because facial features typically coarsen over time, the characteristic facies may not be apparent until later in childhood. |
Frequent infections | 60% | — |
Other skeletal findings | 40%-60% | Including joint laxity and scoliosis |
Epilepsy | 50% | — |
Hearing impairment | 45% | Both sensorineural and conductive hearing loss has been reported. |
Eye issues | ~40% | Ptosis, strabismus, myopia |
Congenital heart defects | 35% | — |
Genitourinary malformations | 33% | — |
Behavioral issues | 25% | May include hyperactivity /or aggressiveness Typically, individuals with a clinical diagnosis of CSS have either aplasia or hypoplasia of the distal phalanx or absence of the nail, classically involving the fifth finger, but other digits may also be affected. |
Source: GeneReviews — "Coffin-Siris Syndrome"
PIGV | Mabry syndrome (OMIM 239300) | AR | DD, seizures, coarse facial features, hypoplastic 5th digits, serum concentrations of ALP | — |
SMARCA2 | Nicolaides-Baraitser syndrome (NCBRS) | AD | See . | See . |
TBC1D24 | DOORS syndrome (See TBC1D24-Related Disorders.) | AR | Deafness, onychodystrophy, osteodystrophy, ID, seizures | Features in common w/CSS incl hypoplastic terminal phalanges /or nail anomalies, deafness, neurologic abnormalities. |
Source: GeneReviews — "Coffin-Siris Syndrome"