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An autosomal dominant non-syndromic intellectual disability that has material basis in an autosomal dominant mutation of EHMT1 on chromosome 9q34.3.
Features include always present findings: Bilateral tonic-clonic seizure, Seizure, Generalized-onset seizure, and Focal-onset seizure and others; and very common findings: Intellectual disability, Feeding difficulties, Global developmental delay, and Recurrent infections. 86 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 21 | Bilateral tonic-clonic seizure, Seizure, Depression |
EHMT1 encodes euchromatic histone lysine methyltransferase 1 (1,298 aa). Histone methyltransferase that specifically mono-, di- and trimethylates 'Lys-9' of histone H3 (H3K9me1, H3K9me2 and H3K9me3, respectively) in euchromatin. Highest expression in Cells EBV-transformed lymphocytes (21.6 TPM) and Testis (17.0 TPM).
Kleefstra syndrome 1 is associated with mutations in the EHMT1 gene on chromosome 9.
The EHMT1 protein participates in EHMT1:EHMT2 dimethylates TP53, EHMT1:EHMT2 methylates IL8 promoter, and EHMT1:EHMT2 methylates IL6 promoter pathways.
EHMT1 is classified as a druggable target (Druggable Genome and Enzyme categories) with score 0.0.
Kleefstra syndrome is characterized by intellectual disability, childhood hypotonia, and distinctive facial features. A complex pattern of other findings can also be observed [, , , , , , , , , , ].
Kleefstra syndrome should be suspected in individuals with the following:
Source: GeneReviews — "Kleefstra Syndrome"
No approved treatments are currently available for Kleefstra syndrome 1. The disease remains an area of unmet medical need.
Evaluations Following Initial Diagnosis To establish the extent of disease and needs in an individual diagnosed with Kleefstra syndrome, 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 Kleefstra Syndrome
Cardiac and renal/urologic abnormalities should be monitored as needed.
Source: GeneReviews — "Kleefstra Syndrome"
Phenotype severity distribution: 5 always present features, 4 very common features, 23 common features.
No clinical trials have been registered for Kleefstra syndrome 1.
42 publications have been identified in PubMed for Kleefstra syndrome 1. Research spans Case Report / Case Series (33%), Epidemiology / Natural History (25%), and Review / Meta-Analysis (20%).
Research Type | Count | % of Total |
|---|---|---|
Patient case studies | 13 | 33% |
Data assembled from 6 of 12 sources · Last updated Sep 19, 2026, 7:12 AM UTC
Online Mendelian Inheritance in Man
Common questions about Kleefstra syndrome 1
Head and neck | 6 | U-Shaped upper lip vermilion, Coarse facial features, Microcephaly |
Digestive system | 3 | Gastroesophageal reflux, Feeding difficulties, Chronic constipation |
Blood and immune system | 3 | Recurrent urinary tract infections, Recurrent infections, Recurrent respiratory infections |
Bones and joints | 3 | Joint hypermobility, Sideways curvature of the spine (scoliosis), Excessive outward curvature of the upper spine (kyphosis) |
Heart and blood vessels | 3 | Coronary artery fistula, Ventricular septal defect, Atrial septal defect |
Growth and development | 2 | Short stature, Tall stature |
Kidneys and urinary system | 2 | Recurrent urinary tract infections, Renal cyst |
Ears | 1 | Hearing loss (hearing impairment) |
Eyes | 1 | Strabismus |
Muscles | 1 | Low muscle tone (hypotonia) |
Arms and legs | 1 | Clinodactyly of the 5th finger |
Lungs and breathing | 1 | Recurrent respiratory infections |
Age of onset: adolescence, childhood, at birth.
Kleefstra syndrome has a clinically recognizable phenotype that includes physical, developmental, and behavioral features. Males and females are affected equally [, , , , , ]. Birth weight is usually within the normal or above-normal range; weight increases in childhood, leading to obesity (50%) . The facial appearance is characterized by brachy(-micro)cephaly, broad forehead, unusual shape of eyebrows (arched or straight with synophrys), mildly upslanted palpebral fissures, midface retrusion, thickened ear helices, short nose with anteverted nares, fleshy everted vermilion of the lower lip and exaggerated Cupid's bow or "tented" appearance of the vermilion of the upper lip, and protruding tongue and relative prognathism (, ).
Source: GeneReviews — "Kleefstra Syndrome"
EHMT1 loss of function accounts for the majority of features in Kleefstra syndrome. Current data indicate that individuals with an intragenic EHMT1 pathogenic variant (e.g., a missense, frameshift, or nonsense variant) and those with a small (1-Mb) 9q34.3 deletion have similar clinical findings. Individuals with larger deletions (≥1 Mb), however, generally have more severe intellectual disability and more medical problems, such as congenital anomalies, feeding issues, and respiratory issues. Pulmonary infections and aspiration difficulties in particular appear to be more severe in individuals with larger 9q34 deletions than in those with smaller deletions or intragenic EHMT1 pathogenic variants.
Source: GeneReviews — "Kleefstra Syndrome"
Kleefstra syndrome should be distinguished from other syndromes that include developmental delay, infantile hypotonia, short stature, distinctive facies, and a behavioral phenotype. The most common of these include those in , which can be distinguished using cytogenetic (FISH) and/or molecular analysis. Table 2. Disorders to Consider in the Differential Diagnosis of Kleefstra Syndrome
Disorder | Gene/ GeneticMechanism | MOI | Additional Overlapping Clinical Features |
|---|---|---|---|
Down syndrome | Trisomy 21 | Virtually all de novo | Similar facial characteristics, incl:; Brachycephaly; Protruding tongue; Hypotonia; Hypertelorism; Midface retrusion |
Smith-Magenis syndrome | Deletion or mutation of RAI1 on chromosome 17p11.21 | Virtually all de novo | Lethargy; Sleep disturbance; Midface retrusion |
Pitt-Hopkins syndrome | Haploinsufficiency of TCF4 | Most de novo | Speech is significantly delayed most persons are nonverbal w/receptive language often stronger than expressive language.; Seizures; Sleep disturbance |
Angelman syndrome | Disruption of maternally imprinted UBE3A | See footnote 2. | Receptive language better than expressive language skills; Sleep disturbances w/multiple awakenings; Midface retrusion w/prognathism; See footnote 3 for distinguishing clinical features. KMT2C-associated syndrome4 |
KMT2C | AD | Currently under study to determine overlap; ASD ID | — |
MBD5 haploinsufficiency | See footnote 5. | AD; typically de novo | ASD ID; Seizures; Developmental regression AD = autosomal dominant; ASD = autism spectrum disorder; ID = intellectual disability; MOI = mode of inheritance Approximately 95% of individuals with Smith-Magenis syndrome have the disorder as a result of an interstitial 17p11. |
Source: GeneReviews — "Kleefstra Syndrome"
Genetic testing for EHMT1 is available. Testing is considered confirmatory for diagnosis.
System/Concern |
|---|
Evaluation |
|---|
Comment |
|---|
Constitutional | Weight, height, body mass index (in those age 2 yrs) | Consider referral to nutritionist in those w/obesity. |
Dental | Dental eval | To assess for dental issues, incl retention of primary dentition |
Eyes | Ophthalmologic eval | To assess for refractive errors |
Ears | Audiologic eval | To assess for hearing loss |
Cardiovascular | Echocardiogram EKG | To evaluate for structural heart defects rhythm disturbance; consider referral to cardiologist. |
Respiratory | Assess for history of sleep disturbance. | Consider referral to sleep disorders clinic. Gastrointestinal/ |
Feeding | Assess for signs symptoms of gastroesophageal reflux disease. | — |
Genitourinary | Renal ultrasound | To evaluate for structural renal anomalies hydronephrosis |
Neurologic | Neurologic eval | Consider referral to neurologist. Head MRI |
Behavioral | Neuropsychiatric eval | Persons age 12 mos: screen for behavior concerns incl sleep disturbances, mood issues, psychotic disorders, anxiety, /or findings suggestive of ASD. Miscellaneous/ |
Other | Developmental assessment | Evaluate motor, speech-language, general cognitive, vocational skills. Consultation w/clinical geneticist /or genetic counselor |
Treatment of Manifestations in Individuals with Kleefstra Syndrome Manifestation/Concern | Treatment | Considerations/Other |
Refractive error | Standard treatment | — |
Hearing loss | Auditory amplification as appropriate | See Hereditary Hearing Loss and Deafness Overview. Congenital heart defects |
rhythm disturbance | Standard treatment per cardiologist | — |
Sleep disturbance | Standard treatment | No well-controlled treatment trials have been reported. Gastroesophageal reflux |
disease | Standard treatment | Consider referral to gastroenterologist for those w/severe issues. |
Renal anomalies | Standard treatment | Consider referral to urologist /or nephrologist. |
Seizures | Standard treatment w/ASM by experienced neurologist1 | Many ASMs may be effective; none has been demonstrated effective specifically for this disorder. ASM = anti-seizure medication Education of parents regarding common seizure presentations is appropriate. |
Source: GeneReviews — "Kleefstra 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 — "Kleefstra Syndrome"
View trials for Kleefstra syndrome 1
10 |
25% |
Research summaries | 8 | 20% |
Laboratory research | 8 | 20% |
Other research | 1 | 3% |
Sedláčková L (2026). [PMID: 41914216](https://pubmed.ncbi.nlm.nih.gov/41914216/). *Mol Genet Genomic Med*. [Case Report / Case Series]
Marchetti GB (2026). [PMID: 41654978](https://pubmed.ncbi.nlm.nih.gov/41654978/). *Ital J Pediatr*. [Review / Meta-Analysis]
Yue SL (2026). [PMID: 41652658](https://pubmed.ncbi.nlm.nih.gov/41652658/). *Am J Med Genet A*. [Case Report / Case Series]
Bouman A (2026). [PMID: 41578867](https://pubmed.ncbi.nlm.nih.gov/41578867/). *Genet Med*. [Review / Meta-Analysis]
Dukuze N (2026). [PMID: 42074547](https://pubmed.ncbi.nlm.nih.gov/42074547/). *Genes (Basel)*. [Case Report / Case Series]
Maruyama A (2025). [PMID: 40878694](https://pubmed.ncbi.nlm.nih.gov/40878694/). *Cardiol Young*. [Case Report / Case Series]
Lim CT (2025). [PMID: 40534452](https://pubmed.ncbi.nlm.nih.gov/40534452/). *J Neurochem*. [Review / Meta-Analysis]
Nichols CA (2025). [PMID: 40624551](https://pubmed.ncbi.nlm.nih.gov/40624551/). *Orphanet J Rare Dis*. [Epidemiology / Natural History]
van Till SAL (2025). [PMID: 40829731](https://pubmed.ncbi.nlm.nih.gov/40829731/). *Eur J Med Genet*. [Epidemiology / Natural History]
Connors KL (2025). [PMID: 40612157](https://pubmed.ncbi.nlm.nih.gov/40612157/). *Sage Open Pediatr*. [Epidemiology / Natural History]
AI-curated news mentioning Kleefstra syndrome 1
Updated Jun 4, 2026
IDefine and UT Southwestern will assess a preclinical EHMT1 gene replacement strategy for Kleefstra syndrome. If the approach advances, future development would likely require a more detailed natural history framework, validated or fit-for-purpose clinical outcome measures, and careful selection of age groups most likely to benefit. In neurodevelopmental disorders, the timing of therapeutic intervention may be especially important because some neurologic features arise during early brain development. The collaboration also illustrates the growing role of patient advocacy organizations in de-risking early rare disease research. However, the clinical implications should be viewed cautiously until preclinical results are disclosed and reviewed. At present, the program establishes a research pathway for EHMT1 replacement rather than evidence of therapeutic benefit. IDefine and UT Southwestern announce research collaboration to advance gene therapy for rare disease Kleefstra syndrome. IDefine–The Kleefstra Syndrome Foundation and UT Southwestern Medical Center have entered a 2-year research collaboration to evaluate a preclinical EHMT1 gene replacement strategy for Kleefstra syndrome, a rare neurodevelopmental disorder with no appoved disease-modifying therapy.1 The program is expected to run through April 2028 and will be led by Steven Gray, PhD, professor at UT Southwestern and director of the UTSW Gene Therapy Program. “This landmark research collaboration represents a meaningful step forward in our mission to accelerate research that can lead to a first treatment fo FDA guidance for rare disease gene therapy development emphasizes that small populations, limited natural history data, and uncertainty about clinically meaningful end points can complicate preclinical-to-clinical translation.4
There are currently no approved treatments for the disease. "Advances in gene therapy and CNS-targeted delivery technologies are creating new opportunities to develop potential treatments for complex neurodevelopmental disorders like Kleefstra syndrome," said Dr. ATLANTA, June 3, 2026 /PRNewswire/ -- IDefine – The Kleefstra Syndrome Foundation, a leading patient advocacy organization, today announced a collaboration with UT Southwestern Medical Center to advance development of a potential gene therapy to treat Kleefstra syndrome (KS), a rare neurodevelopmental disorder caused by changes or loss of the EHMT1 gene, which plays a critical role in brain development and function. - Dr. Steven Gray will lead research effort focused on potential therapy to replace the EHMT1 gene in patients with rare neurodevelopmental disorder View original content:https://www.prnewswire.com/news-releases/idefine-and-ut-southwestern-announce-research-collaboration-to-advance-gene-therapy-for-rare-disease-kleefstra-syndrome-302789121.html The two-year research program, led by Steven Gray, PhD, professor at UT Southwestern and director of the UTSW Gene Therapy Program, will evaluate the feasibility and safety of EHMT1 gene replacement therapy using next-generation gene delivery technology designed to target the central nervous system (CNS). "This landmark research collaboration represents a meaningful step forward in our mission to accelerate research that can lead to a first treatment for Kleefstra syndrome," said Eric Scheeff, PhD, chief scientific officer of IDefine. "We are especially honored to support and partner with Dr. Steven Gray and the UT Southwestern Gene Therapy Program in this effort.
/PRNewswire/ -- IDefine – The Kleefstra Syndrome Foundation, a leading patient advocacy organization, today announced a collaboration with UT Southwestern... ATLANTA, June 3, 2026 /PRNewswire/ -- IDefine – The Kleefstra Syndrome Foundation, a leading patient advocacy organization, today announced a collaboration with UT Southwestern Medical Center to advance development of a potential gene therapy to treat Kleefstra syndrome (KS), a rare neurodevelopmental disorder caused by changes or loss of the EHMT1 gene, which plays a critical role in brain development and function. There are currently no approved treatments for the disease. "Advances in gene therapy and CNS-targeted delivery technologies are creating new opportunities to develop potential treatments for complex neurodevelopmental disorders like Kleefstra syndrome," said Dr. - Dr. Steven Gray will lead research effort focused on potential therapy to replace the EHMT1 gene in patients with rare neurodevelopmental disorder The two-year research program, led by Steven Gray, PhD, professor at UT Southwestern and director of the UTSW Gene Therapy Program, will evaluate the feasibility and safety of EHMT1 gene replacement therapy using next-generation gene delivery technology designed to target the central nervous system (CNS). "This landmark research collaboration represents a meaningful step forward in our mission to accelerate research that can lead to a first treatment for Kleefstra syndrome," said Eric Scheeff, PhD, chief scientific officer of IDefine. "We are especially honored to support and partner with Dr. Steven Gray and the UT Southwestern Gene Therapy Program in this effort.