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X-linked alpha thalassaemia mental retardation (ATR-X) syndrome in males is associated with profound developmental delay, facial dysmorphism, genital abnormalities and alpha thalassaemia. Female carriers are usually physically and intellectually normal.
Features include always present findings: Epicanthus, Bilateral tonic-clonic seizure, Seizure, and Low muscle tone (hypotonia) and others. 57 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 7 | Bilateral tonic-clonic seizure, Seizure, Intellectual disability |
Head and neck | 5 | U-Shaped upper lip vermilion, Widely-spaced maxillary central incisors, Microcephaly |
Bones and joints | 3 | Kyphoscoliosis, Sideways curvature of the spine (scoliosis), Excessive outward curvature of the upper spine (kyphosis) |
Blood and immune system | 2 | Hypochromic microcytic anemia, HbH hemoglobin |
Muscles | 2 | Low muscle tone (hypotonia), Brain shrinkage (cerebral atrophy) |
Digestive system | 2 | Gastroesophageal reflux, Constipation |
Arms and legs | 2 | Radial deviation of finger, Tapered finger |
Growth and development | 2 | Postnatal growth retardation, Growth delay |
Heart and blood vessels | 2 | Ventricular septal defect, Perimembranous ventricular septal defect |
Ears | 1 | Inner ear hearing loss (sensorineural hearing impairment) |
Kidneys and urinary system | 1 | Renal agenesis |
A more or less distinctive phenotype is characteristic of alpha-thalassemia X-linked intellectual disability (ATR-X) syndrome. Craniofacial, genital, and developmental manifestations are prominent among the most severely affected individuals . As additional individuals/families have been evaluated using molecular genetic testing, the range of phenotypic variability has broadened, particularly on the mild end of the spectrum. Affected males may have mild, moderate, or profound intellectual disability (ID), even within the same family. Adults in the family described by appeared to have nonsyndromic X-linked ID (XLID), although childhood photographs showed evidence of facial hypotonia. reported 25 affected males in five families with the variant who had variable but overall milder phenotypes . Table 2. Selected Features of Alpha-thalassemia X-linked Intellectual Disability Syndrome
Feature | % of Persons with Feature | Comments |
|---|---|---|
Developmental delay | 100% | A minority never speak or have meaningful speech. |
ATRX encodes ATRX chromatin remodeler (2,492 aa). Involved in transcriptional regulation and chromatin remodeling. Facilitates DNA replication in multiple cellular environments and is required for efficient replication of a subset of genomic loci. Highest expression in Cells EBV-transformed lymphocytes (22.6 TPM) and Ovary (22.6 TPM).
Alpha thalassemia-X-linked intellectual disability syndrome is associated with mutations in the ATRX gene on chromosome X.
The ATRX protein participates in Defective ATRX does not bind DAXX pathway.
ATRX is classified as a druggable target (Clinically Actionable, Dna Repair, and Enzyme categories) with score 4.4.
Pathogenic variants that affect the ATRX zinc finger domain produce severe psychomotor impairment and urogenital anomalies, whereas pathogenic variants in the helicase domains cause milder phenotypes . More severe genital anomalies occur with variants in the plant homeodomain-like domain. A nonsense variant in exon 2 appears to be a common pathogenic variant that results in an overall milder phenotype .
Source: GeneReviews — "Alpha-Thalassemia X-Linked Intellectual Disability Syndrome"
Alpha-thalassemia X-linked intellectual disability (ATR-X) syndrome should be suspected in individuals with the following clinical findings, hematologic findings, and family history.
Clinical findings
Source: GeneReviews — "Alpha-Thalassemia X-Linked Intellectual Disability Syndrome"
Table 3. Genes of Interest in the Differential Diagnosis of Alpha-Thalassemia X-Linked Intellectual Disability Syndrome
Gene(s) | DiffDx Disorder | MOI | Clinical Features of DiffDx Disorder |
|---|---|---|---|
HBA2 | Hemoglobin H (HbH) disease (See Alpha-Thalassemia.) | AR1 | Microcytic hypochromic hemolytic anemia, hepatosplenomegaly, mild jaundice, sometimes thalassemia-like bone changes |
MECP2 duplication syndrome | XL | Severe ID, spasticity, infantile hypotonia, absent or limited speech, seizures, recurrent respiratory infections; Autistic behaviors GI dysfunction observed in several affected boys; 50% of affected males die by early adulthood. | Face is not characteristically hypotonic as in ATR-X syndrome.; Microcephaly is less common.; Downslanted palpebral fissures RPS6KA3 |
Coffin-Lowry syndrome |
Genetic testing for ATRX is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for alpha thalassemia-X-linked intellectual disability syndrome has been reported in the published literature.
No approved treatments are currently available for alpha thalassemia-X-linked intellectual disability syndrome. An additional 1 compound holds orphan drug designation.
While no drugs are FDA-approved specifically for alpha thalassemia-X-linked intellectual disability syndrome, some of the following designated compounds may be used off-label in clinical practice. Treatment decisions should be made in consultation with a specialist familiar with this condition.
The following drugs have received orphan drug designation from the FDA for alpha thalassemia-X-linked intellectual disability syndrome. Orphan designation reflects regulatory interest and does not indicate approval for treatment.
Brand Name | Generic Name | Sponsor | Designated | Exclusivity End | Designation Status |
|---|---|---|---|---|---|
Cutamesine dihydrochloride | Cutamesine dihydrochloride | BioPharma Global, a division of Pace Life Sciences | 2023 | — | Designated |
To establish the extent of disease and needs in an individual diagnosed with alpha-thalassemia X-linked intellectual disability (ATR-X) syndrome, the evaluations summarized (if not performed as part of the evaluation that led to the diagnosis) are recommended.
Table 4.
Recommended Evaluations Following Initial Diagnosis in Individuals with ATR-X Syndrome
System/Concern | Evaluation | Comment
| Assess height, weight, head circumference | In infants children
| Developmental assessment | • To incl motor, adaptive, cognitive, speech-language eval
Eval for early intervention/ speech therapy/ PT OT/ special education
| Neurologic eval | • To assess muscle tone, evidence for spasticity ( reflexes, Babinski response)
To incl EEG MRI if seizures a concern
Gastrointestinal/
| Gastroenterology/ nutrition/ feeding team eval | For:
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 — "Alpha-Thalassemia X-Linked Intellectual Disability Syndrome"
View trials for alpha thalassemia-X-linked intellectual disability syndrome
Table 6. Recommended Surveillance for Individuals with ATR-X Syndrome
System/Concern | Evaluation | Frequency |
|---|---|---|
Growth | Height, weight, head circumference | At each visit in infancy childhood Development |
abnormalities | Follow up w/treating urologist as needed. | At initial visit in infancy Neurologic |
heart defects | Per treating cardiologist | Per treating cardiologist Ophthalmologic |
involvement | Per treating ophthalmologist | Per treating ophthalmologist |
Source: GeneReviews — "Alpha-Thalassemia X-Linked Intellectual Disability Syndrome"
Phenotype severity distribution: 19 always present features.
Estimated prevalence: Unknown (Unknown prevalence).
No clinical trials have been registered for alpha thalassemia-X-linked intellectual disability syndrome.
21 publications have been identified in PubMed for alpha thalassemia-X-linked intellectual disability syndrome. Research spans Basic Science / Preclinical (43%), Case Report / Case Series (24%), and Review / Meta-Analysis (19%).
Research Type | Count | % of Total |
|---|---|---|
Laboratory research | 9 | 43% |
Patient case studies | 5 | 24% |
Research summaries | 4 | 19% |
Other research | 1 | 5% |
Testing and diagnosis research | 1 | 5% |
Disease patterns and progression | 1 | 5% |
Quesnel K (2026). [PMID: 41724591](https://pubmed.ncbi.nlm.nih.gov/41724591/). *Autism Res*. [Basic Science / Preclinical]
Pena-Ortiz MA (2026). [PMID: 41239822](https://pubmed.ncbi.nlm.nih.gov/41239822/). *Glia*. [Basic Science / Preclinical]
Geltman R (2026). [PMID: 41606192](https://pubmed.ncbi.nlm.nih.gov/41606192/). *Nat Rev Immunol*. [Basic Science / Preclinical]
Brott JT (2026). [PMID: 42048321](https://pubmed.ncbi.nlm.nih.gov/42048321/). *PLoS One*. [Basic Science / Preclinical]
Yan S (2025). [PMID: 40443347](https://pubmed.ncbi.nlm.nih.gov/40443347/). *Acta Biochim Biophys Sin (Shanghai)*. [Basic Science / Preclinical]
Aljaafreh S (2025). [PMID: 40896065](https://pubmed.ncbi.nlm.nih.gov/40896065/). *Cureus*. [Case Report / Case Series]
Mizuguchi T (2025). [PMID: 39966947](https://pubmed.ncbi.nlm.nih.gov/39966947/). *Clin Epigenetics*. [Diagnostic / Biomarker]
Magaña-Acosta M (2025). [PMID: 41222108](https://pubmed.ncbi.nlm.nih.gov/41222108/). *Genesis*. [Review / Meta-Analysis]
Patra S (2025). [PMID: 40656040](https://pubmed.ncbi.nlm.nih.gov/40656040/). *Indian J Psychiatry*. [Other]
Ouragini H (2025). [PMID: 40429944](https://pubmed.ncbi.nlm.nih.gov/40429944/). *Int J Mol Sci*. [Case Report / Case Series]
Data assembled from 8 of 12 sources · Last updated Sep 19, 2026, 11:15 AM UTC
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center
Common questions about alpha thalassemia-X-linked intellectual disability syndrome
Intellectual disability | 100% | Variable severity, from mild to profound Characteristic facies; Hypertelorism/telecanthus; Small nose; Tented upper lip; Open mouth |
Prominent lips | 90% | Usually present from birth, but may persist or become less distinctive in adult life. W/age, face may also coarsen w/open mouth, spaced teeth, prominent lips. |
Microcephaly | 75%-85% | Usually present at birth; head size of those w/out microcephaly usually in lower centiles |
Short stature | 60%-70% | Usually present at birth |
Gastrointestinal dysfunction | 70%-80% | A major morbidity; incl: early feeding difficulty, vomiting, reflux, abdominal distention, obstruction, pain, constipation |
Genital anomalies | 70%-80% | Wide range, from minimal hypospadias or undescended testes to normal-appearing female external genitalia |
Neurologic | Hypotonia | 80%-90% |
Source: GeneReviews — "Alpha-Thalassemia X-Linked Intellectual Disability Syndrome"
XL
Severe-to-profound ID in males; Large open mouth prominent lips; Short stature, microcephaly, dental anomalies common; Childhood-onset kyphoscoliosis (often progressive); Life span in some persons |
Short, soft, fleshy hands, often w/hyperextensible tapering fingers; Childhood-onset SIDAs in ~20% of persons2 AR = autosomal recessive; DiffDx = differential diagnosis; GI = gastrointestinal; ID = intellectual disability; MOI = mode of inheritance; XL = X-linked 1. |
Source: GeneReviews — "Alpha-Thalassemia X-Linked Intellectual Disability Syndrome"
Swallowing difficulties aspiration risk
GERD /or recurrent vomiting
Gastric pseudo-obstruction
Constipation
Genital
abnormalities | Physical exam for evidence of a disorder of genital development such as cryptorchidism, hypospadias, ambiguous genitalia, normal female external genitalia in 46,XY individuals | Consultation w/pediatric urologist if surgical intervention required
| Orthopedics/ physical medicine rehab/ PT OT eval | To incl assessment of:
Source: GeneReviews — "Alpha-Thalassemia X-Linked Intellectual Disability Syndrome"