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A group of X-linked syndromes characterized by severe intellectual deficit and facial dysmorphism, with variable other features.
Features include common findings: Seizure; and sometimes findings: Obesity. 68 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Head and neck | 9 | Tented upper lip vermilion, U-Shaped upper lip vermilion, Coarse facial features |
Brain and nerves | 5 | Seizure, Intellectual disability, Severe intellectual disability |
Arms and legs | 4 | Radial deviation of finger, Tapered finger, Lower limb hypertonia |
Digestive system | 3 | Gastroesophageal reflux, Constipation, Vomiting |
Bones and joints | 2 | Kyphoscoliosis, Delayed skeletal maturation |
Eyes | 2 | Damage to the optic nerve (optic atrophy), Ptosis |
Growth and development | 1 | Short stature |
Kidneys and urinary system | 1 | Renal hypoplasia |
Ears | 1 | Inner ear hearing loss (sensorineural hearing impairment) |
Muscles | 1 | Damage to the optic nerve (optic atrophy) |
Blood and immune system | 1 | Abnormality of blood and blood-forming tissues |
Hormones | 1 | Hypogonadism |
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).
Intellectual disability-hypotonic facies syndrome, X-linked, 1 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.
No approved treatments are currently available for intellectual disability-hypotonic facies syndrome, X-linked, 1. The disease remains an area of unmet medical need.
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:
Nutritional status
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"
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 intellectual disability-hypotonic facies syndrome, X-linked, 1
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: 1 common feature.
No clinical trials have been registered for intellectual disability-hypotonic facies syndrome, X-linked, 1.
3 publications have been identified in PubMed for intellectual disability-hypotonic facies syndrome, X-linked, 1. Research spans Review / Meta-Analysis (67%) and Basic Science / Preclinical (33%).
Wang Y (2024). [PMID: 39363269](https://pubmed.ncbi.nlm.nih.gov/39363269/). *BMC Pediatr*. [Review / Meta-Analysis]
Horsthemke B (2024). [PMID: 38854642](https://pubmed.ncbi.nlm.nih.gov/38854642/). *Med Genet*. [Review / Meta-Analysis]
Trajkova S (2024). [PMID: 38751117](https://pubmed.ncbi.nlm.nih.gov/38751117/). *HGG Adv*. [Basic Science / Preclinical]
Data assembled from 7 of 12 sources · Last updated Sep 20, 2026, 5:35 PM UTC
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center
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"