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Disease characteristics. Alpha-thalassemia X-linked intellectual disability (ATRX) syndrome is characterized by distinctive craniofacial features, genital anomalies, severe developmental delays, hypotonia, intellectual disability, and mild-to-moderate anemia secondary to alpha-thalassemia. Craniofacial abnormalities include small head circumference, telecanthus or ocular hypertelorism, small nose, tented upper lip, and prominent or everted lower lip with coarsening of the facial features over time. Although all affected individuals have a normal 46,XY karyotype, genital anomalies range from hypospadias and undescended testicles to severe hypospadias and ambiguous genitalia, to normal-appearing female genitalia. Global developmental delays are evident in infancy and some affected individuals never walk independently or develop significant speech.
Diagnosis/testing. The diagnosis of ATRX syndrome is established in individuals with somatic abnormalities, intellectual disability, hypotonia, abnormal hemoglobin H production, and a family history consistent with X-linked inheritance. ATRX is the only gene in which mutation causes ATRX syndrome.
Management. Treatment of manifestations: Calorie-dense formula and/or gavage feeding as needed for adequate nutrition; anticholinergics, botulinum toxin type A injection of the salivary glands, and/or surgical redirection of the submandibular ducts for excessive drooling; early intervention programs and special education.
Prevention of secondary complications: Antibiotic prophylaxis and vaccination to prevent pneumococcal and meningococcal infection in those with asplenia.
Surveillance: Regular assessment of growth in infancy and childhood; regular monitoring of developmental progress.
Other: Anemia rarely requires treatment.
Genetic counseling. ATRX syndrome is inherited in an X-linked manner. The mother of a proband may be a carrier or the affected individual may have a de novo gene mutation. Carrier women have a 50% chance in each pregnancy of transmitting the ATRX mutation; offspring with a 46,XY karyotype who inherit the ATRX mutation will be affected; offspring with a 46,XX karyotype who inherit the mutation are unaffected female carriers. Affected individuals do not reproduce. Carrier testing for at-risk females and prenatal testing for pregnancies at increased risk are possible if the disease-causing mutation in the family is known.
Alpha-thalassemia X-linked intellectual disability (ATRX) syndrome may be suspected on the basis of characteristic craniofacial, genital, skeletal, and other somatic findings, and laboratory findings of alpha-thalassemia. Of greatest importance clinically is the failure to achieve developmental milestones on schedule. Cognitive function is usually profoundly impaired, although individuals with less severe intellectual disabilities have been reported.
Because the phenotypic findings (with the exception of alpha-thalassemia) overlap with those of other syndromes, clinical diagnosis should be confirmed by molecular genetic testing.
Affected individuals. Hematologic studies show evidence of alpha-thalassemia in approximately 85% of affected individuals with a 46,XY karyotype who have an ATRX mutation [Gibbons et al 2008].
Female carriers. HbH inclusions are found in only about 25% of female carriers [Gibbons et al 1995b].
Gene. ATRX is the only gene known to be associated with ATRX syndrome.
Clinical testing
Note: The finding that carrier females have marked skewing of X-chromosome inactivation (>90:10) has been used as a nonspecific and presumptive test for carrier detection. Non-random X-chromosome inactivation is not unique to ATRX syndrome; thus, the finding of skewed X-chromosome inactivation is not diagnostic and must be used in the context of clinical findings.
Table 1. Summary of Molecular Genetic Testing Used in Alpha-Thalassemia X-Linked Intellectual Disability Syndrome
| Gene Symbol | Test Method | Mutations Detected | Mutation Detection Frequency by Test Method 1 | Test Availability | |
|---|---|---|---|---|---|
| Affected Males 2 | Carrier Females | ||||
| ATRX | Sequence analysis of select exons | Sequence variants in selected exons 3 | 85% 4 | See footnote 5 | Clinical |
| Sequence analysis / mutation scanning | Sequence variants of coding region and splice junctions | 95% 4 | See footnote 5 | ||
| Deletion / duplication analysis 6 | Deletions / duplications | <5% 4 | Unknown | ||
| X-chromosome inactivation study | Skewed X-chromosome inactivation | NA 7 | 95% of carrier females 8 | ||
1. The ability of the test method used to detect a mutation that is present in the indicated gene
2. Approximately 25% of individuals tested on the basis of suggestive clinical findings have the diagnosis confirmed by gene testing [Badens et al 2006a].
3. Sequence analysis of exon 7, exon 8, proximal area of exon 9, and the helicase domains (exons 17-20)
4. Lack of amplification by PCR prior to sequence analysis can suggest a putative exonic or whole-gene deletion on the X chromosome in affected males; confirmation may require additional testing by deletion/duplication analysis.
5. Sequence analysis of genomic DNA cannot detect deletion of an exon(s) or a whole gene on the X chromosome in carrier females.
6. Testing that identifies deletions/duplications not readily detectable by sequence analysis of genomic DNA; a variety of methods including quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), or targeted array GH (gene/segment-specific) may be used. A full array GH analysis that detects deletions/duplications across the genome may also include this gene/segment.
7. Not applicable
8. Greater than 95% of carrier females have marked skewing of X-chromosome inactivation (>90:10).
Interpretation of test results. For issues to consider in interpretation of sequence analysis results, click here.
Confirming the diagnosis in a proband
Carrier testing for at-risk relatives requires prior identification of the disease-causing mutation in the family.
Note: Female carriers are heterozygous for an ATRX mutation but rarely develop clinical findings.
Prenatal diagnosis and preimplantation genetic diagnosis for at-risk pregnancies require prior identification of the disease-causing mutation in the family.
ATRX mutations have been found in several named X-linked mental retardation (XLMR) syndromes (Carpenter-Waziri syndrome, Holmes-Gang syndrome, Chudley-Lowry syndrome), XLMR with spastic paraplegia, XLMR with epilepsy, and nonsyndromic XLMR [Lossi et al 1999, Stevenson 2000, Yntema et al 2002]. These entities should be considered to be in the phenotypic spectrum of ATRX syndrome; there are no compelling reasons to maintain the syndromic names.
ATRX mutations have also been identified in families reported as having Juberg-Marsidi syndrome and Smith-Fineman-Myers syndrome [Villard et al 1999a]. Because ATRX mutations have not been reported in the original families with Juberg-Marsidi syndrome and Smith-Fineman-Myers syndrome, the relationship between ATRX syndrome and these two syndromes is unclear [Schwartz, personal communication 2010]
A more or less distinctive phenotype has emerged from the study of individuals with alpha-thalassemia X-linked intellectual disability (ATRX) syndrome.
Craniofacial, genital, and developmental manifestations are prominent among the most severely affected individuals [Gibbons et al 1995a, Stevenson et al 2000b, Badens et al 2006a]. As clinical experience with the condition has increased and 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. Findings by Guerrini et al [2000] and Yntema et al [2002] confirm this. Both describe families within which affected males have mild, moderate, or profound intellectual disability. Adults in the family described by Yntema et al [2002] appeared to have nonsyndromic XLMR, although childhood photographs showed evidence of facial hypotonia.
A recognizable pattern of craniofacial findings includes small head circumference, upsweep of the frontal hair, telecanthus or ocular hypertelorism, small triangular nose with retracted columella, tented upper lip, prominent or everted lower lip, and open mouth. Irregular anatomy of the pinnae, wide spacing of the teeth, and tongue protrusion are supplemental findings, the latter two adding to a coarseness of the facial appearance, particularly after the first few years of life.
The external genitalia are usually abnormal. The anomalies are often minor, including first-degree hypospadias, undescended testes, and underdevelopment of the scrotum. More severe defects are second- and third-degree hypospadias, micropenis, and ambiguous genitalia. Although all individuals with ATRX syndrome have a normal 46,XY karyotype, occasionally gonadal dysgenesis results in inadequate testosterone production and ambiguous genitalia or even normal-appearing female external genitalia. Although the spectrum of possible genital anomalies in ATRX syndrome is broad, the type of genital anomaly appears to be consistent within a family.
Short stature is typical and may be accompanied by minor skeletal anomalies (brachydactyly, clinodactyly, tapered digits, joint contractures, pectus carinatum, kyphosis, scoliosis, dimples over the lower spine, varus and valgus foot deformation, and pes planus). Stature is less than two standard deviations (SD) below the mean in two-thirds of individuals using standard growth charts; syndrome-specific growth charts are not available.
Major malformations are not common, but ocular coloboma, cleft palate, cardiac defects, inguinal hernia, heterotaxy, and asplenia [Leahy et al 2005] have been reported.
The severe developmental impairment and intellectual disability are the most important clinical manifestations. From the outset, developmental milestones are globally and markedly delayed. Speech and ambulation occur late in childhood. Some affected individuals never walk independently or develop significant speech.
Hypotonia is a hallmark of the condition, contributing to the facial manifestations, drooling, and developmental retardation. Seizures occur in approximately one third of individuals [Gibbons et al 1995a].
The majority of affected individuals have gastrointestinal symptoms that contribute significantly to morbidity. Approximately three fourths have gastroesophageal reflux and one third have chronic constipation. Gastric pseudo-obstruction resulting from abnormal suspension of the stomach and constipation resulting from colon hypoganglionosis have been observed [Martucciello et al 2006]. Aspiration, presumably related to gastroesophageal reflux, has been a fatal complication in some.
Although the neurobehavioral phenotype has not been extensively delineated, most individuals appear affable, but some are emotionally labile with tantrums and bouts of prolonged crying or laughing.
Alpha-thalassemia. A microcytic, hypochromic anemia characteristic of alpha-thalassemia may be seen, but many individuals with ATRX syndrome have normal red cell indices and normal hematocrit/hemoglobin. The mutated ATRX gene apparently down-regulates α-globin gene expression in those individuals with HbH inclusions.
Badens et al [2006a] found that mutations in the ATRX zinc finger domain produce severe psychomotor impairment and urogenital anomalies, whereas mutations in the helicase domains cause milder phenotypes.
Heterozygous females rarely show clinical manifestations.
Penetrance is presumed to be 100% in males as ATRX mutations have not been reported in normal males.
"Alpha-thalassemia X-linked mental retardation syndrome" and "ATRX syndrome" have been the two most widely accepted terms for this disorder; however, the preferred designation alpha-thalassemia X-linked intellectual disability in this GeneReview conforms to current terminology.
Carpenter-Waziri syndrome, Holmes-Gang syndrome, and Chudley-Lowry syndrome are allelic, each reported in a single family, and clinically similar to ATRX syndrome [Abidi et al 1999, Stevenson et al 2000a, Abidi et al 2005]; they are now considered to be in the phenotypic spectrum of ATRX syndrome and thus no compelling reason remains to retain their names.
Such is not the case for Juberg-Marsidi syndrome and Smith-Fineman-Myers syndrome; ATRX mutations have not been found in the original families with Juberg-Marsadid syndrome or Smith-Fineman-Myers syndrome; thus, allelism between these and ATRX syndrome cannot be considered proven.
The prevalence is not known. Over 200 affected individuals are known to the laboratories conducting molecular genetic testing; substantial under-ascertainment, especially of those with milder phenotypes, is probable.
No racial or ethnic concentration of individuals has been reported.
Coffin-Lowry syndrome (CLS) is characterized by severe to profound intellectual disability in males and normal intelligence to profound intellectual disability in heterozygous females. Older males have a characteristic facial appearance, and short, soft, and fleshy hands, often with remarkably hyperextensible tapering fingers. Short stature, microcephaly, and dental anomalies are common. Childhood-onset stimulus-induced drop episodes (SIDEs) may affect 10%-20% of individuals; unexpected tactile or auditory stimuli or excitement triggers a brief collapse but no loss of consciousness. Progressive kyphoscoliosis and early mortality are seen. Mutations in RPS6KA3 (previously known as RSK2) are causative. Inheritance is X-linked.
MECP2 duplication syndrome. Duplication of MECP2 and adjacent genes in Xq28 has been associated with a syndrome of severe intellectual disability, spasticity, hypotonia, absent or limited speech, seizures, and recurrent respiratory infections [Friez et al 2006]. Gastrointestinal symptoms with gastroesophageal reflux and swallowing dysfunction occur in most. Half of affected males die by early adulthood. Marked skewing of X-chromosome inactivation occurs in carrier females. The face is not as characteristically hypotonic as in ATRX syndrome, nor does microcephaly occur as commonly. Molecular testing should be used to confirm the diagnosis in each syndrome.
Alpha-thalassemia results from reduced production of the α chains of adult hemoglobin (designated Hb α2β2). In individuals with developmental delay who are of Mediterranean, Southeast Asian, or African American origin, it is appropriate to determine the α-globin genotype. Individuals with ATRX syndrome have a normal α-globin genotype (αα/αα), whereas those with alpha-thalassemia have deletions of one α-globin gene (α-/αα), two α-globin genes ([α-/α-] or [- -/αα]), or three α-globin genes (- -/-α). Intellectual disability is not a component of alpha-thalassemia involving α-globin production.
Alpha-thalassemia mental retardation chromosome 16 (ATR-16) is the association of alpha-thalassemia and intellectual disability in individuals with a contiguous gene deletion involving the distal short arm of chromosome 16. Such deletions produce alpha-thalassemia by deleting the two genes in cis configuration at 16p13 that encode α-globin chains. Because the chromosomal deletions and rearrangements giving rise to ATR-16 are large and variable, no specific clinical phenotype is observed in ATR-16; this is in contrast to ATRX syndrome, in which the phenotype is more predictable.
To establish the extent of disease in an individual diagnosed with alpha-thalassemia X-linked intellectual disability (ATRX) syndrome, the following evaluations are recommended:
The following treatments are recommended:
Antibiotic prophylaxis and vaccination to prevent pneumococcal and meningococcal infection are reasonable precautions in the rare patient with asplenia [Leahy et al 2005].
Growth should be followed regularly in infancy and childhood and plotted on age-appropriate growth charts. (Syndrome-specific growth charts are not available.)
Developmental progress should be monitored throughout infancy and childhood.
See Genetic Counseling for issues related to testing of at-risk relatives for genetic counseling purposes.
Search ClinicalTrials.gov 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.
Anemia, if present, is mild and rarely requires treatment.
Genetic counseling is the process of providing individuals and families with information on the nature, inheritance, and implications of genetic disorders to help them make informed medical and personal decisions. The following section deals with genetic risk assessment and the use of family history and genetic testing to clarify genetic status for family members. This section is not meant to address all personal, cultural, or ethical issues that individuals may face or to substitute for consultation with a genetics professional. —ED.
Alpha-thalassemia X-linked intellectual disability (ATRX) syndrome is inherited in an X-linked manner.
Parents of a proband
Sibs of a proband
Offspring of a proband. No affected individual has reproduced.
Other family members of a proband. The proband's maternal aunts and their offspring may be at risk of being carriers or being affected.
Carrier testing of at-risk female relatives is possible if the disease-causing mutation has been identified in the family.
Assisted reproduction technologies (ART). Donor eggs may be utilized by carrier females to avoid the risk of transmitting an ATRX mutation. Although experience with ART in ATRX syndrome is limited, one female conceived by IVF had total inactivation of her normal X chromosome and the physical and psychomotor findings typical of ATRX syndrome in males [Badens et al 2006b].
Family planning
DNA banking is the storage of DNA (typically extracted from white blood cells) for possible future use. Because it is likely that testing methodology and our understanding of genes, mutations, and diseases will improve in the future, consideration should be given to banking DNA of affected individuals.
Prenatal testing is possible for pregnancies at increased risk for ATRX syndrome.
High-risk pregnancies. For pregnancies in which the mother has been identified as being heterozygous for the disease-causing ATRX mutation identified in the family, the usual procedure is to determine fetal sex on cells obtained from amniocentesis (usually performed at ~15-18 weeks' gestation) or chorionic villus sampling (usually performed at ~10-12 weeks' gestation). If the fetus has a 46,XY karyotype, DNA can be analyzed to determine if the disease-causing ATRX mutation identified in the family is present.
Note: Gestational age is expressed as menstrual weeks calculated either from the first day of the last normal menstrual period or by ultrasound measurements.
Indeterminate-risk pregnancies. Germline mosaicism has been documented in ATRX syndrome [Bachoo & Gibbons 1999]; thus, the mother of a proband who does not demonstrate the ATRX mutation in her leukocytes is still at risk of having a second affected child. Prenatal diagnosis as described for high-risk pregnancies should be offered for all XY fetuses.
Preimplantation genetic diagnosis (PGD) may be an option for some families in which the disease-causing mutation has been identified.
GeneReviews staff has selected the following disease-specific and/or umbrella support organizations and/or registries for the benefit of individuals with this disorder and their families. GeneReviews is not responsible for the information provided by other organizations. For information on selection criteria, click here.
Information in the Molecular Genetics and OMIM tables may differ from that elsewhere in the GeneReview: tables may contain more recent information. —ED.
Table A. Alpha-Thalassemia X-Linked Intellectual Disability Syndrome: Genes and Databases
| Gene Symbol | Chromosomal Locus | Protein Name | Locus Specific | HGMD |
|---|---|---|---|---|
| ATRX | Xq21 | Transcriptional regulator ATRX | ATRX @ LOVD | ATRX |
Table B. OMIM Entries for Alpha-Thalassemia X-Linked Intellectual Disability Syndrome (View All in OMIM)
Normal allelic variants. The gene extends over 350 kb and includes 35 exons.
Pathologic allelic variants. Although mutations have been distributed throughout ATRX, more than 90% of those reported are in the zinc finger and helicase domains [Villard et al 1999b, Villard & Fontes 2002, Borgione et al 2003, Badens et al 2006a, Argentaro et al 2007, Thienpont et al 2007]. Missense mutations appear more commonly than do frameshift and nonsense mutations. Deletions, insertions, intragenic duplications, and missense, nonsense, and splice mutations have been found (for more information, see Table A ).
Normal gene product. Zinc finger domain functions as a transcription factor; the helicase domains function in the transcription process opening double-stranded DNA. In combination with other chromatin-associated proteins, the ATRX protein appears to play a role in chromatin remodeling, possibly silencing gene expression during development [Xue et al 2003, Ausió et al 2003, Tang et al 2004a, Tang et al 2004b, Kernohan et al 2010].
Abnormal gene product. The mutant ATRX protein down-regulates the α-globin locus, resulting in thalassemia, and probably suppresses expression of other genes by disturbances in transcription and chromatin structure, leading to malformations and intellectual disability [Tang et al 2004a, Tang et al 2004b, Argentaro et al 2007, Nan et al 2007, Ritchie et al 2008, Kernohan et al 2010].
Medical Genetic Searches: A specialized PubMed search designed for clinicians that is located on the PubMed Clinical Queries page 
Web: www.ggc.org
Dr. Stevenson's work focuses on the clinical and laboratory delineation of intellectual disability and birth defects.
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