DiagnosisClinical DiagnosisAlpha-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.TestingAffected 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]. Red blood cell indices. Although microcytic hypochromic anemia may be seen in some affected individuals, many have red cell indices in the normal range [Gibbons et al 1995a].HbH inclusions (β-globin tetramers) in erythrocytes can be demonstrated following incubation of fresh blood smears with 1% brilliant cresyl blue (BCB). The proportion of cells with HbH inclusions ranges from 0.01% to 30% [Gibbons et al 1995b].
Note: (1) HbH inclusions may be demonstrated readily in some individuals, found only in an occasional erythrocyte in some, or observed only after repeated testing in others. (2) The absence of HbH inclusions in 10%-20% of affected individuals and the rarity of inclusions (≤1% of erythrocytes) in an additional 40% of affected individuals diminish the utility of this testing in most clinical settings. Hemoglobin electrophoresis can also demonstrate HbH; however, the test is not highly sensitive and may fail to identify many cases. Rare cases of ATRX syndrome have been identified through the detection of HgH on newborn screening for hemoglobinopathies. Female carriers. HbH inclusions are found in only about 25% of female carriers [Gibbons et al 1995b]. Molecular Genetic TestingGene. ATRX is the only gene known to be associated with ATRX syndrome.Clinical testingSequence analysis and mutation scanning of select exons. Approximately 90% of the known ATRX mutations can be detected using sequence analysis of the zinc finger domain (exon 7, exon 8, proximal area of exon 9) and helicase domains (exons 17-20) [Villard & Fontes 2002, Badens et al 2006a, Argentaro et al 2007]. Note: Exons selected for sequencing may vary among laboratories (Table 1).Sequence analysis or mutation scanning of all exons and splice junctions detect the less common mutations located outside the zinc finger and helicase domains. Deletions and duplications have been reported, but no data are available on mutations in the promoter regions.Deletion/duplication analysis. Array CGH or targeted MLPA detects deletions and duplications in affected males and carrier females [Gibbons et al 2008, Lugtenberg et al 2009]. Only a few such genomic alterations have been identified. 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 SyndromeView in own windowGene SymbolTest MethodMutations DetectedMutation Detection Frequency by Test Method ^{1Test Availability Affected Males 2Carrier FemalesATRXSequence analysis of select exonsSequence variants in selected exons 385% 4See footnote 5Clinical Sequence analysis /
mutation scanningSequence variants of coding region and splice junctions 95% 4See footnote 5Deletion / duplication analysis 6Deletions / duplications<5% 4UnknownX-chromosome inactivation studySkewed X-chromosome inactivationNA 795% of carrier females 8 1. The ability of the test method used to detect a mutation that is present in the indicated gene2. 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 applicable8. 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.Testing StrategyConfirming the diagnosis in a probandSequencing of the ATRX zinc finger domain (also designated the PHD and ADD domain) and helicase domain detects more than 80% of mutations (exons 7, 8, 9, and 17-20 inclusively).A second level of molecular testing includes full-gene sequencing or cDNA sequencing to detect exonic and splice mutations outside the zinc finger and helicase domains.Duplication/deletion analysis may be required to identify whole-exon and whole-gene deletions or duplications and to delineate smaller deletions and duplications not readily resolved by sequencing.Although staining of erythrocytes with BCB to identify HbH inclusions has been a helpful and inexpensive adjunct to diagnosis in the past, its utility is diminished by the fact that in 10%-20% of affected individuals, erythrocytes do not have these inclusions and in 40% of affected individuals, no more than 1% of erythrocytes have these inclusions. Nonetheless, the test may be useful in supporting the diagnosis in individuals with clinical findings of ATRX syndrome in whom molecular genetic testing does not identify a mutation.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.Genetically Related (Allelic) DisordersATRX 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]}

Natural HistoryA 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.

Genotype-Phenotype CorrelationsBadens 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.Badens et al [2006b] reported a girl conceived by in vitro fertilization (IVF) who had craniofacial features, growth retardation, and developmental impairment typical of ATRX syndrome. Leukocyte studies showed marked skewing of X-chromosome inactivation with her mutation-bearing X chromosome being the active X chromosome. The role of IVF in this unique case of female expression is not known.Wada et al [2005] reported moderate intellectual disability without other phenotypic features of ATRX syndrome in a female carrier with random X-chromosome inactivation.

Differential DiagnosisCoffin-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.

ManagementEvaluations Following Initial DiagnosisTo establish the extent of disease in an individual diagnosed with alpha-thalassemia X-linked intellectual disability (ATRX) syndrome, the following evaluations are recommended:Review of medical history for developmental progress and seizuresAssessment of growth in infants and childrenPhysical examination including assessment of facial features, muscle tone, and deep tendon reflexesAuscultation of the heart for evidence of structural defectExamination of the genitalia for cryptorchidism and other anomaliesAssessment of feeding in early childhood for swallowing difficulties, gastroesophageal reflux, and/ or recurrent vomitingOphthalmologic evaluation for strabismus, visual acuity problems, or structural eye defects if indicated by clinical assessmentTreatment of ManifestationsThe following treatments are recommended:Calorie-dense formula and/or gavage feeding to compensate for poor nutritional intakeIf food refusal is an issue, evaluation for gastrointestinal causes such as peptic ulcer diseaseIf drooling is a serious problem, treatment with anticholinergics, botulinum toxin type A injection of the salivary glands and/or surgical redirecting of the submandibular ductsTreatment in the usual manner for gastroesophageal reflux, recurrent respiratory and urinary tract infections, seizures, severe behavior problems, anomalies (e.g., cleft palate, cardiac malformations, cryptorchidism, ambiguous genitalia, hypospadias)Early intervention programs and special educationPrevention of Secondary ComplicationsAntibiotic prophylaxis and vaccination to prevent pneumococcal and meningococcal infection are reasonable precautions in the rare patient with asplenia [Leahy et al 2005].SurveillanceGrowth 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.Evaluation of Relatives at RiskSee Genetic Counseling for issues related to testing of at-risk relatives for genetic counseling purposes.Therapies Under InvestigationSearch 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.OtherAnemia, if present, is mild and rarely requires treatment.

Molecular GeneticsInformation 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 DatabasesView in own windowGene SymbolChromosomal LocusProtein NameLocus SpecificHGMDATRXXq21​.1Transcriptional regulator ATRXATRX @ LOVDATRXData are compiled from the following standard references: gene symbol from HGNC; chromosomal locus, locus name, critical region, complementation group from OMIM; protein name from UniProt. For a description of databases (Locus Specific, HGMD) to which links are provided, click here.Table B. OMIM Entries for Alpha-Thalassemia X-Linked Intellectual Disability Syndrome (View All in OMIM) View in own window 300032ATR-X GENE; ATRX 301040ALPHA-THALASSEMIA/MENTAL RETARDATION SYNDROME, X-LINKED; ATRXNormal 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].