Alpha-Thalassemia X-Linked Intellectual Disability Syndrome
Summary
Clinical characteristics.
Alpha-thalassemia X-linked intellectual disability (ATR-X) syndrome is characterized by distinctive craniofacial features, genital anomalies, hypotonia, and mild-to-profound developmental delay / intellectual disability (DD/ID). Craniofacial abnormalities include small head circumference, telecanthus or widely spaced eyes, short triangular nose, tented upper lip, and thick or everted lower lip with coarsening of the facial features over time. While all affected individuals have a normal 46,XY karyotype, genital anomalies comprise a range from hypospadias and undescended testicles, to severe hypospadias and ambiguous genitalia, to normal-appearing female external genitalia. Alpha-thalassemia, observed in about 75% of affected individuals, is mild and typically does not require treatment. Osteosarcoma has been reported in a few males with germline pathogenic variants.
Diagnosis/testing.
The diagnosis of ATR-X syndrome is established in a proband with suggestive findings, a 46,XY karyotype, and a hemizygous pathogenic variant in ATRX identified by molecular genetic testing.
Management.
Treatment of manifestations: DD/ID, seizures, gastrointestinal manifestations and feeding difficulties, excessive drooling, and genital anomalies are managed per standard of care.
Surveillance: Regular assessment of growth and developmental progress in infancy and childhood.
Genetic counseling.
ATR-X syndrome is inherited in an X-linked manner. The mother of a proband may be heterozygous (i.e., a carrier) or the affected individual may have a de novo pathogenic variant. If the mother of the proband has an ATRX pathogenic variant, the chance of transmitting it in each pregnancy is 50%: sibs with a 46,XY karyotype who inherit the pathogenic variant will be affected; sibs with a 46,XX karyotype who inherit the pathogenic variant will be heterozygous and will rarely show clinical manifestations. Affected males do not reproduce. Once the ATRX pathogenic variant in the family has been identified, carrier testing for at-risk females, prenatal testing for pregnancies at increased risk, and preimplantation genetic testing are possible.
Diagnosis
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
- A recognizable pattern of craniofacial findings including small head circumference, upsweep of the frontal hair, telecanthus or widely spaced eyes, short triangular nose, tented upper lip, thick or everted lower lip, and open mouth. Irregular anatomy of the pinnae, widely spaced teeth, and protruding tongue are supplemental findings, the latter two adding to a coarseness of the facial appearance, particularly after the first few years of life.
- Growth impairment including microcephaly and short stature, usually present at birth
- Genital anomalies (in an individual with a 46,XY karyotype) that can range from hypospadias and undescended testes to ambiguous genitalia to normal external female genitalia
- Developmental delay / intellectual disability, typically in the severe-to-profound range
Hematologic findings. Hematologic studies show evidence of alpha-thalassemia in approximately 75% of males with ATR-X syndrome [Gibbons et al 2008].
- HbH inclusions (β-globin tetramers) in erythrocytes can be demonstrated following incubation of fresh blood smears with 1% brilliant cresyl blue. The proportion of cells with HbH inclusions ranges from 0.01% to 30% [Gibbons et al 1995a]. 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. The absence of HbH inclusions in one fourth 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.
- Red blood cell indices. A microcytic hypochromic anemia characteristic of alpha-thalassemia may be seen in some affected individuals, but many have red cell indices in the normal range [Gibbons et al 1995b].
- Newborn screening. In rare instances, ATR-X syndrome has been identified through the detection of HgH on newborn screening for hemoglobinopathies.
Family history consistent with X-linked inheritance (e.g., no male-to-male transmission). Absence of a known family history does not preclude the diagnosis.
Establishing the Diagnosis
The diagnosis of ATR-X syndrome is established in a male proband with suggestive findings and a hemizygous pathogenic variant in ATRX identified by molecular genetic testing (see Table 1).
Note: Identification of a hemizygous ATRX variant of uncertain significance does not establish or rule out a diagnosis of this disorder.
Molecular Genetic Testing
Molecular genetic testing approaches can include a combination of gene-targeted testing (single-gene testing and multigene panel) and comprehensive genomic testing (exome sequencing, exome array, genome sequencing) depending on the phenotype. Gene-targeted testing requires that the clinician determine which gene(s) are likely involved, whereas genomic testing does not.
Single-gene testing. Sequence analysis of ATRX is performed first to detect small intragenic deletions/insertions and missense, nonsense, and splice site variants. Note: Depending on the sequencing method used, single-exon, multiexon, or whole-gene deletions/duplications may not be detected. If no variant is detected by the sequencing method used, the next step is to perform gene-targeted deletion/duplication analysis to detect exon and whole-gene deletions or duplications.
Multigene panel. An X-linked intellectual disability panel and other multigene panels that include ATRX and other genes of interest (see Differential Diagnosis) are most likely to identify the genetic cause of the condition at the most reasonable cost while limiting identification of variants of uncertain significance and pathogenic variants in genes that do not explain the underlying phenotype. Note: (1) The genes included in the panel and the diagnostic sensitivity of the testing used for each gene vary by laboratory and are likely to change over time. (2) Some multigene panels may include genes not associated with the condition discussed in this GeneReview. (3) In some laboratories, panel options may include a custom laboratory-designed panel and/or custom phenotype-focused exome analysis that includes genes specified by the clinician. (4) Methods used in a panel may include sequence analysis, deletion/duplication analysis, and/or other non-sequencing-based tests.
For an introduction to multigene panels click here. More detailed information for clinicians ordering genetic tests can be found here.
Comprehensive genomic testing. This approach does not require the clinician to determine which genes are likely involved. Exome sequencing is commonly used; genome sequencing is becoming possible in some laboratories.
If exome sequencing is not diagnostic, exome array should be considered to detect (multi)exon deletions or duplications that cannot be detected by sequence analysis.
For an introduction to comprehensive genomic testing click here. More detailed information for clinicians ordering genomic testing can be found here.
Table 1.
Molecular Genetic Testing Used in ATR-X Syndrome
| Gene 1 | Method | Proportion of Probands with a Pathogenic Variant 2 Detectable by Method |
|---|---|---|
| ATRX | Sequence analysis 3, 4 | ~95% 5 |
| Gene-targeted deletion/duplication analysis 6 | ~5% 6 |
- 1.
See Table A. Genes and Databases for chromosome locus and protein.
- 2.
See Molecular Genetics for information on allelic variants detected in this gene.
- 3.
Sequence analysis detects variants that are benign, likely benign, of uncertain significance, likely pathogenic, or pathogenic. Variants may include small intragenic deletions/insertions and missense, nonsense, and splice site variants; typically, exon or whole-gene deletions/duplications are not detected. For issues to consider in interpretation of sequence analysis results, click here.
- 4.
Lack of amplification by PCR prior to sequence analysis can suggest a putative (multi)exon or whole-gene deletion on the X chromosome in affected males; confirmation requires additional testing by gene-targeted deletion/duplication analysis.
- 5.
Based on data from the subscription-based professional view of Human Gene Mutation Database [Stenson et al 2017]
- 6.
Gene-targeted deletion/duplication analysis detects intragenic deletions or duplications. Methods used may include quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), and a gene-targeted microarray designed to detect single-exon deletions or duplications. Gene-targeted deletion/duplication testing will detect deletions ranging from a single exon to the whole gene; however, of note: whole-gene duplications but not deletions have been reported. Breakpoints of large duplications and/or duplication of adjacent genes (e.g., those described by Honda et al [2012], Isrie et al [2012], and Lugtenberg et al [2009]) may not be detected by these methods.
Other Testing
Epigenetic signature analysis / methylation microarray. A characteristic methylation signature identified on epigenetic signature analysis of leukocytes in individuals with ATR-X syndrome [Schenkel et al 2017] may be useful as a first-tier screening test in an individual with an atypical phenotype or as a second-tier test when molecular genetic testing identifies an ATRX variant of uncertain significance.
Clinical Characteristics
Clinical Description
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 [Gibbons et al 1995b, Badens et al 2006a, Stevenson et al 2012].
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 Yntema et al [2002] appeared to have nonsyndromic X-linked ID (XLID), although childhood photographs showed evidence of facial hypotonia. Basehore et al [2015] reported 25 affected males in five families with the p.Arg37Ter variant who had variable but overall milder phenotypes (see Genotype-Phenotype Correlations).
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. | |
| Intellectual disability | 100% | Variable severity, from mild to profound | |
Characteristic facies
| 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% | Contributes to facial phenotype |
| Seizures | 30%-40% | ||
Developmental Impairment / Intellectual Disability
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.
Growth Impairment
Growth impairment with microcephaly and short stature occurs in most individuals with ATR-X syndrome and is often present at birth. Stature is typically short (>2 SD below the mean in 67% of individuals using standard growth charts; syndrome-specific growth charts are not available). Growth above average is exceptional.
Gastrointestinal Manifestations
Gastrointestinal manifestations, present in the majority of individuals, contribute significantly to morbidity. Approximately three fourths have gastroesophageal reflux and one third have chronic constipation. Gastric pseudo-obstruction can result from abnormal suspension of the stomach and constipation can result from colon hypoganglionosis [Martucciello et al 2006]. Aspiration, presumably related to gastroesophageal reflux, has been a fatal complication in some.
Genital Anomalies
Genital anomalies are often minor, including first-degree hypospadias, undescended testes, and underdevelopment of the scrotum. Although all individuals with ATR-X syndrome have a normal 46,XY karyotype, gonadal dysgenesis resulting in inadequate testosterone production can cause more severe defects that can include second- and third-degree hypospadias, small penis, ambiguous genitalia, or even normal-appearing female external genitalia. Although all individuals with ATR-X syndrome have a normal 46,XY karyotype, occasionally gonadal dysgenesis results in inadequate testosterone production and ambiguous genitalia. Although the spectrum of possible genital anomalies in ATR-X syndrome is broad, the type of genital anomaly appears to be consistent within a family.
Hypotonia
Hypotonia, a hallmark of ATR-X syndrome, contributes to the facial manifestations, drooling, developmental delay, and possibly to the gastrointestinal manifestations.
Seizures
Seizures of various types occur in about one third of individuals with ATR-X syndrome but are not a defining manifestation of the syndrome [Gibbons et al 1995b, Stevenson et al 2012, Giacomini et al 2019]. Brain atrophy and white matter abnormalities have been found on MRI and CT imaging [Wada et al 2013].
Other
The neurobehavioral phenotype has not been extensively delineated; however, most individuals appear affable, but some are emotionally labile with tantrums and bouts of prolonged crying or laughing.
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) occur, but do not contribute significantly to morbidity.
Major malformations are not common, but ocular coloboma, cleft palate, cardiac defects, inguinal hernia, heterotaxy, and asplenia [Leahy et al 2005] have been reported.
Although predisposition to tumor development has not been confirmed in individuals with germline ATRX pathogenic variants, four children with ATR-X syndrome have developed osteosarcoma [Ji et al 2017, Masliah-Planchon et al 2018], a finding that contrasts with the well-recognized tumor association of somatic ATRX pathogenic variants (see Cancer and Benign Tumors). Masliah-Planchon et al [2018] provide clinical, histologic, and genetic data supporting the possibility of tumor predisposition associated with germline ATRX pathogenic variants in their report of three instances of osteosarcoma in two males:
- One individual with two metachronous osteosarcomas, the first (of the tibia) diagnosed and successfully treated at age nine years, and the second (of the humerus) diagnosed and successfully treated ten years later at age 20 years
- One child, diagnosed with osteosarcoma of the femur with pulmonary nodules at age four years, who succumbed 18 months later
Heterozygous Females
Heterozygous females rarely show clinical manifestations. Typically, carrier females have marked skewing of X-chromosome inactivation (>90:10) with preferential inactivation of the X chromosome with the ATRX pathogenic variant. Rare exceptions have been reported, including the following:
- A five-generation pedigree in which three females had signs of ATR-X syndrome [Christensen et al 1999]
- Moderate ID without other phenotypic features of ATR-X syndrome in a female carrier with random X-chromosome inactivation [Wada et al 2005]
- A girl conceived by in vitro fertilization (IVF) who had craniofacial features, growth retardation, and developmental impairment typical of ATR-X syndrome [Badens et al 2006b]. Leukocyte studies showed marked skewing of X-chromosome inactivation with her pathogenic variant-bearing X chromosome being the active X chromosome. The role of IVF in this unique case of female expression is not known.
Genotype-Phenotype Correlations
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 [Badens et al 2006a].
More severe genital anomalies occur with variants in the plant homeodomain-like domain.
A nonsense variant in exon 2 (p.Arg37Ter) appears to be a common pathogenic variant that results in an overall milder phenotype [Basehore et al 2015] (see Table 7).
Nomenclature
"Alpha-thalassemia X-linked intellectual disability syndrome" and "ATR-X syndrome" are the preferred designations for this disorder.
ATRX pathogenic variants have been found in several named XLID syndromes (Carpenter-Waziri syndrome, Holmes-Gang syndrome, Chudley-Lowry syndrome, XLID-arch fingerprints – hypotonia), in XLID with spastic paraplegia, in XLID with epilepsy, and in nonsyndromic XLID [Lossi et al 1999, Stevenson 2000, Stevenson et al 2000, Yntema et al 2002, Stevenson et al 2012]. These entities should be considered to be in the phenotypic spectrum of ATR-X syndrome; there are no compelling reasons to maintain the syndromic names.
Note: A family considered to have Juberg-Marsidi syndrome was found to have an ATRX pathogenic variant [Villard et al 1996]. Subsequently, the original family reported with Juberg-Marsidi syndrome was found to have a HUWE1 pathogenic variant, indicating that the family studied by Villard et al [1996] represented a misdiagnosis [Friez et al 2016].
Although two families considered to have Smith-Fineman-Myers syndrome have ATRX pathogenic variants, the original family with Smith-Fineman-Myers has not been restudied. Hence, the relationship of ATR-X syndrome and Smith-Fineman-Myers syndrome is unclear [Villard et al 1999a, Li et al 2020].
Prevalence
The prevalence is not known. More than 200 affected individuals are known to the laboratories conducting molecular genetic testing; substantial underascertainment, especially of those with milder phenotypes, is probable.
No racial or ethnic concentration of individuals has been reported.
Differential Diagnosis
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 | |
|---|---|---|---|---|
| Overlapping w/ATR-X syndrome | Not observed in ATR-X syndrome | |||
| HBA1 HBA2 | Hemoglobin H (HbH) disease (See Alpha-Thalassemia.) | AR 1 | Microcytic hypochromic hemolytic anemia, hepatosplenomegaly, mild jaundice, & sometimes thalassemia-like bone changes |
|
| MECP2 + adjacent genes in Xq28 | MECP2 duplication syndrome | XL |
|
|
| RPS6KA3 | Coffin-Lowry syndrome | XL |
|
|
AR = autosomal recessive; DiffDx = differential diagnosis; GI = gastrointestinal; ID = intellectual disability; MOI = mode of inheritance; XL = X-linked
- 1.
Alpha-thalassemia is usually inherited in an autosomal recessive manner.
- 2.
Childhood-onset SIDAs (stimulus-induced drop attacks) refers to a brief collapse (but no loss of consciousness) triggered by unexpected tactile or auditory stimuli or excitement.
Alpha-thalassemia intellectual disability, chromosome 16-related (ATR-16 syndrome; OMIM 141750) 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 chromosome 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 ATR-X syndrome, in which the phenotype is more predictable.
Management
Evaluations Following Initial Diagnosis
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 in Table 4 (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 |
|---|---|---|
| Growth | Assess height, weight, head circumference | In infants & children |
| Development | Developmental assessment |
|
| Neurologic | Neurologic eval |
|
| Gastrointestinal/ Feeding | Gastroenterology / nutrition / feeding team eval | For:
|
| 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 |
| Musculoskeletal | Orthopedics / physical medicine & rehabilitation / PT/OT eval | To incl assessment of:
|
| Congenital heart defects | Pediatric cardiologist | Septal defects require eval re possible intervention. |
| Ophthalmologic involvement | Ophthalmologic exam | Assess for strabismus, ↓ visual acuity, structural eye defects (e.g., coloboma). |
| Genetic counseling | By genetics professionals 1 | To inform affected individuals & their families re nature, MOI, & implications of ATR-X syndrome in order to facilitate medical & personal decision making |
| Family support/ resources | Assess:
|
GERD = gastroesophageal reflux disease; MOI = mode of inheritance; OT = occupational therapy; PT = physical therapy
- 1.
Medical geneticist, certified genetic counselor, certified advanced genetic nurse
Treatment of Manifestations
Table 5.
Treatment of Manifestations in Individuals with ATR-X Syndrome
| Manifestation/Concern | Treatment | Considerations/Other |
|---|---|---|
| DD/ID | See Developmental Delay / Intellectual Disability Management Issues. | |
| Seizures | Standardized treatment w/AEDs by experienced neurologist |
|
| Gastrointestinal/ Feeding | Feeding therapy; calorie-dense formula; gastrostomy tube placement as needed for persistent feeding issues |
|
| Drooling | Anticholinergics, botulinum toxin type A injection of salivary glands &/or surgical redirecting of submandibular ducts | Options when drooling is a serious problem |
| Genital abnormalities | Per treating urologist | |
| Musculoskeletal | Orthopedics / physical medicine & rehabilitation / PT / OT | Use of durable medical equipment & positioning devices as needed (e.g., wheelchairs, walkers, bath chairs, orthotics, adaptive strollers) |
| Congenital heart defects | Per treating cardiologist | |
| Ophthalmologic involvement | Per treating ophthalmologist |
AED = antiepileptic drug; DD = developmental delay; ID = intellectual disability; OT = occupational therapy; PT = physical therapy
Developmental Disability / Intellectual Disability Management Issues
The following information represents typical management recommendations for individuals with developmental delay