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SATB2-Associated Syndrome

Synonyms: 2q32 Deletion Syndrome, 2q33.1 Microdeletion Syndrome, Glass Syndrome

, MD, , MS, and , PhD.

Author Information and Affiliations

Initial Posting: ; Last Update: June 20, 2024.

Estimated reading time: 38 minutes

Summary

Clinical characteristics.

SATB2-associated syndrome (SAS) is a multisystem disorder in which all affected individuals have developmental delay / intellectual disability that can range from mild to profound but is most commonly moderate to profound. Speech delay and/or absent speech is observed in all affected individuals. Other neurobehavioral manifestations can include jovial or friendly personality, autistic tendencies, agitation or aggressive outbursts, self-injury, impulsivity, hyperactivity, anxiety, difficulty falling asleep or maintaining sleep, and sensory issues. Most affected individuals have hypotonia. EEG abnormalities are frequent but may be without clinically recognizable seizures. While only about 20% of affected individuals have clinical seizures, a subset of affected individuals have electrical status epilepticus in sleep. Craniofacial findings can include nonspecific dysmorphic features, palatal anomalies (cleft palate, high-arched palate, velopharyngeal insufficiency, bifid uvula), and dental anomalies (abnormal shape or size or the upper central incisors, dental crowding, hypodontia, and delayed teeth eruption, among others). Skeletal anomalies can include scoliosis, tibial bowing, and joint contractures. At least one third of individuals have a history of previous fractures and about one quarter of affected individuals have documented low bone mineral density. Other finding can include pre- and postnatal growth restriction, feeding issues, and eye anomalies (strabismus, refractive error). In those with a larger deletion involving SATB2 and adjacent genes, cardiovascular, genitourinary, and ectodermal findings may also be present.

Diagnosis/testing.

The diagnosis of SAS is established in a proband with suggestive findings and identification of one of the following by molecular genetic testing: a heterozygous intragenic SATB2 pathogenic variant; a heterozygous non-recurrent deletion at 2q33.1 that includes SATB2; a chromosome translocation or inversion with a 2q33.1 breakpoint that disrupts SATB2; a chromosomal duplication with breakpoints that encompass SATB2.

Management.

Treatment of manifestations: Standard treatment for developmental delay / intellectual disability, neurobehavioral issues, cleft palate, micrognathia, dental anomalies, scoliosis, tibial bowing, joint contractures, spasticity, epilepsy, undescended testes, inguinal hernia, hypospadias, refractive error, strabismus, and congenital heart defects. For those with feeding issues and/or poor weight gain, feeding therapy is typically recommended, with a low threshold for clinical feeding evaluation and/or radiographic swallowing study if there are signs or symptoms of dysphagia. A gastrostomy tube placement may be required for persistent feeding issues. Sleep disturbance may respond to sleep hygiene healthy habits and potential medical management, as needed. In those with restless sleep, an overnight EEG to explore potential epileptogenic abnormalities may be considered. To address osteopenia / frequent fractures, optimize physical activity and calcium / vitamin D levels; denosumab and bisphosphonates have also been used with no direct comparison between the different options.

Surveillance: At each visit, measure growth parameters, nutrition status, and safety of oral intake; assess for new manifestations, such as seizures or changes in tone; monitor developmental progress and educational needs; assess for anxiety, ADHD, ASD, aggression, & self-injury; evaluate for scoliosis and spine deformities; and assess for signs/symptoms of sleep disturbance. At least annually, dental evaluation with consideration of orthodontics; ophthalmology evaluation; obtain a DXA scan for bone mineral density if z score is below −1; measure alkaline phosphatase level (if previously elevated). Every two years, obtain a DXA scan for bone mineral density if z score is above −1; measure alkaline phosphatase level (if previously normal).

Genetic counseling.

SAS is an autosomal dominant disorder. Almost all probands with SAS reported to date have the disorder as the result of a de novo genetic event. In approximately 1% of affected individuals, SAS is the result of a genetic alteration inherited from a mosaic parent. To date, individuals with SAS are not known to reproduce. Once the genetic alteration has been identified in an affected family member, prenatal and preimplantation genetic testing are possible.

Diagnosis

No formal clinical diagnostic criteria have been established for SATB2-associated syndrome (SAS).

Suggestive Findings

SAS should be suspected in individuals with the following clinical and family history findings.

Clinical findings

  • Typically moderate-to-profound developmental delay or intellectual disability, including severe speech delay and, in some, absence of speech; however, individuals with milder developmental delay affecting predominantly speech have been reported.

AND

  • Any of the following features presenting in infancy or childhood:
    • Infantile hypotonia and feeding difficulties (relatively common)
    • Neurobehavioral/psychiatric manifestations, including autistic tendencies, hyperactivity, and aggressiveness
    • Palatal anomalies, such as cleft palate, bifid uvula, and high-arched palate
    • Dental anomalies, including prominent upper incisors, crowding, and delayed eruption
    • Skeletal anomalies, including osteopenia, bowing of long bones, scoliosis, and increased risk of fractures
    • Dysmorphic facial features (See Clinical Characteristics.)
    • Seizures

Note: Some of the common features can be described using the acronym SATB2: severe speech anomalies; abnormalities of the palate, teeth anomalies, behavioral issues with or without bone or brain anomalies, and onset before age 2.

Family history. Because SAS is typically caused by a de novo pathogenic variant, most probands represent a simplex case (i.e., a single occurrence in a family). However, rare familial cases (multiple affected sibs) due to presumed or confirmed parental mosaicism have been reported [Grelet et al 2019, Qian et al 2019, Zarate et al 2019].

Establishing the Diagnosis

The diagnosis of SAS is established in a proband with suggestive findings and identification of one of the following by molecular genetic testing (see Table 1):

  • A heterozygous intragenic SATB2 pathogenic (or likely pathogenic) variant
  • A heterozygous non-recurrent deletion at 2q33.1 that includes SATB2
  • A chromosome translocation or inversion with a 2q33.1 breakpoint that disrupts SATB2
  • A chromosomal duplication with breakpoints that encompass SATB2

Note: (1) Per ACMG/AMP variant interpretation guidelines, the terms "pathogenic variant" and "likely pathogenic variant" are synonymous in a clinical setting, meaning that both are considered diagnostic and can be used for clinical decision making [Richards et al 2015]. Reference to "pathogenic variants" in this GeneReview is understood to include likely pathogenic variants. (2) Identification of a heterozygous SATB2 variant of uncertain significance does not establish or rule out the diagnosis.

Molecular genetic testing in a child with developmental delay or an older individual with intellectual disability may begin with exome sequencing / genome sequencing [Manickam et al 2021, van der Sanden et al 2023]. Other options include use of chromosomal microarray analysis or a multigene panel. Note: Single-gene testing (sequence analysis of SATB2, followed by gene-targeted deletion/duplication analysis) is rarely useful and typically NOT recommended.

  • Comprehensive genomic testing does not require the clinician to determine which gene(s) are likely involved. Exome sequencing is most commonly used and yields results similar to an intellectual disability multigene panel, with the additional advantage that exome sequencing includes genes recently identified as causing intellectual disability, whereas some multigene panels may not. Genome sequencing is also possible.
    For an introduction to comprehensive genomic testing click here. More detailed information for clinicians ordering genomic testing can be found here.
  • Chromosomal microarray analysis (CMA) uses oligonucleotide or SNP arrays to detect genome-wide large deletions/duplications (including SATB2) that cannot be detected by sequence analysis.
    For an introduction to CMA click here. More detailed information for clinicians ordering genetic tests can be found here.
  • An intellectual disability multigene panel that includes SATB2 and other genes of interest (see Differential Diagnosis) is likely to identify the genetic cause of the condition in a person with a nondiagnostic CMA 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.
  • Karyotype. If a 2q33.1 deletion or duplication is not identified on CMA and an intragenic pathogenic variant has not been identified on either a multigene panel or comprehensive genomic testing (genomic sequencing and exome array), additional options for testing include karyotype. Chromosome translocations with a 2q33.1 breakpoint that disrupts SATB2 have rarely been observed in individuals with SAS (see Table 1).

Table 1.

Molecular Genetic Testing Used in SATB2-Associated Syndrome

Gene 1MethodProportion of Pathogenic Variants 2 Identified by Method
SATB2 Sequence analysis 3~74% 4
Gene-targeted deletion/duplication analysis 5, 6See footnote 7.
CMA 8~25% 4, 9
Karyotype (to detect structural variants)~1% 4, 10
1.

See Table A. Genes and Databases for chromosome locus and protein.

2.

See Molecular Genetics for information on 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 missense, nonsense, and splice site variants and small intragenic deletions/insertions; typically, exon or whole-gene deletions/duplications are not detected. For issues to consider in interpretation of sequence analysis results, click here.

4.
5.

Gene-targeted deletion/duplication analysis detects intragenic deletions or duplications. Methods used may include a range of techniques such as quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), and a gene-targeted microarray designed to detect single-exon deletions or duplications. Exome and genome sequencing may be able to detect deletions/duplications using breakpoint detection or read depth; however, sensitivity can be lower than gene-targeted deletion/duplication analysis.

6.

Gene-targeted deletion/duplication testing will detect deletions ranging from a single exon to the whole gene; however, breakpoints of large deletions and/or deletion of adjacent genes may not be detected by some of these methods.

7.

Note that, although gene-targeted deletion/duplication assays may detect smaller events than genomic deletion/duplication assays, they will detect larger events but may not be able to determine the size. In general, all deletions/duplications detectable through CMA should also be detectable through gene-targeted deletion/duplication assays.

8.

CMA uses oligonucleotide or SNP arrays to detect genome-wide large deletions/duplications (including SATB2) that may not be detected by sequence analysis. The ability to determine the size of the deletion/duplication depends on the type of microarray used and the density of probes in the 2q33.1 region. CMA designs in current clinical use target the 2q33.1 region.

9.

In addition to detecting the 2q33.1 deletion, CMA can identify intragenic deletions and duplications [Rosenfeld et al 2009, Balasubramanian et al 2011, Asadollahi et al 2014, Liedén et al 2014, Kaiser et al 2015, Zarate et al 2019].

10.

Six individuals with a SATB2 disruption resulting from a "balanced translocation" have been described [Brewer et al 1999, FitzPatrick et al 2003, Baptista et al 2008, Tegay et al 2009, Talkowski et al 2012, Rainger et al 2014].

Clinical Characteristics

Clinical Description

SATB2-associated syndrome (SAS) is a multisystem disorder characterized by significant neurodevelopmental compromise with limited or absent speech, behavioral issues, and craniofacial anomalies.

To date, more than 500 individuals have been identified with a pathogenic variant in SATB2 [Bengani et al 2017, Zarate et al 2019, Mouillé et al 2022, Zarate et al 2022, Zarate et al 2024a]. The following description of the phenotypic features associated with this condition is based on these reports.

Table 2.

SATB2-Associated Syndrome: Frequency of Select Features

Finding% of Affected Persons 1Comment
Developmental delay / intellectual disability100%Most commonly in the moderate-to-profound range
Speech delay100%
Craniofacial dysmorphism84%
Dental anomalies98%
Behavioral issues55%
Elevated alkaline phosphatase62%
Cleft palate45%
Abnormal neuroimaging68%
Micrognathia42%
Hypotonia59%
Feeding difficulties68%
Low weight22%
Low bone density26%
Clinical seizures20%
1.

Complete information was not available for some individuals.

Developmental delay (DD) and intellectual disability (ID). All known individuals with SAS have some degree of developmental delay, often with intellectual disability of variable severity (mild to profound).

  • Speech/language. Severe verbal expressive language deficits and childhood apraxia of speech are often observed, while receptive language skills can be more preserved [Zarate & Fish 2017, Thomason et al 2019, Zarate et al 2019, Snijders Blok et al 2021].
    • Most individuals are nonverbal communicators and use gestures, signs, or augmentative and alternative communication (AAC) devices as their primary way to communicate [Thomason et al 2019].
    • For individuals with a heterozygous pathogenic variant within SATB2 (those who do not have a larger deletion of 2q33.1 that includes SATB2 and other genes), mean age at first word is 19.8 months (range: 13-42 months), although some never achieve verbal communication [Zarate et al 2017].
    • In a single study analyzing the long-term history of 49 individuals age 12 years or older with SAS, difficulties with speech were persistent, with 69% of individuals having ten or fewer words of total speech [Zarate et al 2021a].
  • Motor skills. For individuals with a heterozygous pathogenic variant within SATB2 (those who do not have a larger deletion of 2q33.1 that includes SATB2 and other genes), mean age at walking is 20.9 months (range: 11-35 months).
  • Education / daily living. In a single study analyzing the long-term history of 49 individuals age 12 years or older with SAS [Zarate et al 2021a]:
    • More than half of the cohort was able to read single words and type letters on a keyboard independently;
    • For 79% of adults (n=24), the highest level of education was high school, and only one individual was employed;
    • Most individuals required some degree of assistance for activities of daily living and needed supervision to remain home on their own.

Developmental regression and/or cognitive decline has been described once in an adult female with an 8.6-Mb deletion of 2q32.2-q33.1 who progressed from mild to severe intellectual disability and from poor to absent speech between ages six and 12 years [Gregoric Kumperscak et al 2016].

Neurobehavioral/psychiatric/sleep manifestations. A broad spectrum of behavioral findings has been described, including jovial or friendly personality, autistic tendencies, agitation or aggressive outbursts, self-injury, impulsivity, hyperactivity, anxiety, difficulty falling asleep or maintaining sleep, and sensory issues [Bengani et al 2017, Zarate et al 2017, Cotton et al 2020, Bissell et al 2022, Shelley et al 2023]. There is no evidence that affected individuals have a higher rate of sleep apnea compared to the general population; however, electrical status epilepticus in sleep has been reported. Two affected females were described to have Rett syndrome-like phenotypes with limited purposeful hand movements, stereotyped repetitive movements, and bruxism [Lee et al 2016]. Additional behavioral issues include high pain tolerance, obsessive tendencies, and skin picking [Zarate et al 2017].

Other neurologic manifestations

  • Hypotonia, particularly during infancy (59%)
  • Clinical seizures (20%)
  • EEG abnormalities are frequent but may be without clinically recognizable seizures [Zarate et al 2017, Lewis et al 2020]. Electroencephalographic anomalies are particularly common during sleep stages and may include electrical status epilepticus in sleep.
  • Less common neurologic issues include gait abnormalities / ataxia (17%), hypertonicity and/or spasticity (4%), and hyperreflexia (3%).

Neuroimaging. Brain abnormalities, documented in 68% of affected individuals who underwent head MRI, include nonspecific findings. Most commonly, delayed myelination or abnormal white matter hyperintensities are reported [Lewis et al 2020]. Less frequently, described anomalies include enlarged ventricles, agenesis of the corpus callosum, lissencephaly, brain atrophy, and prominent perivascular spaces [Zarate & Fish 2017, Zarate et al 2017, Lewis et al 2020, Lo et al 2022]. Note that these findings are not sufficiently distinct to suggest the diagnosis of SAS.

Dysmorphic facial features are often observed and persist through adulthood. If present, dysmorphic features are nonspecific. The most frequently described features include the following (see Figure 1 A-E) [Bengani et al 2017, Zarate & Fish 2017, Zarate et al 2017, Zarate et al 2018a, Zarate et al 2021b]:

Figure 1. . Facial features of individuals with SATB2-associated syndrome caused by intragenic pathogenic variants in SATB2 (A-D), intragenic deletion of SATB2 (E), and large deletions that include SATB2 and other adjacent genes (F-G).

Figure 1.

Facial features of individuals with SATB2-associated syndrome caused by intragenic pathogenic variants in SATB2 (A-D), intragenic deletion of SATB2 (E), and large deletions that include SATB2 and other adjacent genes (F-G). The most consistently reported (more...)

  • Deep-set eyes
  • Long, smooth philtrum
  • Thin vermilion of the upper lip
  • Abnormal chin morphology

In those with larger 2q33.1 deletions, additional features can include a prominent forehead, high anterior hairline, triangular appearance of the lower face, low-set ears, and/or long face (see Figure 1 F-G) [Zarate & Fish 2017, Zarate et al 2021b].

Craniofacial anomalies / feeding. The combination of craniofacial issues and hypotonia is the most likely explanation for the high frequency of feeding issues present during infancy and beyond. Thomason et al [2019] established that 68% of individuals with SAS had feeding difficulties, including overstuffing, chewing problems, or pharyngeal dysphagia. These feeding difficulties can be seen even in individuals without a palatal defect.

  • Palatal abnormalities documented in 76% of individuals include cleft palate (45%), high-arched palate, velopharyngeal insufficiency, and bifid uvula (3%) [Zarate et al 2019, Perry et al 2023].
  • Micrognathia, diagnosed in 42% of individuals, has rarely required surgical correction.
  • Mandibular hypoplasia and asymmetric jaw have also been documented radiographically [Zarate et al 2024b].

Dental anomalies. A broad range of dental abnormalities have been reported in the literature [Zarate et al 2017, Scott et al 2019, Li et al 2022, Kurosaka et al 2023] or by families [Zarate et al 2017, Scott et al 2019].

  • Dental anomalies include:
    • Abnormal shape or size or the upper central incisors (67%)
    • Dental crowding, hypodontia, and delayed teeth eruption (76%)
    • Pulp stones
    • Malformed crowns and/or diastema
    • Fused incisors
  • Other issues include:
    • Sialorrhea
    • Bruxism
    • Malocclusion
    • Frequent trauma to maxillary anterior teeth
  • Dental radiographs. In a cohort of 18 individuals with SAS, dental radiographs revealed abnormalities in all cases starting at age two years [Scott et al 2018]. The most common findings include:
    • Delayed development of the mandibular second bicuspids (83%)
    • Delayed development of the roots of the permanent teeth (78%)
    • Rotated (56%) or malformed (44%) teeth
    • Taurodontism (44%)

Skeletal findings. A broad range of skeletal issues have been described in individuals with SAS [Zarate et al 2018a, Mouillé et al 2022, Zarate et al 2024b].

  • Fractures/osteopenia. At least one third of individuals have a history of previous fractures.
    • Bone mineral density is reported to be low (z scores two or more standard deviations below the mean on DXA scan) in 26% of affected individuals.
    • Detailed skeletal radiographic characterization in a cohort of individuals with SAS revealed frequent abnormalities such as skeletal demineralization (94%), calvaria digitiform impressions (57%), vertebral compression fractures (35%), metaphyseal long bone striations (68%), and small epiphyses (63%), among others [Mouillé et al 2022].
    • Biochemically, markers of bone formation and resorption are often elevated in individuals with SAS; 62% of affected individuals have elevated alkaline phosphatase levels, often with low vitamin D and high phosphate levels. However, high alkaline phosphatase levels do not seem to predict the presence of low bone density [Mouillé et al 2022, Zarate et al 2024a].
  • Skeletal anomalies may include the following [Zarate et al 2018b, Mouillé et al 2022, Zarate et al 2024a]:
    • Pectus deformities
    • Kyphosis/lordosis
    • Scoliosis
    • Small hands/feet
    • Arachnodactyly
    • Broad thumbs or halluces
    • Clinodactyly
    • Finger contractures
    • Tibial bowing

Growth restriction. Pre- and postnatal growth restriction, particularly with slower-than-expected weight gain, can be seen in individuals with SAS. Individuals with large contiguous chromosomal deletions encompassing SATB2 have more significant issues with growth. Normative growth curves for individuals with SAS have been published [Zarate et al 2022].

Eye findings. Both strabismus (18%) and refractive errors (8%) have been described.

Cardiovascular. For individuals with intragenic pathogenic variants, cardiovascular findings appear to be minimal. However, in individuals with large deletions involving SATB2 and adjacent genes, aortic dilatation, pulmonary hypertension, and septal defects have been reported. See also Genotype-Phenotype Correlations for cardiovascular issues due to loss of specific adjacent genes.

Genitourinary. Small or undescended testicles, inguinal hernias, and hypospadias have been described in males with large deletions involving SATB2 and adjacent genes.

Ectodermal changes. Thin skin, reduced subcutaneous fat, and thin or sparse hair have been described in some affected individuals with large deletions involving SATB2 and adjacent genes.

Other features. Hypothyroidism has rarely been reported [Zarate et al 2024b]. Families often report other symptoms, including gastrointestinal (constipation or diarrhea) and immunologic issues (frequent infections).

Genotype-Phenotype Correlations

SATB2 pathogenic variants

  • More severe clinical phenotype. Using a clinical scoring rubric developed for SAS, individuals with the following types of SATB2 pathogenic variants have a more severe clinical phenotype [Zarate et al 2023; Y Zarate, unpublished data] (see also satb2-portal.broadinstitute.org):
  • Milder clinical phenotype. Missense pathogenic variants located outside the CUT1 or CUT2 domains lead to milder clinical presentations.

Large deletions that include SATB2 and adjacent genes. In general, individuals with larger deletions have a more severe clinical phenotype (see satb2-portal.broadinstitute.org). The following features are more common (or exclusively present) in these affected individuals [Zarate & Fish 2017]:

  • Genitourinary anomalies
  • Cardiac defects
  • Ectodermal changes (other than dental)
  • Growth restriction (65% of individuals with large deletions vs 31% of individuals with intragenic pathogenic variants) [Zarate et al 2021b]

Nomenclature

The term "Glass syndrome" was suggested after a report of a male with a cytogenetically visible 2q32.2-q33.1 deletion that included SATB2 was published [Glass et al 1989]. SATB2 was subsequently identified as the gene associated with this syndrome [FitzPatrick et al 2003]. In this GeneReview, the authors have documented a consistent phenotype independent of the underlying SATB2 genetic alteration. Accordingly, over the last few years, the designation SATB2-associated syndrome has been used consistently in the literature and adopted by the SATB2 Gene Foundation supporting individuals with this syndrome.

Prevalence

Two studies have estimated the frequency of SAS in large cohorts of individuals with undiagnosed intellectual disability / developmental delay to be 0.24%-0.3% [Bengani et al 2017, Zarate et al 2018b]. Larger population studies have calculated the de novo mutation incidence and prevalence of SATB2-associated syndrome to be 3.5-4.9:100,000 births [López-Rivera et al 2020, Gillentine et al 2022].

Differential Diagnosis

In early infancy SATB2-associated syndrome (SAS) can be particularly difficult to diagnose when developmental delay, hypotonia, feeding difficulties, and palatal issues are the only observable features. During infancy and early childhood, many children with SAS are tested for Angelman syndrome and related disorders. Over time, the emergence of dental issues and distinctive behavioral issues along with lack of speech progression should lead clinicians to consider the diagnosis of SAS. Other syndromes that include developmental delay and dental abnormalities, such as KBG syndrome, can also be considered.

Table 3.

Disorders to Consider in the Differential Diagnosis of SATB2-Associated Syndrome

Gene / Genetic MechanismDisorderMOIDD/ID &
Speech Delay
Craniofacial Dysmorphism / AnomaliesDental AnomaliesBehavioral FindingsSkeletal/Other
SATB2 (SATB2 PV; 2q33.1 del that includes SATB2; chromosome translocation or inversion disrupting SATB2; or chromosomal duplication encompassing SATB2)SATB2-associated syndrome (subject of this GeneReview)ADSome degree of ID in all reported persons; severe speech delay in mostAt least minor dysmorphic facial features in most reported persons; 1 craniofacial anomalies include cleft palate & high-arched palateMost common finding: abnormal shape or size of upper central incisors. Other findings (variably seen): crowding, hypodontia, diastema, delayed primary dentitionJovial or friendly personality, autistic tendencies, agitation or aggressive outbursts, hyperactivity, sleeping difficultiesPectus deformities, kyphosis/lordosis, scoliosis, osteopenia
ANKRD11 (ANKRD11 PV or 16q24.3 del that includes ANKRD11) KBG syndrome ADDD, IDDysmorphic facial features include triangular face, low anterior & posterior hairlines, bushy eyebrows, large & prominent ears, & anteverted nostrils w/hypoplastic alae nasi; palatal anomalies not commonMacrodontia of upper central incisorsASD, ADHD, anxiety, temper tantrums, compulsive & aggressive behaviorsBone age often delayed; short stature prevalent; hand anomalies
UBE3A (deficient expression or function of maternally inherited UBE3A allele) 2 Angelman syndrome See footnote 2.Severe DD or ID; severe speech impairmentTypically not assoc w/anomalies seen in SASTypically not assoc w/findings seen in SASUnique behavior w/inappropriate happy demeanor incl frequent laughing, smiling, & excitabilityTypically not assoc w/anomalies seen in SAS

AD = autosomal dominant; ADHD = attention-deficit/hyperactivity disorder; ASD = autism spectrum disorder; DD = developmental delay; del = deletion; ID = intellectual disability; MOI = mode of inheritance; PV = pathogenic variant

1.

Consistent features associated with larger 2q33.1 deletions include prominent forehead or high anterior hairline, thin vermilion of the upper lip, low-set ears, and long face. Consistent features associated with pathogenic missense, nonsense, and frameshift variants include long and flat philtrum and thin vermilion of the upper lip [Zarate & Fish 2017, Zarate et al 2018a, Zarate et al 2019].

2.

Angelman syndrome is caused by disruption of the maternally imprinted UBE3A allele located within the 15q11.2-q13 Angelman syndrome / Prader-Willi syndrome (AS/PWS) region. The risk to sibs of a proband depends on the genetic mechanism leading to the loss of UBE3A function.

Management

No consensus clinical practice guidelines for SATB2-associated syndrome (SAS) have been published. Some broad recommendations have been published [Zarate et al 2017], and dedicated neurologic and skeletal surveillance recommendations have been proposed based on two large cohort studies [Lewis et al 2020, Zarate et al 2024a]. In the absence of published consensus guidelines, the following recommendations are based on the authors' personal experience managing individuals with this disorder.

Evaluations Following Initial Diagnosis

To establish the extent of disease and needs in an individual diagnosed with SAS, the evaluations summarized in Table 4 (if not performed as part of the evaluation that led to diagnosis) are recommended.

Table 4.

SATB2-Associated Syndrome: Recommended Evaluations Following Initial Diagnosis

System/ConcernEvaluationComment
Constitutional Measurement of weight, length/height, growth velocity, & head circumference
  • To evaluate for poor growth
  • SAS-specific growth charts are available. 1
Neurologic Neurologic eval
  • Consider head MRI to evaluate for brain malformations if clinical seizures are present. 2
  • Baseline EEG, preferably incl sleep stages to evaluate for ESES 3
Development Developmental assessment
  • To incl motor, adaptive, cognitive, & speech-language eval
  • Eval for early intervention / special education
Neurobehavioral/
Psychiatric
Neuropsychiatric evalFor persons age >12 mos: screening for concerns incl sleep disturbances, ADHD, anxiety, &/or findings suggestive of ASD
ENT/Mouth Assess for palatal anomalies.Referral to craniofacial team or otolaryngologist as needed
Dental exam for abnormal tooth shape, number, & location (in those whose teeth have erupted)
  • Referral to dentist
  • Consider dental radiographs if/when affected person can cooperate.
Gastrointestinal/
Feeding
Gastroenterology / nutrition / feeding team eval
  • To incl eval of aspiration risk & nutritional status
  • Consider a videofluoroscopic swallowing study.
  • Consider eval for gastrostomy tube placement in persons w/dysphagia &/or aspiration risk.
Musculoskeletal /
Bone health
Measure alkaline phosphatase w/bone-specific fraction, 25-hydroxyvitamin DD, phosphorus, & PTH levels. 4To obtain a baseline for those age ≥3 yrs 5
DXA scan
Consider lateral thoracolumbar radiographs.In children & adults w/low bone density to evaluate for vertebral compression fractures
Orthopedics / physical medicine & rehab / PT & OT evalTo incl assessment of:
  • Gross motor & fine motor skills
  • Scoliosis, kyphosis, tibial bowing, joint contractures
  • Mobility, ADL, & need for adaptive devices
  • Need for PT (to improve gross motor skills) &/or OT (to improve fine motor skills)
Genitourinary Assess for undescended testes, inguinal hernias, & hypospadias in males.In those w/larger deletions incl SATB2 & adjacent genes
Eyes Ophthalmologic evalTo assess for refractive errors & strabismus
Cardiovascular Consider echocardiogram.In those w/larger deletions incl SATB2 & adjacent genes. 6
Genetic counseling By genetics professionals 7To obtain a pedigree & inform affected persons & their families re nature, MOI, & implications of SAS to facilitate medical & personal decision making
Family support
& resources
By clinicians, wider care team, & family support organizationsAssessment of family & social structure to determine need for:

ADHD = attention-deficit/hyperactivity disorder; ADL = activities of daily living; ASD = autism spectrum disorder; DXA = dual-energy x-ray absorptiometry; ESES = electrical status epilepticus in sleep; MOI = mode of inheritance; OT = occupational therapy; PT = physical therapy; PTH = parathyroid hormone

1.
2.

Brain MRI abnormalities were found in 67.7% of affected individuals, although this did not correlate with the frequency of seizures [Lewis et al 2020].

3.

EEG abnormalities are often documented, even with no clinical seizures. However, electrical status epilepticus in sleep has been reported [Lewis et al 2020].

4.

Elevations in alkaline phosphatase have been documented in more than 60% of affected individuals and are due to the bone-specific fraction. These elevations, however, do not seem to predict the presence of low bone density [Zarate et al 2024a]. Calcium levels, when evaluated, have typically been normal, but if vitamin D supplementation is being considered, it would be reasonable to also obtain a serum calcium level.

5.
6.

In addition to structural defects, individuals with deletions involving COL3A1 and COL5A2 have been described with aortic dilatation/dissection, while individuals with deletions that include BMPR2 are at risk for primary pulmonary hypertension [Zarate et al 2021b]; see also Genotype-Phenotype Correlations.

7.

Medical geneticist, certified genetic counselor, certified advanced genetic nurse

Treatment of Manifestations

There is no cure for SAS. Supportive care to improve quality of life, maximize function, and reduce complications is recommended. This ideally involves multidisciplinary care by specialists in relevant fields (see Table 5).

Table 5.

SATB2-Associated Syndrome: Treatment of Manifestations

Manifestation/ConcernTreatmentConsiderations/Other
Developmental delay /
Intellectual disability /
Neurobehavioral issues
See Developmental Delay / Intellectual Disability Management Issues.
Cleft palate, bifid uvula, & micrognathia
  • Standard treatment ideally by craniofacial team
  • Surgical correction of cleft palate
Dental anomalies Standard treatment per dentist
Poor weight gain /
Feeding difficulties
  • Feeding therapy
  • Gastrostomy tube placement may be required for persistent feeding issues.
Low threshold for clinical feeding eval &/or radiographic swallowing study when showing clinical signs or symptoms of dysphagia.
Sleep disturbance Sleep hygiene healthy habits & potential medical mgmt as neededFor those w/restless sleep, obtain an overnight EEG to explore potential epileptogenic abnormalities.
Scoliosis, tibial bowing, & joint contractures Standard treatment per orthopedist
Osteopenia / Frequent fractures
  • Optimize physical activity & calcium / vitamin D levels.
  • Denosumab & bisphosphonates have been used, w/no direct comparison between the different options. 1
  • Denosumab was reported to be used in 1 affected person. 1
  • Pamidronate & zoledronic acid infusions have also been used. 1
  • Oral alendronate was documented to improve bone mineral content in 1 person. 1
  • Long-term response to these treatments is unknown.
Spasticity Orthopedics / physical medicine & rehab / PT & OT incl stretching to help avoid contractures & fallsConsider need for positioning & mobility devices, disability parking placard.
Epilepsy Standardized treatment w/ASM by experienced neurologist
  • Many ASMs may be effective; none has been demonstrated effective specifically for this disorder.
  • Education of parents/caregivers 2
Undescended testes, inguinal hernia, & hypospadias Standard treatment per urologist
Refractive errors & strabismus Standard treatment per ophthalmologist
Congenital heart defects Standard treatment per cardiologist
Family/Community
  • Ensure appropriate social work involvement to connect families w/local resources, respite, & support.
  • Coordinate care to manage multiple subspecialty appointments, equipment, medications, & supplies.
  • Ongoing assessment of need for palliative care involvement &/or home nursing
  • Consider involvement in adaptive sports or Special Olympics.

ASM = anti-seizure medication; OT = occupational therapy; PT = physical therapy

1.
2.

Education of parents/caregivers regarding common seizure presentations is appropriate. For information on non-medical interventions and coping strategies for children diagnosed with epilepsy, see Epilepsy Foundation Toolbox.

Developmental Delay / Intellectual Disability Management Issues

The following information represents typical management recommendations for individuals with developmental delay / intellectual disability in the United States; standard recommendations may vary by country.

Ages 0-3 years. Referral to an early intervention program is recommended for access to occupational, physical, speech, and feeding therapy. In the US, early intervention is a federally funded program available in all states.

Ages 3-5 years. In the US, developmental preschool through the local public school district is recommended. Before placement, an evaluation is made to determine needed services and therapies and an individualized education plan (IEP) is developed.

Ages 5-21 years

  • In the US, an IEP based on the individual's level of function should be developed by the local public school district. Affected children are permitted to remain in the public school district until age 21.
  • Discussion about transition plans including financial, vocation/employment, and medical arrangements should begin at age 12 years. Developmental pediatricians can provide assistance with transition to adulthood.

All ages. Consultation with a developmental pediatrician is recommended to ensure the involvement of appropriate community, state, and educational agencies and to support parents in maximizing quality of life.

Consideration of private supportive therapies based on the affected individual's needs is recommended. Specific recommendations regarding type of therapy can be made by a developmental pediatrician.

In the US:

  • Developmental Disabilities Administration (DDA) enrollment is recommended. DDA is a public agency that provides services and support to qualified individuals. Eligibility differs by state but is typically determined by diagnosis and/or associated cognitive/adaptive disabilities.
  • Families with limited income and resources may also qualify for supplemental security income (SSI) for their child with a disability.

Motor Dysfunction

Gross motor dysfunction

  • Physical therapy is recommended to maximize mobility and to reduce the risk for later-onset orthopedic complications (e.g., contractures, scoliosis, hip dislocation).
  • Consider use of durable medical equipment as needed (e.g., wheelchairs, walkers, bath chairs, orthotics, adaptive strollers).

Fine motor dysfunction. Occupational therapy is recommended for difficulty with fine motor skills that affect adaptive function such as feeding and dressing.

Oral motor dysfunction. Assuming that the individual is safe to eat by mouth, feeding therapy – typically from an occupational or speech therapist – is recommended for affected individuals who have difficulty feeding due to poor oral motor control.

Communication issues. Consider evaluation for alternative means of communication (e.g., augmentative and alternative communication [AAC]) for individuals who have expressive language difficulties.

Neurobehavioral/Psychiatric Concerns

Children may qualify for and benefit from interventions used in treatment of autism spectrum disorder, including applied behavior analysis (ABA). ABA therapy is targeted to the individual child's behavioral, social, and adaptive strengths and weaknesses and typically performed one on one with a board-certified behavior analyst.

Consultation with a developmental pediatrician may be helpful in guiding parents through appropriate behavior management strategies or providing prescription medications, such as medication used to treat attention-deficit/hyperactivity disorder, when necessary.

Concerns about serious aggressive or destructive behavior can be addressed by a pediatric psychiatrist.

Surveillance

To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, the evaluations summarized in Table 6 are recommended.

Table 6.

SATB2-Associated Syndrome: Recommended Surveillance

System/ConcernEvaluationFrequency
Feeding
  • Measurement of growth parameters
  • Eval of nutritional status & safety of oral intake
At each visit
ENT/Mouth Eval by dentist/orthodontistAt least annually
Neurologic
  • Monitor those w/seizures as clinically indicated.
  • Assess for new manifestations such as seizures or changes in tone.
At each visit
Development Monitor developmental progress & educational needs.
Neurobehavioral/
Psychiatric
Assess for anxiety, ADHD, ASD, aggression, & self-injury.
Musculoskeletal / Bone health Evaluate for scoliosis & spine deformities.
Screening for osteopenia with DXA scan
  • Annually if BMD z score is below −1
  • Every 2 yrs if BMD z score is above −1
  • Measure alkaline phosphatase.
  • Consider obtaining vitamin D levels &, if vitamin D supplementation is being considered, serum calcium levels.
  • Annually if elevated
  • Every 2 yrs if normal
Eyes Eval by ophthalmologistAnnually or as clinically indicated
Respiratory Assess for signs/symptoms of sleep disturbance.At each visit
Family/Community Assess family need for social work support (e.g., palliative/respite care, home nursing, other local resources), care coordination, or follow-up genetic counseling if new questions arise (e.g., family planning).

ADHD = attention-deficit/hyperactivity disorder; ASD = autism spectrum disorder; BMD = bone mineral density; DXA = dual-energy x-ray absorptiometry; OT = occupational therapy; PT = physical therapy

Evaluation of Relatives at Risk

See Genetic Counseling for issues related to testing of at-risk relatives for genetic counseling purposes.

Therapies Under Investigation

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.

Genetic Counseling

Genetic counseling is the process of providing individuals and families with information on the nature, mode(s) of 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; it is not meant to address all personal, cultural, or ethical issues that may arise or to substitute for consultation with a genetics professional. —ED.

Mode of Inheritance

SATB2-associated syndrome (SAS) is an autosomal dominant disorder typically caused by a de novo genetic alteration (an intragenic SATB2 pathogenic variant, a non-recurrent deletion at 2q33.1 that includes SATB2, a chromosome translocation or inversion with a 2q33.1 breakpoint that disrupts SATB2, or a chromosomal duplication with breakpoints that encompass SATB2).

Risk to Family Members

Parents of a proband

  • To date, almost all probands with SAS reported in the literature have the disorder as the result of a de novo genetic alteration (as evidenced by either parental genetic testing or absence of clinical features in the parents).
  • In approximately 1% of individuals, SAS is the result of a genetic alteration inherited from a mosaic parent.
    • Sib recurrence due to presumed parental germline mosaicism was reported in two families in which the genetic alteration identified in the affected sibs was not detected in parental leukocyte DNA (in one family, a SATB2 splice pathogenic variant identified in two brothers and, in another family, a 2q33.1 duplication disrupting SATB2 identified in two brothers) [Bengani et al 2017, Zarate et al 2018a]. Sib recurrence due to confirmed paternal germline mosaicism for a small intragenic SATB2 deletion was reported in the father of two children with SAS [Qian et al 2019].
    • Low-level parental somatic mosaicism for a SATB2 intragenic pathogenic variant has been documented in rare families, including a family with four affected sibs who had a parent with a mosaic pathogenic variant [Zarate et al 2018a; Grelet et al 2019; Y Zarate, unpublished data].
  • Recommendations for the evaluation of parents of a proband with SAS include genetic testing capable of detecting the SAS-related genetic alteration identified in the proband. If the proband has a 2q33.1 deletion or duplication encompassing SATB2, evaluation of the parents should include karyotype to determine if either parent is a carrier of a balanced translocation or other predisposing chromosomal anomaly.
  • If the genetic alteration identified in the proband is not identified in either parent, neither parent has a balanced translocation or other predisposing chromosomal anomaly, and parental identity testing has confirmed biological maternity and paternity, the following possibilities should be considered:
    • The proband has a de novo genetic alteration.
    • The proband inherited a pathogenic variant from a parent with germline (or somatic and germline) mosaicism [Bengani et al 2017, Zarate et al 2018a, Grelet et al 2019, Qian et al 2019]. Note: Testing of parental leukocyte DNA may not detect all instances of somatic mosaicism and will not detect a pathogenic variant that is present in the germ (gonadal) cells only.

Sibs of a proband. The risk to the sibs of the proband depends on the genetic status of the proband's parents:

  • Almost all affected individuals reported in the literature to date have had a de novo genetic alteration, suggesting a low risk to sibs. However, the risk to sibs is slightly greater than that of the general population because of the possibility of parental germline mosaicism [Bengani et al 2017, Zarate et al 2018a, Grelet et al 2019, Qian et al 2019].

Offspring of a proband

  • Each child of an individual with a SATB2 pathogenic variant, 2q33.1 deletion, or duplication encompassing SATB2 has a 50% chance of inheriting the genetic alteration. Risk to offspring of an individual with a chromosome translocation depends on the specific structural variant.
  • To date, individuals with SAS are not known to reproduce.

Other family members. Given that all probands with SAS reported to date have the disorder as a result of a de novo genetic alteration or a genetic alteration inherited from a presumed or documented mosaic parent, the risk to other family members is thought to be low.

Related Genetic Counseling Issues

Family planning

  • The optimal time for determination of genetic risk and discussion of the availability of prenatal/preimplantation genetic testing is before pregnancy.
  • It is appropriate to offer genetic counseling (including discussion of potential risks to offspring and reproductive options) to the parents of an affected child.

Prenatal Testing and Preimplantation Genetic Testing

Once the SAS-related genetic alteration has been identified in an affected family member, molecular genetic prenatal and preimplantation genetic testing are possible.

Differences in perspective may exist among medical professionals and within families regarding the use of prenatal and preimplantation genetic testing. While most centers would consider use of prenatal and preimplantation genetic testing to be a personal decision, discussion of these issues may be helpful.

Resources

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.

  • SATB2 Connect
    Australia
    Email: hello@satb2.org.au
  • SATB2 Gene Foundation, Inc.
    Phone: 678-832-9133
    Email: info@satb2gene.org
  • SATB2 Portal
    An interactive resource about SATB2-associated syndrome (SAS) for families, clinicians and researchers.
    Email: yuri.zarate@uky.edu
  • American Cleft Palate-Craniofacial Association
    Phone: 919-933-9044
  • Unique: Understanding Rare Chromosome and Gene Disorders
    United Kingdom
    Phone: +44 (0) 1883 723356
    Email: info@rarechromo.org

Molecular Genetics

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.

SATB2-Associated Syndrome: Genes and Databases

GeneChromosome LocusProteinLocus-Specific DatabasesHGMDClinVar
SATB2 2q33​.1 DNA-binding protein SATB2 SATB2 @ LOVD SATB2 SATB2

Data are compiled from the following standard references: gene from HGNC; chromosome locus from OMIM; protein from UniProt. For a description of databases (Locus Specific, HGMD, ClinVar) to which links are provided, click here.

Table B.

OMIM Entries for SATB2-Associated Syndrome (View All in OMIM)

608148SPECIAL AT-RICH SEQUENCE-BINDING PROTEIN 2; SATB2
612313GLASS SYNDROME; GLASS

Molecular Pathogenesis

SATB2 encodes DNA-binding protein SATB2 (SATB2; also called special AT-rich sequence-binding protein 2), a 733-amino-acid protein with two CUT domains and a homeodomain highly conserved in vertebrates [FitzPatrick et al 2003, Sheehan-Rooney et al 2010].

SATB2 has several cellular/molecular functions. First, SATB2 has been identified as a transcription factor, containing CUT domains and a homeodomain for DNA binding [FitzPatrick et al 2003, Szemes et al 2006]. DNA binding is associated with nuclear matrix-attachment regions (MARs). MARs are DNA regulatory sequences that are involved in chromatin organization and long-range enhancer function. When SATB2 binds MARs, transcription of multiple genes may be activated simultaneously [Dobreva et al 2003, Gyorgy et al 2008]. Multiple mice studies have shown that Satb2 operates with other transcription factors to promote cortical neuron specification [Britanova et al 2005, Alcamo et al 2008, Liu et al 2022], osteoblast maturation [Dobreva et al 2006, Zhang et al 2011, Gong et al 2014], and intestinal development [Gu et al 2022]. In this context, SATB2 can be considered a master regulator of gene regulatory networks (GRNs) critical to the development of multiple tissues including the jaw, brain, and skeleton – tissues affected in humans with SAS [Britanova et al 2006, Dobreva et al 2006, Zarate et al 2015].

Second, SATB2 has been ascribed as a chromatin remodeler with pioneer factor function [Baranek et al 2012, Feurle et al 2021, Pradhan et al 2021, Wahl et al 2024]. For example, SATB2 mediates chromatin looping between enhancers and promoters of neuronal activity-regulated genes, influencing their expression. Genes associated with SATB2-dependent 3D genome changes have been implicated in cognitive ability and risk for neuropsychiatric and neurodevelopmental disorders [Feurle et al 2021, Wahl et al 2024]. Pioneer factors have a further role to prime DNA for gene expression in a cell type-specific manner, which is conferred by the cooperative binding of other transcription factors [Trompouki et al 2011]. SATB2 binding with different cofactors in different cell types may contribute to variation in severity of different specific phenotypes in individuals with SAS.

In mice, Satb2 has been shown to act in a dosage-dependent manner [Britanova et al 2006]. Therefore, insufficient SATB2 dosage may result in the failure to activate specific genetic programs critical to development. Despite the relatively consistent phenotype of individuals with SAS, variability in the severity of clinical findings has been noted.

Mechanism of disease causation. Loss of function [Rosenfeld et al 2009, Leoyklang et al 2013]

Table 7.

SATB2 Pathogenic Variants Referenced in This GeneReview

Reference SequencesDNA Nucleotide ChangePredicted Protein ChangeComment
NM_015265​.4
NP_056080​.1
c.1165C>Tp.Arg389CysMore severe phenotype 1
c.1174G>Ap.Gly392Arg
c.1174G>C

Variants listed in the table have been provided by the authors. GeneReviews staff have not independently verified the classification of variants.

GeneReviews follows the standard naming conventions of the Human Genome Variation Society (varnomen​.hgvs.org). See Quick Reference for an explanation of nomenclature.

1.

SATB2 Portal (satb2-portal​.broadinstitute.org); Y Zarate, unpublished data

Chapter Notes

Author Notes

The SATB2 portal is a website dedicated to SATB2-associated syndrome (SAS). It offers a comprehensive database of variants in SATB2 as well as the associated phenotype.

Dr Yuri Zarate (ude.yku@etaraz.iruy) is actively involved in clinical research regarding individuals with SAS. He would be happy to communicate with persons who have any questions regarding diagnosis of SAS or other considerations.

Contact Dr Yuri Zarate to inquire about review of SATB2 variants of uncertain significance.

Acknowledgments

We would like to acknowledge the continued support of the families we follow with SAS from around the world.

Author History

Katherine Bosanko, MS (2024-present)
Jennifer Fish, PhD (2016-present)
Julie Kaylor, MS; Arkansas Children's Hospital (2016-2024)
Yuri A Zarate, MD (2016-present)

Revision History

  • 20 June 2024 (ma) Comprehensive update posted live
  • 12 October 2017 (ma) Review posted live
  • 19 December 2016 (yaz) Original submission

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