BCL11A-Related Intellectual Disability

Clinical characteristics.

BCL11A-related intellectual disability (BCL11A-ID) is characterized by developmental delay / intellectual disability of variable degree, neonatal hypotonia, microcephaly, distinctive but variable facial characteristics, behavior problems, and asymptomatic persistence of fetal hemoglobin. Growth delay, seizures, and autism spectrum disorder have also been reported in some affected individuals.

Diagnosis/testing.

The diagnosis of BCL11A-ID is established in a proband with suggestive clinical and laboratory findings and a heterozygous pathogenic variant in BCL11A identified by molecular genetic testing.

Management.

Treatment of manifestations: Treatment is primarily supportive and dictated by symptoms. Standard anti-seizure medication for seizure disorder; standard treatment for abnormal vision and/or strabismus, sleep disturbance, scoliosis, joint laxity, gastroesophageal reflux disease (GERD), constipation, and developmental issues.

Surveillance: Assessment of growth parameters, feeding difficulties, GERD, constipation, scoliosis, developmental progress, and behavior at each visit. Monitor seizures as clinically indicated. Assessment of vision and eye alignment as needed.

Genetic counseling.

BCL11A-ID is inherited in an autosomal dominant manner; however, most affected individuals have the disorder as the result of a de novo BCL11A pathogenic variant. Once the BCL11A pathogenic variant has been identified in an affected family member, prenatal testing for a pregnancy at increased risk and preimplantation genetic testing are possible.

Suggestive Findings

BCL11A-ID should be considered in individuals presenting with the following clinical, laboratory, and neuroimaging findings.

Clinical findings

• Mild-to-severe developmental delay or intellectual disability; AND
• Any of the following features presenting in infancy or childhood:
  • Microcephaly
  • Craniofacial features including flat midface, small nares, thin vermilion of the upper lip and everted vermilion of the lower lip [Dias et al 2016] (see Figure 1)
  • External ear anomalies
  • Strabismus
  • Blue sclerae in infancy
  • Generalized hypotonia of infancy
  • Infant feeding difficulties
  • Language delay and/or dyspraxia
  • Joint laxity
  • Behavioral concerns (repetitive behavior, autism spectrum disorder)
  • Sleep disturbance
  • Seizures

Laboratory findings. Persistence of fetal hemoglobin detected by standardized laboratory methods, such as hemoglobin HPLC (high-performance liquid chromatography) or hemoglobin electrophoresis

Nonspecific brain MRI findings. Hypoplasia of the corpus callosum, hypoplasia of the cerebellar vermis, or white matter abnormalities

Establishing the Diagnosis

The diagnosis of BCL11A-ID is established in a proband with suggestive findings by identification of a heterozygous pathogenic (or likely pathogenic) variant in BCL11A on molecular genetic testing (see Table 1).

Note: Per ACMG variant interpretation guidelines, the terms "pathogenic variants" and "likely pathogenic variants" are synonymous in a clinical setting, meaning that both are considered diagnostic and both can be used for clinical decision making. Reference to "pathogenic variants" in this section is understood to include any likely pathogenic variants.

Molecular genetic testing in a child with developmental delay or an older individual with intellectual disability typically begins with chromosomal microarray analysis (CMA). If CMA is not diagnostic, the next step is typically either a multigene panel or exome sequencing.

Note: Single-gene testing (sequence analysis of BCL11A, followed by gene-targeted deletion/duplication analysis) may be considered in individuals with nonfamilial persistence of fetal hemoglobin identified by hematologic assays.

CMA uses oligonucleotide or SNP arrays to detect genome-wide large deletions/duplications (including BCL11A) that cannot be detected by sequence analysis. See Genetically Related Disorders for discussion of individuals who have larger deletions or duplications of the 2p15-p16.1 region, which includes BCL11A and surrounding genes.

An intellectual disability (ID) multigene panel that includes BCL11A and other genes of interest (see Differential Diagnosis) is most 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. Of note, given the rarity of BCL11A-ID, some panels for ID may not include this gene. (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.

Exome sequencing, which does not require the clinician to determine which gene is likely involved, yields results similar to an ID multigene panel but has the advantage that all rare genes recently identified as causing ID are represented, while some newly identified ID genes may not be included on a multigene panel.

For an introduction to comprehensive genomic testing click here. More detailed information for clinicians ordering genomic testing can be found here.

Clinical Description

BCL11A-related intellectual disability (BCL11A-ID) is characterized by developmental delay / intellectual disability of variable degree (from mild to severe, but most frequently in the moderate range), neonatal hypotonia, microcephaly, distinctive but variable facial characteristics, behavior problems, and asymptomatic persistence of fetal hemoglobin (HbF). Growth delay, seizures, and autism spectrum disorder have also been reported in some affected individuals.

To date, 27 individuals have been reported with a pathogenic (or likely pathogenic) variant in BCL11A [Firth et al 2009, De Rubeis et al 2014, Iossifov et al 2014, Peter et al 2014, Balci et al 2015, Deciphering Developmental Disorders Study Group 2015, Dias et al 2016, Cai et al 2017, Landrum et al 2018, Peron et al 2018, Soblet et al 2018, Yoshida et al 2018]; the authors are aware of additional affected individuals. The following description of the phenotypic features associated with this condition is based on the reported cases and the authors' experience.

Developmental delay (DD) and intellectual disability (ID). All individuals with BCL11A-ID present with DD. Speech delay is always present, and gross and fine motor delays are usually seen as well. All affected individuals have ID, with variable levels ranging from mild to severe.

Other neurodevelopmental features:

• Neonatal hypotonia is seen in the majority of affected individuals, and may result in delayed acquisition of motor milestones (average age at walking: ~30 months). Hypotonia may resolve in childhood, though in some it persists into adolescence.
• Infant feeding difficulties are occasionally present and thought to be associated with central hypotonia as opposed to primary dysphagia.
• Ataxia and/or broad-based gait has been reported in three affected individuals.

Epilepsy has been reported in 5/25 affected individuals [Cai et al 2017, Peron et al 2018, Yoshida et al 2018].

• Various types of seizures have been described (including myoclonic, tonic, and atonic seizures; absence seizures; and spasms) without a common electroclinical pattern.
• Age at seizure onset among individuals reported in the literature varied from two months to three years.
• Seizures are usually controlled with single or combined (2) anti-seizure medication(s). Three reported individuals had seizures that were drug resistant [Peron et al 2018, Yoshida et al 2018] (see also Genetically Related Disorders).

Behavior problems. Most individuals reported have presented with behavior problems [Dias et al 2016].

• Autism spectrum disorder has been described in a subset of affected individuals [De Rubeis et al 2014, Iossifov et al 2014, Dias et al 2016, Cai et al 2017].
• Others exhibit autistic-like traits, such as repetitive behaviors.
• Other behavior problems:
  • Attention deficit and self-injurious behaviors have been reported in one person each.
  • Sleep disturbances have been reported in three people.

Hematologic. A key manifestation of BCL11A-ID is the persistence of fetal hemoglobin (HbF) in affected individuals. In individuals from the general population, HbF is high in the second and third trimester of gestation and in the neonatal period, physiologically decreasing after birth and within the first 12 months of life (with a transition to adult hemoglobin). Therefore, age-specific reference values for hemoglobin variants should be used up to age 24 months.

• Elevated HbF (% of total hemoglobin) has been identified in all affected individuals who have been tested [Dias et al 2016, Cai et al 2017, Peron et al 2018, Soblet et al 2018, Yoshida et al 2018].
• Persistence of HbF is not known to cause symptoms, and no affected individuals with hematologic problems have been reported thus far.

Growth. Intrauterine growth restriction (IUGR) and postnatal growth delay are occasionally present [Dias et al 2016, Cai et al 2017, Yoshida et al 2018], but more than half of the affected individuals have normal growth parameters.

Microcephaly (-2 to -3.5 SD) is seen in approximately half of affected individuals [Dias et al 2016, Cai et al 2017, Soblet et al 2018, Yoshida et al 2018].

Eyes. Strabismus has been reported in 10/21 affected individuals [Dias et al 2016, Cai et al 2017, Peron et al 2018] but no other vision or hearing impairments have been documented. Some affected children with pathogenic loss-of-function variants exhibit blue sclerae in infancy (see Genotype-Phenotype Correlations) [Dias et al 2016].

Neuroimaging. Brain MRI is normal in only a minority of affected individuals; however, most abnormal brain MRI findings are mild and/or nonspecific.

• Structural anomalies of the central nervous system can be present, including hypoplasia of the corpus callosum and/or cerebellar vermis [Dias et al 2016, Peron et al 2018].
• White matter abnormalities, including reduced white matter volume, have been reported [Dias et al 2016].

Other associated features

• Musculoskeletal features
  • Joint hypermobility is a common finding (>80%) in individuals with BCL11A-ID.
  • Scoliosis has occasionally been reported [Dias et al 2016, Cai et al 2017].
• Gastrointestinal problems. Infantile feeding problems with poor weight gain, gastroesophageal reflux disease (GERD), and constipation have occasionally been reported [Dias et al 2016].
• Craniofacial features. No specific dysmorphic features have been observed. If present, dysmorphic features are nonspecific.
  • Affected individuals frequently have flat midface, full cheeks, small nares, thin vermilion of the upper lip, and full or everted vermilion of the lower lip [Dias et al 2016, Peron et al 2018].
  • A subset of individuals have external ear anomalies, including overfolded helix, everted ears, and small earlobe [Liang et al 2009, Dias et al 2016, Soblet et al 2018].

Prognosis. BCL11A-ID is a congenital disorder without known regression of skills. Life span and typical cause of death are unknown due to the limited number of individuals reported to date and ascertainment bias toward diagnosis in childhood. However, the lack of life-limiting congenital anomalies in affected individuals suggests a favorable long-term prognosis with appropriate support. The authors are aware of two affected individuals who are alive and well at 19 and 23 years, respectively [Authors, personal observation], demonstrating that survival into adulthood is possible. Since many adults with disabilities have not undergone advanced genetic testing, it is likely that adults with this condition are underrecognized and underreported.

Genotype-Phenotype Correlations

With the limited number of affected individuals reported to date, no statistically significant genotype-phenotype correlations can be made. However, certain features described to date have been seen only in individuals with loss-of-function (nonsense and frameshift) variants [Dias et al 2016, Yoshida et al 2018]:

• Blue sclerae in infancy
• Epicanthal folds
• Micrognathia or retrognathia
• Short stature (mild)

Prevalence

The prevalence of BCL11A-ID is unknown. To date, 27 affected individuals have been reported in the literature.

Evaluations Following Initial Diagnosis

To establish the extent of disease and needs in an individual diagnosed with BCL11A-ID, the evaluations summarized in Table 3 (if not performed as part of the evaluation that led to diagnosis) are recommended.

Treatment of Manifestations

Surveillance

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.

Mode of Inheritance

BCL11A-related intellectual disability (BCL11A-ID) is inherited in an autosomal dominant manner and is typically caused by a de novo pathogenic variant.

Risk to Family Members

Parents of a proband

• Almost all probands reported to date with BCL11A-ID whose parents have undergone molecular genetic testing have the disorder as a result of a de novo BCL11A pathogenic variant.
• One individual diagnosed with BCL11A-ID inherited a pathogenic variant from a heterozygous parent; the clinical status of the heterozygous parent is unknown [Firth et al 2009].
• Molecular genetic testing is recommended for the parents of a proband with an apparent de novo pathogenic variant.
• If the BCL11A pathogenic variant found in the proband cannot be detected in the leukocyte DNA of either parent, the pathogenic variant most likely occurred de novo in the proband. Another possible explanation is that the proband inherited a pathogenic variant from a parent with germline mosaicism. Although theoretically possible, no instances of germline mosaicism have been reported to date.
• Theoretically, if the parent is the individual in whom the BCL11A pathogenic variant first occurred, the parent may have somatic mosaicism for the variant and may be mildly/minimally affected.

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

• If a parent of the proband is affected and/or is known to have the pathogenic variant identified in the proband, the risk to the sibs is 50%. It is not possible to reliably predict clinical severity in sibs who inherit the pathogenic variant.
• If the BCL11A pathogenic variant found in the proband cannot be detected in the leukocyte DNA of either parent, the recurrence risk to sibs is estimated to be 1% because of the theoretic possibility of parental germline mosaicism [Rahbari et al 2016].

Offspring of a proband. Each child of an individual with a BCL11A-ID has a 50% chance of inheriting the BCL11A pathogenic variant. It is not possible to reliably predict clinical severity in offspring who inherit the pathogenic variant.

Other family members. The risk to other family members depends on the status of the proband's parents: if a parent has the BCL11A pathogenic variant, the parent's family members may be at risk. However, given that almost all probands with BCL11A-ID reported to date have the disorder as a result of a de novo BCL11A pathogenic variant, the risk to other family members is presumed 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 parents of affected individuals.

Prenatal Testing and Preimplantation Genetic Testing

Once the BCL11A pathogenic variant has been identified in an affected family member, prenatal testing for a pregnancy at increased risk and preimplantation genetic testing are possible.

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

Molecular Pathogenesis

BCL11A is a COUP-TF-interacting transcription factor that associates with the BRG1- and BRM-associated factor (BAF) swi/snf chromatin remodeling complex [Kadoch et al 2013]. Pathogenic variants in genes encoding the BAF complex are a recurrent cause of intellectual disability [Kosho et al 2014]. BCL11A is highly expressed in developing mouse brain and in postnatal cortex, hippocampus and caudate nucleus, and in B-lymphocytes. BCL11A is expressed in fetal brain [Nowakowski et al 2017], and in adult brain is restricted to neurons [Uhlén et al 2015]. In addition, BCL11A is a transcriptional repressor of fetal hemoglobin (HbF), playing an important role in globin switching [Bauer & Orkin 2011, Liu et al 2018]. In humans, BCL11A is highly expressed in hematopoietic cells, particularly in B lymphoid and erythroid lineages.

Multiple alternatively spliced transcript variants encoding different isoforms have been identified for BCL11A. BCL11A isoforms share a conserved N terminus and at least one Krüppel C2H2-type zinc finger. The three major BCL11A isoforms, -XL, -L, and -S, encode 835, 773, and 243 amino acid peptides, respectively.

Mechanism of disease causation. BCL11A causes disease through a loss-of-function (LOF) mechanism [Dias et al 2016]. Nonsense and frameshift variants as well as partial or whole-gene deletions have been reported. All LOF variants are predicted to undergo nonsense-mediated decay with loss of isoforms X and XL.

Pathogenic missense variants cluster in the N-terminal region of BCL11A. This region is required for localization to the nucleus, via two C2H2 zinc finger domains. N-terminal missense variants affecting BCL11A localization, dimerization, and transcriptional activity, with putative hypomorphic function, also result in a loss-of-function phenotype.

Heterozygous knockout mice have decreased brain size and aberrant brain transcriptional profiles; they present impaired social memory and decreased social interaction [Dias et al 2016]. BCL11A is associated with neocortical development, specifically the neuronal switch from multipolar to bipolar morphology. BCL11A-deficient neurons have been demonstrated to show impaired radial migration and overexpression of Semac3c [Wiegreffe et al 2015].

BCL11A interacts with calcium/calmodulin-dependent serine kinase (CASK), a gene implicated in X-linked intellectual disability (see CASK-Related Disorders). In a cultured model of hippocampal neurons, CASK enhanced the ability of BCL11A to restrict axon outgrowth and branching [Kuo et al 2010]. CASK interacts with the TBR1 transcription factor, which is also highly expressed in deep layers of cortex and is co-located with BCL11A. Heterozygous variants cause intellectual developmental disorder with autism and speech delay (OMIM 604616). BCL11A regulates the expression of TBR1 in the cortex with residues 629-773 appearing crucial in the interaction between TBR1 and BCL11A [Cánovas et al 2015].

BCL11A-specific laboratory considerations. Individuals with BCL11A-related intellectual disability demonstrate persistence of HbF, with significantly higher levels of HbF than age-matched controls. HbF measurement may be performed to assist in the interpretation of variants of unknown significance.

Author Notes

The authors of this GeneReview clinically follow individuals with BCL11A-related intellectual disability and study the condition.

Acknowledgments

The authors would like to thank the patients and families. Cristina Dias's work is supported by the Wellcome Trust (209568/Z/17/Z).

Revision History

• 26 September 2019 (ma) Review posted live
• 11 February 2019 (ap, cd) Original submission

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