Clinical characteristics.

SMARCA2-related Nicolaides-Baraitser syndrome (SMARCA2-NCBRS) is characterized by commonly shared dysmorphic features including sparse scalp hair, prominence of the interphalangeal joints and distal phalanges due to decreased subcutaneous fat, characteristic coarse facial features, microcephaly (typically acquired), seizures, and developmental delay / intellectual disability. Developmental delay / intellectual disability is severe in nearly half of affected individuals, moderate in one third, and mild in the remainder. Nearly one third never develop speech or language skills. Seizures are of various types and can be difficult to manage, requiring multiple anti-seizure medications to achieve reasonable control. Regression or lack of developmental progress has been noted with the onset of seizures in some affected individuals. Behavioral issues can include autistic-like features (perseveration, hyperacusis), with a minority of affected individuals being diagnosed clinically with an autism spectrum disorder. Cryptorchidism is common in males. About half of affected individuals have growth deficiency and short stature. Delayed tooth eruption with hypo- or oligodontia has also been reported. Radiographic findings may include cone-shaped epiphyses, metaphyseal flaring of the phalanges, and shortening of the phalanges, metacarpals, and/or metatarsals (especially of the 4th and 5th rays) of the hands; platyspondyly; flat intervertebral disc space; and pelvic/femoral anomalies. Rare findings include conductive hearing loss, refractive error / astigmatism, and congenital heart defects.

Diagnosis/testing.

The diagnosis of SMARCA2-NCBRS is established in a proband with suggestive findings and a heterozygous SMARCA2 pathogenic variant identified by molecular genetic testing.

Management.

Treatment of manifestations: Standard therapy for developmental delay / intellectual disability, behavioral issues, epilepsy, poor growth, myopia, astigmatism, hearing loss, dental issues, cryptorchidism, and congenital heart defects.

Surveillance: At each visit, measure growth parameters; evaluate nutritional status and safety of oral intake; monitor those with seizures; assess for new manifestations; monitor developmental progress and educational needs; assess for behavioral issues such as short attention span, sensitivity to loud noises, and oral sensitivity; and evaluate mobility and self-help skills. Dental evaluation at least every six months after the eruption of first dentition. Annual audiology evaluation in childhood. Ophthalmology evaluation per treating ophthalmologist.

Genetic counseling.

SMARCA2-NCBRS is expressed in an autosomal dominant manner and typically caused by a de novo SMARCA2 pathogenic variant; the risk to other family members is presumed to be low. Once a SMARCA2 pathogenic variant has been identified in an affected family member, prenatal and preimplantation genetic testing are possible.

Suggestive Findings

SMARCA2-NCBRS should be considered in probands with the following clinical and radiographic findings and family history.

Clinical findings

• Developmental delay / intellectual disability (DD/ID), most commonly in the severe range but with some having either mild or moderate DD/ID
• Sparse scalp hair
• Prominence of the interphalangeal joints and distal phalanges secondary to poor subcutaneous fat distribution (See Figure 1 and Figure 2.)
• Characteristic facial features (see Clinical Description, Facial features) that can be subtle in the newborn period and in early childhood, with coarsening of the face and increased skin wrinkling over time (See Figure 3.)
• Microcephaly
• Seizures

Figure 1.

Prominent interphalangeal joints with reduced fat deposition in the digits

Figure 2.

Moderately prominent interphalangeal joints

Figure 3.

Coarse facies with sparse scalp hair, thin upper lip vermilion, and thick lower lip vermilion

Radiographic findings

• Hand radiographs may show cone-shaped epiphyses, metaphyseal flaring of the phalanges, and shortening of the phalanges, metacarpals, and/or metatarsals (especially of the 4th and 5th rays).
• Abnormal bone age, most often delayed but on occasion advanced for chronologic age
• Platyspondyly, flat intervertebral discs, small pelvis, pubic bone hypoplasia, small femoral heads, and short femoral neck

Family history. Because SMARCA2-NCBRS is typically caused by a de novo pathogenic variant, most probands represent a simplex case (i.e., a single occurrence in a family).

Establishing the Diagnosis

The diagnosis of SMARCA2-NCBRS is established in a proband with suggestive findings and a heterozygous SMARCA2 pathogenic variant identified by molecular genetic testing (see Table 1).

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 SMARCA2 variant of uncertain significance does not establish or rule out the diagnosis (see Epigenetic Signature Analysis / Methylation Array).

Molecular genetic testing approaches can include a combination of gene-targeted testing (single gene testing, multigene panel) and comprehensive genomic testing (exome sequencing, genome sequencing). Gene-targeted testing requires that the clinician determine which gene(s) are likely involved (see Option 1), whereas comprehensive genomic testing does not (see Option 2).

Clinical Description

SMARC2-related Nicolaides-Baraitser syndrome (SMARC2-NCBRS) is characterized by commonly shared dysmorphic features including sparse scalp hair, prominence of the interphalangeal joints and distal phalanges due to decreased subcutaneous fat, characteristic coarse facial features, microcephaly, seizures, and developmental delay / intellectual disability. Seizures are of various types and can be difficult to manage. Developmental delay / intellectual disability is severe in nearly half of affected individuals, moderate in one third, and mild in the remainder. Nearly one third never develop speech or language skills [Nicolaides & Baraitser 1993, Pretegiani et al 2016, Zhang et al 2022].

To date, at least 80 individuals have been identified with a pathogenic variant in SMARCA2 [Zhang et al 2022]. The following description of the phenotypic features associated with this condition is based on these reports.

Developmental delay (DD) and intellectual disability (ID). Nearly half of affected individuals experience severe DD/ID with particular delays in speech and language development. One third of affected individuals exhibit moderate ID, and the remainder have mild ID.

• About 80% of affected individuals experience severe speech delay, and nearly one third of all affected individuals never develop speech or language skills.
• The mean age for sitting is approximately nine months and the mean age for walking independently is 21 months (range: 10 months-5 years).
• Although psychomotor regression is not typical, the high incidence of seizures that progressively worsen has been associated with loss of speech.

Other neurodevelopmental features

• Hypotonia is present in about one third of affected individuals.
• Infant feeding difficulties are present in at least half of affected individuals, although this does not typically require tube feeding.

Epilepsy can be difficult to manage, requiring multiple anti-seizure medications (ASMs) to achieve reasonable control. The age onset of seizures ranges from birth to 14 years; the mean and median age of onset is 20.9 months and 16.5 months, respectively. Various seizure types have been reported, with generalized seizures in roughly half of affected individuals. Affected individuals frequently experience an initial positive response to ASMs, especially levetiracetam and valproic acid, but very rarely does this lead to complete remission of seizures. Regression or lack of developmental progress has been noted with the onset of seizures.

Neurobehavioral/psychiatric manifestations. Behavior issues have been reported in at least 19 affected individuals, with some displaying autistic-like features (such as perseveration and hyperacusis), and at least three clinically diagnosed with autism spectrum disorder. Other reported findings have included short attention span and oral sensitivities.

Growth. About half of affected individuals have low birth weight and the same proportion experience short stature. Only one affected individual is known to be above the 50th centile for height.

Microcephaly tends to be acquired, being noted in almost one third of infants at birth and in two thirds at follow up.

Ectodermal findings

• Scalp hair is usually sparse at birth and becomes increasingly so with age, particularly in the second decade of life. In some, the sparseness improves with time.
• Skin pigmentation appears to be reduced, although affected individuals do not exhibit true cutaneous albinism.
• Poor subcutaneous fat distribution leads to prominent veins; interphalangeal joints are also prominent.
• Delayed tooth eruption is common, often requiring surgical extraction of primary dentition to allow secondary dentition to migrate into place. In one series, teeth were widely spaced in 58.2% of affected individuals, and hypodontia was reported in 18.6% [Sousa et al 2014].

Facial features may include prominent lashes, thick eyebrows, downslanted palpebral fissures, ptosis, anteverted nares, long philtrum, wide mouth, thin upper lip vermilion, and thick lower lip vermilion. The facial features are often subtle in the newborn period and early childhood, with coarsening of the face and increased skin wrinkling over time (see Figure 3).

Musculoskeletal. The distal phalanges widen with age, becoming oval shaped and broad. Additionally, increasing space between the first and second toes can occur over time. Radiographic findings are listed in Suggestive Findings.

Other associated features

• Genitourinary anomalies. Cryptorchidism is observed in most males.
• Hearing loss has been noted in 5%-10% of affected individuals. The nature of the hearing loss is predominantly conductive, although one case of sensorineural has been reported.
• Vision issues such as myopia and astigmatism have been seen in 15% and 6% of affected individuals, respectively. Glaucoma has been reported in two affected individuals [Simmers et al 2022].
• Congenital heart defects (e.g., atrial septal defect, stenosis of the pulmonary artery, coarctation, patent ductus arteriosus, and double aortic arch) have been reported in six affected individuals.

Note: (1) One affected individual had caudal regression, although it is unclear if this is a rare finding in individuals with SMARCA2-NCBRS or a co-occurrence of two rare but unrelated findings [Wang et al 2024]. (2) A different reported individual with a partial SMARCA2 gene deletion that included the ATP binding region had a novel association of hypertrophic obstructive cardiomyopathy [Foley et al 2022]. (3) One individual was noted to have onset of hashitoxicosis in early adolescence, and a link between thyroid tissue and SMARCA2 has been suggested by studies of thyroid volume in people with Hashimoto thyroiditis [Brčić et al 2020, Henriquez-Lopez & McLean 2023].

Prognosis. It is unknown whether life span in SMARCA2-NCBRS is abnormal. One reported individual lived to age 33 years [Sousa et al 2014], 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. The DNA methylation profile in people with SMARCA2-NCBRS differs significantly from normal. People with SMARCA2-NCBRS have been shown to have accelerated epigenetic ages and shortened DNA methylation-based telomere length relative to healthy controls, suggestive of accelerated biological aging [Shinko et al 2022].

Genotype-Phenotype Correlations

No clear clinically relevant genotype-phenotype correlations have been noted; however, all individuals with a pathogenic variant within the C-terminal helicase region of the ATPase domain have severe intellectual disability and epilepsy, a frequency higher than that in individuals with pathogenic variants in other parts of the gene. More than half of all individuals with SMARCA2-NCBRS reported have a pathogenic variant within the C-terminal helicase region [Zhang et al 2022].

Nomenclature

Morin et al [2003] proposed the name Nicolaides-Baraitser syndrome after the authors of the 1993 article in which the earliest known person with NCBRS was described.

Prevalence

The prevalence of SMARCA2-NCBRS is not known, but is estimated to be extremely low. Fewer than 100 affected individuals have been described in the literature.

Evaluations Following Initial Diagnosis

To establish the extent of disease and needs in an individual diagnosed with SMARCA2-NCBRS, the evaluations summarized in Table 4 (if not performed as part of the evaluation that led to diagnosis) are recommended.

Treatment of Manifestations

There is no cure for SMARCA2-NCBRS. 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).

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.

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

SMARCA2-related Nicolaides-Baraitser syndrome (SMARCA2-NCBRS) is an autosomal dominant disorder typically caused by a de novo pathogenic variant.

Risk to Family Members

Parents of a proband

• To date, all individuals diagnosed with SMARCA2-NCBRS have the disorder as the result of a SMARCA2 pathogenic variant that occurred de novo in the proband or, rarely, was inherited from an unaffected mosaic parent [Liu et al 2022].
• Molecular genetic testing is recommended for the parents of the proband to evaluate their genetic status and inform recurrence risk assessment. (Note: Based on data available to date, it is highly unlikely a SMARCA2 heterozygous pathogenic variant would be detected in an apparently asymptomatic parent.)
• If the pathogenic variant identified in the proband is not identified in either parent and parental identity testing has confirmed biological maternity and paternity, the following possibilities should be considered:
  • The proband has a de novo pathogenic variant.
  • The proband inherited a pathogenic variant from a parent with gonadal (or somatic and gonadal) mosaicism. 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:

• If the SMARCA2 pathogenic variant identified in the proband cannot be detected in the leukocyte DNA of either parent, the recurrence risk to sibs is slightly greater than that of the general population because of the possibility of parental gonadal mosaicism.
• If a parent of the proband is known to be heterozygous for the SMARCA2 pathogenic variant identified in the proband, the risk to the sibs of inheriting the variant is 50%.

Offspring of a proband. To date, individuals with SMARCA2-NCBRS are not known to reproduce.

Other family members. Given that all probands reported to date with SMARCA2-NCBRS reported have the disorder as a result of a SMARCA2 pathogenic variant that occurred de novo in the proband or in an unaffected mosaic parent, 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 SMARCA2 pathogenic variant has been identified in an affected family member, 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 health care professionals would consider use of prenatal and preimplantation genetic testing to be a personal decision, discussion of these issues may be helpful.

Molecular Pathogenesis

The SWI/SNF family of ATPase-dependent chromatin remodelers is essential for the regulation of gene expression, differentiation, and development. SMARCA2 encodes probable global transcription activator SNF2L2 (also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2; SMARCA2), which is within the family of helicase-related proteins that share an ATPase domain critical for the coupling of ATP hydrolysis with DNA binding, which in turn results in chromatin remodeling. SMARCA2 is a subunit of the BRG1-associated factors (BAF) complex, the human analog of the SWI/SNF complex. SMARCA2 comprises 34 exons and makes a transcript of 5,879 base pairs. Alternatively spliced transcript variants encoding different isoforms have been found for this gene, which contains a CAG trinucleotide repeat length polymorphism.

Pathogenic variants in SMARCA2 may result in aberrant chromatin remodeling, causing downstream dysregulation of further genes and resulting in the SMARCA2-related Nicolaides-Baraitser syndrome (SMARCA2-NCBRS) phenotype. It is suspected that mutated SMARCA2 is able to incorporate into the SWI/SNF complex that then binds to downstream targets within the genome. In this scenario, remodeling of the nucleosome structure in order to affect gene expression would not be able to occur normally, due to a dominant-negative or gain-of-function effect.

Mutation of other genes within the SWI/SNF complex has been suggested as the cause in individuals who have findings suggestive of SMARCA2-NCBRS but no detectable SMARCA2 pathogenic variant [Van Houdt et al 2012].

Both somatic and germline pathogenic variants affecting the SWI/SNF complex have been associated with tumor suppression, raising the question whether affected individuals containing these pathogenic variants might have increased risk of developing neoplasias. Most people with SMARCA2-NCBRS with these pathogenic variants are children/adolescents who have yet to be followed into adulthood, perhaps contributing to the lack of reported cancers in these individuals [Santen et al 2012].

Mechanism of disease causation. All pathogenic variants cluster within the ATPase SMARCA2 domain (exons 15-25). Gao et al [2019] found in preclinical studies that deletions encompassing all of SMARCA2 did not cause NCBRS, and mice lacking functional Smarca2 did not demonstrate major developmental abnormalities. Additionally, people with NCBRS have solely nontruncating pathogenic variants located exclusively in the SNF2 ATPase domain. Based on these findings, it is believed that pathogenic variants in SMARCA2 most likely cause a dominant-negative or gain-of-function effect.

Author Notes

Omar Abdul-Rahman, MD, studies the clinical features and molecular basis of SMARCA2-related Nicolaides-Baraitser syndrome and is a member of the Nicolaides-Baraitser Syndrome International Consortium.

Revision History

• 6 March 2025 (ma) Comprehensive updated posted live
• 15 October 2015 (me) Review posted live
• 23 July 2015 (oa) Original submission

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