Autism Spectrum Disorders/Intellectual Disability via the IRF2BPL Gene

Autism spectrum disorder (ASD) and intellectual disability (ID) are heterogeneous groups of neurodevelopmental disorders. ASD is characterized by varying degrees of social impairment, limited communication ability, propensity for repetitive behavior(s), and restricted interests (Levy et al. 2009. PubMed ID: 19819542). ID refers to significant impairment of cognitive and adaptive development (intelligence quotient, IQ<70) due to abnormalities of brain structure and/or function (American Association of Intellectual and Developmental Disabilities). ID is not a single entity, but rather a general symptom of neurologic dysfunction that is diagnosed before age 18 in 1%-3% of the population, irrespective of social class and culture (Kaufman et al. 2010. PubMed ID: 21124998; Vissers et al. 2016. PubMed ID: 26503795). In contrast, ASD symptoms usually present by age 3, and diagnosis is based on the degree and severity of symptoms and behaviors (McPartland et al. 2016). ASD and ID are highly comorbid, suggesting shared etiologies in many forms. For ASD specifically, comorbidities have been observed in more than 70% of cases, and include ID, epilepsy, language deficits, and gastrointestinal problems (Sztainberg and Zoghbi. 2016. PubMed ID: 27786181). Recent studies using whole exome trio studies have identified novel gene candidates, with familial and de novo variants from several hundred genes now implicated in the development of ASD and ID (Bourgeron. 2016. PubMed ID: 27289453).

Pathogenic variants in IRF2BPL have been implicated in the development of ASD and ID phenotypes. Specifically, individuals with truncating variants present with hallmark features consisting of global neurologic regression in childhood before age 7, including speech and motor regression, progressive ataxia, and lack of coordination. Individuals also present with seizures after age 2. Other clinical features include late-onset neurological regression (ages 10-17), clusters of asymmetric tonic spasms, clonic seizures with hypsarrhythmia-like pattern via EEG, quadriplegic hypotonic-ataxic cerebral palsy, severe tetraparesis, cerebellar ataxia, dysarthria, nystagmus, hypotonia, dystonia, dysphagia, microcephaly, diffuse or focal brain and cerebellar atrophy, and muscle biopsy anomalies (Marcogliese et al. 2018. PubMed ID: 30057031; Tran Mau-Them et al. 2019. PubMed ID: 30166628). Missense variants result in a milder phenotype; at least two individuals have been reported with global developmental delay, seizures, and autism spectrum disorder without neurodevelopmental regression or movement anomalies (Marcogliese et al. 2018. PubMed ID: 30057031).

Genetic aberrations are reported to be responsible for 50%-90% and 15%-50% of ASD and ID cases, respectively, and inheritance overall is multifactorial (Larsen et al. 2016. PubMed ID: 27790361; Karam et al. 2015. PubMed ID: 25728503). Incidence of ASD is approximately 1 in 68 individuals with a male-to-female ratio of 4:1 (Center for Disease Control 2014. PubMed ID: 24670961). De novo missense and likely gene disrupting variants are 15% and 75% more frequent in ASD patients than unaffected controls, respectively (Iossifov et al. 2014. PubMed ID: 25363768).

IRF2BPL pathogenic variants result in neurodevelopmental regression symptoms in an autosomal dominant manner as all reported individuals are heterozygous for de novo missense or loss of function variants (when parental samples have been available). Copy number variants ranging in size from 185 kb to 19.7 Mb have been reported to encompass IRF2BPL, however phenotypic information is limited. Furthermore, these CNVs encompass multiple genes and thus the specific role of IRF2BPL is unclear (Marcogliese et al. 2018. PubMed ID: 30057031).

The human IRF2BPL (interferon regulatory factor 2 binding protein like, also known as EAP1, enhanced at puberty 1) gene contains a single exon encoding a 796 amino acid protein. The IRF2BPL protein includes an N-terminal zinc-finger domain (residues 10-61), a polyalanine and polyglutamine region (residues 88-102, 103-127, respectively), and a C3HC4-type RING-finger domain (residue 715-762) associated with E3 ubiquitin ligase activity (Marcogliese et al. 2018. PubMed ID: 30057031; Tran Mau-Them et al. 2019. PubMed ID: 30166628). To date, all loss of function variants impact the C-terminal RING-finger domain responsible for ubiquitin ligase activity. RNA analyses on fibroblasts from patients with truncating pathogenic IRF2BPL variants suggest the mutated allele escapes nonsense-mediated decay and yields a truncated protein (Tran Mau-Them et al. 2019. PubMed ID: 30166628).

In vivo function of IRF2BPL is unclear. The IRF2BPL transcript is ubiquitously expressed in humans, but its role in brain development and its regulation of various transcriptional networks is not well-defined. It has been proposed to play a role in puberty initiation in non-human primates and functions as an E3 ubiquitin ligase that targets proteins for degradation. Accumulation of ubiquitinated proteins and the deregulation of E3 ubiquitin ligases is a common mechanism observed in other neurodevelopmental disorders such as Angelman syndrome (Tran Mau-Them et al. 2019. PubMed ID: 30166628; Marcogliese et al. 2018. PubMed ID: 30057031).

Genetic variants have been found responsible in 25-50% of Intellectual Disability (ID) cases, and this percentage increases proportionally with the severity of the phenotype (McLaren and Bryson. 1987. PubMed ID: 3322329). For Autism Spectrum Disorders (ASD), while heritability estimates have been reported as high as 90% (Bailey et al. 1995. PubMed ID: 7792363; Lichtenstein et al. 2010. PubMed ID: 20686188), only 20% of cases can be explained to date using genetic approaches (Devlin and Scherer. 2012. PubMed ID: 22463983).

While IRF2BPL is categorized as a gene with ‘syndromic, strong evidence’ regarding its association with ASD in the Simons Foundation Autism Research Initiative (SFARI) Database (https://gene.sfari.org/database/human-gene/IRF2BPL), no single gene has been reported to account for more than 1% of all ASD cases to date (Hoang et al. 2018. PubMed ID: 28803755). Furthermore, large cohort studies of individuals with neurodevelopmental phenotypes have implicated hundreds of genes (Larsen et al. 2016. PubMed ID: 27790361; Bourgeron. 2016. PubMed ID: 27289453). Therefore, the clinical sensitivity of any single gene test with regard to a neurodevelopmental phenotype is expected to be low (≤1%).

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This test provides almost full coverage of the single coding exon of the IRF2BPL gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

This test does not include variants within c.250 to c.380 (NM_024496) due to sequence complexity.

For coverage of the polyalanine and polyglutamine region, a PCR-based short tandem repeat polymorphism (STRP) assay is utilized. Briefly, PCR products derived from the targeted region are resolved by electrophoresis on an ABI 3730xI capillary sequencer. The number of repeats are determined using the Gene Mapper 5 program.

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).