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Autism Spectrum Disorders/Intellectual Disability via the IRF2BPL Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
12085 IRF2BPL 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
12085IRF2BPL81479 81479,81479 $890 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

18 days on average for standard orders or 13 days on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Greg Fischer, PhD

Clinical Features and Genetics

Clinical Features

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).

Genetics

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).

Clinical Sensitivity - Sequencing with CNV PGxome

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%).

Testing Strategy

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).

Indications for Test

When parental samples have been available, all reported missense and loss of function variants in IRF2BPL have arose de novo. However, individuals with family members having known IRF2BPL variants and/or presenting with global neurological regression in childhood before age 7 (motor regression, speech regression, coordination defects) or pediatric onset seizures after age 2 are candidates for this test.

Gene

Official Gene Symbol OMIM ID
IRF2BPL 611720
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Citations

  • Bailey et al. 1995. PubMed ID: 7792363
  • Bourgeron. 2016. PubMed ID: 27289453
  • Centers for Disease Control and Prevention. 2014. PubMed ID: 24670961
  • Devlin and Scherer. 2012. PubMed ID: 22463983
  • Hoang et al. 2017. PubMed ID: 28803755
  • Iossifov et al. 2014. PubMed ID: 25363768
  • Karam et al. 2015. PubMed ID: 25728503
  • Kaufman et al. 2010. PubMed ID: 21124998
  • Larsen et al. 2016. PubMed ID: 27790361
  • Levy et al. 2009. PubMed ID: 19819542
  • Lichtenstein et al. 2010. PubMed ID: 20686188
  • Marcogliese et al. 2018. PubMed ID: 30057031
  • McLaren and Bryson. 1987. PubMed ID: 3322329
  • McPartland et al. 2016. Encyclopedia of Mental Health. 2: 124-130.
  • Sztainberg and Zoghbi. 2016. PubMed ID: 27786181
  • Tran Mau-Them et al. 2019. PubMed ID: 30166628
  • Vissers et al. 2016. PubMed ID: 26503795

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
Total Price: $
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