DNA icon

Autism Spectrum Disorders via the FOXP1 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
FOXP1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8139FOXP181479 81479,81479 $990 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. If the Sanger option is selected, CNV detection may be ordered through Test #600.

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 platform).

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

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

For Sanger Sequencing click here.

Turnaround Time

3 weeks on average for standard orders or 2 weeks 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.


Genetic Counselors


  • Greg Fischer, PhD

Clinical Features and Genetics

Clinical Features

Autism Spectrum Disorders (ASD) encompass several neurodevelopmental disorders characterized by varying degrees of social impairment, communication ability, and propensity for restricted interests and repetitive behavior(s) which usually present by age 3. Diagnosis is based on the degree and severity of symptoms and behaviors (Diagnostic and Statistical Manual of Mental Disorders (DSM-5); Levy et al. 2009; McPartland et al. 2016). Comorbidities occur in more than 70% of cases and include intellectual disability (ID), epilepsy, language deficits, and gastrointestinal problems (Sztainberg and Zoghbi 2016). ID specifically 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, AAIDD). 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 (Kaufman et al. 2010; Vissers et al. 2016).

The FOXP1 gene has been implicated in sporadic ASD and ID cases and is associated with global developmental delay with moderate to severe language impairment. Specifically, expressive speech impairment and consonant expression is a hallmark trait of individuals with FOXP1-associated ASD and ID (Le Fevre et al. 2013). Facial features include broad forehead, down-slanting or narrow palpebral fissures, short nose with a broad tip, macrocephaly (variable), frontal upsweep of hair, and prominent fingertip pads. Less common features include widely spaced eyes, ptosis of eyelids, smooth philtrum, sparse lateral eyebrows, and epicanthus (Lozano et al. 2015; Le Fevre et al. 2013; Hamdan et al. 2010).


FOXP1 is a member of the human FOX gene family defined by a DNA binding forkhead box (FOX) domain and involvement in immunological, hematological, and embryological development. FOXP1 is enriched within the brain, including the neocortex, hippocampus, and striatum (Ferland et al. 2003; Teramitsu et al. 2004) and is expressed ubiquitously throughout the central nervous system (Teramitsu et al. 2004). Mouse studies have shown a potential role of FOXP1 in control of motor neuron migration and axon trajectory choice (Palmesino et al. 2010). Members of the FOXP subfamily bind DNA as a homo- or heterodimer. For example, FOXP1 has been shown to work cooperatively in mice with FOXP2, which is also implicated in ASD and ID phenotypes (Le Fevre et al. 2013; Shu et al. 2007). Numerous isoforms of FOXP1 have been described, with the most inclusive transcript encompassing 21 exons, of which exons 6-21 are protein coding (Brown et al. 2008).

FOXP1 pathogenic variants are almost exclusively de novo and include whole and partial gene deletions, translocations, missense, nonsense, and frameshift variants. FOXP1-associated ASD and ID features are inherited in an autosomal dominant manner, likely through haploinsufficiency. At least one study has reported dominant negative effects of abnormal FOXP1 protein product impacting both wild type FOXP1 and FOXP2 protein translocation into the nucleus (Lozano et al. 2015).

Clinical Sensitivity - Sequencing with CNV PGxome

Currently, the contribution of de novo and inherited factors to Autism Spectrum Disorders (ASD) risk is estimated to be approximately 50-60% (Krumm et al. 2015) and 25-50% for intellectual disability (ID), with the percentage increasing proportionately with phenotypic severity (McLaren and Bryson 1987). FOXP1 is classified in the Simons Foundation Autism Research Initiative (SFARI) Database as a ‘strong candidate’ gene regarding ASD risk (https://gene.sfari.org/database/human-gene/FOXP1). However, more than 700 genes total have been associated with ASD features (Bourgeron 2016). One comprehensive study investigating shared clinical features of individuals with FOXP1 putative causative variants from multiple studies described 10 individuals (Le Fevre et al. 2013), however the SFARI gene database indicates there have been as many as 24 reports of affected individuals, half of which were also diagnosed with ASD (https://gene.sfari.org/database/human-gene/FOXP1).

Overall, de novo copy number variants (CNVs) are estimated to account for approximately 6% of ASD risk (Lim et al. 2013). The contribution of FOXP1 CNVs specifically is unclear; however, 3p interstitial deletions that encompass either solely FOXP1 or additional genes within this region have been reported by multiple sources (Le Fevre et al. 2013; Palumbo et al. 2013; Horn et al. 2010; Carr et al. 2010; Pariani et al. 2009). Individuals with large deletions affecting FOXP1 and additional genes share broad forehead, short, broad nose, and macrocephaly phenotypes with those having deletions affecting FOXP1 exclusively, suggesting these features may be specific to FOXP1 disruption (Le Fevre et al. 2013).

Testing Strategy

This test provides full coverage of all coding exons of the FOXP1 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).

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

Individuals presenting with expressive speech impairment as well as characteristic facial features such as broad forehead, down-slanting or narrow palpebral fissures, short nose with a broad tip, macrocephaly, hair upsweep, and prominent fingertip pads are potential candidates for this test. Of note, all FOXP1 variants described in which parental DNA was tested revealed the variants occurred de novo, therefore testing with parental samples is highly recommended (Lozano et al. 2015).


Official Gene Symbol OMIM ID
FOXP1 605515
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Bourgeron T. 2016. Comptes Rendus Biologies. 339: 300-7. PubMed ID: 27289453
  • Brown P.J. et al. 2008. Blood. 111: 2816-24. PubMed ID: 18077790
  • Carr C.W. et al. 2010. European Journal of Human Genetics. 18: 1216-20. PubMed ID: 20571508
  • Ferland R.J. et al. 2003. The Journal of Comparative Neurology. 460: 266-79. PubMed ID: 12687690
  • Hamdan F.F. et al. 2010. American Journal of Human Genetics. 87: 671-8. PubMed ID: 20950788
  • Horn D. et al. 2010. Human Mutation. 31: E1851-60. PubMed ID: 20848658
  • Kaufman L. et al. 2010. Journal of Neurodevelopmental Disorders. 2: 182-209. PubMed ID: 21124998
  • Krumm N. et al. 2015. Nature Genetics. 47: 582-8. PubMed ID: 25961944
  • Le Fevre A.K. et al. 2013. American Journal of Medical Genetics. Part A. 161A: 3166-75. PubMed ID: 24214399
  • Levy S.E. et al. 2009. Lancet. 374: 1627-38. PubMed ID: 19819542
  • Lim E.T. et al. 2013. Neuron. 77: 235-42. PubMed ID: 23352160
  • Lozano R. et al. 2015. European Journal of Human Genetics. 23: 1702-7. PubMed ID: 25853299
  • McLaren J., Bryson S.E. 1987. American Journal of Mental Retardation. 92: 243-54. PubMed ID: 3322329
  • McPartland J.C. et al. 2016. Encyclopedia of Mental Health. 2: 124-130
  • Palmesino E. et al. 2010. Plos Biology. 8: e1000446. PubMed ID: 20711475
  • Palumbo O. et al. 2013. Gene. 516: 107-13. PubMed ID: 23287644
  • Pariani M.J. et al. 2009. European Journal of Medical Genetics. 52: 123-7. PubMed ID: 19332160
  • Shu W. et al. 2007. Development. 134: 1991-2000. PubMed ID: 17428829
  • Sztainberg Y, Zoghbi HY. 2016. Nature Neuroscience. 19: 1408-17. PubMed ID: 27786181
  • Teramitsu I. et al. 2004. The Journal of Neuroscience. 24: 3152-63. PubMed ID: 15056695
  • Vissers L.E. et al. 2016. Nature Reviews. Genetics. 17: 9-18. PubMed ID: 26503795


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

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

loading Loading... ×


An error has occurred while calculating the price. Please try again or contact us for assistance.

View Ordering Instructions

1) Select Test Method (Platform)

1) Select Test Type

2) Select Additional Test Options

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
Total Price: loading
Patient Prompt Pay Price: loading
A patient prompt pay discount is available if payment is made by the patient and received prior to the time of reporting.
Show Patient Prompt Pay Price
Copy Text to Clipboard