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FTO-Deficiency Syndrome via the FTO Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
FTO 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
15161FTO81479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

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

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

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

Intellectual disability (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, 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, irrespective of any social class and culture (Kaufman et al. 2010; Vissers et al. 2016). ID and Autism Spectrum Disorders (ASD) are also highly comorbid with each other, suggesting shared etiologies.

FTO-Deficiency Syndrome (also known as Growth Retardation, Developmental Delay, and Facial Dysmorphism) is a rare syndromic from of ID characterized by developmental delay and distinctive dysmorphic features. Other clinical features include: microcephaly, failure to thrive, decreased brain volume, left ventricular hypertrophy, bilateral hearing loss, and in some cases genital anomalies and cleft palate (Daoud et al. 2016; Boissel et al. 2009). Homozygous missense variants within the FTO gene have been identified to segregate with the clinical features of FTO-Deficiency Syndrome in 10 affected individuals from two families.


Intellectual disability is inherited in a multifactorial fashion, with heritability estimates ranging between 15-50% (Larsen et al. 2016; Karam et al. 2015). Approximately 30% more males than females are diagnosed with ID, yet the male-to-female ratio decreases with decreasing IQ (American Psychiatric Association 2000). Co-occurring ASD and ID has a similar male-to-female prevalence ratio of ~4:1 (Christensen et al. 2016). Single nucleotide polymorphisms within the first intron of FTO have also been associated with childhood and adult obesity in multiple human populations and in mouse models (Fawcett et al. 2010; Church et al. 2010).

FTO-Deficiency Syndrome has been reported in individuals with homozygous missense variants in the 2-oxogluterate binding domain of FTO, supporting an autosomal recessive mode of inheritance.

The human FTO gene contains 9 protein-coding exons which encode a 505 amino acid protein. Bacterial and human homologs of FTO are involved in the repair of alkylated DNA and RNA damage from oxidative demethylation. FTO has also been shown to demethylate m6A in mRNA, which plays an important role in gene expression, mRNA processing, and transcript localization (Dominissini et al. 2012). In vitro studies of recombinant human FTO protein with and without a reported missense variant reveal a significant impact on the demethylase activity of the protein (Boissel et al. 2009) The FTO gene (fat mass and obesity-associated) encodes a nuclear iron-dependent oxygenase that is part of the AlkB homologue subfamily (Daoud et al. 2016; Boissel et al. 2009). The FTO protein is hypothesized to be critical for normal development of the nervous and cardiovascular systems through gene regulation (Daoud et al. 2016). The FTO gene is apparently ubiquitously expressed, with highest levels of expression observed in the human central nervous system, liver, and various structures of the heart (Boissel et al. 2009).

Clinical Sensitivity - Sequencing with CNV PG-Select

Genetic variants have been found responsible in 25-50% of ID cases and this percentage increases proportionally with the severity of the phenotype (McLaren and Bryson 1987). To date, a total of 10 homozygous individuals from two families have been reported with missense variants in their FTO gene all presenting with similar clinical features.

Testing Strategy

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

This test provides full coverage of all coding exons of the FTO gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Individuals with family members known to be carriers of pathogenic variants within the FTO gene and/or presenting with severe growth delay and the distinctive features described are good candidates for this test. Of note, missense variants resulting in FTO-Deficiency Syndrome have been reported in families of Arab, Palestinian, or Tunisian decent (Daoud et al. 2016; Boissel et al. 2009). This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in FTO.


Official Gene Symbol OMIM ID
FTO 610966
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • American Psychiatric Association. Diagnostic and Statistical Manual of Mental Disorders, 2000. Text Revision. 4.
  • Boissel S. et al. 2009. American Journal of Human Genetics. 85: 106-11. PubMed ID: 19559399
  • Christensen D.L. et al. 2016. Morbidity and Mortality Weekly Report. 65: 1-23. PubMed ID: 27031587
  • Church C. et al. 2010. Nature Genetics. 42: 1086-92. PubMed ID: 21076408
  • Daoud H. et al. 2016. Journal of Medical Genetics. 53: 200-7. PubMed ID: 26378117
  • Dominissini D. et al. 2012. Nature. 485: 201-6. PubMed ID: 22575960
  • Fawcett K.A., Barroso I. 2010. Trends in Genetics. 26: 266-74. PubMed ID: 20381893
  • Karam S.M. et al. 2015. American Journal of Medical Genetics. Part A. 167: 1204-14. PubMed ID: 25728503
  • Kaufman L. et al. 2010. Journal of Neurodevelopmental Disorders. 2: 182-209. PubMed ID: 21124998
  • Larsen E. et al. 2016. Molecular Autism. 7: 44. PubMed ID: 27790361
  • McLaren J., Bryson S.E. 1987. American Journal of Mental Retardation. 92: 243-54. PubMed ID: 3322329
  • 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

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