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Fragile X Syndrome via FMR1 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
9599 FMR1 81243 81243,81479 $990 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9599FMR181243 81243,81479 $990 Order Options and Pricing

Pricing Comments

**Before ordering DNA sequencing of FMR1 gene, we strongly recommend ordering the CGG repeat expansion test first, unless targeted testing can be performed for a known familial sequence variant.** For methylation analysis required after finding positive results in the CGG expansion test, please contact us for price.

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).

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


  • Li Fan, MD, PhD, FCCMG, FACMG

Clinical Features and Genetics

Clinical Features

Fragile X syndrome (FXS) is the most common genetic cause of intellectual disability in males and the second most common cause in females, with a prevalence of 1:4000 males and 1:6000 females. FXS is characterized by developmental delay, moderate to severe intellectual disability and autistic behaviors. FXS is typically diagnosed at around three years of age when developmental delay becomes pronounced. Physical features of FXS include an elongated face, prominent jaw, broad forehead, prominent ears, macroorchidism in males, flat feet and hyperextensible finger joints (Gallagher and Hallahan 2011). Common behaviors associated with FXS include attention deficit hyperactivity disorder (ADHD), trouble sleeping, anxiety, mood disorders and aggression. Autistic-like behaviors seen in FXS patients include preserveration of speech, motor stereotypies such as hand flapping, restricted interests and poor eye contact. Approximately 30-50% of FXS patients meet the diagnostic criteria for autism, although symptoms tend to be less severe than in patients with idiopathic autism (McCary and Roberts 2013; McDuffie et al. 2014). FXS-related conditions, Fragile X Tremor Ataxia Syndrome (FXTAS) and Fragile X Premature Ovarian Insufficiency (FXPOI) have not been reported in patients with point mutations in the FMR1 gene.


The majority of FXS cases are caused by an expansion of the CGG repeat in the 5' UTR of the FMR1 gene which leads to methylation and silencing of the FMR1 locus. Sequence variants in the FMR1 gene itself have also been reported to cause FXS and are inherited in an X-linked recessive manner. Both nonsense and missense variants in FMR1 have been identified in males and females with FXS or intellectual disability (De Boulle et al. 1993; Lugenbeel et al. 1995; Grønskov et al. 2011). FMR1 encodes the fragile-X mental retardation protein (FMRP) which is an RNA binding protein highly expressed in the brain. FMRP binds RNAs and transports them to synapses for local translation (Liu-Yesucevitz et al. 2011). FMRP is predicted to bind to as much as 4% of all mRNA in the brain and acts as a translational repressor. FXS is caused by loss of FMRP and improper translation of neuronal mRNAs (Bagni et al. 2012). FMRP mRNA targets are enriched for genes implicated in intellectual disability and autism spectrum disorders, suggesting a common molecular mechanism (Ascano et al. 2012). Loss of FMRP results in long, thin dendritic spines in the cortex which reduces neuronal contacts and impairs synaptic plasticity.

Clinical Sensitivity - Sequencing with CNV PGxome

Traditionally, Fragile X testing has consisted of CGG repeat expansion analysis only, therefore limited data is available for the frequency of FMR1 point mutations in FXS patients. A recent study of male patients with an FXS phenotype who tested negative for repeat expansions in both the FMR1 and AFF2 genes identified possibly pathogenic FMR1 missense mutations in 0.56% (3 of 508) of individuals (Handt et al. 2014).

Testing Strategy

This test provides full coverage of all coding exons of the FMR1 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.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Before ordering DNA sequencing of FMR1 gene, we strongly recommend ordering the CGG repeat expansion test first, unless targeted testing can be performed for a known familial sequence variant.

Indications for Test

Candidates for FMR1 sequencing include males with intellectual disability and males/females with family history of FXS who tested negative for FMR1 repeat expansion.


Official Gene Symbol OMIM ID
FMR1 309550
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Fragile X Syndrome XL 300624

Related Test

Fragile X Syndrome via FMR1 CGG Repeat Expansion


  • Ascano M Jr. et al. 2012. Nature. 492: 382-6. PubMed ID: 23235829
  • Bagni C. et al. 2012. The Journal of Clinical Investigation. 122: 4314-22. PubMed ID: 23202739
  • De Boulle K, Verkerk AJ, Reyniers E, Vits L, Hendrickx J, Roy B Van, Bos F Van den, Graaff E de, Oostra BA, Willems PJ. 1993. A point mutation in the FMR-1 gene associated with fragile X mental retardation. Nat. Genet. 3: 31–35. PubMed ID: 8490650
  • Gallagher A., Hallahan B. 2012. Journal of Neurology. 259: 401-13. PubMed ID: 21748281
  • Grønskov K, Brøndum-Nielsen K, Dedic A, Hjalgrim H. 2011. A nonsense mutation in FMR1 causing fragile X syndrome. European Journal of Human Genetics 19: 489–491. PubMed ID: 21267007
  • Handt M, Epplen A, Hoffjan S, Mese K, Epplen JT, Dekomien G. 2014. Point mutation frequency in the FMR1 gene as revealed by fragile X syndrome screening. Molecular and Cellular Probes 28: 279–283. PubMed ID: 25171808
  • Liu-Yesucevitz L. et al. 2011. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 31: 16086-93. PubMed ID: 22072660
  • Lugenbeel KA, Peier AM, Carson NL, Chudley AE, Nelson DL. 1995. Intragenic loss of function mutations demonstrate the primary role of FMR1 in fragile X syndrome. Nat. Genet. 10: 483–485. PubMed ID: 7670500
  • McCary LM., Roberts JE. 2013. Journal of Intellectual Disability Research : Jidr. 57: 803-14. PubMed ID: 22974167
  • McDuffie A. et al. 2015. Journal of Autism and Developmental Disorders. 45: 1925-37. PubMed ID: 24414079


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

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