Fragile X Syndrome via the FMR1 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
483 FMR1$1130.00 81479 Add to Order
Pricing Comment

**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.

Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity

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).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 FMR1$690.00 81479 Add to Order
Pricing Comment

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Over 100

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Turnaround Time

The great majority of tests are completed within 28 days.

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.

Testing Strategy

Testing involves PCR amplification from genomic DNA and bidirectional Sanger sequencing of the coding exons and ~10bp of adjacent noncoding sequences. This testing strategy will reveal coding sequence changes, splice site mutations and small insertions or deletions in the FMR1 gene, but will not detect large deletions in the FMR1 locus. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known mutations or to confirm research results. 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 300624

Related Tests

Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection
Fragile X Syndrome via FMR1 CGG Repeat Expansion
X-Linked Intellectual Disability Sequencing Panel with CNV Detection


Genetic Counselors
  • 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
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Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 10 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of February 2018, we compared 26.8 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 14 years of our lab operation we have Sanger sequenced roughly 14,300 PCR amplicons. Only one error has been identified, and this was an error in analysis of sequence data.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 10 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options

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.
  • 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.


(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.


(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.


(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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