Fragile X (FMR1) With Reflex to Methylation Analysis

Last Literature Review: May 2024 Last Update:
  • Preferred test to diagnose FXS, FXTAS, or FXPOI
  • May be used for carrier screening in individuals with a family history of FXS
  • Prenatal test for women with fragile X premutations or full mutations

Fragile X syndrome (FXS), the most common heritable form of intellectual disability (ID) and autism, is caused by full FMR1 gene mutations. ,  Individuals with an FMR1 gene premutation may develop fragile X-associated tremor ataxia syndrome (FXTAS), fragile X-associated primary ovarian insufficiency (FXPOI), or fragile X-associated neuropsychiatric disorders (FXAND). ,  These tests use triplet repeat-primed polymerase chain reaction (PCR) followed by size analysis using capillary electrophoresis to determine FMR1 CGG repeat length. Methylation-specific PCR is performed to distinguish between premutation and full mutation alleles.

For more information about the laboratory testing strategy for FMR1-related disorders, refer to the ARUP Consult Fragile X (FMR1)-Associated Disorders topic.

Disease Overview

FXS in male individuals is associated with moderate ID, autism, perseverative speech, hyperactivity, social anxiety, hand flapping or biting, poor eye contact, connective tissue anomalies, and characteristic physical features.  Female individuals with FXS are usually less severely affected than males. FXTAS may present with late-onset progressive ataxia and intention tremor or include cognitive impairment and behavioral features.  Female individuals may develop FXPOI, which is characterized by hypergonadotropic hypogonadism before 40 years of age.  Symptoms of FXAND may include anxiety, depression, attention-deficit/hyperactivity disorder (ADHD), or addictive behavior. 

Prevalence

FXS :

  • Male individuals: approximately 1 in 4,000-7,000
  • Female individuals: approximately 1 in 8,000-11,000

Premutation allele :

  • Female individuals: approximately 1 in 150-300
  • Male individuals: approximately 1 in 300-800

Genetics

Gene

FMR1

Inheritance

X-linked , 

Pattern of inheritance is subject to instability of CGG repeat sequence , 

Penetrance

FXS :

  • Male individuals: complete
  • Female individuals: 50% (depending on X-chromosome inactivation)

FXTAS , :

  • Male individuals >50 years: approximately 40% (varies with age and CGG repeat length)
  • Female individuals >50 years: approximately 16-20%

FXPOI , :

  • Approximately 20% (varies by CGG repeat length)

Test Interpretation

Sensitivity/Specificity

  • Clinical sensitivity/specificity: >99% , 
  • Analytic sensitivity/specificity: 99% , 

The estimated precision of sizing for intermediate and premutation alleles is within two to three CGG repeats.

Results

Results Interpretation: Fragile X (FMR1) with Reflex to Methylation Analysis
Allele CategoryNumber of CGG RepeatsMethylation PatternaInterpretation
Normal<45Not assessed

Not affected with FXS or other FMR1-associated disorders

Not a carrier of FXS

Intermediate45-54Not assessed

Not affected with FXS or other FMR1-associated disorders

Genetic counseling may be helpful

Premutation55-200Unmethylated

Not affected with FXS

Carrier of premutation; thus, at increased risk for other FMR1-associated disorders

Genetic counseling is recommended

FMR1 testing is recommended for at-risk family members

Full mutation>200Full

Consistent with a diagnosis of FXS in a male

Increased risk for FXS in a female

Genetic consultation is recommended

FMR1 testing is recommended for at-risk family members

aMethylation pattern is assessed when an expanded allele is detected to distinguish between premutations and full mutations. The methylation reflex is performed if ≥55 CGG repeats are detected in fetal samples, or when ≥100 CGG repeats are detected in blood samples.

Limitations

  • AGG trinucleotide interruptions within the FMR1 CGG repeat tract are not assessed.
  • An estimated CGG repeat number is not provided for full mutations (alleles with >200 repeats).
  • Rare FMR1 variants unrelated to trinucleotide expansion will not be detected.
  • Diagnostic errors can occur due to rare sequence variations.
  • Methylation patterns are not fully established in early gestation; thus, prenatal diagnosis on chorionic villus sampling is not recommended.

References

  1. GeneReviews - FMR1 Disorders

    Hunter JE, Berry-Kravis E, Hipp H, et al. FMR1 disorders. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews. University of Washington, Seattle. Last update Nov 2019; accessed Apr 2024.