Laboratory Test Guide

FMR1-Related Disorders

General Information

Lab Name

FMR1-Related Disorders

Lab Code

FMR1

Epic Name

FMR1-Related Disorders

Description

Fragile X Syndrome (FXS)

FXS, the most common inherited cause of intellectual disability, affects about 1:4,000-6,250 individuals with one X chromosome (typically assigned male sex at birth); clinical features can include varying degrees of cognitive deficits, seizures, and certain characteristic physical issues. Individuals with two X chromosomes (typically assigned female sex at birth) exhibit symptoms at about half the prevalence as individuals with one X chromosome, and symptoms are generally milder in severity. In over 99% of cases, FXS is caused by a full repeat expansion (>200 CGG trinucleotide repeats) in the FMR1 gene.

Fragile X Tremor/Ataxia Syndrome (FXTAS)

FXTAS can occur in individuals with an FMR1 allele in the premutation range (55-200 CGG repeats) and is characterized primarily by intention tremor, cerebellar gait ataxia, and cognitive impairment. Onset of FXTAS is typically between age 60-65 years; for individuals with an FMR1 allele in the premutation range, FXTAS occurs in approximtely 40% of individuals with one X chromosome and 16-20% of individuals with two X chromosomes.

Fragile X-Related Primary Ovarian Insufficiency (FXPOI)

FXPOI can occur in individuals who have ovaries and an FMR1 allele in the premutation range (55-200 CGG repeats) and is characterized by primary ovarian insufficiency prior to the age of 40. FXPOI occurs in approximately 12-28% of individuals who have ovaries and an FMR1 allele in the premutation range.

Note: Individuals with two X chromosomes and an FMR1 allele with <100 CGG repeats could have additional testing to determine probability of allele expansion upon transmission. (see Lab Test Catalog, lab mnemonic [570] for more info).

The Fragile X DNA test performed is the same for FXS, FXTAS, or FXPOI.

Genetic Counseling

Genetic counseling for FMR1-related conditions is complex and challenging. Genetic counseling for patients and families undergoing or considering genetic testing is highly recommended. The laboratory can provide referrals to genetics clinics in the patient’s locale.

References

  • Hall DA and O'Keefe JA. Clinical neurogenetics: fragile x-associated tremor/ataxia syndrome. Neurol Clin 2013, 31:1073-84. 24176424
  • Hunter JE, Berry-Kravis E, Hipp H, et al. FMR1 Disorders. 1998 Jun 16 [Updated 2019 Nov 21]. In: Adam MP, Everman DB, Mirzaa GM, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2022. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1384/
  • Monaghan KG, Lyon E, Spector EB, and erican College of Medical Genetics and Genomics. ACMG Standards and Guidelines for fragile X testing: a revision to the disease-specific supplements to the Standards and Guidelines for Clinical Genetics Laboratories of the American College of Medical Genetics and Genomics. Genet Med 2013, 15:575-86. 23765048
  • Pirozzi F, Tabolacci E, and Neri G. The FRAXopathies: definition, overview, and update. Am J Med Genet A 2011, 155A:1803-16. 21739597
  • Sullivan SD, Welt C, and Sherman S. FMR1 and the continuum of primary ovarian insufficiency. Semin Reprod Med 2011, 29:299-307. 21969264

Synonyms

ataxia, autism, developmental delay, FMR1, Fragile X, Fragile X-associated tremor ataxia syndrome, FXTAS, intellectual disability, POF, POI, premature ovarian failure, primary ovarian insufficiency, tremor

Components

Code Name
FMR1RT FMR1 Result
FMR1A1 FMR1 Allele 1
FMR1A2 FMR1 Allele 2
FMR1CI FMR1 Clin Info
FMR1IN FMR1 Interpretation
FMR1MT FMR1 Method
FMR1DI FMR1 Director

Interpretation

Method

Test performed using polymerase chain reaction (PCR) with capillary electrophoresis to detect expansions of the CGG trinucleotide tract in the 5’UTR of the FMR1 gene.

Note: There are rare FMR1 mutations; less than 1% of individuals affected with FXS do not have an FMR1 allele in the full expansion ("full mutation") range but carry a deletion or point mutation in the FMR1 gene. Pathogenic variants other than the typical CGG repeat expansion (e.g., single nucleotide variants, deletions, complex rearrangements) are not detectable by this assay.

Reference Range

See individual components

Ref. Range Notes

FMR1 is located at chromosome Xq27.3. FMR1 alleles are categorized by number of CCG repeats and methylation status:

  • Non-expanded (“normal”) allele: up to 44 repeats
  • Intermediate (“gray zone”) allele: 45-54 repeats
  • Premutation allele: 55-200 repeats
  • Full expansion (“full mutation”) allele: over 200 repeats

Guidelines

Ordering & Collection

Specimen Type

Blood/Cultured amniocytes or chorionic villus cells/Extracted DNA from approved sample types (blood, chorionic villi, amniocyte). Direct chorionic villi, amniocyte, or amniotic fluid testing require Genetics Director approval. Please call the lab at 206-598-7021

Collection

Acceptable:

  1. Whole blood:5 mL lavender top (EDTA) tube or yellow (ACD) top tube or 2 mL microtainer lavender top tube

  2. Extracted DNA from blood, chorionic villi, and amniocytes: 500 ng (concentration >10 ng/uL)

  3. Cultured amniocytes/chorionic villi: MCC is required for testing fetal samples. See MCC OLTG.

  4. Also acceptable, but requires the Genetics Director's approval and a backup culture. Direct chorionic villi and/or TISSUE: Send 20mg of tissue in a sterile tube or RPMI culture media

    *NOTE: If a fetal sample (cultured amniocytes or chorionic villi) was received, add MCC to the order. Prenatal testing requires concomitant testing for maternal cell contamination (see Online Test Guide, MCC for ordering and specimen requirements). See Special Instructions.

Unacceptable: Heparin green top tubes, buccal swab

Forms & Requisitions

Genetics Requisition

Handling Instructions

SPS specimen handling:

  1. Whole blood sample: store in the refrigerator

  2. Cultured amniocytes/chorionic villi: store at room temperature. Call the Genetics lab upon receipt (206)598-7021.

  3. Extracted DNA: store in the refrigerator

Quantity

requested: Entire specimen
minimum: Blood: 1 mL. If volume is less than 1mL, do not cancel. Send to Genetics lab. Confluent cultured cells: One (1) T25 flask. Extracted DNA: 250 ng

Processing

If fetal tissue (cultured amniocytes or chorionic villi) was received for prenatal testing, consultation with the laboratory is required. Please notify the Genetics lab about prenatal studies via email at geneticshelp@uw.edu or call 206-598-7021.

Performance

LIS Dept Code

Genetics (GEN)

Performing Location(s)

UW-MT Genetics

Attention: Genetics Lab
Clinical lab, Room NW220
University of Washington Medical Center
1959 NE Pacific Street
Seattle, WA 98195

Tel: 206-598–6429 M–F (7:30 AM–4:00 PM)
Fax: 206-598–0304
Lab email: cgateam@uw.edu

Tel (EXOME only): 206-543-0459

Manager
Joe Bernal

Genetic Counselors
Angela Jacobson, MS, LGC
Sandra Coe, MS,LGC
Dru Leistritz, MS, LGC(EXOME testing only)

Variant Review Scientist
Ankita Jhuraney, PhD
Sarah Paolucci, MA, MS, LGC
Catherine A. Darcey, MSc
Daniel W. Serber, PhD, MS, LCGC

Faculty
Jillian Buchan, PhD, FACMG
Runjun Kumar, MD, PhD
Christina Lockwood, PhD, DABCC, DABMGG
Brian Shirts, MD, PhD
Abbye McEwen, MD, PhD
Colin Pritchard, MD, PhD
Vera Paulson, MD, PhD
Eric Konnick, MD, MS
He Fang, PhD

Frequency

Performed weekly. Results within 2-3 weeks.

Available STAT?

No

Billing & Coding

CPT codes

81243

LOINC

81856-7

Interfaced Order Code

UOW4692