XLMR 14, Syndromic: UPF3B Gene Sequencing

Condition Description

In 2007, Tarpey et al. conducted a study of individuals with mental retardation (MR) from 250 families compatible with X linkage. None of these individuals had mutations in any of the XLMR-linked genes identified at the time. Three different mutations in the UPF3B gene (Xq25-q26) were identified in three families. One of these families had a clinical diagnosis of FG syndrome (FGS), while the other two families had clinical diagnoses of Lujan-Fryns syndrome (LFS). They then analyzed 118 affected individuals from a cohort of families with putative XLMR and found a UPF3B mutation in a family with nonsyndromic XLMR. Mental retardation in these families was mild to severe.

Features present in more than half of affected males in the first three families included a slender build with poor musculature, a long and thin face, high arched palate, high nasal bridge, and pectus. Half of the affected individuals had autistic features or behavioral problems. While the clinical phenotype is variable, many of these clinical features are suggestive of LFS and FGS. The affected males from the fourth family had normal physical examinations, and were hence classified as nonsyndromic XLMR.

Carrier females had normal intelligence and normal physical examinations.

For patients with suspected XLMR 14, sequence analysis is recommended as the first step in mutation identification. For patients in whom mutations are not identified by full gene sequencing, deletion/duplication analysis is appropriate.


  • Tarpey et al. Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation. Nature Genetics 2007, 39:1127-1133.
  • OMIM: http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=300676.
  • OMIM: http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=300298.

Genes (1)

Your search may have returned a result for a gene alias. Click here for a full list of genes and their aliases.


This test is indicated for:

  • Confirmation of a clinical diagnosis of XLMR 14
  • Carrier testing in adults with a family history of XLMR 14


PCR amplification of 11 exons contained in the UPF3B gene is performed on the patient's genomic DNA. Direct sequencing of amplification products is performed in both forward and reverse directions, using automated fluorescence dideoxy sequencing methods. The patient's gene sequences are then compared to a normal reference sequence. Sequence variations are classified as mutations, benign variants unrelated to disease, or variations of unknown clinical significance. Variants of unknown clinical significance may require further studies of the patient and/or family members. This assay does not interrogate the promoter region, deep intronic regions, or other regulatory elements, and does not detect large deletions.


Clinical Sensitivity: Unknown. Mutations in the promoter region, some mutations in the introns and other regulatory element mutations cannot be detected by this analysis. Large deletions will not be detected by this analysis. Results of molecular analysis should be interpreted in the context of the patient's biochemical phenotype.

Analytical Sensitivity: ~99%

Specimen Requirements

Listed below are EGL's preferred sample criteria. For any questions, please call 470.378.2200 and ask to speak with a laboratory genetic counselor (eglgc@egl-eurofins.com).
Submit only 1 of the following specimen types
Whole Blood (EDTA)

EDTA (Purple Top)
Infants and Young Children (<2 years of age): 2-3 ml
Children > 2 years of age to 10 years old: 3-5 ml
Older Children & Adults: 5-10 ml
Autopsy: 2-3 ml unclotted cord or cardiac blood
Collection and Shipping
Ship sample at room temperature for receipt at EGL within 72 hours of collection. Do not freeze.

Oragene™ Saliva Collection Kit
Orangene™ Saliva Collection Kit used according to manufacturer instructions. Please contact EGL for a Saliva Collection Kit for patients that cannot provide a blood sample.
Collection and Shipping
Please do not refrigerate or freeze saliva sample. Please store and ship at room temperature.
DNA, Isolated

Isolation using the Perkin Elmer™Chemagen™ Chemagen™ Automated Extraction method or Qiagen™ Puregene kit for DNA extraction is recommended.
Collection and Shipping
Refrigerate until time of shipment in 100 ng/µL in TE buffer. Ship sample at room temperature with overnight delivery.

Special Instructions

Submit copies of diagnostic biochemical test results with the sample, if appropriate. Contact the laboratory if further information is needed.

Sequence analysis is required before deletion/duplication analysis by targeted CGH array. If sequencing is performed outside of EGL Genetics, please submit a copy of the sequencing report with the test requisition.

  • Deletion/duplication analysis of the UPF3B gene by CGH array is available for those individuals in whom sequence analysis is negative.
  • Custom diagnostic mutation analysis (KM) is available to family members if mutations are identified by targeted mutation testing or sequencing analysis.
  • Prenatal testing is available to adult females who are confirmed carriers of mutations. Please contact the laboratory genetic counselor to discuss appropriate testing prior to collecting a prenatal specimen.

How to Order