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Ehlers-Danlos Syndrome with Progressive Kyphosis, Myopathy, and Hearing Loss (EDSKMH) via the FKBP14 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
1614 FKBP14$580.00 81479 Add to Order
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

Because only two reports (Baumann et al. 2012; Aldeeri et al. 2014) have described three pathogenic sequence variants in a total of seven patients, it is difficult to estimate the clinical sensitivity of this test. Analytical sensitivity should be high because all mutations reported are detectable by sequencing.

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Clinical Features

Ehlers-Danlos syndrome (EDS) pertains to a clinically and genetically heterogeneous group of heritable connective tissue disorders that mainly affect the skin, joints, ligaments, blood vessels, and internal organs (Byers and Murray 2012). The clinical hallmarks of EDS include skin hyperelasticity, joint hypermobility, and pronounced tissue fragility. One of the six major types of EDS, Ehlers-Danlos syndrome with kyphoscoliosis or EDS type VIA (OMIM 225400), is characterized by severe congenital muscle hypotonia, progressive kyphoscoliosis, extensive skin hyperelasticity with widened atrophic scars, and joint hypermobility. Other common features include osteopenia without a tendency to fractures, a Marfanoid habitus, microcornea, as well as occasional rupture of the arteries and the eye globe. The features of severe muscle hypotonia and delayed motor development in children often lead to a misdiagnosis of EDS VIA as a primary neuromuscular disease. A neuromuscular workup during the neonatal period generally yields normal results. Muscle weakness and fatigability are common symptoms of EDS, which are mainly due to increased distensibility of tendons, a decline in mechanical efficiency due to inadequate intramuscular connective tissue, and avoidance of exercise because of joint instability and/or weak connective tissue surrounding the muscle spindles (Castori and Voermans 2014). Recent studies have shown that the neuromuscular symptoms of EDS may be partly attributable to mild to moderate myopathic and/or neuropathic alterations caused by changes in composition of the extracellular matrix in muscles and peripheral nerves (Byers and Murray 2014).

One rare variant of EDS VIA is Ehlers-Danlos syndrome with progressive kyphoscoliosis, myopathy, and hearing loss (EDSKMH; OMIM 614557), which presents with the common features of EDS VIA, but with the additional characteristic of sensorineural hearing loss (Baumann et al. 2012). Patients with EDSKMH present with myopathy as determined by clinical, electrophysiological, imaging, as well as muscle biopsy testing.

Genetics

EDSKMH is an autosomal recessive connective tissue disorder that is caused by pathogenic sequence variants in the FK506-binding protein 14 (FKBP14) gene, which encodes for a 22 kDa peptidyl-prolyl cis-trans isomerase (PPIase) that is mainly located in the endoplasmic reticulum (ER) (Baumann et al. 2012). Cis-trans isomerization involving peptidyl-prolyl bonds has been determined to be the rate-limiting step of protein folding, particularly for procollagens, which are largely influenced by the availability of prolyl-residues. The process of protein folding is accelerated by the action of PPIases, which serve as folding catalysts, as well as act as molecular chaperones. In silico analysis has indicated that the putative FKBP14 protein possesses a PPIase FKBP-type domain that comprises two elongation factor (EF)-hand motifs and one retention signal (Boudko et al. 2014). Pathogenic sequence variants in the FKBP14 gene result in FKBP14 deficiency, which in turn causes enlargement of ER cisterns as well as disarray of the extracellular matrix (Baumann et al. 2012).

To date, only two studies have been conducted on EDSKMH via the FKBP14 gene, describing two pathogenic small deletions and one small insertion. In one study, five patients from four families with EDSKMH were determined to be homozygous for a 1-bp insertion within exon 3 (c.362dupC), resulting in a frameshift that is predicted to generate a premature termination codon (p.Glu122Argfs*7) (Baumann et al. 2012). Further examination of another unrelated patient with EDSKMH showed compound heterozygosity for the same 1-bp insertion and a 19-bp deletion (c.42_60del19) that leads to a premature stop codon (p.Thr15*). Electron microscopy and immunofluorescence studies of fibroblasts from these patients showed abnormal distribution and organization of the extracellular matrix, including types I and III collagens, as well as fibronectin. In another study, a three-year-old boy with EDSKMH was determined to be homozygous for a 4-bp deletion (c.197+5_197+8delGTAA) affecting splicing (Aldeeri et al. 2014).

Testing Strategy

Full gene Sanger sequencing of all four coding exons of the FKBP14 gene is performed. The full coding region of each exon plus ~20 bp of flanking non-coding DNA on either side are sequenced.  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.

Indications for Test

Candidates for this test are patients that have been diagnosed with EDSKMH.

Gene

Official Gene Symbol OMIM ID
FKBP14 614505
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Aldeeri AA, Alazami AM, Hijazi H, Alzahrani F, Alkuraya FS. 2014. Excessively redundant umbilical skin as a potential early clinical feature of Morquio syndrome and FKBP14-related Ehlers-Danlos syndrome. Clinical Genetics 86(5): 469-472. PubMed ID: 24773188
  • Baumann M, Giunta C, Krabichler B, Rüschendorf F, Zoppi N, Colombi M, Bittner RE, Quijano-Roy S, Muntoni F, Cirak S, Schreiber G, Zou Y, Hu Y, Romero NB, Carlier RY, Amberger A, Deutschmann A, Straub V, Rohrbach M, Steinmann B, Rostásy K, Karall D, Bönnemann CG, Zschocke J, Fauth C. 2012. Mutations in FKBP14 cause a variant of Ehlers-Danlos syndrome with progressive kyphoscoliosis, myopathy, and hearing loss. American Journal of Human Genetics 90(2): 201-216. PubMed ID: 22265013
  • Baumann M1, Giunta C, Krabichler B, Rüschendorf F, Zoppi N, Colombi M, Bittner RE, Quijano-Roy S, Muntoni F, Cirak S, Schreiber G, Zou Y, Hu Y, Romero NB, Carlier RY, Amberger A, Deutschmann A, Straub V, Rohrbach M, Steinmann B, Rostásy K, Karall D, Bönnemann CG, Zschocke J, Fauth C. 2012. Mutations in FKBP14 cause a variant of Ehlers-Danlos syndrome with progressive kyphoscoliosis, myopathy, and hearing loss. American Journal of Human Genetics 90(2): 201-216.
  • Boudko SP, Ishikawa Y, Nix J, Chapman MS, Bächinger HP. 2014. Structure of human peptidyl-prolyl cis-trans isomerase FKBP22 containing two EF-hand motifs. Protein Science 23(1): 67-75. PubMed ID: 24272907
  • Byers PH, Murray ML. 2012. Heritable collagen disorders: the paradigm of the Ehlers-Danlos syndrome. Journal of Investigative Dermatology 132(E1): E6-11. PubMed ID: 23154631
  • Byers PH, Murray ML. 2014. Ehlers-Danlos syndrome: A showcase of conditions that lead to understanding matrix biology. Matrix Biology 33: 10-15. PubMed ID: 23920413
  • Castori M, Voermans NC. 2014. Neurological manifestations of Ehlers-Danlos syndrome(s): A review. Iran Journal of Neurology 13(4): 190-208. PubMed ID: 25632331
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TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  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 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 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 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

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 20 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.

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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.
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.

SPECIMEN TYPES
WHOLE BLOOD

(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.

DNA

(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.

CELL CULTURE

(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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