Forms

Autosomal Recessive Transient Infantile Liver Failure (LFIT) via the TRMU 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
2954 TRMU$780.00 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

Clinical sensitivity for transient infantile liver failure (LFIT) is difficult to estimate, as fewer than 30 patients have been described to date (Zeharia et al. 2009; Gaignard et al. 2013; Grover et al. 2014; Uusimaa et al. 2011; Kemp et al. 2011). Analytical sensitivity is expected to be high, however, as many of the pathogenic variants reported are either missense changes or small deletions/insertions.

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Clinical Features

Transient infantile liver failure (LFIT) is characterized by acute hepatic failure and hyperlactatemia in 2 to 4-month old infants (Zeharia et al. 2009). Hallmark features of LFIT include feeding difficulties, growth delay, lethargy, jaundiced sclerae, hepatomegaly, and a distended abdomen (Zeharia et al. 2009; Gaignard et al. 2013). Additionally, patients present with high levels of lactate in cerebrospinal fluid and/or blood, indicative of mitochondrial dysfunction. To date, fewer than 30 patients have been identified with LFIT worldwide (Zeharia et al. 2009; Gaignard et al. 2013; Grover et al. 2015; Uusimaa et al. 2011; Kemp et al. 2011).

Given the rarity of this disorder, the long-term prognosis for a LFIT-affected child is still uncertain. In one study, however, LFIT patients who survived the initial acute hepatic event fully recovered normal liver function within 3-4 months, and did not have a second episode (longest follow-up: 14 years) (Zeharia et al. 2009).

Genetics

Transient infantile liver failure (LFIT) is an autosomal recessive disorder linked to defects in mitochondrial tRNA modification (Zeharia et al. 2009). The TRMU gene, located on chromosome 22q13.31, spans 11 exons and produces a mitochondrial-specific tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase. This enzyme is essential for the 2-thiolation of uridine at the wobble position of the mitochondrial tRNA-Lys, tRNA-Glu, and tRNA-Gln (Umeda et al. 2005; Sasarman et al. 2011). Consequently, loss or inactivation of TRMU results in severe reduction of this post-transcriptional modification, although the exact molecular consequence of such a defect is still in dispute (Zeharia et al. 2009; Sasarman et al. 2011).

A number of different pathogenic variants have been documented for TRMU-associated LFIT. Missense variants that alter highly conserved residues are documented most frequently; in particular, the variants c.229T>C (p.Tyr77His) and c.835G>A (p.Val279Met) are commonly reported (Zeharia et al. 2009; Gaignard et al. 2013; Grover et al. 2014; Uusimaa et al. 2011). Several other types of inactivating variants have also been described, including small out-of-frame insertions/deletions or splicing variants (Zeharia et al. 2009; Uusimaa et al. 2011; Gaignard et al. 2013). 

A thorough differential diagnosis for LFIT is critical to rule out causative infections or similar genetic disorders. Heritable, non-reversible infantile liver failure has been associated with mitochondrial DNA depletion syndrome, which can be caused by loss-of-function variants in nuclear-encoded genes such as DGUOK, POLG, and MPV17 (Mandel et al. 2001; Naviaux and Nguyen 2004; Spinazzola et al. 2006). In contrast to the genetic disorders linked to these genes, TRMU-associated transient infantile liver failure patients have normal mtDNA levels (Zeharia et al. 2009).

Testing Strategy

Full gene sequencing of TRMU is performed, with bidirectional sequencing of exons 1-11. 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

TRMU sequencing should be considered for patients who present with acute liver failure within the first few months of life, or for individuals with a family history of transient infantile liver failure.  We will also sequence the TRMU gene to determine carrier status.

Gene

Official Gene Symbol OMIM ID
TRMU 610230
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Liver Failure Acute Infantile AR 613070

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Gaignard P. et al. 2013. JIMD Reports. 11: 117-23. PubMed ID: 23625533
  • Grover Z. et al. 2015. JIMD Reports. 21: 109-13. PubMed ID: 25665837
  • Kemp J. et al. 2011. Brain: A Journal of Neurology. 134: 183-95. PubMed ID: 21169334
  • Mandel H. et al. 2001. Nature Genetics. 29:337-41. PubMed ID: 11687800
  • Naviaux R. and Nguyen K. 2004. Annals of Neurology. 55: 706-12. PubMed ID: 15122711
  • Sasarman F. et al. 2011. Human Molecular Genetics. 20: 4634-43. PubMed ID: 21890497
  • Spinazzola A. et al. 2006. Nature Genetics. 38: 570-5. PubMed ID: 16582910
  • Umeda N. et al. 2005. The Journal of Biological Chemistry. 280: 1613-24. PubMed ID: 15509579
  • Uusimaa J. et al. 2011. Journal of Medical Genetics. 48: 660-8. PubMed ID: 21931168
  • Zeharia A. et al. 2009. American Journal of Human Genetics. 85: 401-7. PubMed ID: 19732863
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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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