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Perrault Syndrome Type 4 via the LARS2 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
1549 LARS2$1160.00 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

Based on the limited number of reports on LARS2 variants, the clinical sensitivity cannot be determined. The analytical sensitivity of bi-directional sequencing is high because all LARS2 causative mutations reported to date are detectable by this method.

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 LARS2$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Features

Perrault syndrome is a sex-influenced disorder that is characterized by progressive, sensorineural deafness coupled with ovarian dysgenesis or premature ovarian failure (streak gonads) and infertility in females; however, this syndrome often goes undetected until puberty or during child-bearing age (Pierce et al. 2010). Perrault syndrome also affects males and is mainly characterized by progressive hearing loss. Affected females are karyotypically 46,XX and infertile; affected males are 46,XY and fertile. Some patients diagnosed with Perrault syndrome also develop neurologic abnormalities, which include mild mental retardation, cerebellar ataxia, and disruptions involving the peripheral nervous system (Huyghe et al. 2006). 

Diagnosing Perrault syndrome in a male patient can be very challenging, especially in the absence of a sister that presents specific symptoms of the syndrome. The average age at diagnosis of Perrault syndrome in females is 22 years old, which is often ascertained by a delay in puberty and the development of sensorineural deafness. Hearing loss in Perrault syndrome is always bilateral, although the severity can be variable (ranging from mild to profound deafness). Ovarian dysgenesis occurs in all female Perrault syndrome patients and is often validated by amenorrhea; however, males do not show any gonadal defects. Approximately 50% of patients with Perrault syndrome show delayed growth, with height often below the third percentile.

Genetics

Perrault syndrome follows an autosomal recessive pattern of inheritance and is caused by variants in several genes, including the LARS2 gene, also known as the LEURS or PRLTS4 gene, which has been localized to chromosomal band 3p21.3 (Pierce et al. 2010, Pierce et al. 2013). However, a recent study involving two families affected by premature ovarian failure and hearing loss has identified three LARS2 variants in five affected children (Pierce et al. 2013).

The LARS2 gene consists of 20 exons and encodes a mitochondrial leucyl-tRNA synthetase 2 protein, also called leucine translase and leucine tRNA ligase, which plays a major role in aminoacylation (Lue et al. 2007; Hsu et al. 2008). The protein is generally expressed as a soluble protein (Ling et al. 2005). Variants in the LARS2 have also been implicated in the etiology of mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) and type 2 diabetes (Kadowaki et al. 1994; Li et al. 2010; M’t Hart et al. 2005; Reiling et al. 2010; Karicheva et al. 2011). Other genes implicated in the development of Perrault syndrome include CLPP, HSD17B4 and HARS2.

Mitochondrial leucyl-tRNA synthetase 2 is a 903-amino acid polypeptide that is highly expressed in tissues characterized by high metabolic rates, including skeletal muscles, kidney, and heart (Higashikata et al. 2001). Aside from aminoacylation, this protein also facilitates in the association of the mRNA strand to ribosomes, which is an essential step in protein synthesis (Chomyn et al. 2000). This enzyme also assists in the modification of the wobble U base, which is related to the incorporation of the correct amino acid in the growing polypeptide strand (Sasarman et al. 2008).

Most cases of Perrault syndrome are simultaneously reported in at least two female members of a family. In cases wherein two brothers are involved, these individuals often present a relatively mild phenotype. Only a few variants in the LARS2 gene have been reported, which include two missense mutations and one small deletion (Pierce et al. 2013). There is also evidence that the leucyl-tRNA synthetase 2 protein plays an important role in the respiratory chain (King et al. 1992).

Testing Strategy

Full gene sequencing of all coding exons of the LARS2 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

Individuals presenting with hearing loss and an enlargement of the vestibular aqueduct can be offered the LARS2 gene test. The individual should have completed otologic and audiologic tests, as well as ancillary testing such as CT imaging of the inner ear to determine abnormalities in the temporal bone. Audioprofiling may also assist in determining the rate of progressive hearing loss each year. Cascade testing or successive testing of family members to trace the inheritance pattern of the identified mutation may be offered when the patient has been identified as the index case or proband.

Gene

Official Gene Symbol OMIM ID
LARS2 604544
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Perrault Syndrome 4 615300

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Chomyn A, Enriquez JA, Micol V, Fernandez-Silva P, Attardi G. 2000. The mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episode syndrome-associated human mitochondrial tRNALeu(UUR) mutation causes aminoacylation deficiency and concomitant reduced association of mRNA with ribosomes. Journal of Biological Chemistry 275: 19198-19209. PubMed ID: 10858457
  • Higashikata T, Koyama J, Shimada H, Yazaki M, Owa M, Ikeda S. 2001. An 80-year-old mitochondrial disease patient with A3243G tRNA(Leu(UUR)) gene presenting cardiac dysfunction as the main symptom. Internal Medicine 40: 405-408. PubMed ID: 11393411
  • Hsu JL, Martinis SA. 2008. A flexible peptide tether controls accessibility of a unique C-terminal RNA-binding domain in leucyl-tRNA synthetases. Journal of Molecular Biology 376: 482-491. PubMed ID: 18155724
  • Huyghe S, Schmalbruch H, Hulshagen L, Veldhoven PV, Baes M, Hartmann D. 2006. Peroxisomal multifunctional protein-2 deficiency causes motor deficits and glial lesions in the adult central nervous system. American Journal of Pathology 168:1321-1334. PubMed ID: 16565505
  • Kadowaki T, Kadowaki H, Mori Y, Tobe K, Sakuta R, Suzuki Y, Tanabe Y, Sakura H, Awata T, Goto Y, et al. 1994. A subtype of diabetes mellitus associated with a mutation of mitochondrial DNA. New England Journal of Medicine 330: 962-968. PubMed ID: 8121460
  • Karicheva OZ, Kolesnikova OA, Schirtz T, Vysokikh MY, Mager-Heckel AM, Lombès A, Boucheham A, Krasheninnikov IA, Martin RP, Entelis N, Tarassov I. 2011. Correction of the consequences of mitochondrial 3243A>G mutation in the MT-TL1 gene causing the MELAS syndrome by tRNA import into mitochondria. Nucleic Acids Research 39: 8173-8186. PubMed ID: 21724600
  • King MP, Koga Y, Davidson M, Schon EA. 1992. Defects in mitochondrial protein synthesis and respiratory chain activity segregate with the tRNA(Leu(UUR)) mutation associated with mitochondrial myopathy, encephalopathy, lactic acidosis, and strokelike episodes. Molecular and Cellular Biology 12: 480-490. PubMed ID: 1732728
  • Li R, Guan MX. 2010. Human mitochondrial leucyl-tRNA synthetase corrects mitochondrial dysfunctions due to the tRNALeu(UUR) A3243G mutation, associated with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like symptoms and diabetes. Molecular and Cellular Biology 30: 2147-2154. PubMed ID: 20194621
  • Ling C, Yao YN, Zheng YG, Wei H, Wang L, Wu XF, Wang ED. 2005. The C-terminal appended domain of human cytosolic leucyl-tRNA synthetase is indispensable in its interaction with arginyl-tRNA synthetase in the multi-tRNA synthetase complex. Journal of Biological Chemistry 280: 34755-34763. PubMed ID: 16055448
  • Lue SW, Kelley SO. 2007. A single residue in leucyl-tRNA synthetase affecting amino acid specificity and tRNA aminoacylation. Biochemistry 46: 4466-4472. PubMed ID: 17378584
  • M't Hart LM, Hansen T, Rietveld I, Dekker JM, Nijpels G, Janssen GM, Arp PA, Uitterlinden AG, Jørgensen T, Borch-Johnsen K, Pols HA, Pedersen O, van Duijn CM, Heine RJ, Maassen JA.2005. Evidence that the mitochondrial leucyl tRNA synthetase (LARS2) gene represents a novel type 2 diabetes susceptibility gene. Diabetes 54: 1892-1895. PubMed ID: 15919814
  • Pierce SB , Walsh T, Chisholm KM, Lee MK, Thornton AM, Fiumara A, Opitz JM, Levy-Lahad E, Klevit RE, King MC. 2010. Mutations in the DBP-deficiency protein HSD17B4 cause ovarian dysgenesis, hearing loss, and ataxia of Perrault Syndrome. American Journal of Human Genetics 87: 282-288. PubMed ID: 20673864
  • Pierce SB, Gersak K, Michaelson-Cohen R, Walsh T, Lee MK, Malach D, Klevit RE, King MC, Levy-Lahad E. 2013. Mutations in LARS2, encoding mitochondrial leucyl-tRNA synthetase, lead to premature ovarian failure and hearing loss in Perrault syndrome. American Journal of Human Genetics 92: 614-620. PubMed ID: 23541342
  • Reiling E, Jafar-Mohammadi B, van 't Riet E, Weedon MN, van Vliet-Ostaptchouk JV, Hansen T, Saxena R, van Haeften TW, Arp PA, Das S, Nijpels G, Groenewoud MJ, van Hove EC, Uitterlinden AG, Smit JW, Morris AD, Doney AS, Palmer CN, Guiducci C, Hattersley AT, Frayling TM, Pedersen O, Slagboom PE, Altshuler DM, Groop L, Romijn JA, Maassen JA, Hofker MH, Dekker JM, McCarthy MI, 't Hart LM. 2010. Genetic association analysis of LARS2 with type 2 diabetes. Diabetologia 53: 103-110. PubMed ID: 19847392
  • Sasarman F, Antonicka H, Shoubridge EA.2008. The A3243G tRNALeu(UUR) MELAS mutation causes amino acid misincorporation and a combined respiratory chain assembly defect partially suppressed by overexpression of EFTu and EFG2. Human Molecular Genetics 17: 3697-3707. PubMed ID: 18753147
Order Kits
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.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

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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