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LIG4 Syndrome via the LIG4 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
1711 LIG4$680.00 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 is unknown due to the limited number of cases reported. Analytical sensitivity should be high as all reported mutations are detectable by sequencing.

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Clinical Features
LIG4 syndrome, also known as Ligation IV syndrome, is characterized by microcephaly, unusual facial features, growth and developmental delay, skin anomalies, pancytopenia, and combined immunodeficiency. Facial features have been described as "bird like" (beak-like nose and micrognathia). An affected individual's skin is photosensitive and can have psoriatic-like lesions. Additionally, patients may have telangiectasias, leukemia, lymphoma, and bone marrow abnormalities (O’Driscoll et al. 2001; Chistiakov et al. 2009). Malignancies have been reported in 25% of reported cases, although cancer risks may be higher because most patients have an early death (Murray et al. 2014). LIG4 syndrome is a clinically heterogeneous disorder as a patient has also been described to have lymphopenia, extreme radiosensitivity, severe dysmaturity, corpus callosum agenesis, polysyndactyly, dysmorphic appearance, and erythema (IJspeert et al. 2013). It is an extremely rare syndrome (i.e. <20 cases described) with an estimated prevalence of 1 in 1,000,000 (http://www.orpha.net/).
Genetics
LIG4 syndrome is an autosomal recessive disorder caused by pathogenic variants in the LIG4 gene. This gene encodes a ligase that is involved in double stranded break repair during V(D)J recombination and non-homologous end-joining (NHEJ) (IJspeert et al. 2013). The ligase forms a complex with other NHEJ proteins, such as the X-ray repair cross complementing protein 4 (XRCC4) and is important in the final step in ligating DNA strands during NHEJ (Helleday et al. 2007). Cell lines from affected patients show radiosensitivity and chromosome instability (O’Driscoll et al. 2001). Biallelic null alleles are embryonic lethal, so that individuals with LIG4 syndrome have at least one hypomorphic allele. Pathogenic variants observed in the C-terminal and XRCC4-binding domain have a greater deleterious effect than variants outside of these regions (Chistiakov et al. 2009). Reported pathogenic variants include missense, nonsense, and small insertions and deletions (Human Mutation Gene Database).
Testing Strategy
DNA ligase 4 is encoded by one exon from the LIG4 gene on chromosome 13q33-q34. Testing is accomplished by amplifying the coding exon and ~20 bp of adjacent noncoding sequence, then determining the nucleotide sequence using standard dideoxy Sanger sequencing methods and a capillary electrophoresis instrument. We will also sequence any single portion (Test #100) or portions of this exon (Test #200) in family members of patients with a known mutation or to confirm research results.
Indications for Test
Individuals suspected of having LIG4 syndrome. Family members may also be tested to determine carrier status of an identified variant in the LIG4 gene. This test is specifically designed for heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.

Gene

Official Gene Symbol OMIM ID
LIG4 601837
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Lig4 Syndrome 606593

Related Tests

Name
Ataxia telangiectasia Syndrome via the ATM Gene
Nijmegen Breakage Syndrome via the NBN Gene
Seckel Syndrome, Primary Microcephaly and Familial Cutaneous Telangiectasia and Cancer Syndrome via the ATR Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Chistiakov DA, Voronova NV, Chistiakov AP. 2009. Ligase IV syndrome. European Journal of Medical Genetics 52: 373–378. PubMed ID: 19467349
  • Helleday T, Lo J, Vangent D, Engelward B. 2007. DNA double-strand break repair: From mechanistic understanding to cancer treatment. DNA Repair 6: 923–935. PubMed ID: 17363343
  • Human Gene Mutation Database (Bio-base).
  • IJspeert H, Warris A, Flier M, Reisli I, Keles S, Chishimba S, Dongen JJ, Gent DC, Burg M. 2013. Clinical Spectrum of LIG4 Deficiency Is Broadened with Severe Dysmaturity, Primordial Dwarfism, and Neurological Abnormalities. Hum Mutat 34: 1611–1614. PubMed ID: 24027040
  • Murray JE, Bicknell LS, Yigit G, Duker AL, Kogelenberg M van, Haghayegh S, Wieczorek D, Kayserili H, Albert MH, Wise CA, Brandon J, Kleefstra T, Warris A, van der Flier M, Bamforth JS, Doonanco K, Adès L, Ma A, Field M, Johnson D, Shackley F, Firth H, Woods CG, Nürnberg P, Gatti RA, Hurles M, Bober MB, Wollnik B, Jackson AP. 2014. Extreme Growth Failure is a Common Presentation of Ligase IV Deficiency. Human Mutation 35: 76–85. PubMed ID: 24123394
  • O’Driscoll M, Cerosaletti KM, Girard P-M, Dai Y, Stumm M, Kysela B, Hirsch B, Gennery A, Palmer SE, Seidel J, Gatti RA, Varon R, Oettinger MA, Neitzel H, Jeggo PA, Concannon P. 2001. DNA ligase IV mutations identified in patients exhibiting developmental delay and immunodeficiency. Molecular Cell 8: 1175–1185. PubMed ID: 11779494
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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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