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Fish-Eye Disease and Norum Disease via the LCAT 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
2012 LCAT$650.00 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
A mutation screening in Netherlands patients with low HDL levels identified LCAT pathogenic variants in 29% (28 of the 98) of patients and 18 of them carried the same variant (p.Thr147Ile), suggesting that it is a founder mutation (Holleboom et al. 2011).

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Clinical Features
Fish eye disease (FED) is due to the deficiency of plasma lecithin-cholesterol acyltransferase (alpha-LCAT deficiency) and is referred to as incomplete or partial LCAT deficiency. FED is characterized by severe corneal opacities due to abnormal corneal lipid deposition, causing impaired vision which eventually leads to blindness. Other symptoms include dyslipoproteinaemia, which is characterized by increased levels of very low and low density lipoproteins (VLDL and LDL) and a 90% reduction in the level of high-density lipoprotein (HDL) (Carlson 1982; Carlson and Philipson 1979).

Clinically, FED differs from other familial conditions with deficiency of HDL such as Tangier disease, Milano-AI-apoprotein disease, and familial LCAT-deficiency (FLD) (due to alpha- and beta-LCAT deficiency referred as complete LCAT deficiency, also known as Norum disease). FLD is a severe form of disease and apart from corneal opacification patients present with normochromic anemia and  progressive renal failure (by 4th to 5th decade) (Carlson 1982).
Genetics
FED and FLD are autosomal recessive disorders. Both are due to homozygous or compound heterozygous pathogenic variants in LCAT (Holleboom et al. 2011). Missense variants dispersed in different regions of the LCAT gene were reported in both FLD and FED cases, which suggests several functionally important structural domains (Funke et al. 1993). Looking at the documented pathogenic variants in the Human Gene Mutation Database, protein truncating variants were reported in only FLD cases (HGMD). No other genotype-pyhentype correlations have been reported. LCAT pathogenic variants were highly prevalent in patients with low HDL cholesterol levels in the Netherlands due to the founder mutation p.Thr147Ile (Holleboom et al. 2011). So far, over 100 pathogenic variants (missense, nonsense, splicing, small and gross deletions and duplications and small indels) have been reported in LCAT (HGMD).

LCAT encodes a highly conserved enzyme lecithin:cholesterol acyltransferase (LCAT) that catalyzes the formation of most plasma cholesterol ester and plays an important role in the reverse transport of cholesterol from peripheral tissue to the liver (Maeda et al. 1991).
Testing Strategy
This test involves bidirectional DNA Sanger sequencing of all coding exons and ~ 20 bp of flanking noncoding sequence of the LCAT gene. 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
All Fish eye disease and familial LCAT-deficiency patients and all patients with high density lipoprotein deficiency are candidates.

Gene

Official Gene Symbol OMIM ID
LCAT 606967
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Diseases

Name Inheritance OMIM ID
Fish-Eye Disease 136120
Norum Disease 245900

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Carlson LA. 1982. European journal of clinical investigation. 12: 41-53. PubMed ID: 6802651
  • Carlson LA., Philipson B. 1979. Lancet (London, England). 2: 922-4. PubMed ID: 91022
  • Funke H. et al. 1993. The Journal of clinical investigation. 91: 677-83. PubMed ID: 8432868
  • Holleboom AG. et al. 2011. Human mutation. 32: 1290-8. PubMed ID: 21901787
  • Human Gene Mutation Database (Bio-base).
  • Maeda E. et al. 1991. Biochemical and biophysical research communications. 178: 460-6. PubMed ID: 1859405
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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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