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Posterior Microphthalmia via the PRSS56 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
2013 PRSS56$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
In a mutational screening of 25 MCOP affected patients from 13 families, 19 Saudi patients (~75%) were homozygous for PRSS56 mutations, 1 Indian and 1 Saudi patient had mutations in MFRP, and in 4 Saudi patients no causative variants were detected. All patients had a similar phenotype (Nowilaty et al. 2013).

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Clinical Features
Posterior microphthalmos (MCOP) is a relatively rare, isolated malformation of the eye. Clinically, MCOP is characterized by extreme hyperopia, retinal folding, normal anterior segment with a small posterior segment, steep corneal curvatures, shallow anterior chamber, thick lenses and scleral wall, reduced visual acuity and strabismic amblyopia. Funduscopy findings include crowded optical discs, tortuous vessels, and an abnormal foveal avascular zone. Affected individuals are at-risk for narrow-angle glaucoma, chorioretinal pathology including uveal effusion and amblyopia due to the abnormally small eye size (Hmani-Aifa et al. 2009; Gal et al. 2011; Said et al. 2013).
Genetics
To date, pathogenic variants in two genes MFRP (encodes membrane frizzled-related protein) and PRSS56 (encodes a serine protease) have been reported to be causative for autosomal recessive Posterior microphthalmia (arMCOP) (Said et al. 2013).

PRSS56, which encodes a trypsin-like serine protease, is classified as a member of the chymotrypsin family as the encoded protein carries a highly conserved triad consisting of Asp191-His145-Ser286 (similar to trypsin triad Asp102-His57-Ser195), which is required for the catalytic activity of the protein (Gal et al. 2011).

MCOP was found to be highly prevalent in the Faroe Islands due to a founder effect (carrier frequency 3.2%). Patients of the Faroese families were either homozygous for c.926G>C (p.Trp309Ser) or compound heterozygous for c.926G>C and c.526C>G (p.Arg176Gly) variants in PRSS56. Molecular modeling of the p.Trp309Ser variant showed substantially reduced enzyme affinity and reactivity toward in vivo protein substrates. A homozygous single nucleotide deletion c.1066dupC was identified in five arMCOP patients from a consanguineous Tunisian family, which is predicted to result in translational frameshift and protein truncation (p.Gln356Argfs*148). In the Saudi population, PRSS56 pathogenic variants were shown to be the major cause of arMCOP (Orr et al. 2011; Gal et al. 2011; Said et al. 2013; Nowilaty et al. 2013). So far, over 20 pathogenic variants (missense variants and single nucleotide duplications) have been reported in the PRSS56 gene, which the majority are missense variants (90%) (Human Gene Mutation Database; Orr et al. 2011; Gal et al. 2011).
Testing Strategy
This test involves bidirectional DNA Sanger sequencing of all coding exons and ~ 20 bp of flanking noncoding sequence of the PRSS56 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 patients with symptoms suggestive of posterior segment anomalies are candidates.

Gene

Official Gene Symbol OMIM ID
PRSS56 613858
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Microphthalmia, Isolated 6 613517

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Gal A, Rau I, El Matri L, Kreienkamp H-J, Fehr S, Baklouti K, Chouchane I, Li Y, Rehbein M, Fuchs J, Fledelius HC, Vilhelmsen K, Schorderet DF, Munier FL, Ostergaard E, Thompson DA, Rosenberg T. 2011. Autosomal-Recessive Posterior Microphthalmos Is Caused by Mutations in PRSS56, a Gene Encoding a Trypsin-Like Serine Protease. The American Journal of Human Genetics 88: 382–390. PubMed ID: 21397065
  • Hmani-Aifa M, Salem S Ben, Benzina Z, Bouassida W, Messaoud R, Turki K, Khairallah M, Rebaï A, Fakhfekh F, Söderkvist P, Ayadi H. 2009. A genome-wide linkage scan in Tunisian families identifies a novel locus for non-syndromic posterior microphthalmia to chromosome 2q37.1. Hum. Genet. 126: 575–587. PubMed ID: 19526372
  • Human Gene Mutation Database (Bio-base).
  • Nowilaty SR, Khan AO, Aldahmesh MA, Tabbara KF, Al-Amri A, Alkuraya FS. 2013. Biometric and molecular characterization of clinically diagnosed posterior microphthalmos. Am. J. Ophthalmol. 155: 361–372.e7. PubMed ID: 23127749
  • Orr A, Dubé M-P, Zenteno JC, Jiang H, Asselin G, Evans SC, Caqueret A, Lakosha H, Letourneau L, Marcadier J, Matsuoka M, Macgillivray C, Nightingale M, Papillon-Cavanagh S, Perry S, Provost S, Ludman M, Guernsey DL, Samuels ME. 2011. Mutations in a novel serine protease PRSS56 in families with nanophthalmos. Molecular vision 17: 1850. PubMed ID: 21850159
  • Said MB, Chouchène E, Salem SB, Daoud K, Largueche L, Bouassida W, Benzina Z, Ayadi H, Söderkvist P, Matri L, Hmani-Aifa M. 2013. Posterior microphthalmia and nanophthalmia in Tunisia caused by a founder c.1059_1066insC mutation of the PRSS56 gene. Gene 528: 288–294. PubMed ID: 23820083
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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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