Forms

Protein S Deficiency via the PROS1 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
Order Kits
TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
1654 PROS1$910.00 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 study of 53 patients with laboratory tests indicating Protein S deficiency (decreased Protein S activity or free antigen levels), mutation in the PROS1 gene was found in 38 (71%) (Biguzzi et al. 2005). Individuals with a familial history of thrombophilia identify a causative mutation in the F5, F2, SERPINC1, PROC, or PROS1 gene in about half of cases. Of those cases, PROS1 mutations represent between 1-3% of individuals with an identifiable hereditable cause for venous thromboembolism (Varga and Kujovich 2012). Analytical sensitivity is ~95% for detection of causative variants in the PROS1 gene as gross deletions represent a minority of cases and would not be detected by sequencing.

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 PROS1$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

Protein S deficiency is a disorder that increases the risk of developing abnormal clots, especially deep vein thrombosis (DVT) within the legs and arms. Symptoms can range greatly from asymptomatic to life-threatening with severe clotting called purpura fulminans appearing shortly after birth. The vast clinical spectrum of Protein S deficiency is due to the influence of environmental factors including increased age, surgery, inactivity, pregnancy, smoking, and oral contraceptives as well as other genetic risk factors such as Factor V Leiden and Prothrombin 20210G>A (Varga and Kujovich 2012). Mild Protein S deficiency is the most prevalent form, occurring in about 1 in 500 individuals. Protein S deficiency may also be acquired through chronic inflammation, liver disease, and vitamin K deficiency, making diagnosis of the hereditable form more difficult (Marlar and Gausman 2011). Anticoagulation therapies such as warfarin have been used to mitigate clotting in patients with Protein S deficiency. Genetic testing may aid in differential diagnosis between inherited and acquired forms of Protein S deficiency as well as from protein C deficiency, antithrombin deficiency, and other hypercoagulability disorders (Varga and Kujovich 2012).

Genetics

Protein S deficiency is inherited in an autosomal dominant manner with variable penetrance due to mutations in the PROS1 gene. Rare compound heterozygous individuals typically have a severe form of the disease. Causative variants have been found throughout the PROS1 gene with missense, nonsense, insertions/deletions alterations, and splice site alterations representing 45%, 18%, 18%, and 14% of cases respectively (Gandrille et al. 2000; Biguzzi et al. 2005). Large deletions have been reported in a minority of cases (Pintao et al. 2009). Disease penetrance is incomplete, but linked to the degree of protein S activity loss. Thrombophilia risk is also increased through environmental factors and mutations in the F5 (Factor V Leiden), F2 (Prothrombin 20210), PROC, and SERPINC1 genes (Caspers M et al. 2012). Protein S functions as a cofactor for Protein C where together this complex functions to down regulate thrombin formation through degradation of pro-coagulation factors V and VIII (Marlar and Gausman 2011).

Testing Strategy

This test involves bidirectional Sanger sequencing using genomic DNA of all coding exons in the PROS1 gene plus ~20bp of flanking non-coding DNA on each side. We will also sequence any single exon (Test #100) in family members of patients with known mutation or to confirm research results.

Indications for Test

Patients with biochemical evidence showing decreased Protein S activity are ideal candidates as this is diagnostic for all three forms of Protein S deficiency. Individuals with type I form, representing ~80% cases, also have decreased free and total Protein S antigen levels. Type II individuals have unaffected Protein S antigen levels and type III only show decreases in free Protein S antigen. Patients with a strong family history of thrombophilia are also candidates for testing (Marlar and Gausman 2011).

Gene

Official Gene Symbol OMIM ID
PROS1 176880
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Biguzzi E, Razzari C, Lane DA, Castaman G, Cappellari A, Bucciarelli P, Fontana G, Margaglione M, D’Andrea G, Simmonds RE, Rezende SM, Preston R, et al. 2005. Molecular diversity and thrombotic risk in protein S deficiency: The PROSIT study. Human Mutation 25: 259–269. PubMed ID: 15712227
  • Caspers M, Pavlova A, Driesen J, Harbrecht U, Klamroth R, Kadar J, Fischer R, Kemkes-Matthes B, Oldenburg J. 2012. Deficiencies of antithrombin, protein C and protein S - practical experience in genetic analysis of a large patient cohort. Thromb. Haemost. 108: 247–257. PubMed ID: 22627591
  • Gandrille S, Borgel D, Eschwege-Gufflet V, Aillaud MF, Dreyfus M, Matheron C, Gaussem P, Abgrall JF, Jude B, Sie P. 1995. Identification of 15 different candidate causal point mutations and three polymorphisms in 19 patients with protein S deficiency using a scanning method for the analysis of the protein S active gene. Blood 85: 130–138. PubMed ID: 11127877
  • Marlar RA, Gausman JN. 2011. Protein S abnormalities: A diagnostic nightmare. American Journal of Hematology 86: 418–421. PubMed ID: 21523802
  • Pintao MC, Garcia AA, Borgel D, Alhenc-Gelas M, Spek CA, Visser MCH de, Gandrille S, Reitsma PH. 2009. Gross deletions/duplications in PROS1 are relatively common in point mutation-negative hereditary protein S deficiency. Human Genetics 126: 449–456. PubMed ID: 19466456
  • Varga EA, Kujovich JL. 2012. Management of inherited thrombophilia: guide for genetics professionals. Clin. Genet. 81: 7–17. PubMed ID: 21707594
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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