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Test Code F2NGS F2 Gene, Next-Generation Sequencing, Varies


Advisory Information


This genetic test should only be considered if clinical and family history, initial coagulation screens, and initial factor II (FII) tests (activity and antigen) indicate a diagnosis of factor II deficiency.

 

This test is not intended to evaluate for the F2 c.*97G>A alteration (historically known as G20210A) associated with prothrombin-related thrombophilia. If testing for the F2 c.*97G>A alteration (G20210A) is desired instead of full-gene sequencing, order PTNT / Prothrombin G20210A Mutation, Blood.



Shipping Instructions


Ambient and refrigerate specimens must arrive within 7 days (168 hours of draw), and frozen specimens must arrive within 14 days (336 hours of draw).

 

Collect and package specimen as close to shipping time as possible.



Necessary Information


Rare Coagulation Disorder Patient Information is required, see Special Instructions. Testing may proceed without the patient information, however, the information aids in providing a more thorough interpretation. Ordering providers are strongly encouraged to fill out the form and send with the specimen.



Specimen Required


Submit only 1 of the following specimens:

 

Specimen Type: Peripheral blood

Container/Tube:

Preferred: Lavender top (EDTA)

Acceptable: Yellow top (ACD) or green top (sodium citrate)

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send specimen in original tube.

Specimen Stability: Ambient (preferred)/Refrigerated/Frozen

 

Specimen Type: Extracted DNA

Container/Tube: 1.5- to 2-mL tube

Specimen Volume: Entire specimen

Collection Instructions:

1. Label specimen as extracted DNA and source of specimen.

2. Provide indication of volume and concentration of the DNA.

Specimen Stability: Frozen (preferred)/Refrigerated/Ambient


Forms

1. Rare Coagulation Disorder Patient Information (T824) is required, see Special Instructions. Fax the completed form to 507-284-1759.

2. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file. The following documents are available in Special Instructions:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing-Spanish (T826)

3. If not ordering electronically, complete, print, and send a Coagulation Test Request (T753) with the specimen.

Secondary ID

65167

Useful For

Ascertaining a causative alteration in F2 and the affected region of prothrombin protein in an individual clinically diagnosed with factor II deficiency

 

Carrier testing for close family members of an individual with a factor II deficiency diagnosis

 

This test is not intended for prenatal diagnosis.

Testing Algorithm

The clinical workup for factor II deficiency (F2D) begins with special coagulation testing for factor II. See  F_2 / Coagulation Factor II Activity Assay, Plasma.

 

Genetic testing for F2D is indicated if:

-Prothrombin (factor II) activity is reduced (less than 80% of normal)

-Acquired causes of factor II deficiency have been excluded (eg, vitamin K deficiency, warfarin anticoagulation use, liver disease, etc)

 

Prothrombin antigen testing, to distinguish between type I and type II deficiencies, may be helpful in cases where genetic testing results yield variants of uncertain significance.

Method Name

Custom Sequence Capture and Targeted Next-Generation Sequencing (NGS) followed by Polymerase Chain Reaction (PCR) and Sanger Sequencing when appropriate

Reporting Name

F2 Gene, Full Gene NGS

Specimen Type

Varies

Specimen Minimum Volume

Blood: 1 mL
Extracted DNA: 100 mcL at 50 ng/mcL concentration

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred) 7 days
  Frozen  14 days
  Refrigerated  7 days

Reject Due To

Gross hemolysis OK
Gross lipemia OK

Clinical Information

Factor II (FII) deficiency (F2D) is a bleeding diathesis. Symptoms include subcutaneous and muscle hematomas, prolonged post-injury bleeding, bleeding into joint spaces, and mucosal tract bleeds.

 

Hereditary factor II deficiency is thought to be extremely rare, with an estimated prevalence of 1 in 2 million. If genetic in origin, F2D is inherited in an autosomal recessive manner. Both males and females may be affected if homozygous or compound heterozygous for pathogenic alterations in F2. Heterozygotes are typically asymptomatic, although both post-trauma excessive bleeding and post-operative bleeding have been described in carriers.

 

Factor II is also known as prothrombin and is produced by the F2 gene. Prothrombin is proteolytically cleaved to form thrombin during the coagulation cascade. Thrombin has multiple roles in the hemostatic response to injury. These roles include the stimulation of platelets to form a platelet plug, the cleavage of fibrinogen to form fibrin clot, the activation of factors V and VIII by the excision of their central domains, and the activation of protein C and protein S to start the inhibition of the coagulation process. A significant deficiency (less than 1% to 5%) in the amount of functional prothrombin can cause abnormal spontaneous or post traumatic bleeding. It has been estimated that the minimum level of functional prothrombin needed to prevent these symptoms is 10% to 20% of normal.(1) Alterations in the F2 gene that interfere with the production or function of prothrombin disrupt the coagulation cascade and can lead to bleeding complications.

 

FII deficiency is classified into 2 types. Mutations in the F2 gene that interfere with the production of prothrombin lead to lower levels of the protein in blood causing type I F2D, or hypoprothrombinemia. Type I F2D may be classified as mild, moderate or severe based on the factor level in plasma. A factor level of less than 5% is considered a severe deficiency and is characterized by severe bleeding symptoms with bleeding typically occurring spontaneously. Moderate deficiency is defined as 5% to 10% activity and mild deficiency is greater than 10%. Individuals who are heterozygous for a pathogenic F2 alteration typically have factor levels of 30% to 60%.

 

Mutations in F2 that create a dysfunctional protein that is produced in normal amounts but isn’t as active cause type II F2D, or dysprothrombinemia. Individuals with type II F2D  alterations have bleeding of variable severity that is typically less severe than in type I F2D. Cases of compound heterozygosity for both a hypoprothrombinemia mutation and a dysprothrombinemia mutation in the same person have been reported. Additionally, a complete absence of prothrombin is thought to be incompatible with life.

 

Genetic testing is indicated if a coagulation screen shows prolonged prothrombin time (PT), prolonged activated partial thromboplastin time (aPTT), normal thrombin time (TT), and reduced levels of prothrombin (factor II) activity. Prothrombin antigen testing helps to distinguish between type I and type II deficiencies.

 

Causes of acquired (non-genetic) factor II deficiency that should be excluded prior to genetic testing include long-term use of antibiotics, impaired vitamin K absorption, liver disease, the obstruction of bile, and warfarin anticoagulation. Cases of an acquired factor II inhibitor can occur in the presence of a lupus anticoagulant, autoimmune disorders or during infection or lymphoma.(2) A small number of cases are suspected to have been drug induced (quinidine in one case and phenytoin in another).

Reference Values

An interpretive report will be provided

Interpretation

An interpretive report will be provided.

 

Evaluation and categorization of variants is performed using the most recent published American College of Medical Genetics and Genomics (ACMG) recommendations as a guideline. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

 

Consultations with the Mayo Clinic Special Coagulation Clinic, Molecular Hematopathology Laboratory, or Thrombophilia Center are available for DNA diagnosis cases. This may be especially helpful in complex cases or in situations where the diagnosis is atypical or uncertain.

Clinical Reference

1. Palla R, Peyvandi F, Shapiro AD: Rare bleeding disorders: diagnosis and treatment. Blood 2015;125(13):2052-2061

2. Mulliez SM, De Keyser F, Verbist C, et al: Lupus anti-coagulant-hypoprothrombinemia syndrome: report of two cases and review of the literature. Lupus 2015;94(4):713-715

3. Lancellotti S, Basso M, De Cristofaro R: Congenital Prothrombin Deficiency: An Update. Semin Thromb Hemost 2013;39(6):596-606

4. Pozzi N, Chen Z, Gohara DW, et al: Crystal structure of prothrombin reveals conformational flexibility and mechanism of action. J Biol Chem. 2013;288(31):22734-22744

5. Lane DA, Philippou H, Huntington JA: Directing Thrombin. Blood 2005;106(8):2605-2612

Day(s) and Time(s) Performed

Performed weekly; Varies

Analytic Time

21 days

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.

CPT Code Information

81479

LOINC Code Information

Test ID Test Order Name Order LOINC Value
F2NGS F2 Gene, Full Gene NGS 94237-5

 

Result ID Test Result Name Result LOINC Value
113019 F2NGS Result 50397-9
113013 Alterations Detected 82939-0
113012 Interpretation 69047-9
113014 Additional Information 48767-8
113015 Method 85069-3
113016 Disclaimer 62364-5
113017 Panel Gene List 24477-2
113018 Reviewed By 18771-6