Test Catalog

Test ID: ATNGS    
Antithrombin Deficiency, SERPINC1 Gene, Next-Generation Sequencing, Varies

Useful For Suggests clinical disorders or settings where the test may be helpful

Ascertaining a causative alteration in SERPINC1 and the affected region of antithrombin (AT) protein in an individual clinically diagnosed with antithrombin deficiency


Genetic confirmation of a clinical AT deficiency diagnosis, particularly in patients with borderline low AT activity levels


Prognosis and risk assessment based on the genotype-phenotype correlations


Ascertaining alteration status of family members related to an individual with a confirmed SERPINC1 alteration for the purposes of informing clinical management and genetic counseling


Evaluating individuals with apparent heparin resistance


This test is not intended for prenatal diagnosis

Genetics Test Information Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test detects pathogenic alterations in the SERPINC1 gene to delineate the underlying molecular defect in a patient with a laboratory diagnosis of antithrombin (AT) deficiency based on a reduced AT activity or antigen.


The gene target for this test is:

Gene name (transcript): SERPINC1 (GRCh37 [hg19] NM_000488)

Chromosomal location: 1q25.1

Testing Algorithm Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

The clinical workup for antithrombin deficiency begins with an antithrombin (AT) activity assay (see ATTF / Antithrombin Activity, Plasma). An abnormal result is considered less than 80% of normal activity.


Genetic testing for AT deficiency is indicated if:

-AT activity assay is less than 80%

-There is a clinical suspicion for hereditary deficiency of antithrombin due to family history or atypical clinical presentation


If AT activity results are abnormal, an antithrombin antigen assay is usually performed to determine the quantity of antithrombin present (ATTI / Antithrombin Antigen, Plasma). This is done to distinguish between type I AT deficiency (characterized by reduced AT activity and antigen) and type II AT deficiency (low activity and normal antigen).

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Antithrombin (AT) deficiency is a rare hereditary thrombophilia that puts patients at a significantly increased risk of venous thromboembolism. In selected cases, patients manifest heparin resistance. Individuals with AT deficiency are at increased risk for venous thromboembolism (VTE) and late (2nd or 3rd trimester) pregnancy loss.(1,2) It has been estimated that individuals with inherited AT deficiency have a 16-fold increase in risk of VTE compared to individuals without AT deficiency.(4) Women with AT deficiency are at particularly high risk for developing clots during pregnancy and after delivery.(5)


Hereditary AT deficiency is uncommon, with prevalence in the general population of 1 in 2000 to 5000.(1, 2) Hereditary AT deficiency is inherited in an autosomal dominant manner with variable penetrance. Both men and women may be affected.


AT deficiency is a result of defects in the concentration or function of AT, a natural anticoagulant in blood plasma. AT is the major inhibitor of blood coagulation by inactivating thrombin and factor Xa. The SERPINC1 gene encodes for antithrombin. Genetic testing of SERPINC1 is indicated if plasma AT activity assay is abnormally low (ie, typically less than 80% of normal or lower than the reference range established in the local laboratory). AT activity testing should not be performed during acute thrombosis or illness as these could cause a temporary reduction in AT levels. Likewise, it should not be performed while the patient is taking an anticoagulant such as heparin (which may falsely lower levels) or an oral direct factor Xa inhibitor (eg, rivaroxaban, apixaban or edoxaban), which may falsely elevate AT levels.


Additionally, causes of acquired (non-genetic) AT deficiency are much more common than inherited AT deficiency and should be excluded prior to genetic testing. These causes of acquired AT deficiency include liver disease, acute thrombosis, heparin therapy, nephrotic syndrome, disseminated intravascular coagulation, and effects of chemotherapeutic agents such an L-asparaginase. These and other acquired causes of AT deficiency should be excluded prior to genetic testing.

Reference Values Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretive report will be provided

Interpretation Provides information to assist in interpretation of the test results

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, and 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.

Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances


Some individuals may have a mutation that is not identified by the methods performed. The absence of a mutation, therefore, does not eliminate the possibility of antithrombin (AT) deficiency. This assay does not distinguish between germline and somatic alterations, particularly with variant allele frequencies (VAF) significantly lower than 50%. Test results should be interpreted in context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.


Technical Limitations:

Next-generation sequencing (NGS) may not detect all types of genetic variants. Additionally, rare polymorphisms may be present that could lead to false negative or positive results. Therefore test results should be interpreted in the context of antithrombin activity and antigen measurements, clinical findings, family history, and other laboratory data. If results do not match clinical findings, consider alternative methods for analyzing these genes, such as Sanger sequencing or large deletion/duplication analysis. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.


If multiple alterations are identified, NGS is not able to distinguish between alterations that are found in the same allele ("in cis") and alterations found on different alleles ("in trans"). This limitation may complicate diagnosis or classification and has implications for inheritance and genetic counseling. To resolve these cases, molecular results must be correlated with clinical history, activity and antigen measurements, and family studies.


Unless reported or predicted to cause disease, alterations found deep in the intron or alterations that do not result in an amino acid substitution are not reported. These and common polymorphisms identified for this patient are available upon request.


Reclassification of Variants Policy:

At this time, it is not standard practice for the laboratory to systematically review likely pathogenic variants or variants of uncertain significance that are detected and reported. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.

Clinical Reference Recommendations for in-depth reading of a clinical nature

1. Patnaik MM, Moll S: Inherited Antithrombin deficiency: a review. Haemophilia 2008;14(6):1229-1239

2. Blajchamn MA, Austin RC, Fernandez-Rachubinski F, et al: Blood 1992;80(9):2159-2171

3. Patnaik MM, Guenther J, Pruthi RK, et al: The Potential Role of Molecular Analysis in Hereditary Antithrombin (AT) Deficiency Diagnosis and Management. Blood 2009;114:2976 (Abstract)

4. Di Minno MN, Ambrosino P, Ageno W, et al: Natural anticoagulants deficiency and the risk of venous thromboembolism: a meta-analysis of observational studies. Thromb Haemost 2015;135(5):923-932

5. Rogenhofer N, Bohlmann MK, Beuter-Winkler P, et al: Prevention, management and extent of adverse pregnancy outcomes in women with hereditary antithrombin deficiency. Ann Hematol 2014;93(3):385-392

6. Luxembourg B, Delev D, Geisen C, et al: Molecular basis of antithrombin deficiency. Thromb Haemost 2011;105(4):635-646

Special Instructions Library of PDFs including pertinent information and forms related to the test