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PTEN Hamartoma Tumor Syndrome via the PTEN Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
PTEN 81321 81321,81323 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7513PTEN81321 81321,81323 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Eric Bend, PhD

Clinical Features and Genetics

Clinical Features

PTEN hamartoma tumor syndrome (PHTS) is a cluster of related clinical conditions, all caused by germline variants in the PTEN tumor suppressor gene (OMIM 601728). Included in PHTS are Cowden syndrome (CS; OMIM 158350), Bannayan-Riley-Ruvalcaba syndrome (BRRS; OMIM 153480), Proteus (PS; OMIM 176920) and Proteus-like syndromes, and VACTERL association with hydrocephalus (OMIM 276950). While each PHTS condition has its own unique pathognomonic features (see for example Blumenthal & Dennis, Eur J Hum Genet 16:1289-1300, 2008), hamartomatous overgrowth, macrocephaly, and vascular malformations appear to be common to all conditions (Zhou et al. Lancet 358:210-211, 2001). A presumptive diagnosis of PHTS is typically made based on clinical symptoms, but a definitive diagnosis requires the identification of a heterozygous PTEN variant. Patients with a germline variant in PTEN have a 5-10 fold higher chance of developing cancer at a much earlier age (<30 years old) than the general population (Eng, Hum Mut 22:183-198, 2003). In addition to confirming the diagnosis of PHTS, testing patients for a germline PTEN variant is essential to accurately assess their risk for cancer and to make appropriate recommendations regarding prevention and treatment of malignancy.


PTEN hamartoma tumor syndrome inherited in an autosomal dominant manner, and PTEN is the only known gene to be associated with the disease. In addition to PHTS, germline variants in PTEN have been identified in 16% of patients with autism spectrum disorders (ASD) and macrocephaly, 12.5% of patients with adenomatous and hyperplastic polyps, and 5% of women with at least two different types of cancer (Zbuk & Eng Nat Rev Cancer 7:35-45, 2007; Lintas & Persico J Med Genet 46:1-8, 2009). To date, ~230 variants have been reported for the PTEN gene, and most (~95%) are detectable by DNA sequencing (Human Gene Mutation Database, www.hgmd.cf.ac.uk). The PTEN gene consists of 9 exons and encodes a dual lipid and protein phosphatase. Variants have been reported throughout the coding region, and sequencing of all 9 exons is recommended (Eng Hum Mut 22:183-198, 2003). Five variants have also been reported within the minimal promoter about 800 bp upstream of the start codon and sequencing of this region is also recommended (Teresi et al. Am J Hum Genet 81:756-767, 2007).

Clinical Sensitivity - Sequencing with CNV PG-Select

This test is predicted to detect causative variants in ~80% of patients with CS, ~65% of patients with BRRS, and ~20% of patients with PS (Eng Hum Mutat 22:183-198, 2003).

Testing Strategy

This test provides full coverage of all coding exons of the PTEN gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

In addition to the regions described above, this testing includes coverage of the PTEN minimal promoter region (positions -1239 to -765 relative to the start codon).

Indications for Test

Candidates for this test are patients with PHTS or autism with macrocephaly, women presenting with multiple primary cancers, and relatives of patients with a known germline PTEN variant. This test is specifically designed for heritable germline variants and is not appropriate for the detection of somatic variants in tumor tissue.


Official Gene Symbol OMIM ID
PTEN 601728
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Cowden and Cowden-like Syndromes via the PIK3CA Gene
Hereditary Breast and Ovarian Cancer - High Risk and Lynch Syndrome Panel
Hereditary Endometrial Cancer Panel


  • Blumenthal GM, Dennis PA. 2008. PTEN hamartoma tumor syndromes. European Journal of Human Genetics 16: 1289–1300. PubMed ID: 18781191
  • Eng C. 2003. PTEN: One Gene, Many Syndromes. Human Mutation 22: 183–198. PubMed ID: 12938083
  • Human Gene Mutation Database.
  • Lintas C, Persico AM. 2009. Autistic phenotypes and genetic testing: state-of-the-art for the clinical geneticist. Journal of medical genetics 46: 1–8. PubMed ID: 18728070
  • Teresi RE, Zbuk KM, Pezzolesi MG, Waite KA, Eng C. 2007. Cowden Syndrome–Affected Patients with PTEN Promoter Mutations Demonstrate Abnormal Protein Translation. The American Journal of Human Genetics 81: 756–767. PubMed ID: 17847000
  • Zbuk KM, Eng C. 2006. Cancer phenomics: RET and PTEN as illustrative models. Nature Reviews Cancer 7: 35–45. PubMed ID: 17167516
  • Zhou X-P, Hampel H, Thiele H, Gorlin RJ, Hennekam R, Parisi M, Winter RM, Eng C. 2001. Association of germline mutation in the PTEN tumour suppressor gene and Proteus and Proteus-like syndromes. The Lancet 358: 210–211. PubMed ID: 11476841


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

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.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

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.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

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View Ordering Instructions

1) Select Test Method (Platform)

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2) Select Additional Test Options

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
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