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Tooth Agenesis via the PAX9 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
PAX9 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8803PAX981479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information. If the Sanger option is selected, CNV detection may be ordered through Test #600.

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

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

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


  • Megan Piazza, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Tooth agenesis is congenital absence of one or more permanent dentition, which does not include absence of third molars. It can be further divided into three subtypes: hypodontia defined as missing of less than 6 teeth, oligodontia defined as missing of 6 or more permanent teeth, and anodontia which is complete absence of permanent teeth. Tooth agenesis can occur as isolated cases or can be associated with syndromes, such as cleft lip and /or cleft palate, and ectodermal dysplasia (De Coster et al. 2009). It is currently known to be caused by pathogenic variants in at least following genes: MXS1, PAX9, AXIN2, EDA, EDARADD, WNT10A, and LTBP3.


Pathogenic variants in the PAX9 gene cause autosomal dominant selective tooth agenesis 3. The PAX9 protein coded by the PAX9 gene is a member of the paired box family of transcription factors that plays a key role during fetal development. To date, ~40 unique pathogenic variants have been reported. They are: missense (53%), nonsense (13%), small deletion/insertion (25%), and gross deletion/insertion (8%) (Stockton et al. 2000; Das et al. 2002; Bergendal et al. 2011; Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

In one study, PAX9 pathogenic variants were identified in 4% of 93 unrelated Swedish probands with a clinical diagnosis of isolated oligodontia (Bergendal et al. 2011). Gross deletions/insertions account for ~8% of reported PAX9 pathogenic variants (Das et al. 2002; Human Gene Mutation Database).

Three gross deletions/insertions have been reported in the PAX9 gene that account for ~8% of reported PAX9 pathogenic variants (Das et al. 2002; Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the PAX9 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

Candidates for this test are patients with symptoms consistent with tooth agenesis and the family members of patients who have known PAX9 pathogenic variants.


Official Gene Symbol OMIM ID
PAX9 167416
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Tooth Agenesis, Selective, 3 AD 604625

Related Tests

Ectodermal Dysplasia via the EDA Gene
Ectodermal Dysplasia via the EDARADD Gene


  • Bergendal B, Klar J, Stecksén-Blicks C, Norderyd J, Dahl N. 2011. Isolated oligodontia associated with mutations in EDARADD, AXIN2, MSX1, and PAX9 genes. Am. J. Med. Genet. 155: 1616–1622. PubMed ID: 21626677
  • Das P, Hai M, Elcock C, Leal SM, Brown DT, Brook AH, Patel PI. 2003. Novel missense mutations and a 288-bp exonic insertion in PAX9 in families with autosomal dominant hypodontia. Am. J. Med. Genet. 118A: 35–42. PubMed ID: 11941488
  • De Coster PJ, Marks LA, Martens LC, Huysseune A. 2009. Dental agenesis: genetic and clinical perspectives. Journal of Oral Pathology & Medicine 38: 1–17. PubMed ID: 18771513
  • Human Gene Mutation Database (Bio-base).
  • Stockton DW, Das P, Goldenberg M, D’Souza RN, Patel PI. 2000. Mutation of PAX9 is associated with oligodontia. Nat Genet 24: 18–19. PubMed ID: 10615120


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

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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View Ordering Instructions

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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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