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Tooth Agenesis Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
AXIN2 81479,81479
DSPP 81479,81479
EDA 81479,81479
EDAR 81479,81479
EDARADD 81479,81479
LTBP3 81479,81479
MSX1 81479,81479
PAX9 81479,81479
WNT10A 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
3021Genes x (9)81479 81479(x18) $990 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our Custom Panel tool.

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).

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 defined as the congenital absence of one or more teeth excluding the third molars. It has an incidence from 1.6 -6.9% in different populations (Al-Ani et al. 2017. PubMed ID: 28401166). Tooth agenesis occurs more in permanent teeth than in deciduous teeth, with most patients missing one or two permanent second premolars and upper later incisors. Tooth agenesis can occur in isolated cases, or as a primary feature related to different syndromes. For example, missing teeth is a primary feature of ectodermal dysplasia, which is a clinically and genetically heterogeneous disorder characterized by abnormal development of hair, teeth, nails or sweat glands. The majority of genes related to tooth agenesis are involved in the Wnt signaling pathway that regulates tooth formation and tooth homeostasis (Tamura and Nemoto. 2016. PubMed ID: 28408959).


This panel includes genes associated with a variety of genetic conditions that lead to tooth agenesis or impact tooth health or function and includes ectodermal dysplasia, tooth agenesis with or without orofacial cleft, oligodontia-colorectal cancer syndrome, oligodontia, deafness with dentinogenesis, dentin dysplasia type II, and Shields type II and III dentinogenesis imperfecta. Tooth agenesis disorders are genetically heterogenous and can be inherited in an autosomal dominant, autosomal recessive, and X-linked manner. All types of variants have been reported in the genes within this panel, including missense; nonsense; small deletions, duplications, insertions, and indels; splicing; and regulatory variants. Copy number variants have also been reported in several of these genes (Das et al. 2003. PubMed ID: 12605438; Jezewski et al. 2003. PubMed ID: 12807959; Nieminen et al. 2003. PubMed ID: 14630905; Lammi et al. 2004. PubMed ID: 15042511; Cluzeau et al. 2011. PubMed ID: 20979233; Iglesias et al. 2014. PubMed ID: 24901346; Huckert et al. 2015. PubMed ID: 25669657; Human Gene Mutation Database). 

See individual gene summaries for information about molecular biology of gene products and spectra of pathogenic variants.

Clinical Sensitivity - Sequencing with CNV PGxome

Pathogenic variants in EDA, EDAR, WNT10A, and EDARADD are responsible for ~90% of clinically diagnosed hypohidrotic ectodermal dysplasia patients (Cluzeau et al. 2011. PubMed ID: 20979233). MSX1 pathogenic variants were found in ~2% of patients affected with non-syndromic cleft lip and palate (Jezewski et al. 2003. PubMed ID: 12807959). In another study including 7 genes in Wnt signaling pathways (MSX1, AXIN2, PAX9, EDA, EDAR, EDARADD, and WNT10A), 44% of studied probands were found to have a pathogenic variant in one of these genes (Arte et al. 2013. PubMed ID: 23991204). Clinical sensitivity for LTBP3 is currently unknown due to limitations in the medical literature. Analytical sensitivity for LTBP3 may be high because all reported pathogenic variants are detectable by sequencing.

Large deletions account for ~10% of deleterious variants found in EDA and ~1% of deleterious copy number variants are large insertions, duplications, or indels (Human Gene Mutation Database). Only a few large copy number variants have been identified in EDAR and WNT10A (Human Gene Mutation Database). Large copy number variants in PAX9 account for ~8% of reported pathogenic variants (Human Gene Mutation Database). Limited large copy number variants have been reported in the DSPP, EDARADD, LTBP3, and MSX1 genes (Human Gene Mutation Database). To our knowledge, no large copy number variants have been reported in the AXIN2 gene (Human Gene Mutation Database).

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel provides 100% coverage of all coding exons of the genes 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

Patients with tooth agenesis are candidates for this test.


Official Gene Symbol OMIM ID
AXIN2 604025
DSPP 125485
EDA 300451
EDAR 604095
EDARADD 606603
LTBP3 602090
MSX1 142983
PAX9 167416
WNT10A 606268
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test



  • Al-Ani et al. 2017. PubMed ID: 28401166
  • Arte et al. 2013. PubMed ID: 23991204
  • Cluzeau et al. 2011. PubMed ID: 20979233
  • Das et al. 2003. PubMed ID: 12605438
  • Huckert et al. 2015. PubMed ID: 25669657
  • Human Gene Mutation Database (Bio-base).
  • Iglesias et al. 2014. PubMed ID: 24901346
  • Jezewski et al. 2003. PubMed ID: 12807959
  • Lammi. 2004. PubMed ID: 15042511
  • Nieminen et al. 2003. PubMed ID: 14630905
  • Tamura and Nemoto. 2016. PubMed ID: 28408959


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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