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Waardenburg Syndrome Type IID via the SNAI2 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
SNAI2 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9051SNAI281479 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


  • Ben Dorshorst, PhD

Clinical Features and Genetics

Clinical Features

Waardenburg syndrome (WS) is an auditory-pigmentary disorder characterized by congenital sensorineural hearing loss and pigmentary abnormalities of the hair, including a white forelock, and pigmentary changes of the iris such as heterochromia. WS is classified into 4 main types depending on the clinical symptoms and has causative mutations in different genes (Pingault et al. 2010).

WS I : Auditory-pigmentary abnormalities along with dystopia canthorum (lateral displacement of the inner canthi), caused by mutations in PAX3.

WS II : Auditory-pigmentary abnormalities without dystopia canthorum, caused by mutations in MITF, SNAI2, and SOX10.

WS III : Type I with musculo-skeletal abnormalities of the upper limb (Klein-Waardenburg syndrome), caused by mutations in PAX3.

WS IV : Type II with Hirschsprung disease (Waardenburg-Shah syndrome), caused by mutations in EDN3, EDNRB, and SOX10.

WS type II is typified by sensorineural hearing loss and heterochromia iridum is observed in approximately 77% and 47% of affected individuals respectively, and is much more common than WS type I (Liu et al. 1995). Dystopia canthorum is NOT observed in WS II. Other clinical manifestations such as the classic white forelock are more common in WS1.


WS type IID is an autosomal recessive syndrome caused by homozygous deletions of the SNAI2 gene. The snail family zinc finger 2 (SNAI2), or SLUG as it is sometimes called, is a transcription factor that plays a role in formation of tissues, particularly the neural crest during embryonic development (Perez-Mancera et al. 2007). Lack of snail 2 may disrupt the development of melanocytes in certain areas of the skin, hair, eyes, and inner ear, leading to hearing loss and the patchy loss of pigmentation that are characteristic features of Waardenburg syndrome, type II. Limited studies evaluating the role of SNAI2 mutations in Waardenburg syndrome suggest that it plays a minor role in WS2 (Pingault et al. 2010). Mutations identified so far are solely homozygous deletions (Sánchez-Martín et al. 2002), no point mutations have been identified. Mutations in SNAI2 are also known to be causative for Piebaldism (Sánchez-Martín et al. 2003).

Clinical Sensitivity - Sequencing with CNV PGxome

Limited studies identify deletions of SNAI2 to be responsible for WS2 (Sánchez-Martín et al. 2002). Since extensive studies evaluating the role of SNAI2 point mutations have not been carried out, the clinical sensitivity of our sequencing test is currently unknown.

Testing Strategy

This test provides full coverage of all coding exons of the SNAI2 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

Diagnostic criteria for Waardenburg syndrome type II (WSII) were outlined (Liu et al. 1995) and include three important indicators: congenital sensorineural hearing loss, complete heterochromia iridum (irides of different color), and absence of Dystopia canthorum. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in SNAI2.


Official Gene Symbol OMIM ID
SNAI2 602150
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Partial Albinism AD 172800
Waardenburg Syndrome, Type 2D AR 608890

Related Test

Waardenburg Syndrome Panel


  • Liu XZ, Newton VE, Read AP. 1995. Waardenburg syndrome type II: phenotypic findings and diagnostic criteria. Am. J. Med. Genet. 55: 95–100. PubMed ID: 7702105
  • Perez-Mancera PA, Bermejo-Rodriguez C, Gonzalez-Herrero I, Herranz M, Flores T, Jimenez R, Sanchez-Garcia I. 2007. Adipose tissue mass is modulated by SLUG (SNAI2). Human Molecular Genetics 16: 2972–2986. PubMed ID: 17905753
  • Pingault V, Ente D, Dastot-Le Moal F, Goossens M, Marlin S, Bondurand N. 2010. Review and update of mutations causing Waardenburg syndrome. Human Mutation 31: 391–406. PubMed ID: 20127975
  • Sánchez-Martín M, Pérez-Losada J, Rodríguez-García A, González-Sánchez B, Korf BR, Kuster W, Moss C, Spritz RA, Sánchez-García I. 2003. Deletion of the SLUG (SNAI2) gene results in human piebaldism. Am. J. Med. Genet. A 122A: 125–132. PubMed ID: 12955764
  • Sánchez-Martín M, Rodríguez-García A, Pérez-Losada J, Sagrera A, Read AP, Sánchez-García I. 2002. SLUG (SNAI2) deletions in patients with Waardenburg disease. Human molecular genetics 11: 3231–3236. PubMed ID: 12444107


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