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Usher Syndrome Type 3 via the CLRN1 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
CLRN1 81404 81404,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7605CLRN181404 81404,81479 $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


  • Ben Dorshorst, PhD

Clinical Features and Genetics

Clinical Features

Usher syndrome is a clinically heterogeneous disorder characterized by progressive retinitis pigmentosa (RP) and sensorineural hearing impairment, with or without vestibular abnormalities. Three types are recognized based on the age of onset, severity of symptoms, and the vestibular involvement (Smith et al. Am J Med Genet 50:32-38, 1994). Patients with Usher syndrome type 3 (USH3 OMIM 276902) are born with normal hearing and vision. Hearing loss usually begins during childhood or early teens, and RP begins in the teens. Vestibular involvement may occur later in life. Features of RP include night blindness progressing to constriction of the peripheral visual field with eventually loss of central vision, abnormal fundus with bone-spicule deposits/attenuated retinal vessels, and abnormal electroretinographic (ERG) findings (Daiger et al. Arch Ophthalmol 125:151-158, 2007).


Usher Syndrome Type 3 (USH3) is an autosomal recessive disease that is caused by variants in the CLRN1 gene (Joensuu et al. Am J Hum Genet 69:673-684, 2001). CLRN1 encodes clarin-1, which is presumed to be involved in sensory synapses (Adato et al. Eur J Hum Genet 10:339-350, 2002). To date, about 20 CLRN1 causative variants have been reported. Variants include missense, nonsense, splicing, and small insertions or deletions. Although most CLRN1 variants are private, a nonsense variant (c.528T>G, p.Tyr176Stop) appears to be common in Finnish USH3 families, and a missense variant (c.144T>G, p.Asn48Lys) was found in several USH3 families in the Ashkenazi Jewish population (Fields et al. Am J Hum Genet 71:607-617, 2002).

Clinical Sensitivity - Sequencing with CNV PG-Select

Unknown at this time.

Testing Strategy

This test provides full coverage of all coding exons of the CLRN1 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Patients with combined, progressive postlingual sensorineural hearing loss and RP, with or without vestibular abnormality. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in CLRN1.


Official Gene Symbol OMIM ID
CLRN1 606397
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Usher Syndrome, Type 3 AR 276902

Related Test

Retinitis Pigmentosa Panel


  • Adato, A., et.al. (2002). "USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses." Eur J Hum Genet 10(6): 339-50. PubMed ID: 12080385
  • Daiger et al. 2007. PubMed ID: 17296890
  • Fields, R. R., et.al. (2002). "Usher syndrome type III: revised genomic structure of the USH3 gene and identification of novel mutations." Am J Hum Genet 71(3): 607-17. PubMed ID: 12145752
  • Joensuu, T., et.al. (2001). "Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3." Am J Hum Genet 69(4): 673-84. PubMed ID: 11524702
  • Smith R.J.H. et al. 1994. American Journal of Medical Genetics. 50: 32-8. PubMed ID: 8160750


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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