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CLRN1 gene
Reviewed by Medicinsk Expert•Last updated: 2026-10-22•Gene

CLRN1 gene

The CLRN1 gene provides instructions for making the protein clarin 1, which is essential for normal hearing and vision.

Normal Function

The CLRN1 gene provides information for making a protein called clarin 1. This protein is probably involved in normal hearing and vision. Clarin 1 has been found in several areas of the body, including sensory cells in the inner ear called hair cells. These cells help transmit sound and motion signals to the brain. This protein is also active in the retina, which is the light-sensing tissue that lines the back of the eye. Although the function of clarin 1 has not been determined, studies suggest that it plays a role in communication between nerve cells (neurons) in the inner ear and in the retina. Clarin 1 may be important for the development and function of synapses, which are junctions between neurons where cell-to-cell communication occurs.

Health Conditions Related to Genetic Changes

Usher syndrome

At least 15 mutations in the CLRN1 gene have been identified in people with Usher syndrome type III, which is characterized by a combination of hearing loss and vision loss. Some affected individuals also have problems with balance and coordination. CLRN1 gene mutations cause a form of the condition known as Usher syndrome type IIIA (USH3A). This form of Usher syndrome is rare in most countries, although it represents about 40 percent of all Usher syndrome cases in the Finnish population.

Several CLRN1 gene mutations change single protein building blocks (amino acids) in the clarin 1 protein. In some cases, these mutations lead to the production of an abnormally short version of the protein or prevent the production of any functional clarin 1. Other mutations insert or delete small amounts of DNA in the CLRN1 gene, which probably impairs the normal function of the protein. It is unclear how a missing or altered clarin 1 protein leads to the signs and symptoms of Usher syndrome type IIIA.

Two particular CLRN1 gene mutations are most common in families of Finnish ancestry:

  • One mutation, sometimes called Finmajor and written as Tyr176Ter or Y176X, leads to the production of an abnormally short, nonfunctional version of clarin 1.
  • The other mutation, written as Met120Lys or M120K and also known as Finminor, substitutes the amino acid lysine for the amino acid methionine at protein position 120. This mutation appears to disrupt the protein's normal function.

Retinitis pigmentosa

CLRN1 gene mutations have also been associated with retinitis pigmentosa.

Other Names for This Gene

  • USH3
  • USH3A
  • USH3A_HUMAN
  • Usher syndrome 3A
  • Usher syndrome type 3 protein

Frequently Asked Questions

While there is no cure that restores the lost function of clarin‑1, supportive therapies are available. Hearing aids, cochlear implants, and assistive listening devices can improve auditory perception. For vision loss, low‑vision aids, prescription glasses, and adaptive technologies help maintain independence. Regular monitoring by audiologists and ophthalmologists is essential to adjust interventions as the disease progresses.
DNA sequencing test that targets the CLRN1 gene is performed on a blood or saliva sample. The test looks for known pathogenic variants and also scans for novel changes in the coding regions and splice sites. If a mutation is found, it is compared to databases of Usher syndrome variants to confirm its pathogenicity.
Hearing loss in CLRN1-related Usher syndrome often begins in childhood or adolescence and may present as difficulty understanding speech in noisy environments or frequent requests for repetition. Vision loss usually starts with night blindness or difficulty seeing in low light, progressing to tunnel vision. Balance issues, such as frequent falls or dizziness, can also appear. Early audiologic and ophthalmologic evaluations are recommended when these symptoms arise.
CLRN1 mutations are inherited in an autosomal recessive pattern. If both parents carry a pathogenic variant, each child has a 25 % chance of being affected, a 50 % chance of being a carrier, and a 25 % chance of being unaffected. Genetic counseling and carrier testing for family members can clarify individual risks.
Source: MedlinePlus, National Library of Medicine

MedlinePlus brings together authoritative health information from the National Library of Medicine (NLM), the National Institutes of Health (NIH), and other government agencies and health-related organizations.

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