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Genetics Home Reference: your guide to understanding genetic conditions     A service of the U.S. National Library of Medicine®


Reviewed February 2007

What is the official name of the CLRN1 gene?

The official name of this gene is “clarin 1.”

CLRN1 is the gene's official symbol. The CLRN1 gene is also known by other names, listed below.

What is the normal function of the CLRN1 gene?

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

How are changes in the CLRN1 gene related to health conditions?

Usher syndrome - caused by mutations in the CLRN1 gene

At least 10 mutations in the CLRN1 gene have been identified in people with Usher syndrome. Several of these 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 cell from making any functional clarin 1. Other mutations insert or delete small amounts of DNA in the CLRN1 gene, which probably impairs the normal function of clarin 1. Researchers have not determined how a missing or altered clarin 1 protein leads to the signs and symptoms of Usher syndrome.

Two particular CLRN1 mutations have been identified in families of Finnish ancestry. One mutation, sometimes called Finn(major) and written as Tyr176Ter, leads to the production of an abnormally short, nonfunctional version of clarin 1. The other mutation, Met120Lys, also known as Finn(minor), substitutes the amino acid lysine for the amino acid methionine at protein position 120. This mutation may disrupt the protein's normal function.

Where is the CLRN1 gene located?

Cytogenetic Location: 3q25

Molecular Location on chromosome 3: base pairs 150,918,911 to 150,973,020

(Homo sapiens Annotation Release 107, GRCh38.p2) (NCBI (

The CLRN1 gene is located on the long (q) arm of chromosome 3 at position 25.

The CLRN1 gene is located on the long (q) arm of chromosome 3 at position 25.

More precisely, the CLRN1 gene is located from base pair 150,918,911 to base pair 150,973,020 on chromosome 3.

See How do geneticists indicate the location of a gene? ( in the Handbook.

Where can I find additional information about CLRN1?

You and your healthcare professional may find the following resources about CLRN1 helpful.

You may also be interested in these resources, which are designed for genetics professionals and researchers.

What other names do people use for the CLRN1 gene or gene products?

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

See How are genetic conditions and genes named? ( in the Handbook.

What glossary definitions help with understanding CLRN1?

acids ; amino acid ; cell ; DNA ; gene ; hair cells ; lysine ; methionine ; mutation ; nerve cell ; protein ; retina ; sensory cells ; syndrome ; tissue

You may find definitions for these and many other terms in the Genetics Home Reference Glossary.


  • Adato A, Vreugde S, Joensuu T, Avidan N, Hamalainen R, Belenkiy O, Olender T, Bonne-Tamir B, Ben-Asher E, Espinos C, Millán JM, Lehesjoki AE, Flannery JG, Avraham KB, Pietrokovski S, Sankila EM, Beckmann JS, Lancet D. USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses. Eur J Hum Genet. 2002 Jun;10(6):339-50. (
  • Ahmed ZM, Riazuddin S, Riazuddin S, Wilcox ER. The molecular genetics of Usher syndrome. Clin Genet. 2003 Jun;63(6):431-44. Review. (
  • Aller E, Jaijo T, Oltra S, Alió J, Galán F, Nájera C, Beneyto M, Millán JM. Mutation screening of USH3 gene (clarin-1) in Spanish patients with Usher syndrome: low prevalence and phenotypic variability. Clin Genet. 2004 Dec;66(6):525-9. (
  • Fields RR, Zhou G, Huang D, Davis JR, Möller C, Jacobson SG, Kimberling WJ, Sumegi J. Usher syndrome type III: revised genomic structure of the USH3 gene and identification of novel mutations. Am J Hum Genet. 2002 Sep;71(3):607-17. Epub 2002 Jul 16. (
  • Joensuu T, Hämäläinen R, Yuan B, Johnson C, Tegelberg S, Gasparini P, Zelante L, Pirvola U, Pakarinen L, Lehesjoki AE, de la Chapelle A, Sankila EM. Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3. Am J Hum Genet. 2001 Oct;69(4):673-84. Epub 2001 Aug 27. Erratum in: Am J Hum Genet 2001 Nov;69(5):1160. (
  • NCBI Gene (
  • Reiners J, Nagel-Wolfrum K, Jürgens K, Märker T, Wolfrum U. Molecular basis of human Usher syndrome: deciphering the meshes of the Usher protein network provides insights into the pathomechanisms of the Usher disease. Exp Eye Res. 2006 Jul;83(1):97-119. Epub 2006 Mar 20. Review. (


The resources on this site should not be used as a substitute for professional medical care or advice. Users seeking information about a personal genetic disease, syndrome, or condition should consult with a qualified healthcare professional. See How can I find a genetics professional in my area? ( in the Handbook.

Reviewed: February 2007
Published: February 1, 2016