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CLRN1

clarin 1

The CLRN1 gene provides instructions for producing clarin 1, a protein thought to be essential for normal hearing and vision, particularly within the inner ear and retina. The CLRN1 gene encodes the clarin 1 protein, which plays a role in sensory cells of the inner ear and the retina, critical for transmitting sound, motion, and visual signals.

Chromosome 3q25.1 Various HGNC:12605 Tier C
CLRN1 3q25.1 p arm q arm 3

CLRN1 is located on the long (q) arm of chromosome 3, at band 3q25.1. Arm ratio per GRCh38 - banding schematic.

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Clinical tests that include this

Carrier Screening panel
CLRN1 is 1 of 1,008 genes on this panel
Expanded carrier screening for recessive and X-linked conditions

Overview

The CLRN1 gene, also known by alternative names such as USH3 and USH3A, carries the genetic blueprint for a protein called clarin 1. This protein is believed to be important for the proper function of sensory cells involved in both hearing and vision. Studies suggest clarin 1 is particularly active in the inner ear's hair cells, which are vital for transmitting sound and motion signals, as well as in the retina, the light-sensitive tissue at the back of the eye.

What the gene does

The clarin 1 protein, encoded by the CLRN1 gene, is thought to play a crucial role in the normal development and function of the sensory systems responsible for hearing and sight. It is found in sensory cells within the inner ear, specifically hair cells, which are responsible for converting sound vibrations into electrical signals that the brain can interpret. Additionally, clarin 1 is present in the retina, the part of the eye that detects light. While its precise molecular mechanism is still being investigated, research indicates that clarin 1 may facilitate communication between nerve cells, known as neurons, in both the inner ear and the retina. This communication is vital for the development and proper functioning of synapses, the specialised junctions through which neurons transmit signals to one another.

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Chromosome location

The CLRN1 gene is located on chromosome 3, specifically at position 3q25.1. This position indicates its precise address within the human genome, helping to identify its placement relative to other genes and genetic markers on the long arm of chromosome 3.

Protein structure

The clarin 1 protein comprises 232 amino acids. Domain architecture has not been experimentally characterised in detail for this protein.

Key variants

Genetic variations within the CLRN1 gene can lead to alterations in the clarin 1 protein, potentially affecting its structure or function. These changes can disrupt the protein's ability to support normal hearing and vision, contributing to the development of associated conditions. Different types of genetic changes have been identified within the CLRN1 gene.

The table below shows the top 10 pathogenic or likely-pathogenic variants currently classified in ClinVar for CLRN1.
View all on ClinVar →

Sample of pathogenic variants

10 pathogenic / likely-pathogenic variants from ClinVar, ranked by review status (expert-panel-reviewed first). This is a sample; recurrent founder variants in a specific population may not appear here - see the full ClinVar listing via the link above.

Variant (HGVS) Protein change Classification Evidence Associated condition
c.138del
Deletion
 p.Val47fs Pathogenic/Likely pathogenic ★★☆☆ Retinitis pigmentosa 61
c.149C>A
single nucleotide variant
 p.Ser50Ter Pathogenic ★★☆☆ Retinitis pigmentosa 61
c.190_200dup
Duplication
 p.His67fs Pathogenic/Likely pathogenic ★★☆☆ Retinitis pigmentosa 61
c.190G>C
single nucleotide variant
 p.Gly64Arg Pathogenic/Likely pathogenic ★★☆☆ Retinitis pigmentosa 61
c.253+6T>C
single nucleotide variant
 - Pathogenic/Likely pathogenic ★★☆☆ Retinitis pigmentosa 61
c.513T>A
single nucleotide variant
 p.Tyr171Ter Pathogenic/Likely pathogenic ★★☆☆ Retinitis pigmentosa 61
c.528T>A
single nucleotide variant
 p.Tyr176Ter Pathogenic/Likely pathogenic ★★☆☆ Retinitis pigmentosa 61
c.555T>A
single nucleotide variant
 p.Tyr185Ter Pathogenic/Likely pathogenic ★★☆☆ Retinitis pigmentosa 61
c.563C>A
single nucleotide variant
 p.Ser188Ter Pathogenic ★★☆☆ Usher syndrome
c.591del
Deletion
 p.Phe197fs Pathogenic ★★☆☆ Neuronal ceroid lipofuscinosis

Evidence stars indicate ClinVar review status. Individual variant interpretation should always be performed by a qualified clinical laboratory - many variants remain classified as Variants of Uncertain Significance (VUS) pending more research.

Associated conditions

Variants in the CLRN1 gene are primarily associated with Usher syndrome type 3 (USH3A), a rare inherited disorder. This condition is characterised by progressive hearing loss, often beginning in childhood, followed by a gradual loss of vision due to retinitis pigmentosa. Some individuals with Usher syndrome type 3 may also experience issues with balance and coordination.

  • Usher syndrome type 3
    Hearing Loss
    AR
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UK clinical status

The CLRN1 gene is included in several UK NHS Genomic Medicine Service national test panels. It is covered on the 'Monogenic hearing loss' panel (R67) and the 'Retinal disorders' panel (R32), indicating its recognised clinical significance for these conditions within the UK healthcare system.

Green-listed
High evidence · clinically actionable in NHS testing
Included in NHS GMS signed-off panels
Monogenic hearing loss · R67 NHS GMS → Retinal disorders · R32 NHS GMS →
NHS Genomic Medicine Service Jeen carrier screening

Sources: NHS GMS PanelApp · Genomics England PanelApp · NHS National Genomic Test Directory

Frequently asked questions

What is the CLRN1 gene?

The CLRN1 gene provides instructions for making the clarin 1 protein, which is believed to be important for the normal functioning of sensory cells involved in hearing and vision, particularly in the inner ear and retina.

What health conditions are associated with CLRN1 gene variants?

Variants in the CLRN1 gene are primarily associated with Usher syndrome type 3 (USH3A), a condition characterised by progressive hearing loss and vision impairment due to retinitis pigmentosa.

How does the clarin 1 protein work?

While its exact mechanism is still being researched, the clarin 1 protein is thought to facilitate communication between nerve cells (neurons) in the inner ear and retina, which is crucial for the development and function of synapses, the junctions where cells communicate.

References

  1. Geng R, Melki S, Chen DH. The mechanosensory structure of the hair cell requires clarin-1, a protein encoded by Usher syndrome III causative gene. The Journal of neuroscience : the official journal of the Society for Neuroscience. 2012. PMID: 22787034
  2. Khan MI, Kersten FF, Azam M. CLRN1 mutations cause nonsyndromic retinitis pigmentosa. Ophthalmology. 2011. PMID: 21310491
  3. Geng R, Geller SF, Hayashi T. Usher syndrome IIIA gene clarin-1 is essential for hair cell function and associated neural activation. Human molecular genetics. 2009. PMID: 19414487
  4. Isosomppi J, Västinsalo H, Geller SF. Disease-causing mutations in the CLRN1 gene alter normal CLRN1 protein trafficking to the plasma membrane. Molecular vision. 2009. PMID: 19753315
  5. Aller E, Jaijo T, Oltra S. Mutation screening of USH3 gene (clarin-1) in Spanish patients with Usher syndrome: low prevalence and phenotypic variability. Clinical genetics. 2004. PMID: 15521980
  6. Adato A, Vreugde S, Joensuu T. USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses. European journal of human genetics : EJHG. 2002. PMID: 12080385
  7. Fields RR, Zhou G, Huang D. Usher syndrome type III: revised genomic structure of the USH3 gene and identification of novel mutations. American journal of human genetics. 2002. PMID: 12145752
  8. Joensuu T, Hämäläinen R, Yuan B. Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3. American journal of human genetics. 2001. PMID: 11524702
Educational content. This page is not medical or genetic advice, is not individually reviewed by a clinician for each reader, and should not replace a consultation with a qualified healthcare professional or genetic counsellor. If you are considering genetic testing or acting on a test result, book a consultation.
Data sources Last updated 20 September 2026. Content compiled from HGNC · MedlinePlus Genetics · ClinGen · Genomics England PanelApp · NHS National Genomic Test Directory · ClinVar · UniProt · AlphaFold .