CLRN1 Gene: Clarin-1 and Usher Syndrome Type III
Essential gene for retinal and cochlear hair cell function
Gene Information Card
| Symbol | CLRN1 |
|---|---|
| Full Name | Clarin 1 |
| Gene Type | Protein coding |
| Chromosomal Location | 3q25.1 |
| NCBI Gene ID | 7401 ncbi.nlm.nih.gov/gene/7401 |
| Ensembl ID | ENSG00000163646 |
| UniProt ID | P58418 |
| OMIM ID | 606397 |
| HGNC ID | 2095 |
| Aliases | USH3A, RP61, clarin-1 |
Description
CLRN1 encodes clarin-1, a four-transmembrane-domain protein essential for the development and maintenance of hair cells in the inner ear and photoreceptor cells in the retina. Mutations in CLRN1 cause Usher syndrome type III (USH3), characterized by progressive hearing loss and retinitis pigmentosa. The protein is involved in synaptic ribbon formation and calcium homeostasis.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Usher syndrome type III (USH3) | Loss-of-function mutations in CLRN1 disrupt clarin-1 protein, leading to progressive sensorineural hearing loss and retinitis pigmentosa. | ClinVar, OMIM |
| Retinitis pigmentosa 61 (RP61) | CLRN1 mutations cause non-syndromic retinitis pigmentosa via photoreceptor degeneration. | OMIM, NCBI |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Cochlea | — | High |
| Retina | — | High |
| Testis | — | Moderate |
| Brain | — | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| ARPE-19 (retinal pigment epithelium) | — | Expressed |
| HEK293 | — | Expressed in transfected models |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.528T>A (p.N176K) | Missense | Found in USH3 patients | Loss of function |
| c.144T>G (p.Y48*) | Nonsense | Rare | Loss of function |
| c.149C>T (p.T50M) | Missense | Reported in USH3 | Loss of function |
Mutation functional classification
Loss of Function (LOF)
Most CLRN1 mutations result in loss of clarin-1 function, leading to hair cell and photoreceptor degeneration.
Gain of Function (GOF)
No gain-of-function mutations reported.
Dominant Negative (DN)
No dominant-negative mutations reported; inheritance is autosomal recessive.
View complete mutation data：
Gene Ontology (GO)
| • plasma membrane (GO:0005886) | • integral component of membrane (GO:0016021) |
| • sensory perception of sound (GO:0007605) | • visual perception (GO:0007601) |
| • nervous system development (GO:0007399) |
Pathways
• Usher syndrome pathway
• Photoreceptor cell maintenance
Protein Summary
Clarin-1 is a 232-amino-acid transmembrane protein with four membrane-spanning domains. It localizes to the plasma membrane of hair cell stereocilia and photoreceptor synapses. The protein interacts with other Usher syndrome proteins (e.g., harmonin, cadherin 23) and is critical for synaptic ribbon integrity and calcium signaling. Loss of clarin-1 leads to progressive sensory deficits.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| CLRN1 Knockout HEK293 Cell Line | EDJ-KQ3269 | Human | 7401 | Details Get a Quote |
| CLRN1 Knockout HeLa Cell Line | EDJ-KQ54734 | Human | 7401 | Details Get a Quote |
| CLRN1 Knockout A-549 Cell Line | EDJ-KQ63227 | Human | 7401 | Details Get a Quote |
| CLRN1 Knockout HCT 116 Cell Line | EDJ-KQ71692 | Human | 7401 | Details Get a Quote |
