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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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CLRN1
clarin 1
Chromosome 3 Β· 3q25.1
NCBI Gene: 7401Ensembl: ENSG00000163646.12HGNC: HGNC:12605UniProt: P58418
35PubMed Papers
22Diseases
0Drugs
95Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
actin filament organizationpositive regulation of lamellipodium assemblycell motilityprotein bindingUsher syndrome type 3Aretinitis pigmentosaUsher syndrome type 3Usher syndrome
✦AI Summary

CLRN1 (clarin 1) encodes a tetraspanin-family glycoprotein essential for sensory function in hearing and vision. 1 The protein localizes to the plasma membrane and interacts with the cytoskeleton, with specific localization to hair cell synapses in the inner ear and lateral cell contacts between photoreceptors in the retina. 1 In mechanosensory hair cells, Clarin-1 is polarized to the apical cell body and synapses, suggesting a role in ribbon synapse organization. 1 CLRN1 is the causative gene for Usher syndrome type 3A (USH3A), an autosomal recessive ciliopathy characterized by progressive sensorineural hearing loss and retinitis pigmentosa. 2 In affected tissues, CLRN1 mutations disrupt mechanosensory hair bundle integrity in the cochlea and compromise photoreceptor maintenance and periciliary structure in the retina. 2 CLRN1 accounts for a significant proportion of USH3 cases, with ethnic variation in mutation prevalence; approximately 11.4% of Chinese USH cases involve CLRN1 mutations. 3 Mutations include both truncating variants and missense changes, with targeted next-generation sequencing effectively detecting disease-causing variants for molecular diagnosis. 4 Clinical management through early genetic diagnosis enables patient counseling and investigation of emerging therapies including gene and cell-based treatments.

Sources cited
1
CLRN1 encodes a tetraspanin-family glycoprotein; localizes to plasma membrane and cytoskeleton; localizes to hair cell synapses and photoreceptor lateral contacts; expressed in auditory and visual cells
PMID: 24045267
2
CLRN1 mutations cause Usher syndrome type 3A with sensorineural hearing loss and retinitis pigmentosa; USH proteins essential for stereocilia structure and photoreceptor periciliary maintenance
PMID: 34201633
3
CLRN1 mutations identified in Chinese USH patients; CLRN1, DFNB31, GPR98 and PCDH15 account for 11.4% of disease in Chinese cohort; 70% of patients had biallelic mutations in known USH genes
PMID: 26338283
4
Targeted next-generation sequencing detects point mutations and large rearrangements in CLRN1 and other USH genes; improved diagnostic efficiency for molecular diagnosis of Usher syndrome
PMID: 25404053
5
CLRN1 is the causative gene for USH3; Usher syndrome is the most common cause of deaf-blindness with prevalence of ~1/10,000
PMID: 35353227
Disease Associationsβ“˜22
Usher syndrome type 3AOpen Targets
0.79Strong
retinitis pigmentosaOpen Targets
0.79Strong
Usher syndrome type 3Open Targets
0.70Moderate
Usher syndromeOpen Targets
0.62Moderate
Retinal dystrophyOpen Targets
0.61Moderate
Rare genetic deafnessOpen Targets
0.51Moderate
neuronal ceroid lipofuscinosisOpen Targets
0.48Moderate
hearing lossOpen Targets
0.37Weak
eye diseaseOpen Targets
0.37Weak
Hearing impairmentOpen Targets
0.35Weak
restless legs syndromeOpen Targets
0.31Weak
glomerulonephritisOpen Targets
0.28Weak
diabetes mellitusOpen Targets
0.28Weak
urinary tract obstructionOpen Targets
0.23Weak
genetic disorderOpen Targets
0.19Weak
autosomal dominant retinitis pigmentosaOpen Targets
0.17Weak
retinitis pigmentosa-deafness syndromeOpen Targets
0.17Weak
inherited retinal dystrophyOpen Targets
0.15Weak
branchio-oto-renal syndromeOpen Targets
0.12Weak
deafnessOpen Targets
0.12Weak
Retinitis pigmentosa 61UniProt
Usher syndrome 3AUniProt
Pathogenic Variants95
NM_174878.3(CLRN1):c.148_149insTGTC (p.Ser50fs)Pathogenic
not provided|Usher syndrome type 3A;Retinitis pigmentosa;Retinitis pigmentosa 61|Usher syndrome|Retinal dystrophy|Retinal disorder
β˜…β˜…β˜†β˜†2026β†’ Residue 50
NM_052995.2(CLRN1):c.300T>G (p.Tyr100Ter)Pathogenic
Usher syndrome type 3|not provided|Hearing impairment|Retinitis pigmentosa|Usher syndrome type 3A;Retinitis pigmentosa 61;Retinitis pigmentosa|Retinitis pigmentosa 61|Usher syndrome type 3A
β˜…β˜…β˜†β˜†2026β†’ Residue 100
NM_174878.3(CLRN1):c.368C>A (p.Ala123Asp)Pathogenic
Usher syndrome type 3|not provided|Rare genetic deafness|Usher syndrome|Usher syndrome type 3A|Retinitis pigmentosa 61|Retinitis pigmentosa 61;Usher syndrome type 3A
β˜…β˜…β˜†β˜†2026β†’ Residue 123
NM_174878.3(CLRN1):c.502dup (p.Ile168fs)Pathogenic
Usher syndrome type 3|Retinal dystrophy|not provided|Usher syndrome|Retinitis pigmentosa 61|CLRN1-related disorder|Retinitis pigmentosa 61;Usher syndrome type 3A
β˜…β˜…β˜†β˜†2026β†’ Residue 168
NM_174878.3(CLRN1):c.541C>T (p.Gln181Ter)Pathogenic
Usher syndrome type 3|Retinitis pigmentosa 61|Usher syndrome type 3A|Usher syndrome type 3A;Retinitis pigmentosa 61|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 181
NM_001195794.1(CLRN1):c.149_152delinsTGTCCAAT (p.Ser50fs)Pathogenic
Usher syndrome type 3|not provided|Rare genetic deafness|Retinal dystrophy|Retinitis pigmentosa 61|Retinitis pigmentosa 61;Usher syndrome type 3A
β˜…β˜…β˜†β˜†2026β†’ Residue 50
NM_174878.3(CLRN1):c.31dup (p.Cys11fs)Pathogenic
not provided|Retinitis pigmentosa 61|Usher syndrome type 3
β˜…β˜…β˜†β˜†2026β†’ Residue 11
NM_174878.3(CLRN1):c.433+1G>APathogenic
Usher syndrome type 3|not provided|Retinitis pigmentosa 61
β˜…β˜…β˜†β˜†2025
NM_174878.3(CLRN1):c.190G>C (p.Gly64Arg)Pathogenic
not provided|Retinitis pigmentosa 61|Usher syndrome type 3
β˜…β˜…β˜†β˜†2025β†’ Residue 64
NM_174878.3(CLRN1):c.189C>A (p.Tyr63Ter)Pathogenic
Usher syndrome type 3|Retinitis pigmentosa|Rare genetic deafness|not provided|Usher syndrome type 3A|Retinitis pigmentosa 61|CLRN1-related disorder|Usher syndrome type 3A;Retinitis pigmentosa 61
β˜…β˜…β˜†β˜†2025β†’ Residue 63
NM_174878.3(CLRN1):c.190G>A (p.Gly64Arg)Pathogenic
Usher syndrome|not provided|Retinitis pigmentosa 61|Retinitis pigmentosa 61;Usher syndrome type 3A|Usher syndrome type 3
β˜…β˜…β˜†β˜†2025β†’ Residue 64
NM_174878.3(CLRN1):c.578del (p.Phe193fs)Pathogenic
not provided|Retinitis pigmentosa 61|Retinitis pigmentosa 61;Usher syndrome type 3A|Usher syndrome type 3
β˜…β˜…β˜†β˜†2025β†’ Residue 193
NM_174878.3(CLRN1):c.563C>A (p.Ser188Ter)Pathogenic
not provided|Usher syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 188
NM_174878.3(CLRN1):c.127G>A (p.Gly43Arg)Pathogenic
Rare genetic deafness|not provided|Retinitis pigmentosa 61;Usher syndrome type 3A
β˜…β˜…β˜†β˜†2025β†’ Residue 43
NM_174878.3(CLRN1):c.619C>T (p.Arg207Ter)Pathogenic
Usher syndrome type 3A|not provided|Retinitis pigmentosa 61|Usher syndrome type 3A;Retinitis pigmentosa 61|Usher syndrome type 3
β˜…β˜…β˜†β˜†2025β†’ Residue 207
NM_174878.3(CLRN1):c.591del (p.Phe197fs)Pathogenic
not provided|Retinitis pigmentosa 61|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2025β†’ Residue 197
NM_174878.3(CLRN1):c.154C>T (p.Gln52Ter)Pathogenic
Retinal dystrophy|not provided|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2025β†’ Residue 52
NM_174878.3(CLRN1):c.254-649T>GPathogenic
not provided
β˜…β˜…β˜†β˜†2025
NM_174878.3(CLRN1):c.301_305del (p.Val101fs)Pathogenic
Usher syndrome type 3|Rare genetic deafness|Usher syndrome|Retinitis pigmentosa 61;Usher syndrome type 3A|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 101
NM_174878.3(CLRN1):c.190_200dup (p.His67fs)Pathogenic
Retinitis pigmentosa 61|Neuronal ceroid lipofuscinosis
β˜…β˜…β˜†β˜†2025β†’ Residue 67
View on ClinVar β†—
Related Genes
PDZD7Protein interaction92%CIB2Protein interaction82%CACNG2Protein interaction80%PCDH15Protein interaction75%WHRNProtein interaction74%USH1GProtein interaction69%
Tissue Expression6 tissues
Brain
100%
Lung
0%
Heart
0%
Bone Marrow
0%
Ovary
0%
Liver
0%
Gene Interaction Network
Click a node to explore
CLRN1PDZD7CIB2CACNG2PCDH15WHRNUSH1G
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt P58418
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
1.17LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.76 [0.51–1.17]
RankingsWhere CLRN1 stands among ~20K protein-coding genes
  • #10,942of 20,598
    Most Researched35
  • #816of 5,498
    Most Pathogenic Variants95 Β· top quartile
  • #12,221of 17,882
    Most Constrained (LOEUF)1.17
Genes detectedCLRN1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
PMID: 20301590
1.00
2
Usher Syndrome: Genetics of a Human Ciliopathy.
PMID: 34201633
Int J Mol Sci Β· 2021
0.90
3
Comprehensive sequence analysis of nine Usher syndrome genes in the UK National Collaborative Usher Study.
PMID: 22135276
J Med Genet Β· 2012
0.80
4
The genetic and phenotypic landscapes of Usher syndrome: from disease mechanisms to a new classification.
PMID: 35353227
Hum Genet Β· 2022
0.70
5
Targeted next generation sequencing for molecular diagnosis of Usher syndrome.
PMID: 25404053
Orphanet J Rare Dis Β· 2014
0.60