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Tbio Clarin-1

May have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells and presumably also in analogous synapses within the retina.

This gene encodes a protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIIa. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

 Comments

Property Summary

NCBI Gene PubMed Count 28
PubMed Score 47.78
PubTator Score 49.36

Knowledge Summary

Patent

No data available

TINX Plot

  Disease (6)

Disease Target Count
Usher Syndrome, Type III 2
Disease Target Count P-value
ovarian cancer 8491 1.3e-06
aldosterone-producing adenoma 664 1.9e-02
Disease Target Count Z-score Confidence
Usher syndrome 34 7.224 3.6
Disease Target Count Z-score Confidence
Sensorineural hearing loss 107 4.47 2.2
Blindness 84 3.984 2.0
Disease Target Count
Usher syndrome 3A 1

Expression

  Differential Expression (2)

Disease log2 FC p
aldosterone-producing adenoma 2.360 1.9e-02
ovarian cancer -1.500 1.3e-06

Synonym

Accession P58418 D3DNJ3 E1ACU9 Q8N6A9
Symbols RP61
USH3
USH3A

Gene

CLRN1

  Ortholog (1)

Species Source Disease
Chimp OMA EggNOG

 UniProt Keyword (16)

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 GO Component (4)

 GO Process (9)

 Compartment GO Term (19)

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 IMPC Phenotype (5)

 OMIM Phenotype (2)

 MGI Phenotype (4)

 HCA RNA Cell Line (42)

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Gene RIF (15)

PMID Text
25743179 This is the first report of Usher syndrome type 3 with a CLRN1 gene mutation in Asian populations.
23304067 Two novel mutations in the CLRN1 gene, p.R207X and p.I168N, have been found in patients with Usher syndrome type 3.
22964989 High-resolution measures of retinal structure demonstrate patterns of cone loss associated with CLRN1 mutations.
22787034 This study confirmed using a novel mouse model carrying a Clrn1N48K knock-in mutation to investigate the consequence of the missense mutation N48K in mCLRN1 in vivo.
22681893 Possible digenism could not be excluded in two families segregating genomic variations in both MYO7A and USH2A, and two families with CLRN1 and USH2A.
21675857 Here we describe a novel deletion in CLRN1. Our data support previously reported intra familial variability in the clinical features of Usher syndrome type I and III.
21310491 Retinitis pigmentosa-associated mutations p.Pro31Leu and p.Leu154Trp may represent hypomorphic mutations, because substituted amino acids in transmembrane domains remain polar.
20717163 The complexity of the CLRN1 gene and the identification of multiple splice variants may partially explain why mutations in CLRN1 result in substantial variation in clinical phenotype.
19753315 Part of the pathogenesis of USH3 may be associated with defective intracellular trafficking as well as decreased stability of mutant CLRN1 proteins.
19683999 Observational study of gene-disease association and genetic testing. (HuGE Navigator)
19423712 clarin-1 has a role in the regulation and homeostasis of actin filaments
18281613 USH3A and USH2A share patterns of rod and cone dysfunction and retinal structural abnormalities.
12145752 revised structure of USH3 gene: new translation start site, 5' untranslated region, and transcript encoding 232-amino acid protein; four new disease-causing mutations; identified mouse and rat orthologues, and two human paralogues on chromosomes 4 and 10
12080385 a role for clarin-1 in hair cell and photoreceptor cell synapses, as well as a common pathophysiological pathway for different Usher syndromes
11524702 Mutations in the USH3 gene underlie Usher syndrome type 3.

AA Sequence 

MPSQQKKIIFCMAGVFSFACALGVVTALGTPLWIKATVLCKTGALLVNASGQELDKFMGEMQYGLFHGEG      1 - 70
VRQCGLGARPFRFSFFPDLLKAIPVSIHVNVILFSAILIVLTMVGTAFFMYNAFGKPFETLHGPLGLYLL     71 - 140
SFISGSCGCLVMILFASEVKIHHLSEKIANYKEGTYVYKTQSEKYTTSFWVIFFCFFVHFLNGLLIRLAG    141 - 210
FQFPFAKSKDAETTNVAADLMY                                                    211 - 232
//

Text Mined References (29)

PMID Year Title
25743179 2015 Identification of a novel CLRN1 gene mutation in Usher syndrome type 3: two case reports.
24618850 2014 Massively parallel DNA sequencing facilitates diagnosis of patients with Usher syndrome type 1.
23304067 2012 Two novel disease-causing mutations in the CLRN1 gene in patients with Usher syndrome type 3.
22964989 2013 Cone structure in patients with usher syndrome type III and mutations in the Clarin 1 gene.
22787034 2012 The mechanosensory structure of the hair cell requires clarin-1, a protein encoded by Usher syndrome III causative gene.
22681893 2013 Extended mutation spectrum of Usher syndrome in Finland.
21675857 2011 A novel 5-bp deletion in Clarin 1 in a family with Usher syndrome.
21310491 2011 CLRN1 mutations cause nonsyndromic retinitis pigmentosa.
20717163 2011 Alternative splice variants of the USH3A gene Clarin 1 (CLRN1).
19753315 2009 Disease-causing mutations in the CLRN1 gene alter normal CLRN1 protein trafficking to the plasma membrane.
19683999 2010 Microarray-based mutation analysis of 183 Spanish families with Usher syndrome.
19423712 2009 Clarin-1, encoded by the Usher Syndrome III causative gene, forms a membranous microdomain: possible role of clarin-1 in organizing the actin cytoskeleton.
18484607 2008 UMD-USHbases: a comprehensive set of databases to record and analyse pathogenic mutations and unclassified variants in seven Usher syndrome causing genes.
18281613 2008 Retinal disease in Usher syndrome III caused by mutations in the clarin-1 gene.
18273898 2008 Spectrum of USH2A mutations in Scandinavian patients with Usher syndrome type II.
16641997 2006 The DNA sequence, annotation and analysis of human chromosome 3.
15650299 Serial audiometry and speech recognition findings in Finnish Usher syndrome type III patients.
15521980 2004 Mutation screening of USH3 gene (clarin-1) in Spanish patients with Usher syndrome: low prevalence and phenotypic variability.
15489334 2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
14569126 2003 Genetic homogeneity and phenotypic variability among Ashkenazi Jews with Usher syndrome type III.
12477932 2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.
12145752 2002 Usher syndrome type III: revised genomic structure of the USH3 gene and identification of novel mutations.
12080385 2002 USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses.
11524702 2001 Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3.
10704288 2000 A sequence-ready map of the Usher syndrome type III critical region on chromosome 3q.
10364543 1999 Possible interaction between USH1B and USH3 gene products as implied by apparent digenic deafness inheritance.
8975700 1996 Refined mapping of the Usher syndrome type III locus on chromosome 3, exclusion of candidate genes, and identification of the putative mouse homologous region.
8889548 1996 Normalization and subtraction: two approaches to facilitate gene discovery.
7711740 1995 Assignment of an Usher syndrome type III (USH3) gene to chromosome 3q.