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CLRN1 clarin 1 [ Homo sapiens (human) ]

Gene ID: 7401, updated on 5-Mar-2024

Summary

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Official Symbol
CLRN1provided by HGNC
Official Full Name
clarin 1provided by HGNC
Primary source
HGNC:HGNC:12605
See related
Ensembl:ENSG00000163646 MIM:606397; AllianceGenome:HGNC:12605
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RP61; USH3; USH3A
Summary
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]
Expression
Biased expression in adrenal (RPKM 2.0), duodenum (RPKM 0.5) and 1 other tissue See more
Orthologs
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Genomic context

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See CLRN1 in Genome Data Viewer
Location:
3q25.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (150926163..150972999, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (153677250..153724083, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (150643950..150690786, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909447 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14819 Neighboring gene SIAH2 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:150523844-150524366 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:150524367-150524888 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:150539149-150539823 Neighboring gene NANOG hESC enhancer GRCh37_chr3:150566660-150567161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14820 Neighboring gene uncharacterized LOC124909446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14821 Neighboring gene MINDY family member 4B Neighboring gene Sharpr-MPRA regulatory region 9248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:150643693-150644193 Neighboring gene CLRN1 antisense RNA 1 Neighboring gene uncharacterized LOC124909448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14822 Neighboring gene Sharpr-MPRA regulatory region 19 Neighboring gene mediator complex subunit 12L Neighboring gene RNA, 5S ribosomal pseudogene 145

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Retinal Phenotype of Patients with CLRN1-Associated Usher 3A Syndrome in French Light4Deaf Cohort. Smirnov VM, et al. Invest Ophthalmol Vis Sci, 2022 Apr 1. PMID 35481838, Free PMC Article
  2. A deep intronic CLRN1 (USH3A) founder mutation generates an aberrant exon and underlies severe Usher syndrome on the Arabian Peninsula. Khan AO, et al. Sci Rep, 2017 May 3. PMID 28469144, Free PMC Article
  3. Identification of a novel CLRN1 gene mutation in Usher syndrome type 3: two case reports. Yoshimura H, et al. Ann Otol Rhinol Laryngol, 2015 May. PMID 25743179
  4. Two novel disease-causing mutations in the CLRN1 gene in patients with Usher syndrome type 3. García-García G, et al. Mol Vis, 2012. PMID 23304067, Free PMC Article
  5. Cone structure in patients with usher syndrome type III and mutations in the Clarin 1 gene. Ratnam K, et al. JAMA Ophthalmol, 2013 Jan. PMID 22964989, Free PMC Article

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Retinal Phenotype of Patients with CLRN1-Associated Usher 3A Syndrome in French Light4Deaf Cohort.
    Title: Retinal Phenotype of Patients with CLRN1-Associated Usher 3A Syndrome in French Light4Deaf Cohort.
  2. Extending the spectrum of CLRN1- and ABCA4-associated inherited retinal dystrophies caused by novel and recurrent variants using exome sequencing.
    Title: Extending the spectrum of CLRN1- and ABCA4-associated inherited retinal dystrophies caused by novel and recurrent variants using exome sequencing.
  3. Studied role of clarin1 (CLRN1) in activation of hair cell mechanotransduction function through an unconventional secretory pathway, and the possibility this activation may be therapeutic to prevent hair cell dysfunction.
    Title: Unconventional secretory pathway activation restores hair cell mechanotransduction in an USH3A model.
  4. Study founds 1 deep intronic CLRN1 (USH3A) founder mutation generates an aberrant exon that underlies severe Usher syndrome in a family on the Arabian Peninsula.
    Title: A deep intronic CLRN1 (USH3A) founder mutation generates an aberrant exon and underlies severe Usher syndrome on the Arabian Peninsula.
  5. We report here novel homozygous mutations in various genes causing USH, extending the spectrum of causative mutations. We also prove combined sequencing techniques as useful tools to identify novel disease-causing mutations. To the best of our knowledge, this is the largest report of a genetic analysis of Israeli and Palestinian families (n = 74) with different USH subtypes.
    Title: The Genetics of Usher Syndrome in the Israeli and Palestinian Populations.
  6. This is the first report of Usher syndrome type 3 with a CLRN1 gene mutation in Asian populations.
    Title: Identification of a novel CLRN1 gene mutation in Usher syndrome type 3: two case reports.
  7. Possible digenism could not be excluded in two families segregating genomic variations in both MYO7A and USH2A, and two families with CLRN1 and USH2A.
    Title: Extended mutation spectrum of Usher syndrome in Finland.
  8. Two novel mutations in the CLRN1 gene, p.R207X and p.I168N, have been found in patients with Usher syndrome type 3.
    Title: Two novel disease-causing mutations in the CLRN1 gene in patients with Usher syndrome type 3.
  9. High-resolution measures of retinal structure demonstrate patterns of cone loss associated with CLRN1 mutations.
    Title: Cone structure in patients with usher syndrome type III and mutations in the Clarin 1 gene.
  10. 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.
    Title: The mechanosensory structure of the hair cell requires clarin-1, a protein encoded by Usher syndrome III causative gene.
Submit: New GeneRIF Correction See all GeneRIFs (20)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Retinitis pigmentosa
MedGen: C0035334 OMIM: 268000 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
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Retinitis pigmentosa 61
MedGen: C3280041 OMIM: 614180 GeneReviews: Not available
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Usher syndrome type 3A
MedGen: C5779850 OMIM: 276902 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within actin filament organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in auditory receptor cell stereocilium organization IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cell motility IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in equilibrioception IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in equilibrioception IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in photoreceptor cell maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within positive regulation of lamellipodium assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in sensory perception of light stimulus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in sensory perception of sound IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in visual perception IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in basal part of cell IEA
Inferred from Electronic Annotation
more info
  
located_in lamellipodium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in microtubule cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
located_in microvillus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in stereocilium IEA
Inferred from Electronic Annotation
more info
  
located_in trans-Golgi network transport vesicle IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
clarin-1
Names
Usher syndrome type-3 protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009168.1 RefSeqGene

    Range
    5001..51837
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_700

mRNA and Protein(s)

  1. NM_001195794.1 → NP_001182723.1  clarin-1 isoform d

    See identical proteins and their annotated locations for NP_001182723.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) encodes the longest isoform (d).
    Source sequence(s)
    AF482697, AF495717, HM626132
    Consensus CDS
    CCDS56285.1
    UniProtKB/Swiss-Prot
    P58418
    Related
    ENSP00000329158.4, ENST00000328863.8

  2. NM_001256819.2 → NP_001243748.1  clarin-1 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has multiple differences in the coding region, compared to variant 5, one of which results in a translational frameshift. The resulting isoform (e) has a distinct C-terminus and is shorter than isoform d.
    Source sequence(s)
    AC020636, BM666773
    UniProtKB/TrEMBL
    C9JYI2
    Related
    ENSP00000419892.2, ENST00000468836.2

  3. NM_052995.2 → NP_443721.1  clarin-1 isoform c

    See identical proteins and their annotated locations for NP_443721.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains multiple differences in the UTRs and coding region compared to variant 5. The resulting isoform (c) contains shorter and distinct N- and C-termini, compared to isoform d.
    Source sequence(s)
    AF388366
    Consensus CDS
    CCDS35492.1
    UniProtKB/Swiss-Prot
    P58418
    Related
    ENSP00000295911.2, ENST00000295911.6

  4. NM_174878.3 → NP_777367.1  clarin-1 isoform a

    See identical proteins and their annotated locations for NP_777367.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame exon in the 3' coding region, compared to variant 5. The resulting isoform (a) is shorter than isoform d.
    Source sequence(s)
    AF482697, AF495717
    Consensus CDS
    CCDS3153.1
    UniProtKB/Swiss-Prot
    D3DNJ3, E1ACU9, P58418, Q8N6A9
    Related
    ENSP00000322280.1, ENST00000327047.6

RNA

  1. NR_046380.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) has an additional exon in the 5' region, compared to variant 5. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 5, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC020636, AF482697, AF495717, BC074970, HM626132

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    150926163..150972999 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    153677250..153724083 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_174880.1: Suppressed sequence

    Description
    NM_174880.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P58418.2 GenPept UniProtKB/Swiss-Prot:P58418

Gene LinkOut

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