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    CLRN1 clarin 1 [ Homo sapiens (human) ]

    Gene ID: 7401, updated on 2-May-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
    mouse all
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    Genomic context

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    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
    		Compare labs
    Retinitis pigmentosa 61
    MedGen: C3280041 OMIM: 614180 GeneReviews: Not available
    		Compare labs
    Usher syndrome type 3A
    MedGen: C5779850 OMIM: 276902 GeneReviews: Not available
    		Compare labs

    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 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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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