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    CLRN1 clarin 1 [ Homo sapiens (human) ]

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

    Summary

    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
    NEW
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    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001195794.1NP_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_001256819.2NP_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_052995.2NP_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_174878.3NP_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.