Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P58418

- CLRN1_HUMAN

UniProt

P58418 - CLRN1_HUMAN

Protein

Clarin-1

Gene

CLRN1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 109 (01 Oct 2014)
      Sequence version 2 (06 Feb 2007)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    Functioni

    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.1 Publication

    GO - Biological processi

    1. actin filament organization Source: MGI
    2. cell motility Source: MGI
    3. equilibrioception Source: HGNC
    4. photoreceptor cell maintenance Source: HGNC
    5. positive regulation of lamellipodium assembly Source: MGI
    6. response to stimulus Source: UniProtKB-KW
    7. sensory perception of light stimulus Source: HGNC
    8. sensory perception of sound Source: HGNC
    9. visual perception Source: UniProtKB-KW

    Keywords - Biological processi

    Hearing, Sensory transduction, Vision

    Protein family/group databases

    TCDBi9.A.46.1.1. the clarin (clrn) family.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Clarin-1
    Alternative name(s):
    Usher syndrome type-3 protein
    Gene namesi
    Name:CLRN1
    Synonyms:USH3A
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 3

    Organism-specific databases

    HGNCiHGNC:12605. CLRN1.

    Subcellular locationi

    GO - Cellular componenti

    1. integral component of membrane Source: UniProtKB-KW
    2. lamellipodium Source: MGI
    3. microvillus Source: MGI
    4. plasma membrane Source: MGI

    Keywords - Cellular componenti

    Membrane

    Pathology & Biotechi

    Involvement in diseasei

    Usher syndrome 3A (USH3A) [MIM:276902]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH3 is characterized by postlingual, progressive hearing loss, variable vestibular dysfunction, and onset of retinitis pigmentosa symptoms, including nyctalopia, constriction of the visual fields, and loss of central visual acuity, usually by the second decade of life.5 Publications
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti40 – 401C → G in USH3A. 1 Publication
    VAR_054555
    Natural varianti48 – 481N → K in USH3A. 2 Publications
    VAR_030345
    Natural varianti105 – 1051S → P in USH3A. 1 Publication
    VAR_054556
    Natural varianti120 – 1201M → K in USH3A. 1 Publication
    VAR_012241
    Natural varianti150 – 1501L → P in USH3A. 1 Publication
    VAR_030346
    Natural varianti153 – 1542IL → M in USH3A.
    VAR_012242
    Retinitis pigmentosa 61 (RP61) [MIM:614180]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti31 – 311P → L in RP61; the mutant protein is retained in the endoplasmic reticulum. 1 Publication
    VAR_066673
    Natural varianti154 – 1541L → W in RP61; the mutant protein is retained in the endoplasmic reticulum. 1 Publication
    VAR_066674

    Keywords - Diseasei

    Deafness, Disease mutation, Retinitis pigmentosa, Usher syndrome

    Organism-specific databases

    MIMi276902. phenotype.
    614180. phenotype.
    Orphaneti791. Retinitis pigmentosa.
    231183. Usher syndrome type 3.
    PharmGKBiPA37231.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 232232Clarin-1PRO_0000065729Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi48 – 481N-linked (GlcNAc...)Sequence Analysis

    Keywords - PTMi

    Glycoprotein

    Proteomic databases

    PaxDbiP58418.
    PRIDEiP58418.

    PTM databases

    PhosphoSiteiP58418.

    Expressioni

    Tissue specificityi

    Widely expressed. Found in the retina.

    Gene expression databases

    ArrayExpressiP58418.
    BgeeiP58418.
    CleanExiHS_CLRN1.
    GenevestigatoriP58418.

    Organism-specific databases

    HPAiHPA054636.

    Interactioni

    Protein-protein interaction databases

    STRINGi9606.ENSP00000322280.

    Structurei

    3D structure databases

    ProteinModelPortaliP58418.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei8 – 2821HelicalSequence AnalysisAdd
    BLAST
    Transmembranei101 – 12121HelicalSequence AnalysisAdd
    BLAST
    Transmembranei135 – 15521HelicalSequence AnalysisAdd
    BLAST
    Transmembranei186 – 20621HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the clarin family.Curated

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG44698.
    HOGENOMiHOG000060265.
    HOVERGENiHBG061269.
    InParanoidiP58418.
    OMAiWWSRERR.
    OrthoDBiEOG7MD4QW.
    PhylomeDBiP58418.
    TreeFamiTF331875.

    Family and domain databases

    InterProiIPR026748. Clarin.
    IPR004031. PMP22/EMP/MP20/Claudin.
    [Graphical view]
    PANTHERiPTHR31548. PTHR31548. 1 hit.
    PfamiPF13903. Claudin_2. 1 hit.
    [Graphical view]

    Sequences (3)i

    Sequence statusi: Complete.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Note: Additional isoforms seem to exist.

    Isoform 1 (identifier: P58418-3) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MPSQQKKIIF CMAGVFSFAC ALGVVTALGT PLWIKATVLC KTGALLVNAS    50
    GQELDKFMGE MQYGLFHGEG VRQCGLGARP FRFSFFPDLL KAIPVSIHVN 100
    VILFSAILIV LTMVGTAFFM YNAFGKPFET LHGPLGLYLL SFISGSCGCL 150
    VMILFASEVK IHHLSEKIAN YKEGTYVYKT QSEKYTTSFW VIFFCFFVHF 200
    LNGLLIRLAG FQFPFAKSKD AETTNVAADL MY 232
    Length:232
    Mass (Da):25,719
    Last modified:February 6, 2007 - v2
    Checksum:i2713C621FEBE4281
    GO
    Isoform 2 (identifier: P58418-1) [UniParc]FASTAAdd to Basket

    Also known as: A

    The sequence of this isoform differs from the canonical sequence as follows:
         1-85: MPSQQKKIIF...LGARPFRFSF → MQALQQQPV
         191-232: VIFFCFFVHFLNGLLIRLAGFQFPFAKSKDAETTNVAADLMY → LTKGHS

    Show »
    Length:120
    Mass (Da):13,421
    Checksum:i959B081E7665A2D1
    GO
    Isoform 3 (identifier: P58418-4) [UniParc]FASTAAdd to Basket

    Also known as: 0-2-2b-3

    The sequence of this isoform differs from the canonical sequence as follows:
         144-144: S → SVALWLPATRHQAQ

    Show »
    Length:245
    Mass (Da):27,192
    Checksum:i024BFE7B5C3788D3
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti7 – 71K → I.
    Corresponds to variant rs3796241 [ dbSNP | Ensembl ].
    VAR_053825
    Natural varianti31 – 311P → L in RP61; the mutant protein is retained in the endoplasmic reticulum. 1 Publication
    VAR_066673
    Natural varianti40 – 401C → G in USH3A. 1 Publication
    VAR_054555
    Natural varianti48 – 481N → K in USH3A. 2 Publications
    VAR_030345
    Natural varianti105 – 1051S → P in USH3A. 1 Publication
    VAR_054556
    Natural varianti120 – 1201M → K in USH3A. 1 Publication
    VAR_012241
    Natural varianti150 – 1501L → P in USH3A. 1 Publication
    VAR_030346
    Natural varianti153 – 1542IL → M in USH3A.
    VAR_012242
    Natural varianti154 – 1541L → W in RP61; the mutant protein is retained in the endoplasmic reticulum. 1 Publication
    VAR_066674

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 8585MPSQQ…FRFSF → MQALQQQPV in isoform 2. 1 PublicationVSP_022868Add
    BLAST
    Alternative sequencei144 – 1441S → SVALWLPATRHQAQ in isoform 3. 1 PublicationVSP_043303
    Alternative sequencei191 – 23242VIFFC…ADLMY → LTKGHS in isoform 2. 1 PublicationVSP_022869Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF388366 mRNA. Translation: AAL09581.1.
    AF482697 mRNA. Translation: AAN07148.1.
    AF495717 mRNA. Translation: AAM88774.1.
    HM626132 mRNA. Translation: ADM63096.1.
    AC020636 Genomic DNA. No translation available.
    CH471052 Genomic DNA. Translation: EAW78814.1.
    CH471052 Genomic DNA. Translation: EAW78815.1.
    BC074970 mRNA. Translation: AAH74970.1.
    BC074971 mRNA. Translation: AAH74971.1.
    CCDSiCCDS3153.1. [P58418-3]
    CCDS35492.1. [P58418-1]
    CCDS56285.1. [P58418-4]
    RefSeqiNP_001182723.1. NM_001195794.1. [P58418-4]
    NP_443721.1. NM_052995.2. [P58418-1]
    NP_777367.1. NM_174878.2. [P58418-3]
    UniGeneiHs.745448.

    Genome annotation databases

    EnsembliENST00000295911; ENSP00000295911; ENSG00000163646. [P58418-1]
    ENST00000327047; ENSP00000322280; ENSG00000163646. [P58418-3]
    ENST00000328863; ENSP00000329158; ENSG00000163646. [P58418-4]
    GeneIDi7401.
    KEGGihsa:7401.
    UCSCiuc003eyj.3. human. [P58418-1]
    uc003eyk.1. human. [P58418-3]
    uc021xfs.1. human. [P58418-4]

    Polymorphism databases

    DMDMi125987806.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Web resourcesi

    Mutations of the USH3A gene

    Retina International's Scientific Newsletter

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF388366 mRNA. Translation: AAL09581.1 .
    AF482697 mRNA. Translation: AAN07148.1 .
    AF495717 mRNA. Translation: AAM88774.1 .
    HM626132 mRNA. Translation: ADM63096.1 .
    AC020636 Genomic DNA. No translation available.
    CH471052 Genomic DNA. Translation: EAW78814.1 .
    CH471052 Genomic DNA. Translation: EAW78815.1 .
    BC074970 mRNA. Translation: AAH74970.1 .
    BC074971 mRNA. Translation: AAH74971.1 .
    CCDSi CCDS3153.1. [P58418-3 ]
    CCDS35492.1. [P58418-1 ]
    CCDS56285.1. [P58418-4 ]
    RefSeqi NP_001182723.1. NM_001195794.1. [P58418-4 ]
    NP_443721.1. NM_052995.2. [P58418-1 ]
    NP_777367.1. NM_174878.2. [P58418-3 ]
    UniGenei Hs.745448.

    3D structure databases

    ProteinModelPortali P58418.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 9606.ENSP00000322280.

    Protein family/group databases

    TCDBi 9.A.46.1.1. the clarin (clrn) family.

    PTM databases

    PhosphoSitei P58418.

    Polymorphism databases

    DMDMi 125987806.

    Proteomic databases

    PaxDbi P58418.
    PRIDEi P58418.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000295911 ; ENSP00000295911 ; ENSG00000163646 . [P58418-1 ]
    ENST00000327047 ; ENSP00000322280 ; ENSG00000163646 . [P58418-3 ]
    ENST00000328863 ; ENSP00000329158 ; ENSG00000163646 . [P58418-4 ]
    GeneIDi 7401.
    KEGGi hsa:7401.
    UCSCi uc003eyj.3. human. [P58418-1 ]
    uc003eyk.1. human. [P58418-3 ]
    uc021xfs.1. human. [P58418-4 ]

    Organism-specific databases

    CTDi 7401.
    GeneCardsi GC03M150643.
    GeneReviewsi CLRN1.
    HGNCi HGNC:12605. CLRN1.
    HPAi HPA054636.
    MIMi 276902. phenotype.
    606397. gene.
    614180. phenotype.
    neXtProti NX_P58418.
    Orphaneti 791. Retinitis pigmentosa.
    231183. Usher syndrome type 3.
    PharmGKBi PA37231.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG44698.
    HOGENOMi HOG000060265.
    HOVERGENi HBG061269.
    InParanoidi P58418.
    OMAi WWSRERR.
    OrthoDBi EOG7MD4QW.
    PhylomeDBi P58418.
    TreeFami TF331875.

    Miscellaneous databases

    GeneWikii CLRN1.
    GenomeRNAii 7401.
    NextBioi 28970.
    PROi P58418.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P58418.
    Bgeei P58418.
    CleanExi HS_CLRN1.
    Genevestigatori P58418.

    Family and domain databases

    InterProi IPR026748. Clarin.
    IPR004031. PMP22/EMP/MP20/Claudin.
    [Graphical view ]
    PANTHERi PTHR31548. PTHR31548. 1 hit.
    Pfami PF13903. Claudin_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), VARIANTS USH3A LYS-120 AND 153-ILE-LEU-154 DELINS MET.
    2. "Usher syndrome type III: revised genomic structure of the USH3 gene and identification of novel mutations."
      Fields R.R., Zhou G., Huang D., Davis J.R., Moeller C., Jacobson S.G., Kimberling W.J., Sumegi J.
      Am. J. Hum. Genet. 71:607-617(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANTS USH3A LYS-48 AND PRO-150.
    3. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT USH3A LYS-48, FUNCTION.
      Tissue: Retina.
    4. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), ALTERNATIVE SPLICING.
      Tissue: Retina.
    5. "The DNA sequence, annotation and analysis of human chromosome 3."
      Muzny D.M., Scherer S.E., Kaul R., Wang J., Yu J., Sudbrak R., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J.
      , Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R., Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Wei S., Wheeler D.A., Wright M.W., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clendenning J., Clerc-Blankenburg K.P., Chen R., Chen Z., Davis C., Delgado O., Dinh H.H., Dong W., Draper H., Ernst S., Fu G., Gonzalez-Garay M.L., Garcia D.K., Gillett W., Gu J., Hao B., Haugen E., Havlak P., He X., Hennig S., Hu S., Huang W., Jackson L.R., Jacob L.S., Kelly S.H., Kube M., Levy R., Li Z., Liu B., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Palmeiri A., Pasternak S., Perez L.M., Phelps K.A., Plopper F.J., Qiang B., Raymond C., Rodriguez R., Saenphimmachak C., Santibanez J., Shen H., Shen Y., Subramanian S., Tabor P.E., Verduzco D., Waldron L., Wang J., Wang J., Wang Q., Williams G.A., Wong G.K.-S., Yao Z., Zhang J., Zhang X., Zhao G., Zhou J., Zhou Y., Nelson D., Lehrach H., Reinhardt R., Naylor S.L., Yang H., Olson M., Weinstock G., Gibbs R.A.
      Nature 440:1194-1198(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    7. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    8. "Mutation screening of USH3 gene (clarin-1) in Spanish patients with Usher syndrome: low prevalence and phenotypic variability."
      Aller E., Jaijo T., Oltra S., Alio J., Galan F., Najera C., Beneyto M., Millan J.M.
      Clin. Genet. 66:525-529(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT USH3A GLY-40.
    9. "Spectrum of USH2A mutations in Scandinavian patients with Usher syndrome type II."
      Dreyer B., Brox V., Tranebjaerg L., Rosenberg T., Sadeghi A.M., Moeller C., Nilssen O.
      Hum. Mutat. 29:451-451(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT USH3A PRO-105.
    10. Cited for: VARIANTS RP61 LEU-31 AND TRP-154, CHARACTERIZATION OF VARIANTS RP61 LEU-31 AND TRP-154.

    Entry informationi

    Entry nameiCLRN1_HUMAN
    AccessioniPrimary (citable) accession number: P58418
    Secondary accession number(s): D3DNJ3, E1ACU9, Q8N6A9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 5, 2001
    Last sequence update: February 6, 2007
    Last modified: October 1, 2014
    This is version 109 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 3
      Human chromosome 3: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3