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Protein

Clarin-1

Gene

CLRN1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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. auditory receptor cell stereocilium organization Source: Ensembl
  3. cell motility Source: MGI
  4. equilibrioception Source: HGNC
  5. photoreceptor cell maintenance Source: HGNC
  6. positive regulation of lamellipodium assembly Source: MGI
  7. response to stimulus Source: UniProtKB-KW
  8. sensory perception of light stimulus Source: HGNC
  9. sensory perception of sound Source: HGNC
  10. visual perception Source: UniProtKB-KW
Complete GO annotation...

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 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:12605. CLRN1.

Subcellular locationi

Topology

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

GO - Cellular componenti

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

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Involvement in diseasei

Usher syndrome 3A (USH3A)6 Publications

The disease is caused by mutations affecting the gene represented in this entry.

Disease descriptionUSH 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.

See also OMIM:276902
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. 1 Publication
VAR_012242
Natural varianti168 – 1681I → N in USH3A. 1 Publication
VAR_071434
Retinitis pigmentosa 61 (RP61)1 Publication

The disease is caused by mutations affecting the gene represented in this entry.

Disease descriptionA 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.

See also OMIM:614180
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

BgeeiP58418.
CleanExiHS_CLRN1.
ExpressionAtlasiP58418. baseline and differential.
GenevestigatoriP58418.

Organism-specific databases

HPAiHPA054636.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000322280.

Structurei

3D structure databases

ProteinModelPortaliP58418.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the clarin family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG44698.
GeneTreeiENSGT00750000117609.
HOGENOMiHOG000060265.
HOVERGENiHBG061269.
InParanoidiP58418.
OMAiQYGLFHG.
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. AlignAdd to basket

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

        10         20         30         40         50
MPSQQKKIIF CMAGVFSFAC ALGVVTALGT PLWIKATVLC KTGALLVNAS
60 70 80 90 100
GQELDKFMGE MQYGLFHGEG VRQCGLGARP FRFSFFPDLL KAIPVSIHVN
110 120 130 140 150
VILFSAILIV LTMVGTAFFM YNAFGKPFET LHGPLGLYLL SFISGSCGCL
160 170 180 190 200
VMILFASEVK IHHLSEKIAN YKEGTYVYKT QSEKYTTSFW VIFFCFFVHF
210 220 230
LNGLLIRLAG FQFPFAKSKD AETTNVAADL MY
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. 1 Publication
VAR_012242
Natural varianti154 – 1541L → W in RP61; the mutant protein is retained in the endoplasmic reticulum. 1 Publication
VAR_066674
Natural varianti168 – 1681I → N in USH3A. 1 Publication
VAR_071434

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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliP58418.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000322280.

Protein family/group databases

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

PTM databases

PhosphoSiteiP58418.

Polymorphism databases

DMDMi125987806.

Proteomic databases

PaxDbiP58418.
PRIDEiP58418.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi7401.
GeneCardsiGC03M150643.
GeneReviewsiCLRN1.
HGNCiHGNC:12605. CLRN1.
HPAiHPA054636.
MIMi276902. phenotype.
606397. gene.
614180. phenotype.
neXtProtiNX_P58418.
Orphaneti791. Retinitis pigmentosa.
231183. Usher syndrome type 3.
PharmGKBiPA37231.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG44698.
GeneTreeiENSGT00750000117609.
HOGENOMiHOG000060265.
HOVERGENiHBG061269.
InParanoidiP58418.
OMAiQYGLFHG.
OrthoDBiEOG7MD4QW.
PhylomeDBiP58418.
TreeFamiTF331875.

Miscellaneous databases

GeneWikiiCLRN1.
GenomeRNAii7401.
NextBioi28970.
PROiP58418.
SOURCEiSearch...

Gene expression databases

BgeeiP58418.
CleanExiHS_CLRN1.
ExpressionAtlasiP58418. baseline and differential.
GenevestigatoriP58418.

Family and domain databases

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

Publicationsi

« Hide 'large scale' publications
  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(2001) [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(2005) [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(2003) [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(2003) [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(2007) [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.
  11. "Two novel disease-causing mutations in the CLRN1 gene in patients with Usher syndrome type 3."
    Garcia-Garcia G., Aparisi M.J., Rodrigo R., Sequedo M.D., Espinos C., Rosell J., Olea J.L., Mendivil M.P., Ramos-Arroyo M.A., Ayuso C., Jaijo T., Aller E., Millan J.M.
    Mol. Vis. 18:3070-3078(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT USH3A ASN-168.

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: March 4, 2015
This is version 112 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.