Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P58418 (CLRN1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 108. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Clarin-1
Alternative name(s):
Usher syndrome type-3 protein
Gene names
Name:CLRN1
Synonyms:USH3A
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length232 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.3

Subcellular location

Membrane; Multi-pass membrane protein Potential.

Tissue specificity

Widely expressed. Found in the retina.

Involvement in disease

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.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.1 Ref.2 Ref.3 Ref.8 Ref.9

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.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.10

Sequence similarities

Belongs to the clarin family.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: P58418-3)

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.
Isoform 2 (identifier: P58418-1)

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
Isoform 3 (identifier: P58418-4)

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

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 232232Clarin-1
PRO_0000065729

Regions

Transmembrane8 – 2821Helical; Potential
Transmembrane101 – 12121Helical; Potential
Transmembrane135 – 15521Helical; Potential
Transmembrane186 – 20621Helical; Potential

Amino acid modifications

Glycosylation481N-linked (GlcNAc...) Potential

Natural variations

Alternative sequence1 – 8585MPSQQ…FRFSF → MQALQQQPV in isoform 2.
VSP_022868
Alternative sequence1441S → SVALWLPATRHQAQ in isoform 3.
VSP_043303
Alternative sequence191 – 23242VIFFC…ADLMY → LTKGHS in isoform 2.
VSP_022869
Natural variant71K → I.
Corresponds to variant rs3796241 [ dbSNP | Ensembl ].
VAR_053825
Natural variant311P → L in RP61; the mutant protein is retained in the endoplasmic reticulum. Ref.10
VAR_066673
Natural variant401C → G in USH3A. Ref.8
VAR_054555
Natural variant481N → K in USH3A. Ref.2 Ref.3
VAR_030345
Natural variant1051S → P in USH3A. Ref.9
VAR_054556
Natural variant1201M → K in USH3A. Ref.1
VAR_012241
Natural variant1501L → P in USH3A. Ref.2
VAR_030346
Natural variant153 – 1542IL → M in USH3A.
VAR_012242
Natural variant1541L → W in RP61; the mutant protein is retained in the endoplasmic reticulum. Ref.10
VAR_066674

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified February 6, 2007. Version 2.
Checksum: 2713C621FEBE4281

FASTA23225,719
        10         20         30         40         50         60 
MPSQQKKIIF CMAGVFSFAC ALGVVTALGT PLWIKATVLC KTGALLVNAS GQELDKFMGE 

        70         80         90        100        110        120 
MQYGLFHGEG VRQCGLGARP FRFSFFPDLL KAIPVSIHVN VILFSAILIV LTMVGTAFFM 

       130        140        150        160        170        180 
YNAFGKPFET LHGPLGLYLL SFISGSCGCL VMILFASEVK IHHLSEKIAN YKEGTYVYKT 

       190        200        210        220        230 
QSEKYTTSFW VIFFCFFVHF LNGLLIRLAG FQFPFAKSKD AETTNVAADL MY 

« Hide

Isoform 2 (A) [UniParc].

Checksum: 959B081E7665A2D1
Show »

FASTA12013,421
Isoform 3 (0-2-2b-3) [UniParc].

Checksum: 024BFE7B5C3788D3
Show »

FASTA24527,192

References

« Hide 'large scale' references
[1]"Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3."
Joensuu T., Haemaelaeinen R., Yuan B., Johnson C., Tegelberg S., Gasparini P., Zelante L., Pirvola U., Pakarinen L., Lehesjoki A.-E., de la Chapelle A., Sankila E.-M.
Am. J. Hum. Genet. 69:673-684(2001) [PubMed] [Europe PMC] [Abstract]
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]"USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses."
Adato A., Vreugde S., Joensuu T., Avidan N., Hamalainen R., Belenkiy O., Olender T., Bonne-Tamir B., Ben-Asher E., Espinos C., Millan J.M., Lehesjoki A.-E., Flannery J.G., Avraham K.B., Pietrokovski S., Sankila E.-M., Beckmann J.S., Lancet D.
Eur. J. Hum. Genet. 10:339-350(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT USH3A LYS-48, FUNCTION.
Tissue: Retina.
[4]"Alternative splice variants of the USH3A gene Clarin 1 (CLRN1)."
Vastinsalo H., Jalkanen R., Dinculescu A., Isosomppi J., Geller S., Flannery J.G., Hauswirth W.W., Sankila E.M.
Eur. J. Hum. Genet. 19:30-35(2011) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
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]"CLRN1 mutations cause nonsyndromic retinitis pigmentosa."
Khan M.I., Kersten F.F., Azam M., Collin R.W., Hussain A., Shah S.T., Keunen J.E., Kremer H., Cremers F.P., Qamar R., den Hollander A.I.
Ophthalmology 118:1444-1448(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS RP61 LEU-31 AND TRP-154, CHARACTERIZATION OF VARIANTS RP61 LEU-31 AND TRP-154.

Web resources

Mutations of the USH3A gene

Retina International's Scientific Newsletter

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS3153.1. [P58418-3]
CCDS35492.1. [P58418-1]
CCDS56285.1. [P58418-4]
RefSeqNP_001182723.1. NM_001195794.1. [P58418-4]
NP_443721.1. NM_052995.2. [P58418-1]
NP_777367.1. NM_174878.2. [P58418-3]
UniGeneHs.745448.

3D structure databases

ProteinModelPortalP58418.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING9606.ENSP00000322280.

Protein family/group databases

TCDB9.A.46.1.1. the clarin (clrn) family.

PTM databases

PhosphoSiteP58418.

Polymorphism databases

DMDM125987806.

Proteomic databases

PaxDbP58418.
PRIDEP58418.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000295911; ENSP00000295911; ENSG00000163646. [P58418-1]
ENST00000327047; ENSP00000322280; ENSG00000163646. [P58418-3]
ENST00000328863; ENSP00000329158; ENSG00000163646. [P58418-4]
GeneID7401.
KEGGhsa:7401.
UCSCuc003eyj.3. human. [P58418-1]
uc003eyk.1. human. [P58418-3]
uc021xfs.1. human. [P58418-4]

Organism-specific databases

CTD7401.
GeneCardsGC03M150643.
GeneReviewsCLRN1.
HGNCHGNC:12605. CLRN1.
HPAHPA054636.
MIM276902. phenotype.
606397. gene.
614180. phenotype.
neXtProtNX_P58418.
Orphanet791. Retinitis pigmentosa.
231183. Usher syndrome type 3.
PharmGKBPA37231.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG44698.
HOGENOMHOG000060265.
HOVERGENHBG061269.
InParanoidP58418.
OMAWWSRERR.
OrthoDBEOG7MD4QW.
PhylomeDBP58418.
TreeFamTF331875.

Gene expression databases

ArrayExpressP58418.
BgeeP58418.
CleanExHS_CLRN1.
GenevestigatorP58418.

Family and domain databases

InterProIPR026748. Clarin.
IPR004031. PMP22/EMP/MP20/Claudin.
[Graphical view]
PANTHERPTHR31548. PTHR31548. 1 hit.
PfamPF13903. Claudin_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GeneWikiCLRN1.
GenomeRNAi7401.
NextBio28970.
PROP58418.
SOURCESearch...

Entry information

Entry nameCLRN1_HUMAN
AccessionPrimary (citable) accession number: P58418
Secondary accession number(s): D3DNJ3, E1ACU9, Q8N6A9
Entry history
Integrated into UniProtKB/Swiss-Prot: December 5, 2001
Last sequence update: February 6, 2007
Last modified: July 9, 2014
This is version 108 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 3

Human chromosome 3: entries, gene names and cross-references to MIM