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UniProtKB/Swiss-Prot entry O43405


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name COCH_HUMAN
Primary accession number O43405
Secondary accession numbers None
Integrated into Swiss-Prot on May 30, 2000
Sequence was last modified on June 1, 1998 (Sequence version 1)
Annotations were last modified on    June 16, 2009 (Entry version 98)
Name and origin of the protein
Protein name Cochlin [Precursor]
Synonym COCH-5B2
Gene name
Name: COCH
Synonyms: COCH5B2
ORFNames: UNQ257/PRO294
From
Homo sapiens (Human) [TaxID: 9606] 
Taxonomy Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo.
Protein existence 1: Evidence at protein level;
References
[1]
NUCLEOTIDE SEQUENCE [MRNA].
TISSUE=Cochlea;
DOI=10.1006/geno.1997.5067; PubMed=9441737 [NCBI, ExPASy, EBI, Israel, Japan]
Robertson N.G., Skvorak A.B., Yin Y., Weremowicz S., Johnson K.R., Kovatch K.A., Battey J.F., Bieber F.R., Morton C.C.;
"Mapping and characterization of a novel cochlear gene in human and in mouse: a positional candidate gene for a deafness disorder, DFNA9.";
Genomics 46:345-354(1997).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
DOI=10.1101/gr.1293003; PubMed=12975309 [NCBI, ExPASy, EBI, Israel, Japan]
Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J., Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P., Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E., Heldens S., Huang A., Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D., Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L., Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C., Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J., Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M.;
"The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment.";
Genome Res. 13:2265-2270(2003).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANTS ARG-135; ASN-281; SER-352 AND VAL-402.
SeattleSNPs variation discovery resource;
Submitted (FEB-2005) to the EMBL/GenBank/DDBJ databases.
[4]
GLYCOSYLATION, SUBCELLULAR LOCATION, AND PROTEOLYTIC PROCESSING.
DOI=10.1136/jmg.40.7.479; PubMed=12843317 [NCBI, ExPASy, EBI, Israel, Japan]
Robertson N.G., Hamaker S.A., Patriub V., Aster J.C., Morton C.C.;
"Subcellular localisation, secretion, and post-translational processing of normal cochlin, and of mutants causing the sensorineural deafness and vestibular disorder, DFNA9.";
J. Med. Genet. 40:479-486(2003).
[5]
INTERACTION WITH SLC44A2.
DOI=10.1007/s10162-007-0099-2; PubMed=17926100 [NCBI, ExPASy, EBI, Israel, Japan]
Kommareddi P.K., Nair T.S., Raphael Y., Telian S.A., Kim A.H., Arts H.A., El-Kashlan H.K., Carey T.E.;
"Cochlin isoforms and their interaction with CTL2 (SLC44A2) in the inner ear.";
J. Assoc. Res. Otolaryngol. 8:435-446(2007).
[6]
STRUCTURE BY NMR OF 27-126.
DOI=10.1093/emboj/20.19.5347; PubMed=11574466 [NCBI, ExPASy, EBI, Israel, Japan]
Liepinsh E., Trexler M., Kaikkonen A., Weigelt J., Banyai L., Patthy L., Otting G.;
"NMR structure of the LCCL domain and implications for DFNA9 deafness disorder.";
EMBO J. 20:5347-5353(2001).
[7]
VARIANTS DFNA9 GLY-66; GLU-88 AND ARG-117.
DOI=10.1038/3118; PubMed=9806553 [NCBI, ExPASy, EBI, Israel, Japan]
Robertson N.G., Lu L., Heller S., Merchant S.N., Eavey R.D., McKenna M., Nadol J.B. Jr., Miyamoto R.T., Linthicum F.H. Jr., Neto J.F.L., Hudspeth A.J., Seidman C.E., Morton C.C., Seidman J.G.;
"Mutations in a novel cochlear gene cause DFNA9, a human nonsyndromic deafness with vestibular dysfunction.";
Nat. Genet. 20:299-303(1998).
[8]
VARIANT DFNA9 SER-51.
DOI=10.1093/hmg/8.2.361; PubMed=9931344 [NCBI, ExPASy, EBI, Israel, Japan]
de Kok Y.J.M., Bom S.J.H., Brunt T.M., Kemperman M.H., van Beusekom E., van der Velde-Visser S.D., Robertson N.G., Morton C.C., Huygen P.L.M., Verhagen W.I.M., Brunner H.G., Cremers C.W.R.J., Cremers F.P.M.;
"A Pro51Ser mutation in the COCH gene is associated with late onset autosomal dominant progressive sensorineural hearing loss with vestibular defects.";
Hum. Mol. Genet. 8:361-366(1999).
[9]
VARIANT DFNA9 SER-51.
DOI=10.1093/hmg/8.8.1425; PubMed=10400989 [NCBI, ExPASy, EBI, Israel, Japan]
Fransen E., Verstreken M., Verhagen W.I.M., Wuyts F.L., Huygen P.L.M., D'Haese P., Robertson N.G., Morton C.C., McGuirt W.T., Smith R.J.H., Declau F., Van de Heyning P.H., Van Camp G.;
"High prevalence of symptoms of Meniere's disease in three families with a mutation in the COCH gene.";
Hum. Mol. Genet. 8:1425-1429(1999).
[10]
VARIANT DFNA9 ASN-109.
DOI=10.1002/humu.37; PubMed=11295836 [NCBI, ExPASy, EBI, Israel, Japan]
Kamarinos M., McGill J., Lynch M., Dahl H.-H.M.;
"Identification of a novel COCH mutation, I109N, highlights the similar clinical features observed in DFNA9 families.";
Hum. Mutat. 17:351-351(2001).
[11]
ERRATUM.
Kamarinos M., McGill J., Lynch M., Dahl H.-H.M.;
Hum. Mutat. 18:547-548(2001).
[12]
VARIANT DFNA9 THR-119.
DOI=10.1038/sj.ejhg.5201043; PubMed=14512963 [NCBI, ExPASy, EBI, Israel, Japan]
Usami S., Takahashi K., Yuge I., Ohtsuka A., Namba A., Abe S., Fransen E., Patthy L., Otting G., Van Camp G.;
"Mutations in the COCH gene are a frequent cause of autosomal dominant progressive cochleo-vestibular dysfunction, but not of Meniere's disease.";
Eur. J. Hum. Genet. 11:744-748(2003).
[13]
CHARACTERIZATION OF VARIANTS DFNA9 SER-51; GLY-66; GLU-88; ASN-109 AND ARG-117.
DOI=10.1007/s00439-003-0992-7; PubMed=12928864 [NCBI, ExPASy, EBI, Israel, Japan]
Grabski R., Szul T., Sasaki T., Timpl R., Mayne R., Hicks B., Sztul E.;
"Mutations in COCH that result in non-syndromic autosomal dominant deafness (DFNA9) affect matrix deposition of cochlin.";
Hum. Genet. 113:406-416(2003).
[14]
DISEASE.
DOI=10.1097/00129492-200109000-00009; PubMed=11568667 [NCBI, ExPASy, EBI, Israel, Japan]
Boulassel M.-R., Tomasi J.-P., Deggouj N., Gersdorff M.;
"COCH5B2 is a target antigen of anti-inner ear antibodies in autoimmune inner ear diseases.";
Otol. Neurotol. 22:614-618(2001).
Comments
  • SUBUNIT: Interacts with SLC44A2.
  • SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix.
  • TISSUE SPECIFICITY: Expressed in inner ear structures; the cochlea and the vestibule.
  • PTM: N-glycosylated.
  • PTM: A 50 kDa form is created by proteolytic cleavage.
  • DISEASE: Defects in COCH are the cause of non-syndromic sensorineural deafness autosomal dominant type 9 (DFNA9) [MIM:601369]. DFNA9 is a form of sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. DFNA9 is characterized by onset in the fourth or fifth decade of life and initially involves the high frequencies. Deafness is progressive and usually complete by the sixth decade. In addition to cochlear involvement, DFNA9 patients also exhibit a spectrum of vestibular dysfunctions. Penetrance of the vestibular symptoms is often incomplete, and some patients are minimally affected, whereas others suffer from severe balance disturbances and episodes of vertigo. Affected individuals have mucopolysaccharide depositions in the channels of the cochlear and vestibular nerves. These depositions apparently cause strangulation and degeneration of dendritic fibers.
  • DISEASE: Defects in COCH may contribute to Meniere disease [MIM:156000]. Meniere disease is an autosomal dominant disorder characterized by hearing loss associated with episodic vertigo. Antibodies against COCH are found in 10% of Meniere patients.
  • SIMILARITY: Contains 1 LCCL domain.
  • SIMILARITY: Contains 2 VWFA domains.
  • WEB RESOURCE: Name=Protein Spotlight; Note=The Japanese Horseshoe Crab and Deafness - Issue 4 of November 2000; URL="http://www.expasy.org/spotlight/back_issues/sptlt004.shtml";.
  • WEB RESOURCE: Name=Hereditary hearing loss homepage; Note=Gene page; URL="http://webhost.ua.ac.be/hhh/";.
  • WEB RESOURCE: Name=GeneReviews; URL="http://www.genetests.org/query?gene=COCH";.
  • WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/coch/";.
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
AF006740; AAC39545.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AY358900; AAQ89259.1; -; mRNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AY916789; AAW82432.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
IPI IPI00012386; -.
RefSeq NP_001128530.1; -.
NP_004077.1; -.
UniGene Hs.21016
3D structure databases
PDB
1JBI; NMR; -; A=28-124.[ExPASy / RCSB / EBI]
PDBsum 1JBI; -.
ModBase O43405.
PTM databases
PhosphoSite O43405; -.
Organism-specific databases
GeneCards GC14P030413; -.
H-InvDB HIX0022288; -.
HGNC HGNC:2180; COCH.
GenAtlas COCH.
MIM 156000; phenotype. [NCBI / EBI]
601369; phenotype. [NCBI / EBI]
603196; gene. [NCBI / EBI]
Orphanet 45360; Meniere disease.
87884; Nonsyndromic genetic deafness.
PharmGKB PA26693; -.
Gene expression databases
ArrayExpress O43405; -.
Bgee O43405; -.
CleanEx HS_COCH; -.
GermOnline ENSG00000100473; Homo sapiens.
Ontologies
GO
GO:0005615; Cellular component: extracellular space (inferred from electronic annotation from UniProtKB-SubCell).
GO:0005578; Cellular component: proteinaceous extracellular matrix (inferred from electronic annotation from UniProtKB-SubCell).
GO:0007605; Biological process: sensory perception of sound (traceable author statement from ProtInc).
QuickGo view.
Family and domain databases
InterPro IPR004043; LCCL.
IPR002035; VWF_A.
Graphical view of domain structure.
Gene3D G3DSA:2.170.130.20; LCCL; 1.
Pfam PF03815; LCCL; 1.
PF00092; VWA; 2.
Pfam graphical view of domain structure.
SMART SM00603; LCCL; 1.
SM00327; VWA; 2.
SMART graphical view of domain structure.
PROSITE PS50820; LCCL; 1.
PS50234; VWFA; 2.
PROSITE graphical view of domain structure (profiles).
Proteomic databases
PRIDE O43405; -.
Genome annotation databases
Ensembl ENSG00000100473; Homo sapiens. [Contig view]
GeneID 1690; -.
KEGG hsa:1690; -.
Phylogenomic databases
HOGENOM O43405; -.
HOVERGEN O43405; -.
OMA O43405; FISNIAK.
Other
NextBio 6926; -.
SOURCE COCH; Homo sapiens.
ProtoNet O43405.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
3D-structure; Deafness; Disease mutation; Disulfide bond; Extracellular matrix; Glycoprotein; Hearing; Non-syndromic deafness; Polymorphism; Repeat; Secreted; Signal.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom   To Length Description FTId
SIGNAL   1    24  24     Potential. 
CHAIN   25   550  526     Cochlin. PRO_0000020968
DOMAIN   28   121  94     LCCL. 
DOMAIN   165   346  182     VWFA 1. 
DOMAIN   367   537  171     VWFA 2. 
CARBOHYD   100   100        N-linked (GlcNAc...) (Potential). 
CARBOHYD   221   221        N-linked (GlcNAc...) (Potential). 
DISULFID   34    50         
DISULFID   54    74         
VARIANT   51    51  1     P -> S (in DFNA9; Meniere disease; does not affect protein deposition to the extracellular matrix). VAR_008532 
VARIANT   66    66  1     V -> G (in DFNA9; affects protein deposition to the extracellular matrix). VAR_008533 
VARIANT   88    88  1     G -> E (in DFNA9; affects protein deposition to the extracellular matrix). VAR_008534 
VARIANT   109   109  1     I -> N (in DFNA9; affects protein deposition to the extracellular matrix). VAR_008535 
VARIANT   117   117  1     W -> R (in DFNA9; does not affect protein deposition to the extracellular matrix). VAR_008536 
VARIANT   119   119  1     A -> T (in DFNA9). VAR_017175 
VARIANT   135   135  1     G -> R (in dbSNP:rs28400035 [NCBI]). VAR_022259 
VARIANT   281   281  1     D -> N (in dbSNP:rs28362775 [NCBI]). VAR_022260 
VARIANT   352   352  1     T -> S (in dbSNP:rs1045644 [NCBI]). VAR_011925 
VARIANT   402   402  1     I -> V (in dbSNP:rs28362778 [NCBI]). VAR_022261 
VARIANT   518   518  1     E -> G (in dbSNP:rs17097468 [NCBI]). VAR_050896 
VARIANT   532   532  1     P -> S (in dbSNP:rs1801963 [NCBI]). VAR_011926 
TURN   38    40  3      
STRAND   43    50  8      
STRAND   56    58  3      
STRAND   61    68  8      
HELIX   73    80  8      
STRAND   88    95  8      
STRAND   110   112  3      
Sequence information
Length: 550 AA [This is the length of the unprocessed precursor] Molecular weight: 59483 Da [This is the MW of the unprocessed precursor] CRC64: 74D7D51290098B30 [This is a checksum on the sequence]
        10         20         30         40         50         60 
MSAAWIPALG LGVCLLLLPG PAGSEGAAPI AITCFTRGLD IRKEKADVLC PGGCPLEEFS 

        70         80         90        100        110        120 
VYGNIVYASV SSICGAAVHR GVISNSGGPV RVYSLPGREN YSSVDANGIQ SQMLSRWSAS 

       130        140        150        160        170        180 
FTVTKGKSST QEATGQAVST AHPPTGKRLK KTPEKKTGNK DCKADIAFLI DGSFNIGQRR 

       190        200        210        220        230        240 
FNLQKNFVGK VALMLGIGTE GPHVGLVQAS EHPKIEFYLK NFTSAKDVLF AIKEVGFRGG 

       250        260        270        280        290        300 
NSNTGKALKH TAQKFFTVDA GVRKGIPKVV VVFIDGWPSD DIEEAGIVAR EFGVNVFIVS 

       310        320        330        340        350        360 
VAKPIPEELG MVQDVTFVDK AVCRNNGFFS YHMPNWFGTT KYVKPLVQKL CTHEQMMCSK 

       370        380        390        400        410        420 
TCYNSVNIAF LIDGSSSVGD SNFRLMLEFV SNIAKTFEIS DIGAKIAAVQ FTYDQRTEFS 

       430        440        450        460        470        480 
FTDYSTKENV LAVIRNIRYM SGGTATGDAI SFTVRNVFGP IRESPNKNFL VIVTDGQSYD 

       490        500        510        520        530        540 
DVQGPAAAAH DAGITIFSVG VAWAPLDDLK DMASKPKESH AFFTREFTGL EPIVSDVIRG 

       550 
ICRDFLESQQ 

O43405 in FASTA format

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