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Aliases for COCH Gene

Aliases for COCH Gene

  • Cochlin 2 3 3 5
  • Coagulation Factor C Homolog, Cochlin (Limulus Polyphemus) 2 3
  • COCH-5B2 3 4
  • COCH5B2 3 4
  • Coagulation Factor C (Limulus Polyphemus Homolog); Cochlin 2
  • DFNA9 3

External Ids for COCH Gene

Previous HGNC Symbols for COCH Gene

  • DFNA31
  • DFNA9

Previous GeneCards Identifiers for COCH Gene

  • GC14P028719
  • GC14P025131
  • GC14P029333
  • GC14P030413
  • GC14P031343
  • GC14P011460

Summaries for COCH Gene

Entrez Gene Summary for COCH Gene

  • The protein encoded by this gene is highly conserved in human, mouse, and chicken, showing 94% and 79% amino acid identity of human to mouse and chicken sequences, respectively. Hybridization to this gene was detected in spindle-shaped cells located along nerve fibers between the auditory ganglion and sensory epithelium. These cells accompany neurites at the habenula perforata, the opening through which neurites extend to innervate hair cells. This and the pattern of expression of this gene in chicken inner ear paralleled the histologic findings of acidophilic deposits, consistent with mucopolysaccharide ground substance, in temporal bones from DFNA9 (autosomal dominant nonsyndromic sensorineural deafness 9) patients. Mutations that cause DFNA9 have been reported in this gene. Alternative splicing results in multiple transcript variants encoding the same protein. Additional splice variants encoding distinct isoforms have been described but their biological validities have not been demonstrated. [provided by RefSeq, Oct 2008]

GeneCards Summary for COCH Gene

COCH (Cochlin) is a Protein Coding gene. Diseases associated with COCH include Deafness, Autosomal Dominant 9 and Nonsyndromic Deafness. Gene Ontology (GO) annotations related to this gene include collagen binding. An important paralog of this gene is VIT.

UniProtKB/Swiss-Prot for COCH Gene

  • Plays a role in the control of cell shape and motility in the trabecular meshwork.

Gene Wiki entry for COCH Gene

Additional gene information for COCH Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COCH Gene

Genomics for COCH Gene

GeneHancer (GH) Regulatory Elements for COCH Gene

Promoters and enhancers for COCH Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14I030873 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 557.4 +0.2 191 1.9 ATF1 ARID4B SIN3A DMAP1 ZNF2 ZNF48 SLC30A9 POLR2B GLIS2 E2F8 COCH AP4S1 LOC100506071
GH14I030848 Enhancer 1 Ensembl ENCODE 12.2 -25.3 -25274 1.3 PKNOX1 MAX ZNF384 EBF1 CEBPG RAD21 YY1 RELA HNF4G ZNF143 COCH ENSG00000258558
GH14I030822 Enhancer 0.9 ENCODE 7.6 -52.2 -52234 0.2 SMAD1 ARNT NCOA2 TCF12 GATA2 ATF7 NCOA1 MBD2 GMEB1 SMARCA4 ENSG00000258558 RPL27P1 GC14P030822 G2E3 COCH
GH14I031273 Enhancer 0.8 Ensembl ENCODE 4.1 +399.5 399459 1.1 GATAD2A CTCF JUN BATF KMT2B RAD21 ZNF316 IKZF1 SMC3 FOS ENSG00000203546 HECTD1 COCH NARSP1 GC14M031259 ENSG00000199291 LOC105370436
GH14I030850 Enhancer 0.2 ENCODE 12.2 -24.4 -24397 0.1 COCH ENSG00000258558
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around COCH on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the COCH gene promoter:

Genomic Locations for COCH Gene

Genomic Locations for COCH Gene
chr14:30,874,514-30,895,079
(GRCh38/hg38)
Size:
20,566 bases
Orientation:
Plus strand
chr14:31,343,720-31,364,271
(GRCh37/hg19)

Genomic View for COCH Gene

Genes around COCH on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COCH Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COCH Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COCH Gene

Proteins for COCH Gene

  • Protein details for COCH Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43405-COCH_HUMAN
    Recommended name:
    Cochlin
    Protein Accession:
    O43405
    Secondary Accessions:
    • A8K9K9
    • D3DS84
    • Q96IU6

    Protein attributes for COCH Gene

    Size:
    550 amino acids
    Molecular mass:
    59483 Da
    Quaternary structure:
    • Monomer (PubMed:22610276). May form homodimer (PubMed:22610276). Interacts with type II collagen (PubMed:22610276). Interacts with SLC44A2 (PubMed:17926100). Interacts with ANXA2 (PubMed:21886777).

    Three dimensional structures from OCA and Proteopedia for COCH Gene

    Alternative splice isoforms for COCH Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COCH Gene

Post-translational modifications for COCH Gene

No data available for DME Specific Peptides for COCH Gene

Domains & Families for COCH Gene

Gene Families for COCH Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted secreted proteins
  • Transporters

Suggested Antigen Peptide Sequences for COCH Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with COCH: view

No data available for UniProtKB/Swiss-Prot for COCH Gene

Function for COCH Gene

Molecular function for COCH Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the control of cell shape and motility in the trabecular meshwork.

Phenotypes From GWAS Catalog for COCH Gene

Gene Ontology (GO) - Molecular Function for COCH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21886777
GO:0005518 collagen binding IDA 22610276
genes like me logo Genes that share ontologies with COCH: view
genes like me logo Genes that share phenotypes with COCH: view

Human Phenotype Ontology for COCH Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for COCH Gene

MGI Knock Outs for COCH:

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for COCH Gene

Localization for COCH Gene

Subcellular locations from UniProtKB/Swiss-Prot for COCH Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COCH gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 2
plasma membrane 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for COCH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0031012 extracellular matrix IEA,IDA 22610276
GO:0070062 extracellular exosome IDA,HDA 23376485
genes like me logo Genes that share ontologies with COCH: view

Pathways & Interactions for COCH Gene

No Data Available

Gene Ontology (GO) - Biological Process for COCH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007605 sensory perception of sound IEA --
GO:0008360 regulation of cell shape IMP 21886777
GO:0042742 defense response to bacterium IEA --
GO:0045089 positive regulation of innate immune response IEA --
genes like me logo Genes that share ontologies with COCH: view

No data available for Pathways by source and SIGNOR curated interactions for COCH Gene

Drugs & Compounds for COCH Gene

(1) Drugs for COCH Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with COCH: view

Transcripts for COCH Gene

Unigene Clusters for COCH Gene

Coagulation factor C homolog, cochlin (Limulus polyphemus):
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for COCH Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c · 2d · 2e · 2f ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b
SP1: - - - - - - -
SP2: - - - - -
SP3: - - - - -
SP4: - - - - - - - -
SP5: - - - - - - - -
SP6: -
SP7:
SP8: - - - - -
SP9: -
SP10:
SP11: -

Relevant External Links for COCH Gene

GeneLoc Exon Structure for
COCH
ECgene alternative splicing isoforms for
COCH

Expression for COCH Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COCH Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COCH Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x12.9), Brain - Putamen (basal ganglia) (x9.0), and Brain - Caudate (basal ganglia) (x8.6).

Protein differential expression in normal tissues from HIPED for COCH Gene

This gene is overexpressed in Cerebrospinal fluid (25.6), Seminal vesicle (8.8), Urine (7.5), Vitreous humor (7.4), and Pancreatic juice (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for COCH Gene



NURSA nuclear receptor signaling pathways regulating expression of COCH Gene:

COCH

SOURCE GeneReport for Unigene cluster for COCH Gene:

Hs.21016

mRNA Expression by UniProt/SwissProt for COCH Gene:

O43405-COCH_HUMAN
Tissue specificity: Expressed in inner ear structures; the cochlea and the vestibule.

Evidence on tissue expression from TISSUES for COCH Gene

  • Kidney(4.1)
  • Lung(4.1)
  • Nervous system(3.9)
  • Pancreas(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COCH Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • head
  • inner ear
  • middle ear
  • outer ear
Thorax:
  • heart
  • heart valve
Limb:
  • forearm
General:
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with COCH: view

Primer Products

No data available for Protein tissue co-expression partners for COCH Gene

Orthologs for COCH Gene

This gene was present in the common ancestor of animals.

Orthologs for COCH Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COCH 33 34
  • 99.76 (n)
dog
(Canis familiaris)
Mammalia COCH 33 34
  • 93.27 (n)
cow
(Bos Taurus)
Mammalia COCH 33 34
  • 92.12 (n)
mouse
(Mus musculus)
Mammalia Coch 33 16 34
  • 89.39 (n)
oppossum
(Monodelphis domestica)
Mammalia COCH 34
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COCH 34
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves COCH 33 34
  • 76.52 (n)
lizard
(Anolis carolinensis)
Reptilia COCH 34
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia coch 33
  • 67.3 (n)
zebrafish
(Danio rerio)
Actinopterygii coch 33 34
  • 61.97 (n)
worm
(Caenorhabditis elegans)
Secernentea mup-4 34
  • 5 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 12 (a)
OneToOne
Species where no ortholog for COCH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for COCH Gene

ENSEMBL:
Gene Tree for COCH (if available)
TreeFam:
Gene Tree for COCH (if available)

Paralogs for COCH Gene

Paralogs for COCH Gene

genes like me logo Genes that share paralogs with COCH: view

Variants for COCH Gene

Sequence variations from dbSNP and Humsavar for COCH Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs1045644 benign, not specified, Nonsyndromic Hearing Loss, Dominant 30,885,890(+) C/G coding_sequence_variant, missense_variant
rs121908927 pathogenic, Deafness, autosomal dominant 9, Deafness, autosomal dominant, 9 (DFNA9) [MIM:601369] 30,877,686(+) T/C/G coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs121908928 pathogenic, uncertain-significance, Deafness, autosomal dominant 9, not specified, Deafness, autosomal dominant, 9 (DFNA9) [MIM:601369] 30,878,834(+) G/A/T coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs121908929 pathogenic, Deafness, autosomal dominant 9, Deafness, autosomal dominant, 9 (DFNA9) [MIM:601369] 30,878,920(+) T/C coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs121908930 pathogenic, Deafness, autosomal dominant 9, Deafness, autosomal dominant, 9 (DFNA9) [MIM:601369] 30,878,897(+) T/A/C coding_sequence_variant, genic_upstream_transcript_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for COCH Gene

Variant ID Type Subtype PubMed ID
nsv832762 CNV loss 17160897
nsv564169 CNV gain 21841781
esv33189 CNV loss 17666407
dgv3605n54 CNV loss 21841781

Variation tolerance for COCH Gene

Residual Variation Intolerance Score: 58% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.94; 89.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COCH Gene

Human Gene Mutation Database (HGMD)
COCH
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COCH

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COCH Gene

Disorders for COCH Gene

MalaCards: The human disease database

(25) MalaCards diseases for COCH Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
deafness, autosomal dominant 9
  • dfna9
nonsyndromic deafness
  • nonsyndromic hearing loss
non-syndromic genetic deafness
  • isolated genetic deafness
autosomal dominant non-syndromic sensorineural deafness type dfna
  • autosomal dominant isolated neurosensory deafness type dfna
vestibular disease
  • vertigo, vestibular disorder
- elite association - COSMIC cancer census association via MalaCards
Search COCH in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

COCH_HUMAN
  • Deafness, autosomal dominant, 9 (DFNA9) [MIM:601369]: A form of non-syndromic hearing loss characterized by onset in the fourth or fifth decade of life and initially involves the high frequencies. Hearing loss 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. {ECO:0000269 PubMed:10400989, ECO:0000269 PubMed:11295836, ECO:0000269 PubMed:12928864, ECO:0000269 PubMed:14512963, ECO:0000269 PubMed:16835921, ECO:0000269 PubMed:17561763, ECO:0000269 PubMed:18312449, ECO:0000269 PubMed:22610276, ECO:0000269 PubMed:22931125, ECO:0000269 PubMed:23993205, ECO:0000269 PubMed:25388789, ECO:0000269 PubMed:9806553, ECO:0000269 PubMed:9931344}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for COCH

genes like me logo Genes that share disorders with COCH: view

No data available for Genatlas for COCH Gene

Publications for COCH Gene

  1. Cochlin isoforms and their interaction with CTL2 (SLC44A2) in the inner ear. (PMID: 17926100) Kommareddi PK … Carey TE (Journal of the Association for Research in Otolaryngology : JARO 2007) 3 4 22 58
  2. Subcellular localisation, secretion, and post-translational processing of normal cochlin, and of mutants causing the sensorineural deafness and vestibular disorder, DFNA9. (PMID: 12843317) Robertson NG … Morton CC (Journal of medical genetics 2003) 3 4 22 58
  3. Mutations in COCH that result in non-syndromic autosomal dominant deafness (DFNA9) affect matrix deposition of cochlin. (PMID: 12928864) Grabski R … Sztul E (Human genetics 2003) 3 4 22 58
  4. NMR structure of the LCCL domain and implications for DFNA9 deafness disorder. (PMID: 11574466) Liepinsh E … Otting G (The EMBO journal 2001) 3 4 22 58
  5. Identification of a novel COCH mutation, I109N, highlights the similar clinical features observed in DFNA9 families. (PMID: 11295836) Kamarinos M … Dahl H (Human mutation 2001) 3 4 22 58

Products for COCH Gene

Sources for COCH Gene

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