COCH cochlin [Homo sapiens (human)] - Gene

Summary

Official Symbol: COCHprovided by HGNC
Official Full Name: cochlinprovided by HGNC
Primary source: HGNC:HGNC:2180
See related: Ensembl:ENSG00000100473 MIM:603196; AllianceGenome:HGNC:2180
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: DFNA9; COCH5B2; DFNB110; COCH-5B2
Summary: 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]
Expression: Biased expression in pancreas (RPKM 45.5), prostate (RPKM 16.0) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 14q12

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (30874559..30895615)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (25072046..25093101)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (31343765..31359824)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interaural and sex differences in the natural evolution of hearing levels in pre-symptomatic and symptomatic carriers of the p.Pro51Ser variant in the COCH gene.
Title: Interaural and sex differences in the natural evolution of hearing levels in pre-symptomatic and symptomatic carriers of the p.Pro51Ser variant in the COCH gene.
Evaluation of hearing levels and vestibular function and the impact on cognitive performance in (pre)-symptomatic patients with DFNA9: protocol for a prospective longitudinal study (Rosetta study).
Title: Evaluation of hearing levels and vestibular function and the impact on cognitive performance in (pre)-symptomatic patients with DFNA9: protocol for a prospective longitudinal study (Rosetta study).
Inhibiting KCNMA1-AS1 promotes osteogenic differentiation of HBMSCs via miR-1303/cochlin axis.
Title: Inhibiting KCNMA1-AS1 promotes osteogenic differentiation of HBMSCs via miR-1303/cochlin axis.
Genotype-Phenotype Correlations of Pathogenic COCH Variants in DFNA9: A HuGE Systematic Review and Audiometric Meta-Analysis.
Title: Genotype-Phenotype Correlations of Pathogenic COCH Variants in DFNA9: A HuGE Systematic Review and Audiometric Meta-Analysis.
Does Vestibulo-Ocular Reflex (VOR) Gain Correlate With Radiological Findings in the Semi-Circular Canals in Patients Carrying the p.Pro51Ser (P51S) COCH Variant Causing DFNA9? Relationship Between the Three-Dimensional Video Head Impulse Test (vHIT) and MR/CT Imaging.
Title: Does Vestibulo-Ocular Reflex (VOR) Gain Correlate With Radiological Findings in the Semi-Circular Canals in Patients Carrying the p.Pro51Ser (P51S) COCH Variant Causing DFNA9? Relationship Between the Three-Dimensional Video Head Impulse Test (vHIT) and MR/CT Imaging.
On the pathophysiology of DFNA9: Effect of pathogenic variants in the COCH gene on inner ear functioning in human and transgenic mice.
Title: On the pathophysiology of DFNA9: Effect of pathogenic variants in the COCH gene on inner ear functioning in human and transgenic mice.
Genotype-phenotype Correlation Study in a Large Series of Patients Carrying the p.Pro51Ser (p.P51S) Variant in COCH (DFNA9): Part I-A Cross-sectional Study of Hearing Function in 111 Carriers.
Title: Genotype-phenotype Correlation Study in a Large Series of Patients Carrying the p.Pro51Ser (p.P51S) Variant in COCH (DFNA9): Part I-A Cross-sectional Study of Hearing Function in 111 Carriers.
Homozygote loss-of-function variants in the human COCH gene underlie hearing loss.
Title: Homozygote loss-of-function variants in the human COCH gene underlie hearing loss.
Cochlin-cleaved LCCL is a dual-armed regulator of the innate immune response in the cochlea during inflammation.
Title: Cochlin-cleaved LCCL is a dual-armed regulator of the innate immune response in the cochlea during inflammation.
A Novel COCH Mutation Affects the vWFA2 Domain and Leads to a Relatively Mild DFNA9 Phenotype.
Title: A Novel COCH Mutation Affects the vWFA2 Domain and Leads to a Relatively Mild DFNA9 Phenotype.

Submit: New GeneRIF Correction See all GeneRIFs (59)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal dominant nonsyndromic hearing loss 9 MedGen: C1832425 OMIM: 601369 GeneReviews: Genetic Hearing Loss Overview	Compare labs
Hearing loss, autosomal recessive 110 MedGen: C4748162 OMIM: 618094 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D14S670E (e-PCR)
- UniSTS:8531

WI-12411 (e-PCR)
- UniSTS:64920

COCH__4606 (e-PCR)
- UniSTS:466126

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables collagen binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in regulation of cell shape	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in collagen-containing extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: cochlin

Names: coagulation factor C homolog, cochlin (Limulus polyphemus)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008211.3 RefSeqGene

Range

5002..21061

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001135058.2 → NP_001128530.1 cochlin isoform b precursor

See identical proteins and their annotated locations for NP_001128530.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) uses an alternate in-frame splice junction in the 5' end compared to variant 3. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 1 and 2 encode the same isoform (b).

Source sequence(s)

AF006740, AL049830, AY358900

Consensus CDS

CCDS9640.1

UniProtKB/Swiss-Prot

A8K9K9, D3DS84, O43405, Q96IU6

UniProtKB/TrEMBL

A0A2R8Y3T0

Related

ENSP00000496360.1, ENST00000644874.2

Conserved Domains (3) summary

smart00603
Location:30 → 112

LCCL; LCCL domain

cd01472
Location:366 → 527

vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...

cd01482
Location:164 → 328

vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
NM_001347720.2 → NP_001334649.1 cochlin isoform a precursor

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents the longest transcript and encodes the longer isoform (a).

Source sequence(s)

AL049830

Consensus CDS

CCDS86382.1

UniProtKB/TrEMBL

A0A2R8Y3T0, A0A2U3TZE7

Related

ENSP00000216361.5, ENST00000216361.9
NM_004086.3 → NP_004077.1 cochlin isoform b precursor

See identical proteins and their annotated locations for NP_004077.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and uses an alternate in-frame splice junction in the 5' end compared to variant 3. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 1 and 2 encode the same isoform (b).

Source sequence(s)

AF006740, AL049830

Consensus CDS

CCDS9640.1

UniProtKB/Swiss-Prot

A8K9K9, D3DS84, O43405, Q96IU6

UniProtKB/TrEMBL

A0A2R8Y3T0

Related

ENSP00000379862.3, ENST00000396618.9

Conserved Domains (3) summary

smart00603
Location:30 → 112

LCCL; LCCL domain

cd01472
Location:366 → 527

vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...

cd01482
Location:164 → 328

vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

30874559..30895615

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047431063.1 → XP_047287019.1 cochlin isoform X2

UniProtKB/TrEMBL

A0A2U3TZE7
XM_047431062.1 → XP_047287018.1 cochlin isoform X1
XM_047431064.1 → XP_047287020.1 cochlin isoform X4

UniProtKB/Swiss-Prot

A8K9K9, D3DS84, O43405, Q96IU6

Related

ENSP00000494838.1, ENST00000643575.1
XM_017021071.2 → XP_016876560.1 cochlin isoform X2

UniProtKB/TrEMBL

A0A2R8Y3T0, A0A2U3TZE7
XM_024449506.1 → XP_024305274.1 cochlin isoform X3

UniProtKB/TrEMBL

A0A2R8Y3T0

Related

ENSP00000493569.1, ENST00000555117.2

Conserved Domains (3) summary

smart00603
Location:30 → 112

LCCL; LCCL domain

cd01472
Location:385 → 546

vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...

cl00057
Location:164 → 347

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...