Noise induced hearing loss

disease
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Also known as hearing loss, noise-induced, susceptibility toNIHLnoise-induced hearing loss

Summary

Noise induced hearing loss (MONDO:0013098) is a disease with 9 cohort genes (3 GWAS associations across 4 studies) and 21 clinical trials. Top therapeutic interventions include methylprednisolone, zonisamide, and disufenton sodium.

At a glance

  • Cohort genes: 9
  • GWAS associations: 3
  • ClinVar variants: 1
  • Clinical trials: 21

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namenoise induced hearing loss
Mondo IDMONDO:0013098
EFOEFO:1001254
MeSHD006317
NCITC34664
SNOMED CT73415002
UMLSC0018781
MedGen5455
Is cancer (heuristic)no

Also known as: hearing loss, noise-induced, susceptibility to · NIHL · noise-induced hearing loss

Data availability: 1 ClinVar variant · 3 GWAS associations (4 studies).

Disease family

Classification path: disease › human disease › disease by body system or component › auditory system disorderhearing disorderhearing loss disordernoise induced hearing loss

Related subtypes (10): Johanson-Blizzard syndrome, nonsyndromic genetic hearing loss, sudden hearing loss disorder, sensorineural hearing loss disorder, conductive hearing loss disorder, central hearing loss, X-linked deafness, auditory neuropathy, hearing loss, mixed conductive-sensorineural, drug-induced hearing loss

Genetics & variants

GWAS landscape

3 GWAS associations across 4 studies. Top hits map to 3 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs75987595e-07NCL?12.75
rs350758901e-06AUTS2G3.17
rs100811912e-06PTPRN2A1.99

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90081540Backman JD202116,06913,961Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90085526Backman JD202116,06913,961Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST011920Niu Y2020890Genome-wide association study identifies 7q11.22 and 7q36.3 associated with noise-induced hearing loss among Chinese population.
GCST003006Grondin Y2015190Genetic Polymorphisms Associated with Hearing Threshold Shift in Subjects during First Encounter with Occupational Impulse Noise.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding0
Tier 2: splice/UTR0
Tier 3: regulatory0
Tier 4: intronic/intergenic3

MAF distribution

BucketVariants
common (>=0.05)3
low_freq (0.01-0.05)0
rare (<0.01)0
unknown0

Functional consequences

ConsequenceCount
intron_variant3

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs75987592231457245C>A,G,T0.05intron_variantNCL5e-07Tier 4: intronic/intergenic
rs35075890770713244A>C,G,T0.05intron_variantAUTS21e-06Tier 4: intronic/intergenic
rs100811917158530114A>C,G,T0.05intron_variantPTPRN22e-06Tier 4: intronic/intergenic

ClinVar germline variants

1 retrieved; paginated sample, class counts are floors:

1 benign

ClinVarVariant (HGVS)GeneClassificationReview
132651NM_000219.6(KCNE1):c.112A>G (p.Ser38Gly)KCNE1Benigncriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 7 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
AUTS2Orphanet:352490Autism spectrum disorder due to AUTS2 deficiency
AUTS2Orphanet:641372B-lymphoblastic leukemia/lymphoma with t(7;9)(q11.2;p13.2)
DYNC2I1Orphanet:474Jeune syndrome
DYNC2I1Orphanet:93271Short rib-polydactyly syndrome, Verma-Naumoff type
KCNE1Orphanet:101016Romano-Ward syndrome
KCNE1Orphanet:334Hereditary atrial fibrillation
KCNE1Orphanet:90647Jervell and Lange-Nielsen syndrome

Cohort genes → proteins

9 cohort genes, 9 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only8
multi_evidence1

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
VIPR2HGNC:12695ENSG00000106018P41587Vasoactive intestinal polypeptide receptor 2gwas
AUTS2HGNC:14262ENSG00000158321Q8WXX7Autism susceptibility gene 2 proteingwas
GALNT17HGNC:16347ENSG00000185274Q6IS24Polypeptide N-acetylgalactosaminyltransferase 17gwas
DYNC2I1HGNC:21862ENSG00000126870Q8WVS4Cytoplasmic dynein 2 intermediate chain 1gwas
NCAPG2HGNC:21904ENSG00000146918Q86XI2Condensin-2 complex subunit G2gwas
ESYT2HGNC:22211ENSG00000117868A0FGR8Extended synaptotagmin-2gwas
KCNE1HGNC:6240ENSG00000180509P15382Potassium voltage-gated channel subfamily E member 1clinvar
NUCLEOLINHGNC:7667ENSG00000115053P19338Nucleolingwas
PTPRN2HGNC:9677ENSG00000155093Q92932Receptor-type tyrosine-protein phosphatase N2gwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
VIPR2Vasoactive intestinal polypeptide receptor 2G protein-coupled receptor activated by the neuropeptides vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (ADCYAP1/PACAP).
AUTS2Autism susceptibility gene 2 proteinComponent of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development.
GALNT17Polypeptide N-acetylgalactosaminyltransferase 17May catalyze the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor.
DYNC2I1Cytoplasmic dynein 2 intermediate chain 1Acts as one of several non-catalytic accessory components of the cytoplasmic dynein 2 complex (dynein-2 complex), a motor protein complex that drives the movement of cargos along microtubules within cilia and flagella in concert with the i…
NCAPG2Condensin-2 complex subunit G2Regulatory subunit of the condensin-2 complex, a complex which establishes mitotic chromosome architecture and is involved in physical rigidity of the chromatid axis.
ESYT2Extended synaptotagmin-2Tethers the endoplasmic reticulum to the cell membrane and promotes the formation of appositions between the endoplasmic reticulum and the cell membrane.
KCNE1Potassium voltage-gated channel subfamily E member 1Ancillary protein that functions as a regulatory subunit of the voltage-gated potassium (Kv) channel complex composed of pore-forming and potassium-conducting alpha subunits and of regulatory beta subunits.
NUCLEOLINNucleolinNucleolin is the major nucleolar protein of growing eukaryotic cells.
PTPRN2Receptor-type tyrosine-protein phosphatase N2Plays a role in vesicle-mediated secretory processes.

Protein-family classification

Druggable: 3 · Difficult: 1 · Unknown: 5 · Druggable fraction: 0.33

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Ion channel112.4×0.256
Phosphatase19.3×0.256
GPCR12.7×0.519
Scaffold/PPI11.9×0.519
Other/Unknown51.0×0.641

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
VIPR2GPCRyesGPCR_2_secretin-like, GPCR_2_VIP_rcpt, GPCR_2_extracellular_dom
AUTS2Other/UnknownnoAUTS2
GALNT17Other/UnknownnoRicin_B_lectin, Glyco_trans_2-like, Nucleotide-diphossugar_trans
DYNC2I1Scaffold/PPInoWD40_rpt, WD40/YVTN_repeat-like_dom_sf, WD40_repeat_dom_sf
NCAPG2Other/UnknownnoARM-like, ARM-type_fold, Condensin2_G2
ESYT2Other/UnknownnoC2_dom, SMP_LBD, C2_domain_sf
KCNE1Ion channelyesK_chnl_KCNE, KCNE1
NUCLEOLINOther/UnknownnoRRM_dom, RRM_euk-type, Nucleotide-bd_a/b_plait_sf
PTPRN2Phosphataseyes3.1.3.48PTP_cat, Tyr_Pase_dom, Tyr_Pase_cat

Expression context

Cohort genes with no expression data: 0.

9 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)9
unknown0

Top tissues across cohort

TissueCohort genes
cortical plate2
ganglionic eminence2
ventricular zone2
apex of heart1
heart left ventricle1
mucosa of stomach1
tibia1
cerebellar vermis1
dorsal root ganglion1
trigeminal ganglion1
right uterine tube1
sperm1
sural nerve1
oocyte1
secondary oocyte1
calcaneal tendon1
layer of synovial tissue1
saphenous vein1
blood1
leukocyte1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
VIPR2169broadmarkermucosa of stomach, apex of heart, heart left ventricle
AUTS2292ubiquitousmarkercortical plate, tibia, ganglionic eminence
GALNT17199broadmarkertrigeminal ganglion, dorsal root ganglion, cerebellar vermis
DYNC2I1269ubiquitousmarkersural nerve, right uterine tube, sperm
NCAPG2217ubiquitousmarkerventricular zone, secondary oocyte, oocyte
ESYT2261ubiquitousmarkerlayer of synovial tissue, calcaneal tendon, saphenous vein
KCNE1121broadmarkerblood, monocyte, leukocyte
NUCLEOLIN165ubiquitousmarkerventricular zone, ganglionic eminence, cortical plate
PTPRN2254broadmarkerlateral nuclear group of thalamus, middle temporal gyrus, lateral globus pallidus

Protein interactions among cohort

Intra-cohort edges: 4.

Hub genes (top 10 by interactor count)

SymbolInteractor count
NUCLEOLIN5,960
NCAPG21,831
AUTS21,700
ESYT21,684
PTPRN21,491
VIPR21,488
KCNE11,005
DYNC2I1955
GALNT17852

Intra-cohort edges

ABSources
AUTS2GALNT17string_interaction
DYNC2I1ESYT2string_interaction
DYNC2I1NCAPG2string_interaction
ESYT2NCAPG2string_interaction

Structural data

PDB: 7 · AlphaFold-only: 2 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
KCNE1P153825
DYNC2I1Q8WVS44
ESYT2A0FGR84
NUCLEOLINP193384
VIPR2P415873
PTPRN2Q929323
NCAPG2Q86XI21

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
GALNT17Q6IS2490.68
AUTS2Q8WXX741.89

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 19. Enrichment computed across 9 evidence-associated genes (9 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 9 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Glycosphingolipid transport1158.6×0.050ESYT2
Assembly and Release of Dengue Virus Virions1158.6×0.050NUCLEOLIN
Phase 3 - rapid repolarisation1126.9×0.050KCNE1
Phase 2 - plateau phase184.6×0.056KCNE1
Respiratory syncytial virus (RSV) attachment and entry155.2×0.068NUCLEOLIN
Glucagon-type ligand receptors138.5×0.080VIPR2
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known133.4×0.080AUTS2
Intraflagellar transport122.3×0.101DYNC2I1
O-linked glycosylation of mucins120.5×0.101GALNT17
Condensation of Prophase Chromosomes117.4×0.103NCAPG2
Transcriptional regulation by RUNX1116.3×0.103AUTS2
Cardiac conduction112.1×0.126KCNE1
Muscle contraction18.6×0.158KCNE1
G alpha (s) signalling events18.1×0.158VIPR2
Major pathway of rRNA processing in the nucleolus and cytosol16.9×0.173NUCLEOLIN
Neutrophil degranulation12.6×0.375PTPRN2
RNA Polymerase II Transcription12.5×0.375AUTS2
Gene expression (Transcription)12.0×0.428AUTS2
Generic Transcription Pathway11.7×0.460AUTS2

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 9 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
vestibular nucleus development1936.2×0.023KCNE1
secretory granule organization1374.5×0.023KCNE1
regulation of secretion1312.1×0.023PTPRN2
obsolete endoplasmic reticulum-plasma membrane tethering1312.1×0.023ESYT2
negative regulation of protein targeting to membrane1312.1×0.023KCNE1
negative regulation of delayed rectifier potassium channel activity1312.1×0.023KCNE1
positive regulation of chromosome condensation1234.1×0.023NCAPG2
regulation of potassium ion transport1208.1×0.023KCNE1
cardiac muscle cell contraction1187.2×0.023KCNE1
membrane repolarization during action potential1187.2×0.023KCNE1
membrane repolarization during cardiac muscle cell action potential1187.2×0.023KCNE1
dendrite extension1187.2×0.023AUTS2
membrane repolarization during ventricular cardiac muscle cell action potential1187.2×0.023KCNE1
positive regulation of chromosome separation1187.2×0.023NCAPG2
epithelial cell maturation1170.2×0.023KCNE1
positive regulation of transcription of nucleolar large rRNA by RNA polymerase I1170.2×0.023NUCLEOLIN
insulin secretion involved in cellular response to glucose stimulus1144.0×0.023PTPRN2
positive regulation of chromosome segregation1144.0×0.023NCAPG2
membrane repolarization1144.0×0.023KCNE1
intraciliary retrograde transport1124.8×0.023DYNC2I1
potassium ion export across plasma membrane1117.0×0.023KCNE1
inner cell mass cell proliferation1110.1×0.023NCAPG2
ventricular cardiac muscle cell action potential1110.1×0.023KCNE1
positive regulation of potassium ion transmembrane transport1110.1×0.023KCNE1
chromosome condensation193.6×0.025NCAPG2
regulation of ventricular cardiac muscle cell membrane repolarization193.6×0.025KCNE1
neurotransmitter secretion178.0×0.028PTPRN2
cardiac muscle cell action potential involved in contraction178.0×0.028KCNE1
positive regulation of Rac protein signal transduction172.0×0.030AUTS2
regulation of potassium ion transmembrane transport169.3×0.030KCNE1

Therapeutics

Drugs indicated for this disease

0 approved, 1 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
MethioninePhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Vatiquinone.

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 2 · Phased (≥1): 2 · Undrugged: 7

Druggability breadth: 4 of 9 evidence-associated genes (44%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
KCNE1AMBRISENTAN

Top cohort targets by molecule count

SymbolMoleculesMax phase
KCNE1144
VIPR223
AUTS200
GALNT1700
DYNC2I100
NCAPG200
ESYT200
NUCLEOLIN00
PTPRN200

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
AMBRISENTAN4KCNE1
DULOXETINE4KCNE1
PALONOSETRON4KCNE1
DARUNAVIR4KCNE1
DARIFENACIN4KCNE1
TOLTERODINE4KCNE1
SOLIFENACIN4KCNE1
EVEROLIMUS4KCNE1
RALTEGRAVIR4KCNE1
MARAVIROC4KCNE1
ALVIMOPAN4KCNE1
NEBIVOLOL4KCNE1
SUNITINIB4KCNE1
NELFINAVIR4KCNE1
AVIPTADIL3VIPR2
MK-08932VIPR2

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
KCNE1117Functional:63, Binding:47, ADMET:6, Toxicity:1
VIPR227Functional:14, Binding:13
NUCLEOLIN8Binding:8
ESYT21Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
PTPRN23.1.3.48protein-tyrosine-phosphatase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
KCNE1117

Pharmacogenomics

Cohort genes with a PharmGKB record: 9; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

16 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
AMBRISENTAN4KCNE1
DULOXETINE4KCNE1
PALONOSETRON4KCNE1
DARUNAVIR4KCNE1
DARIFENACIN4KCNE1
TOLTERODINE4KCNE1
SOLIFENACIN4KCNE1
EVEROLIMUS4KCNE1
RALTEGRAVIR4KCNE1
MARAVIROC4KCNE1
ALVIMOPAN4KCNE1
NEBIVOLOL4KCNE1
SUNITINIB4KCNE1
NELFINAVIR4KCNE1
AVIPTADIL3VIPR2
MK-08932VIPR2

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1KCNE1
BPhased (≥1) drug, not yet approved1VIPR2
CDruggable family + PDB, no drug1PTPRN2
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug6AUTS2, GALNT17, DYNC2I1, NCAPG2, ESYT2, NUCLEOLIN

Undrugged target profiles

7 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
AUTS20
GALNT170
DYNC2I10
NCAPG20
ESYT21
NUCLEOLIN8
PTPRN20

Clinical trials & evidence

Clinical trials

Clinical trials: 21.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified9
PHASE25
PHASE13
PHASE1/PHASE22
PHASE31
EARLY_PHASE11

Top trials by phase / activity

NCTPhaseStatusTitle
NCT02903355PHASE3TERMINATEDPhase 3 Clinical Trial: D-methionine to Reduce Noise-Induced Hearing Loss (NIHL)
NCT07304024PHASE1/PHASE2RECRUITINGA Treatment for a Form of Age-Related Central Auditory Processing Disorder Consisting of Clemastine Fumarate Plus Engineered Sound
NCT00808470PHASE2COMPLETEDMicronutrients to Prevent Noise-induced Hearing Loss
NCT02049073PHASE1/PHASE2WITHDRAWNPrevention of Noise-induced Hearing Loss
NCT02257983PHASE2COMPLETEDProtective Effects of EPI-743 on Noise-Induced Hearing Loss
NCT02779192PHASE2UNKNOWNA Phase 2b Study of SPI-1005 to Prevent Acute Noise Induced Hearing Loss
NCT04120116PHASE2COMPLETEDFX-322 in Adults With Stable Sensorineural Hearing Loss
NCT05086276PHASE2COMPLETEDFX-322 in Adults With Acquired Sensorineural Hearing Loss
NCT02259595PHASE1COMPLETEDStudy to Determine the Safety, Tolerability, and Pharmacokinetic Profile of HPN-07 and HPN-07 Plus NAC
NCT04601909PHASE1COMPLETEDFX-322 in Adults With Age-Related Sensorineural Hearing Loss
NCT04629664PHASE1COMPLETEDFX-322 in Adults With Severe Sensorineural Hearing Loss
NCT07472023EARLY_PHASE1ENROLLING_BY_INVITATIONRegenerative Medicine and Stem Cell-Based Interventions for Inner Ear Trauma, Tinnitus, and Sensorineural Hearing Loss
NCT06729632Not specifiedRECRUITINGNon-Invasive System to Deliver Therapeutic Hypothermia for Protection Against Noise-Induced Hearing Loss
NCT07513077Not specifiedRECRUITINGPrevention of Noise-Induced Hearing Loss in Primary Education
NCT07534098Not specifiedNOT_YET_RECRUITINGIntervention for Hearing Health Among Native Americans
NCT01454895Not specifiedCOMPLETEDTest of a Web-based Intervention to Promote Hearing Protector Use
NCT01727492Not specifiedUNKNOWNPrevention of Noise-induced Damage by Use of Antioxidants
NCT02472821Not specifiedCOMPLETEDTest of Hearing Health Education Programs for Farm and Rural Youth
NCT04183361Not specifiedUNKNOWNABR Characteristics and Salivary Cortisone Concentration in Noise-exposed Workers
NCT05511753Not specifiedUNKNOWNThe Effect of Acupuncture on Patients With Noise-induced Hearing Loss
NCT05636488Not specifiedUNKNOWNDetermination of the Effects of Noise Level in the Operating Room

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
METHYLPREDNISOLONE41
ZONISAMIDE41
DISUFENTON SODIUM31
EBSELEN31
VATIQUINONE31
CHEMBL123426801