Otosclerosis

disease
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Also known as otosclerosis (disease)

Summary

Otosclerosis (MONDO:0005349) is a disease (an umbrella term covering 11 Mondo subtypes) caused by SMARCA4 (GenCC Strong), with 2 cohort genes (53 GWAS associations across 6 studies) and 21 clinical trials. Top therapeutic interventions include acetylcysteine and tiludronic acid.

At a glance

  • Causal gene: SMARCA4 (GenCC Strong)
  • Umbrella term: 11 Mondo subtypes
  • Cohort genes: 2
  • GWAS associations: 53
  • Clinical trials: 21

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameotosclerosis
Mondo IDMONDO:0005349
EFOEFO:0004213
MeSHD010040
OMIM166800
Orphanet2794
DOIDDOID:12185
ICD-10-CMH80
ICD-111242649410
NCITC185242
SNOMED CT11543004
UMLSC0029899
MedGen10508
GARD0027719
Is cancer (heuristic)no

Also known as: otosclerosis · otosclerosis (disease)

Data availability: 53 GWAS associations (6 studies) · 1 GenCC gene-disease record · 1 HPO phenotype · 2 cell lines.

Disease family

An umbrella term covering 11 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › auditory system disorderinner ear disorderotosclerosis

Related subtypes (14): bilateral hyperactive labyrinth, labyrinthine bilateral reactive loss, labyrinthitis, labyrinthine unilateral reactive loss, unilateral hyperactive labyrinth, vestibular disorder, cochlear disorder, bilateral hypoactive labyrinth, unilateral hypoactive labyrinth, motion sickness, X-linked mixed hearing loss with perilymphatic gusher, autoimmune inner ear disease, enlarged vestibular aqueduct syndrome, inner ear neoplasm

Subtypes (11): otosclerosis 1, otosclerosis 2, otosclerosis 3, congenital corneal opacities, cornea guttata, and corectopia, otosclerosis 5, otosclerosis 4, otosclerosis 7, otosclerosis 8, otosclerosis 10, otosclerosis 11, otosclerosis 12

Genetics & variants

GWAS landscape

53 GWAS associations across 6 studies. Top hits map to 39 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs772490842e-23LINC00536 - EIF3HG1.31
rs118682071e-22LINC01482C1.34
rs122700544e-20LTBP3T0.75
rs105928363e-18MARK3C1.25
rs719001421e-15LINC02644 - ZNF438G0.82
rs79951582e-15COL4A2, COL4A2-AS2G0.82
rs393753e-14RELNC1.21
rs7919031e-13IP6K3C0.83
rs49173e-12AHSG, HRG-AS1C0.84
rs1818315143e-12HSP90AB3P - SPP1T12.3
rs131924575e-11SUPT3HA1.21
rs46369037e-11IRX5 - MTND5P34T1.28
rs672845501e-10RPS3AP2 - PTX4T1.17
rs116839213e-10ANAPC1G1.17
rs5536529e-10MAML2A1.3
rs731722961e-09LINC02341 - TNFSF11A1.26
rs4851072e-09CLDN23 - MFHAS1G1.16
rs27620492e-09DLEU1C1.16
rs2016940674e-09LYPLAL1-AS1 - ZC3H11BT1.19
rs48770804e-09SEMA4DA0.83
rs60668251e-08PREX1G1.16
rs39141322e-08RELN?1.54
rs664871182e-08DNMT1A1.16
rs21186123e-08SMAD3T0.85
rs81051613e-08TGFB1C0.83
rs44647514e-08CD109T1.14
rs803399794e-08NAMAG1.15
rs60661315e-08EYA2C1.14
rs108062315e-08LINC02542C0.87
rs616844696e-08LINC00326T1.14

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90129575Ramo JT20233,504861,198Genome-wide screen of otosclerosis in population biobanks: 27 loci and shared associations with skeletal structure.
GCST90473490UK Biobank Whole-Genome Sequencing Consortium20251,024457,416Whole-genome sequencing of 490,640 UK Biobank participants.
GCST90481949Verma A2024531450,305Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90436038Zhou W2018310404,888Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST000345Schrauwen I20093020A genome-wide analysis identifies genetic variants in the RELN gene associated with otosclerosis.
GCST90043819Jiang L2021288456,060A generalized linear mixed model association tool for biobank-scale data.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding1
Tier 2: splice/UTR2
Tier 3: regulatory1
Tier 4: intronic/intergenic46

MAF distribution

BucketVariants
common (>=0.05)42
low_freq (0.01-0.05)2
rare (<0.01)6
unknown0

Functional consequences

ConsequenceCount
intron_variant32
intergenic_variant14
regulatory_region_variant1
3_prime_UTR_variant1
missense_variant1
5_prime_UTR_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs772490848116560300A>C,G0.3regulatory_region_variantLINC00536 - EIF3H2e-23Tier 3: regulatory
rs118682071768679579T>C0.23intron_variantLINC014821e-22Tier 4: intronic/intergenic
rs122700541165555077C>T0.22intron_variantLTBP34e-20Tier 4: intronic/intergenic
rs1059283614103471817CAAT>C0.34intron_variantMARK33e-18Tier 4: intronic/intergenic
rs719001421030775254GCTTCTGGCTTAAGC>G,GCTTCTGGCTTAAGCCTTCTGGCTTAAGC0.41intergenic_variantLINC02644 - ZNF4381e-15Tier 4: intronic/intergenic
rs799515813110459370A>G0.453_prime_UTR_variantCOL4A2, COL4A2-AS22e-15Tier 2: splice/UTR
rs393757103837624A>C,T0.41intron_variantRELN3e-14Tier 4: intronic/intergenic
rs791903633734868G>C0.5intron_variantIP6K31e-13Tier 4: intronic/intergenic
rs49173186619924T>A,C0.36missense_variantAHSG, HRG-AS13e-12Tier 1: coding
rs181831514487901594C>T0.002intron_variantHSP90AB3P - SPP13e-12Tier 4: intronic/intergenic
rs13192457644887654C>A,G,T0.44intron_variantSUPT3H5e-11Tier 4: intronic/intergenic
rs46369031654995451C>T0.12intergenic_variantIRX5 - MTND5P347e-11Tier 4: intronic/intergenic
rs67284550161480948C>T0.42intergenic_variantRPS3AP2 - PTX41e-10Tier 4: intronic/intergenic
rs116839212111714056T>A,C,G0.38intergenic_variantANAPC13e-10Tier 4: intronic/intergenic
rs5536521196200151G>A,C,T0.08intron_variantMAML29e-10Tier 4: intronic/intergenic
rs731722961342525753G>A0.11intergenic_variantLINC02341 - TNFSF111e-09Tier 4: intronic/intergenic
rs48510788723898C>G0.47intron_variantCLDN23 - MFHAS12e-09Tier 4: intronic/intergenic
rs27620491350248227G>C0.39intron_variantDLEU12e-09Tier 4: intronic/intergenic
rs2016940671219593024TGA>T0.33intergenic_variantLYPLAL1-AS1 - ZC3H11B4e-09Tier 4: intronic/intergenic
rs4877080989398813T>A,C,G0.28intron_variantSEMA4D4e-09Tier 4: intronic/intergenic
rs60668252048723580A>G,T0.32intron_variantPREX11e-08Tier 4: intronic/intergenic
rs39141327103886922C>A,T0.23intron_variantRELN2e-08Tier 4: intronic/intergenic
rs664871181910142669G>A0.3intron_variantDNMT12e-08Tier 4: intronic/intergenic
rs21186121567108152C>A,T0.21intron_variantSMAD33e-08Tier 4: intronic/intergenic
rs81051611941333726T>C0.16intron_variantTGFB13e-08Tier 4: intronic/intergenic
rs4464751673707844G>C,T0.46intron_variantCD1094e-08Tier 4: intronic/intergenic
rs80339979999889431GA>G0.36intron_variantNAMA4e-08Tier 4: intronic/intergenic
rs60661312046941020T>C,G0.45intron_variantEYA25e-08Tier 4: intronic/intergenic
rs10806231681968979T>C0.39intron_variantLINC025425e-08Tier 4: intronic/intergenic
rs616844696132953615TATCTATAAGTGA>T,TATCTATAAGTGAATCTATAAGTGA0.43intergenic_variantLINC003266e-08Tier 4: intronic/intergenic

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 14 · Orphanet: 6 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
SMARCA4StrongAutosomal dominantotosclerosis14

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SMARCA4Orphanet:1465Coffin-Siris syndrome
SMARCA4Orphanet:231108Rhabdoid tumor predisposition syndrome
SMARCA4Orphanet:370396Small cell carcinoma of the ovary
SMARCA4Orphanet:466962SMARCA4-deficient sarcoma of thorax
RELNOrphanet:101046Epilepsy with auditory features
RELNOrphanet:89844Lissencephaly syndrome, Norman-Roberts type

Cohort genes → proteins

2 cohort genes, 2 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only1
multi_evidence1

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SMARCA4HGNC:11100ENSG00000127616P51532SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4gencc
RELNHGNC:9957ENSG00000189056P78509Reelingwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SMARCA4SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4ATPase involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology).
RELNReelinExtracellular matrix serine protease secreted by pioneer neurons that plays a role in layering of neurons in the cerebral cortex and cerebellum by coordinating cell positioning during neurodevelopment.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 2 · Druggable fraction: 0.0

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
Other/Unknown21.8×0.312

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SMARCA4Other/UnknownnoSNF2_N, Bromodomain, Helicase_C-like
RELNOther/UnknownnoEGF, Reeler_dom, EGF_extracell

Expression context

Cohort genes with no expression data: 0.

2 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)2
unknown0

Top tissues across cohort

TissueCohort genes
cervix squamous epithelium1
cortical plate1
ganglionic eminence1
cerebellar vermis1
cerebellum1
olfactory bulb1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SMARCA4295ubiquitousmarkerganglionic eminence, cortical plate, cervix squamous epithelium
RELN254broadmarkerolfactory bulb, cerebellar vermis, cerebellum

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
SMARCA48,138
RELN2,305

Structural data

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

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
SMARCA4P5153231
RELNP785091

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 33. Enrichment computed across 2 evidence-associated genes (2 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 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Reelin signalling pathway1951.7×0.022RELN
Formation of the non-canonical BAF (ncBAF) complex1335.9×0.022SMARCA4
Formation of the canonical BAF (cBAF) complex1317.2×0.022SMARCA4
Formation of the polybromo-BAF (pBAF) complex1317.2×0.022SMARCA4
Formation of the embryonic stem cell BAF (esBAF) complex1300.5×0.022SMARCA4
Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)1228.4×0.022SMARCA4
EGR2 and SOX10-mediated initiation of Schwann cell myelination1184.2×0.022SMARCA4
Regulation of endogenous retroelements1184.2×0.022SMARCA4
Interleukin-7 signaling1158.6×0.022SMARCA4
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known1150.3×0.022SMARCA4
Regulation of MITF-M-dependent genes involved in pigmentation1132.8×0.023SMARCA4
MITF-M-dependent gene expression190.6×0.028SMARCA4
RMTs methylate histone arginines173.2×0.028SMARCA4
Transcriptional regulation by RUNX1173.2×0.028SMARCA4
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)173.2×0.028SMARCA4
Formation of the beta-catenin:TCF transactivating complex160.1×0.028SMARCA4
Negative Regulation of CDH1 Gene Transcription160.1×0.028SMARCA4
TCF dependent signaling in response to WNT158.9×0.028SMARCA4
Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs)158.9×0.028SMARCA4
MITF-M-regulated melanocyte development157.1×0.028SMARCA4
Signaling by WNT156.0×0.028SMARCA4
Chromatin organization140.8×0.037SMARCA4
Chromatin modifying enzymes136.1×0.038SMARCA4
Epigenetic regulation of gene expression135.7×0.038SMARCA4
Signaling by Interleukins132.1×0.041SMARCA4
Nervous system development121.5×0.058SMARCA4
Cytokine Signaling in Immune system120.4×0.059SMARCA4
RNA Polymerase II Transcription111.3×0.102SMARCA4
Gene expression (Transcription)18.9×0.124SMARCA4
Generic Transcription Pathway17.5×0.141SMARCA4

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
spinal cord patterning18426.0×0.005RELN
positive regulation of lateral motor column neuron migration18426.0×0.005RELN
lateral motor column neuron migration12808.7×0.006RELN
positive regulation of glucose mediated signaling pathway12808.7×0.006SMARCA4
cerebral cortex tangential migration12106.5×0.006RELN
regulation of synaptic activity12106.5×0.006RELN
RNA polymerase I preinitiation complex assembly11685.2×0.006SMARCA4
NMDA glutamate receptor clustering11685.2×0.006RELN
postsynaptic density protein 95 clustering11404.3×0.006RELN
positive regulation of small GTPase mediated signal transduction11053.2×0.006RELN
receptor localization to synapse11053.2×0.006RELN
ventral spinal cord development1936.2×0.006RELN
positive regulation of synapse maturation1936.2×0.006RELN
postsynaptic density assembly1936.2×0.006RELN
radial glial cell differentiation1766.0×0.006RELN
positive regulation of transcription of nucleolar large rRNA by RNA polymerase I1766.0×0.006SMARCA4
interneuron migration1766.0×0.006RELN
regulation of behavior1702.2×0.006RELN
reelin-mediated signaling pathway1601.9×0.006RELN
positive regulation of signal transduction by p53 class mediator1601.9×0.006SMARCA4
layer formation in cerebral cortex1561.7×0.006RELN
neural retina development1468.1×0.006SMARCA4
negative regulation of androgen receptor signaling pathway1468.1×0.006SMARCA4
glial cell differentiation1443.5×0.006RELN
host-mediated activation of viral transcription1443.5×0.006SMARCA4
response to pain1443.5×0.006RELN
positive regulation of dendritic spine morphogenesis1443.5×0.006RELN
nucleosome disassembly1401.2×0.007SMARCA4
protein localization to synapse1383.0×0.007RELN
regulation of neuron differentiation1366.4×0.007RELN

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
Tiludronic AcidPhase 3 (in late-stage trials)

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 1 · Undrugged: 1

Druggability breadth: 1 of 2 evidence-associated genes (50%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
SMARCA422
RELN00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
MOLIBRESIB2SMARCA4
CAMIBIRSTAT2SMARCA4

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

SymbolAssaysType breakdown
SMARCA4230Binding:207, ADMET:12, Functional:11

Cohort genes with high screening signal

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

SymbolChEMBL assays
SMARCA4230

Pharmacogenomics

Cohort genes with a PharmGKB record: 2; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

2 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)
MOLIBRESIB2SMARCA4
CAMIBIRSTAT2SMARCA4

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved1SMARCA4
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug1RELN

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
RELN0

Clinical trials & evidence

Clinical trials

Clinical trials: 21.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified19
PHASE41
PHASE31

Top trials by phase / activity

NCTPhaseStatusTitle
NCT00525551PHASE4COMPLETEDEfficacy of Acetylcysteine in Patients Undergoing Surgery for Otosclerosis
NCT01617057PHASE3TERMINATEDTherapeutic Efficacy of Tiludronic Acid on Inner Ear Involvement in Advanced Otosclerosis
NCT05921578Not specifiedRECRUITINGCone-beam CT in the Diagnosis and Surgical Treatment of Otosclerosis.
NCT07304999Not specifiedNOT_YET_RECRUITINGSurgical and Audiological Outcomes of Endoscopic Stapes Surgery
NCT00222417Not specifiedUNKNOWNAudiometric Parameters in Conductive Hearing Loss and Middle Ear Disease
NCT01855425Not specifiedCOMPLETEDCone Beam CT for Diagnosis of Select Otorhinolaryngology (ENT) Indications at Lower Dose
NCT02019888Not specifiedCOMPLETEDWide Frequency Band Test of Hearing in Veterans
NCT02435446Not specifiedTERMINATEDCone Beam and CT Scan for the Diagnosis of Otosclerosis (TACOS)
NCT02456272Not specifiedCOMPLETEDHearing Aid Versus Surgical Rehabilitation as Treatment of Otosclerosis: Pilot Study
NCT02901093Not specifiedCOMPLETEDQuantification of Prosthesis Penetration With Conebeam in Otosclerosis
NCT03888079Not specifiedCOMPLETEDPatient Satisfaction After Surgery for Otosclerosis Under Local ou General Anesthesia
NCT04908839Not specifiedCOMPLETEDValidation of the French Version of the Stapesplasty Outcome Test 25 (SPOT-25)
NCT05214053Not specifiedTERMINATEDCone Beam vs MDCT for Diagnosis and Pre-operative Evaluation of Otosclerosis
NCT05799404Not specifiedUNKNOWNStapes Footplate Thickness Measured With UHR-CT
NCT05987215Not specifiedUNKNOWNInterest of Using Deep Learning Algorithm for Otosclerosis Detection on Temporal Bone High Resolution CT
NCT06022471Not specifiedUNKNOWNOutcome of Stapes Surgery in Otosclerotic Patients With Tinnitus Using Tinnitogram
NCT06179251Not specifiedUNKNOWNKNOW HOW TO POSITION THE SACCULE AND UTRICULE IN SCANNING
NCT06221007Not specifiedCOMPLETEDLong-Term Results of Bone Cement in Stapes Surgery
NCT06283836Not specifiedCOMPLETEDDexmedetomidine vs. Remifentanil Conscious Sedation for Stapedotomy/Stapedectomy
NCT06323863Not specifiedUNKNOWNUltra-high Resolution CT: the End of Stapes Prosthesis Measurement Misestimation
NCT06618053Not specifiedCOMPLETEDThe Cost-effectiveness of Stapes Surgery for Otosclerosis Performed Under Local Versus General Anesthesia

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
ACETYLCYSTEINE41
TILUDRONIC ACID41