Autosomal dominant nonsyndromic hearing loss 65

disease
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Also known as autosomal dominant deafness 65autosomal dominant nonsyndromic deafness 65autosomal dominant nonsyndromic deafness caused by mutation in TBC1D24autosomal dominant nonsyndromic deafness type 65deafness, autosomal dominant 65deafness, autosomal dominant type 65DFNA65TBC1D24 autosomal dominant nonsyndromic deafness

Summary

Autosomal dominant nonsyndromic hearing loss 65 (MONDO:0014470) is a disease caused by TBC1D24 (GenCC Strong), with 5 cohort genes.

At a glance

  • Causal gene: TBC1D24 (GenCC Strong)
  • Cohort genes: 5
  • ClinVar variants: 748

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameautosomal dominant nonsyndromic hearing loss 65
Mondo IDMONDO:0014470
OMIM616044
DOIDDOID:0110586
UMLSC3892048
MedGen856147
GARD0018140
Is cancer (heuristic)no

Also known as: autosomal dominant deafness 65 · autosomal dominant nonsyndromic deafness 65 · autosomal dominant nonsyndromic deafness caused by mutation in TBC1D24 · autosomal dominant nonsyndromic deafness type 65 · deafness, autosomal dominant 65 · deafness, autosomal dominant type 65 · DFNA65 · TBC1D24 autosomal dominant nonsyndromic deafness

Data availability: 748 ClinVar variants · 3 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › autosomal genetic disease › autosomal dominant disease › autosomal dominant nonsyndromic hearing lossautosomal dominant nonsyndromic hearing loss 65

Related subtypes (75): autosomal dominant nonsyndromic hearing loss 1, autosomal dominant nonsyndromic hearing loss 2A, autosomal dominant nonsyndromic hearing loss 4A, autosomal dominant nonsyndromic hearing loss 6, autosomal dominant nonsyndromic hearing loss 5, autosomal dominant nonsyndromic hearing loss 10, autosomal dominant nonsyndromic hearing loss 11, autosomal dominant nonsyndromic hearing loss 9, autosomal dominant nonsyndromic hearing loss 7, autosomal dominant nonsyndromic hearing loss 12, autosomal dominant nonsyndromic hearing loss 3A, autosomal dominant nonsyndromic hearing loss 13, autosomal dominant nonsyndromic hearing loss 15, autosomal dominant nonsyndromic hearing loss 17, autosomal dominant nonsyndromic hearing loss 16, autosomal dominant nonsyndromic hearing loss 20, autosomal dominant nonsyndromic hearing loss 23, autosomal dominant nonsyndromic hearing loss 25, autosomal dominant nonsyndromic hearing loss 18, autosomal dominant nonsyndromic hearing loss 24, autosomal dominant nonsyndromic hearing loss 22, autosomal dominant nonsyndromic hearing loss 30, autosomal dominant nonsyndromic hearing loss 36, autosomal dominant nonsyndromic hearing loss 21, autosomal dominant nonsyndromic hearing loss 44, autosomal dominant nonsyndromic hearing loss 48, autosomal dominant nonsyndromic hearing loss 41, autosomal dominant nonsyndromic hearing loss 49, autosomal dominant nonsyndromic hearing loss 43, autosomal dominant nonsyndromic hearing loss 28, autosomal dominant nonsyndromic hearing loss 31, autosomal dominant nonsyndromic hearing loss 47, autosomal dominant auditory neuropathy 1, autosomal dominant nonsyndromic hearing loss 53, autosomal dominant nonsyndromic hearing loss 27, autosomal dominant nonsyndromic hearing loss 59, autosomal dominant nonsyndromic hearing loss 3B, autosomal dominant nonsyndromic hearing loss 2B, autosomal dominant nonsyndromic hearing loss 50, autosomal dominant nonsyndromic hearing loss 51, autosomal dominant nonsyndromic hearing loss 64, autosomal dominant nonsyndromic hearing loss 33, autosomal dominant nonsyndromic hearing loss 4B, autosomal dominant nonsyndromic hearing loss 56, autosomal dominant nonsyndromic hearing loss 54, autosomal dominant nonsyndromic hearing loss 58, autosomal dominant nonsyndromic hearing loss 67, autosomal dominant nonsyndromic hearing loss 40, autosomal dominant nonsyndromic hearing loss 69, autosomal dominant nonsyndromic hearing loss 68, autosomal dominant nonsyndromic hearing loss 70, autosomal dominant nonsyndromic hearing loss 66, hearing loss, autosomal dominant 74, hearing loss, autosomal dominant 77, hearing loss, autosomal dominant 81, hearing loss, autosomal dominant 82, hearing loss, autosomal dominant 83, hearing loss, autosomal dominant 84, hearing loss, autosomal dominant 80, hearing loss, autosomal dominant 37, hearing loss, autosomal dominant 75, hearing loss, autosomal dominant 76, hearing loss, autosomal dominant 71, hearing loss, autosomal dominant 72, hearing loss, autosomal dominant 73, hearing loss, autosomal dominant 34, with or without inflammation, hearing loss, autosomal dominant 78, hearing loss, autosomal dominant 79, hearing loss, autosomal dominant 85, hearing loss, autosomal dominant 86, hearing loss, autosomal dominant 87, hearing loss, autosomal dominant 88, hearing loss, autosomal dominant 89, hearing loss, autosomal dominant 90, autosomal dominant nonsyndromic hearing loss 91

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

600 retrieved; paginated sample, class counts are floors:

273 uncertain significance, 193 likely benign, 54 conflicting classifications of pathogenicity, 38 pathogenic, 18 benign/likely benign, 11 pathogenic/likely pathogenic, 7 likely pathogenic, 6 benign

ClinVarVariant (HGVS)GeneClassificationReview
3243524NC_000016.9:g.(?2550259)(3154076_?)delFLYWCH1Pathogeniccriteria provided, single submitter
1029242NM_001199107.2(TBC1D24):c.965+2T>CTBC1D24Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1066340NM_001199107.2(TBC1D24):c.115G>C (p.Ala39Pro)TBC1D24Pathogeniccriteria provided, single submitter
1071941NM_001199107.2(TBC1D24):c.642_793del (p.Trp215fs)TBC1D24Pathogeniccriteria provided, multiple submitters, no conflicts
1072207NM_001199107.2(TBC1D24):c.715del (p.Val239fs)TBC1D24Pathogeniccriteria provided, single submitter
133246NM_001199107.2(TBC1D24):c.533C>T (p.Ser178Leu)TBC1D24Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1357131NM_001199107.2(TBC1D24):c.1397del (p.Pro466fs)TBC1D24Pathogeniccriteria provided, single submitter
1369893NM_001199107.2(TBC1D24):c.56del (p.Ile19fs)TBC1D24Pathogeniccriteria provided, single submitter
1378399NM_001199107.2(TBC1D24):c.979A>T (p.Lys327Ter)TBC1D24Pathogeniccriteria provided, single submitter
1397090NM_001199107.2(TBC1D24):c.1540C>T (p.Gln514Ter)TBC1D24Pathogeniccriteria provided, single submitter
1402576NC_000016.9:g.(?2546150)(2550959_?)delTBC1D24Pathogeniccriteria provided, single submitter
1451981NM_001199107.2(TBC1D24):c.1141dup (p.Arg381fs)TBC1D24Pathogeniccriteria provided, single submitter
1453407NM_001199107.2(TBC1D24):c.636G>A (p.Trp212Ter)TBC1D24Pathogeniccriteria provided, single submitter
1456664NM_001199107.2(TBC1D24):c.752del (p.Phe251fs)TBC1D24Pathogeniccriteria provided, multiple submitters, no conflicts
1459471NM_001199107.2(TBC1D24):c.806del (p.Ile269fs)TBC1D24Pathogeniccriteria provided, single submitter
1473155NM_001199107.2(TBC1D24):c.706G>A (p.Gly236Ser)TBC1D24Pathogeniccriteria provided, single submitter
183152NM_001199107.2(TBC1D24):c.119G>T (p.Arg40Leu)TBC1D24Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1966628NM_001199107.2(TBC1D24):c.1505dup (p.Ser503fs)TBC1D24Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1970211NM_001199107.2(TBC1D24):c.668_669delinsAA (p.Cys223Ter)TBC1D24Pathogeniccriteria provided, single submitter
2035641NM_001199107.2(TBC1D24):c.1574del (p.Gly525fs)TBC1D24Pathogeniccriteria provided, single submitter
207499NM_001199107.2(TBC1D24):c.457G>A (p.Glu153Lys)TBC1D24Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
207503NM_001199107.2(TBC1D24):c.680G>T (p.Arg227Leu)TBC1D24Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
207505NM_001199107.2(TBC1D24):c.845C>G (p.Pro282Arg)TBC1D24Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
207507NM_001199107.2(TBC1D24):c.475del (p.Leu159fs)TBC1D24Pathogeniccriteria provided, multiple submitters, no conflicts
2101220NM_001199107.2(TBC1D24):c.1402_1409dup (p.Ser472fs)TBC1D24Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2121170NM_001199107.2(TBC1D24):c.1488del (p.Met497fs)TBC1D24Pathogeniccriteria provided, single submitter
2127078NM_001199107.2(TBC1D24):c.270_286del (p.Pro91fs)TBC1D24Pathogeniccriteria provided, single submitter
2163597NM_001199107.2(TBC1D24):c.132G>A (p.Trp44Ter)TBC1D24Pathogeniccriteria provided, multiple submitters, no conflicts
2938575NM_001199107.2(TBC1D24):c.1078del (p.Arg360fs)TBC1D24Pathogeniccriteria provided, single submitter
2942773NM_001199107.2(TBC1D24):c.309dup (p.Tyr104fs)TBC1D24Pathogeniccriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 21 · Orphanet: 9 · 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
TBC1D24StrongAutosomal dominantautosomal dominant nonsyndromic hearing loss 6521

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
TBC1D24Orphanet:163727Rolandic epilepsy-paroxysmal exercise-induced dystonia-writer’s cramp syndrome
TBC1D24Orphanet:293181Epilepsy of infancy with migrating focal seizures
TBC1D24Orphanet:352582Familial infantile myoclonic epilepsy
TBC1D24Orphanet:352587Focal epilepsy-intellectual disability-cerebro-cerebellar malformation
TBC1D24Orphanet:352596Progressive myoclonic epilepsy with dystonia
TBC1D24Orphanet:79500DOORS syndrome
TBC1D24Orphanet:90635Rare autosomal dominant non-syndromic sensorineural deafness type DFNA
TBC1D24Orphanet:90636Rare autosomal recessive non-syndromic sensorineural deafness type DFNB
CCNFOrphanet:803Amyotrophic lateral sclerosis

Cohort genes → proteins

5 cohort genes, 5 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence5

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
TBC1D24HGNC:29203ENSG00000162065Q9ULP9TBC1 domain family member 24gencc,clinvar
CCNFHGNC:1591ENSG00000162063P41002Cyclin-Fclinvar
MLST8HGNC:24825ENSG00000167965Q9BVC4Target of rapamycin complex subunit LST8clinvar
FLYWCH1HGNC:25404ENSG00000059122Q4VC44FLYWCH-type zinc finger-containing protein 1clinvar
EME2HGNC:27289ENSG00000197774A4GXA9Structure-specific endonuclease subunit EME2clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
TBC1D24TBC1 domain family member 24May act as a GTPase-activating protein for Rab family protein(s).
CCNFCyclin-FSubstrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins.
MLST8Target of rapamycin complex subunit LST8Subunit of both mTORC1 and mTORC2, which regulates cell growth and survival in response to nutrient and hormonal signals. mTORC1 is activated in response to growth factors or amino acids.
FLYWCH1FLYWCH-type zinc finger-containing protein 1Transcription cofactor.
EME2Structure-specific endonuclease subunit EME2Non-catalytic subunit of the structure-specific, heterodimeric DNA endonuclease MUS81-EME2 which is involved in the maintenance of genome stability.

Protein-family classification

Druggable: 0 · Difficult: 2 · Unknown: 3 · 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
Scaffold/PPI13.5×0.608
Transcription factor11.6×0.608
Other/Unknown31.1×0.608

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
TBC1D24Other/UnknownnoRab-GAP-TBC_dom, TLDc_dom, Rab-GAP_TBC_sf
CCNFOther/UnknownnoF-box_dom, Cyclin_C-dom, Cyclin_N
MLST8Scaffold/PPInoWD40_rpt, Quinoprotein_ADH-like_sf, WD40/YVTN_repeat-like_dom_sf
FLYWCH1Transcription factornoZnf_FLYWCH, FLYWCH_N, FWCH1/FWCH2
EME2Other/UnknownnoERCC4_domain, Mms4/EME1/EME2, EME1/EME2_C

Expression context

Cohort genes with no expression data: 0.

5 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)5
unknown0

Top tissues across cohort

TissueCohort genes
cerebellar hemisphere3
right hemisphere of cerebellum3
cerebellar cortex2
Brodmann (1909) area 231
middle temporal gyrus1
parotid gland1
hair follicle1
olfactory bulb1
type B pancreatic cell1
oviduct epithelium1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
TBC1D24227ubiquitousmarkerparotid gland, Brodmann (1909) area 23, middle temporal gyrus
CCNF213ubiquitousmarkertype B pancreatic cell, olfactory bulb, hair follicle
MLST8263ubiquitousmarkerright hemisphere of cerebellum, cerebellar hemisphere, cerebellar cortex
FLYWCH1249ubiquitousmarkerright hemisphere of cerebellum, cerebellar hemisphere, cerebellar cortex
EME2231ubiquitousmarkeroviduct epithelium, right hemisphere of cerebellum, cerebellar hemisphere

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
CCNF6,626
MLST82,702
EME21,255
TBC1D241,016
FLYWCH1826

Structural data

PDB: 4 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
MLST8Q9BVC445
CCNFP410021
FLYWCH1Q4VC441
EME2A4GXA91

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
TBC1D24Q9ULP984.46

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 52. Enrichment computed across 5 evidence-associated genes (4 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 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Dengue virus modulates apoptosis1178.4×0.038MLST8
Regulation of TP53 Expression and Degradation1129.8×0.038MLST8
mTORC1-mediated signalling1119.0×0.038MLST8
Regulation of T cell activation by CD28 family1105.7×0.038MLST8
Constitutive Signaling by AKT1 E17K in Cancer1105.7×0.038MLST8
VEGFR2 mediated vascular permeability1102.0×0.038MLST8
Cellular response to heat stress198.5×0.038MLST8
Energy dependent regulation of mTOR by LKB1-AMPK198.5×0.038MLST8
CD28 dependent PI3K/Akt signaling198.5×0.038MLST8
Co-stimulation by CD28195.2×0.038MLST8
PI3K/AKT Signaling in Cancer192.1×0.038MLST8
Rab regulation of trafficking192.1×0.038TBC1D24
HSF1-dependent transactivation179.3×0.038MLST8
Resolution of D-loop Structures through Holliday Junction Intermediates175.1×0.038EME2
Response of endothelial cells to shear stress175.1×0.038MLST8
Regulation of TP53 Degradation173.2×0.038MLST8
Fanconi Anemia Pathway169.6×0.038EME2
MTOR signalling166.4×0.038MLST8
TBC/RABGAPs164.9×0.038TBC1D24
Cellular responses to mechanical stimuli164.9×0.038MLST8
Adaptive Immune System214.9×0.038CCNF, MLST8
PTEN Regulation157.1×0.041MLST8
Signaling by VEGF154.9×0.041MLST8
Amino acids regulate mTORC1150.1×0.043MLST8
Regulation of PTEN gene transcription144.6×0.046MLST8
Cellular response to starvation141.4×0.047MLST8
High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells140.2×0.047MLST8
Autophagy137.1×0.050MLST8
VEGFA-VEGFR2 Pathway134.8×0.051MLST8
Regulation of TP53 Activity133.2×0.051MLST8

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 5 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
re-entry into mitotic cell cycle11123.5×0.015CCNF
negative regulation of cellular response to oxidative stress1842.6×0.015TBC1D24
positive regulation of pentose-phosphate shunt1842.6×0.015MLST8
negative regulation of centrosome duplication1674.1×0.015CCNF
TORC2 signaling1306.4×0.019MLST8
cellular response to osmotic stress1240.7×0.019MLST8
positive regulation of neuron migration1198.3×0.019TBC1D24
resolution of meiotic recombination intermediates1187.2×0.019EME2
mitotic intra-S DNA damage checkpoint signaling1187.2×0.019EME2
positive regulation of lipid biosynthetic process1177.4×0.019MLST8
positive regulation of dendrite morphogenesis1177.4×0.019TBC1D24
TORC1 signaling1160.5×0.019MLST8
TOR signaling1153.2×0.019MLST8
DNA damage response221.4×0.019MLST8, FLYWCH1
positive regulation of glycolytic process1134.8×0.020MLST8
positive regulation of excitatory postsynaptic potential1105.3×0.021TBC1D24
positive regulation of TOR signaling199.1×0.021MLST8
cellular response to nutrient levels193.6×0.021MLST8
axon development191.1×0.021TBC1D24
placenta development188.7×0.021CCNF
synaptic vesicle endocytosis186.4×0.021TBC1D24
replication fork processing184.3×0.021EME2
dendrite development178.4×0.022TBC1D24
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process174.9×0.022CCNF
positive regulation of actin filament polymerization166.1×0.024MLST8
telomere maintenance153.5×0.028EME2
negative regulation of autophagy151.9×0.028MLST8
double-strand break repair140.6×0.034EME2
G1/S transition of mitotic cell cycle140.1×0.034CCNF
positive regulation of cell growth136.6×0.036MLST8

Therapeutics

Drug target analysis

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

Druggability breadth: 1 of 5 evidence-associated genes (20%) 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
MLST8EVEROLIMUS

Top cohort targets by molecule count

SymbolMoleculesMax phase
MLST8134
TBC1D2400
CCNF00
FLYWCH100
EME200

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
EVEROLIMUS4MLST8
SIROLIMUS4MLST8
DACTOLISIB3MLST8
OMIPALISIB2MLST8
VISTUSERTIB2MLST8
OSI-0272MLST8
SAPANISERTIB2MLST8
ONATASERTIB2MLST8
CC-1152MLST8
PAXALISIB2MLST8
BIMIRALISIB2MLST8
AZD-80551MLST8
RMC-55521MLST8

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

SymbolAssaysType breakdown
MLST8275Binding:275

Cohort genes with high screening signal

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

SymbolChEMBL assays
MLST8275

Pharmacogenomics

Cohort genes with a PharmGKB record: 5; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

13 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)
EVEROLIMUS4MLST8
SIROLIMUS4MLST8
DACTOLISIB3MLST8
OMIPALISIB2MLST8
VISTUSERTIB2MLST8
OSI-0272MLST8
SAPANISERTIB2MLST8
ONATASERTIB2MLST8
CC-1152MLST8
PAXALISIB2MLST8
BIMIRALISIB2MLST8
AZD-80551MLST8
RMC-55521MLST8

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1MLST8
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug4TBC1D24, CCNF, FLYWCH1, EME2

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
TBC1D240
CCNF0
FLYWCH10
EME20

Clinical trials & evidence

Clinical trials

Clinical trials: 0.