Autosomal recessive nonsyndromic hearing loss 4

disease
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Also known as autosomal recessive deafness 4 with enlarged vestibular aqueductautosomal recessive nonsyndromic deafness 4autosomal recessive nonsyndromic deafness type 4deafness, autosomal recessive 4, with enlarged vestibular aqueductDFNB4enlarged vestibular aqueductenlarged vestibular aqueduct, digenicneurosensory nonsyndromic recessive deafness 4

Summary

Autosomal recessive nonsyndromic hearing loss 4 (MONDO:0010933) is a disease caused by SLC26A4 (GenCC Definitive), with 5 cohort genes and 2 clinical trials.

At a glance

  • Causal gene: SLC26A4 (GenCC Definitive)
  • Cohort genes: 5
  • ClinVar variants: 857
  • Clinical trials: 2

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameautosomal recessive nonsyndromic hearing loss 4
Mondo IDMONDO:0010933
MeSHC566366
OMIM600791
DOIDDOID:0110498
UMLSC3538946
MedGen761234
GARD0022584
Is cancer (heuristic)no

Also known as: autosomal recessive deafness 4 with enlarged vestibular aqueduct · autosomal recessive nonsyndromic deafness 4 · autosomal recessive nonsyndromic deafness type 4 · deafness, autosomal recessive 4, with enlarged vestibular aqueduct · DFNB4 · enlarged vestibular aqueduct · enlarged vestibular aqueduct, digenic · neurosensory nonsyndromic recessive deafness 4

Data availability: 857 ClinVar variants · 5 GenCC gene-disease records · 1 cell line.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › autosomal genetic disease › autosomal recessive diseasehearing loss, autosomal recessiveautosomal recessive nonsyndromic hearing loss 4

Related subtypes (101): autosomal recessive nonsyndromic hearing loss 5, autosomal recessive nonsyndromic hearing loss 1A, autosomal recessive nonsyndromic hearing loss 2, autosomal recessive nonsyndromic hearing loss 3, autosomal recessive nonsyndromic hearing loss 6, autosomal recessive nonsyndromic hearing loss 7, autosomal recessive nonsyndromic hearing loss 9, autosomal recessive nonsyndromic hearing loss 8, autosomal recessive nonsyndromic hearing loss 12, autosomal recessive nonsyndromic hearing loss 15, autosomal recessive nonsyndromic hearing loss 18A, autosomal recessive nonsyndromic hearing loss 17, autosomal recessive nonsyndromic hearing loss 13, autosomal recessive nonsyndromic hearing loss 21, autosomal recessive nonsyndromic hearing loss 14, autosomal recessive nonsyndromic hearing loss 16, autosomal recessive nonsyndromic hearing loss 20, autosomal recessive nonsyndromic hearing loss 26, autosomal recessive nonsyndromic hearing loss 27, autosomal recessive nonsyndromic hearing loss 22, autosomal recessive nonsyndromic hearing loss 31, autosomal recessive nonsyndromic hearing loss 30, autosomal recessive nonsyndromic hearing loss 33, autosomal recessive nonsyndromic hearing loss 37, autosomal recessive nonsyndromic hearing loss 38, autosomal recessive nonsyndromic hearing loss 40, autosomal recessive nonsyndromic hearing loss 39, autosomal recessive nonsyndromic hearing loss 35, autosomal recessive nonsyndromic hearing loss 32, autosomal recessive nonsyndromic hearing loss 36, autosomal recessive nonsyndromic hearing loss 48, autosomal recessive nonsyndromic hearing loss 23, autosomal recessive nonsyndromic hearing loss 42, autosomal recessive nonsyndromic hearing loss 46, autosomal recessive nonsyndromic hearing loss 53, autosomal recessive nonsyndromic hearing loss 28, autosomal recessive nonsyndromic hearing loss 51, autosomal recessive nonsyndromic hearing loss 47, autosomal recessive nonsyndromic hearing loss 55, autosomal recessive nonsyndromic hearing loss 62, autosomal recessive nonsyndromic hearing loss 49, autosomal recessive nonsyndromic hearing loss 44, autosomal recessive nonsyndromic hearing loss 66, autosomal recessive nonsyndromic hearing loss 59, autosomal recessive nonsyndromic hearing loss 65, autosomal recessive nonsyndromic hearing loss 67, autosomal recessive nonsyndromic hearing loss 68, autosomal recessive nonsyndromic hearing loss 24, autosomal recessive nonsyndromic hearing loss 63, autosomal recessive nonsyndromic hearing loss 45, autosomal recessive nonsyndromic hearing loss 1B, autosomal recessive nonsyndromic hearing loss 71, autosomal recessive nonsyndromic hearing loss 77, autosomal recessive nonsyndromic hearing loss 25, autosomal recessive nonsyndromic hearing loss 79, autosomal recessive nonsyndromic hearing loss 84A, autosomal recessive nonsyndromic hearing loss 85, autosomal recessive nonsyndromic hearing loss 91, autosomal recessive nonsyndromic hearing loss 83, autosomal recessive nonsyndromic hearing loss 74, autosomal recessive nonsyndromic hearing loss 61, autosomal recessive nonsyndromic hearing loss 89, autosomal recessive nonsyndromic hearing loss 29, autosomal recessive nonsyndromic hearing loss 96, autosomal recessive nonsyndromic hearing loss 86, autosomal recessive nonsyndromic hearing loss 98, autosomal recessive nonsyndromic hearing loss 93, autosomal recessive nonsyndromic hearing loss 70, autosomal recessive nonsyndromic hearing loss 84B, autosomal recessive nonsyndromic hearing loss 18B, autosomal recessive nonsyndromic hearing loss 88, autosomal recessive nonsyndromic hearing loss 76, autosomal recessive nonsyndromic hearing loss 101, autosomal recessive nonsyndromic hearing loss 102, autosomal recessive nonsyndromic hearing loss 103, autosomal recessive nonsyndromic hearing loss 104, autosomal recessive nonsyndromic hearing loss 97, hearing loss, autosomal recessive 111, hearing loss, autosomal recessive 118, with cochlear aplasia, hearing loss, autosomal recessive 119, hearing loss, autosomal recessive 117, hearing loss, autosomal recessive 112, hearing loss, autosomal recessive 113, hearing loss, autosomal recessive 100, hearing loss, autosomal recessive 94, hearing loss, autosomal recessive 114, hearing loss, autosomal recessive 115, hearing loss, autosomal recessive 99, hearing loss, autosomal recessive 106, hearing loss, autosomal recessive 107, hearing loss, autosomal recessive 108, hearing loss, autosomal recessive 57, hearing loss, autosomal recessive 109, hearing loss, autosomal recessive 116, hearing loss, autosomal recessive 110, hearing loss, autosomal recessive 120, hearing loss, autosomal recessive 121, hearing loss, autosomal recessive 122, hearing loss, autosomal recessive 123, autosomal recessive nonsyndromic hearing loss 124, hearing loss, autosomal recessive 125

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:

182 uncertain significance, 125 likely pathogenic, 103 pathogenic, 83 conflicting classifications of pathogenicity, 76 pathogenic/likely pathogenic, 13 benign, 9 likely benign, 9 benign/likely benign

ClinVarVariant (HGVS)GeneClassificationReview
424816NM_000441.1(SLC26A4):c.[349C>T];[578C>T]Pathogenicno assertion criteria provided
3775116NM_012188.5(FOXI1):c.748dup (p.Asp250fs)FOXI1Pathogeniccriteria provided, single submitter
1033030NM_000441.2(SLC26A4):c.2184_2187dup (p.Gln730fs)LOC123956210Pathogeniccriteria provided, single submitter
188869NM_000441.2(SLC26A4):c.2127del (p.Phe709fs)LOC123956210Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1929401NM_000441.2(SLC26A4):c.2113C>T (p.Gln705Ter)LOC123956210Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3601760NM_000441.2(SLC26A4):c.2116T>C (p.Cys706Arg)LOC123956210Pathogeniccriteria provided, single submitter
3601761NM_000441.2(SLC26A4):c.2128G>T (p.Asp710Tyr)LOC123956210Pathogeniccriteria provided, single submitter
1033029NM_000441.2(SLC26A4):c.1615-2A>GSLC26A4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1065203NM_000441.2(SLC26A4):c.1786C>T (p.Gln596Ter)SLC26A4Pathogeniccriteria provided, single submitter
1065204NM_000441.2(SLC26A4):c.317C>A (p.Ala106Asp)SLC26A4Pathogeniccriteria provided, multiple submitters, no conflicts
1065207NM_000441.2(SLC26A4):c.387del (p.Phe130fs)SLC26A4Pathogeniccriteria provided, multiple submitters, no conflicts
1065210NM_000441.2(SLC26A4):c.754T>C (p.Ser252Pro)SLC26A4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1065211NM_000441.2(SLC26A4):c.415+2T>CSLC26A4Pathogeniccriteria provided, single submitter
1065212NM_000441.2(SLC26A4):c.1991C>T (p.Ala664Val)SLC26A4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1065213NM_000441.2(SLC26A4):c.1299dup (p.Ala434fs)SLC26A4Pathogenicno assertion criteria provided
1068420NM_000441.2(SLC26A4):c.1803+2T>CSLC26A4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1069712NM_000441.2(SLC26A4):c.1614+1G>TSLC26A4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1070843NM_000441.2(SLC26A4):c.1984dup (p.Cys662fs)SLC26A4Pathogeniccriteria provided, multiple submitters, no conflicts
1073256NM_000441.2(SLC26A4):c.25G>T (p.Glu9Ter)SLC26A4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1073278NM_000441.2(SLC26A4):c.1150-1G>TSLC26A4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1073634NM_000441.2(SLC26A4):c.1343C>A (p.Ser448Ter)SLC26A4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1074192NM_000441.2(SLC26A4):c.2026del (p.Leu676fs)SLC26A4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1075541NM_000441.2(SLC26A4):c.170C>A (p.Ser57Ter)SLC26A4Pathogeniccriteria provided, multiple submitters, no conflicts
1075641NM_000441.2(SLC26A4):c.1150-1G>ASLC26A4Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1185073NM_000441.2(SLC26A4):c.593_600+8delSLC26A4Pathogenicno assertion criteria provided
1185667NM_000441.2(SLC26A4):c.3G>A (p.Met1Ile)SLC26A4Pathogenicno assertion criteria provided
1185668NM_000441.2(SLC26A4):c.79T>C (p.Tyr27His)SLC26A4Pathogenicno assertion criteria provided
1185669NM_000441.2(SLC26A4):c.305-1G>ASLC26A4Pathogenicno assertion criteria provided
1185671NM_000441.2(SLC26A4):c.600+2T>CSLC26A4Pathogenicno assertion criteria provided
1185672NM_000441.2(SLC26A4):c.667_669dup (p.Phe223dup)SLC26A4Pathogenicno assertion criteria provided

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 17 · Orphanet: 12 · 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
SLC26A4DefinitiveAutosomal recessiveautosomal recessive nonsyndromic hearing loss 410
FOXI1LimitedAutosomal recessiveautosomal recessive nonsyndromic hearing loss 47

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
FOXI1Orphanet:402041Autosomal recessive distal renal tubular acidosis
FOXI1Orphanet:705Pendred syndrome
SLC26A4Orphanet:705Pendred syndrome
SLC26A4Orphanet:90636Rare autosomal recessive non-syndromic sensorineural deafness type DFNB
SLC26A4Orphanet:95713Athyreosis
SLC26A4Orphanet:95720Thyroid hypoplasia
TJP2Orphanet:238475Familial hypercholanemia
TJP2Orphanet:480483Progressive familial intrahepatic cholestasis type 4
TJP2Orphanet:90635Rare autosomal dominant non-syndromic sensorineural deafness type DFNA
KCNJ10Orphanet:199343EAST syndrome
KCNJ10Orphanet:705Pendred syndrome
KCNJ10Orphanet:98809Paroxysmal kinesigenic dyskinesia

Cohort genes → proteins

5 cohort genes, 4 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence5

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
FOXI1HGNC:3815ENSG00000168269Q12951Forkhead box protein I1gencc,clinvar
SLC26A4HGNC:8818ENSG00000091137O43511Pendringencc,clinvar
TJP2HGNC:11828ENSG00000119139Q9UDY2Tight junction protein 2clinvar
SLC26A4-AS1HGNC:22385ENSG00000233705SLC26A4 antisense RNA 1clinvar
KCNJ10HGNC:6256ENSG00000177807P78508ATP-sensitive inward rectifier potassium channel 10clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
FOXI1Forkhead box protein I1Transcriptional activator required for the development of normal hearing, sense of balance and kidney function.
SLC26A4PendrinSodium-independent transporter of chloride and iodide.
TJP2Tight junction protein 2Plays a role in tight junctions and adherens junctions.
KCNJ10ATP-sensitive inward rectifier potassium channel 10May be responsible for potassium buffering action of glial cells in the brain.

Protein-family classification

Druggable: 2 · Difficult: 2 · Unknown: 1 · Druggable fraction: 0.4

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 channel122.3×0.157
Transporter115.6×0.157
Scaffold/PPI13.5×0.429
Transcription factor11.6×0.595
Other/Unknown10.4×0.983

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
FOXI1Transcription factornoFork_head_dom, TF_fork_head_CS_1, TF_fork_head_CS_2
SLC26A4TransporteryesSLC26A/SulP_fam, STAS_dom, SLC26A/SulP_dom
TJP2Scaffold/PPInoSH3_domain, PDZ, ZO
SLC26A4-AS1Other/Unknownno
KCNJ10Ion channelyesK_chnl_inward-rec_Kir1.2, K_chnl_inward-rec_Kir_cyto, Ig_E-set

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
right lobe of thyroid gland2
thyroid gland2
adult mammalian kidney1
metanephros cortex1
olfactory segment of nasal mucosa1
palpebral conjunctiva1
corpus callosum1
descending thoracic aorta1
thoracic aorta1
left lobe of thyroid gland1
C1 segment of cervical spinal cord1
globus pallidus1
medial globus pallidus1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
FOXI146tissue_specificmarkermetanephros cortex, adult mammalian kidney, olfactory segment of nasal mucosa
SLC26A4190tissue_specificmarkerpalpebral conjunctiva, right lobe of thyroid gland, thyroid gland
TJP2134ubiquitousmarkercorpus callosum, descending thoracic aorta, thoracic aorta
SLC26A4-AS1164tissue_specificmarkerright lobe of thyroid gland, thyroid gland, left lobe of thyroid gland
KCNJ10185tissue_specificmarkerC1 segment of cervical spinal cord, medial globus pallidus, globus pallidus

Protein interactions among cohort

Intra-cohort edges: 3.

Hub genes (top 10 by interactor count)

SymbolInteractor count
TJP22,916
KCNJ101,862
SLC26A41,648
FOXI11,523
SLC26A4-AS10

Intra-cohort edges

ABSources
FOXI1KCNJ10string_interaction
FOXI1SLC26A4string_interaction
KCNJ10SLC26A4string_interaction

Structural data

PDB: 2 · AlphaFold-only: 2 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
KCNJ10P785084
TJP2Q9UDY22

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
SLC26A4O4351182.72
FOXI1Q1295160.03

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 25. Enrichment computed across 5 evidence-associated genes (3 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 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Defective SLC26A4 causes Pendred syndrome (PDS)13806.7×0.007SLC26A4
Potassium transport channels11268.9×0.010KCNJ10
Inorganic anion exchange by SLC26 transporters1423.0×0.014SLC26A4
G protein gated Potassium channels1380.7×0.014KCNJ10
Apoptotic cleavage of cell adhesion proteins1346.1×0.014TJP2
Inwardly rectifying K+ channels1237.9×0.015KCNJ10
Activation of GABAB receptors1200.3×0.015KCNJ10
Signaling by Hippo1181.3×0.015TJP2
GABA B receptor activation1181.3×0.015KCNJ10
Activation of G protein gated Potassium channels1131.3×0.017KCNJ10
Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits1131.3×0.017KCNJ10
GABA receptor activation1105.7×0.020KCNJ10
SLC transporter disorders168.0×0.028SLC26A4
RHOB GTPase cycle151.4×0.032TJP2
RHOC GTPase cycle148.8×0.032TJP2
Disorders of transmembrane transporters146.4×0.032SLC26A4
Potassium Channels144.8×0.032KCNJ10
R-HSA-425393143.3×0.032SLC26A4
Neurotransmitter receptors and postsynaptic signal transmission133.4×0.039KCNJ10
Transmission across Chemical Synapses125.4×0.047KCNJ10
RHOA GTPase cycle124.9×0.047TJP2
SLC-mediated transmembrane transport119.7×0.057SLC26A4
Neuronal System114.8×0.072KCNJ10
Transport of small molecules18.4×0.119SLC26A4
Disease14.4×0.212SLC26A4

GO biological processes 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.

GO termCohort genesFoldFDRSample cohort genes
glutamate reuptake12106.5×0.010KCNJ10
inorganic anion transport11404.3×0.010SLC26A4
positive regulation of blood-brain barrier permeability1842.6×0.010TJP2
iodide transport1601.9×0.010SLC26A4
regulation of membrane permeability1601.9×0.010TJP2
protein localization to cell-cell junction1468.1×0.010TJP2
homotypic cell-cell adhesion1421.3×0.010TJP2
regulation of pH1351.1×0.010SLC26A4
establishment of endothelial intestinal barrier1351.1×0.010TJP2
regulation of resting membrane potential1324.1×0.010KCNJ10
intestinal absorption1300.9×0.010TJP2
sulfate transmembrane transport1300.9×0.010SLC26A4
cellular response to potassium ion1263.3×0.010KCNJ10
central nervous system myelination1247.8×0.010KCNJ10
regulation of long-term neuronal synaptic plasticity1247.8×0.010KCNJ10
potassium ion homeostasis1191.5×0.011KCNJ10
embryo development ending in birth or egg hatching1183.2×0.011FOXI1
regulation of monoatomic ion transmembrane transport1183.2×0.011KCNJ10
cell-cell junction organization1156.0×0.012TJP2
adult walking behavior1123.9×0.014KCNJ10
maintenance of blood-brain barrier1120.4×0.014TJP2
potassium ion import across plasma membrane191.6×0.018KCNJ10
inner ear morphogenesis175.2×0.021FOXI1
non-motile cilium assembly172.6×0.021KCNJ10
chloride transmembrane transport159.3×0.024SLC26A4
regulation of protein localization151.4×0.027SLC26A4
potassium ion transport147.9×0.028KCNJ10
monoatomic ion transport139.0×0.033SLC26A4
anatomical structure morphogenesis134.8×0.035FOXI1
potassium ion transmembrane transport134.0×0.035KCNJ10

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 5

Druggability breadth: 2 of 5 evidence-associated genes (40%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
FOXI100
SLC26A400
TJP200
SLC26A4-AS100
KCNJ1000

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

SymbolAssaysType breakdown
SLC26A437Binding:37
KCNJ1010Binding:10

Pharmacogenomics

Cohort genes with a PharmGKB record: 4; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

0 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.

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug1KCNJ10
DDruggable family + AlphaFold only, no drug1SLC26A4
EDifficult family or no structure, no drug3FOXI1, TJP2, SLC26A4-AS1

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
FOXI10
SLC26A437
TJP20
SLC26A4-AS10
KCNJ1010

Clinical trials & evidence

Clinical trials

Clinical trials: 2.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified2

Top trials by phase / activity

NCTPhaseStatusTitle
NCT02798783Not specifiedCOMPLETEDEnlarged Vestibular Aqueduct Registry
NCT04934605Not specifiedUNKNOWNGenotype-phenotype Correlation of SLC26A4 in CI Patients With EVA