Autosomal recessive nonsyndromic hearing loss 29

Summary

Autosomal recessive nonsyndromic hearing loss 29 (MONDO:0013537) is a disease caused by CLDN14 (GenCC Definitive), with 2 cohort genes.

At a glance

• Causal gene: CLDN14 (GenCC Definitive)
• Cohort genes: 2
• ClinVar variants: 75

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	autosomal recessive nonsyndromic hearing loss 29
Mondo ID	MONDO:0013537
OMIM	614035
DOID	DOID:0110487
UMLS	C3279660
MedGen	481290
GARD	0022641
Is cancer (heuristic)	no

Also known as: autosomal recessive deafness 29 · autosomal recessive nonsyndromic deafness 29 · autosomal recessive nonsyndromic deafness caused by mutation in CLDN14 · autosomal recessive nonsyndromic deafness type 29 · autosomal recessive nonsyndromic hearing loss 29 · CLDN14 autosomal recessive nonsyndromic deafness · deafness, autosomal recessive 29 · deafness, autosomal recessive type 29 · DFNB29

Data availability: 75 ClinVar variants · 2 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 recessive disease › hearing loss, autosomal recessive › autosomal recessive nonsyndromic hearing loss 29

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 4, 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 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

75 retrieved; paginated sample, class counts are floors:

37 uncertain significance, 15 conflicting classifications of pathogenicity, 8 pathogenic, 6 benign, 3 pathogenic/likely pathogenic, 3 benign/likely benign, 2 likely benign, 1 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
1064997	NM_001146079.2(CLDN14):c.89G>A (p.Trp30Ter)	CLDN14	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
189332	NM_001146079.2(CLDN14):c.167G>A (p.Trp56Ter)	CLDN14	Pathogenic	criteria provided, single submitter
3601010	NM_001146079.2(CLDN14):c.554_556del (p.Cys185_Gln186delinsTer)	CLDN14	Pathogenic	criteria provided, single submitter
3601931	NM_001146079.2(CLDN14):c.167_168del (p.Trp56fs)	CLDN14	Pathogenic	criteria provided, single submitter
3601941	NM_001146079.2(CLDN14):c.285C>A (p.Cys95Ter)	CLDN14	Pathogenic	criteria provided, single submitter
3601952	NM_001146079.2(CLDN14):c.355_361del (p.Ile119fs)	CLDN14	Pathogenic	criteria provided, single submitter
4845581	NM_001146079.2(CLDN14):c.202C>T (p.Arg68Ter)	CLDN14	Pathogenic	criteria provided, single submitter
189331	NM_001146079.2(CLDN14):c.242G>A (p.Arg81His)	CLDN14-AS1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
189333	NM_001146079.2(CLDN14):c.694G>A (p.Gly232Arg)	CLDN14-AS1	Pathogenic/Likely pathogenic	no assertion criteria provided
4850	NM_001146079.2(CLDN14):c.398del (p.Met133fs)	CLDN14-AS1	Pathogenic	no assertion criteria provided
4851	NM_001146079.2(CLDN14):c.254T>A (p.Val85Asp)	CLDN14-AS1	Pathogenic	criteria provided, single submitter
599168	NM_001146079.2(CLDN14):c.191G>A (p.Cys64Tyr)	CLDN14	Likely pathogenic	no assertion criteria provided
196574	NM_001146079.2(CLDN14):c.*10G>C	CLDN14	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
290065	NM_001146079.2(CLDN14):c.321C>T (p.Cys107=)	CLDN14	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
339888	NM_001146079.2(CLDN14):c.522G>A (p.Ser174=)	CLDN14	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
339895	NM_001146079.2(CLDN14):c.-75G>T	CLDN14	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
44085	NM_001146079.2(CLDN14):c.621C>T (p.Thr207=)	CLDN14	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
44089	NM_001146079.2(CLDN14):c.690C>T (p.His230=)	CLDN14	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
896237	NM_001146079.2(CLDN14):c.681G>A (p.Ser227=)	CLDN14	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
898997	NM_001146079.2(CLDN14):c.-5G>A	CLDN14	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
228519	NM_001146079.2(CLDN14):c.488C>T (p.Ala163Val)	CLDN14-AS1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
339889	NM_001146079.2(CLDN14):c.450G>T (p.Pro150=)	CLDN14-AS1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
339893	NM_001146079.2(CLDN14):c.-46G>A	CLDN14-AS1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
4852	NM_001146079.2(CLDN14):c.301G>A (p.Gly101Arg)	CLDN14-AS1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
64487	NM_001146079.2(CLDN14):c.18G>A (p.Val6=)	CLDN14-AS1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
895962	NM_001146079.2(CLDN14):c.*48G>A	CLDN14-AS1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
898996	NM_001146079.2(CLDN14):c.129C>T (p.Ala43=)	CLDN14-AS1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1065076	NM_001146079.2(CLDN14):c.364G>A (p.Gly122Ser)	CLDN14	Uncertain significance	criteria provided, multiple submitters, no conflicts
3065219	NM_001146079.2(CLDN14):c.639_645del (p.Ala215fs)	CLDN14	Uncertain significance	criteria provided, single submitter
339884	NM_001146079.2(CLDN14):c.*107G>A	CLDN14	Uncertain significance	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 4 · Orphanet: 1 · 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.

Gene	Classification	Inheritance	Disease	Records
CLDN14	Definitive	Autosomal recessive	nonsyndromic genetic hearing loss	4

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
CLDN14	Orphanet:90636	Rare autosomal recessive non-syndromic sensorineural deafness type DFNB

Cohort genes → proteins

2 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	2

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
CLDN14	HGNC:2035	ENSG00000159261	O95500	Claudin-14	gencc,clinvar
LNCTSI	HGNC:56660	ENSG00000230479		lncRNA TGF-beta/SMAD3 pathway interacting	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
CLDN14	Claudin-14	Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium-independent cell-adhesion activity.

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.

Family	Genes	Fold	FDR
Other/Unknown	2	1.8×	0.312

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
CLDN14	Other/Unknown	no		PMP22/EMP/MP20/Claudin, Claudin, Claudin_CS
LNCTSI	Other/Unknown	no

Expression context

Cohort genes with no expression data: 0.

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

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	2
unknown	0

Top tissues across cohort

Tissue	Cohort genes
liver	1
male germ line stem cell (sensu Vertebrata) in testis	1
right lobe of liver	1
gastrocnemius	1
muscle of leg	1
skeletal muscle tissue	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
CLDN14	84	tissue_specific	marker	right lobe of liver, liver, male germ line stem cell (sensu Vertebrata) in testis
LNCTSI	115		yes	skeletal muscle tissue, muscle of leg, gastrocnemius

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
CLDN14	772
LNCTSI	0

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
CLDN14	O95500	80.00

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 1. Enrichment computed across 2 evidence-associated genes (1 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 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Tight junction interactions	1	368.4×	0.003	CLDN14

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
calcium-independent cell-cell adhesion	1	802.5×	0.005	CLDN14
bicellular tight junction assembly	1	330.4×	0.006	CLDN14
protein-containing complex assembly	1	113.9×	0.012	CLDN14
cell adhesion	1	37.5×	0.027	CLDN14

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 2

Druggability breadth: 0 of 2 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
CLDN14	0	0
LNCTSI	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; 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):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	2	CLDN14, LNCTSI

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
CLDN14	0	—
LNCTSI	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.