Autosomal recessive nonsyndromic hearing loss 79

Summary

Autosomal recessive nonsyndromic hearing loss 79 (MONDO:0013215) is a disease caused by TPRN (GenCC Definitive), with 2 cohort genes.

At a glance

• Causal gene: TPRN (GenCC Definitive)
• Cohort genes: 2
• ClinVar variants: 33

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	autosomal recessive nonsyndromic hearing loss 79
Mondo ID	MONDO:0013215
MeSH	C567651
OMIM	613307
DOID	DOID:0110526
UMLS	C2750082
MedGen	413222
GARD	0022633
Is cancer (heuristic)	no

Also known as: autosomal recessive deafness 79 · autosomal recessive nonsyndromic deafness 79 · autosomal recessive nonsyndromic deafness caused by mutation in TPRN · autosomal recessive nonsyndromic deafness type 79 · autosomal recessive nonsyndromic hearing loss 79 · deafness, autosomal recessive 79 · deafness, autosomal recessive type 79 · DFNB79 · TPRN autosomal recessive nonsyndromic deafness

Data availability: 33 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 recessive disease › hearing loss, autosomal recessive › autosomal recessive nonsyndromic hearing loss 79

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 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

33 retrieved; paginated sample, class counts are floors:

10 pathogenic, 8 uncertain significance, 6 conflicting classifications of pathogenicity, 4 benign, 3 likely pathogenic, 2 pathogenic/likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
627483	NM_001128228.3(TPRN):c.53G>A (p.Trp18Ter)	LOC130003093	Pathogenic	no assertion criteria provided
2627632	NM_001128228.3(TPRN):c.301G>T (p.Glu101Ter)	TMEM203	Pathogenic	criteria provided, single submitter
134	NM_001128228.3(TPRN):c.1239G>A (p.Trp413Ter)	TPRN	Pathogenic/Likely pathogenic	no assertion criteria provided
135	NM_001128228.3(TPRN):c.1427del (p.Pro476fs)	TPRN	Pathogenic	no assertion criteria provided
136	NM_001128228.3(TPRN):c.227_237dup (p.Leu80fs)	TPRN	Pathogenic	no assertion criteria provided
137	NM_001128228.3(TPRN):c.225_235del (p.Gly76fs)	TPRN	Pathogenic	criteria provided, multiple submitters, no conflicts
138	NM_001128228.3(TPRN):c.1530del (p.Thr511fs)	TPRN	Pathogenic	no assertion criteria provided
1806299	NM_001128228.3(TPRN):c.943dup (p.Leu315fs)	TPRN	Pathogenic	criteria provided, multiple submitters, no conflicts
3601942	NM_001128228.3(TPRN):c.650del (p.Gly217fs)	TPRN	Pathogenic	criteria provided, single submitter
3780737	NM_001128228.3(TPRN):c.1031del (p.Pro344fs)	TPRN	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
4687959	NM_001128228.3(TPRN):c.412del (p.Glu138fs)	TPRN	Pathogenic	criteria provided, single submitter
4796608	NM_001128228.3(TPRN):c.1671del (p.Tyr558fs)	TPRN	Pathogenic	criteria provided, single submitter
3069168	NM_001128228.3(TPRN):c.1525_1532del (p.Pro509fs)	TPRN	Likely pathogenic	criteria provided, single submitter
3780738	NM_001128228.3(TPRN):c.503_521del (p.Arg168fs)	TPRN	Likely pathogenic	criteria provided, single submitter
627484	NM_001128228.3(TPRN):c.1159G>T (p.Glu387Ter)	TPRN	Likely pathogenic	no assertion criteria provided
1607222	NM_001128228.3(TPRN):c.1700C>T (p.Thr567Ile)	TPRN	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
165576	NM_001128228.3(TPRN):c.2057C>T (p.Pro686Leu)	TPRN	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
228025	NM_001128228.3(TPRN):c.2023G>A (p.Ala675Thr)	TPRN	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
281979	NM_001128228.3(TPRN):c.655C>A (p.Arg219Ser)	TPRN	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
286302	NM_001128228.3(TPRN):c.1468G>A (p.Val490Met)	TPRN	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
618440	NM_001128228.3(TPRN):c.1094A>G (p.Gln365Arg)	TPRN	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1199833	NM_001128228.3(TPRN):c.1725+5G>A	TPRN	Uncertain significance	criteria provided, multiple submitters, no conflicts
1478433	NM_001128228.3(TPRN):c.770C>T (p.Pro257Leu)	TPRN	Uncertain significance	criteria provided, multiple submitters, no conflicts
288938	NM_001128228.3(TPRN):c.691C>T (p.Arg231Trp)	TPRN	Uncertain significance	criteria provided, multiple submitters, no conflicts
3328333	NM_001128228.3(TPRN):c.1852G>A (p.Glu618Lys)	TPRN	Uncertain significance	criteria provided, multiple submitters, no conflicts
3892703	NM_001128228.3(TPRN):c.1019C>T (p.Ser340Phe)	TPRN	Uncertain significance	criteria provided, single submitter
3892705	NM_001128228.3(TPRN):c.1918G>T (p.Val640Leu)	TPRN	Uncertain significance	criteria provided, single submitter
440352	NM_001128228.3(TPRN):c.1936G>A (p.Glu646Lys)	TPRN	Uncertain significance	criteria provided, multiple submitters, no conflicts
811203	NM_001128228.3(TPRN):c.1696C>T (p.Leu566Phe)	TPRN	Uncertain significance	criteria provided, multiple submitters, no conflicts
165579	NM_001128228.3(TPRN):c.1818GGA[8] (p.Glu621del)	TPRN	Benign	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · 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
TPRN	Definitive	Autosomal recessive	nonsyndromic genetic hearing loss	5

Orphanet rare-disease linkage (cohort genes)

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

Cohort genes → proteins

2 cohort genes, 2 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	2

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
TPRN	HGNC:26894	ENSG00000176058	Q4KMQ1	Taperin	gencc,clinvar
TMEM203	HGNC:28217	ENSG00000187713	Q969S6	Transmembrane protein 203	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
TPRN	Taperin	Essential for hearing.
TMEM203	Transmembrane protein 203	Involved in the regulation of cellular calcium homeotasis.

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)
TPRN	Other/Unknown	no		Phostensin/Taperin_N_dom, Phostensin/Taperin_PP1-bd_dom, PPP1R18/Tprn
TMEM203	Other/Unknown	no		TM_Fragile-X-F-assoc

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)

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

Top tissues across cohort

Tissue	Cohort genes
body of pancreas	1
mucosa of transverse colon	1
right hemisphere of cerebellum	1
apex of heart	1
gastrocnemius	1
heart left ventricle	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
TPRN	197	ubiquitous	marker	mucosa of transverse colon, body of pancreas, right hemisphere of cerebellum
TMEM203	134	ubiquitous	marker	apex of heart, heart left ventricle, gastrocnemius

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
TPRN	894
TMEM203	615

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
TPRN	Q4KMQ1	1

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
TMEM203	Q969S6	84.89

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 2. 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
Sensory processing of sound by outer hair cells of the cochlea	1	203.9×	0.006	TPRN
Sensory processing of sound by inner hair cells of the cochlea	1	163.1×	0.006	TPRN

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 term	Cohort genes	Fold	FDR	Sample cohort genes
stereocilium maintenance	1	2106.5×	0.002	TPRN
auditory receptor cell stereocilium organization	1	421.3×	0.006	TPRN
intracellular calcium ion homeostasis	1	72.6×	0.023	TMEM203
sensory perception of sound	1	50.5×	0.025	TPRN
spermatogenesis	1	17.6×	0.056	TMEM203

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
TPRN	0	0
TMEM203	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

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	TPRN, TMEM203

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)
TPRN	0	—
TMEM203	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.