Autosomal recessive nonsyndromic hearing loss 63

disease
On this page

Also known as autosomal recessive deafness 63autosomal recessive nonsyndromic deafness 63autosomal recessive nonsyndromic deafness caused by mutation in LRTOMTautosomal recessive nonsyndromic deafness type 63deafness, autosomal recessive 63deafness, autosomal recessive type 63DFNB63LRTOMT autosomal recessive nonsyndromic deafness

Summary

Autosomal recessive nonsyndromic hearing loss 63 (MONDO:0012670) is a disease caused by LRTOMT (GenCC Definitive), with 5 cohort genes.

At a glance

  • Causal gene: LRTOMT (GenCC Definitive)
  • Cohort genes: 5
  • ClinVar variants: 102

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameautosomal recessive nonsyndromic hearing loss 63
Mondo IDMONDO:0012670
MeSHC566951
OMIM611451
DOIDDOID:0110515
UMLSC1969621
MedGen409872
GARD0022627
Is cancer (heuristic)no

Also known as: autosomal recessive deafness 63 · autosomal recessive nonsyndromic deafness 63 · autosomal recessive nonsyndromic deafness caused by mutation in LRTOMT · autosomal recessive nonsyndromic deafness type 63 · autosomal recessive nonsyndromic hearing loss 63 · deafness, autosomal recessive 63 · deafness, autosomal recessive type 63 · DFNB63 · LRTOMT autosomal recessive nonsyndromic deafness

Data availability: 102 ClinVar variants · 4 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 diseasehearing loss, autosomal recessiveautosomal recessive nonsyndromic hearing loss 63

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 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

102 retrieved; paginated sample, class counts are floors:

67 uncertain significance, 12 pathogenic, 10 conflicting classifications of pathogenicity, 9 likely pathogenic, 2 likely benign, 1 pathogenic/likely pathogenic, 1 benign

ClinVarVariant (HGVS)GeneClassificationReview
208717NM_001145308.5(LRTOMT):c.614_617dup (p.Ser207fs)ANAPC15Pathogeniccriteria provided, multiple submitters, no conflicts
3601219NM_001145308.5(LRTOMT):c.426T>A (p.Cys142Ter)ANAPC15Pathogeniccriteria provided, single submitter
3601221NM_001145308.5(LRTOMT):c.555+2T>GANAPC15Pathogeniccriteria provided, single submitter
1687602NM_145309.6(LRRC51):c.340_346del (p.Ile114fs)LRRC51Pathogeniccriteria provided, single submitter
179792NM_001145308.5(LRTOMT):c.358+4A>CLRTOMTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3601216NM_001145308.5(LRTOMT):c.314G>A (p.Trp105Ter)LRTOMTPathogeniccriteria provided, single submitter
3601217NM_001145308.5(LRTOMT):c.315G>A (p.Trp105Ter)LRTOMTPathogeniccriteria provided, single submitter
543NM_001145308.5(LRTOMT):c.242G>A (p.Arg81Gln)LRTOMTPathogeniccriteria provided, multiple submitters, no conflicts
544NM_001145308.5(LRTOMT):c.313T>C (p.Trp105Arg)LRTOMTPathogenicno assertion criteria provided
545NM_001145308.5(LRTOMT):c.328G>A (p.Glu110Lys)LRTOMTPathogenicno assertion criteria provided
1804950NM_001145308.5(LRTOMT):c.199C>T (p.Arg67Ter)TOMTPathogeniccriteria provided, single submitter
3601215NM_001145308.5(LRTOMT):c.307del (p.Asp103fs)TOMTPathogeniccriteria provided, single submitter
546NM_001145308.5(LRTOMT):c.333C>G (p.Tyr111Ter)TOMTPathogenicno assertion criteria provided
430723Multiple allelesLikely pathogenicno assertion criteria provided
1705515NM_001145308.5(LRTOMT):c.566del (p.Ile189fs)ANAPC15Likely pathogeniccriteria provided, single submitter
3601220NM_001145308.5(LRTOMT):c.476T>G (p.Leu159Arg)ANAPC15Likely pathogeniccriteria provided, single submitter
3601222NM_001145308.5(LRTOMT):c.641T>C (p.Leu214Pro)ANAPC15Likely pathogeniccriteria provided, single submitter
3601223NM_001145308.5(LRTOMT):c.849del (p.Gln284fs)ANAPC15Likely pathogeniccriteria provided, single submitter
627450NM_001145308.5(LRTOMT):c.384_385insCTCG (p.Glu129fs)ANAPC15Likely pathogenicno assertion criteria provided
3601218NM_001145308.5(LRTOMT):c.347G>A (p.Gly116Glu)LRTOMTLikely pathogeniccriteria provided, single submitter
632174NM_001145308.5(LRTOMT):c.172C>T (p.Arg58Ter)LRTOMTLikely pathogeniccriteria provided, single submitter
3601214NM_001145308.5(LRTOMT):c.242G>C (p.Arg81Pro)TOMTLikely pathogeniccriteria provided, single submitter
305994NM_001145308.5(LRTOMT):c.503C>T (p.Thr168Met)ANAPC15Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
305996NM_001145308.5(LRTOMT):c.585C>T (p.Asp195=)ANAPC15Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
226718NM_145309.6(LRRC51):c.352G>C (p.Gly118Arg)LRRC51Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
227535NM_001145308.5(LRTOMT):c.397G>C (p.Ala133Pro)LRTOMTConflicting classifications of pathogenicitycriteria provided, conflicting classifications
305986NM_145309.6(LRRC51):c.255C>T (p.Asp85=)LRTOMTConflicting classifications of pathogenicitycriteria provided, conflicting classifications
305991NM_001145308.5(LRTOMT):c.209G>A (p.Arg70Gln)LRTOMTConflicting classifications of pathogenicitycriteria provided, conflicting classifications
44038NM_001145308.5(LRTOMT):c.222A>G (p.Ser74=)LRTOMTConflicting classifications of pathogenicitycriteria provided, conflicting classifications
44039NM_001145308.5(LRTOMT):c.352G>A (p.Val118Ile)LRTOMTConflicting classifications of pathogenicitycriteria provided, conflicting classifications

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · Orphanet: 2 · 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
LRTOMTDefinitiveUnknownautosomal recessive nonsyndromic hearing loss 635

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
LRTOMTOrphanet:90636Rare autosomal recessive non-syndromic sensorineural deafness type DFNB
NUMA1Orphanet:520Acute promyelocytic leukemia

Cohort genes → proteins

5 cohort genes, 4 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence5

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
LRTOMTHGNC:25033ENSG00000284922leucine rich transmembrane and O-methyltransferase domain containinggencc,clinvar
ANAPC15HGNC:24531ENSG00000110200P60006Anaphase-promoting complex subunit 15clinvar
LRRC51HGNC:55526ENSG00000184154Q96E66Leucine-rich repeat-containing protein 51clinvar
TOMTHGNC:55527ENSG00000284844Q8WZ04Transmembrane O-methyltransferaseclinvar
NUMA1HGNC:8059ENSG00000137497Q14980Nuclear mitotic apparatus protein 1clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
ANAPC15Anaphase-promoting complex subunit 15Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle.
TOMTTransmembrane O-methyltransferaseCatalyzes the O-methylation, and thereby the inactivation, of catecholamine neurotransmitters and catechol hormones.
NUMA1Nuclear mitotic apparatus protein 1Microtubule (MT)-binding protein that plays a role in the formation and maintenance of the spindle poles and the alignement and the segregation of chromosomes during mitotic cell division.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 5 · 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/Unknown51.8×0.054

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
LRTOMTOther/Unknownno
ANAPC15Other/UnknownnoANAPC15
LRRC51Other/UnknownnoLeu-rich_rpt, LRR_dom_sf
TOMTOther/UnknownnoSAM_O-MeTrfase, SAM-dependent_MTases_sf
NUMA1Other/UnknownnoNuMA_N_HOOK, NuMA_LGNBD, MT-Golgi_org_protein

Expression context

Cohort genes with no expression data: 0.

3 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)1
broad (>20)4
unknown0

Top tissues across cohort

TissueCohort genes
right testis3
left testis2
right uterine tube2
male germ line stem cell (sensu Vertebrata) in testis1
testis1
apex of heart1
bone marrow cell1
primordial germ cell in gonad1
ventricular zone1
body of uterus1
endocervix1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
LRTOMT130ubiquitousyesmale germ line stem cell (sensu Vertebrata) in testis, right testis, testis
ANAPC15276ubiquitousmarkerapex of heart, right testis, left testis
LRRC51136ubiquitousmarkerright testis, left testis, right uterine tube
TOMT14yesprimordial germ cell in gonad, bone marrow cell, ventricular zone
NUMA1294ubiquitousmarkerright uterine tube, body of uterus, endocervix

Protein interactions among cohort

Intra-cohort edges: 2.

Hub genes (top 10 by interactor count)

SymbolInteractor count
NUMA14,282
TOMT1,448
ANAPC15937
LRRC51720
LRTOMT0

Intra-cohort edges

ABSources
LRRC51LRTOMTbiogrid_interaction
LRTOMTTOMTbiogrid_interaction

Structural data

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

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
ANAPC15P6000618
NUMA1Q149805

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
LRRC51Q96E6691.31
TOMTQ8WZ0490.73

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 46. 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
Enzymatic degradation of dopamine by COMT21903.3×1e-05LRTOMT, LRRC51
Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components1158.6×0.030ANAPC15
Phosphorylation of the APC/C1135.9×0.030ANAPC15
Inactivation of APC/C via direct inhibition of the APC/C complex1129.8×0.030ANAPC15
Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase1129.8×0.030ANAPC15
Aberrant regulation of mitotic exit in cancer due to RB1 defects1129.8×0.030ANAPC15
APC/C:Cdc20 mediated degradation of Cyclin B1114.2×0.030ANAPC15
APC-Cdc20 mediated degradation of Nek2A1105.7×0.030ANAPC15
APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint1105.7×0.030ANAPC15
Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins1102.0×0.030ANAPC15
Aberrant regulation of mitotic cell cycle due to RB1 defects1102.0×0.030ANAPC15
Diseases of mitotic cell cycle198.5×0.030ANAPC15
Mitotic Prophase192.1×0.030NUMA1
APC/C:Cdc20 mediated degradation of mitotic proteins189.2×0.030ANAPC15
APC/C-mediated degradation of cell cycle proteins184.0×0.030ANAPC15
Regulation of mitotic cell cycle184.0×0.030ANAPC15
DNA Replication Pre-Initiation179.3×0.030ANAPC15
Regulation of APC/C activators between G1/S and early anaphase177.2×0.030ANAPC15
Switching of origins to a post-replicative state175.1×0.030ANAPC15
Synthesis of DNA175.1×0.030ANAPC15
Transcriptional Regulation by VENTX166.4×0.033ANAPC15
DNA Replication159.5×0.035ANAPC15
Autodegradation of Cdh1 by Cdh1:APC/C147.6×0.038ANAPC15
APC/C:Cdc20 mediated degradation of Securin147.6×0.038ANAPC15
S Phase145.3×0.038ANAPC15
Cdc20:Phospho-APC/C mediated degradation of Cyclin A143.3×0.038ANAPC15
APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1142.6×0.038ANAPC15
CDK-mediated phosphorylation and removal of Cdc6142.6×0.038ANAPC15
Mitotic Spindle Checkpoint139.6×0.040ANAPC15
Assembly of the pre-replicative complex134.8×0.043ANAPC15

GO biological processes 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.

GO termCohort genesFoldFDRSample cohort genes
anastral spindle assembly15617.3×0.002NUMA1
positive regulation of protein localization to spindle pole body15617.3×0.002NUMA1
positive regulation of mitotic spindle elongation15617.3×0.002NUMA1
catecholamine catabolic process12808.7×0.003TOMT
regulation of metaphase plate congression11123.5×0.004NUMA1
positive regulation of protein localization to cell cortex11123.5×0.004NUMA1
positive regulation of hair follicle development1802.5×0.004NUMA1
regulation of mitotic cell cycle spindle assembly checkpoint1702.2×0.004ANAPC15
positive regulation of spindle assembly1702.2×0.004NUMA1
auditory receptor cell development1624.1×0.004TOMT
positive regulation of intracellular transport1561.7×0.004NUMA1
dopamine catabolic process1561.7×0.004TOMT
positive regulation of chromosome separation1561.7×0.004NUMA1
cell division230.8×0.004ANAPC15, NUMA1
astral microtubule organization1432.1×0.005NUMA1
positive regulation of chromosome segregation1432.1×0.005NUMA1
dopamine metabolic process1330.4×0.006TOMT
regulation of mitotic spindle organization1280.9×0.006NUMA1
protein branched polyubiquitination1280.9×0.006ANAPC15
positive regulation of keratinocyte differentiation1267.5×0.006NUMA1
regulation of meiotic cell cycle1255.3×0.006ANAPC15
anaphase-promoting complex-dependent catabolic process1234.1×0.006ANAPC15
positive regulation of microtubule polymerization1224.7×0.006NUMA1
developmental process1224.7×0.006TOMT
nucleus organization1187.2×0.007NUMA1
microtubule bundle formation1170.2×0.008NUMA1
establishment of mitotic spindle orientation1160.5×0.008NUMA1
positive regulation of BMP signaling pathway1151.8×0.008NUMA1
protein K11-linked ubiquitination1130.6×0.009ANAPC15
meiotic cell cycle181.4×0.014NUMA1

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · 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).

Top cohort targets by molecule count

SymbolMoleculesMax phase
NUMA112
LRTOMT00
ANAPC1500
LRRC5100
TOMT00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
MOLIBRESIB2NUMA1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

SymbolAssaysType breakdown
NUMA18Binding:8

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

1 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)
MOLIBRESIB2NUMA1

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved1NUMA1
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug4LRTOMT, ANAPC15, LRRC51, TOMT

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
LRTOMT0
ANAPC150
LRRC510
TOMT0

Clinical trials & evidence

Clinical trials

Clinical trials: 0.