LRTOMT

Chr 11AR

leucine rich transmembrane and O-methyltransferase domain containing

Also known as: CFAP111, DFNB63, LRRC51, LRRC51-TOMT

NCBI Gene: 220074ENSG00000284922UniProt: Q96E66

This locus represents naturally occurring readthrough transcription between the neighboring LRRC51 (leucine-rich repeat containing 51) and TOMT (transmembrane O-methyltransferase) genes on chromosome 11. The readthrough transcript encodes a fusion protein that shares sequence identity with each individual gene product. Multiple reports implicate mutations in this gene in nonsyndromic deafness.[provided by RefSeq, Feb 2021]

Primary Disease Associations & Inheritance

Deafness, autosomal recessive 63MIM #611451
AR
289
ClinVar variants
34
Pathogenic / LP
—
pLI score
0
Active trials
Clinical Summary— LRTOMT
🧬
Gene-Disease Validity (ClinGen)
autosomal recessive nonsyndromic hearing loss 63 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

📋
ClinVar Variants
34 Pathogenic / Likely Pathogenic· 168 VUS of 289 total submissions
Some data sources returned errors (1)

gnomad: Error: Gene not found

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

ClinVar Variant Classifications

289 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic24
Likely Pathogenic10
VUS168
Likely Benign55
Benign15
Conflicting17
24
Pathogenic
10
Likely Pathogenic
168
VUS
55
Likely Benign
15
Benign
17
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
6
3
15
0
24
Likely Pathogenic
4
4
2
0
10
VUS
1
118
42
7
168
Likely Benign
1
9
20
25
55
Benign
0
2
13
0
15
Conflicting
—17
Total121369232289

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

LRTOMT · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Deafness, autosomal recessive 63

MIM #611451

Molecular basis of disorder known

Autosomal recessive
📖
GeneReview available — LRTOMT
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
A novel pathogenic variant in the LRTOMT gene causes autosomal recessive non-syndromic hearing loss in an Iranian family.
Sarmadi A et al.·BMC Med Genet
2020
Identification a novel pathogenic LRTOMT mutation in Mauritanian families with nonsyndromic deafness.
Salame M et al.·Eur Arch Otorhinolaryngol
2023
Analysis of p.Gly12Valfs*2, p.Trp24* and p.Trp77Arg mutations in GJB2 and p.Arg81Gln variant in LRTOMT among non syndromic hearing loss Egyptian patients: implications for genetic diagnosis.
Gibriel AA et al.·Mol Biol Rep
2019Cohort
Novel mutations in LRTOMT associated with moderate progressive hearing loss in autosomal recessive inheritance.
Ichinose A et al.·Ann Otol Rhinol Laryngol
2015Case report
Delineation of Homozygous Variants Associated with Prelingual Sensorineural Hearing Loss in Pakistani Families.
Noman M et al.·Genes (Basel)
2019
Homozygous Missense Variants in FOXI1 and TMPRSS3 Genes Associated with Non-syndromic Deafness in Moroccan Families.
AitRaise I et al.·Biochem Genet
2024
Deep analysis of the LRTOMTc.242G>A variant in non-syndromic hearing loss North African patients and the Berber population: Implications for genetic diagnosis and genealogical studies.
Mosrati MA et al.·Mol Genet Genomic Med
2021Cohort
Molecular aetiology of ski-slope hearing loss and audiological course of cochlear implantees.
Kim Y et al.·Eur Arch Otorhinolaryngol
2022
Epidemiology, etiology, genetic variants in non- syndromic hearing loss in Iran: A systematic review and meta-analysis.
Aliazami F et al.·Int J Pediatr Otorhinolaryngol
2023Meta-analysis
Mutations in eight small DFNB genes are not a frequent cause of non-syndromic hereditary hearing loss in Czech patients.
Marková S et al.·Int J Pediatr Otorhinolaryngol
2016Cohort
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools