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Aliases for LRTOMT Gene

Aliases for LRTOMT Gene

  • Leucine Rich Transmembrane And O-Methyltransferase Domain Containing 2 3 5
  • EC 2.1.1.6 4 61
  • LRRC51 3 4
  • Leucine Rich Transmembrane And 0-Methyltransferase Domain Containing 3
  • Leucine-Rich Repeat-Containing Protein 51 3
  • Leucine Rich Repeat Containing 51 2
  • Transmembrane O-Methyltransferase 3
  • Deafness, Autosomal Recessive 63 2
  • Catechol O-Methyltransferase 2 4
  • Protein LRTOMT1 4
  • Protein LRTOMT2 4
  • CFAP111 3
  • DFNB63 3
  • COMT2 4
  • TOMT 4

External Ids for LRTOMT Gene

Previous HGNC Symbols for LRTOMT Gene

  • LRRC51
  • DFNB63

Previous GeneCards Identifiers for LRTOMT Gene

  • GC11P071471
  • GC11P071792
  • GC11P068084

Summaries for LRTOMT Gene

Entrez Gene Summary for LRTOMT Gene

  • This gene includes two transcript forms. The short form has one open reading frame (ORF), which encodes the leucine-rich repeats (LRR)-containing protein of unknown function. This protein is called LRTOMT1 or LRRC51. The long form has two alternative ORFs; the upstream ORF has the same translation start codon as used in the short form and the resulting transcript is a candidate for nonsense-mediated decay, and the downstream ORF encodes a different protein, which is a transmembrane catechol-O-methyltransferase and is called LRTOMT2, TOMT or COMT2. The COMT2 is essential for auditory and vestibular function. Defects in the COMT2 can cause nonsyndromic deafness. Alternatively spliced transcript variants from each transcript form have been found for this gene. [provided by RefSeq, Sep 2012]

GeneCards Summary for LRTOMT Gene

LRTOMT (Leucine Rich Transmembrane And O-Methyltransferase Domain Containing) is a Protein Coding gene. Diseases associated with LRTOMT include Deafness, Autosomal Recessive 63 and Dfnb63 Nonsyndromic Hearing Loss And Deafness. Among its related pathways are noradrenaline and adrenaline degradation. GO annotations related to this gene include O-methyltransferase activity and catechol O-methyltransferase activity. An important paralog of this gene is COMT.

UniProtKB/Swiss-Prot for LRTOMT Gene

  • Catalyzes the O-methylation, and thereby the inactivation, of catecholamine neurotransmitters and catechol hormones (By similarity). Required for auditory function.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRTOMT Gene

Genomics for LRTOMT Gene

Regulatory Elements for LRTOMT Gene

Enhancers for LRTOMT Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G071995 1.5 Ensembl ENCODE dbSUPER 14.7 -81.8 -81821 5.1 PKNOX1 TCF12 GATA2 NCOA1 REST TBX21 ZNF592 MBD2 SMARCA4 MYNN LRTOMT LOC100133315 RNF121 LAMTOR1 ANAPC15 FAM86C1 GC11P072002 IL18BP
GH11G072098 1.4 ENCODE dbSUPER 15.5 +21.5 21479 6.0 HDGF PKNOX1 FOXA2 MLX CREB3L1 ARNT AGO1 ARID4B SIN3A DMAP1 FAM86C1 LRTOMT NUMA1 OR7E128P ENSG00000204971 LAMTOR1
GH11G071942 1.6 Ensembl ENCODE dbSUPER 10.2 -133.8 -133824 7.3 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 YY1 FOS KAT8 MEF2D MIER3 LOC100128494 NUMA1 IL18BP LRTOMT FAM86C1 PIR62264
GH11G072037 1.3 ENCODE dbSUPER 11.8 -39.5 -39482 6.7 HDGF PKNOX1 FOXA2 MLX WRNIP1 ARID4B SIN3A FEZF1 YY1 SLC30A9 LRTOMT NUMA1 FAM86C1 LOC100128494 LAMTOR1 ANAPC15 FOLR3 IL18BP RNF121 PHOX2A
GH11G071991 1.4 FANTOM5 Ensembl ENCODE 10.5 -88.7 -88656 1.3 PKNOX1 MXI1 TBL1XR1 BACH1 BMI1 YY1 ARID3A EED RELB ETV6 FOLR3 LRTOMT NUMA1 RNF121 LOC100133315 PHOX2A OR7E128P IL18BP PIR62264
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LRTOMT on UCSC Golden Path with GeneCards custom track

Promoters for LRTOMT Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000041650 -131 2001 HDGF PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZBTB7B YY1 ZNF766

Genomic Location for LRTOMT Gene

Chromosome:
11
Start:
72,080,331 bp from pter
End:
72,110,782 bp from pter
Size:
30,452 bases
Orientation:
Plus strand

Genomic View for LRTOMT Gene

Genes around LRTOMT on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRTOMT Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRTOMT Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRTOMT Gene

Proteins for LRTOMT Gene

  • Protein details for LRTOMT Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WZ04-TOMT_HUMAN
    Recommended name:
    Transmembrane O-methyltransferase
    Protein Accession:
    Q8WZ04
    Secondary Accessions:
    • B7Z816

    Protein attributes for LRTOMT Gene

    Size:
    291 amino acids
    Molecular mass:
    32155 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • In primates, this protein is produced by a bicistronic gene which also produces the LRRC51 protein from an overlapping reading frame. In rodents, these proteins are produced by 2 separate adjacent genes which together are orthologous to the single primate gene.
    SequenceCaution:
    • Sequence=AAL55772.1; Type=Frameshift; Positions=91; Evidence={ECO:0000305};

    Alternative splice isoforms for LRTOMT Gene

    UniProtKB/Swiss-Prot:
  • Protein details for LRTOMT Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96E66-LRC51_HUMAN
    Recommended name:
    Leucine-rich repeat-containing protein 51
    Protein Accession:
    Q96E66
    Secondary Accessions:
    • B2R7X1
    • B6CZ35
    • B6CZ36
    • B6CZ37
    • B6CZ38
    • B6CZ39
    • B7Z5I4

    Protein attributes for LRTOMT Gene

    Size:
    192 amino acids
    Molecular mass:
    22206 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • In primates, this protein is produced by a bicistronic gene which also produces the TOMT protein from an overlapping reading frame. In rodents, these proteins are produced by 2 separate adjacent genes which together are orthologous to the single primate gene.

    Alternative splice isoforms for LRTOMT Gene

neXtProt entry for LRTOMT Gene

Selected DME Specific Peptides for LRTOMT Gene

Q8WZ04:
  • GATVLADHVLFPGAPRFLQY
  • RDCLSGLRIEERAFSYV
  • YLRDLQLLEAHALLP
  • KGQILMRLVEEKAPACVLELGT
  • RLLTVERD
  • LPDFPAIKDGIAQLTY

Post-translational modifications for LRTOMT Gene

Domains & Families for LRTOMT Gene

Gene Families for LRTOMT Gene

Suggested Antigen Peptide Sequences for LRTOMT Gene

Graphical View of Domain Structure for InterPro Entry

Q8WZ04

UniProtKB/Swiss-Prot:

LRC51_HUMAN :
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. Cation-dependent O-methyltransferase family.
Family:
  • Belongs to the class I-like SAM-binding methyltransferase superfamily. Cation-dependent O-methyltransferase family.
genes like me logo Genes that share domains with LRTOMT: view

Function for LRTOMT Gene

Molecular function for LRTOMT Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol.
UniProtKB/Swiss-Prot Function:
Catalyzes the O-methylation, and thereby the inactivation, of catecholamine neurotransmitters and catechol hormones (By similarity). Required for auditory function.

Enzyme Numbers (IUBMB) for LRTOMT Gene

Gene Ontology (GO) - Molecular Function for LRTOMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008168 methyltransferase activity IEA --
GO:0008171 O-methyltransferase activity IEA --
GO:0016206 catechol O-methyltransferase activity TAS,ISS --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with LRTOMT: view
genes like me logo Genes that share phenotypes with LRTOMT: view

Human Phenotype Ontology for LRTOMT Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for LRTOMT

CRISPR Products

miRNA for LRTOMT Gene

miRTarBase miRNAs that target LRTOMT

Inhibitory RNA Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for LRTOMT Gene

Localization for LRTOMT Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRTOMT Gene

Isoform 1: Membrane; Single-pass membrane protein.
Isoform 2: Cytoplasm.
Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRTOMT gene
Compartment Confidence
plasma membrane 1
extracellular 1
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for LRTOMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005737 cytoplasm IEA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LRTOMT: view

Pathways & Interactions for LRTOMT Gene

genes like me logo Genes that share pathways with LRTOMT: view

Pathways by source for LRTOMT Gene

1 BioSystems pathway for LRTOMT Gene

Interacting Proteins for LRTOMT Gene

Gene Ontology (GO) - Biological Process for LRTOMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006584 catecholamine metabolic process IEA --
GO:0007605 sensory perception of sound ISS 18794526
GO:0032259 methylation IEA --
GO:0042135 neurotransmitter catabolic process IEA --
GO:0042424 catecholamine catabolic process ISS 18794526
genes like me logo Genes that share ontologies with LRTOMT: view

No data available for SIGNOR curated interactions for LRTOMT Gene

Drugs & Compounds for LRTOMT Gene

(4) Drugs for LRTOMT Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guaiacol Approved Pharma 0
S-Adenosylmethionine Approved Nutra 0
Pyrocatechol Experimental Pharma 0
s-adenosylhomocysteine Experimental Pharma 0
genes like me logo Genes that share compounds with LRTOMT: view

Transcripts for LRTOMT Gene

Unigene Clusters for LRTOMT Gene

Leucine rich transmembrane and 0-methyltransferase domain containing:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for LRTOMT Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b ^ 9a · 9b · 9c ^ 10
SP1: - - - -
SP2: - -
SP3: - - - - -
SP4: - - -
SP5:
SP6: -
SP7: - - - - - -
SP8: - - - - - -
SP9: - -
SP10: - - - - - - - - -

Relevant External Links for LRTOMT Gene

GeneLoc Exon Structure for
LRTOMT
ECgene alternative splicing isoforms for
LRTOMT

Expression for LRTOMT Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRTOMT Gene

mRNA differential expression in normal tissues according to GTEx for LRTOMT Gene

This gene is overexpressed in Testis (x7.2).

Protein differential expression in normal tissues from HIPED for LRTOMT Gene

This gene is overexpressed in Fetal Liver (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LRTOMT Gene



Protein tissue co-expression partners for LRTOMT Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LRTOMT Gene:

LRTOMT

SOURCE GeneReport for Unigene cluster for LRTOMT Gene:

Hs.317243

Evidence on tissue expression from TISSUES for LRTOMT Gene

  • Nervous system(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LRTOMT Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
  • inner ear
  • middle ear
  • outer ear
  • skull
General:
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with LRTOMT: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for LRTOMT Gene

Orthologs for LRTOMT Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRTOMT Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRTOMT 34
  • 99.54 (n)
cow
(Bos Taurus)
Mammalia LRTOMT 35
  • 96 (a)
OneToOne
TOMT 34
  • 89.89 (n)
mouse
(Mus musculus)
Mammalia Tomt 34 16 35
  • 86.56 (n)
rat
(Rattus norvegicus)
Mammalia Tomt 34
  • 85.66 (n)
dog
(Canis familiaris)
Mammalia LRTOMT 35
  • 85 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LRTOMT 35
  • 80 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LRTOMT 35
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100490284 34
  • 63.4 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.15885 34
zebrafish
(Danio rerio)
Actinopterygii comtb 35
  • 33 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6621 35
  • 22 (a)
OneToOne
Species where no ortholog for LRTOMT was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LRTOMT Gene

ENSEMBL:
Gene Tree for LRTOMT (if available)
TreeFam:
Gene Tree for LRTOMT (if available)

Paralogs for LRTOMT Gene

Variants for LRTOMT Gene

Sequence variations from dbSNP and Humsavar for LRTOMT Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs137853185 Pathogenic, Deafness, autosomal recessive, 63 (DFNB63) [MIM:611451] 72,106,094(+) GGAGC(A/G)GGCCT downstream-variant-500B, reference, missense
rs137853186 Pathogenic, Deafness, autosomal recessive, 63 (DFNB63) [MIM:611451] 72,106,165(+) ACCAC(C/T)GGAGC downstream-variant-500B, reference, missense
rs137853187 Pathogenic, Deafness, autosomal recessive, 63 (DFNB63) [MIM:611451] 72,106,180(+) GCTGC(A/G)AGTAC downstream-variant-500B, reference, missense
rs61741195 Benign, Deafness, autosomal recessive, 63 (DFNB63) [MIM:611451] 72,108,672(+) GAGTC(A/G/T)GGCAG intron-variant, reference, missense
rs758115449 Deafness, autosomal recessive, 63 (DFNB63) [MIM:611451] 72,108,037(+) GGGTC(A/G)CCTTC intron-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for LRTOMT Gene

Variant ID Type Subtype PubMed ID
nsv384 CNV insertion 18451855
nsv428262 CNV gain+loss 18775914
nsv825989 CNV loss 20364138

Variation tolerance for LRTOMT Gene

Gene Damage Index Score: 1.98; 36.54% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LRTOMT Gene

Human Gene Mutation Database (HGMD)
LRTOMT
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRTOMT

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRTOMT Gene

Disorders for LRTOMT Gene

MalaCards: The human disease database

(8) MalaCards diseases for LRTOMT Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
deafness, autosomal recessive 63
  • autosomal recessive nonsyndromic deafness 63
dfnb63 nonsyndromic hearing loss and deafness
  • dfnb 63 nonsyndromic hearing loss and deafness
autosomal recessive non-syndromic sensorineural deafness type dfnb
  • autosomal recessive isolated neurosensory deafness type dfnb
autosomal recessive nonsyndromic deafness
deafness, autosomal recessive
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

LRC51_HUMAN
  • Deafness, autosomal recessive, 63 (DFNB63) [MIM:611451]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269 PubMed:18794526, ECO:0000269 PubMed:18953341}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for LRTOMT

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LRTOMT
genes like me logo Genes that share disorders with LRTOMT: view

No data available for Genatlas for LRTOMT Gene

Publications for LRTOMT Gene

  1. A catechol-O-methyltransferase that is essential for auditory function in mice and humans. (PMID: 18794526) Du X. … Beutler B. (Proc. Natl. Acad. Sci. U.S.A. 2008) 2 3 4 64
  2. Mutations of LRTOMT, a fusion gene with alternative reading frames, cause nonsyndromic deafness in humans. (PMID: 18953341) Ahmed Z.M. … Kremer H. (Nat. Genet. 2008) 2 3 4 64
  3. Novel mutations in LRTOMT associated with moderate progressive hearing loss in autosomal recessive inheritance. (PMID: 25788562) Ichinose A. … Usami S. (Ann. Otol. Rhinol. Laryngol. 2015) 3 64
  4. The c.242G>A mutation in LRTOMT gene is responsible for a high prevalence of deafness in the Moroccan population. (PMID: 23053991) Charif M. … Barakat A. (Mol. Biol. Rep. 2012) 3 64
  5. A 1 bp deletion in the dual reading frame deafness gene LRTOMT causes a frameshift from the first into the second reading frame. (PMID: 21739586) Vanwesemael M. … Van Camp G. (Am. J. Med. Genet. A 2011) 3 64

Products for LRTOMT Gene

Sources for LRTOMT Gene

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