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    LRTOMT leucine rich transmembrane and O-methyltransferase domain containing [ Homo sapiens (human) ]

    Gene ID: 220074, updated on 5-Mar-2024

    Summary

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    Official Symbol
    LRTOMTprovided by HGNC
    Official Full Name
    leucine rich transmembrane and O-methyltransferase domain containingprovided by HGNC
    Primary source
    HGNC:HGNC:25033
    See related
    Ensembl:ENSG00000284922 MIM:612414; AllianceGenome:HGNC:25033
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TOMT; DFNB63; LRRC51; CFAP111; LRRC51-TOMT
    Summary
    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]
    Expression
    Broad expression in testis (RPKM 6.2), thyroid (RPKM 2.2) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    Location:
    11q13.4
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (72080850..72110782)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (72007754..72037672)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (71791896..71821828)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene nuclear mitotic apparatus protein 1 Neighboring gene uncharacterized LOC124902815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:71790999-71791954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:71791955-71792909 Neighboring gene microRNA 3165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5180 Neighboring gene leucine rich repeat containing 51 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3713 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:71814909-71815429 Neighboring gene uncharacterized LOC124902837 Neighboring gene late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:71823011-71823548 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:71823549-71824086 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:71824087-71824624 Neighboring gene anaphase promoting complex subunit 15 Neighboring gene transmembrane O-methyltransferase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:71849877-71850378 Neighboring gene ribulose-5-phosphate-3-epimerase pseudogene 6 Neighboring gene folate receptor gamma

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. 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, 2021 Oct. PMID 34514748, Free PMC Article
    2. 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 Jun 9. PMID 32517708, Free PMC Article
    3. Novel mutations in LRTOMT associated with moderate progressive hearing loss in autosomal recessive inheritance. Ichinose A, et al. Ann Otol Rhinol Laryngol, 2015 May. PMID 25788562
    4. The c.242G>A mutation in LRTOMT gene is responsible for a high prevalence of deafness in the Moroccan population. Charif M, et al. Mol Biol Rep, 2012 Dec. PMID 23053991
    5. A 1 bp deletion in the dual reading frame deafness gene LRTOMT causes a frameshift from the first into the second reading frame. Vanwesemael M, et al. Am J Med Genet A, 2011 Aug. PMID 21739586

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification a novel pathogenic LRTOMT mutation in Mauritanian families with nonsyndromic deafness.
      Title: Identification a novel pathogenic LRTOMT mutation in Mauritanian families with nonsyndromic deafness.
    2. 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.
      Title: 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.
    3. A novel pathogenic variant in the LRTOMT gene causes autosomal recessive non-syndromic hearing loss in an Iranian family.
      Title: A novel pathogenic variant in the LRTOMT gene causes autosomal recessive non-syndromic hearing loss in an Iranian family.
    4. Results indicate that mutations in the LRT)MT gene lead to alterations in the LRTOMT2 protein and might be involved in progressive sensorineural hearing loss.
      Title: Novel mutations in LRTOMT associated with moderate progressive hearing loss in autosomal recessive inheritance.
    5. LRTOMT gene is the second cause of congenital hearing impairment in Moroccan patients.
      Title: The c.242G>A mutation in LRTOMT gene is responsible for a high prevalence of deafness in the Moroccan population.
    6. A 1 bp deletion in the dual reading frame deafness gene LRTOMT causes a frameshift from the first into the second reading frame.
      Title: A 1 bp deletion in the dual reading frame deafness gene LRTOMT causes a frameshift from the first into the second reading frame.
    7. A genome wide linkage analysis of nonsyndromic deafness segregating in a consanguineous Pakistani family (PKDF537) was used to identify DFNB63, a new locus for congenital profound sensorineural hearing loss.
      Title: Autosomal recessive nonsyndromic deafness locus DFNB63 at chromosome 11q13.2-q13.3.
    8. The locus associated with ARNSHI
      Title: A novel locus for autosomal recessive nonsyndromic hearing impairment, DFNB63, maps to chromosome 11q13.2-q13.4.
    9. Haplotype analysis defined a 5.55 Mb critical region between microsatellite markers D11S4136 and D11S4081.
      Title: Localization of a novel autosomal recessive non-syndromic hearing impairment locus DFNB63 to chromosome 11q13.3-q13.4.
    10. nonsense mutation in the human ortholog of the murine Comt2 gene that causes nonsyndromic deafness
      Title: A catechol-O-methyltransferase that is essential for auditory function in mice and humans.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Autosomal recessive nonsyndromic hearing loss 63
    MedGen: C1969621 OMIM: 611451 GeneReviews: Genetic Hearing Loss Overview
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included genes: LRRC51, TOMT

    Homology

    Clone Names

    • FLJ52451

    General protein information

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    Preferred Names
    transmembrane O-methyltransferase
    Names
    leucine rich transmembrane and 0-methyltransferase domain containing
    NP_001138780.1
    NP_001138781.1
    NP_001138782.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_021423.1 RefSeqGene

      Range
      4996..35447
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001145308.5 → NP_001138780.1  transmembrane O-methyltransferase isoform LRTOMT2a

      See identical proteins and their annotated locations for NP_001138780.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) represents the long transcript form. It has multiple differences from variant 1. This variant lacks the upstream open reading frame as seen in the other variants of the long transcript form. The encoded isoform (LRTOMT2a) is a transmembrane catechol-O-methyltransferase. This protein is supported by Western blot as reported in PMID:18953341. Variants 4 and 5 encode the same isoform LRTOMT2a.
      Source sequence(s)
      AK302772, BX115135, EU627069
      Consensus CDS
      CCDS44668.1
      UniProtKB/Swiss-Prot
      B7Z816, Q8WZ04
      Related
      ENSP00000305742.7, ENST00000307198.11
      Conserved Domains (1) summary
      cl17173
      Location:88 → 249
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    2. NM_001145309.4 → NP_001138781.1  transmembrane O-methyltransferase isoform LRTOMT2a

      See identical proteins and their annotated locations for NP_001138781.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5), also known as D', represents the long transcript form. It lacks the 3' terminal exon and includes several alternate exons, compared to variant 1. This variant encodes isoform LRTOMT2a, which is a transmembrane catechol-O-methyltransferase and is supported by Western blot as reported in PMID: 18953341. Variants 4 and 5 encode the same isoform LRTOMT2a.
      Source sequence(s)
      AP000812, AP002490
      UniProtKB/Swiss-Prot
      B7Z816, Q8WZ04
      Conserved Domains (1) summary
      cl17173
      Location:88 → 249
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    3. NM_001145310.4 → NP_001138782.1  transmembrane O-methyltransferase isoform LRTOMT2b

      See identical proteins and their annotated locations for NP_001138782.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6), also known as E', represents the long transcript form. It lacks the 3' terminal exon and includes several alternate exons, compared to variant 1. This variant encodes isoform LRTOMT2b, which lacks an internal segment including the transmembrane region, compared to isoform LRTOMT2a. Isoform LRTOMT2b is a catechol-O-methyltransferase, which is supported by Western blot as reported in PMID: 18953341.
      Source sequence(s)
      AP000812, AP002490
      UniProtKB/Swiss-Prot
      Q8WZ04
      Conserved Domains (1) summary
      cl17173
      Location:48 → 209
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      72080850..72110782
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      72007754..72037672
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_073187.2: Suppressed sequence

      Description
      NR_073187.2: This RefSeq was permanently suppressed because this transcript has been represented by NM_001145309.3.

    2. NR_073188.2: Suppressed sequence

      Description
      NR_073188.2: This RefSeq was permanently suppressed because this transcript has been represented by NM_001145310.3.
    Nucleotide Protein
    Heading Accession and Version

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