LOCUS       NM_001145309            3311 bp    mRNA    linear   PRI 06-AUG-2023
DEFINITION  Homo sapiens leucine rich transmembrane and O-methyltransferase
            domain containing (LRTOMT), transcript variant 5, mRNA.
ACCESSION   NM_001145309
VERSION     NM_001145309.4
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3311)
  AUTHORS   Salame M, Bonnet C, Moctar ECM, Brahim SM, Dedy A, Vetah LA, Veten
            F, Hamed CT, Petit C and Houmeida A.
  TITLE     Identification a novel pathogenic LRTOMT mutation in Mauritanian
            families with nonsyndromic deafness
  JOURNAL   Eur Arch Otorhinolaryngol 280 (9), 4057-4063 (2023)
   PUBMED   36928321
  REMARK    GeneRIF: Identification a novel pathogenic LRTOMT mutation in
            Mauritanian families with nonsyndromic deafness.
REFERENCE   2  (bases 1 to 3311)
  AUTHORS   Mosrati MA, Fadhlaoui-Zid K, Benammar-Elgaaied A, Gibriel AA, Ben
            Said M and Masmoudi S.
  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
  JOURNAL   Mol Genet Genomic Med 9 (10), e1810 (2021)
   PUBMED   34514748
  REMARK    GeneRIF: 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.
REFERENCE   3  (bases 1 to 3311)
  AUTHORS   Sarmadi A, Nasrniya S, Soleimani Farsani M, Narrei S, Nouri Z,
            Sepehrnejad M, Nilforoush MH, Abtahi H and Tabatabaiefar MA.
  TITLE     A novel pathogenic variant in the LRTOMT gene causes autosomal
            recessive non-syndromic hearing loss in an Iranian family
  JOURNAL   BMC Med Genet 21 (1), 127 (2020)
   PUBMED   32517708
  REMARK    GeneRIF: A novel pathogenic variant in the LRTOMT gene causes
            autosomal recessive non-syndromic hearing loss in an Iranian
            family.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3311)
  AUTHORS   Ichinose A, Moteki H, Hattori M, Nishio SY and Usami S.
  TITLE     Novel mutations in LRTOMT associated with moderate progressive
            hearing loss in autosomal recessive inheritance
  JOURNAL   Ann Otol Rhinol Laryngol 124 Suppl 1, 142S-147S (2015)
   PUBMED   25788562
  REMARK    GeneRIF: 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.
REFERENCE   5  (bases 1 to 3311)
  AUTHORS   Charif M, Bounaceur S, Abidi O, Nahili H, Rouba H, Kandil M,
            Boulouiz R and Barakat A.
  TITLE     The c.242G>A mutation in LRTOMT gene is responsible for a high
            prevalence of deafness in the Moroccan population
  JOURNAL   Mol Biol Rep 39 (12), 11011-11016 (2012)
   PUBMED   23053991
  REMARK    GeneRIF: LRTOMT gene is the second cause of congenital hearing
            impairment in Moroccan patients.
REFERENCE   6  (bases 1 to 3311)
  AUTHORS   Du X, Schwander M, Moresco EM, Viviani P, Haller C, Hildebrand MS,
            Pak K, Tarantino L, Roberts A, Richardson H, Koob G, Najmabadi H,
            Ryan AF, Smith RJ, Muller U and Beutler B.
  TITLE     A catechol-O-methyltransferase that is essential for auditory
            function in mice and humans
  JOURNAL   Proc Natl Acad Sci U S A 105 (38), 14609-14614 (2008)
   PUBMED   18794526
  REMARK    GeneRIF: nonsense mutation in the human ortholog of the murine
            Comt2 gene that causes nonsyndromic deafness
REFERENCE   7  (bases 1 to 3311)
  AUTHORS   Kalay E, Caylan R, Kiroglu AF, Yasar T, Collin RW, Heister JG,
            Oostrik J, Cremers CW, Brunner HG, Karaguzel A and Kremer H.
  TITLE     A novel locus for autosomal recessive nonsyndromic hearing
            impairment, DFNB63, maps to chromosome 11q13.2-q13.4
  JOURNAL   J Mol Med (Berl) 85 (4), 397-404 (2007)
   PUBMED   17211611
  REMARK    GeneRIF: The locus associated with ARNSHI
REFERENCE   8  (bases 1 to 3311)
  AUTHORS   Tlili A, Masmoudi S, Dhouib H, Bouaziz S, Rebeh IB, Chouchen J,
            Turki K, Benzina Z, Charfedine I, Drira M and Ayadi H.
  TITLE     Localization of a novel autosomal recessive non-syndromic hearing
            impairment locus DFNB63 to chromosome 11q13.3-q13.4
  JOURNAL   Ann Hum Genet 71 (Pt 2), 271-275 (2007)
   PUBMED   17166180
  REMARK    GeneRIF: Haplotype analysis defined a 5.55 Mb critical region
            between microsatellite markers D11S4136 and D11S4081.
REFERENCE   9  (bases 1 to 3311)
  AUTHORS   Khan SY, Riazuddin S, Tariq M, Anwar S, Shabbir MI, Riazuddin SA,
            Khan SN, Husnain T, Ahmed ZM, Friedman TB and Riazuddin S.
  TITLE     Autosomal recessive nonsyndromic deafness locus DFNB63 at
            chromosome 11q13.2-q13.3
  JOURNAL   Hum Genet 120 (6), 789-793 (2007)
   PUBMED   17066295
  REMARK    GeneRIF: 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.
REFERENCE   10 (bases 1 to 3311)
  AUTHORS   Shearer,A.E., Hildebrand,M.S., Schaefer,A.M. and Smith,R.J.H.
  TITLE     Genetic Hearing Loss Overview
  JOURNAL   (in) Adam MP, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW
            and Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301607
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AP002490.4 and AP000812.4.
            
            On Nov 30, 2019 this sequence version replaced NM_001145309.3.
            
            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].
            
            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.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: EU627069.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2148093
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-36                AP002490.4         170074-170109
            37-120              AP002490.4         177521-177604
            121-257             AP002490.4         178253-178389
            258-463             AP000812.4         382-587
            464-612             AP000812.4         1834-1982
            613-661             AP000812.4         11850-11898
            662-936             AP000812.4         12822-13096
            937-1133            AP000812.4         14809-15005
            1134-3311           AP000812.4         15491-17668
FEATURES             Location/Qualifiers
     source          1..3311
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11q13.4"
     gene            1..3311
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /note="leucine rich transmembrane and O-methyltransferase
                     domain containing"
                     /db_xref="GeneID:220074"
                     /db_xref="HGNC:HGNC:25033"
                     /db_xref="MIM:612414"
     exon            1..36
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /inference="alignment:Splign:2.1.0"
     exon            37..120
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /inference="alignment:Splign:2.1.0"
     exon            121..257
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /inference="alignment:Splign:2.1.0"
     exon            258..463
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /inference="alignment:Splign:2.1.0"
     exon            464..612
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /inference="alignment:Splign:2.1.0"
     CDS             579..1454
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /EC_number="2.1.1.6"
                     /note="isoform LRTOMT2a is encoded by transcript variant
                     5; leucine rich transmembrane and 0-methyltransferase
                     domain containing"
                     /codon_start=1
                     /product="transmembrane O-methyltransferase isoform
                     LRTOMT2a"
                     /protein_id="NP_001138781.1"
                     /db_xref="GeneID:220074"
                     /db_xref="HGNC:HGNC:25033"
                     /db_xref="MIM:612414"
                     /translation="MGTPWRKRKGIAGPGLPDLSCALVLQPRAQVGTMSPAIALAFLP
                     LVVTLLVRYRHYFRLLVRTVLLRSLRDCLSGLRIEERAFSYVLTHALPGDPGHILTTL
                     DHWSSRCEYLSHMGPVKGQILMRLVEEKAPACVLELGTYCGYSTLLIARALPPGGRLL
                     TVERDPRTAAVAEKLIRLAGFDEHMVELIVGSSEDVIPCLRTQYQLSRADLVLLAHRP
                     RCYLRDLQLLEAHALLPAGATVLADHVLFPGAPRFLQYAKSCGRYRCRLHHTGLPDFP
                     AIKDGIAQLTYAGPG"
     exon            613..661
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /inference="alignment:Splign:2.1.0"
     exon            662..936
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /inference="alignment:Splign:2.1.0"
     exon            937..1133
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /inference="alignment:Splign:2.1.0"
     exon            1134..3311
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2104..2109
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /note="hexamer: AATAGA"
     polyA_site      2125
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /note="major polyA site"
     regulatory      2139..2144
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /note="hexamer: ATTAAA"
     regulatory      2143..2148
                     /regulatory_class="polyA_signal_sequence"
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
                     /note="hexamer: AAGAAA"
     polyA_site      2159
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
     polyA_site      2167
                     /gene="LRTOMT"
                     /gene_synonym="CFAP111; DFNB63; LRRC51; LRRC51-TOMT; TOMT"
ORIGIN      
        1 agtgggacgc caagactgga gaggaagcga ctgcggggag tatttccatt ttaaccggaa
       61 acaatccctg aacccacagg aatgaatgcc taatggtgga gtttcagcca tcagtgacag
      121 gctgaaccca gactcccagg gcacctgctt gcacctttga atgatggcct gaactatgaa
      181 caaacgggac tatatgaaca cttcggtaca ggagccccct cttgactact ccttcagaag
      241 catccacgtc attcaagatc tggtaaatga ggagccaagg acaggactac gaccactgaa
      301 gcgttcaaag tcggggaaat cactgaccca gtccctgtgg ctgaataaca atgttctcaa
      361 tgatctgaga gacttcaacc aggtggcttc acagctgttg gagcacccag agaacctggc
      421 ctggatcgac ctgtccttta atgacctgac ttccattgac cctgtcctaa caactttctt
      481 caacctgagt gtcctctatc ttcacggcaa cagcatccag cgcctggggg aggtgaataa
      541 gctggctgtc cttcctcggc tccgtagcct gacactccat gggaacccca tggaggaaga
      601 gaaagggtat agcaggccct ggactccccg acctgtcctg tgctctggtc ctccagccca
      661 gggcccaggt agggaccatg tcccctgcca ttgcattggc cttcctgcca ctggtggtaa
      721 cattgctggt gcggtaccgg cactacttcc gattgctggt gcgcacggtc ttgctgcgaa
      781 gcctccgaga ctgcctgtca gggctgcgga tcgaggagcg ggccttcagc tacgtgctca
      841 cccatgccct gcccggtgac cctggtcaca tcctcaccac cctggaccac tggagcagcc
      901 gctgcgagta cttgagccac atggggcctg tcaaaggtca gatcctgatg cggctggtgg
      961 aggagaaggc ccctgcttgt gtgctggaat tgggaaccta ctgtggatac tctaccctgc
     1021 ttattgcccg agccctgccc cctgggggtc gccttcttac tgtggagcgg gacccacgca
     1081 cggcagcagt ggctgaaaaa ctcatccgcc tggccggctt tgatgagcac atggtggagc
     1141 tcatcgtggg cagctcagag gacgtgatcc cgtgcctacg cacccagtat cagctgagtc
     1201 gggcagacct ggtgctcctg gcacaccggc cacgatgtta cctgagggac ctgcagctgc
     1261 tggaggccca tgccctactg ccagcaggtg ccaccgtgct ggctgaccat gtgctcttcc
     1321 ctggtgcacc ccgcttcttg cagtatgcta agagctgtgg ccgctaccgc tgccgcctcc
     1381 accacactgg ccttccagac ttccctgcca tcaaggatgg aatagctcag ctcacctatg
     1441 ctggaccagg ctgaggtcca ggcccagggg tacttactga tgcccacccc cacccccacc
     1501 caagcaggga cctcaaaatc ccctcccttt cctgtttggg gccttgacac acgctgggct
     1561 cagggctagg gagtctctct tcccacctct gacctctttc agcctctaca ctgacctcaa
     1621 gtgtcaagtt ctatcaggct gcttggtctc actaggcccc ctctttccag agagaaccat
     1681 ggactgacag caagaagcct gagctcccga cccagctctg tcactgattt gctgagtgac
     1741 tccaagggaa tccccacctt gctctgagat ttaatcttct ctcttaacac gaaggaagct
     1801 ggatgggaga gctccagggg cctcccagtt ctcggcctca gaaagcctcc catcctcagc
     1861 ccatgccatt ctgggtggga tcagaggaag tggcaatgag ttagacgccc tgcaggaata
     1921 gctggatgca agctgggcca gagaaaatgg cacagaaccc tggacccagg gccagggatg
     1981 ccctggcctt ccctaactct ggcccaccta gccaattagg tgtggctgat gtcccttgag
     2041 tgccctcttc ctaaagccca aaagaagatg ctggactcct ctgggcccca ccaacaaata
     2101 gggaatagac atgggtggaa aatcactcct ttgtctttat taaagaaact tagaccagac
     2161 ctggcaatca aggggtgagg tactggccag gaaggtggag taggtttcag gccctgggga
     2221 tttcaagtgc agactgatgg cctgggaggg gccaaagaga ccagatcctg gcagcagctg
     2281 aggaggtgcc caagggcact ttcaggcact ggggccatca gctggttctg tgggcagggg
     2341 ttgggggttg ggatgcaggg tagtttgggc tggcctggaa tctccctgag gccaccctgc
     2401 cttgtctacc tagatcatcc actggtcctg atcctgttcg ttgccttcca tgtccacctg
     2461 gagaggaggc tgggtgtggg tggggagggg cctcagccag cctcagcccc agatcctgcc
     2521 cctggctgga tccagggttt ctgtacccct tggccatcaa ctgggtcagg agcaagggtc
     2581 caggaacaga ggccctcccc catacccctt gcctacctca ttgacctctc catcatccgg
     2641 tgactcattg tagtcattca tctcgtccat gtcctgcata tcctcatcat cctctgagtc
     2701 ctcttcacta tcctcatcat cttcatcatc ctcttcttcc tcgtcatcat agtgctggtg
     2761 ggcaggacag agcctgtaag ccctacaggc ctgcatggac cagttcaaga actgacccac
     2821 ttgagcctct ctctagggcc aatgaatgac cccctacccc gacactccct ccttgagtct
     2881 agcaggctgg tgcatgttct gcaggacctt aatgctaggc ccaatgccca ccccttctat
     2941 ctcccctttt aggcttttac ccagatctga gaaccacaac tgctctgggt cagagacagg
     3001 acattcagaa ttagagcaga gcctcggtcc actgcggccc ccacacaggc cccacctgct
     3061 agagccactc acctctgagg ctggcttgcc aataggaacc aggttgttgt ctttctccgc
     3121 gatgctttgg agctgtgggc aaaggcacag aggaacaagg ccagagccca agtagggcag
     3181 gtcaggggca tgggactggc ccattctgcc cagaagacaa cccacacgtg ttggggagaa
     3241 gcttcctccc agttctcagg gagatacaat ccctttcttg tcatctgcca tttatgaact
     3301 tgatccaaat a
//
