LOCUS       NM_174878               2087 bp    mRNA    linear   PRI 11-OCT-2024
DEFINITION  Homo sapiens clarin 1 (CLRN1), transcript variant 1, mRNA.
ACCESSION   NM_174878 NM_174879
VERSION     NM_174878.3
KEYWORDS    RefSeq; MANE Select.
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 2087)
  AUTHORS   Smirnov,V.M., Nassisi,M., Mohand-Said,S., Bonnet,C., Aubois,A.,
            Devisme,C., Dib,T., Zeitz,C., Loundon,N., Marlin,S., Petit,C.,
            Bodaghi,B., Sahel,J.A. and Audo,I.
  TITLE     Retinal Phenotype of Patients with CLRN1-Associated Usher 3A
            Syndrome in French Light4Deaf Cohort
  JOURNAL   Invest Ophthalmol Vis Sci 63 (4), 25 (2022)
   PUBMED   35481838
  REMARK    GeneRIF: Retinal Phenotype of Patients with CLRN1-Associated Usher
            3A Syndrome in French Light4Deaf Cohort.
REFERENCE   2  (bases 1 to 2087)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   3  (bases 1 to 2087)
  AUTHORS   Abu-Ameerh,M., Mohammad,H., Dardas,Z., Barham,R., Ali,D.,
            Bijawi,M., Tawalbeh,M., Amr,S., Hatmal,M.M., Al-Bdour,M., Awidi,A.
            and Azab,B.
  TITLE     Extending the spectrum of CLRN1- and ABCA4-associated inherited
            retinal dystrophies caused by novel and recurrent variants using
            exome sequencing
  JOURNAL   Mol Genet Genomic Med 8 (3), e1123 (2020)
   PUBMED   31968401
  REMARK    GeneRIF: Extending the spectrum of CLRN1- and ABCA4-associated
            inherited retinal dystrophies caused by novel and recurrent
            variants using exome sequencing.
REFERENCE   4  (bases 1 to 2087)
  AUTHORS   Gopal,S.R., Lee,Y.T., Stepanyan,R., McDermott,B.M. Jr. and
            Alagramam,K.N.
  TITLE     Unconventional secretory pathway activation restores hair cell
            mechanotransduction in an USH3A model
  JOURNAL   Proc Natl Acad Sci U S A 116 (22), 11000-11009 (2019)
   PUBMED   31097578
  REMARK    GeneRIF: Studied role of clarin1 (CLRN1) in activation of hair cell
            mechanotransduction function through an unconventional secretory
            pathway, and the possibility this activation may be therapeutic to
            prevent hair cell dysfunction.
REFERENCE   5  (bases 1 to 2087)
  AUTHORS   Vastinsalo,H., Jalkanen,R., Dinculescu,A., Isosomppi,J., Geller,S.,
            Flannery,J.G., Hauswirth,W.W. and Sankila,E.M.
  TITLE     Alternative splice variants of the USH3A gene Clarin 1 (CLRN1)
  JOURNAL   Eur J Hum Genet 19 (1), 30-35 (2011)
   PUBMED   20717163
  REMARK    GeneRIF: The complexity of the CLRN1 gene and the identification of
            multiple splice variants may partially explain why mutations in
            CLRN1 result in substantial variation in clinical phenotype.
REFERENCE   6  (bases 1 to 2087)
  AUTHORS   Baux,D., Faugere,V., Larrieu,L., Le Guedard-Mereuze,S., Hamroun,D.,
            Beroud,C., Malcolm,S., Claustres,M. and Roux,A.F.
  TITLE     UMD-USHbases: a comprehensive set of databases to record and
            analyse pathogenic mutations and unclassified variants in seven
            Usher syndrome causing genes
  JOURNAL   Hum Mutat 29 (8), E76-E87 (2008)
   PUBMED   18484607
REFERENCE   7  (bases 1 to 2087)
  AUTHORS   Joensuu,T., Hamalainen,R., Lehesjoki,A.E., de la Chapelle,A. and
            Sankila,E.M.
  TITLE     A sequence-ready map of the Usher syndrome type III critical region
            on chromosome 3q
  JOURNAL   Genomics 63 (3), 409-416 (2000)
   PUBMED   10704288
REFERENCE   8  (bases 1 to 2087)
  AUTHORS   Adato,A., Kalinski,H., Weil,D., Chaib,H., Korostishevsky,M. and
            Bonne-Tamir,B.
  TITLE     Possible interaction between USH1B and USH3 gene products as
            implied by apparent digenic deafness inheritance
  JOURNAL   Am J Hum Genet 65 (1), 261-265 (1999)
   PUBMED   10364543
REFERENCE   9  (bases 1 to 2087)
  AUTHORS   Joensuu,T., Blanco,G., Pakarinen,L., Sistonen,P., Kaariainen,H.,
            Brown,S., Chapelle,A. and Sankila,E.M.
  TITLE     Refined mapping of the Usher syndrome type III locus on chromosome
            3, exclusion of candidate genes, and identification of the putative
            mouse homologous region
  JOURNAL   Genomics 38 (3), 255-263 (1996)
   PUBMED   8975700
REFERENCE   10 (bases 1 to 2087)
  AUTHORS   Fahim,A.T., Daiger,S.P. and Weleber,R.G.
  TITLE     Nonsyndromic Retinitis Pigmentosa Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301590
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AF482697.1 and AF495717.1.
            
            On Jun 2, 2019 this sequence version replaced NM_174878.2.
            
            Summary: This gene encodes a protein that contains a cytosolic
            N-terminus, multiple helical transmembrane domains, and an
            endoplasmic reticulum membrane retention signal, TKGH, in the
            C-terminus. The encoded protein may be important in development and
            homeostasis of the inner ear and retina. Mutations within this gene
            have been associated with Usher syndrome type IIIa. Multiple
            transcript variants encoding distinct isoforms have been identified
            for this gene. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) lacks an in-frame exon in the
            3' coding region, compared to variant 5. The resulting isoform (a)
            is shorter than isoform d.
            
            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 :: AF495717.1, AF482697.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2144835, SAMN03267753
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000327047.6/ ENSP00000322280.1
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1020              AF482697.1         274-1293
            1021-1032           AF495717.1         1034-1045
            1033-1346           AF482697.1         1304-1617
            1347-2087           AF495717.1         1360-2100
FEATURES             Location/Qualifiers
     source          1..2087
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3q25.1"
     gene            1..2087
                     /gene="CLRN1"
                     /gene_synonym="RP61; USH3; USH3A"
                     /note="clarin 1"
                     /db_xref="GeneID:7401"
                     /db_xref="HGNC:HGNC:12605"
                     /db_xref="MIM:606397"
     exon            1..272
                     /gene="CLRN1"
                     /gene_synonym="RP61; USH3; USH3A"
                     /inference="alignment:Splign:2.1.0"
     CDS             20..718
                     /gene="CLRN1"
                     /gene_synonym="RP61; USH3; USH3A"
                     /note="isoform a is encoded by transcript variant 1; Usher
                     syndrome type-3 protein"
                     /codon_start=1
                     /product="clarin-1 isoform a"
                     /protein_id="NP_777367.1"
                     /db_xref="CCDS:CCDS3153.1"
                     /db_xref="GeneID:7401"
                     /db_xref="HGNC:HGNC:12605"
                     /db_xref="MIM:606397"
                     /translation="MPSQQKKIIFCMAGVFSFACALGVVTALGTPLWIKATVLCKTGA
                     LLVNASGQELDKFMGEMQYGLFHGEGVRQCGLGARPFRFSFFPDLLKAIPVSIHVNVI
                     LFSAILIVLTMVGTAFFMYNAFGKPFETLHGPLGLYLLSFISGSCGCLVMILFASEVK
                     IHHLSEKIANYKEGTYVYKTQSEKYTTSFWVIFFCFFVHFLNGLLIRLAGFQFPFAKS
                     KDAETTNVAADLMY"
     exon            273..452
                     /gene="CLRN1"
                     /gene_synonym="RP61; USH3; USH3A"
                     /inference="alignment:Splign:2.1.0"
     exon            453..2087
                     /gene="CLRN1"
                     /gene_synonym="RP61; USH3; USH3A"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 acagaagccg tttctcatca tgccaagcca acagaagaaa atcatttttt gcatggccgg
       61 agtgttcagt tttgcatgtg ccctcggagt tgtgacagcc ttggggacac cgttgtggat
      121 caaagccact gtcctctgca aaacgggagc tctgctcgtc aatgcctcag ggcaggagct
      181 ggacaagttt atgggtgaaa tgcagtacgg gcttttccac ggagagggtg tgaggcagtg
      241 tgggttggga gcaaggccct ttcggttctc attttttcca gatttgctca aagcaatccc
      301 agtgagcatc cacgtcaatg tcattctctt ctctgccatc cttattgtgt taaccatggt
      361 ggggacagcc ttcttcatgt acaatgcttt tggaaaacct tttgaaactc tgcatggtcc
      421 cctagggctg taccttttga gcttcatttc aggctcctgt ggctgtcttg tcatgatatt
      481 gtttgcctct gaagtgaaaa tccatcacct ctcagaaaaa attgcaaatt ataaagaagg
      541 gacttatgtc tacaaaacgc aaagtgaaaa atataccacc tcattctggg tcattttctt
      601 ttgctttttt gttcattttc tgaatgggct cctaatacga cttgctggat ttcagttccc
      661 ttttgcaaaa tctaaagacg cagaaacaac taatgtagct gcagatctaa tgtactgaaa
      721 ggcaaacctt tctataattt tacaagggag tagacttgct ttggtcactt ttagatgtgg
      781 ttaattttgc atatcctttt agtctgcata tattaaagca tcaggaccct tcgtgacaat
      841 gtttacaaat tacgtactaa ggatacaggc tggaaagtaa gggaagcaga aggaaggctt
      901 tgaaaagttg ttttatctgg tgggaaattg cttgacccag gtagtcaaag gcagttgact
      961 agaatcgaca aattgttact ccatatatat atatgtgtgt gtgtgtgtgt gtgtgtgtgt
     1021 gtaagatgtc ttcctatcaa aaagatatca aaggcacatg gaatatattt taataaaaac
     1081 aaataatatc tctaatatat ccacacattt gttgccagat ttcagaaaac tgagctgcaa
     1141 tcgctttcct aaaacagtag tgtattaaat gaacatctat aaaatgtatc aacacacatt
     1201 ttaaaaaatt tgtttaaagt atactcttag gccaggcgtg gtgactcaca cctgtaattc
     1261 cagcacttca ggaggccaag gtgggaagat catttgagtt caggagttcg agttacagcc
     1321 tgggcaataa agtgagaccc tgtcactaac aaaattaaaa aataaaataa atataaaata
     1381 taggctttaa aaaagcatag tcttattaac catgtctgtt ggtcaaaatc tgcaaactct
     1441 aaaagaagaa aagaagaaaa aaccaagctt agggtatttt tcctcccgtg cctgagtccc
     1501 aattacattc acgacagtac tttcaatgaa cataattgtt aggaccactg aggaatcatg
     1561 aaaaatgatc tctgcttagt acatttgatg caaaatgact tattaggggc tgtttttcta
     1621 gctatagtgt ctcgagtact aatatgcaat tatgaaaatt atattaaatc tgggattatg
     1681 acggtatcac tgtatcatct tggtcttgtt ctggctgtca ccaagcatga cccaggtcaa
     1741 cttttttttt cccctgaatt acccatcaaa ttgatctgca gctgactaaa ggccacagct
     1801 gagcctggaa ctgacccttc cttcatcctc aacctgctgt cctccagaaa gcaccaagga
     1861 aaaagcagag aatgacagca aacagatcac taggcctctg accacaggtg ctgagtactc
     1921 agcagccctc atataatagg tttgaaagta ctccttaaaa taaaacactg tttccctttg
     1981 gaactattta caaggatgaa acaaccgtat acctgagaaa taacttgctc tggtgtcaat
     2041 tcgctattcg ccagcagaca tcagaacaca ccgagtttcc agatgct
//
