LOCUS       NM_017882               2228 bp    mRNA    linear   PRI 08-OCT-2024
DEFINITION  Homo sapiens CLN6 transmembrane ER protein (CLN6), transcript
            variant 1, mRNA.
ACCESSION   NM_017882
VERSION     NM_017882.3
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 2228)
  AUTHORS   Ilyas,M., Tariq,F., Ishaq,R., Habiba,U., Bibi,F., Khan,S.N.,
            Ali,Y., Haider,S., Efthymiou,S., Abdullah,U., Raja,G.K. and
            Shaiq,P.A.
  TITLE     Whole exome sequencing identifies variable expressivity of CLN6
            variants in Progressive myoclonic epilepsy affected families
  JOURNAL   Epilepsy Res 201, 107283 (2024)
   PUBMED   38382230
  REMARK    GeneRIF: Whole exome sequencing identifies variable expressivity of
            CLN6 variants in Progressive myoclonic epilepsy affected families.
REFERENCE   2  (bases 1 to 2228)
  AUTHORS   Badilla-Porras,R., Echeverri-McCandless,A., Weimer,J.M.,
            Ulate-Campos,A., Soto-Rodriguez,A., Gutierrez-Mata,A.,
            Hernandez-Con,L., Bogantes-Ledezma,S., Balmaceda-Meza,A.,
            Brudvig,J. and Sanabria-Castro,A.
  TITLE     Neuronal Ceroid Lipofuscinosis Type 6 (CLN6) clinical findings and
            molecular diagnosis: Costa Rica's experience
  JOURNAL   Orphanet J Rare Dis 17 (1), 13 (2022)
   PUBMED   35012600
  REMARK    GeneRIF: Neuronal Ceroid Lipofuscinosis Type 6 (CLN6) clinical
            findings and molecular diagnosis: Costa Rica's experience.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2228)
  AUTHORS   Onodera,M., Tsujimoto,S., Doi,S., Yamashita,A., Yamazaki,T.,
            Makifuchi,T. and Inazu,T.
  TITLE     p.Asn77Lys homozygous CLN6 mutation in two unrelated Japanese
            patients with Kufs disease, an adult onset neuronal ceroid
            lipofuscinosis
  JOURNAL   Clin Chim Acta 523, 191-195 (2021)
   PUBMED   34597687
  REMARK    GeneRIF: p.Asn77Lys homozygous CLN6 mutation in two unrelated
            Japanese patients with Kufs disease, an adult onset neuronal ceroid
            lipofuscinosis.
REFERENCE   4  (bases 1 to 2228)
  AUTHORS   Shiro,Y., Yamashita,A., Watanabe,K. and Yamazaki,T.
  TITLE     CLN6's luminal tail-mediated functional interference between CLN6
            mutants as a novel pathomechanism for the neuronal ceroid
            lipofuscinoses
  JOURNAL   Biomed Res 42 (4), 129-138 (2021)
   PUBMED   34380921
  REMARK    GeneRIF: CLN6's luminal tail-mediated functional interference
            between CLN6 mutants as a novel pathomechanism for the neuronal
            ceroid lipofuscinoses.
REFERENCE   5  (bases 1 to 2228)
  AUTHORS   Wheeler,R.B., Sharp,J.D., Schultz,R.A., Joslin,J.M., Williams,R.E.
            and Mole,S.E.
  TITLE     The gene mutated in variant late-infantile neuronal ceroid
            lipofuscinosis (CLN6) and in nclf mutant mice encodes a novel
            predicted transmembrane protein
  JOURNAL   Am J Hum Genet 70 (2), 537-542 (2002)
   PUBMED   11727201
  REMARK    GeneRIF: gene mutated in variant late-infantile neuronal ceroid
            lipofuscinosis (CLN6) and in nclf mutant mice encodes a novel
            predicted transmembrane protein
REFERENCE   6  (bases 1 to 2228)
  AUTHORS   Holopainen,J.M., Saarikoski,J., Kinnunen,P.K. and Jarvela,I.
  TITLE     Elevated lysosomal pH in neuronal ceroid lipofuscinoses (NCLs)
  JOURNAL   Eur J Biochem 268 (22), 5851-5856 (2001)
   PUBMED   11722572
REFERENCE   7  (bases 1 to 2228)
  AUTHORS   Dawson,G. and Cho,S.
  TITLE     Batten's disease: clues to neuronal protein catabolism in lysosomes
  JOURNAL   J Neurosci Res 60 (2), 133-140 (2000)
   PUBMED   10740217
  REMARK    Review article
REFERENCE   8  (bases 1 to 2228)
  AUTHORS   Sharp,J.D., Wheeler,R.B., Lake,B.D., Savukoski,M., Jarvela,I.E.,
            Peltonen,L., Gardiner,R.M. and Williams,R.E.
  TITLE     Loci for classical and a variant late infantile neuronal ceroid
            lipofuscinosis map to chromosomes 11p15 and 15q21-23
  JOURNAL   Hum Mol Genet 6 (4), 591-595 (1997)
   PUBMED   9097964
REFERENCE   9  (bases 1 to 2228)
  AUTHORS   Mole,S.E. and Williams,R.E.
  TITLE     Neuronal Ceroid-Lipofuscinoses - RETIRED CHAPTER, FOR HISTORICAL
            REFERENCE ONLY
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301601
REFERENCE   10 (bases 1 to 2228)
  AUTHORS   Klein,C., Lohmann,K., Marras,C. and Munchau,A.
  TITLE     Hereditary Dystonia Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301334
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BM149330.1, AK027604.1,
            BC013130.1, CN427564.1, BC010849.1 and CA446197.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_017882.2.
            
            Summary: This gene is one of eight which have been associated with
            neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten
            disease, NCL comprises a class of autosomal recessive,
            neurodegenerative disorders affecting children. The genes
            responsible likely encode proteins involved in the degradation of
            post-translationally modified proteins in lysosomes. The primary
            defect in NCL disorders is thought to be associated with lysosomal
            storage function. [provided by RefSeq, Oct 2008].
            
            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 :: AK000568.1, BC010849.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000249806.11/ ENSP00000249806.5
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-18                BM149330.1         17-34
            19-984              AK027604.1         1-966
            985-1236            BC013130.1         850-1101
            1237-1241           CN427564.1         17-21
            1242-1896           BC010849.1         1166-1820
            1897-2228           CA446197.1         17-348              c
FEATURES             Location/Qualifiers
     source          1..2228
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="15"
                     /map="15q23"
     gene            1..2228
                     /gene="CLN6"
                     /gene_synonym="CLN4A; CLN6A; HsT18960; nclf"
                     /note="CLN6 transmembrane ER protein"
                     /db_xref="GeneID:54982"
                     /db_xref="HGNC:HGNC:2077"
                     /db_xref="MIM:606725"
     exon            1..227
                     /gene="CLN6"
                     /gene_synonym="CLN4A; CLN6A; HsT18960; nclf"
                     /inference="alignment:Splign:2.1.0"
     CDS             145..1080
                     /gene="CLN6"
                     /gene_synonym="CLN4A; CLN6A; HsT18960; nclf"
                     /note="isoform 1 is encoded by transcript variant 1;
                     ceroid-lipofuscinosis neuronal protein 6;
                     ceroid-lipofuscinosis neuronal 6 late infantile;
                     ceroid-lipofuscinosis, neuronal 6, late infantile"
                     /codon_start=1
                     /product="ceroid-lipofuscinosis neuronal protein 6 isoform
                     1"
                     /protein_id="NP_060352.1"
                     /db_xref="CCDS:CCDS10227.1"
                     /db_xref="GeneID:54982"
                     /db_xref="HGNC:HGNC:2077"
                     /db_xref="MIM:606725"
                     /translation="MEATRRRQHLGATGGPGAQLGASFLQARHGSVSADEAARTAPFH
                     LDLWFYFTLQNWVLDFGRPIAMLVFPLEWFPLNKPSVGDYFHMAYNVITPFLLLKLIE
                     RSPRTLPRSITYVSIIIFIMGASIHLVGDSVNHRLLFSGYQHHLSVRENPIIKNLKPE
                     TLIDSFELLYYYDEYLGHCMWYIPFFLILFMYFSGCFTASKAESLIPGPALLLVAPSG
                     LYYWYLVTEGQIFILFIFTFFAMLALVLHQKRKRLFLDSNGLFLFSSFALTLLLVALW
                     VAWLWNDPVLRKKYPGVIYVPEPWAFYTLHVSSRH"
     exon            228..342
                     /gene="CLN6"
                     /gene_synonym="CLN4A; CLN6A; HsT18960; nclf"
                     /inference="alignment:Splign:2.1.0"
     exon            343..441
                     /gene="CLN6"
                     /gene_synonym="CLN4A; CLN6A; HsT18960; nclf"
                     /inference="alignment:Splign:2.1.0"
     exon            442..630
                     /gene="CLN6"
                     /gene_synonym="CLN4A; CLN6A; HsT18960; nclf"
                     /inference="alignment:Splign:2.1.0"
     exon            631..686
                     /gene="CLN6"
                     /gene_synonym="CLN4A; CLN6A; HsT18960; nclf"
                     /inference="alignment:Splign:2.1.0"
     exon            687..809
                     /gene="CLN6"
                     /gene_synonym="CLN4A; CLN6A; HsT18960; nclf"
                     /inference="alignment:Splign:2.1.0"
     exon            810..2228
                     /gene="CLN6"
                     /gene_synonym="CLN4A; CLN6A; HsT18960; nclf"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2210..2215
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CLN6"
                     /gene_synonym="CLN4A; CLN6A; HsT18960; nclf"
                     /note="hexamer: AATACA"
     polyA_site      2228
                     /gene="CLN6"
                     /gene_synonym="CLN4A; CLN6A; HsT18960; nclf"
                     /note="major polyA site"
ORIGIN      
        1 ctgttcctcc cgagggccgc gcgctctcgc cggcccgccc cgaaccgccc cgcgctggga
       61 atttgcggcg gcctccgccg gggcagccga gctgaaccgg tctcttcctc ggaaaggcag
      121 ggccgagggg cctgcggggc agccatggag gcgacgcgga ggcggcagca cctgggagcg
      181 acgggcggcc caggcgcgca gctgggcgcc tccttcctgc aggccaggca tggctctgtg
      241 agcgctgatg aggctgcccg cacggctccc ttccacctcg acctctggtt ctacttcaca
      301 ctgcagaact gggttctgga ctttgggcgt cccattgcca tgctggtatt ccctctcgag
      361 tggtttccac tcaacaagcc cagtgttggg gactacttcc acatggccta caacgtcatc
      421 acgccctttc tcttgctcaa gctcatcgag cggtcccccc gcaccctgcc acgctccatc
      481 acgtacgtga gcatcatcat cttcatcatg ggtgccagca tccacctggt gggtgactct
      541 gtcaaccacc gcctgctctt cagtggctac cagcaccacc tgtctgtccg tgagaacccc
      601 atcatcaaga atctcaagcc ggagacgctg atcgactcct ttgagctgct ctactattat
      661 gatgagtacc tgggtcactg catgtggtac atccccttct tcctcatcct cttcatgtac
      721 ttcagcggct gctttactgc ctctaaagct gagagcttga ttccagggcc tgccctgctc
      781 ctggtggcac ccagtggcct gtactactgg tacctggtca ccgagggcca gatcttcatc
      841 ctcttcatct tcaccttctt cgccatgctg gccctcgtcc tgcaccagaa gcgcaagcgc
      901 ctcttcctgg acagcaacgg cctcttcctc ttctcctcct tcgcactgac cctcttgctt
      961 gtggcgctct gggtcgcctg gctgtggaat gaccctgttc tcaggaagaa gtacccgggt
     1021 gtcatctacg tccctgagcc ctgggctttc tacacccttc acgtcagcag tcggcactga
     1081 gtccctggca ccaggctctg gcgctctgct gggtgggagg gtgggccatg gagggcatct
     1141 gaatacagga gtaggggggg tgtgggtgtg taaccagaga ccgagagcat gagtggggtg
     1201 tgcctcgtgt gcgtggattc gtgtgtgtgt gtgtgtgtgt cttgtatatg tgtgcgcaga
     1261 gtgcatcatt ttcagactct actatttccg tcaagtttct gtttgatttg gatcatctca
     1321 ggatcggatt ctgttttaga gtgtttctgg gccaggatcc gggcccctgc cctcctctgc
     1381 acctgaccac actccctact cagggctagt ctgttcttcc cggacatctt ctggtagccg
     1441 tgcaggagag ggctgggtgg ggcagaggcc aggaggggac ctggtgtgtc acctgcccac
     1501 cacctggctc atccctcagg cccaccctga ccctacatta cataggttac gtcagcctac
     1561 tgtggctgtt gagcaaagca tttctccttt ctgggcctca tttgcactag atgggcctgt
     1621 ggtcccaaag taggtcagta ggttggggtt gctgacaccc cttgggtgca gctttgggac
     1681 agatgagtgg ctctgtcctg tcactgccct ctccctgcct gggggctatg tgcactccag
     1741 acccctgccc aggctcaggc ccatgaggta tggagacacc ctggccccca ggagctggag
     1801 gcaccgccca ctcccctggc attccagctt tgcaggtgac cctcctctac ccaaagctct
     1861 gtccccctgc tcccactcca gaagaactgc ggcacgcgct tcgggcagcc tagccacagg
     1921 ctttgagcgc ctgcattcct gggggctgga gggtggggtg ccaaaggccc tgagcaaaag
     1981 ccagagctcc tctcatcaaa gcctttacaa ggtgctgggc ccagaggctt tgccttgaca
     2041 gagtggccca gggtttcaag ggaggaggaa cctcccccta cctaggaccc ttcctgtggg
     2101 gggtctacag agtcagggac agaagggaag ggacccacag gaagtcacag tggtgcccag
     2161 ggatgtgtca gcccccagcc acggggacgc gggattcaag aatgaagtaa atacagtcac
     2221 agccccaa
//
