LOCUS       NM_006493               5243 bp    mRNA    linear   PRI 12-OCT-2024
DEFINITION  Homo sapiens CLN5 intracellular trafficking protein (CLN5),
            transcript variant 1, mRNA.
ACCESSION   NM_006493
VERSION     NM_006493.4
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 5243)
  AUTHORS   Medoh,U.N., Hims,A., Chen,J.Y., Ghoochani,A., Nyame,K., Dong,W. and
            Abu-Remaileh,M.
  TITLE     The Batten disease gene product CLN5 is the lysosomal
            bis(monoacylglycero)phosphate synthase
  JOURNAL   Science 381 (6663), 1182-1189 (2023)
   PUBMED   37708259
  REMARK    GeneRIF: The Batten disease gene product CLN5 is the lysosomal
            bis(monoacylglycero)phosphate synthase.
REFERENCE   2  (bases 1 to 5243)
  AUTHORS   Wang,Y., Wang,H. and Wang,C.
  TITLE     Lysosomal dysfunction, autophagic defects, and CLN5 accumulation
            underlie the pathogenesis of KCTD7-mutated neuronal ceroid
            lipofuscinoses
  JOURNAL   Autophagy 19 (6), 1876-1878 (2023)
   PUBMED   36368077
  REMARK    GeneRIF: Lysosomal dysfunction, autophagic defects, and CLN5
            accumulation underlie the pathogenesis of KCTD7-mutated neuronal
            ceroid lipofuscinoses.
REFERENCE   3  (bases 1 to 5243)
  AUTHORS   Luebben,A.V., Bender,D., Becker,S., Crowther,L.M., Erven,I.,
            Hofmann,K., Soding,J., Klemp,H., Bellotti,C., Stauble,A., Qiu,T.,
            Kathayat,R.S., Dickinson,B.C., Gartner,J., Sheldrick,G.M.,
            Kratzner,R. and Steinfeld,R.
  TITLE     Cln5 represents a new type of cysteine-based S-depalmitoylase
            linked to neurodegeneration
  JOURNAL   Sci Adv 8 (15), eabj8633 (2022)
   PUBMED   35427157
  REMARK    GeneRIF: Cln5 represents a new type of cysteine-based
            S-depalmitoylase linked to neurodegeneration.
REFERENCE   4  (bases 1 to 5243)
  AUTHORS   Basak,I., Hansen,R.A., Ward,M.E. and Hughes,S.M.
  TITLE     Deficiency of the Lysosomal Protein CLN5 Alters Lysosomal Function
            and Movement
  JOURNAL   Biomolecules 11 (10), 1412 (2021)
   PUBMED   34680045
  REMARK    GeneRIF: Deficiency of the Lysosomal Protein CLN5 Alters Lysosomal
            Function and Movement.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 5243)
  AUTHORS   Klockars,T., Savukoski,M., Isosomppi,J., Laan,M., Jarvela,I.,
            Petrukhin,K., Palotie,A. and Peltonen,L.
  TITLE     Efficient construction of a physical map by fiber-FISH of the CLN5
            region: refined assignment and long-range contig covering the
            critical region on 13q22
  JOURNAL   Genomics 35 (1), 71-78 (1996)
   PUBMED   8661106
REFERENCE   6  (bases 1 to 5243)
  AUTHORS   Savukoski,M., Kestila,M., Williams,R., Jarvela,I., Sharp,J.,
            Harris,J., Santavuori,P., Gardiner,M. and Peltonen,L.
  TITLE     Defined chromosomal assignment of CLN5 demonstrates that at least
            four genetic loci are involved in the pathogenesis of human ceroid
            lipofuscinoses
  JOURNAL   Am J Hum Genet 55 (4), 695-701 (1994)
   PUBMED   7942847
REFERENCE   7  (bases 1 to 5243)
  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   8  (bases 1 to 5243)
  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
REFERENCE   9  (bases 1 to 5243)
  AUTHORS   Perlman,S.
  TITLE     Hereditary Ataxia Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301317
REFERENCE   10 (bases 1 to 5243)
  AUTHORS   Carpenter,S., Karpati,G., Andermann,F., Jacob,J.C. and Andermann,E.
  TITLE     The ultrastructural characteristics of the abnormal cytosomes in
            Batten-Kufs' disease
  JOURNAL   Brain 100 Pt 1, 137-156 (1977)
   PUBMED   193610
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC001226.1.
            
            On Jun 2, 2019 this sequence version replaced NM_006493.3.
            
            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].
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            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 :: SRR1803612.29164.1,
                                           SRR1803612.5105.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000377453.9/ ENSP00000366673.5
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-191               AC001226.1         23490-23680
            192-357             AC001226.1         26472-26637
            358-583             AC001226.1         27311-27536
            584-5243            AC001226.1         31867-36526
FEATURES             Location/Qualifiers
     source          1..5243
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="13"
                     /map="13q22.3"
     gene            1..5243
                     /gene="CLN5"
                     /note="CLN5 intracellular trafficking protein"
                     /db_xref="GeneID:1203"
                     /db_xref="HGNC:HGNC:2076"
                     /db_xref="MIM:608102"
     exon            1..191
                     /gene="CLN5"
                     /inference="alignment:Splign:2.1.0"
     CDS             19..1095
                     /gene="CLN5"
                     /EC_number="3.1.2.22"
                     /note="isoform 1 is encoded by transcript variant 1;
                     ceroid-lipofuscinosis neuronal protein 5;
                     ceroid-lipofuscinosis, neuronal 5; BMP synthase CLN5;
                     S-depalmitoylase CLN5; palmitoyl protein thioesterase
                     CLN5; bis(monoacylglycero)phosphate synthase CLN5"
                     /codon_start=1
                     /product="bis(monoacylglycero)phosphate synthase CLN5
                     isoform 1"
                     /protein_id="NP_006484.2"
                     /db_xref="CCDS:CCDS9456.2"
                     /db_xref="GeneID:1203"
                     /db_xref="HGNC:HGNC:2076"
                     /db_xref="MIM:608102"
                     /translation="MAQEVDTAQGAEMRRGAGAARGRASWCWALALLWLAVVPGWSRV
                     SGIPSRRHWPVPYKRFDFRPKPDPYCQAKYTFCPTGSPIPVMEGDDDIEVFRLQAPVW
                     EFKYGDLLGHLKIMHDAIGFRSTLTGKNYTMEWYELFQLGNCTFPHLRPEMDAPFWCN
                     QGAACFFEGIDDVHWKENGTLVQVATISGNMFNQMAKWVKQDNETGIYYETWNVKASP
                     EKGAETWFDSYDCSKFVLRTFNKLAEFGAEFKNIETNYTRIFLYSGEPTYLGNETSVF
                     GPTGNKTLGLAIKRFYYPFKPHLPTKEFLLSLLQIFDAVIVHKQFYLFYNFEYWFLPM
                     KFPFIKITYEEIPLPIRNKTLSGL"
     exon            192..357
                     /gene="CLN5"
                     /inference="alignment:Splign:2.1.0"
     exon            358..583
                     /gene="CLN5"
                     /inference="alignment:Splign:2.1.0"
     exon            584..5243
                     /gene="CLN5"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1437..1442
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CLN5"
                     /note="hexamer: AATAAA"
     polyA_site      1459
                     /gene="CLN5"
                     /note="major polyA site"
     regulatory      2622..2627
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CLN5"
                     /note="hexamer: ATTAAA"
     polyA_site      2643
                     /gene="CLN5"
                     /note="major polyA site"
     regulatory      3730..3735
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CLN5"
                     /note="hexamer: ATTATA"
     polyA_site      3753
                     /gene="CLN5"
ORIGIN      
        1 agtactgggt gcagcctgat ggcgcaggag gtagacacgg cacagggcgc cgagatgcgg
       61 cggggcgcgg gcgcggctcg gggacgcgct tcctggtgct gggccctggc gctgctttgg
      121 ctcgcggtgg ttccgggctg gtcccgggtc tcgggcatcc cctcccggcg ccactggccg
      181 gtgccctaca agcgctttga cttccgtcca aaacctgatc cttattgtca agctaagtat
      241 actttctgtc caactggctc acctatccca gttatggagg gtgatgatga cattgaagtt
      301 tttcgattac aagccccagt atgggaattt aaatatggag acctcctggg acacttgaaa
      361 attatgcatg atgccattgg attcagaagt acattaactg gcaagaacta cacaatggaa
      421 tggtatgaac ttttccaact tggcaactgt acatttcccc atctccgacc tgaaatggat
      481 gcccctttct ggtgtaatca aggcgctgcc tgcttttttg agggaattga tgatgttcac
      541 tggaaggaaa atgggacatt agttcaagta gcaactatat caggaaacat gttcaaccaa
      601 atggcaaagt gggtgaaaca ggacaatgaa acaggaattt attatgagac atggaatgta
      661 aaagccagcc cagaaaaggg ggcagagaca tggtttgatt cctacgactg ttccaaattt
      721 gtgttaagga cctttaacaa gttggctgaa tttggagcag agttcaagaa catagaaacc
      781 aactatacaa gaatatttct ttacagtgga gaacctactt atctgggaaa tgaaacatct
      841 gtttttgggc caacaggaaa caagactctt ggtttagcca taaaaagatt ttattacccc
      901 ttcaaaccac atttgccaac taaagaattt ctgttgagtc tcttgcaaat ttttgatgca
      961 gtgattgtgc acaaacagtt ctatttgttt tataattttg aatattggtt tttacctatg
     1021 aaattccctt ttattaaaat aacatatgaa gaaatccctt tacctatcag aaacaaaaca
     1081 ctctctggtt tataaaacac cttaattcta ctgctctttt ttctccaatc accagcatct
     1141 gtttttcagg gggtgatttt acttttgtga attccttagc ctttcttcct tggtgcataa
     1201 agttaaaatg cacatcagca gaattgctgc atattaacat ctcaggactc ttctcttgta
     1261 aagaagctga aattcgtact atattggcca aagtgagcga gttaggtgat cttggtttca
     1321 atttccgagc ctttgttaat atggagaatt atggttcata tcagttatgt aggacctttg
     1381 gacccagggt cctacagata gatatggtgt gcccagattt taaaaatacc ttcaaaaata
     1441 aaaaatacat tcagtgacat tttcatggtg ggagctcttc tttctgatat ggcagttaca
     1501 ctttttcact taagtgcttt agtttagact aactttacaa cttctataac ttttggaacc
     1561 aagtttagta tagtctgatt acattccatt cacctaactt tagacattcg tttagacacc
     1621 ataactggag tgattgtgct tctagatgtg gcaaatccag tgttaacaca tatttctggc
     1681 tgagattttg gaactagcta gtaactggct tgtgttcttt aagcatacta acatcactaa
     1741 atcttaggat ttaggattgc tgtaaagatg taagttgtgt atgtttggca ggtcacattg
     1801 aatggcagtg ataatgatta atcaaagaac aaatgtcatc cttgatcttg cctaatgtag
     1861 tttatgtgcc aaactttcca gggttttgta gtcacctaga ttttaagctg atagcatagt
     1921 gcttcagcgg ttcttctaac cggggtatgc aggaacatgg ctgcagacac gtttgggtaa
     1981 acaggcacct tctgacttct tcattgtttc ctgtagttct ccctcttccc acaaagctgt
     2041 cagcgcagtg gaagaggttg cacttctccg agagaggaca ggtttctgtt aagatcacca
     2101 agtagctgtg ctttaattag agccagacaa gctttcaagg tcctttaagt atttgatgat
     2161 caactgaaca cgtttctatt caaggagaaa acaccattca gtaagaagat ggagtagata
     2221 tcagataaaa caattcacgt ttaatatgta aatgtaccaa ttatgtgatt cagtttcaac
     2281 tttcaagtac ttcctgagag gttagtacat tattattgag ctctcacaga aagcttaatc
     2341 atagatataa ttaacctgat ccaaatgagt aaagtggacc ttagaaaggc taagtgatct
     2401 ttctctggct atccagctag tagtaatgaa gtcaggtctt gaaccccggt tctgctgact
     2461 gaattggatg cactatagta caggctttta gcaccgaagt gtggtcctca gaccagtgcc
     2521 tgccaaccag atgttactgg tctgtgagga aataagtaca gatactgaca ggaagctttt
     2581 ataaacaatt tattggagtg tttttgtttc tgttgggtct aattaaaaaa attggagctt
     2641 gtattttatg tgtctttggt cttattttgt ctaggaattc atttttgctg ggtttttttt
     2701 tttcaactgt agtcccacaa cagtctgaaa ataacccagt caccagatat cttcctcaaa
     2761 tacagaggga gaactttctt tcacgcctcc tttagcctgt cgactcctta taataatgcc
     2821 taaatattcc aaattaatac tgcctcttta acctgctaat tgttttcaca atgttacaag
     2881 aaaacttgga tctgtgcatt atcaccatct agtggctaaa ctcaggcaac acgaacttct
     2941 accaaactca ggaaattgct ctggaaaaac tacaggattt tggatttcca gaactgcctt
     3001 gaagagacaa agattcttgt accaagtttt ggtcaactgc aaatcaaaga acttggttat
     3061 gcagggaaaa caaatgagga tatctgtacc tggaactttt aaacaagatt ctaatagtta
     3121 tgtgaaaaaa gcattcaaga tttttgagta ggcacagtgg cttacgcctg taatcctatc
     3181 actttgcgaa actgaggtgg tggaaggatc actgaaggtc gggagttcaa gaccagcctg
     3241 gccaatgtgg tgaaaccccg tttctcctaa aattaaaaaa aaaaaaaaaa agctaggggt
     3301 ggtggtccat gcctgtaatc ccagctacac gtgaggctaa ggcaggagaa tcacttgaac
     3361 ccaggaggca gaggttgcag tgagctgaga tggcgccact gcactccagc ctgggcgaca
     3421 gagcgagact ccgtctcaaa aaaaaagcat tcaagatttt tcattgttcc taagaatctt
     3481 aattaaatga agacagaaag catcataaag tcaggtaact acagcacaga cagcattaac
     3541 atttacaaaa gtatttctta agaattaaac ctgtcagctc tacttacaag atgtagagct
     3601 ttcaggtgaa gatgattcaa gaacatgctt tcaaaatagt agttgagaaa ccaaaacata
     3661 gccacgcaga aatctgccaa ttaagttttg ctgccctttg agcaatatga cttaatgtga
     3721 tttactttaa ttataactta agtacaactt aaatgcagtt tctattttgc tattgttata
     3781 gatgtaggct gggtgcggtg gcttatgcct gtaatcctaa cacatacttt gggaggccaa
     3841 ggtggacgga tcacttgagg tcaggagttc gagaccagcc tggccaacat ggtgaaaccc
     3901 cgtctctact gaaaatacaa aaattagctg gttgtggtgg agcatgcctg tagtcccagc
     3961 tacttgggag gctgaggcag gagaatcact tgaatccagg aggtggaggt tcccacgagc
     4021 caagatcgca ccactgcact ccagcctggc aacagagtga gactccgtct caaaaaaatg
     4081 ttgtagatgt ataaaattta tacattttta gtctgactag ggctttagag tgaatatatc
     4141 tcctcattaa tctggcacaa aattagttaa gtaagtatac ccacaaagtg tcatctaata
     4201 tattgttgca tgtagaggaa aacacagtga agaaacctac taactttatt tggaaccctc
     4261 aatattggtg gctccttaaa aattggagaa aaaaatcaag tcttaggaag tcttatccag
     4321 ttttatggtc tgctgtggtg gcacttaatg aattacctgg aattatagtt cctgtaagat
     4381 gttttatttt ttaaatagtt ggcaggctat acaaagagtg atgttccaaa actacacaca
     4441 tgctttttcc ctgttcacaa aggcaaacag gctggccaaa gtgtttccag catcttcgtc
     4501 atatttaccc tttattatcc aagtggtttc ctgctcttca aaccttcctt tcaaaatttt
     4561 gtctcctact taaaacaagt taggattatt tatcctttta ttggactgat tattctaagg
     4621 ataagctctt acttcacttt cggagtaaaa ggctttgtgc cctttttaaa gttgggtgtc
     4681 agcaagcagc tggaattttc ctgcctggta aaattaaaac cagccccaca aactggggtt
     4741 ggagtctgtg caaagctcat tactatctat gtgtggggta gaaattatag tgtgttaaag
     4801 gacctagtgt aaaaaaaaaa aattttaaag gacctagtgg aggcttgaac cttcttcaca
     4861 tgaacgtctt cctttcagcc taaagttctt aaaatgcact aaattgactt aatcttcaat
     4921 catacctatt ttttctgata tggttacaac agcccaaatt accaagataa gttgaaagcc
     4981 agtaaaacaa tgaaaataat ttcaatagtt gaaaaactat tctaatttat ataaagacat
     5041 ttatctctaa aaagactggt tgggttcaag gacccttaaa gactgattct atgtctaaat
     5101 aatctgtttt ataagttctc attctgaatg cagaaagaac ctattatttt ctgtataaaa
     5161 atttaaaaat ttatatttca tggtaggttt taaatttcct atttctttag gcatcagagc
     5221 ttatttcaag aatagattcc atg
//
