LOCUS       NM_022575               2708 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens VPS16 core subunit of CORVET and HOPS complexes
            (VPS16), transcript variant 1, mRNA.
ACCESSION   NM_022575
VERSION     NM_022575.4
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 2708)
  AUTHORS   Monfrini,E., Avanzino,L., Palermo,G., Bonato,G., Brescia,G.,
            Ceravolo,R., Cantarella,G., Mandich,P., Prokisch,H., Storm Van's
            Gravesande,K., Straccia,G., Elia,A., Reale,C., Panteghini,C.,
            Zorzi,G., Eleopra,R., Erro,R., Carecchio,M., Garavaglia,B.,
            Zech,M., Romito,L. and Di Fonzo,A.
  TITLE     Dominant VPS16 Pathogenic Variants: Not Only Isolated Dystonia
  JOURNAL   Mov Disord Clin Pract 11 (1), 87-93 (2024)
   PUBMED   38291845
  REMARK    GeneRIF: Dominant VPS16 Pathogenic Variants: Not Only Isolated
            Dystonia.
REFERENCE   2  (bases 1 to 2708)
  AUTHORS   Gong,X., Chen,T., Lin,C., Ping,H., Tong,X., Zhang,K., Chen,Z.,
            Cai,C., Lu,Z. and Ke,H.
  TITLE     Bioinformatics Analysis of the Prognostic Significance of VPS16 in
            Hepatocellular Carcinoma and Its Role in Drug Screening
  JOURNAL   Biomed Res Int 2023, 2501596 (2023)
   PUBMED   37124933
  REMARK    GeneRIF: Bioinformatics Analysis of the Prognostic Significance of
            VPS16 in Hepatocellular Carcinoma and Its Role in Drug Screening.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2708)
  AUTHORS   Zhang,B., Ma,Y., Niu,H. and Liu,Z.
  TITLE     Overexpression of VPS16 correlates with tumor progression and
            chemoresistance in colorectal cancer
  JOURNAL   Biochem Biophys Res Commun 607, 81-88 (2022)
   PUBMED   35367832
  REMARK    GeneRIF: Overexpression of VPS16 correlates with tumor progression
            and chemoresistance in colorectal cancer.
REFERENCE   4  (bases 1 to 2708)
  AUTHORS   Cho,N.H., Cheveralls,K.C., Brunner,A.D., Kim,K., Michaelis,A.C.,
            Raghavan,P., Kobayashi,H., Savy,L., Li,J.Y., Canaj,H., Kim,J.Y.S.,
            Stewart,E.M., Gnann,C., McCarthy,F., Cabrera,J.P., Brunetti,R.M.,
            Chhun,B.B., Dingle,G., Hein,M.Y., Huang,B., Mehta,S.B.,
            Weissman,J.S., Gomez-Sjoberg,R., Itzhak,D.N., Royer,L.A., Mann,M.
            and Leonetti,M.D.
  TITLE     OpenCell: Endogenous tagging for the cartography of human cellular
            organization
  JOURNAL   Science 375 (6585), eabi6983 (2022)
   PUBMED   35271311
REFERENCE   5  (bases 1 to 2708)
  AUTHORS   Yildiz,Y., Kosukcu,C., Aygun,D., Akcaboy,M., Oztek Celebi,F.Z.,
            Tasci Yildiz,Y., Sahin,G., Aytekin,C., Yuksel,D., Lay,I.,
            Ozgul,R.K. and Dursun,A.
  TITLE     Homozygous missense VPS16 variant is associated with a novel
            disease, resembling mucopolysaccharidosis-plus syndrome in two
            siblings
  JOURNAL   Clin Genet 100 (3), 308-317 (2021)
   PUBMED   34013567
  REMARK    GeneRIF: Homozygous missense VPS16 variant is associated with a
            novel disease, resembling mucopolysaccharidosis-plus syndrome in
            two siblings.
REFERENCE   6  (bases 1 to 2708)
  AUTHORS   Schroder,B., Wrocklage,C., Pan,C., Jager,R., Kosters,B.,
            Schafer,H., Elsasser,H.P., Mann,M. and Hasilik,A.
  TITLE     Integral and associated lysosomal membrane proteins
  JOURNAL   Traffic 8 (12), 1676-1686 (2007)
   PUBMED   17897319
REFERENCE   7  (bases 1 to 2708)
  AUTHORS   Girard,A., Sachidanandam,R., Hannon,G.J. and Carmell,M.A.
  TITLE     A germline-specific class of small RNAs binds mammalian Piwi
            proteins
  JOURNAL   Nature 442 (7099), 199-202 (2006)
   PUBMED   16751776
REFERENCE   8  (bases 1 to 2708)
  AUTHORS   Deloukas,P., Matthews,L.H., Ashurst,J., Burton,J., Gilbert,J.G.,
            Jones,M., Stavrides,G., Almeida,J.P., Babbage,A.K., Bagguley,C.L.,
            Bailey,J., Barlow,K.F., Bates,K.N., Beard,L.M., Beare,D.M.,
            Beasley,O.P., Bird,C.P., Blakey,S.E., Bridgeman,A.M., Brown,A.J.,
            Buck,D., Burrill,W., Butler,A.P., Carder,C., Carter,N.P.,
            Chapman,J.C., Clamp,M., Clark,G., Clark,L.N., Clark,S.Y.,
            Clee,C.M., Clegg,S., Cobley,V.E., Collier,R.E., Connor,R.,
            Corby,N.R., Coulson,A., Coville,G.J., Deadman,R., Dhami,P.,
            Dunn,M., Ellington,A.G., Frankland,J.A., Fraser,A., French,L.,
            Garner,P., Grafham,D.V., Griffiths,C., Griffiths,M.N., Gwilliam,R.,
            Hall,R.E., Hammond,S., Harley,J.L., Heath,P.D., Ho,S., Holden,J.L.,
            Howden,P.J., Huckle,E., Hunt,A.R., Hunt,S.E., Jekosch,K.,
            Johnson,C.M., Johnson,D., Kay,M.P., Kimberley,A.M., King,A.,
            Knights,A., Laird,G.K., Lawlor,S., Lehvaslaiho,M.H., Leversha,M.,
            Lloyd,C., Lloyd,D.M., Lovell,J.D., Marsh,V.L., Martin,S.L.,
            McConnachie,L.J., McLay,K., McMurray,A.A., Milne,S., Mistry,D.,
            Moore,M.J., Mullikin,J.C., Nickerson,T., Oliver,K., Parker,A.,
            Patel,R., Pearce,T.A., Peck,A.I., Phillimore,B.J.,
            Prathalingam,S.R., Plumb,R.W., Ramsay,H., Rice,C.M., Ross,M.T.,
            Scott,C.E., Sehra,H.K., Shownkeen,R., Sims,S., Skuce,C.D.,
            Smith,M.L., Soderlund,C., Steward,C.A., Sulston,J.E., Swann,M.,
            Sycamore,N., Taylor,R., Tee,L., Thomas,D.W., Thorpe,A., Tracey,A.,
            Tromans,A.C., Vaudin,M., Wall,M., Wallis,J.M., Whitehead,S.L.,
            Whittaker,P., Willey,D.L., Williams,L., Williams,S.A., Wilming,L.,
            Wray,P.W., Hubbard,T., Durbin,R.M., Bentley,D.R., Beck,S. and
            Rogers,J.
  TITLE     The DNA sequence and comparative analysis of human chromosome 20
  JOURNAL   Nature 414 (6866), 865-871 (2001)
   PUBMED   11780052
REFERENCE   9  (bases 1 to 2708)
  AUTHORS   Kim,B.Y., Kramer,H., Yamamoto,A., Kominami,E., Kohsaka,S. and
            Akazawa,C.
  TITLE     Molecular characterization of mammalian homologues of class C Vps
            proteins that interact with syntaxin-7
  JOURNAL   J Biol Chem 276 (31), 29393-29402 (2001)
   PUBMED   11382755
REFERENCE   10 (bases 1 to 2708)
  AUTHORS   Huizing,M., Didier,A., Walenta,J., Anikster,Y., Gahl,W.A. and
            Kramer,H.
  TITLE     Molecular cloning and characterization of human VPS18, VPS 11,
            VPS16, and VPS33
  JOURNAL   Gene 264 (2), 241-247 (2001)
   PUBMED   11250079
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BU845142.1, AF308801.1 and
            BM468030.1.
            
            On Nov 23, 2018 this sequence version replaced NM_022575.3.
            
            Summary: Vesicle mediated protein sorting plays an important role
            in segregation of intracellular molecules into distinct organelles.
            Genetic studies in yeast have identified more than 40 vacuolar
            protein sorting (VPS) genes involved in vesicle transport to
            vacuoles. This gene encodes the human homolog of yeast class C
            Vps16 protein. The mammalian class C Vps proteins are predominantly
            associated with late endosomes/lysosomes, and like their yeast
            counterparts, may mediate vesicle trafficking steps in the
            endosome/lysosome pathway. Two transcript variants encoding
            different isoforms have been found for this gene. [provided by
            RefSeq, Jul 2009].
            
            Transcript Variant: This variant (1) encodes the longer isoform
            (1).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript 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 :: SRR3476690.940372.1,
                                           SRR1163655.61091.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000380445.8/ ENSP00000369810.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-322               BU845142.1         26-347
            323-2332            AF308801.1         307-2316
            2333-2708           BM468030.1         354-729
FEATURES             Location/Qualifiers
     source          1..2708
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="20"
                     /map="20p13"
     gene            1..2708
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /note="VPS16 core subunit of CORVET and HOPS complexes"
                     /db_xref="GeneID:64601"
                     /db_xref="HGNC:HGNC:14584"
                     /db_xref="MIM:608550"
     exon            1..83
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     CDS             31..2550
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /note="isoform 1 is encoded by transcript variant 1;
                     vacuolar protein sorting protein 16; vacuolar protein
                     sorting-associated protein 16 homolog; vacuolar protein
                     sorting 16 homolog; VPS16, CORVET/HOPS core subunit"
                     /codon_start=1
                     /product="vacuolar protein sorting-associated protein 16
                     homolog isoform 1"
                     /protein_id="NP_072097.2"
                     /db_xref="CCDS:CCDS13036.1"
                     /db_xref="GeneID:64601"
                     /db_xref="HGNC:HGNC:14584"
                     /db_xref="MIM:608550"
                     /translation="MDCYTANWNPLGDSAFYRKYELYSMDWDLKEELRDCLVAAAPYG
                     GPIALLRNPWRKEKAASVRPVLDIYSASGMPLASLLWKSGPVVSLGWSAEEELLCVQE
                     DGAVLVYGLHGDFRRHFSMGNEVLQNRVLDARIFHTEFGSGVAILTGAHRFTLSANVG
                     DLKLRRMPEVPGLQSAPSCWTVLCQDRVAHILLAVGPDLYLLDHAACSAVTPPGLAPG
                     VSSFLQMAVSFTYRHLALFTDTGYIWMGTASLKEKLCEFNCNIRAPPKQMVWCSRPRS
                     KERAVVVAWERRLMVVGDAPESIQFVLDEDSYLVPELDGVRIFSRSTHEFLHEVPAAS
                     EEIFKIASMAPGALLLEAQKEYEKESQKADEYLREIQELGQLTQAVQQCIEAAGHEHQ
                     PDMQKSLLRAASFGKCFLDRFPPDSFVHMCQDLRVLNAVRDYHIGIPLTYSQYKQLTI
                     QVLLDRLVLRRLYPLAIQICEYLRLPEVQGVSRILAHWACYKVQQKDVSDEDVARAIN
                     QKLGDTPGVSYSDIAARAYGCGRTELAIKLLEYEPRSGEQVPLLLKMKRSKLALSKAI
                     ESGDTDLVFTVLLHLKNELNRGDFFMTLRNQPMALSLYRQFCKHQELETLKDLYNQDD
                     NHQELGSFHIRASYAAEERIEGRVAALQTAADAFYKAKNEFAAKATEDQMRLLRLQRR
                     LEDELGGQFLDLSLHDTVTTLILGGHNKRAEQLARDFRIPDKRLWWLKLTALADLEDW
                     EELEKFSKSKKSPIGYLPFVEICMKQHNKYEAKKYASRVGPEQKVKALLLVGDVAQAA
                     DVAIEHRNEAELSLVLSHCTGATDGATADKIQRARAQAQKK"
     exon            84..172
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            173..270
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            271..399
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            400..544
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            545..660
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            661..783
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            784..839
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            840..929
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            930..1024
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            1025..1101
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            1102..1233
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            1234..1361
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            1362..1397
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            1398..1506
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            1507..1641
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            1642..1750
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            1751..1848
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            1849..1956
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            1957..2034
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            2035..2204
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            2205..2301
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            2302..2405
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     exon            2406..2708
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2689..2694
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /note="hexamer: AATAAA"
     polyA_site      2708
                     /gene="VPS16"
                     /gene_synonym="DYT30; hVPS16"
                     /note="major polyA site"
ORIGIN      
        1 ggtgcttccc agctgccgtc tgcaccagcc atggactgct acacggcgaa ctggaaccca
       61 ctcggggact ctgcctttta ccggaaatat gagctgtaca gcatggactg ggacctgaag
      121 gaggaactca gggattgcct ggtggctgct gcaccctatg ggggccccat tgcactgctg
      181 aggaacccct ggcggaagga gaaagctgct agtgtgaggc cagtgctcga tatatactct
      241 gcttccggca tgcctctggc cagcctgctg tggaagagtg gacccgtggt gtccctgggc
      301 tggtcagctg aggaggagct gctctgtgtg caggaagatg gtgctgtact ggtttatggg
      361 cttcatggtg acttccggag acacttcagc atgggcaatg aagtgctcca gaaccgggtt
      421 ctggatgccc ggatctttca cactgagttt ggttccggag tggccatcct cacaggggcc
      481 caccgcttca ccctcagtgc caatgtgggt gacctcaaac tccgccggat gccagaggtg
      541 ccaggtctgc aaagtgcacc ctcctgctgg actgtgctgt gccaggaccg agtggcacac
      601 attcttctgg ctgtggggcc tgacctttac ctcttggacc atgcagcctg ctccgcagtg
      661 acgccccctg gcctggcccc aggagtaagc agcttcctac agatggctgt ctccttcacc
      721 taccgacacc tggcactctt cacagacaca ggctacatct ggatggggac agcatcactc
      781 aaggagaagc tatgtgagtt caactgcaac atccgggcac ctccaaagca gatggtctgg
      841 tgcagccgtc ctcgtagcaa ggagagggcc gtggtggtgg cctgggaaag gcggctgatg
      901 gtggtgggcg atgcacccga gagcatccag tttgtgctgg atgaggactc ctacctggtg
      961 cctgagctcg atggggtccg catcttctcc cgcagcaccc acgagttcct gcatgaggtt
     1021 ccagcggcca gcgaggaaat cttcaaaatt gcctcaatgg cccccggggc gctgctcctg
     1081 gaggctcaga aggagtatga gaaagagagc cagaaggcgg acgagtacct gcgggagatc
     1141 caggagctgg gccagctgac ccaggccgtg cagcagtgca ttgaggctgc aggacatgag
     1201 caccagccag acatgcagaa gagtctgctc agggccgcct ccttcggaaa gtgtttcctg
     1261 gacagatttc cacccgacag cttcgtgcac atgtgtcagg acctgcgtgt gctcaatgct
     1321 gttcgggact atcacatcgg gatcccgctc acctatagcc aatataagca gctcaccatc
     1381 caggtgctgc tggacaggct cgtgttgcgg agactttacc ccctggccat ccagatatgc
     1441 gagtacttgc gccttcctga agtacagggc gtcagcagga tcctggccca ctgggcctgc
     1501 tacaaggtgc aacagaagga tgtctcagat gaggatgtgg ctcgagccat taaccagaag
     1561 ctgggggaca cgcctggtgt ctcttactcc gacattgctg cacgagccta tggttgtggc
     1621 cgcacggagc tggccatcaa gctgctggag tatgagccac gctcagggga gcaggtaccc
     1681 cttctcctaa agatgaagag gagcaaactg gcactaagca aggccatcga gagcggggac
     1741 actgacctgg tgttcacggt gttgctgcac ctgaagaacg agctgaaccg aggagatttt
     1801 ttcatgaccc ttcggaatca gcccatggcc ctcagtttgt accgacagtt ctgtaagcat
     1861 caggagctag agacgctgaa ggacctttac aatcaggatg acaatcacca ggaattgggc
     1921 agcttccaca tccgagccag ctatgctgca gaagagcgta ttgaggggcg agtagcagct
     1981 ctgcagacag ccgccgatgc cttctacaag gccaagaatg agtttgcagc caaggctaca
     2041 gaggatcaaa tgcggctcct acggctgcag cggcgcctag aagacgagct ggggggccag
     2101 ttcctagacc tgtctctaca tgacacagtt accaccctca ttcttggcgg tcacaacaag
     2161 cgtgcagagc agctggcacg tgacttccgc atccctgaca agaggctctg gtggctgaag
     2221 ctgactgccc tggcagattt ggaagattgg gaagagctag agaagttttc caagagcaag
     2281 aaatcaccca ttggctacct gccttttgtg gagatctgca tgaaacaaca taacaaatac
     2341 gaagccaaga agtatgcttc ccgcgtgggt cccgagcaga aggtcaaggc tttgcttctt
     2401 gttggcgatg tggctcaggc tgcagatgtg gccatcgaac accggaatga ggctgagctg
     2461 agcctcgtat tgtcccactg cacgggagcc acagatgggg ccacagctga caagattcaa
     2521 cgggccaggg cacaagccca gaagaagtga ggagtccatc ctgtacatct caagcaaggg
     2581 gttcctcccc tagcacctgg gcttggcaga agggccatag ttcatccagc tcctccccta
     2641 gagcaatgct gaggagcggg ggcatggtag cagggctgtc tggttttaaa taaagttgga
     2701 acacttca
//
