U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    VPS33B VPS33B late endosome and lysosome associated [ Homo sapiens (human) ]

    Gene ID: 26276, updated on 28-Oct-2024

    Summary

    Official Symbol
    VPS33Bprovided by HGNC
    Official Full Name
    VPS33B late endosome and lysosome associatedprovided by HGNC
    Primary source
    HGNC:HGNC:12712
    See related
    Ensembl:ENSG00000184056 MIM:608552; AllianceGenome:HGNC:12712
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    KDIDAR; PFIC12
    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 is a member of the Sec-1 domain family, and encodes the human ortholog of rat Vps33b which is homologous to the yeast class C Vps33 protein. The mammalian class C vacuolar protein sorting proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Mutations in this gene are associated with arthrogryposis-renal dysfunction-cholestasis syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
    Expression
    Ubiquitous expression in brain (RPKM 5.8), testis (RPKM 4.9) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See VPS33B in Genome Data Viewer
    Location:
    15q26.1
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (90998416..91022621, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (88757999..88782209, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (91541646..91565851, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene PRC1 antisense RNA 1 Neighboring gene protein regulator of cytokinesis 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:91526592-91527791 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:91537071-91537938 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:91537939-91538805 Neighboring gene uncharacterized LOC124903556 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:91547812-91547974 Neighboring gene uncharacterized LOC105370970 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:91564908-91565524 Neighboring gene VPS33B divergent transcript Neighboring gene golgin A2 pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Arthrogryposis, renal dysfunction, and cholestasis 1
    MedGen: C1859722 OMIM: 208085 GeneReviews: Not available
    Compare labs
    Cholestasis, progressive familial intrahepatic, 12
    MedGen: C5774311 OMIM: 620010 GeneReviews: Not available
    Compare labs
    Keratoderma-ichthyosis-deafness syndrome, autosomal recessive
    MedGen: C5774200 OMIM: 620009 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ14848

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-containing complex binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    NOT involved_in autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in collagen fibril organization IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within collagen metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endosome organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT involved_in endosome to lysosome transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in intracellular transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in lysosome localization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in megakaryocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in melanosome localization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in membrane fusion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within peptidyl-lysine hydroxylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in phagosome-lysosome fusion NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in platelet alpha granule organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of platelet aggregation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in skin morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within vesicle-mediated transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of CORVET complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT part_of HOPS complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of HOPS complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in clathrin-coated vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
     
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in platelet alpha granule IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in recycling endosome IEA
    Inferred from Electronic Annotation
    more info
     
    part_of vesicle tethering complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 

    General protein information

    Preferred Names
    vacuolar protein sorting-associated protein 33B
    Names
    vacuolar protein sorting 33 homolog B
    vacuolar protein sorting 33-like protein B

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_012162.1 RefSeqGene

      Range
      4983..29188
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_884

    mRNA and Protein(s)

    1. NM_001289148.1NP_001276077.1  vacuolar protein sorting-associated protein 33B isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AK074863, AK293688, CB048637, DC397488
      Consensus CDS
      CCDS73783.1
      UniProtKB/TrEMBL
      B7Z1N4, F5H008
      Related
      ENSP00000444053.1, ENST00000535906.1
      Conserved Domains (1) summary
      pfam00995
      Location:32578
      Sec1; Sec1 family
    2. NM_001289149.1NP_001276078.1  vacuolar protein sorting-associated protein 33B isoform 3

      See identical proteins and their annotated locations for NP_001276078.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in its 5' UTR and uses a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK074863, CB048637, DC397488
      UniProtKB/TrEMBL
      B7Z6M7
      Conserved Domains (1) summary
      pfam00995
      Location:10514
      Sec1; Sec1 family
    3. NM_018668.5NP_061138.3  vacuolar protein sorting-associated protein 33B isoform 1

      See identical proteins and their annotated locations for NP_061138.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AF201694, AF308803, DC397488
      Consensus CDS
      CCDS10369.1
      UniProtKB/Swiss-Prot
      B3KQF6, Q96K14, Q9H267, Q9NRP6, Q9NSF3
      UniProtKB/TrEMBL
      A0A0S2Z577, B7Z1N4
      Related
      ENSP00000327650.4, ENST00000333371.8
      Conserved Domains (1) summary
      pfam00995
      Location:37605
      Sec1; Sec1 family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      90998416..91022621 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005254887.2XP_005254944.1  vacuolar protein sorting-associated protein 33B isoform X1

      See identical proteins and their annotated locations for XP_005254944.1

      UniProtKB/TrEMBL
      B7Z6M7
      Conserved Domains (1) summary
      pfam00995
      Location:10514
      Sec1; Sec1 family
    2. XM_047432383.1XP_047288339.1  vacuolar protein sorting-associated protein 33B isoform X1

    3. XM_011521449.3XP_011519751.1  vacuolar protein sorting-associated protein 33B isoform X2

      UniProtKB/TrEMBL
      B7Z6M7
      Conserved Domains (1) summary
      pfam00995
      Location:23497
      Sec1; Sec1 family
    4. XM_047432384.1XP_047288340.1  vacuolar protein sorting-associated protein 33B isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      88757999..88782209 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377722.1XP_054233697.1  vacuolar protein sorting-associated protein 33B isoform X1

    2. XM_054377721.1XP_054233696.1  vacuolar protein sorting-associated protein 33B isoform X1

    3. XM_054377723.1XP_054233698.1  vacuolar protein sorting-associated protein 33B isoform X2

    4. XM_054377724.1XP_054233699.1  vacuolar protein sorting-associated protein 33B isoform X3