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

Gene ID: 26276, updated on 17-Jun-2019

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
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
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

Genomic context

See VPS33B in Genome Data Viewer
Location:
15q26.1
Exon count:
24
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (90998416..91022839, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (91541774..91565833, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene PRC1 antisense RNA 1 Neighboring gene RCC1 domain containing 1 Neighboring gene protein regulator of cytokinesis 1 Neighboring gene uncharacterized LOC105370970 Neighboring gene VPS33B divergent transcript Neighboring gene golgin A2 pseudogene Neighboring gene synaptic vesicle glycoprotein 2B Neighboring gene uncharacterized LOC105370972

Genomic regions, transcripts, and products

Expression

  • Project title: 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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Arthrogryposis renal dysfunction cholestasis syndrome
MedGen: C1859722 OMIM: 208085 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ14848

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
NOT autophagosome maturation IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
endosome organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT endosome to lysosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
lysosome localization IDA
Inferred from Direct Assay
more info
PubMed 
melanosome localization IDA
Inferred from Direct Assay
more info
PubMed 
membrane fusion IMP
Inferred from Mutant Phenotype
more info
PubMed 
peptidyl-lysine hydroxylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
platelet alpha granule organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
vesicle docking involved in exocytosis IEA
Inferred from Electronic Annotation
more info
 
vesicle-mediated transport IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
HOPS complex IDA
Inferred from Direct Assay
more info
PubMed 
NOT HOPS complex IDA
Inferred from Direct Assay
more info
PubMed 
clathrin-coated vesicle IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
early endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
late endosome IDA
Inferred from Direct Assay
more info
PubMed 
late endosome membrane IEA
Inferred from Electronic Annotation
more info
 
lysosomal membrane IEA
Inferred from Electronic Annotation
more info
 
lysosome IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
platelet alpha granule IDA
Inferred from Direct Assay
more info
PubMed 
recycling endosome IEA
Inferred from Electronic Annotation
more info
 

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)

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/Swiss-Prot
    Q9H267
    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/Swiss-Prot
    Q9H267
    Conserved Domains (1) summary
    pfam00995
    Location:10514
    Sec1; Sec1 family
  3. NM_018668.4NP_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, CB048637, DC397488
    Consensus CDS
    CCDS10369.1
    UniProtKB/Swiss-Prot
    Q9H267
    UniProtKB/TrEMBL
    A0A0S2Z577
    Related
    ENSP00000327650.3, ENST00000333371.7
    Conserved Domains (1) summary
    pfam00995
    Location:37605
    Sec1; Sec1 family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    90998416..91022839 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017022075.2XP_016877564.1  vacuolar protein sorting-associated protein 33B isoform X3

  2. XM_011521448.1XP_011519750.1  vacuolar protein sorting-associated protein 33B isoform X1

    See identical proteins and their annotated locations for XP_011519750.1

    UniProtKB/Swiss-Prot
    Q9H267
    Conserved Domains (1) summary
    pfam00995
    Location:10514
    Sec1; Sec1 family
  3. XM_017022076.1XP_016877565.1  vacuolar protein sorting-associated protein 33B isoform X3

  4. XM_011521449.2XP_011519751.1  vacuolar protein sorting-associated protein 33B isoform X2

    Conserved Domains (1) summary
    pfam00995
    Location:23497
    Sec1; Sec1 family
  5. XM_005254887.1XP_005254944.1  vacuolar protein sorting-associated protein 33B isoform X1

    See identical proteins and their annotated locations for XP_005254944.1

    UniProtKB/Swiss-Prot
    Q9H267
    Conserved Domains (1) summary
    pfam00995
    Location:10514
    Sec1; Sec1 family

RNA

  1. XR_001751213.2 RNA Sequence

    Related
    ENST00000574755.5
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