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Aliases for VPS33B Gene

Aliases for VPS33B Gene

  • VPS33B, Late Endosome And Lysosome Associated 2 3 5
  • Vacuolar Protein Sorting 33 Homolog B (Yeast) 2
  • Vacuolar Protein Sorting 33B (Yeast Homolog) 2
  • HVPS33B 4

External Ids for VPS33B Gene

Previous GeneCards Identifiers for VPS33B Gene

  • GC15P087731
  • GC15M084982
  • GC15M089129
  • GC15M089271
  • GC15M089342
  • GC15M091541
  • GC15M067652

Summaries for VPS33B Gene

Entrez Gene Summary for VPS33B Gene

  • 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]

GeneCards Summary for VPS33B Gene

VPS33B (VPS33B, Late Endosome And Lysosome Associated) is a Protein Coding gene. Diseases associated with VPS33B include Arthrogryposis, Renal Dysfunction, And Cholestasis 1 and Vps33b-Related Arthrogryposis, Renal Dysfunction, And Cholestasis Syndrome. An important paralog of this gene is VPS33A.

UniProtKB/Swiss-Prot for VPS33B Gene

  • May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membrane docking/fusion reactions of late endosomes/lysosomes. Mediates phagolysosomal fusion in macrophages (PubMed:18474358). Proposed to be involved in endosomal maturation implicating VIPAS39. In epithelial cells, the VPS33B:VIPAS39 complex may play a role in the apical recycling pathway and in the maintenance of the apical-basolateral polarity (PubMed:20190753). Seems to be involved in the sorting of specific cargos from the trans-Golgi network to alpha-granule-destined multivesicular bodies (MVBs) promoting MVBs maturation in megakaryocytes (By similarity).

Gene Wiki entry for VPS33B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS33B Gene

Genomics for VPS33B Gene

Regulatory Elements for VPS33B Gene

Enhancers for VPS33B Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH15G090991 1.4 Ensembl ENCODE 23.6 +28.9 28947 4.3 CREB3L1 MLX AGO1 ZFP64 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC RCCD1 ENSG00000259314 VPS33B LOC101926911 UNC45A NIFKP5 ENSG00000270322 ENSG00000259212 FES PRC1
GH15G091021 1.1 ENCODE 12.1 +0.3 270 2.0 HDGF ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766 ZNF143 ZNF207 RCCD1 ENSG00000259314 VPS33B UNC45A LOC101926911 LOC105370970
GH15G090988 0.9 Ensembl ENCODE 12.3 +34.0 34020 0.8 HDGF PKNOX1 NFIB GATAD2B ARID3A GATA3 IKZF1 HMBOX1 IKZF2 RCCD1 LOC101926911 VPS33B PRC1 GC15M090978 ENSG00000200142
GH15G090986 0.6 ENCODE 12.3 +35.6 35616 0.2 ZNF362 CEBPG DPF2 ATF2 ATF3 ZSCAN5C CREB1 NBN MLLT1 LOC101926911 VPS33B HDDC3 ENSG00000224441 UNC45A GC15M090978 PRC1 ENSG00000200142
GH15G090989 0.5 Ensembl 12.3 +33.3 33321 0.2 ZNF362 ARID3A MAFG ZNF18 RCCD1 VPS33B LOC101926911 PRC1 GC15M090978 ENSG00000200142
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VPS33B on UCSC Golden Path with GeneCards custom track

Promoters for VPS33B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000081160 121 1401 HDGF ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF766 ZNF143 ZNF207

Genomic Location for VPS33B Gene

Chromosome:
15
Start:
90,998,416 bp from pter
End:
91,022,621 bp from pter
Size:
24,206 bases
Orientation:
Minus strand

Genomic View for VPS33B Gene

Genes around VPS33B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS33B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS33B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS33B Gene

Proteins for VPS33B Gene

  • Protein details for VPS33B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H267-VP33B_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 33B
    Protein Accession:
    Q9H267
    Secondary Accessions:
    • B3KQF6
    • Q96K14
    • Q9NRP6
    • Q9NSF3

    Protein attributes for VPS33B Gene

    Size:
    617 amino acids
    Molecular mass:
    70585 Da
    Quaternary structure:
    • Interacts with RAB11A and VIPAS39. Associates with adaptor protein complex 3 (AP-3), clathrin:AP-3 and clathrin:HGS complexes (PubMed:21411634). Interacts with M.tuberculosis PtpA.

    Alternative splice isoforms for VPS33B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS33B Gene

Post-translational modifications for VPS33B Gene

  • Phosphorylated on tyrosine residues. Dephosphorylation by M.tuberculosis PtpA is necessary to induce the reduction of host phagolysosome fusion in M.tuberculosis-infected macrophages.
  • Ubiquitination at posLast=304304
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS33B Gene

Domains & Families for VPS33B Gene

Protein Domains for VPS33B Gene

Graphical View of Domain Structure for InterPro Entry

Q9H267

UniProtKB/Swiss-Prot:

VP33B_HUMAN :
  • Belongs to the STXBP/unc-18/SEC1 family.
Family:
  • Belongs to the STXBP/unc-18/SEC1 family.
genes like me logo Genes that share domains with VPS33B: view

No data available for Gene Families for VPS33B Gene

Function for VPS33B Gene

Molecular function for VPS33B Gene

UniProtKB/Swiss-Prot Function:
May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membrane docking/fusion reactions of late endosomes/lysosomes. Mediates phagolysosomal fusion in macrophages (PubMed:18474358). Proposed to be involved in endosomal maturation implicating VIPAS39. In epithelial cells, the VPS33B:VIPAS39 complex may play a role in the apical recycling pathway and in the maintenance of the apical-basolateral polarity (PubMed:20190753). Seems to be involved in the sorting of specific cargos from the trans-Golgi network to alpha-granule-destined multivesicular bodies (MVBs) promoting MVBs maturation in megakaryocytes (By similarity).

Gene Ontology (GO) - Molecular Function for VPS33B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with VPS33B: view
genes like me logo Genes that share phenotypes with VPS33B: view

Human Phenotype Ontology for VPS33B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VPS33B Gene

MGI Knock Outs for VPS33B:

Animal Model Products

CRISPR Products

miRNA for VPS33B Gene

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for VPS33B Gene

Localization for VPS33B Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS33B Gene

Late endosome membrane; Peripheral membrane protein; Cytoplasmic side. Lysosome membrane; Peripheral membrane protein; Cytoplasmic side. Early endosome. Cytoplasmic vesicle, clathrin-coated vesicle. Recycling endosome. Note=Colocalizes in clusters with VIPAS39 at cytoplasmic organelles (PubMed:19109425). Colocalizes with RAB11A and VIPAS39 on recycling endosomes (PubMed:22753090). Colocalizes with AP-3, clathrin, Rab5 and Rab7b (PubMed:21411634). Colocalizes with M.tuberculosis PtpA in the cytosol of tuberculosis-infected macrophages and associates with phagosomes (PubMed:18474358). {ECO:0000269 PubMed:18474358, ECO:0000269 PubMed:19109425, ECO:0000269 PubMed:21411634, ECO:0000269 PubMed:22753090}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VPS33B gene
Compartment Confidence
lysosome 5
endosome 5
cytosol 3
mitochondrion 2
peroxisome 1
nucleus 1

Gene Ontology (GO) - Cellular Components for VPS33B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 15052268
GO:0005764 lysosome IDA,IEA 15052268
GO:0005765 lysosomal membrane IEA --
GO:0005768 endosome IEA --
GO:0005769 early endosome IEA --
genes like me logo Genes that share ontologies with VPS33B: view

Pathways & Interactions for VPS33B Gene

SuperPathways for VPS33B Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS33B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006904 vesicle docking involved in exocytosis IEA --
GO:0007032 endosome organization IMP 23918659
GO:0008333 NOT endosome to lysosome transport IMP 25783203
GO:0015031 protein transport IMP 15052268
genes like me logo Genes that share ontologies with VPS33B: view

No data available for Pathways by source and SIGNOR curated interactions for VPS33B Gene

Drugs & Compounds for VPS33B Gene

No Compound Related Data Available

Transcripts for VPS33B Gene

Unigene Clusters for VPS33B Gene

Vacuolar protein sorting 33 homolog B (yeast):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS33B Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11
SP1: -
SP2:
SP3: - -
SP4:
SP5: - - -

Relevant External Links for VPS33B Gene

GeneLoc Exon Structure for
VPS33B
ECgene alternative splicing isoforms for
VPS33B

Expression for VPS33B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VPS33B Gene

Protein differential expression in normal tissues from HIPED for VPS33B Gene

This gene is overexpressed in Peripheral blood mononuclear cells (20.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VPS33B Gene



Protein tissue co-expression partners for VPS33B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS33B Gene:

VPS33B

SOURCE GeneReport for Unigene cluster for VPS33B Gene:

Hs.745007

mRNA Expression by UniProt/SwissProt for VPS33B Gene:

Q9H267-VP33B_HUMAN
Tissue specificity: Ubiquitous; highly expressed in testis and low expression in the lung.

Evidence on tissue expression from TISSUES for VPS33B Gene

  • Nervous system(3.4)
  • Blood(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS33B Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • chin
  • ear
  • eye
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • outer ear
  • pituitary gland
  • skull
Thorax:
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • abdominal wall
  • biliary tract
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
Pelvis:
  • pelvis
  • placenta
  • ureter
  • urinary bladder
  • uterus
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • coagulation system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with VPS33B: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for VPS33B Gene

Orthologs for VPS33B Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for VPS33B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS33B 34 35
  • 99.51 (n)
dog
(Canis familiaris)
Mammalia VPS33B 34 35
  • 92.49 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS33B 35
  • 92 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VPS33B 34 35
  • 91.25 (n)
mouse
(Mus musculus)
Mammalia Vps33b 34 16 35
  • 91.25 (n)
rat
(Rattus norvegicus)
Mammalia Vps33b 34
  • 90.71 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 60 (a)
OneToMany
-- 35
  • 56 (a)
OneToMany
-- 35
  • 40 (a)
OneToMany
chicken
(Gallus gallus)
Aves VPS33B 34 35
  • 77.16 (n)
lizard
(Anolis carolinensis)
Reptilia VPS33B 35
  • 79 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps33b 34
  • 69.96 (n)
zebrafish
(Danio rerio)
Actinopterygii vps33b 34 35
  • 69.23 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8451 34
fruit fly
(Drosophila melanogaster)
Insecta CG5127 36
  • 21 (a)
Vps33B 35
  • 20 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea vps-33.2 34 35
  • 43.82 (n)
C56C10.1 36
  • 27 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS33 35
  • 19 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 46 (a)
OneToOne
Species where no ortholog for VPS33B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VPS33B Gene

ENSEMBL:
Gene Tree for VPS33B (if available)
TreeFam:
Gene Tree for VPS33B (if available)

Paralogs for VPS33B Gene

Paralogs for VPS33B Gene

(1) SIMAP similar genes for VPS33B Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with VPS33B: view

Variants for VPS33B Gene

Sequence variations from dbSNP and Humsavar for VPS33B Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs121434385 Pathogenic, Arthrogryposis, renal dysfunction and cholestasis syndrome 1 (ARCS1) [MIM:208085] 91,022,161(-) TCTGC(C/T)GGAGC nc-transcript-variant, upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs139829189 Arthrogryposis, renal dysfunction and cholestasis syndrome 1 (ARCS1) [MIM:208085] 91,006,702(+) CTTGG(A/G)AGCAA nc-transcript-variant, reference, missense
rs1057519063 Pathogenic 91,013,842(-) CTGGC(C/T)GAACT nc-transcript-variant, downstream-variant-500B, reference, stop-gained, utr-variant-5-prime
rs121434383 Pathogenic 90,999,963(-) AGCGG(C/T)GAAGC nc-transcript-variant, reference, stop-gained
rs121434384 Pathogenic 91,002,143(-) ATCTG(A/C/T)GAAGA nc-transcript-variant, reference, synonymous-codon, stop-gained

Structural Variations from Database of Genomic Variants (DGV) for VPS33B Gene

Variant ID Type Subtype PubMed ID
dgv757e212 CNV loss 25503493
esv2672368 CNV deletion 23128226
esv3581818 CNV loss 25503493
nsv1053084 CNV gain 25217958
nsv833090 CNV loss 17160897
nsv833091 CNV loss 17160897
nsv976964 CNV duplication 23825009

Variation tolerance for VPS33B Gene

Residual Variation Intolerance Score: 5.76% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.81; 34.12% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VPS33B Gene

Human Gene Mutation Database (HGMD)
VPS33B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS33B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS33B Gene

Disorders for VPS33B Gene

MalaCards: The human disease database

(6) MalaCards diseases for VPS33B Gene - From: OMIM, ClinVar, GeneTests, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
arthrogryposis, renal dysfunction, and cholestasis 1
  • arc syndrome
vps33b-related arthrogryposis, renal dysfunction, and cholestasis syndrome
  • arthrogryposis, renal dysfunction, and cholestasis 1
cholestasis
  • bile occlusion
myh-9 related disease
  • sebastian syndrome
bile duct disease
  • bile duct disorder nos
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

VP33B_HUMAN
  • Arthrogryposis, renal dysfunction and cholestasis syndrome 1 (ARCS1) [MIM:208085]: A multisystem disorder, characterized by neurogenic arthrogryposis multiplex congenita, renal tubular dysfunction and neonatal cholestasis with bile duct hypoplasia and low gamma glutamyl transpeptidase activity. Platelet dysfunction is common. {ECO:0000269 PubMed:15052268, ECO:0000269 PubMed:18853461, ECO:0000269 PubMed:20190753, ECO:0000269 PubMed:22753090, ECO:0000269 PubMed:23918659}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for VPS33B

Genetic Association Database (GAD)
VPS33B
Human Genome Epidemiology (HuGE) Navigator
VPS33B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VPS33B
genes like me logo Genes that share disorders with VPS33B: view

No data available for Genatlas for VPS33B Gene

Publications for VPS33B Gene

  1. Mycobacterium tuberculosis virulence is mediated by PtpA dephosphorylation of human vacuolar protein sorting 33B. (PMID: 18474358) Bach H. … Av-Gay Y. (Cell Host Microbe 2008) 3 4 22 64
  2. Vps33B is required for delivery of endocytosed cargo to lysosomes. (PMID: 26403612) Galmes R. … Klumperman J. (Traffic 2015) 2 3 64
  3. Structural basis of Vps33A recruitment to the human HOPS complex by Vps16. (PMID: 23901104) Graham S.C. … Owen D.J. (Proc. Natl. Acad. Sci. U.S.A. 2013) 3 4 64
  4. Vps33b pathogenic mutations preferentially affect VIPAS39/SPE-39-positive endosomes. (PMID: 23918659) Tornieri K. … Faundez V. (Hum. Mol. Genet. 2013) 3 4 64
  5. Associations among genotype, clinical phenotype, and intracellular localization of trafficking proteins in ARC syndrome. (PMID: 22753090) Smith H. … Gissen P. (Hum. Mutat. 2012) 3 4 64

Products for VPS33B Gene

Sources for VPS33B Gene

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