VPS33B

General Information

Full gene name:vacuolar protein sorting 33 homolog B (yeast) Entrez Gene ID:26276 Location:15q26.1 Synonyms: Type:protein-coding

User SNPs

SNPs given by the user that are near or inside this gene:

SNP	Distance (bp)	Direction
rs8042680	20437	downstream

NCBI 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 Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. [provided by RefSeq, Jul 2008]

OMIM

OMIM ID:`OMIM ID 613401 `_

Allelic Variants (Selected Examples)

.0001 ARTHROGRYPOSIS, RENAL DYSFUNCTION, AND CHOLESTASIS 2

In a Turkish proband with arthrogryposis, renal dysfunction, and cholestasis-2 (613404), Cullinane et al. (2010) identified homozygosity for a 535C-T transition in the VIPAR gene, resulting in a gln179-to-ter (Q179X) substitution. The mutation segregated with disease in the family and was not found in at least 200 ethnically matched chromosomes.

.0002 ARTHROGRYPOSIS, RENAL DYSFUNCTION, AND CHOLESTASIS 2

In a Croatian proband with arthrogryposis, renal dysfunction, and cholestasis-2 (613404), Cullinane et al. (2010) identified homozygosity for a 5-bp deletion (748delACAGA) in the VIPAR gene, causing a frameshift and a premature termination codon. The mutation segregated with disease in the family and was not found in at least 200 ethnically matched chromosomes.

.0003 ARTHROGRYPOSIS, RENAL DYSFUNCTION, AND CHOLESTASIS 2

In an Italian proband with arthrogryposis, renal dysfunction, and cholestasis-2 (613404), Cullinane et al. (2010) identified homozygosity for a 658C-T transition in the VIPAR gene, resulting in an arg220-to-ter (R220X) substitution. A Turkish ARCS proband was found to be compound heterozygous for R220X and an 873C-T transition in the VIPAR gene, resulting in a gln291-to-ter (Q291X; 613404.0004) substitution. Both mutations segregated with disease in the families and were not found in at least 200 ethnically matched chromosomes, respectively.

.0004 ARTHROGRYPOSIS, RENAL DYSFUNCTION, AND CHOLESTASIS 2

See 613404.0003 and Cullinane et al. (2010).

.0005 ARTHROGRYPOSIS, RENAL DYSFUNCTION, AND CHOLESTASIS 2

In a Turkish proband with arthrogryposis, renal dysfunction, and cholestasis-2 (613404), Cullinane et al. (2010) identified homozygosity for a 2T-G transversion in the VIPAR gene, resulting in a met1-to-arg (M1R) substitution at the start codon, predicted to cause failure of translation. The mutation segregated with disease in the family and was not found in at least 200 ethnically matched chromosomes.

NCBI Phenotypes

• Gene Reviews
• Arthrogryposis renal dysfunction cholestasis syndrome
• OMIM
• GTR

Gene Ontology

• vesicle docking involved in exocytosis
• late endosome
• lysosome
• protein binding
• platelet alpha granule
• platelet alpha granule organization
• vesicle-mediated transport
• cellular membrane fusion
• cytoplasm
• lysosomal membrane
• late endosome membrane
• perinuclear region of cytoplasm
• protein transport
• HOPS complex
• melanosome localization
• lysosome localization

KEGG Pathways

No pathways found linked to this gene.

GeneRIFs

• Genetic deletion of ptpA attenuates Mycobacterium tuberculosis growth in human macrophages and identify VPS33B, a regulator of membrane fusion, as a PtpA substrate. [PMID 18474358]
• We assessed the clinical characteristics and investigated the VPS33B mutations in Korean patients with ARC (arthrogryposis, renal dysfunction, and cholestasis) syndrome. [PMID 19274792]
• Observational study of gene-disease association. (HuGE Navigator) [PMID 18367154]
• Two-hybrid [PMID 21900206]
• Two-hybrid [PMID 21900206]
• Affinity Capture-MS [PMID 21906983]
• A and B classes reflect the evolution of organelle/tissue-specific functions [PMID 15790593]
• VPS33B is involved in intracellular vesicle trafficking [PMID 16123220]
• The present observations indicate that VPS33B deficiency results in abnormal secretion of lamellar granules, which underlies ichthyosis in ARC syndrome. [PMID 18347289]
• Positive Genetic [PMID 22318606]
• encodes a homolog of the class C yeast vacuolar protein sorting gene, that contains a Sec1-like domain important in the regulation of vesicle-to-target SNARE complex formation and subsequent membrane fusion [PMID 15052268]
• Two-hybrid [PMID 16189514]

PubMed Articles

Recent articles:

• Lin YY et al. “Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.” Nature. 2012 Feb 8;482(7384):251-5. PMID 22318606
• Kim W et al. “Systematic and quantitative assessment of the ubiquitin-modified proteome.” Mol Cell. 2011 Oct 21;44(2):325-40. PMID 21906983
• Wagner SA et al. “A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.” Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. PMID 21890473
• Vinayagam A et al. “A directed protein interaction network for investigating intracellular signal transduction.” Sci Signal. 2011 Sep 6;4(189):rs8. PMID 21900206
• Danielsen JM et al. “Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.” Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. PMID 21139048
• Jang JY et al. “Clinical characteristics and VPS33B mutations in patients with ARC syndrome.” J Pediatr Gastroenterol Nutr. 2009 Mar;48(3):348-54. PMID 19274792
• Zhu GD et al. “SPE-39 family proteins interact with the HOPS complex and function in lysosomal delivery.” Mol Biol Cell. 2009 Feb;20(4):1223-40. PMID 19109425
• Liang C et al. “Beclin1-binding UVRAG targets the class C Vps complex to coordinate autophagosome maturation and endocytic trafficking.” Nat Cell Biol. 2008 Jul;10(7):776-87. PMID 18552835
• Verma R et al. “Linkage disequilibrium mapping of a chromosome 15q25-26 major depression linkage region and sequencing of NTRK3.” Biol Psychiatry. 2008 Jun 15;63(12):1185-9. PMID 18367154
• Bach H et al. “Mycobacterium tuberculosis virulence is mediated by PtpA dephosphorylation of human vacuolar protein sorting 33B.” Cell Host Microbe. 2008 May 15;3(5):316-22. PMID 18474358

Top Pubmed articles linked to gene VPS33B matching any search term:

• Jang JY et al. “Clinical characteristics and VPS33B mutations in patients with ARC syndrome.” J Pediatr Gastroenterol Nutr. 2009 Mar;48(3):348-54. PMID 19274792