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Aliases for VIPAS39 Gene

Aliases for VIPAS39 Gene

  • VPS33B Interacting Protein, Apical-Basolateral Polarity Regulator, Spe-39 Homolog 2 3 5
  • C14orf133 3 4
  • HSPE-39 3 4
  • SPE39 3 4
  • VIPAR 3 4
  • VPS33B-Interacting Protein Involved In Polarity And Apical Protein Restriction 3
  • VPS33B-Interacting Protein In Apical-Basolateral Polarity Regulator 4
  • VPS33B-Interacting Protein In Polarity And Apical Restriction 4
  • Apical-Basolateral Polarity Regulator 2
  • Chromosome 14 Open Reading Frame 133 2
  • VPS33B Interacting Protein 2
  • SPE-39 3
  • VPS16B 3

External Ids for VIPAS39 Gene

Previous HGNC Symbols for VIPAS39 Gene

  • C14orf133

Previous GeneCards Identifiers for VIPAS39 Gene

  • GC14M077895

Summaries for VIPAS39 Gene

Entrez Gene Summary for VIPAS39 Gene

  • This gene encodes a protein involved in the sorting of lysosomal proteins. Mutations in this gene are associated with ARCS2 (arthrogryposis, renal dysfunction, and cholestasis-2). Alternative splicing results in multiple transcript variants.[provided by RefSeq, Jul 2010]

GeneCards Summary for VIPAS39 Gene

VIPAS39 (VPS33B Interacting Protein, Apical-Basolateral Polarity Regulator, Spe-39 Homolog) is a Protein Coding gene. Diseases associated with VIPAS39 include arthrogryposis, renal dysfunction, and cholestasis 2 and vipas39-related arthrogryposis, renal dysfunction, and cholestasis syndrome.

UniProtKB/Swiss-Prot for VIPAS39 Gene

  • Proposed to be involved in endosomal maturation implicating in part VPS33B. In epithelial cells, the VPS33B:VIPAS39 complex may play a role in the apical RAB11A-dependent recycling pathway and in the maintenance of the apical-basolateral polarity (PubMed:20190753). May play a role in lysosomal trafficking, probably via association with the core HOPS complex in a discrete population of endosomes; the functions seems to be indepenedent of VPS33B (PubMed:19109425). May play a role in vesicular trafficking during spermatogenesis (By similarity). May be involved in direct or indirect transcriptional regulation of E-cadherin (By similarity).

Gene Wiki entry for VIPAS39 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VIPAS39 Gene

Genomics for VIPAS39 Gene

Regulatory Elements for VIPAS39 Gene

Enhancers for VIPAS39 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around VIPAS39 on UCSC Golden Path with GeneCards custom track

Promoters for VIPAS39 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around VIPAS39 on UCSC Golden Path with GeneCards custom track

Genomic Location for VIPAS39 Gene

Chromosome:
14
Start:
77,426,675 bp from pter
End:
77,457,952 bp from pter
Size:
31,278 bases
Orientation:
Minus strand

Genomic View for VIPAS39 Gene

Genes around VIPAS39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VIPAS39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VIPAS39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VIPAS39 Gene

Proteins for VIPAS39 Gene

  • Protein details for VIPAS39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H9C1-SPE39_HUMAN
    Recommended name:
    Spermatogenesis-defective protein 39 homolog
    Protein Accession:
    Q9H9C1
    Secondary Accessions:
    • B4DPI6
    • O95434
    • Q9H7E1
    • Q9H9I9

    Protein attributes for VIPAS39 Gene

    Size:
    493 amino acids
    Molecular mass:
    57005 Da
    Quaternary structure:
    • Interacts with VPS33B (PubMed:19109425, PubMed:23901104). Associates with the homotypic fusion and vacuole protein sorting (HOPS) complex; impaired by VPS33B (PubMed:19109425, PubMed:23918659, PubMed:22753090). A possible interaction with VPS33A is reported conflictingly (PubMed:19109425, PubMed:23901104). Interacts with RAB11A (PubMed:20190753).
    SequenceCaution:
    • Sequence=AAD09624.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=BAB14951.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for VIPAS39 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VIPAS39 Gene

Proteomics data for VIPAS39 Gene at MOPED

Post-translational modifications for VIPAS39 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for VIPAS39 Gene

Domains & Families for VIPAS39 Gene

Protein Domains for VIPAS39 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VIPAS39 Gene

Graphical View of Domain Structure for InterPro Entry

Q9H9C1

UniProtKB/Swiss-Prot:

SPE39_HUMAN :
  • Belongs to the SPE39 family.
Family:
  • Belongs to the SPE39 family.
genes like me logo Genes that share domains with VIPAS39: view

No data available for Gene Families for VIPAS39 Gene

Function for VIPAS39 Gene

Molecular function for VIPAS39 Gene

UniProtKB/Swiss-Prot Function:
Proposed to be involved in endosomal maturation implicating in part VPS33B. In epithelial cells, the VPS33B:VIPAS39 complex may play a role in the apical RAB11A-dependent recycling pathway and in the maintenance of the apical-basolateral polarity (PubMed:20190753). May play a role in lysosomal trafficking, probably via association with the core HOPS complex in a discrete population of endosomes; the functions seems to be indepenedent of VPS33B (PubMed:19109425). May play a role in vesicular trafficking during spermatogenesis (By similarity). May be involved in direct or indirect transcriptional regulation of E-cadherin (By similarity).

Phenotypes for VIPAS39 Gene

genes like me logo Genes that share phenotypes with VIPAS39: view

Human Phenotype Ontology for VIPAS39 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for VIPAS39 Gene

miRTarBase miRNAs that target VIPAS39

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for VIPAS39 Gene

Localization for VIPAS39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VIPAS39 Gene

Cytoplasm. Cytoplasmic vesicle. Early endosome. Recycling endosome. Late endosome. Note=Colocalizes in clusters with VPS33B at cytoplasmic organelles (PubMed:19109425).

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VIPAS39 Gene COMPARTMENTS Subcellular localization image for VIPAS39 gene
Compartment Confidence
endosome 5
nucleus 3
cytosol 2
lysosome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for VIPAS39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 20190753
GO:0030897 colocalizes_with HOPS complex IDA 19109425
genes like me logo Genes that share ontologies with VIPAS39: view

Pathways & Interactions for VIPAS39 Gene

SuperPathways for VIPAS39 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VIPAS39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006886 intracellular protein transport IMP 19109425
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with VIPAS39: view

No data available for Pathways by source and SIGNOR curated interactions for VIPAS39 Gene

Drugs & Compounds for VIPAS39 Gene

No Compound Related Data Available

Transcripts for VIPAS39 Gene

Unigene Clusters for VIPAS39 Gene

VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for VIPAS39 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17
SP1: -
SP2:
SP3:
SP4:
SP5:

Relevant External Links for VIPAS39 Gene

GeneLoc Exon Structure for
VIPAS39
ECgene alternative splicing isoforms for
VIPAS39

Expression for VIPAS39 Gene

mRNA expression in normal human tissues for VIPAS39 Gene

Protein differential expression in normal tissues from HIPED for VIPAS39 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (23.8), Fetal Brain (8.4), and Prostate (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for VIPAS39 Gene



SOURCE GeneReport for Unigene cluster for VIPAS39 Gene Hs.16157

genes like me logo Genes that share expression patterns with VIPAS39: view

Protein tissue co-expression partners for VIPAS39 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for VIPAS39 Gene

Orthologs for VIPAS39 Gene

This gene was present in the common ancestor of animals.

Orthologs for VIPAS39 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia VIPAS39 35
  • 91.55 (n)
  • 96.47 (a)
VIPAS39 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VIPAS39 35
  • 92.43 (n)
  • 97.36 (a)
VIPAS39 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vipas39 35
  • 88.77 (n)
  • 95.55 (a)
Vipas39 16
Vipas39 36
  • 95 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia VIPAS39 35
  • 99.66 (n)
  • 100 (a)
VIPAR 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vipas39 35
  • 89.71 (n)
  • 94.78 (a)
oppossum
(Monodelphis domestica)
Mammalia VIPAS39 36
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 85 (a)
OneToMany
-- 36
  • 84 (a)
OneToMany
chicken
(Gallus gallus)
Aves VIPAR 35
  • 74.59 (n)
  • 80.99 (a)
VIPAS39 36
  • 81 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VIPAS39 36
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vipas39 35
  • 68.23 (n)
  • 72.24 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.3364 35
zebrafish
(Danio rerio)
Actinopterygii vipas39 35
  • 65.49 (n)
  • 65.01 (a)
xbp1 35
vipas39 36
  • 65 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001233 35
  • 42.8 (n)
  • 31.92 (a)
fruit fly
(Drosophila melanogaster)
Insecta Vps16B 35
  • 43.56 (n)
  • 30.06 (a)
Vps16B 36
  • 27 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea spe-39 36
  • 21 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 34 (a)
OneToOne
Species with no ortholog for VIPAS39:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 VIPAS39 Gene

ENSEMBL:
Gene Tree for VIPAS39 (if available)
TreeFam:
Gene Tree for VIPAS39 (if available)

Paralogs for VIPAS39 Gene

(1) SIMAP similar genes for VIPAS39 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with VIPAS39: view

No data available for Paralogs for VIPAS39 Gene

Variants for VIPAS39 Gene

Sequence variations from dbSNP and Humsavar for VIPAS39 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs7143671 -- 77,430,301(+) TAATT(A/C)ACAAA intron-variant
rs8018711 -- 77,455,406(+) CCTGA(A/G)CTTGG intron-variant
rs760252 -- 77,449,862(+) GAACT(C/T)AAGGC intron-variant
rs8006819 -- 77,438,943(+) ATATC(A/G)TAATC intron-variant
rs7148149 -- 77,444,825(+) catcc(A/G)cccac intron-variant

Variation tolerance for VIPAS39 Gene

Residual Variation Intolerance Score: 18.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.21; 39.83% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VIPAS39 Gene

HapMap Linkage Disequilibrium report
VIPAS39
Human Gene Mutation Database (HGMD)
VIPAS39

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for VIPAS39 Gene

Disorders for VIPAS39 Gene

MalaCards: The human disease database

(5) MalaCards diseases for VIPAS39 Gene - From: OMIM, ClinVar, GeneTests, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SPE39_HUMAN
  • Arthrogryposis, renal dysfunction and cholestasis syndrome 2 (ARCS2) [MIM:613404]: 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. Note=The disease is caused by mutations affecting the gene represented in this entry. In liver, CEACAM5 and ABCB11 are mislocalized and E-cadherin expression is decreased.

Relevant External Links for VIPAS39

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VIPAS39
genes like me logo Genes that share disorders with VIPAS39: view

No data available for Genatlas for VIPAS39 Gene

Publications for VIPAS39 Gene

  1. Vps33b pathogenic mutations preferentially affect VIPAS39/SPE-39-positive endosomes. (PMID: 23918659) Tornieri K. … Faundez V. (Hum. Mol. Genet. 2013) 2 3 4 67
  2. Associations among genotype, clinical phenotype, and intracellular localization of trafficking proteins in ARC syndrome. (PMID: 22753090) Smith H. … Gissen P. (Hum. Mutat. 2012) 2 3
  3. The VPS33B-binding protein VPS16B is required in megakaryocyte and platelet I+-granule biogenesis. (PMID: 23002115) Urban D. … Kahr W.H. (Blood 2012) 2 3
  4. Mutations in VIPAR cause an arthrogryposis, renal dysfunction and cholestasis syndrome phenotype with defects in epithelial polarization. (PMID: 20190753) Cullinane A.R. … Gissen P. (Nat. Genet. 2010) 2 3
  5. SPE-39 family proteins interact with the HOPS complex and function in lysosomal delivery. (PMID: 19109425) Zhu G.D. … L'hernault S.W. (Mol. Biol. Cell 2009) 2 3

Products for VIPAS39 Gene

Sources for VIPAS39 Gene

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