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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, Apical-Basolateral Polarity Regulator 2
  • VPS33B-Interacting Protein In Polarity And Apical Restriction 4
  • Spermatogenesis-Defective Protein 39 Homolog 3
  • Chromosome 14 Open Reading Frame 133 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

Additional gene information for VIPAS39 Gene

No data available for CIViC summary , 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 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
GH14H077021 2.3 VISTA FANTOM5 ENCODE dbSUPER 29.6 +423.6 423573 25.6 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D ZNF585B SNW1 ALKBH1 RPL22P2 VIPAS39 POMT2 IRF2BPL ZMYND19P1 GPATCH2L RPL21P10 CIPC
GH14H076767 1.4 Ensembl ENCODE dbSUPER 37.4 +689.5 689467 2.2 PKNOX1 ZFP64 BATF TCF12 RUNX3 CREM IKZF2 ZC3H11A REST ELF1 VIPAS39 SNW1 ZMYND19P1 ALKBH1 IRF2BPL GPATCH2L RPL22P2 POMT2 ENSG00000259081 VASH1
GH14H077096 1.4 ENCODE dbSUPER 35.7 +359.5 359488 4.4 HDGF PKNOX1 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B YY1 SNW1 VIPAS39 ZMYND19P1 RPL22P2 ALKBH1 IRF2BPL GPATCH2L RPL21P10 POMT2 CIPC
GH14H077614 1.3 ENCODE dbSUPER 34.6 -158.3 -158271 2.7 HDGF PKNOX1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZBTB7B YY1 SLC30A9 SNW1 VIPAS39 ALKBH1 RPL22P2 ADCK1 ZMYND19P1 SPTLC2 RPL21P10 IRF2BPL RN7SL587P
GH14H077301 1.5 Ensembl ENCODE dbSUPER 24.3 +152.9 152869 6.5 PKNOX1 FOXA2 ATF1 ARID4B SIN3A FEZF1 ZNF2 ZNF207 ATF7 FOS VIPAS39 IRF2BPL GSTZ1 ALKBH1 NGB MIR1260A ZDHHC22 ENSG00000201384 SAMD15 TMED8
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000071155 -48 2801 PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 YBX1 ZNF2 YY1

Genomic Locations for VIPAS39 Gene

Genomic Locations for VIPAS39 Gene
chr14:77,426,675-77,457,952
(GRCh38/hg38)
Size:
31,278 bases
Orientation:
Minus strand
chr14:77,893,018-77,924,295
(GRCh37/hg19)

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

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

Gene Families for VIPAS39 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

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

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 From GWAS Catalog for VIPAS39 Gene

Gene Ontology (GO) - Molecular Function for VIPAS39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with VIPAS39: view
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 Models for VIPAS39 Gene

MGI Knock Outs for VIPAS39:

Animal Model Products

miRNA for VIPAS39 Gene

miRTarBase miRNAs that target VIPAS39

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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
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 VIPAS39 gene
Compartment Confidence
golgi apparatus 5
endosome 5
nucleus 3
cytosol 2
lysosome 1

Gene Ontology (GO) - Cellular Components for VIPAS39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 20190753
GO:0005768 endosome IEA --
GO:0005769 early endosome IDA,IEA 19109425
GO:0005770 late endosome IEA,IDA 19109425
GO:0005794 Golgi apparatus IDA 27435297
genes like me logo Genes that share ontologies with VIPAS39: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VIPAS39 Gene

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:0006355 regulation of transcription, DNA-templated IEA --
GO:0006810 transport IEA --
GO:0006886 intracellular protein transport IMP 19109425
GO:0007283 spermatogenesis 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:

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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



Protein tissue co-expression partners for VIPAS39 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VIPAS39 Gene:

VIPAS39

SOURCE GeneReport for Unigene cluster for VIPAS39 Gene:

Hs.16157

Evidence on tissue expression from TISSUES for VIPAS39 Gene

  • Kidney(4.3)
  • Liver(4.2)
  • Skin(4.2)
  • Nervous system(3.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VIPAS39 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 VIPAS39: view

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
chimpanzee
(Pan troglodytes)
Mammalia VIPAR 34
  • 100 (a)
OneToOne
VIPAS39 33
  • 99.66 (n)
dog
(Canis familiaris)
Mammalia VIPAS39 33 34
  • 92.43 (n)
cow
(Bos Taurus)
Mammalia VIPAS39 34 33
  • 91.55 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vipas39 33
  • 89.71 (n)
oppossum
(Monodelphis domestica)
Mammalia VIPAS39 34
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vipas39 16 34 33
  • 88.77 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 85 (a)
OneToMany
-- 34
  • 84 (a)
OneToMany
chicken
(Gallus gallus)
Aves VIPAS39 34
  • 81 (a)
OneToOne
VIPAR 33
  • 74.59 (n)
lizard
(Anolis carolinensis)
Reptilia VIPAS39 34
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vipas39 33
  • 68.23 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.3364 33
zebrafish
(Danio rerio)
Actinopterygii vipas39 34 33
  • 65.49 (n)
OneToOne
xbp1 33
fruit fly
(Drosophila melanogaster)
Insecta Vps16B 33 34
  • 43.56 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001233 33
  • 42.8 (n)
worm
(Caenorhabditis elegans)
Secernentea spe-39 34
  • 21 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 34 (a)
OneToOne
Species where no ortholog for VIPAS39 was found in the sources mined by GeneCards:
  • 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
rs200370925 Pathogenic 77,442,636(+) CTGTC(A/G)CACCT nc-transcript-variant, reference, stop-gained
rs267607171 Pathogenic 77,435,885(-) ACATA(C/T)AGGAC nc-transcript-variant, reference, stop-gained
rs267607172 Pathogenic 77,454,101(-) GTAGA(G/T)GAATC nc-transcript-variant, reference, missense
rs267607173 Pathogenic 77,444,311(-) CCTTA(C/T)AGGAC intron-variant, nc-transcript-variant, reference, stop-gained
rs794726653 Pathogenic 77,441,075(-) TAGAA(-/CAGAA)GAGCT nc-transcript-variant, reference, frameshift-variant

Structural Variations from Database of Genomic Variants (DGV) for VIPAS39 Gene

Variant ID Type Subtype PubMed ID
nsv832835 CNV gain 17160897
nsv1362 CNV deletion 18451855
nsv1041985 CNV loss 25217958

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

Human Gene Mutation Database (HGMD)
VIPAS39
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VIPAS39

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VIPAS39 Gene

Disorders for VIPAS39 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
arthrogryposis, renal dysfunction, and cholestasis 2
  • arthrogryposis, renal dysfunction and cholestasis syndrome 2
vipas39-related arthrogryposis, renal dysfunction, and cholestasis syndrome
  • arthrogryposis, renal dysfunction, and cholestasis 2
neurogenic arthrogryposis multiplex congenita
  • amc neurogenic type
cholestasis
  • bile occlusion
arthrogryposis, renal dysfunction, and cholestasis 1
  • arc syndrome
- 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 (Human molecular genetics 2013) 2 3 4 60
  2. Associations among genotype, clinical phenotype, and intracellular localization of trafficking proteins in ARC syndrome. (PMID: 22753090) Smith H … Gissen P (Human mutation 2012) 2 3 4 60
  3. Mutations in VIPAR cause an arthrogryposis, renal dysfunction and cholestasis syndrome phenotype with defects in epithelial polarization. (PMID: 20190753) Cullinane AR … Gissen P (Nature genetics 2010) 2 3 4 60
  4. SPE-39 family proteins interact with the HOPS complex and function in lysosomal delivery. (PMID: 19109425) Zhu GD … L'hernault SW (Molecular biology of the cell 2009) 2 3 4 60
  5. Structural basis of Vps33A recruitment to the human HOPS complex by Vps16. (PMID: 23901104) Graham SC … Owen DJ (Proceedings of the National Academy of Sciences of the United States of America 2013) 3 4 60

Products for VIPAS39 Gene

Sources for VIPAS39 Gene

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