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Aliases for VPS50 Gene

Aliases for VPS50 Gene

  • VPS50, EARP/GARPII Complex Subunit 2 3 5
  • Coiled-Coil Domain-Containing Protein 132 3 4
  • Coiled-Coil Domain Containing 132 2 3
  • EARP/GARPII Complex Subunit VPS50 3 4
  • Syndetin 2 3
  • CCDC132 3 4
  • KIAA1861 4
  • VPS54L 3

External Ids for VPS50 Gene

Previous HGNC Symbols for VPS50 Gene

  • CCDC132

Summaries for VPS50 Gene

GeneCards Summary for VPS50 Gene

VPS50 (VPS50, EARP/GARPII Complex Subunit) is a Protein Coding gene.

UniProtKB/Swiss-Prot for VPS50 Gene

  • Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane. Within the EARP complex, required to tether the complex to recycling endosomes. Not involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN).

Gene Wiki entry for VPS50 Gene

Additional gene information for VPS50 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS50 Gene

Genomics for VPS50 Gene

GeneHancer (GH) Regulatory Elements for VPS50 Gene

Promoters and enhancers for VPS50 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07I093231 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 556 -0.2 -195 2.1 PKNOX1 SMAD1 FOXA2 ARNT ARID4B SIN3A ZNF2 YY1 POLR2B ZNF766 VPS50 HEPACAM2 KRIT1 LOC105375403 PEX1 SAMD9L GATAD1 FAM133B BET1
GH07I092423 Enhancer 1.5 FANTOM5 Ensembl ENCODE 21.5 -807.6 -807639 2.2 HDGF PKNOX1 CLOCK MLX ARNT ARID4B NEUROD1 SIN3A YBX1 DMAP1 KRIT1 ENSG00000243107 FAM133B GATAD1 VPS50 AKAP9 PEX1 CYP51A1-AS1 MTERF1 CHCHD4P1
GH07I093115 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE 4.3 -115.0 -114975 4.6 RB1 RFX5 YY1 ZNF121 RCOR1 ATF7 ETV6 FOS NFYA NFYC SAMD9 SAMD9L VPS50 GC07P093054
GH07I093145 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 4.5 -85.1 -85070 3.6 PKNOX1 ATF1 ZBTB40 ZNF766 RUNX3 CAVIN1 ZBTB11 ZNF592 ZNF148 MEF2D SAMD9L ENSG00000243107 KRIT1 GATAD1 PEX1 FAM133B BET1 LOC105375403 VPS50 GC07P093141
GH07I093228 Enhancer 0.7 ENCODE 5.2 -3.9 -3917 0.2 CTCF FOXA2 CEBPG ZNF2 RAD21 FOXK2 SCRT2 ZNF143 SMC3 GATAD2A SAMD9L VPS50 HEPACAM2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VPS50 on UCSC Golden Path with GeneCards custom track

Genomic Locations for VPS50 Gene

Genomic Locations for VPS50 Gene
chr7:93,232,340-93,361,123
(GRCh38/hg38)
Size:
128,784 bases
Orientation:
Plus strand
chr7:92,861,653-92,988,338
(GRCh37/hg19)

Genomic View for VPS50 Gene

Genes around VPS50 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS50 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS50 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS50 Gene

Proteins for VPS50 Gene

  • Protein details for VPS50 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96JG6-VPS50_HUMAN
    Recommended name:
    Syndetin
    Protein Accession:
    Q96JG6
    Secondary Accessions:
    • B3KX22
    • D1MQ00
    • F5H5U7
    • Q75N07
    • Q8WVK3
    • Q9H5C6

    Protein attributes for VPS50 Gene

    Size:
    964 amino acids
    Molecular mass:
    111174 Da
    Quaternary structure:
    • Component of the endosome-associated retrograde protein (EARP) complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin (PubMed:25799061). Interacts with EIPR1 (By similarity).
    Miscellaneous:
    • Was named syndetin after the Greek syndeo, which means connect or tether.
    SequenceCaution:
    • Sequence=BAB15701.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB47490.2; Type=Frameshift; Positions=2; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS50 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS50 Gene

Post-translational modifications for VPS50 Gene

No Post-translational modifications

No data available for DME Specific Peptides for VPS50 Gene

Domains & Families for VPS50 Gene

Gene Families for VPS50 Gene

Protein Domains for VPS50 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VPS50 Gene

Graphical View of Domain Structure for InterPro Entry

Q96JG6

UniProtKB/Swiss-Prot:

VPS50_HUMAN :
  • Belongs to the syndetin family.
Family:
  • Belongs to the syndetin family.
genes like me logo Genes that share domains with VPS50: view

Function for VPS50 Gene

Molecular function for VPS50 Gene

UniProtKB/Swiss-Prot Function:
Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane. Within the EARP complex, required to tether the complex to recycling endosomes. Not involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN).

Phenotypes From GWAS Catalog for VPS50 Gene

Gene Ontology (GO) - Molecular Function for VPS50 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000149 SNARE binding IDA 25799061
GO:0005515 protein binding IPI 25799061
genes like me logo Genes that share ontologies with VPS50: view
genes like me logo Genes that share phenotypes with VPS50: view

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VPS50 Gene

Localization for VPS50 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS50 Gene

Recycling endosome.

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 VPS50 gene
Compartment Confidence
extracellular 5
endosome 5
nucleus 3
cytosol 3
plasma membrane 2
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (1)
  • Plasma membrane (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VPS50 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IEA --
GO:0016020 membrane HDA,IDA 19946888
GO:0055037 recycling endosome IEA,IDA 25799061
GO:0070062 extracellular exosome IDA,HDA 19056867
GO:1990745 EARP complex IDA 25799061
genes like me logo Genes that share ontologies with VPS50: view

Pathways & Interactions for VPS50 Gene

SuperPathways for VPS50 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS50 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0015031 protein transport IEA --
GO:0032456 endocytic recycling IMP 25799061
GO:0042147 NOT retrograde transport, endosome to Golgi IMP 25799061
genes like me logo Genes that share ontologies with VPS50: view

No data available for Pathways by source and SIGNOR curated interactions for VPS50 Gene

Drugs & Compounds for VPS50 Gene

No Compound Related Data Available

Transcripts for VPS50 Gene

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS50 Gene

No ASD Table

Relevant External Links for VPS50 Gene

GeneLoc Exon Structure for
VPS50
ECgene alternative splicing isoforms for
VPS50

Expression for VPS50 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of VPS50 Gene:

VPS50

mRNA Expression by UniProt/SwissProt for VPS50 Gene:

Q96JG6-VPS50_HUMAN
Tissue specificity: Ubiquitous, with higher expression in brain and skeletal muscle.

Evidence on tissue expression from TISSUES for VPS50 Gene

  • Nervous system(4.9)
  • Liver(4.2)
  • Lung(4.2)
  • Skin(4.2)
genes like me logo Genes that share expression patterns with VPS50: view

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS50 Gene

Orthologs for VPS50 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS50 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CCDC132 34 33
  • 99.65 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CCDC132 34 33
  • 93.6 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CCDC132 34 33
  • 93.19 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ccdc132 33
  • 89.94 (n)
mouse
(Mus musculus)
Mammalia Ccdc132 34 33
  • 89.56 (n)
OneToOne
Vps50 16
oppossum
(Monodelphis domestica)
Mammalia CCDC132 34
  • 67 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CCDC132 34
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves CCDC132 34 33
  • 81.96 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CCDC132 34
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ccdc132 33
  • 77.8 (n)
zebrafish
(Danio rerio)
Actinopterygii CCDC132 (2 of 2) 34
  • 87 (a)
OneToMany
CCDC132 (1 of 2) 34
  • 84 (a)
OneToMany
si:ch211-287b5.1 33
  • 71.38 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4996 33 34
  • 47.08 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000343 33
  • 42.89 (n)
worm
(Caenorhabditis elegans)
Secernentea C44B9.1 33
  • 44.59 (n)
vesa-1 34
  • 28 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G27900 33
  • 43.28 (n)
rice
(Oryza sativa)
Liliopsida Os10g0546300 33
  • 41.87 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 48 (a)
OneToOne
Species where no ortholog for VPS50 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VPS50 Gene

ENSEMBL:
Gene Tree for VPS50 (if available)
TreeFam:
Gene Tree for VPS50 (if available)

Paralogs for VPS50 Gene

No data available for Paralogs for VPS50 Gene

Variants for VPS50 Gene

Sequence variations from dbSNP and Humsavar for VPS50 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs1000020324 -- 93,321,367(+) C/T downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1000066698 -- 93,359,503(+) A/G 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1000072921 -- 93,330,292(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000137743 -- 93,293,496(+) C/G genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000158572 -- 93,297,008(+) T/A genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for VPS50 Gene

Variant ID Type Subtype PubMed ID
nsv607801 CNV loss 21841781
nsv528267 CNV loss 19592680
nsv1124973 CNV duplication 24896259

Variation tolerance for VPS50 Gene

Residual Variation Intolerance Score: 8.22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.11; 51.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS50 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS50

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS50 Gene

Disorders for VPS50 Gene

No disorders were found for VPS50 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VPS50 Gene

Publications for VPS50 Gene

  1. EARP is a multisubunit tethering complex involved in endocytic recycling. (PMID: 25799061) Schindler C … Bonifacino JS (Nature cell biology 2015) 2 3 4 58
  2. Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11347906) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 2 3 4 58
  3. Toward a comprehensive map of the effectors of rab GTPases. (PMID: 25453831) Gillingham AK … Munro S (Developmental cell 2014) 2 3 58
  4. CCDC132 is highly expressed in atopic dermatitis T cells. (PMID: 21472204) Matsumoto Y … Oshida T (Molecular medicine reports 2010) 3 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for VPS50 Gene

Sources for VPS50 Gene

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