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Aliases for VPS53 Gene

Aliases for VPS53 Gene

  • VPS53, GARP Complex Subunit 2 3 5
  • Vacuolar Protein Sorting-Associated Protein 53 Homolog 3
  • Vacuolar Protein Sorting 53 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 53 (Yeast) 2
  • HVps53L 3
  • Pp13624 3
  • HCCS1 3
  • PCH2E 3

External Ids for VPS53 Gene

Previous GeneCards Identifiers for VPS53 Gene

  • GC17M000366
  • GC17M000381

Summaries for VPS53 Gene

Entrez Gene Summary for VPS53 Gene

  • This gene encodes a protein with sequence similarity to the yeast Vps53p protein. Vps53p is involved in retrograde vesicle trafficking in late Golgi. [provided by RefSeq, Jul 2008]

GeneCards Summary for VPS53 Gene

VPS53 (VPS53, GARP Complex Subunit) is a Protein Coding gene. Diseases associated with VPS53 include Pontocerebellar Hypoplasia, Type 2E and Cerebral Atrophy. Among its related pathways are Golgi-to-ER retrograde transport and Retrograde transport at the Trans-Golgi-Network.

UniProtKB/Swiss-Prot for VPS53 Gene

  • Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD (PubMed:15878329, PubMed:18367545). 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 (PubMed:25799061).

Additional gene information for VPS53 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS53 Gene

Genomics for VPS53 Gene

Regulatory Elements for VPS53 Gene

Enhancers for VPS53 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
GH17H000599 1.6 FANTOM5 Ensembl ENCODE 34.9 +119.7 119706 4 PKNOX1 ATF1 ARNT TCF12 ZNF766 GATA2 ELK1 ATF7 NCOA1 MBD2 VPS53 RFLNB LOC105371430 C17orf97 FAM57A GEMIN4 GC17P000599 GC17M000605
GH17H000713 1.1 ENCODE 41 +6.2 6161 3 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207 VPS53 GEMIN4 PRPF8 FAM57A ENSG00000262920 ENSG00000262228 DBIL5P TIMM22 GLOD4 NXN
GH17H000689 1.6 FANTOM5 Ensembl ENCODE dbSUPER 28.1 +28.7 28715 7 SIN3A RFX5 SCRT2 RCOR1 FOS DEK CEBPB NR2F2 ZNF217 ZFP69B VPS53 FAM57A C17orf97 RFLNB DOC2B TIMM22 GEMIN4 ENSG00000263015 GC17M000676 GC17P000714
GH17H000533 1.1 Ensembl ENCODE dbSUPER 39.1 +186.8 186837 2 FOXA2 POLR2A CEBPA MAX WT1 MYC RAD21 NR2F2 VPS53 RFLNB ENSG00000263015 GC17M000536 GC17P000528
GH17H000537 1.1 Ensembl ENCODE dbSUPER 39.1 +183.3 183281 2 MAFF ZNF316 CEBPB MAFG CEBPG EMSY MAFK VPS53 RFLNB C17orf97 GC17M000536 GC17P000528
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VPS53 on UCSC Golden Path with GeneCards custom track

Genomic Location for VPS53 Gene

Chromosome:
17
Start:
508,668 bp from pter
End:
721,717 bp from pter
Size:
213,050 bases
Orientation:
Minus strand

Genomic View for VPS53 Gene

Genes around VPS53 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS53 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS53 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS53 Gene

Proteins for VPS53 Gene

  • Protein details for VPS53 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5VIR6-VPS53_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 53 homolog
    Protein Accession:
    Q5VIR6
    Secondary Accessions:
    • A8K2S8
    • B3FH42
    • Q8WYW3
    • Q9BRR2
    • Q9BY02
    • Q9NV25

    Protein attributes for VPS53 Gene

    Size:
    699 amino acids
    Molecular mass:
    79653 Da
    Quaternary structure:
    • Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54 (PubMed:15878329). Component of the endosome-associated retrograde protein (EARP) complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin (PubMed:25799061).
    SequenceCaution:
    • Sequence=AAL55842.1; Type=Frameshift; Positions=562; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS53 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS53 Gene

Post-translational modifications for VPS53 Gene

  • Ubiquitination at Lys102
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for VPS53

No data available for DME Specific Peptides for VPS53 Gene

Domains & Families for VPS53 Gene

Gene Families for VPS53 Gene

Protein Domains for VPS53 Gene

Suggested Antigen Peptide Sequences for VPS53 Gene

Graphical View of Domain Structure for InterPro Entry

Q5VIR6

UniProtKB/Swiss-Prot:

VPS53_HUMAN :
  • Belongs to the VPS53 family.
Family:
  • Belongs to the VPS53 family.
genes like me logo Genes that share domains with VPS53: view

Function for VPS53 Gene

Molecular function for VPS53 Gene

UniProtKB/Swiss-Prot Function:
Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD (PubMed:15878329, PubMed:18367545). 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 (PubMed:25799061).

Phenotypes From GWAS Catalog for VPS53 Gene

Gene Ontology (GO) - Molecular Function for VPS53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15878329
genes like me logo Genes that share ontologies with VPS53: view
genes like me logo Genes that share phenotypes with VPS53: view

Human Phenotype Ontology for VPS53 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VPS53 Gene

MGI Knock Outs for VPS53:

Animal Model Products

CRISPR Products

miRNA for VPS53 Gene

miRTarBase miRNAs that target VPS53

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for VPS53
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for VPS53 Gene

Localization for VPS53 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS53 Gene

Golgi apparatus, trans-Golgi network membrane; Peripheral membrane protein. Endosome membrane; Peripheral membrane protein. Recycling endosome. Note=Localizes to the trans-Golgi network as part of the GARP complex, while it localizes to recycling endosomes as part of the EARP complex (PubMed:25799061). {ECO:0000269 PubMed:25799061}.

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 VPS53 gene
Compartment Confidence
cytosol 5
golgi apparatus 5
endosome 5
peroxisome 1
nucleus 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VPS53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000938 GARP complex IDA 19620288
GO:0005768 endosome IEA --
GO:0005794 Golgi apparatus IDA,IEA 15878329
GO:0005802 trans-Golgi network IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with VPS53: view

Pathways & Interactions for VPS53 Gene

genes like me logo Genes that share pathways with VPS53: view

Gene Ontology (GO) - Biological Process for VPS53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0007041 lysosomal transport IMP 25799061
GO:0015031 protein transport IEA --
GO:0032456 endocytic recycling IMP 25799061
GO:0042147 retrograde transport, endosome to Golgi IMP,IBA 25799061
genes like me logo Genes that share ontologies with VPS53: view

No data available for SIGNOR curated interactions for VPS53 Gene

Drugs & Compounds for VPS53 Gene

No Compound Related Data Available

Transcripts for VPS53 Gene

Unigene Clusters for VPS53 Gene

Vacuolar protein sorting 53 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for VPS53
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for VPS53 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24 ^ 25 ^
SP1: - - -
SP2: - - - - -
SP3:

ExUns: 26
SP1:
SP2:
SP3:

Relevant External Links for VPS53 Gene

GeneLoc Exon Structure for
VPS53
ECgene alternative splicing isoforms for
VPS53

Expression for VPS53 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VPS53 Gene

Protein differential expression in normal tissues from HIPED for VPS53 Gene

This gene is overexpressed in Bone (18.7), Peripheral blood mononuclear cells (7.5), and Lymph node (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VPS53 Gene



Protein tissue co-expression partners for VPS53 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS53 Gene:

VPS53

SOURCE GeneReport for Unigene cluster for VPS53 Gene:

Hs.461819

Evidence on tissue expression from TISSUES for VPS53 Gene

  • Liver(4.2)
  • Nervous system(3.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS53 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
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:
  • peripheral nerve
  • peripheral nervous system
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with VPS53: view

Primer 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 VPS53 Gene

Orthologs for VPS53 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS53 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS53 33 34
  • 99.57 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS53 34
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS53 33 34
  • 91.81 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VPS53 34
  • 91 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VPS53 33 34
  • 90.71 (n)
mouse
(Mus musculus)
Mammalia Vps53 33 16 34
  • 89.45 (n)
rat
(Rattus norvegicus)
Mammalia Vps53 33
  • 89.2 (n)
chicken
(Gallus gallus)
Aves VPS53 33 34
  • 82.52 (n)
lizard
(Anolis carolinensis)
Reptilia VPS53 34
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100496110 33
  • 75.16 (n)
zebrafish
(Danio rerio)
Actinopterygii vps53 33 34
  • 77.87 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006623 33
  • 59.2 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG3338 33 34
  • 57.93 (n)
worm
(Caenorhabditis elegans)
Secernentea vps-53 33 34
  • 49.37 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS53 34
  • 21 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons HIT1 33
  • 48.66 (n)
rice
(Oryza sativa)
Liliopsida Os01g0906200 33
  • 47.9 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 59 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU03024 33
  • 47.24 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vps53 33
  • 41.81 (n)
Species where no ortholog for VPS53 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • 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 VPS53 Gene

ENSEMBL:
Gene Tree for VPS53 (if available)
TreeFam:
Gene Tree for VPS53 (if available)

Paralogs for VPS53 Gene

No data available for Paralogs for VPS53 Gene

Variants for VPS53 Gene

Sequence variations from dbSNP and Humsavar for VPS53 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs587777465 Pathogenic, Pontocerebellar hypoplasia 2E (PCH2E) [MIM:615851] 532,843(+) TCACC(C/T)GTTCT nc-transcript-variant, reference, missense
rs587777466 Pathogenic 562,498(+) CAGGA(C/T)TCACT intron-variant
rs1057518257 Uncertain significance 628,179(-) TAATA(C/T)TCTAG nc-transcript-variant, reference, missense
rs1000008068 -- 582,247(+) CCCTC(-/AGAACCTCAGTGCATTCTG)AGAAC intron-variant
rs1000049054 -- 606,967(+) GCACA(C/T)TCTAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VPS53 Gene

Variant ID Type Subtype PubMed ID
dgv1396n106 CNV tandem duplication 24896259
dgv1675e59 CNV duplication 20981092
dgv3070n100 CNV gain 25217958
dgv3071n100 CNV gain 25217958
dgv3072n100 CNV gain 25217958
dgv3073n100 CNV gain 25217958
dgv521e199 CNV deletion 23128226
dgv5386n54 CNV gain 21841781
dgv5387n54 CNV loss 21841781
dgv5388n54 CNV loss 21841781
dgv5389n54 CNV gain 21841781
dgv5390n54 CNV loss 21841781
dgv5391n54 CNV loss 21841781
dgv5392n54 CNV loss 21841781
esv1001912 CNV deletion 20482838
esv1004113 CNV deletion 20482838
esv1159433 CNV insertion 17803354
esv1215226 CNV insertion 17803354
esv1330743 CNV deletion 17803354
esv1335456 CNV deletion 17803354
esv1350659 CNV insertion 17803354
esv1357787 CNV deletion 17803354
esv1392031 CNV deletion 17803354
esv1395254 CNV deletion 17803354
esv1467116 CNV insertion 17803354
esv1490863 CNV deletion 17803354
esv1520334 CNV deletion 17803354
esv1545947 CNV deletion 17803354
esv1679501 CNV insertion 17803354
esv1712223 CNV deletion 17803354
esv1714830 CNV deletion 17803354
esv1749886 CNV insertion 17803354
esv1753121 CNV insertion 17803354
esv2031997 CNV deletion 18987734
esv2052813 CNV deletion 18987734
esv21577 CNV loss 19812545
esv2212170 CNV deletion 18987734
esv2261698 CNV deletion 18987734
esv2332044 CNV deletion 18987734
esv2396313 CNV deletion 18987734
esv24077 CNV loss 19812545
esv2422420 CNV duplication 17116639
esv2540286 CNV insertion 19546169
esv26118 CNV gain 19812545
esv2630451 CNV deletion 19546169
esv2661341 CNV deletion 23128226
esv2662231 CNV deletion 23128226
esv2674580 CNV deletion 23128226
esv2715313 CNV deletion 23290073
esv2715314 CNV deletion 23290073
esv2715315 CNV deletion 23290073
esv2715316 CNV deletion 23290073
esv2715317 CNV deletion 23290073
esv2715319 CNV deletion 23290073
esv2715320 CNV deletion 23290073
esv2715321 CNV deletion 23290073
esv2715322 CNV deletion 23290073
esv2715323 CNV deletion 23290073
esv2715324 CNV deletion 23290073
esv2715325 CNV deletion 23290073
esv2715326 CNV deletion 23290073
esv2715327 CNV deletion 23290073
esv2715328 CNV deletion 23290073
esv2715330 CNV deletion 23290073
esv2715331 CNV deletion 23290073
esv2715332 CNV deletion 23290073
esv2715333 CNV deletion 23290073
esv2715334 CNV deletion 23290073
esv2715335 CNV deletion 23290073
esv2715336 CNV deletion 23290073
esv2715337 CNV deletion 23290073
esv2715338 CNV deletion 23290073
esv2715339 CNV deletion 23290073
esv2715341 CNV deletion 23290073
esv2715342 CNV deletion 23290073
esv2715343 CNV deletion 23290073
esv2715344 CNV deletion 23290073
esv2715345 CNV deletion 23290073
esv2715346 CNV deletion 23290073
esv2715347 CNV deletion 23290073
esv27374 CNV gain+loss 19812545
esv2758672 CNV loss 17122850
esv28623 CNV gain 19812545
esv3174902 CNV deletion 24192839
esv3368962 CNV duplication 20981092
esv3553952 CNV deletion 23714750
esv3553954 CNV deletion 23714750
esv3553956 CNV deletion 23714750
esv3582454 CNV loss 25503493
esv3582455 CNV loss 25503493
esv3582457 CNV loss 25503493
esv3639625 CNV gain 21293372
esv3639626 CNV gain 21293372
esv3639627 CNV gain 21293372
esv3639628 CNV loss 21293372
esv3639629 CNV loss 21293372
esv3639630 CNV gain 21293372
esv3639631 CNV loss 21293372
esv3639633 CNV loss 21293372
esv3639634 CNV loss 21293372
esv3892944 CNV gain 25118596
esv4014 CNV loss 18987735
esv5641 CNV loss 19470904
esv997699 CNV deletion 20482838
nsv1057000 CNV gain 25217958
nsv1063272 CNV gain 25217958
nsv1064955 CNV gain 25217958
nsv1066827 CNV gain 25217958
nsv1070374 CNV deletion 25765185
nsv1071322 CNV deletion 25765185
nsv1109038 CNV deletion 24896259
nsv1112291 CNV deletion 24896259
nsv1112292 CNV deletion 24896259
nsv1112293 CNV deletion 24896259
nsv1117175 CNV tandem duplication 24896259
nsv111966 CNV deletion 16902084
nsv1131124 CNV deletion 24896259
nsv1134582 CNV deletion 24896259
nsv1146926 CNV deletion 26484159
nsv1147081 CNV deletion 26484159
nsv1940 CNV insertion 18451855
nsv428332 CNV loss 18775914
nsv457627 CNV gain 19166990
nsv457631 CNV gain 19166990
nsv469805 CNV loss 16826518
nsv469891 CNV loss 16826518
nsv472994 CNV novel sequence insertion 20440878
nsv477906 CNV novel sequence insertion 20440878
nsv479118 CNV novel sequence insertion 20440878
nsv479160 CNV novel sequence insertion 20440878
nsv522031 CNV gain 19592680
nsv573948 CNV gain 21841781
nsv574063 CNV gain 21841781
nsv574064 CNV loss 21841781
nsv574065 CNV gain+loss 21841781
nsv574067 CNV gain 21841781
nsv574075 CNV loss 21841781
nsv574077 CNV loss 21841781
nsv574081 CNV loss 21841781
nsv574085 CNV loss 21841781
nsv574086 CNV gain 21841781
nsv574087 CNV loss 21841781
nsv574090 CNV gain 21841781
nsv9485 CNV gain 18304495
nsv952093 CNV duplication 24416366
nsv954570 CNV deletion 24416366
nsv955404 CNV deletion 24416366
nsv978347 CNV duplication 23825009

Variation tolerance for VPS53 Gene

Residual Variation Intolerance Score: 12% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.66; 82.88% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VPS53 Gene

Human Gene Mutation Database (HGMD)
VPS53
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS53

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS53 Gene

Disorders for VPS53 Gene

MalaCards: The human disease database

(3) MalaCards diseases for VPS53 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
pontocerebellar hypoplasia, type 2e
  • pontocerebellar hypoplasia type 2a
cerebral atrophy
leukodystrophy, hypomyelinating, 6
  • hld
- elite association - COSMIC cancer census association via MalaCards
Search VPS53 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VPS53_HUMAN
  • Pontocerebellar hypoplasia 2E (PCH2E) [MIM:615851]: A neurodegenerative disorder characterized by progressive cerebello-cerebral atrophy, profound mental retardation, progressive microcephaly, spasticity, and early-onset epilepsy. {ECO:0000269 PubMed:24577744}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for VPS53

Genetic Association Database (GAD)
VPS53
Human Genome Epidemiology (HuGE) Navigator
VPS53
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VPS53
genes like me logo Genes that share disorders with VPS53: view

No data available for Genatlas for VPS53 Gene

Publications for VPS53 Gene

  1. Characterization of the human GARP (Golgi associated retrograde protein) complex. (PMID: 15878329) Liewen H … Stenner-Liewen F (Experimental cell research 2005) 2 3 4 60
  2. EARP is a multisubunit tethering complex involved in endocytic recycling. (PMID: 25799061) Schindler C … Bonifacino JS (Nature cell biology 2015) 3 4 60
  3. Ang2/fat-free is a conserved subunit of the Golgi-associated retrograde protein complex. (PMID: 20685960) Pérez-Victoria FJ … Bonifacino JS (Molecular biology of the cell 2010) 3 4 60
  4. Dual roles of the mammalian GARP complex in tethering and SNARE complex assembly at the trans-golgi network. (PMID: 19620288) Pérez-Victoria FJ … Bonifacino JS (Molecular and cellular biology 2009) 3 22 60
  5. Requirement of the human GARP complex for mannose 6-phosphate-receptor-dependent sorting of cathepsin D to lysosomes. (PMID: 18367545) Pérez-Victoria FJ … Bonifacino JS (Molecular biology of the cell 2008) 3 4 60

Products for VPS53 Gene

Sources for VPS53 Gene

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