Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
55275
Gene name Gene Name - the full gene name approved by the HGNC.
VPS53 subunit of GARP complex
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
VPS53
Synonyms (NCBI Gene) Gene synonyms aliases
HCCS1, PCH2E, hVps53L, pp13624
Disease Acronyms (UniProt) Disease acronyms from UniProt database
PCH2E
Chromosome Chromosome number
17
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
17p13.3
Summary Summary of gene provided in NCBI Entrez 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]
SNPs SNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs200594402 G>A Likely-pathogenic Non coding transcript variant, stop gained, coding sequence variant
rs587777465 T>C Pathogenic Coding sequence variant, missense variant, non coding transcript variant, genic downstream transcript variant
rs587777466 C>T Pathogenic Intron variant
rs768997239 ACTT>- Likely-pathogenic Splice donor variant, non coding transcript variant, intron variant, coding sequence variant
rs1447478732 ->AG Likely-pathogenic Non coding transcript variant, intron variant, frameshift variant, 5 prime UTR variant, genic upstream transcript variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT023608 hsa-miR-1-3p Proteomics 18668040
MIRT046870 hsa-miR-221-3p CLASH 23622248
MIRT043781 hsa-miR-328-3p CLASH 23622248
MIRT038949 hsa-miR-28-3p CLASH 23622248
MIRT036899 hsa-miR-877-3p CLASH 23622248
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0000938 Component GARP complex IBA 21873635
GO:0000938 Component GARP complex IDA 19620288, 25799061
GO:0005515 Function Protein binding IPI 3172165, 15878329, 20685960, 25799061, 28514442
GO:0005794 Component Golgi apparatus IDA 15878329
GO:0005829 Component Cytosol IDA
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
615850 25608 ENSG00000141252
Protein
UniProt ID Q5VIR6
Protein name Vacuolar protein sorting-associated protein 53 homolog
Protein function Acts as a 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 bet
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF04100 Vps53_N 39 453 Vps53-like, N-terminal Family
Sequence
MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNAVEYINTLFPTEQSLAN
IDEVVNKIRLKIRRLDDNIRTVVRGQTNVGQDGRQALEEAQKAIQQLFGKIKDIKDKAEK
SEQMVKEITRDIKQLDHAKRHLTTSITTLNHLHMLAGGVDSLEAMTRRRQYGEVANLLQG
VMNVLEHFHKYMGIPQIRQLSERVKAAQTELGQQILADFEEAFPSQGTKRPGGPSNVLRD
ACLVANILDPRIKQEIIKKFIKQHLSEYLVLFQENQDVAWLDKIDRRYAWIKRQLVDYEE
KYGRMFPREWCMAERIAVEFCHVTRAELAKIMRTRAKEIEVKLLLFAIQRTTNFEGFLAK
RFSGCTLTDGTLKKLESPPPSTNPFLEDEPTPEMEELATEKGDLDQPKKPKAPDNPFHGI
VSKCFEPHLYVYIESQDKNLGELIDRFVADFKA
QGPPKPNTDEGGAVLPSCADLFVYYKK
CMVQCSQLSTGEPMIALTTIFQKYLREYAWKILSGNLPKTTTSSGGLTISSLLKEKEGSE
VAKFTLEELCLICNILSTAEYCLATTQQLEEKLKEKVDVSLIERINLTGEMDTFSTVISS
SIQLLVQDLDAACDPALTAMSKMQWQNVEHVGDQSPYVTSVILHIKQNVPIIRDNLASTR
KYFTQFCVKFANSFIPKFITHLFKCKPISMVGAEQLLLDTHSLKMVLLDLPSISSQVVRK
APASYTKIVVKGMTRAEMILKVVMAPHEPLVVFVDNYIKLLTDCNTETFQKILDMKGLKR
SEQSSMLELLRQRLPAPPSGAESSGSLSLTAPTPEQESSRIRKLEKLIKKRL
Sequence length 832
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Retrograde transport at the Trans-Golgi-Network
Associated diseases Disease information provided by ClinVar, GenCC, and GWAS databases.
Causal
Disease term Disease name dbSNP ID References
Developmental delay Global developmental delay rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291
View all (32 more)
2920088
Mental retardation Intellectual Disability rs5742905, rs267607136, rs267607137, rs2131714307, rs267607038, rs267607042, rs80338685, rs137853127, rs80338815, rs28940893, rs387906309, rs121908096, rs121908099, rs587784365, rs121918315
View all (1024 more)
2920088
Hypotonia Neonatal Hypotonia rs141138948, rs397517172, rs869312824, rs1583169151
Osteoporosis Osteoporosis rs72658152, rs72667023, rs587776916, rs72656370, rs768615287
Unknown
Disease term Disease name Evidence References Source
Cerebellar Hypoplasia pontocerebellar hypoplasia, type 13 GenCC
Progressive Cerebello-Cerebral Atrophy progressive cerebello-cerebral atrophy GenCC
Diabetes Diabetes GWAS
Glioblastoma Glioblastoma CRISPR screening of E3 ubiquitin ligases reveals Ring Finger Protein 185 as a novel tumor suppressor in glioblastoma repressed by promoter hypermethylation and miR-587 GWAS, CBGDA
Associations from Text Mining
Disease Name Relationship Type References
Atrophy Associate 26357016
Deafness Associate 39842660
Epilepsy Associate 39842660
Heart Diseases Associate 39842660
Intellectual Disability Associate 32209057
Liver Diseases Associate 39842660
Microcephaly Associate 39842660
Microcephaly with Mental Retardation and Digital Anomalies Associate 32209057
Muscular Atrophy Spinal Associate 26357016
Nervous System Diseases Associate 39842660