Gene Gene information from NCBI Gene database.
Entrez ID 55275
Gene name VPS53 subunit of GARP complex
Gene symbol VPS53
Synonyms (NCBI Gene)
HCCS1PCH2EhVps53Lpp13624
Chromosome 17
Chromosome location 17p13.3
Summary 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.
6
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.
1347
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 (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
32
GO ID Ontology Definition Evidence Reference
GO:0000938 Component GARP complex IBA
GO:0000938 Component GARP complex IDA 19620288, 25799061
GO:0000938 Component GARP complex IEA
GO:0000938 Component GARP complex NAS 25799061
GO:0005515 Function Protein binding IPI 3172165, 15878329, 20685960, 25799061, 28514442, 33961781
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
615850 25608 ENSG00000141252
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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 associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
104
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Pontocerebellar hypoplasia type 2E Pathogenic; Likely pathogenic rs587777465, rs587777466, rs200594402, rs1447478732, rs1472685858 RCV000128407
RCV000128408
RCV000674147
RCV005029568
RCV001009626
Pontoneocerebellar hypoplasia Likely pathogenic; Pathogenic rs587777466, rs776733428 RCV002298475
RCV002308571
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Acute myeloid leukemia Likely benign; Benign rs117255969, rs61644407, rs79657649 RCV005914959
RCV005896506
RCV005900041
Cervical cancer Likely benign rs117255969 RCV005914961
Cholangiocarcinoma Likely benign; Benign rs117255969, rs61644407, rs56807006, rs11657527 RCV005914964
RCV005896511
RCV005896504
RCV005902329
Colon adenocarcinoma Uncertain significance; Benign rs750886235, rs61644407, rs79657649 RCV005932560
RCV005896505
RCV005900040
Associations from Text MiningDisease associations identified through Pubtator
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