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 (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
38
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Pontocerebellar hypoplasia type 2E Pathogenic; Likely pathogenic rs587777465, rs587777466, rs200594402, rs1447478732, rs1472685858 RCV000128407
RCV000128408
RCV000674147
RCV005029568
RCV001009626
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Pontoneocerebellar hypoplasia Likely pathogenic; Pathogenic rs587777466, rs776733428 RCV002298475
RCV002308571
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Likely benign; Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma Likely benign; Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Atrophy Atrophy Pubtator 26357016 Associate
★☆☆☆☆
Found in Text Mining only
Cerebellar atrophy Cerebellar atrophy HPO_DG
★☆☆☆☆
Found in Text Mining only
Cerebral atrophy Cerebral Atrophy HPO_DG
★☆☆☆☆
Found in Text Mining only
cervical cancer Cervical Cancer BEFREE 11857354
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervix carcinoma Cervix carcinoma BEFREE 11857354
★☆☆☆☆
Found in Text Mining only
Colorectal Carcinoma Colorectal Cancer BEFREE 18617915
★☆☆☆☆
Found in Text Mining only
Complete atrioventricular block Complete Atrioventricular Block BEFREE 28189396
★☆☆☆☆
Found in Text Mining only
Congenital pontocerebellar hypoplasia Pontoneocerebellar hypoplasia GENOMICS_ENGLAND_DG 24577744
★☆☆☆☆
Found in Text Mining only
Deafness Deafness Pubtator 39842660 Associate
★☆☆☆☆
Found in Text Mining only
Dwarfism Dwarfism HPO_DG
★☆☆☆☆
Found in Text Mining only