Human Gene VPS54 (ENST00000272322.9) from GENCODE V39
  Description: Homo sapiens VPS54 subunit of GARP complex (VPS54), transcript variant 1, mRNA. (from RefSeq NM_016516)
RefSeq Summary (NM_016516): This gene encodes for a protein that in yeast forms part of a trimeric vacuolar-protein-sorting complex that is required for retrograde transport of proteins from prevacuoles to the late Golgi compartment. As in yeast, mammalian Vps54 proteins contain a coiled-coil region and dileucine motifs. Alternative splicing results in multiple transcript variants encoding different isoforms [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000272322.9
Gencode Gene: ENSG00000143952.20
Transcript (Including UTRs)
   Position: hg38 chr2:63,892,150-64,019,428 Size: 127,279 Total Exon Count: 23 Strand: -
Coding Region
   Position: hg38 chr2:63,893,430-63,983,999 Size: 90,570 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2022-01-17 08:30:34

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr2:63,892,150-64,019,428)mRNA (may differ from genome)Protein (977 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Vacuolar protein sorting-associated protein 54; AltName: Full=Hepatocellular carcinoma protein 8; AltName: Full=Tumor antigen HOM-HCC-8; AltName: Full=Tumor antigen SLP-8p;
FUNCTION: May be involved in retrograde transport from early and late endosomes to the late Golgi. 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.
SUBUNIT: Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54.
SIMILARITY: Belongs to the VPS54 family.
SEQUENCE CAUTION: Sequence=BAA92134.1; Type=Erroneous initiation;

-  MalaCards Disease Associations
  MalaCards Gene Search: VPS54
Diseases sorted by gene-association score: amyotrophic lateral sclerosis 1 (0)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 13.56 RPKM in Pituitary
Total median expression: 378.32 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -289.70511-0.567 Picture PostScript Text
3' UTR -302.201280-0.236 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019515 - Vacuolar_sorting-assoc_54
IPR012501 - Vps54

Pfam Domains:
PF10475 - Vacuolar-sorting protein 54, of GARP complex
PF07928 - Vps54-like protein

ModBase Predicted Comparative 3D Structure on Q9P1Q0
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
Protein SequenceProtein SequenceProtein Sequence  Protein Sequence
AlignmentAlignmentAlignment  Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019905 syntaxin binding

Biological Process:
GO:0006896 Golgi to vacuole transport
GO:0007041 lysosomal transport
GO:0015031 protein transport
GO:0040007 growth
GO:0042147 retrograde transport, endosome to Golgi
GO:0048873 homeostasis of number of cells within a tissue
GO:0050881 musculoskeletal movement
GO:0060052 neurofilament cytoskeleton organization

Cellular Component:
GO:0000938 GARP complex
GO:0005654 nucleoplasm
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0032588 trans-Golgi network membrane
GO:0048471 perinuclear region of cytoplasm

-  Descriptions from all associated GenBank mRNAs
  BC041868 - Homo sapiens vacuolar protein sorting 54 homolog (S. cerevisiae), mRNA (cDNA clone MGC:43704 IMAGE:5271464), complete cds.
AF102177 - Homo sapiens tumor antigen SLP-8p (HCC8) mRNA, complete cds.
BC030275 - Homo sapiens vacuolar protein sorting 54 homolog (S. cerevisiae), mRNA (cDNA clone MGC:39932 IMAGE:3917367), complete cds.
AK292889 - Homo sapiens cDNA FLJ78648 complete cds, highly similar to Homo sapiens vacuolar protein sorting 54 (yeast) (VPS54), transcript variant 2, mRNA.
AK292669 - Homo sapiens cDNA FLJ77625 complete cds, highly similar to Homo sapiens vacuolar protein sorting 54 (VPS54), transcript variant 1, mRNA.
KJ893937 - Synthetic construct Homo sapiens clone ccsbBroadEn_03331 VPS54 gene, encodes complete protein.
AY444798 - Homo sapiens vacuolar sorting protein 54 long isoform (VPS54) mRNA, complete cds, alternatively spliced.
DQ891080 - Synthetic construct clone IMAGE:100003710; FLH169138.01X; RZPDo839G1194D vacuolar protein sorting 54 (S. cerevisiae) (VPS54) gene, encodes complete protein.
DQ894262 - Synthetic construct Homo sapiens clone IMAGE:100008722; FLH169134.01L; RZPDo839G1193D vacuolar protein sorting 54 (S. cerevisiae) (VPS54) gene, encodes complete protein.
AK002205 - Homo sapiens cDNA FLJ11343 fis, clone PLACE1010811.
AL137604 - Homo sapiens mRNA; cDNA DKFZp434F0411 (from clone DKFZp434F0411); partial cds.
AK094019 - Homo sapiens cDNA FLJ36700 fis, clone UTERU2009131, highly similar to Rattus norvegicus mRNA for Vps54-like protein.
AK124436 - Homo sapiens cDNA FLJ42445 fis, clone BLADE2008539, highly similar to Homo sapiens tumor antigen SLP-8p (HCC8).
JD137424 - Sequence 118448 from Patent EP1572962.
JD087466 - Sequence 68490 from Patent EP1572962.
AL359939 - Homo sapiens mRNA; cDNA DKFZp434I1019 (from clone DKFZp434I1019).
CR749701 - Homo sapiens mRNA; cDNA DKFZp434I1019 (from clone DKFZp434I1019).
AK025545 - Homo sapiens cDNA: FLJ21892 fis, clone HEP03336, highly similar to AF102177 Homo sapiens tumor antigen SLP-8p (HCC8) mRNA.
JD297319 - Sequence 278343 from Patent EP1572962.
JD299901 - Sequence 280925 from Patent EP1572962.
JD281868 - Sequence 262892 from Patent EP1572962.
JD347708 - Sequence 328732 from Patent EP1572962.
JD041777 - Sequence 22801 from Patent EP1572962.
JD376353 - Sequence 357377 from Patent EP1572962.
AK126141 - Homo sapiens cDNA FLJ44153 fis, clone THYMU2031579.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9P1Q0 (Reactome details) participates in the following event(s):

R-HSA-6811431 RAB6:GTP binds the GARP and COG complexes, t-SNAREs and endosome-derived vesicles
R-HSA-6814674 Tethering of late endosome-derived vesicles by GARP, STX10:ST16:VTI1A and Golgins
R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000272322.1, ENST00000272322.2, ENST00000272322.3, ENST00000272322.4, ENST00000272322.5, ENST00000272322.6, ENST00000272322.7, ENST00000272322.8, HCC8, NM_016516, Q5VIR5, Q86YF7, Q8N6G3, Q9NPV0, Q9NT07, Q9NUJ0, Q9P1Q0, uc002scq.1, uc002scq.2, uc002scq.3, uc002scq.4, uc002scq.5, VPS54_HUMAN
UCSC ID: ENST00000272322.9
RefSeq Accession: NM_016516
Protein: Q9P1Q0 (aka VPS54_HUMAN)
CCDS: CCDS33208.1, CCDS46302.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.