Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	51542
Gene name	VPS54 subunit of GARP complex
Gene symbol	VPS54
Synonyms (NCBI Gene)	HCC8PPP1R164SLP-8pVPS54LWRhVps54L
Chromosome	2
Chromosome location	2p15-p14
Summary	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 c

Show/Hide all (54)

miRTarBase ID	miRNA	Experiments	Reference
MIRT027414	hsa-miR-98-5p	Microarray	19088304
MIRT028839	hsa-miR-26b-5p	Microarray	19088304
MIRT030672	hsa-miR-21-5p	Microarray	18591254
MIRT037142	hsa-miR-877-3p	CLASH	23622248
MIRT726119	hsa-miR-92a-3p	HITS-CLIP	22473208
MIRT726117	hsa-miR-92b-3p	HITS-CLIP	22473208
MIRT726118	hsa-miR-32-5p	HITS-CLIP	22473208
MIRT1487377	hsa-miR-4420	CLIP-seq
MIRT1487378	hsa-miR-4772-3p	CLIP-seq
MIRT1487379	hsa-miR-489	CLIP-seq
MIRT1487380	hsa-miR-494	CLIP-seq
MIRT1487381	hsa-miR-596	CLIP-seq
MIRT1487382	hsa-miR-891b	CLIP-seq
MIRT2146749	hsa-miR-1183	CLIP-seq
MIRT2146750	hsa-miR-25	CLIP-seq
MIRT2146751	hsa-miR-32	CLIP-seq
MIRT2146752	hsa-miR-363	CLIP-seq
MIRT2146753	hsa-miR-367	CLIP-seq
MIRT2146754	hsa-miR-4317	CLIP-seq
MIRT2146755	hsa-miR-4325	CLIP-seq
MIRT1487379	hsa-miR-489	CLIP-seq
MIRT2146756	hsa-miR-7	CLIP-seq
MIRT2146757	hsa-miR-92a	CLIP-seq
MIRT2146758	hsa-miR-92b	CLIP-seq
MIRT2146750	hsa-miR-25	CLIP-seq
MIRT2146751	hsa-miR-32	CLIP-seq
MIRT2146752	hsa-miR-363	CLIP-seq
MIRT2146753	hsa-miR-367	CLIP-seq
MIRT2146754	hsa-miR-4317	CLIP-seq
MIRT2146755	hsa-miR-4325	CLIP-seq
MIRT2146756	hsa-miR-7	CLIP-seq
MIRT2146757	hsa-miR-92a	CLIP-seq
MIRT2146758	hsa-miR-92b	CLIP-seq
MIRT2146750	hsa-miR-25	CLIP-seq
MIRT2146751	hsa-miR-32	CLIP-seq
MIRT2146752	hsa-miR-363	CLIP-seq
MIRT2146753	hsa-miR-367	CLIP-seq
MIRT2146754	hsa-miR-4317	CLIP-seq
MIRT2146755	hsa-miR-4325	CLIP-seq
MIRT2146756	hsa-miR-7	CLIP-seq
MIRT2146757	hsa-miR-92a	CLIP-seq
MIRT2146758	hsa-miR-92b	CLIP-seq
MIRT2463326	hsa-miR-4452	CLIP-seq
MIRT1487380	hsa-miR-494	CLIP-seq
MIRT2463327	hsa-miR-605	CLIP-seq
MIRT2463326	hsa-miR-4452	CLIP-seq
MIRT1487380	hsa-miR-494	CLIP-seq
MIRT2463327	hsa-miR-605	CLIP-seq
MIRT2463326	hsa-miR-4452	CLIP-seq
MIRT1487380	hsa-miR-494	CLIP-seq
MIRT2463327	hsa-miR-605	CLIP-seq
MIRT2463326	hsa-miR-4452	CLIP-seq
MIRT1487380	hsa-miR-494	CLIP-seq
MIRT2463327	hsa-miR-605	CLIP-seq

Show/Hide all (70)

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:0001701	Process	In utero embryonic development	IEA
GO:0005515	Function	Protein binding	IPI	3172165, 15878329, 20685960, 25799061, 32814053, 33961781
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	IEA
GO:0005794	Component	Golgi apparatus	IDA	15878329
GO:0005794	Component	Golgi apparatus	IEA
GO:0005802	Component	Trans-Golgi network	IDA	25799061
GO:0005802	Component	Trans-Golgi network	IMP	25795912
GO:0005829	Component	Cytosol	IEA
GO:0006309	Process	Apoptotic DNA fragmentation	IEA
GO:0006622	Process	Protein targeting to lysosome	IEA
GO:0006623	Process	Protein targeting to vacuole	IEA
GO:0006874	Process	Intracellular calcium ion homeostasis	IEA
GO:0006896	Process	Golgi to vacuole transport	IBA
GO:0006941	Process	Striated muscle contraction	IEA
GO:0007005	Process	Mitochondrion organization	IEA
GO:0007033	Process	Vacuole organization	IEA
GO:0007041	Process	Lysosomal transport	IMP	25799061
GO:0007274	Process	Neuromuscular synaptic transmission	IEA
GO:0007519	Process	Skeletal muscle tissue development	IEA
GO:0008104	Process	Intracellular protein localization	IEA
GO:0010467	Process	Gene expression	IEA
GO:0010992	Process	Ubiquitin recycling	IEA
GO:0014004	Process	Microglia differentiation	IEA
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	ISS
GO:0019905	Function	Syntaxin binding	IBA
GO:0022904	Process	Respiratory electron transport chain	IEA
GO:0030149	Process	Sphingolipid catabolic process	IEA
GO:0032588	Component	Trans-Golgi network membrane	TAS
GO:0034394	Process	Protein localization to cell surface	IEA
GO:0035108	Process	Limb morphogenesis	IEA
GO:0035128	Process	Post-embryonic forelimb morphogenesis	IEA
GO:0035249	Process	Synaptic transmission, glutamatergic	IEA
GO:0040008	Process	Regulation of growth	IEA
GO:0042147	Process	Retrograde transport, endosome to Golgi	IBA
GO:0042147	Process	Retrograde transport, endosome to Golgi	IEA
GO:0042147	Process	Retrograde transport, endosome to Golgi	IMP	25799061
GO:0042147	Process	Retrograde transport, endosome to Golgi	NAS	25799061
GO:0045047	Process	Protein targeting to ER	IEA
GO:0045202	Component	Synapse	IEA
GO:0046677	Process	Response to antibiotic	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	IDA	15878329
GO:0048515	Process	Spermatid differentiation	IEA
GO:0048630	Process	Skeletal muscle tissue growth	IEA
GO:0048708	Process	Astrocyte differentiation	IEA
GO:0048812	Process	Neuron projection morphogenesis	IEA
GO:0048872	Process	Homeostasis of number of cells	IEA
GO:0048873	Process	Homeostasis of number of cells within a tissue	IEA
GO:0050881	Process	Musculoskeletal movement	IEA
GO:0051402	Process	Neuron apoptotic process	IEA
GO:0051592	Process	Response to calcium ion	IEA
GO:0051932	Process	Synaptic transmission, GABAergic	IEA
GO:0051938	Process	L-glutamate import	IEA
GO:0060052	Process	Neurofilament cytoskeleton organization	IEA
GO:0060173	Process	Limb development	IEA
GO:0061744	Process	Motor behavior	IEA
GO:0070493	Process	Thrombin-activated receptor signaling pathway	IEA
GO:0071393	Process	Cellular response to progesterone stimulus	IEA
GO:0090119	Process	Vesicle-mediated cholesterol transport	IEA
GO:0097049	Process	Motor neuron apoptotic process	IEA
GO:0097719	Process	Neural tissue regeneration	IEA
GO:0150076	Process	Neuroinflammatory response	IEA
GO:2000672	Process	Negative regulation of motor neuron apoptotic process	IEA

MIM	HGNC	e!Ensembl
614633	18652	ENSG00000143952

Q9P1Q0

Protein name

Vacuolar protein sorting-associated protein 54 (Hepatocellular carcinoma protein 8) (Tumor antigen HOM-HCC-8) (Tumor antigen SLP-8p)

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
PF10475	Vps54_N	198 → 364	Vacuolar-sorting protein 54, of GARP complex	Family
PF07928	Vps54	736 → 868	Vps54-like protein	Family

Sequence

MASSHSSSPVPQGSSSDVFFKIEVDPSKHIRPVPSLPDVCPKEPTGDSHSLYVAPSLVTD
QHRWTVYHSKVNLPAALNDPRLAKRESDFFTKTWGLDFVDTEVIPSFYLPQISKEHFTVY
QQEISQREKIHERCKNICPPKDTFERTLLHTHDKSRTDLEQVPKIFMKPDFALDDSLTFN
SVLPWSHFNTAGGKGNRDAASSKLLQEKLSHYLDIVEVNIAHQISLRSEAFFHAMTSQHE
LQDYLRKTSQAVKMLRDKIAQIDKVMCEGSLHILRLALTRNNCVKVYNKLKLMATVHQTQ
PTVQVLLSTSEFVGALDLIATTQEVLQQELQGIHSFRHLGSQLCELEKLIDKMMIAEFST
YSHSDLNRPLEDDCQVLEEERLISLVFGLLKQRKLNFLEIYGEKMVITAKNIIKQCVINK
VSQTEEIDTDVVVKLADQMRMLNFPQWFDLLKDIFSKFTIFLQRVKATLNIIHSVVLSVL
DKNQRTRELEEISQQKNAAKDNSLDTEVAYLIHEGMFISDAFGEGELTPIAVDTTSQRNA
SPNSEPCSSDSVSEPECTTDSSSSKEHTSSSAIPGGVDIMVSEDMKLTDSELGKLANNIQ
ELLYSASDICHDRAVKFLMSRAKDGFLEKLNSMEFITLSRLMETFILDTEQICGRKSTSL
LGALQSQAIKFVNRFHEERKTKLSLLLDNERWKQADVPAEFQDLVDSLSDGKIALPEKKS
GATEERKPAEVLIVEGQQYAVVGTVLLLIRIILEYCQCVDNIPSVTTDMLTRLSDLLKYF
NSRSCQLVLGAGALQVVGLKTITTKNLALSSRCLQLIVHYIPVIRAHFEARLPPKQYSML
RHFDHITKDYHDHIAEISAKLVAIMDSLFDKLLSKYEVKAPVPSACFRNICKQMTKMHEA
IFDLLPEEQTQMLFLRINASYKLHLKKQLSHLNVINDGGPQNGLVTADVAFYTGNLQALK
GLKDLDLNMAEIWEQKR

Sequence length

977

Interactions

View interactions

	Reactome
			Retrograde transport at the Trans-Golgi-Network

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)

Show/Hide Unknown Diseases (16)

Phenotype Name	Clinical Significance	Source	Evidence Score
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.
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar GWAS catalog	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Familial cancer of breast	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROTIC DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Tooth agenesis	Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

VPS54 (VPS54 subunit of GARP complex)