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	6293
Gene name	VPS52 subunit of GARP complex
Gene symbol	VPS52
Synonyms (NCBI Gene)	ARE1SAC2SACM2LdJ1033B10.5
Chromosome	6
Chromosome location	6p21.32
Summary	This gene encodes a protein that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and

174

Show/Hide all (174)

miRTarBase ID	miRNA	Experiments	Reference
MIRT651672	hsa-miR-7109-3p	HITS-CLIP	23824327
MIRT651671	hsa-miR-330-3p	HITS-CLIP	23824327
MIRT651670	hsa-miR-105-5p	HITS-CLIP	23824327
MIRT651669	hsa-miR-7853-5p	HITS-CLIP	23824327
MIRT651668	hsa-miR-4719	HITS-CLIP	23824327
MIRT651667	hsa-miR-205-5p	HITS-CLIP	23824327
MIRT651666	hsa-miR-4252	HITS-CLIP	23824327
MIRT651665	hsa-miR-6791-3p	HITS-CLIP	23824327
MIRT651664	hsa-miR-6829-3p	HITS-CLIP	23824327
MIRT651663	hsa-miR-513b-5p	HITS-CLIP	23824327
MIRT651673	hsa-miR-6771-3p	HITS-CLIP	23824327
MIRT651672	hsa-miR-7109-3p	HITS-CLIP	23824327
MIRT651671	hsa-miR-330-3p	HITS-CLIP	23824327
MIRT651670	hsa-miR-105-5p	HITS-CLIP	23824327
MIRT651669	hsa-miR-7853-5p	HITS-CLIP	23824327
MIRT651668	hsa-miR-4719	HITS-CLIP	23824327
MIRT651667	hsa-miR-205-5p	HITS-CLIP	23824327
MIRT651666	hsa-miR-4252	HITS-CLIP	23824327
MIRT651665	hsa-miR-6791-3p	HITS-CLIP	23824327
MIRT651664	hsa-miR-6829-3p	HITS-CLIP	23824327
MIRT651663	hsa-miR-513b-5p	HITS-CLIP	23824327
MIRT491962	hsa-miR-142-3p	PAR-CLIP	23592263
MIRT491961	hsa-miR-302f	PAR-CLIP	23592263
MIRT491960	hsa-miR-7161-3p	PAR-CLIP	23592263
MIRT491958	hsa-miR-4779	PAR-CLIP	23592263
MIRT491959	hsa-miR-4255	PAR-CLIP	23592263
MIRT491957	hsa-miR-4459	PAR-CLIP	23592263
MIRT491956	hsa-miR-665	PAR-CLIP	23592263
MIRT491954	hsa-miR-655-5p	PAR-CLIP	23592263
MIRT491955	hsa-miR-4663	PAR-CLIP	23592263
MIRT491953	hsa-miR-7160-5p	PAR-CLIP	23592263
MIRT491952	hsa-miR-8077	PAR-CLIP	23592263
MIRT491950	hsa-miR-6731-5p	PAR-CLIP	23592263
MIRT491951	hsa-miR-8085	PAR-CLIP	23592263
MIRT491949	hsa-miR-3175	PAR-CLIP	23592263
MIRT491948	hsa-miR-124-5p	PAR-CLIP	23592263
MIRT491946	hsa-miR-3671	PAR-CLIP	23592263
MIRT491947	hsa-miR-6807-5p	PAR-CLIP	23592263
MIRT491945	hsa-miR-628-5p	PAR-CLIP	23592263
MIRT491944	hsa-miR-3591-5p	PAR-CLIP	23592263
MIRT491943	hsa-miR-607	PAR-CLIP	23592263
MIRT491942	hsa-miR-4728-5p	PAR-CLIP	23592263
MIRT651672	hsa-miR-7109-3p	HITS-CLIP	23824327
MIRT651671	hsa-miR-330-3p	HITS-CLIP	23824327
MIRT651670	hsa-miR-105-5p	HITS-CLIP	23824327
MIRT651669	hsa-miR-7853-5p	HITS-CLIP	23824327
MIRT651668	hsa-miR-4719	HITS-CLIP	23824327
MIRT651667	hsa-miR-205-5p	HITS-CLIP	23824327
MIRT651666	hsa-miR-4252	HITS-CLIP	23824327
MIRT651665	hsa-miR-6791-3p	HITS-CLIP	23824327
MIRT651664	hsa-miR-6829-3p	HITS-CLIP	23824327
MIRT651663	hsa-miR-513b-5p	HITS-CLIP	23824327
MIRT651673	hsa-miR-6771-3p	HITS-CLIP	23824327
MIRT651672	hsa-miR-7109-3p	HITS-CLIP	23824327
MIRT651671	hsa-miR-330-3p	HITS-CLIP	23824327
MIRT651670	hsa-miR-105-5p	HITS-CLIP	23824327
MIRT651669	hsa-miR-7853-5p	HITS-CLIP	23824327
MIRT651668	hsa-miR-4719	HITS-CLIP	23824327
MIRT651667	hsa-miR-205-5p	HITS-CLIP	23824327
MIRT651666	hsa-miR-4252	HITS-CLIP	23824327
MIRT651665	hsa-miR-6791-3p	HITS-CLIP	23824327
MIRT651664	hsa-miR-6829-3p	HITS-CLIP	23824327
MIRT651663	hsa-miR-513b-5p	HITS-CLIP	23824327
MIRT491962	hsa-miR-142-3p	PAR-CLIP	23592263
MIRT491961	hsa-miR-302f	PAR-CLIP	23592263
MIRT491960	hsa-miR-7161-3p	PAR-CLIP	23592263
MIRT491958	hsa-miR-4779	PAR-CLIP	23592263
MIRT491959	hsa-miR-4255	PAR-CLIP	23592263
MIRT491957	hsa-miR-4459	PAR-CLIP	23592263
MIRT491956	hsa-miR-665	PAR-CLIP	23592263
MIRT491954	hsa-miR-655-5p	PAR-CLIP	23592263
MIRT491955	hsa-miR-4663	PAR-CLIP	23592263
MIRT491953	hsa-miR-7160-5p	PAR-CLIP	23592263
MIRT491952	hsa-miR-8077	PAR-CLIP	23592263
MIRT491950	hsa-miR-6731-5p	PAR-CLIP	23592263
MIRT491951	hsa-miR-8085	PAR-CLIP	23592263
MIRT491949	hsa-miR-3175	PAR-CLIP	23592263
MIRT491948	hsa-miR-124-5p	PAR-CLIP	23592263
MIRT491946	hsa-miR-3671	PAR-CLIP	23592263
MIRT491947	hsa-miR-6807-5p	PAR-CLIP	23592263
MIRT491945	hsa-miR-628-5p	PAR-CLIP	23592263
MIRT491944	hsa-miR-3591-5p	PAR-CLIP	23592263
MIRT491943	hsa-miR-607	PAR-CLIP	23592263
MIRT491942	hsa-miR-4728-5p	PAR-CLIP	23592263
MIRT1487124	hsa-miR-1202	CLIP-seq
MIRT1487125	hsa-miR-1304	CLIP-seq
MIRT1487126	hsa-miR-140-5p	CLIP-seq
MIRT1487127	hsa-miR-1827	CLIP-seq
MIRT1487128	hsa-miR-2682	CLIP-seq
MIRT1487129	hsa-miR-3194-5p	CLIP-seq
MIRT1487130	hsa-miR-34a	CLIP-seq
MIRT1487131	hsa-miR-34c-5p	CLIP-seq
MIRT1487132	hsa-miR-3613-3p	CLIP-seq
MIRT1487133	hsa-miR-3664-3p	CLIP-seq
MIRT1487134	hsa-miR-3972	CLIP-seq
MIRT1487135	hsa-miR-4257	CLIP-seq
MIRT1487136	hsa-miR-4271	CLIP-seq
MIRT1487137	hsa-miR-4436a	CLIP-seq
MIRT1487138	hsa-miR-4499	CLIP-seq
MIRT1487139	hsa-miR-449a	CLIP-seq
MIRT1487140	hsa-miR-449b	CLIP-seq
MIRT1487141	hsa-miR-449c	CLIP-seq
MIRT1487142	hsa-miR-4513	CLIP-seq
MIRT1487143	hsa-miR-4658	CLIP-seq
MIRT1487144	hsa-miR-4704-3p	CLIP-seq
MIRT1487145	hsa-miR-4725-3p	CLIP-seq
MIRT1487146	hsa-miR-4756-3p	CLIP-seq
MIRT1487147	hsa-miR-4758-5p	CLIP-seq
MIRT1487148	hsa-miR-4765	CLIP-seq
MIRT1487149	hsa-miR-5095	CLIP-seq
MIRT1487150	hsa-miR-526b	CLIP-seq
MIRT1487151	hsa-miR-548v	CLIP-seq
MIRT1487152	hsa-miR-617	CLIP-seq
MIRT2146641	hsa-miR-3153	CLIP-seq
MIRT2146642	hsa-miR-3173-3p	CLIP-seq
MIRT2146643	hsa-miR-3545-5p	CLIP-seq
MIRT2146644	hsa-miR-4463	CLIP-seq
MIRT2146645	hsa-miR-4494	CLIP-seq
MIRT2146646	hsa-miR-4668-5p	CLIP-seq
MIRT2146647	hsa-miR-4795-5p	CLIP-seq
MIRT2146648	hsa-miR-542-3p	CLIP-seq
MIRT2146649	hsa-miR-635	CLIP-seq
MIRT2146650	hsa-miR-671-5p	CLIP-seq
MIRT2367238	hsa-miR-1184	CLIP-seq
MIRT2367239	hsa-miR-1205	CLIP-seq
MIRT2367240	hsa-miR-1262	CLIP-seq
MIRT1487125	hsa-miR-1304	CLIP-seq
MIRT1487127	hsa-miR-1827	CLIP-seq
MIRT2367241	hsa-miR-18a	CLIP-seq
MIRT2367242	hsa-miR-18b	CLIP-seq
MIRT2367243	hsa-miR-21	CLIP-seq
MIRT1487128	hsa-miR-2682	CLIP-seq
MIRT2367244	hsa-miR-3147	CLIP-seq
MIRT2367245	hsa-miR-3158-5p	CLIP-seq
MIRT2367246	hsa-miR-3166	CLIP-seq
MIRT2146642	hsa-miR-3173-3p	CLIP-seq
MIRT2367247	hsa-miR-3189-3p	CLIP-seq
MIRT2367248	hsa-miR-3192	CLIP-seq
MIRT1487133	hsa-miR-3664-3p	CLIP-seq
MIRT2367249	hsa-miR-4267	CLIP-seq
MIRT1487136	hsa-miR-4271	CLIP-seq
MIRT2367250	hsa-miR-4300	CLIP-seq
MIRT2367251	hsa-miR-4425	CLIP-seq
MIRT1487137	hsa-miR-4436a	CLIP-seq
MIRT2367252	hsa-miR-4455	CLIP-seq
MIRT2146644	hsa-miR-4463	CLIP-seq
MIRT2367253	hsa-miR-4493	CLIP-seq
MIRT2146645	hsa-miR-4494	CLIP-seq
MIRT1487138	hsa-miR-4499	CLIP-seq
MIRT1487141	hsa-miR-449c	CLIP-seq
MIRT1487142	hsa-miR-4513	CLIP-seq
MIRT2367254	hsa-miR-4701-3p	CLIP-seq
MIRT2367255	hsa-miR-4713-3p	CLIP-seq
MIRT1487145	hsa-miR-4725-3p	CLIP-seq
MIRT2367256	hsa-miR-4731-5p	CLIP-seq
MIRT2367257	hsa-miR-4735-3p	CLIP-seq
MIRT1487146	hsa-miR-4756-3p	CLIP-seq
MIRT2367258	hsa-miR-4761-5p	CLIP-seq
MIRT2367259	hsa-miR-4771	CLIP-seq
MIRT2146648	hsa-miR-542-3p	CLIP-seq
MIRT2367260	hsa-miR-544	CLIP-seq
MIRT2367261	hsa-miR-590-5p	CLIP-seq
MIRT2367262	hsa-miR-609	CLIP-seq
MIRT1487152	hsa-miR-617	CLIP-seq
MIRT2146650	hsa-miR-671-5p	CLIP-seq
MIRT2367263	hsa-miR-920	CLIP-seq
MIRT1487132	hsa-miR-3613-3p	CLIP-seq
MIRT1487150	hsa-miR-526b	CLIP-seq
MIRT1487151	hsa-miR-548v	CLIP-seq
MIRT1487152	hsa-miR-617	CLIP-seq
MIRT1487132	hsa-miR-3613-3p	CLIP-seq
MIRT1487150	hsa-miR-526b	CLIP-seq
MIRT1487151	hsa-miR-548v	CLIP-seq
MIRT1487152	hsa-miR-617	CLIP-seq

Show/Hide all (35)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000938	Component	GARP complex	IBA
GO:0000938	Component	GARP complex	IDA	25799061
GO:0000938	Component	GARP complex	NAS	25799061
GO:0005515	Function	Protein binding	IPI	15878329, 18985028, 20163565, 20685960, 21516116, 23932592, 25416956, 25799061, 26496610, 26871637, 28514442, 29892012, 31515488, 32296183, 33961781, 36217029
GO:0005768	Component	Endosome	IEA
GO:0005794	Component	Golgi apparatus	IDA	15878329
GO:0005794	Component	Golgi apparatus	IEA
GO:0005829	Component	Cytosol	IEA
GO:0006605	Process	Protein targeting	IEA
GO:0006896	Process	Golgi to vacuole transport	IBA
GO:0007041	Process	Lysosomal transport	IBA
GO:0007041	Process	Lysosomal transport	IDA	25799061
GO:0010008	Component	Endosome membrane	IEA
GO:0010668	Process	Ectodermal cell differentiation	IEA
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IDA	25799061
GO:0016020	Component	Membrane	IEA
GO:0019905	Function	Syntaxin binding	IBA
GO:0019905	Function	Syntaxin binding	IPI	15878329
GO:0032456	Process	Endocytic recycling	IBA
GO:0032456	Process	Endocytic recycling	IMP	25799061
GO:0032456	Process	Endocytic recycling	NAS	25799061
GO:0032588	Component	Trans-Golgi network membrane	TAS
GO:0042147	Process	Retrograde transport, endosome to Golgi	IBA
GO:0042147	Process	Retrograde transport, endosome to Golgi	NAS	25799061
GO:0048471	Component	Perinuclear region of cytoplasm	IDA	15878329
GO:0048611	Process	Embryonic ectodermal digestive tract development	IEA
GO:0055037	Component	Recycling endosome	IDA	25799061
GO:0055037	Component	Recycling endosome	IEA
GO:0055037	Component	Recycling endosome	NAS	25799061
GO:0090119	Process	Vesicle-mediated cholesterol transport	IEA
GO:0098793	Component	Presynapse	IEA
GO:0098794	Component	Postsynapse	IEA
GO:1990745	Component	EARP complex	IDA	25799061
GO:1990745	Component	EARP complex	IPI	25799061

MIM	HGNC	e!Ensembl
603443	10518	ENSG00000223501

Q8N1B4

Protein name

Vacuolar protein sorting-associated protein 52 homolog (SAC2 suppressor of actin mutations 2-like protein)

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
PF04129	Vps52	94 → 601	Vps52 / Sac2 family	Family

Sequence

MAAAATMAAAARELVLRAGTSDMEEEEGPLAGGPGLQEPLQLGELDITSDEFILDEVDVH
IQANLEDELVKEALKTGVDLRHYSKQVELELQQIEQKSIRDYIQESENIASLHNQITACD
AVLERMEQMLGAFQSDLSSISSEIRTLQEQSGAMNIRLRNRQAVRGKLGELVDGLVVPSA
LVTAILEAPVTEPRFLEQLQELDAKAAAVREQEARGTAACADVRGVLDRLRVKAVTKIRE
FILQKIYSFRKPMTNYQIPQTALLKYRFFYQFLLGNERATAKEIRDEYVETLSKIYLSYY
RSYLGRLMKVQYEEVAEKDDLMGVEDTAKKGFFSKPSLRSRNTIFTLGTRGSVISPTELE
APILVPHTAQRGEQRYPFEALFRSQHYALLDNSCREYLFICEFFVVSGPAAHDLFHAVMG
RTLSMTLKHLDSYLADCYDAIAVFLCIHIVLRFRNIAAKRDVPALDRYWEQVLALLWPRF
ELILEMNVQSVRSTDPQRLGGLDTRPHYITRRYAEFSSALVSINQTIPNERTMQLLGQLQ
VEVENFVLRVAAEFSSRKEQLVFLINNYDMMLGVLMERAADDSKEVESFQQLLNARTQEF
IEELLSPPFGGLVAFVKEAEALIERGQAERLRGEEARVTQLIRGFGSSWKSSVESLSQDV
MRSFTNFRNGTSIIQGALTQLIQLYHRFHRVLSQPQLRALPARAELINIHHLMVELKKHK
PNF

Sequence length

723

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 (6)

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.
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATIC NEOPLASMS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

VPS52 (VPS52 subunit of GARP complex)