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

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	55610
Gene name	VPS50 subunit of EARP/GARPII complex
Gene symbol	VPS50
Synonyms (NCBI Gene)	CCDC132NEDMSCVPS54L
Chromosome	7
Chromosome location	7q21.2-q21.3

188

Show/Hide all (188)

miRTarBase ID	miRNA	Experiments	Reference
MIRT574089	hsa-miR-548ac	HITS-CLIP	19536157
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	19536157
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	19536157
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	19536157
MIRT574084	hsa-miR-548z	HITS-CLIP	19536157
MIRT574085	hsa-miR-3613-3p	HITS-CLIP	19536157
MIRT574083	hsa-miR-607	HITS-CLIP	19536157
MIRT574082	hsa-miR-1305	HITS-CLIP	19536157
MIRT574080	hsa-miR-335-3p	HITS-CLIP	19536157
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	19536157
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574082	hsa-miR-1305	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574082	hsa-miR-1305	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574085	hsa-miR-3613-3p	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574085	hsa-miR-3613-3p	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574082	hsa-miR-1305	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574082	hsa-miR-1305	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574082	hsa-miR-1305	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574082	hsa-miR-1305	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574082	hsa-miR-1305	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574082	hsa-miR-1305	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574085	hsa-miR-3613-3p	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574082	hsa-miR-1305	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574082	hsa-miR-1305	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574082	hsa-miR-1305	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574082	hsa-miR-1305	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	HITS-CLIP	23824327
MIRT574087	hsa-miR-548bb-3p	HITS-CLIP	23824327
MIRT574088	hsa-miR-548d-3p	HITS-CLIP	23824327
MIRT574086	hsa-miR-548h-3p	HITS-CLIP	23824327
MIRT574084	hsa-miR-548z	HITS-CLIP	23824327
MIRT574083	hsa-miR-607	HITS-CLIP	23824327
MIRT574080	hsa-miR-335-3p	HITS-CLIP	23824327
MIRT574081	hsa-miR-4668-5p	HITS-CLIP	23824327
MIRT574089	hsa-miR-548ac	PAR-CLIP	20371350
MIRT574087	hsa-miR-548bb-3p	PAR-CLIP	20371350
MIRT574088	hsa-miR-548d-3p	PAR-CLIP	20371350
MIRT574086	hsa-miR-548h-3p	PAR-CLIP	20371350
MIRT574084	hsa-miR-548z	PAR-CLIP	20371350
MIRT574085	hsa-miR-3613-3p	PAR-CLIP	20371350
MIRT574083	hsa-miR-607	PAR-CLIP	20371350
MIRT574082	hsa-miR-1305	PAR-CLIP	20371350
MIRT574080	hsa-miR-335-3p	PAR-CLIP	20371350
MIRT574081	hsa-miR-4668-5p	PAR-CLIP	20371350
MIRT442207	hsa-miR-548az-5p	PAR-CLIP	22100165
MIRT442206	hsa-miR-548t-5p	PAR-CLIP	22100165
MIRT442205	hsa-miR-106a-5p	PAR-CLIP	22100165
MIRT442204	hsa-miR-106b-5p	PAR-CLIP	22100165
MIRT442203	hsa-miR-17-5p	PAR-CLIP	22100165
MIRT442202	hsa-miR-20a-5p	PAR-CLIP	22100165
MIRT442201	hsa-miR-20b-5p	PAR-CLIP	22100165
MIRT442200	hsa-miR-519d-3p	PAR-CLIP	22100165
MIRT442199	hsa-miR-526b-3p	PAR-CLIP	22100165
MIRT442198	hsa-miR-93-5p	PAR-CLIP	22100165
MIRT442196	hsa-miR-6755-5p	PAR-CLIP	22100165
MIRT442197	hsa-miR-6847-5p	PAR-CLIP	22100165
MIRT442195	hsa-miR-4257	PAR-CLIP	22100165
MIRT442194	hsa-miR-5189-3p	PAR-CLIP	22100165
MIRT442193	hsa-miR-197-5p	PAR-CLIP	22100165
MIRT442192	hsa-miR-3132	PAR-CLIP	22100165
MIRT442191	hsa-miR-4650-3p	PAR-CLIP	22100165
MIRT442190	hsa-miR-127-5p	PAR-CLIP	22100165

Show/Hide all (23)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000149	Function	SNARE binding	IBA
GO:0000149	Function	SNARE binding	IDA	25799061
GO:0005515	Function	Protein binding	IPI	3172165, 25799061, 26496610, 28514442, 33961781
GO:0005768	Component	Endosome	IEA
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0032456	Process	Endocytic recycling	IBA
GO:0032456	Process	Endocytic recycling	IDA	25799061
GO:0032456	Process	Endocytic recycling	IEA
GO:0032456	Process	Endocytic recycling	IEA
GO:0032456	Process	Endocytic recycling	IMP	25799061
GO:0032456	Process	Endocytic recycling	NAS	25799061
GO:0042147	Process	Retrograde transport, endosome to Golgi	IMP	25799061
GO:0048471	Component	Perinuclear region of cytoplasm	IEA
GO:0055037	Component	Recycling endosome	IDA	25799061
GO:0055037	Component	Recycling endosome	IEA
GO:0055037	Component	Recycling endosome	NAS	25799061
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:1990745	Component	EARP complex	IBA
GO:1990745	Component	EARP complex	IDA	25799061
GO:1990745	Component	EARP complex	IEA
GO:1990745	Component	EARP complex	IPI	25799061

MIM	HGNC	e!Ensembl
616465	25956	ENSG00000004766

Q96JG6

Protein name

Syndetin (Coiled-coil domain-containing protein 132) (EARP/GARPII complex subunit VPS50)

Protein function

Acts as a component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane. Within the EARP

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF10475	Vps54_N	54 → 345	Vacuolar-sorting protein 54, of GARP complex	Family
PF10474	DUF2451	723 → 957	Protein of unknown function C-terminus (DUF2451)	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous, with higher expression in brain and skeletal muscle. {ECO:0000269|PubMed:21472204}.

Sequence

MQKIKSLMTRQGLKSPQESLSDLGAIESLRVPGKEEFRELREQPSDPQAEQELINSIEQV
YFSVDSFDIVKYELEKLPPVLNLQELEAYRDKLKQQQAAVSKKVADLILEKQPAYVKELE
RVTSLQTGLQLAAVICTNGRRHLNIAKEGFTQASLGLLANQRKRQLLIGLLKSLRTIKTL
QRTDVRLSEMLEEEDYPGAIQLCLECQKAASTFKHYSCISELNSKLQDTLEQIEEQLDVA
LSKICKNFDINHYTKVQQAYRLLGKTQTAMDQLHMHFTQAIHNTVFQVVLGYVELCAGNT
DTKFQKLQYKDLCTHVTPDSYIPCLADLCKALWEVMLSYYRTMEWHEKHDNEDTASASEG
SNMIGTEETNFDRGYIKKKLEHGLTRIWQDVQLKVKTYLLGTDLSIFKYDDFIFVLDIIS
RLMQVGEEFCGSKSEVLQESIRKQSVNYFKNYHRTRLDELRMFLENETWELCPVKSNFSI
LQLHEFKFMEQSRSPSVSPSKQPVSTSSKTVTLFEQYCSGGNPFEIQANHKDEETEDVLA
SNGYESDEQEKSAYQEYDSDSDVPEELKRDYVDEQTGDGPVKSVSRETLKSRKKSDYSLN
KVNAPILTNTTLNVIRLVGKYMQMMNILKPIAFDVIHFMSQLFDYYLYAIYTFFGRNDSL
ESTGLGLSSSRLRTTLNRIQESLIDLEVSADPTATLTAAEERKEKVPSPHLSHLVVLTSG
DTLYGLAERVVATESLVFLAEQFEFLQPHLDAVMPAVKKPFLQQFYSQTVSTASELRKPI
YWIVAGKALDYEQMLLLMANVKWDVKEIMSQHNIYVDALLKEFEQFNRRLNEVSKRVRIP
LPVSNILWEHCIRLANRTIVEGYANVKKCSNEGRALMQLDFQQFLMKLEKLTDIRPIPDK
EFVETYIKAYYLTENDMERWIKEHREYSTKQLTNLVNVCLGSHINKKARQKLLAAIDDID
RPKR

Sequence length

964

Interactions

View interactions

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 Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis	Pathogenic; Likely pathogenic	rs745695719, rs2116989385, rs1262620713, rs2546603981	RCV001804216 RCV001804217 RCV003988998 RCV004555185	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (2)

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.
AMENORRHEA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSYCHIATRIC DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (5)

Disease Name	Disease (Merged)	Source	PMID	Evidence Score
Associations from Text Mining Disease associations identified through text mining
IGA Glomerulonephritis	Glomerulonephritis	BEFREE	26370181	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	31814760	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	31814760	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	31814760	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	31814760	★★★★★ ★☆☆☆☆ Found in Text Mining only

VPS50 (VPS50 subunit of EARP/GARPII complex)