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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	55823
Gene name	VPS11 core subunit of CORVET and HOPS complexes
Gene symbol	VPS11
Synonyms (NCBI Gene)	DYT32END1HLD12HLD12; DYT32PEP5RNF108hVPS11
Chromosome	11
Chromosome location	11q23.3
Summary	Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuol

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SNP ID	Visualize variation	Clinical significance	Consequence
rs34757931	T>G	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant

121

Show/Hide all (121)

miRTarBase ID	miRNA	Experiments	Reference
MIRT043320	hsa-miR-331-3p	CLASH	23622248
MIRT1485833	hsa-miR-1207-5p	CLIP-seq
MIRT1485834	hsa-miR-1237	CLIP-seq
MIRT1485835	hsa-miR-133a	CLIP-seq
MIRT1485836	hsa-miR-133b	CLIP-seq
MIRT1485837	hsa-miR-2117	CLIP-seq
MIRT1485838	hsa-miR-31	CLIP-seq
MIRT1485839	hsa-miR-3153	CLIP-seq
MIRT1485840	hsa-miR-3157-5p	CLIP-seq
MIRT1485841	hsa-miR-3168	CLIP-seq
MIRT1485842	hsa-miR-3182	CLIP-seq
MIRT1485843	hsa-miR-3194-5p	CLIP-seq
MIRT1485844	hsa-miR-3606	CLIP-seq
MIRT1485845	hsa-miR-3614-3p	CLIP-seq
MIRT1485846	hsa-miR-3616-3p	CLIP-seq
MIRT1485847	hsa-miR-3653	CLIP-seq
MIRT1485848	hsa-miR-3714	CLIP-seq
MIRT1485849	hsa-miR-4253	CLIP-seq
MIRT1485850	hsa-miR-4257	CLIP-seq
MIRT1485851	hsa-miR-4273	CLIP-seq
MIRT1485852	hsa-miR-4289	CLIP-seq
MIRT1485853	hsa-miR-4303	CLIP-seq
MIRT1485854	hsa-miR-4423-5p	CLIP-seq
MIRT1485855	hsa-miR-4446-3p	CLIP-seq
MIRT1485856	hsa-miR-4504	CLIP-seq
MIRT1485857	hsa-miR-4645-5p	CLIP-seq
MIRT1485858	hsa-miR-4649-3p	CLIP-seq
MIRT1485859	hsa-miR-4663	CLIP-seq
MIRT1485860	hsa-miR-4673	CLIP-seq
MIRT1485861	hsa-miR-4675	CLIP-seq
MIRT1485862	hsa-miR-4691-3p	CLIP-seq
MIRT1485863	hsa-miR-4691-5p	CLIP-seq
MIRT1485864	hsa-miR-4693-3p	CLIP-seq
MIRT1485865	hsa-miR-4707-3p	CLIP-seq
MIRT1485866	hsa-miR-4709-3p	CLIP-seq
MIRT1485867	hsa-miR-4711-3p	CLIP-seq
MIRT1485868	hsa-miR-4712-3p	CLIP-seq
MIRT1485869	hsa-miR-4721	CLIP-seq
MIRT1485870	hsa-miR-4726-3p	CLIP-seq
MIRT1485871	hsa-miR-4741	CLIP-seq
MIRT1485872	hsa-miR-4753-3p	CLIP-seq
MIRT1485873	hsa-miR-4763-3p	CLIP-seq
MIRT1485874	hsa-miR-4779	CLIP-seq
MIRT1485875	hsa-miR-542-3p	CLIP-seq
MIRT1485876	hsa-miR-592	CLIP-seq
MIRT1485877	hsa-miR-599	CLIP-seq
MIRT1485878	hsa-miR-614	CLIP-seq
MIRT1485879	hsa-miR-628-5p	CLIP-seq
MIRT1485880	hsa-miR-940	CLIP-seq
MIRT1485854	hsa-miR-4423-5p	CLIP-seq
MIRT1485857	hsa-miR-4645-5p	CLIP-seq
MIRT1485860	hsa-miR-4673	CLIP-seq
MIRT1485863	hsa-miR-4691-5p	CLIP-seq
MIRT1485854	hsa-miR-4423-5p	CLIP-seq
MIRT1485857	hsa-miR-4645-5p	CLIP-seq
MIRT1485860	hsa-miR-4673	CLIP-seq
MIRT1485863	hsa-miR-4691-5p	CLIP-seq
MIRT1485833	hsa-miR-1207-5p	CLIP-seq
MIRT2659989	hsa-miR-1233	CLIP-seq
MIRT1485834	hsa-miR-1237	CLIP-seq
MIRT2659990	hsa-miR-1285	CLIP-seq
MIRT1485838	hsa-miR-31	CLIP-seq
MIRT1485839	hsa-miR-3153	CLIP-seq
MIRT1485840	hsa-miR-3157-5p	CLIP-seq
MIRT1485841	hsa-miR-3168	CLIP-seq
MIRT1485842	hsa-miR-3182	CLIP-seq
MIRT2659991	hsa-miR-3187-5p	CLIP-seq
MIRT1485843	hsa-miR-3194-5p	CLIP-seq
MIRT1485844	hsa-miR-3606	CLIP-seq
MIRT1485845	hsa-miR-3614-3p	CLIP-seq
MIRT1485846	hsa-miR-3616-3p	CLIP-seq
MIRT1485847	hsa-miR-3653	CLIP-seq
MIRT1485848	hsa-miR-3714	CLIP-seq
MIRT2659992	hsa-miR-3945	CLIP-seq
MIRT1485849	hsa-miR-4253	CLIP-seq
MIRT2659993	hsa-miR-4292	CLIP-seq
MIRT1485853	hsa-miR-4303	CLIP-seq
MIRT1485855	hsa-miR-4446-3p	CLIP-seq
MIRT1485856	hsa-miR-4504	CLIP-seq
MIRT1485858	hsa-miR-4649-3p	CLIP-seq
MIRT1485861	hsa-miR-4675	CLIP-seq
MIRT1485862	hsa-miR-4691-3p	CLIP-seq
MIRT1485864	hsa-miR-4693-3p	CLIP-seq
MIRT1485866	hsa-miR-4709-3p	CLIP-seq
MIRT1485868	hsa-miR-4712-3p	CLIP-seq
MIRT1485869	hsa-miR-4721	CLIP-seq
MIRT1485871	hsa-miR-4741	CLIP-seq
MIRT1485873	hsa-miR-4763-3p	CLIP-seq
MIRT1485874	hsa-miR-4779	CLIP-seq
MIRT1485875	hsa-miR-542-3p	CLIP-seq
MIRT2659994	hsa-miR-612	CLIP-seq
MIRT1485880	hsa-miR-940	CLIP-seq
MIRT1485833	hsa-miR-1207-5p	CLIP-seq
MIRT2659989	hsa-miR-1233	CLIP-seq
MIRT2659990	hsa-miR-1285	CLIP-seq
MIRT1485838	hsa-miR-31	CLIP-seq
MIRT1485839	hsa-miR-3153	CLIP-seq
MIRT1485841	hsa-miR-3168	CLIP-seq
MIRT2659991	hsa-miR-3187-5p	CLIP-seq
MIRT1485844	hsa-miR-3606	CLIP-seq
MIRT1485846	hsa-miR-3616-3p	CLIP-seq
MIRT1485847	hsa-miR-3653	CLIP-seq
MIRT1485848	hsa-miR-3714	CLIP-seq
MIRT2659992	hsa-miR-3945	CLIP-seq
MIRT1485849	hsa-miR-4253	CLIP-seq
MIRT2659993	hsa-miR-4292	CLIP-seq
MIRT1485853	hsa-miR-4303	CLIP-seq
MIRT1485855	hsa-miR-4446-3p	CLIP-seq
MIRT1485856	hsa-miR-4504	CLIP-seq
MIRT1485858	hsa-miR-4649-3p	CLIP-seq
MIRT1485861	hsa-miR-4675	CLIP-seq
MIRT1485864	hsa-miR-4693-3p	CLIP-seq
MIRT1485866	hsa-miR-4709-3p	CLIP-seq
MIRT1485868	hsa-miR-4712-3p	CLIP-seq
MIRT1485869	hsa-miR-4721	CLIP-seq
MIRT1485871	hsa-miR-4741	CLIP-seq
MIRT1485873	hsa-miR-4763-3p	CLIP-seq
MIRT1485874	hsa-miR-4779	CLIP-seq
MIRT1485875	hsa-miR-542-3p	CLIP-seq
MIRT2659994	hsa-miR-612	CLIP-seq
MIRT1485880	hsa-miR-940	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0005515	Function	Protein binding	IPI	11382755, 21148287, 22493164, 23901104, 25266290, 25416956, 25500191, 26496610, 28325809, 28514442, 29778605, 32296183, 32814053, 33422265, 33961781, 35271311
GO:0005764	Component	Lysosome	IDA	21148287
GO:0005764	Component	Lysosome	IDA	11382755, 21802320
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	HDA	17897319
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005768	Component	Endosome	IBA
GO:0005768	Component	Endosome	IDA	20682791
GO:0005768	Component	Endosome	IEA
GO:0005769	Component	Early endosome	IDA	21148287
GO:0005769	Component	Early endosome	IEA
GO:0005770	Component	Late endosome	IDA	21148287
GO:0005770	Component	Late endosome	IDA	11382755
GO:0005776	Component	Autophagosome	IEA
GO:0006886	Process	Intracellular protein transport	IEA
GO:0006904	Process	Vesicle docking involved in exocytosis	IBA
GO:0006914	Process	Autophagy	IEA
GO:0007032	Process	Endosome organization	IBA
GO:0007033	Process	Vacuole organization	IBA
GO:0008270	Function	Zinc ion binding	IEA
GO:0008333	Process	Endosome to lysosome transport	IMP	25783203
GO:0010008	Component	Endosome membrane	TAS
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016192	Process	Vesicle-mediated transport	IEA
GO:0016567	Process	Protein ubiquitination	IMP	31015428
GO:0019904	Function	Protein domain specific binding	IPI	21148287
GO:0019905	Function	Syntaxin binding	IDA	11382755
GO:0030136	Component	Clathrin-coated vesicle	IEA
GO:0030139	Component	Endocytic vesicle	IDA	20682791
GO:0030674	Function	Protein-macromolecule adaptor activity	IBA
GO:0030897	Component	HOPS complex	IBA
GO:0030897	Component	HOPS complex	IDA	19109425, 23901104, 24554770, 37821429
GO:0030897	Component	HOPS complex	NAS	24554770
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0031647	Process	Regulation of protein stability	HMP	24270810
GO:0031902	Component	Late endosome membrane	IEA
GO:0033147	Process	Negative regulation of intracellular estrogen receptor signaling pathway	IGI	31015428
GO:0033263	Component	CORVET complex	NAS	31092635
GO:0034058	Process	Endosomal vesicle fusion	IMP	21148287
GO:0034058	Process	Endosomal vesicle fusion	NAS	24554770, 31092635
GO:0035542	Process	Regulation of SNARE complex assembly	NAS	24554770, 31092635
GO:0045732	Process	Positive regulation of protein catabolic process	IMP	21148287
GO:0046872	Function	Metal ion binding	IEA
GO:0048284	Process	Organelle fusion	IBA
GO:0061630	Function	Ubiquitin protein ligase activity	IMP	31015428
GO:0099023	Component	Vesicle tethering complex	IEA
GO:1902115	Process	Regulation of organelle assembly	IMP	21148287
GO:1903955	Process	Positive regulation of protein targeting to mitochondrion	HMP	24270810
GO:2000643	Process	Positive regulation of early endosome to late endosome transport	IMP	21148287

MIM	HGNC	e!Ensembl
608549	14583	ENSG00000160695

Q9H270

Protein name

Vacuolar protein sorting-associated protein 11 homolog (hVPS11) (RING finger protein 108)

Protein function

Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act as a core component of the putative HOPS and CORVET endosomal tethering complexes

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00637	Clathrin	412 → 548	Region in Clathrin and VPS	Family
PF13923	zf-C3HC4_2	821 → 860		Domain
PF12451	VPS11_C	864 → 908	Vacuolar protein sorting protein 11 C terminal	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous. Expression was highest in heart and low in lung.

Sequence

MAAYLQWRRFVFFDKELVKEPLSNDGAAPGATPASGSAASKFLCLPPGITVCDSGRGSLV
FGDMEGQIWFLPRSLQLTGFQAYKLRVTHLYQLKQHNILASVGEDEEGINPLVKIWNLEK
RDGGNPLCTRIFPAIPGTEPTVVSCLTVHENLNFMAIGFTDGSVTLNKGDITRDRHSKTQ
ILHKGNYPVTGLAFRQAGKTTHLFVVTTENVQSYIVSGKDYPRVELDTHGCGLRCSALSD
PSQDLQFIVAGDECVYLYQPDERGPCFAFEGHKLIAHWFRGYLIIVSRDRKVSPKSEFTS
RDSQSSDKQILNIYDLCNKFIAYSTVFEDVVDVLAEWGSLYVLTRDGRVHALQEKDTQTK
LEMLFKKNLFEMAINLAKSQHLDSDGLAQIFMQYGDHLYSKGNHDGAVQQYIRTIGKLEP
SYVIRKFLDAQRIHNLTAYLQTLHRQSLANADHTTLLLNCYTKLKDSSKLEEFIKKKSES
EVHFDVETAIKVLRQAGYYSHALYLAENHAHHEWYLKIQLEDIKNYQEALRYIGKLPFEQ
AESNMKRYGKILMHHIPEQTTQLLKGLCTDYRPSLEGRSDREAPGCRANSEEFIPIFANN
PRELKAFLEHMSEVQPDSPQGIYDTLLELRLQNWAHEKDPQVKEKLHAEAISLLKSGRFC
DVFDKALVLCQMHDFQDGVLYLYEQGKLFQQIMHYHMQHEQYRQVISVCERHGEQDPSLW
EQALSYFARKEEDCKEYVAAVLKHIENKNLMPPLLVVQTLAHNSTATLSVIRDYLVQKLQ
KQSQQIAQDELRVRRYREETTRIRQEIQELKASPKIFQKTKCSICNSALELPSVHFLCGH
SFHQHCFESYSESDADCPTCLPENRKVMDMIRAQEQKRDLHDQFQHQLRCSNDSFSVIAD
YFGRGVFNKLTLLTDPPTARLTSSLEAGLQRDLLMHSRRGT

Sequence length

941

Interactions

View interactions

	KEGG
	Autophagy - animal Efferocytosis Salmonella infection

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Dystonia 32	Pathogenic	rs2134735270	RCV001787247
Hypomyelinating leukodystrophy 12	Pathogenic; Likely pathogenic	rs2134766485, rs34757931	RCV001787246 RCV000203530
Leukoencephalopathy	Likely pathogenic; Pathogenic	rs34757931	RCV000202610

Show/Hide Unknown Diseases (13)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign	rs36008744, rs115245779	RCV005909407 RCV005902559
Adrenocortical carcinoma, hereditary	Benign	rs36008744	RCV005909408
Clear cell carcinoma of kidney	Benign	rs36008744	RCV005909409
Hepatocellular carcinoma	Benign	rs3825061, rs15818	RCV005914024 RCV005909416
Lung cancer	Benign	rs36008744	RCV005909414
Nonpapillary renal cell carcinoma	Likely benign	rs1784302	RCV005934645
Ovarian serous cystadenocarcinoma	Benign; Likely benign	rs36008744, rs1784302	RCV005909411 RCV005934646
Sarcoma	Benign	rs36008744	RCV005909410
Thymoma	Uncertain significance	rs782349615	RCV005928470
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	rs36008744, rs1784302	RCV005909413 RCV005934647
Uterine carcinosarcoma	Benign	rs36008744	RCV005909412
Uterine corpus endometrial carcinoma	Benign	rs36008744, rs115245779	RCV005909415 RCV005902560
VPS11-related disorder	Likely benign; Benign	rs782054802, rs150766222, rs141677018	RCV003966353 RCV003927173 RCV003970862

Show/Hide Text Mining Associations (15)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Blindness	Associate	27473128
Buschke Ollendorff syndrome	Associate	22132895
Demyelinating Diseases	Associate	27473128
Developmental Disabilities	Associate	27473128
Dystonia	Associate	33452836
Enterocolitis Necrotizing	Associate	28770467
Hearing Loss	Associate	27473128
Hypoxia	Associate	23509317
Lysosomal Storage Diseases	Associate	27473128, 33452836
Microcephaly	Associate	27473128
Neoplasms	Associate	23509317
No Reflow Phenomenon	Associate	28770467
Parkinson Disease	Associate	31199560
Quadriplegia	Associate	27473128
Seizures	Associate	27473128

VPS11 (VPS11 core subunit of CORVET and HOPS complexes)