VPS16 (VPS16 core subunit of CORVET and HOPS complexes)

Gene

• Entrez ID: 64601
• Gene name: VPS16 core subunit of CORVET and HOPS complexes
• Gene symbol: VPS16
• Synonyms (NCBI Gene): DYT30, hVPS16
• Chromosome: 20
• Chromosome location: 20p13
• 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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT019172	hsa-miR-335-5p	Microarray	18185580
MIRT1486062	hsa-miR-1237	CLIP-seq
MIRT1486063	hsa-miR-1291	CLIP-seq
MIRT1486064	hsa-miR-328	CLIP-seq
MIRT1486065	hsa-miR-4480	CLIP-seq
MIRT1486066	hsa-miR-4726-3p	CLIP-seq
MIRT1486067	hsa-miR-4727-5p	CLIP-seq
MIRT1486068	hsa-miR-4769-3p	CLIP-seq
MIRT1486069	hsa-miR-764	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003779	Function	Actin binding	IBA
GO:0005515	Function	Protein binding	IPI	11382755, 20190753, 23901104, 24554770, 25266290, 25783203, 26496610, 28013294, 29778605, 33422265, 33961781, 35271311
GO:0005737	Component	Cytoplasm	IEA
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	IEA
GO:0005769	Component	Early endosome	IDA	19109425
GO:0005769	Component	Early endosome	IEA
GO:0005770	Component	Late endosome	IDA	11382755, 19109425
GO:0005776	Component	Autophagosome	IEA
GO:0006886	Process	Intracellular protein transport	IEA
GO:0006914	Process	Autophagy	IEA
GO:0007033	Process	Vacuole organization	IEA
GO:0008333	Process	Endosome to lysosome transport	IMP	25783203
GO:0010008	Component	Endosome membrane	IEA
GO:0010008	Component	Endosome membrane	TAS
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016197	Process	Endosomal transport	IBA
GO:0030136	Component	Clathrin-coated vesicle	IEA
GO:0030424	Component	Axon	IEA
GO:0030897	Component	HOPS complex	IBA
GO:0030897	Component	HOPS complex	IDA	19109425, 23901104, 24554770, 25783203, 37821429
GO:0030897	Component	HOPS complex	NAS	24554770
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0031902	Component	Late endosome membrane	IEA
GO:0033263	Component	CORVET complex	NAS	31092635
GO:0034058	Process	Endosomal vesicle fusion	NAS	24554770, 31092635
GO:0035542	Process	Regulation of SNARE complex assembly	NAS	24554770, 31092635
GO:0042144	Process	Vacuole fusion, non-autophagic	IBA
GO:0043025	Component	Neuronal cell body	IEA
GO:0051015	Function	Actin filament binding	IEA
GO:0055037	Component	Recycling endosome	IDA	19109425
GO:0097352	Process	Autophagosome maturation	IMP	25783203
GO:0098793	Component	Presynapse	IEA
GO:0099023	Component	Vesicle tethering complex	IEA

Other IDs

• MIM: 608550
• HGNC: 14584
• e!Ensembl: ENSG00000215305

Protein

• UniProt ID: Q9H269
• Protein name: Vacuolar protein sorting-associated protein 16 homolog (hVPS16)
• 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
• PDB: 4BX9
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04841	Vps16_N	4 → 420	Vps16, N-terminal region	Family
  PF04840	Vps16_C	517 → 835	Vps16, C-terminal region	Family

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitous.
• Sequence:

  MDCYTANWNPLGDSAFYRKYELYSMDWDLKEELRDCLVAAAPYGGPIALLRNPWRKEKAA
  SVRPVLDIYSASGMPLASLLWKSGPVVSLGWSAEEELLCVQEDGAVLVYGLHGDFRRHFS
  MGNEVLQNRVLDARIFHTEFGSGVAILTGAHRFTLSANVGDLKLRRMPEVPGLQSAPSCW
  TVLCQDRVAHILLAVGPDLYLLDHAACSAVTPPGLAPGVSSFLQMAVSFTYRHLALFTDT
  GYIWMGTASLKEKLCEFNCNIRAPPKQMVWCSRPRSKERAVVVAWERRLMVVGDAPESIQ
  FVLDEDSYLVPELDGVRIFSRSTHEFLHEVPAASEEIFKIASMAPGALLLEAQKEYEKES
  QKADEYLREIQELGQLTQAVQQCIEAAGHEHQPDMQKSLLRAASFGKCFLDRFPPDSFVH
  MCQDLRVLNAVRDYHIGIPLTYSQYKQLTIQVLLDRLVLRRLYPLAIQICEYLRLPEVQG
  VSRILAHWACYKVQQKDVSDEDVARAINQKLGDTPGVSYSDIAARAYGCGRTELAIKLLE
  YEPRSGEQVPLLLKMKRSKLALSKAIESGDTDLVFTVLLHLKNELNRGDFFMTLRNQPMA
  LSLYRQFCKHQELETLKDLYNQDDNHQELGSFHIRASYAAEERIEGRVAALQTAADAFYK
  AKNEFAAKATEDQMRLLRLQRRLEDELGGQFLDLSLHDTVTTLILGGHNKRAEQLARDFR
  IPDKRLWWLKLTALADLEDWEELEKFSKSKKSPIGYLPFVEICMKQHNKYEAKKYASRVG
  PEQKVKALLLVGDVAQAADVAIEHRNEAELSLVLSHCTGATDGATADKIQRARAQAQKK

• Sequence length: 839

Pathways

KEGG:

Autophagy - animal
Efferocytosis
Salmonella infection

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Dystonia 30	Pathogenic; Likely pathogenic	rs2146669693, rs1600004624, rs2146664989, rs367642720, rs2146673211, rs2515137975, rs2515114359, rs374769660, rs1422519039	RCV001375927 RCV001375929 RCV001375930 RCV001375931 RCV002468659 RCV002468812 RCV003444075 RCV001375928 RCV002468629	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
VPS16-associated disorder	Pathogenic	rs374769660	RCV001254053	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
VPS16-related disorder	Likely pathogenic	rs2089253964	RCV004753396	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Autism	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISTIC DISORDER	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Coarse facial features	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Decreased total neutrophil count	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Peripheral neuropathy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Splenomegaly	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	37124933	Associate	★☆☆☆☆ Found in Text Mining only
Choreoathetosis Hypothyroidism And Neonatal Respiratory Distress	Choreoathetosis	Pubtator	38291845	Associate	★☆☆☆☆ Found in Text Mining only
Dystonia	Dystonia	Pubtator	38291845	Associate	★☆☆☆☆ Found in Text Mining only
Dystonia, Primary	Dystonia	BEFREE	27174565		★☆☆☆☆ Found in Text Mining only
Dystonic Disorders	Dystonia	Pubtator	38291845	Associate	★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	Pubtator	34250953	Associate	★☆☆☆☆ Found in Text Mining only