VPS11 VPS11 core subunit of CORVET and HOPS complexes [Homo sapiens (human)] - Gene

Summary

Official Symbol: VPS11provided by HGNC
Official Full Name: VPS11 core subunit of CORVET and HOPS complexesprovided by HGNC
Primary source: HGNC:HGNC:14583
See related: Ensembl:ENSG00000160695 MIM:608549; AllianceGenome:HGNC:14583
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: END1; PEP5; HLD12; RNF108; hVPS11; HLD12; DYT32
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 vacuoles. This gene encodes the human homolog of yeast class C Vps11 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
Expression: Ubiquitous expression in thyroid (RPKM 16.0), bone marrow (RPKM 14.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q23.3

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (119067818..119081972)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (119088176..119102362)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (118938529..118952682)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Overexpression of VPS11 antagonizes the promoting effect of miR-542-3p on Mycobacterium tuberculosis survival in macrophages by regulating autophagy.
Title: Overexpression of VPS11 antagonizes the promoting effect of miR-542-3p on Mycobacterium tuberculosis survival in macrophages by regulating autophagy.
A Novel Homozygous VPS11 Variant May Cause Generalized Dystonia.
Title: A Novel Homozygous VPS11 Variant May Cause Generalized Dystonia.
Study characterized the ubiquitinomes of Vps11/18 and demonstrated that these two factors are involved in the regulation of signal transduction by protein ubiquitination. VPS11/18 regulate several signaling factors and pathways, including Wnt, estrogen receptor alpha (ERalpha), and NFkappaB.
Title: Vps11 and Vps18 of Vps-C membrane traffic complexes are E3 ubiquitin ligases and fine-tune signalling.
Underlining the presumed pathogenic potential of VPS11 defects.
Title: The second report of a new hypomyelinating disease due to a defect in the VPS11 gene discloses a massive lysosomal involvement.
our study reveals a defect in VPS11 as the underlying etiology for an autosomal recessive leukoencephalopathy disorder associated with a dysfunctional autophagy-lysosome trafficking pathway
Title: A Founder Mutation in VPS11 Causes an Autosomal Recessive Leukoencephalopathy Linked to Autophagic Defects.
In Ashkenazi-Jewish patients, syndrome with hypomyelination, developmental delay, increasing appendicular spasticity, truncal hypotonia and acquired microcephaly is associated with VPS11 missense mutation, p.Cys846Gly.
Title: Hypomyelination and developmental delay associated with VPS11 mutation in Ashkenazi-Jewish patients.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Dystonia 32 MedGen: C5562029 OMIM: 619637 GeneReviews: Not available	Compare labs
Hypomyelinating leukodystrophy 12 MedGen: C4225247 OMIM: 616683 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-Z40836 (e-PCR)
- UniSTS:12041

A004G17 (e-PCR)
- UniSTS:45322

D11S3369 (e-PCR)
- UniSTS:152611

G54074 (e-PCR)
- UniSTS:109456

WI-11749 (e-PCR)
- UniSTS:81315

MARC_7601-7602:992008552:1 (e-PCR)
- UniSTS:231352

MARC_7601-7602:996687999:1 (e-PCR)
- UniSTS:231352

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-macromolecule adaptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables syntaxin binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in autophagy	IEA Inferred from Electronic Annotation more info
involved_in endosomal vesicle fusion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endosomal vesicle fusion	NAS Non-traceable Author Statement more info	PubMed
involved_in endosome organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in endosome to lysosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of intracellular estrogen receptor signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in organelle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of early endosome to late endosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein targeting to mitochondrion	HMP more info	PubMed
involved_in protein ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of SNARE complex assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of organelle assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein stability	HMP more info	PubMed
involved_in vacuole organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle docking involved in exocytosis	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of CORVET complex	NAS Non-traceable Author Statement more info	PubMed
part_of HOPS complex	IBA Inferred from Biological aspect of Ancestor more info
part_of HOPS complex	IDA Inferred from Direct Assay more info	PubMed
part_of HOPS complex	NAS Non-traceable Author Statement more info	PubMed
located_in autophagosome	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated vesicle	IEA Inferred from Electronic Annotation more info
colocalizes_with early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endocytic vesicle	IDA Inferred from Direct Assay more info	PubMed
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	TAS Traceable Author Statement more info
colocalizes_with late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	HDA more info	PubMed
colocalizes_with lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 11 homolog

Names: RING finger protein 108; VPS11, CORVET/HOPS core subunit; vacuolar protein sorting 11 homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029670.2 RefSeqGene

Range

5037..19191

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001290185.2 → NP_001277114.1 vacuolar protein sorting-associated protein 11 homolog isoform 2

See identical proteins and their annotated locations for NP_001277114.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in its 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AK302973, BC065563, BI561271

Consensus CDS

CCDS76485.1

UniProtKB/Swiss-Prot

Q8WY89, Q96EP8, Q9H270, Q9H6D9, Q9HCS6

UniProtKB/TrEMBL

B7Z879

Related

ENSP00000481807.1, ENST00000614944.4

Conserved Domains (5) summary

smart00299
Location:401 → 525

CLH; Clathrin heavy chain repeat homology

cd00162
Location:811 → 850

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam00637
Location:407 → 526

Clathrin; Region in Clathrin and VPS

pfam12451
Location:852 → 897

VPS11_C; Vacuolar protein sorting protein 11 C terminal

cl02567
Location:132 → 282

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001378218.1 → NP_001365147.1 vacuolar protein sorting-associated protein 11 homolog isoform 3

Status: REVIEWED

Source sequence(s)

AP003392, KF511489

UniProtKB/Swiss-Prot

Q8WY89, Q96EP8, Q9H270, Q9H6D9, Q9HCS6

Conserved Domains (4) summary

cd16688
Location:824 → 867

RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins

pfam00637
Location:415 → 540

Clathrin; Region in Clathrin and VPS

pfam12451
Location:868 → 911

VPS11_C; Vacuolar protein sorting protein 11 C terminal

cl29593
Location:146 → 296

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001378219.1 → NP_001365148.1 vacuolar protein sorting-associated protein 11 homolog isoform 4

Status: REVIEWED

Source sequence(s)

AP003392, KF511489

UniProtKB/Swiss-Prot

Q8WY89, Q96EP8, Q9H270, Q9H6D9, Q9HCS6

Conserved Domains (4) summary

cd16688
Location:824 → 867

RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins

pfam00637
Location:421 → 540

Clathrin; Region in Clathrin and VPS

pfam12451
Location:868 → 911

VPS11_C; Vacuolar protein sorting protein 11 C terminal

cl29593
Location:142 → 292

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001378220.1 → NP_001365149.1 vacuolar protein sorting-associated protein 11 homolog isoform 5

Status: REVIEWED

Source sequence(s)

AP003392, KF511489

UniProtKB/Swiss-Prot

Q8WY89, Q96EP8, Q9H270, Q9H6D9, Q9HCS6

Conserved Domains (4) summary

cd16688
Location:815 → 858

RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins

pfam00637
Location:406 → 531

Clathrin; Region in Clathrin and VPS

pfam12451
Location:859 → 902

VPS11_C; Vacuolar protein sorting protein 11 C terminal

cl29593
Location:142 → 292

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001378221.1 → NP_001365150.1 vacuolar protein sorting-associated protein 11 homolog isoform 6

Status: REVIEWED

Source sequence(s)

AP003392, KF511489

UniProtKB/Swiss-Prot

Q8WY89, Q96EP8, Q9H270, Q9H6D9, Q9HCS6

Conserved Domains (4) summary

cd16688
Location:814 → 857

RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins

pfam00637
Location:405 → 530

Clathrin; Region in Clathrin and VPS

pfam12451
Location:858 → 901

VPS11_C; Vacuolar protein sorting protein 11 C terminal

cl29593
Location:136 → 286

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_021729.6 → NP_068375.3 vacuolar protein sorting-associated protein 11 homolog isoform 1

See identical proteins and their annotated locations for NP_068375.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AP003392, KF511489

Consensus CDS

CCDS73404.1

UniProtKB/Swiss-Prot

Q8WY89, Q96EP8, Q9H270, Q9H6D9, Q9HCS6

UniProtKB/TrEMBL

A0A087WXL6

Related

ENSP00000481126.1, ENST00000621676.5

Conserved Domains (5) summary

smart00299
Location:411 → 535

CLH; Clathrin heavy chain repeat homology

cd00162
Location:821 → 860

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam00637
Location:417 → 536

Clathrin; Region in Clathrin and VPS

pfam12451
Location:862 → 907

VPS11_C; Vacuolar protein sorting protein 11 C terminal

cl02567
Location:142 → 292

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RNA

NR_165447.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003392, KF511489
NR_165448.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003392, KF511489
NR_165449.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003392, KF511489
NR_165450.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003392, KF511489

Related

ENST00000622309.4
NR_165451.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003392, KF511489
NR_165452.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003392, KF511489
NR_165453.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003392, KF511489
NR_165454.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003392, KF511489