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

Gene ID: 55823, updated on 4-Jan-2025

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
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Genomic context

See VPS11 in Genome Data Viewer
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_000011.10Genomic Context describing neighboring genes Neighboring gene HYOU1 antisense RNA 1 Neighboring gene hypoxia up-regulated 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5617 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118927013-118927514 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118927515-118928014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5618 Neighboring gene uncharacterized LOC124902769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5620 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118955192-118955889 Neighboring gene hydroxymethylbilane synthase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118963458-118963970 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118965105-118965668 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118965669-118966232 Neighboring gene dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 Neighboring gene H2A.X variant histone

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Pathways from PubChem

Interactions

General gene information

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding  
enables nucleotide binding  
enables protein binding PubMed 
enables protein domain specific binding PubMed 
enables protein-macromolecule adaptor activity  
enables syntaxin binding PubMed 
enables ubiquitin protein ligase activity PubMed 
Process Evidence Code Pubs
involved_in autophagy  
involved_in endosomal vesicle fusion PubMed 
involved_in endosomal vesicle fusion PubMed 
involved_in endosome organization  
involved_in endosome to lysosome transport PubMed 
involved_in intracellular protein transport  
involved_in negative regulation of intracellular estrogen receptor signaling pathway PubMed 
involved_in organelle fusion  
involved_in positive regulation of early endosome to late endosome transport PubMed 
involved_in positive regulation of protein catabolic process PubMed 
involved_in positive regulation of protein targeting to mitochondrion PubMed 
involved_in protein ubiquitination PubMed 
involved_in regulation of SNARE complex assembly PubMed 
involved_in regulation of organelle assembly PubMed 
involved_in regulation of protein stability PubMed 
involved_in vacuole organization  
involved_in vesicle docking involved in exocytosis  
Component Evidence Code Pubs
part_of CORVET complex PubMed 
part_of HOPS complex  
part_of HOPS complex PubMed 
part_of HOPS complex PubMed 
located_in autophagosome  
located_in clathrin-coated vesicle  
colocalizes_with early endosome PubMed 
located_in endocytic vesicle PubMed 
is_active_in endosome  
located_in endosome PubMed 
located_in endosome membrane  
colocalizes_with late endosome PubMed 
located_in late endosome PubMed 
located_in late endosome membrane  
located_in lysosomal membrane PubMed 
colocalizes_with lysosome PubMed 
located_in lysosome PubMed 

General protein information

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

  1. NG_029670.2 RefSeqGene

    Range
    5037..19191
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001290185.2NP_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:401525
    CLH; Clathrin heavy chain repeat homology
    cd00162
    Location:811850
    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:407526
    Clathrin; Region in Clathrin and VPS
    pfam12451
    Location:852897
    VPS11_C; Vacuolar protein sorting protein 11 C terminal
    cl02567
    Location:132282
    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 ...
  2. NM_001378218.1NP_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:824867
    RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins
    pfam00637
    Location:415540
    Clathrin; Region in Clathrin and VPS
    pfam12451
    Location:868911
    VPS11_C; Vacuolar protein sorting protein 11 C terminal
    cl29593
    Location:146296
    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 ...
  3. NM_001378219.1NP_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:824867
    RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins
    pfam00637
    Location:421540
    Clathrin; Region in Clathrin and VPS
    pfam12451
    Location:868911
    VPS11_C; Vacuolar protein sorting protein 11 C terminal
    cl29593
    Location:142292
    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 ...
  4. NM_001378220.1NP_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:815858
    RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins
    pfam00637
    Location:406531
    Clathrin; Region in Clathrin and VPS
    pfam12451
    Location:859902
    VPS11_C; Vacuolar protein sorting protein 11 C terminal
    cl29593
    Location:142292
    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 ...
  5. NM_001378221.1NP_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:814857
    RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins
    pfam00637
    Location:405530
    Clathrin; Region in Clathrin and VPS
    pfam12451
    Location:858901
    VPS11_C; Vacuolar protein sorting protein 11 C terminal
    cl29593
    Location:136286
    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 ...
  6. NM_021729.6NP_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:411535
    CLH; Clathrin heavy chain repeat homology
    cd00162
    Location:821860
    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:417536
    Clathrin; Region in Clathrin and VPS
    pfam12451
    Location:862907
    VPS11_C; Vacuolar protein sorting protein 11 C terminal
    cl02567
    Location:142292
    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

  1. NR_165447.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP003392, KF511489
  2. NR_165448.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP003392, KF511489
  3. NR_165449.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP003392, KF511489
  4. NR_165450.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP003392, KF511489
    Related
    ENST00000622309.4
  5. NR_165451.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP003392, KF511489
  6. NR_165452.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP003392, KF511489
  7. NR_165453.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP003392, KF511489
  8. NR_165454.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP003392, KF511489

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    119067818..119081972
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427256.1XP_047283212.1  vacuolar protein sorting-associated protein 11 homolog isoform X1

RNA

  1. XR_947859.3 RNA Sequence

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646203.1 Reference GRCh38.p14 PATCHES

    Range
    89417..103571
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331618.1XP_054187593.1  vacuolar protein sorting-associated protein 11 homolog isoform X1

RNA

  1. XR_008485725.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    119088176..119102362
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369352.1XP_054225327.1  vacuolar protein sorting-associated protein 11 homolog isoform X1

RNA

  1. XR_008488420.1 RNA Sequence

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