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Aliases for VPS11 Gene

Aliases for VPS11 Gene

  • VPS11, CORVET/HOPS Core Subunit 2 3 5
  • RING Finger Protein 108 3 4
  • RNF108 3 4
  • HVPS11 3 4
  • Vacuolar Protein Sorting-Associated Protein 11 Homolog 3
  • Vacuolar Protein Sorting 11 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 11 (Yeast Homolog) 2
  • Vacuolar Protein Sorting 11 Homolog 3
  • HLD12 3
  • END1 3
  • PEP5 3

External Ids for VPS11 Gene

Previous GeneCards Identifiers for VPS11 Gene

  • GC11P135438
  • GC11P120450
  • GC11P118972
  • GC11P118476
  • GC11P118443
  • GC11P118938
  • GC11P114878

Summaries for VPS11 Gene

Entrez Gene Summary for VPS11 Gene

  • 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]

GeneCards Summary for VPS11 Gene

VPS11 (VPS11, CORVET/HOPS Core Subunit) is a Protein Coding gene. Diseases associated with VPS11 include Leukodystrophy, Hypomyelinating, 12 and Brain Small Vessel Disease With Or Without Ocular Anomalies. Gene Ontology (GO) annotations related to this gene include nucleotide binding and syntaxin binding.

UniProtKB/Swiss-Prot for VPS11 Gene

  • 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 which are proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes. The CORVET complex is proposed to function as a Rab5 effector to mediate early endosome fusion probably in specific endosome subpopulations (PubMed:11382755, PubMed:23351085, PubMed:24554770, PubMed:25266290, PubMed:25783203). Required for fusion of endosomes and autophagosomes with lysosomes (PubMed:25783203). Involved in cargo transport from early to late endosomes and required for the transition from early to late endosomes (PubMed:21148287). Involved in the retrograde Shiga toxin transport (PubMed:23593995).

Gene Wiki entry for VPS11 Gene

Additional gene information for VPS11 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS11 Gene

Genomics for VPS11 Gene

GeneHancer (GH) Regulatory Elements for VPS11 Gene

Promoters and enhancers for VPS11 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J119066 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 687.9 0.0 -6 2.2 HDGF PKNOX1 CLOCK MLX ARNT ZFP64 ARID4B SIN3A DMAP1 YY1 VPS11 ENSG00000272186 HYOU1 DPAGT1 HMBS ARCN1 H2AFX C2CD2L KMT2A ENSG00000254909
GH11J119055 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 685.9 -10.6 -10555 3 HDGF CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 YY1 E2F8 ZNF143 VPS11 HYOU1 GC11P119057 RPL5P30 KMT2A HINFP UBE4A HMBS PIR44546
GH11J118433 Promoter/Enhancer 2.7 VISTA EPDnew Ensembl ENCODE dbSUPER 43.4 -629.6 -629604 8.2 CLOCK ZFP64 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 KMT2A VPS11 HINFP ARCN1 TMEM25 CCDC84 IFT46 UBE4A THY1 BCL9L
GH11J119084 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 46.7 +17.6 17637 2.2 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A DMAP1 ZBTB7B YY1 SLC30A9 HMBS VPS11 SETP16 ENSG00000254892 ENSG00000254909 ENSG00000245869 ENSG00000254428 ARCN1 UBE4A BCL9L
GH11J119090 Promoter/Enhancer 2 Ensembl ENCODE dbSUPER 48.7 +26.0 25980 5.9 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC ZFP41 GLIS1 GC11M119097 H2AFX KMT2A HINFP UBE4A RPL5P30 ARCN1 BCL9L VPS11 CCDC84
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS11 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VPS11 gene promoter:
  • p53
  • MyoD
  • TFIID
  • TBP
  • Gfi-1

Genomic Locations for VPS11 Gene

Genomic Locations for VPS11 Gene
chr11:119,067,692-119,081,978
(GRCh38/hg38)
Size:
14,287 bases
Orientation:
Plus strand
chr11:118,938,403-118,952,688
(GRCh37/hg19)
Size:
14,286 bases
Orientation:
Plus strand

Genomic View for VPS11 Gene

Genes around VPS11 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS11 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS11 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS11 Gene

Proteins for VPS11 Gene

  • Protein details for VPS11 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H270-VPS11_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 11 homolog
    Protein Accession:
    Q9H270
    Secondary Accessions:
    • Q8WY89
    • Q96EP8
    • Q9H6D9
    • Q9HCS6

    Protein attributes for VPS11 Gene

    Size:
    941 amino acids
    Molecular mass:
    107837 Da
    Quaternary structure:
    • Core component of at least two putative endosomal tethering complexes, the homotypic fusion and vacuole protein sorting (HOPS) complex and the class C core vacuole/endosome tethering (CORVET) complex. Their common core is composed of the class C Vps proteins VPS11, VPS16, VPS18 and VPS33A, which in HOPS further associates with VPS39 and VPS41 and in CORVET with VPS8 and TGFBRAP1 (PubMed:11382755, PubMed:20434987, PubMed:23351085, PubMed:23901104, PubMed:25266290, PubMed:25783203). Interacts with TGFBRAP1, MON1B, STX7, STX17, EZR, RDX, MSN, ECPAS (PubMed:11382755, PubMed:20682791, PubMed:21148287, PubMed:24554770, PubMed:25266290). Interacts with RAB5C (By similarity). Associates with adaptor protein complex 3 (AP-3) and clathrin:AP-3 complexes (By similarity).
    SequenceCaution:
    • Sequence=AAG23761.1; Type=Frameshift; Positions=439, 924; Evidence={ECO:0000305}; Sequence=BAB15320.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

neXtProt entry for VPS11 Gene

Post-translational modifications for VPS11 Gene

  • Ubiquitination at posLast=909909 and posLast=8484
  • Modification sites at PhosphoSitePlus

Other Protein References for VPS11 Gene

No data available for DME Specific Peptides for VPS11 Gene

Domains & Families for VPS11 Gene

Gene Families for VPS11 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for VPS11 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H270

UniProtKB/Swiss-Prot:

VPS11_HUMAN :
  • Belongs to the VPS11 family.
Family:
  • Belongs to the VPS11 family.
genes like me logo Genes that share domains with VPS11: view

Function for VPS11 Gene

Molecular function for VPS11 Gene

UniProtKB/Swiss-Prot 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 which are proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes. The CORVET complex is proposed to function as a Rab5 effector to mediate early endosome fusion probably in specific endosome subpopulations (PubMed:11382755, PubMed:23351085, PubMed:24554770, PubMed:25266290, PubMed:25783203). Required for fusion of endosomes and autophagosomes with lysosomes (PubMed:25783203). Involved in cargo transport from early to late endosomes and required for the transition from early to late endosomes (PubMed:21148287). Involved in the retrograde Shiga toxin transport (PubMed:23593995).

Phenotypes From GWAS Catalog for VPS11 Gene

Gene Ontology (GO) - Molecular Function for VPS11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0005488 binding IEA --
GO:0005515 protein binding IPI 11382755
GO:0019904 protein domain specific binding IPI 21148287
GO:0019905 syntaxin binding IDA 11382755
genes like me logo Genes that share ontologies with VPS11: view
genes like me logo Genes that share phenotypes with VPS11: view

Human Phenotype Ontology for VPS11 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for VPS11 Gene

miRTarBase miRNAs that target VPS11

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS11

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for VPS11 Gene

Localization for VPS11 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS11 Gene

Endosome. Late endosome membrane; Peripheral membrane protein; Cytoplasmic side. Lysosome membrane; Peripheral membrane protein; Cytoplasmic side. Early endosome. Cytoplasmic vesicle. Cytoplasmic vesicle, autophagosome. Cytoplasmic vesicle, clathrin-coated vesicle.

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for VPS11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005764 colocalizes_with lysosome IEA,IDA 21148287
GO:0005765 lysosomal membrane HDA,IEA 17897319
GO:0005768 endosome IDA,IEA 20682791
GO:0005769 colocalizes_with early endosome IDA,IEA 21148287
genes like me logo Genes that share ontologies with VPS11: view

No data available for Subcellular locations from COMPARTMENTS for VPS11 Gene

Pathways & Interactions for VPS11 Gene

SuperPathways for VPS11 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IEA --
GO:0006904 vesicle docking involved in exocytosis IBA --
GO:0006914 autophagy IEA --
GO:0007032 endosome organization IBA --
GO:0007040 lysosome organization IBA --
genes like me logo Genes that share ontologies with VPS11: view

No data available for Pathways by source and SIGNOR curated interactions for VPS11 Gene

Drugs & Compounds for VPS11 Gene

No Compound Related Data Available

Transcripts for VPS11 Gene

Unigene Clusters for VPS11 Gene

Vacuolar protein sorting 11 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS11

Alternative Splicing Database (ASD) splice patterns (SP) for VPS11 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3a · 3b · 3c · 3d ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^
SP1: - - - - -
SP2: - - - - - - - -
SP3: - -
SP4:
SP5: -
SP6: -
SP7:
SP8: - -

ExUns: 14 ^ 15 ^ 16a · 16b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for VPS11 Gene

GeneLoc Exon Structure for
VPS11
ECgene alternative splicing isoforms for
VPS11

Expression for VPS11 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VPS11 Gene

Protein differential expression in normal tissues from HIPED for VPS11 Gene

This gene is overexpressed in Tonsil (40.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VPS11 Gene



Protein tissue co-expression partners for VPS11 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS11 Gene:

VPS11

SOURCE GeneReport for Unigene cluster for VPS11 Gene:

Hs.234282

mRNA Expression by UniProt/SwissProt for VPS11 Gene:

Q9H270-VPS11_HUMAN
Tissue specificity: Ubiquitous. Expression was highest in heart and low in lung.
genes like me logo Genes that share expression patterns with VPS11: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS11 Gene

Orthologs for VPS11 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS11 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS11 33
  • 99.86 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS11 34
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS11 34 33
  • 92.81 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VPS11 34 33
  • 92.45 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Vps11 16 34 33
  • 91.36 (n)
rat
(Rattus norvegicus)
Mammalia Vps11 33
  • 91.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VPS11 34
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS11 34 33
  • 75.75 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS11 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps11 33
  • 72.05 (n)
Str.9475 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.7968 33
zebrafish
(Danio rerio)
Actinopterygii vps11 34 33
  • 71.4 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002665 33
  • 51.9 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG32350 34
  • 20 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea R06F6.2 35
  • 27 (a)
vps-11 34
  • 26 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PEP5 34
  • 21 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons VPS11 33
  • 53.09 (n)
rice
(Oryza sativa)
Liliopsida Os04g0382700 33
  • 51.8 (n)
wheat
(Triticum aestivum)
Liliopsida Ta.8374 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 49 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU05422 33
  • 48.2 (n)
Species where no ortholog for VPS11 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for VPS11 Gene

ENSEMBL:
Gene Tree for VPS11 (if available)
TreeFam:
Gene Tree for VPS11 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VPS11: view image

Paralogs for VPS11 Gene

(1) SIMAP similar genes for VPS11 Gene using alignment to 2 proteins:

  • VPS11_HUMAN
  • U3KPW6_HUMAN
genes like me logo Genes that share paralogs with VPS11: view

No data available for Paralogs for VPS11 Gene

Variants for VPS11 Gene

Sequence variations from dbSNP and Humsavar for VPS11 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs34757931 pathogenic, Leukoencephalopathy, Leukodystrophy, hypomyelinating, 12 119,081,189(+) T/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
VAR_076393 Leukodystrophy, hypomyelinating, 12 (HLD12) [MIM:616683] p.Cys846Gly
rs1000064376 -- 119,078,513(+) A/G intron_variant
rs1000491172 -- 119,067,515(+) C/G upstream_transcript_variant
rs1000737270 -- 119,072,686(+) G/A intron_variant

Variation tolerance for VPS11 Gene

Gene Damage Index Score: 10.24; 90.54% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS11 Gene

Human Gene Mutation Database (HGMD)
VPS11
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS11

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for VPS11 Gene

Disorders for VPS11 Gene

MalaCards: The human disease database

(2) MalaCards diseases for VPS11 Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search VPS11 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VPS11_HUMAN
  • Leukodystrophy, hypomyelinating, 12 (HLD12) [MIM:616683]: An autosomal recessive neurologic disorder characterized by developmental delay, spasticity, truncal hypotonia, acquired microcephaly, intellectual disability with variable seizure disorder, accompanied by thin corpus callosum, paucity of white matter and delayed myelination. {ECO:0000269 PubMed:26307567}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for VPS11

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VPS11: view

No data available for Genatlas for VPS11 Gene

Publications for VPS11 Gene

  1. Characterization of the Mammalian CORVET and HOPS Complexes and Their Modular Restructuring for Endosome Specificity. (PMID: 26463206) van der Kant R … Neefjes J (The Journal of biological chemistry 2015) 2 3 58
  2. Hypomyelination and developmental delay associated with VPS11 mutation in Ashkenazi-Jewish patients. (PMID: 26307567) Edvardson S … Elpeleg O (Journal of medical genetics 2015) 3 4 58
  3. Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome Fusion with Endosomes and Autophagosomes. (PMID: 25783203) Wartosch L … Luzio JP (Traffic (Copenhagen, Denmark) 2015) 3 4 58
  4. The HOPS complex mediates autophagosome-lysosome fusion through interaction with syntaxin 17. (PMID: 24554770) Jiang P … Mizushima N (Molecular biology of the cell 2014) 3 4 58
  5. Mammalian CORVET is required for fusion and conversion of distinct early endosome subpopulations. (PMID: 25266290) Perini ED … Zerial M (Traffic (Copenhagen, Denmark) 2014) 3 4 58

Products for VPS11 Gene

Sources for VPS11 Gene

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