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Aliases for VPS41 Gene

Aliases for VPS41 Gene

  • VPS41, HOPS Complex Subunit 2 3
  • VPS41 HOPS Complex Subunit 3 5
  • S53 3 4
  • Vacuolar Protein Sorting 41 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 41 (Yeast Homolog) 2
  • Vacuolar Protein Sorting 41 (Yeast) 2
  • Vacuolar Protein Sorting 41 Homolog 3
  • Vacuolar Assembly Protein 41 3
  • HVps41p 3
  • HVPS41 3
  • HVSP41 3

External Ids for VPS41 Gene

Previous GeneCards Identifiers for VPS41 Gene

  • GC07M038409
  • GC07M038470
  • GC07M038504
  • GC07M038536
  • GC07M038913
  • GC07M039137
  • GC07M039370

Summaries for VPS41 Gene

Entrez Gene Summary for VPS41 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 ortholog of yeast Vps41 protein which is also conserved in Drosophila, tomato, and Arabidopsis. Expression studies in yeast and human indicate that this protein may be involved in the formation and fusion of transport vesicles from the Golgi. Several transcript variants encoding different isoforms have been described for this gene, however, the full-length nature of not all is known. [provided by RefSeq, Jul 2008]

GeneCards Summary for VPS41 Gene

VPS41 (VPS41, HOPS Complex Subunit) is a Protein Coding gene. GO annotations related to this gene include binding and GTPase binding.

UniProtKB/Swiss-Prot for VPS41 Gene

  • Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act in part as a core component of the putative HOPS endosomal tethering complexe is 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 (PubMed:23351085). Involved in homotypic vesicle fusions between late endosomes and in heterotypic fusions between late endosomes and lysosomes implicated in degradation of endocytosed cargo (PubMed:9159129, PubMed:23167963, PubMed:25445562, PubMed:25908847). Required for fusion of autophagosomes with lysosomes (PubMed:25783203). May link the HOPS complex to endosomal Rab7 via its association with RILP and to lysosomal membranes via its association with ARL8B, suggesting that these interactions may bring the compartments to close proximity for fusion (PubMed:25445562, PubMed:25908847). Involved in the direct trans-Golgi network to late endosomes transport of lysosomal membrane proteins independently of HOPS (PubMed:23322049). Involved in sorting to the regulated secretory pathway presumably implicating the AP-3 adaptor complex (By similarity). May play a role in HOPS-independent function in the regulated secretory pathway (PubMed:24210660).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS41 Gene

Genomics for VPS41 Gene

Regulatory Elements for VPS41 Gene

Genomic Location for VPS41 Gene

Chromosome:
7
Start:
38,722,963 bp from pter
End:
38,932,394 bp from pter
Size:
209,432 bases
Orientation:
Minus strand

Genomic View for VPS41 Gene

Genes around VPS41 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS41 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS41 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS41 Gene

Proteins for VPS41 Gene

  • Protein details for VPS41 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P49754-VPS41_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 41 homolog
    Protein Accession:
    P49754
    Secondary Accessions:
    • E9PF36
    • Q86TP8
    • Q99851
    • Q99852

    Protein attributes for VPS41 Gene

    Size:
    854 amino acids
    Molecular mass:
    98566 Da
    Quaternary structure:
    • Component of the putative homotypic fusion and vacuole protein sorting (HOPS) complex; the core of which composed of the class C Vps proteins VPS11, VPS16, VPS18 and VPS33A, is associated with VPS39 and VPS41 (PubMed:23351085, PubMed:25445562, PubMed:25908847). Interacts with RILP, MON1B (PubMed:20434987, PubMed:25445562). Interacts with ARL8B (GTP-bound form); involved in recruitment to lysosomes and probably hierarchial assembly of the HOPS complex at lysosomal membranes (PubMed:25908847). In vitro can self-assemble into a lattice (PubMed:24210660). Associates with adaptor protein complex 3 (AP-3) and clathrin:AP-3 complexes (PubMed:21411634).
    Miscellaneous:
    • Protective against both alpha-synuclein and neurotoxic-mediated injury in invertebrate and cellular models of Parkinsons disease (PD); the function requires the AP-3 adaptor complex and the HOPS complex.

    Alternative splice isoforms for VPS41 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS41 Gene

Proteomics data for VPS41 Gene at MOPED

Post-translational modifications for VPS41 Gene

  • Ubiquitination at Lys 762
  • Modification sites at PhosphoSitePlus

Antibody Products

No data available for DME Specific Peptides for VPS41 Gene

Domains & Families for VPS41 Gene

Suggested Antigen Peptide Sequences for VPS41 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P49754

UniProtKB/Swiss-Prot:

VPS41_HUMAN :
  • Belongs to the VPS41 family.
  • Contains 1 CHCR (clathrin heavy-chain) repeat.
Family:
  • Belongs to the VPS41 family.
Similarity:
  • Contains 1 CHCR (clathrin heavy-chain) repeat.
  • Contains 1 RING-type zinc finger.
genes like me logo Genes that share domains with VPS41: view

No data available for Gene Families for VPS41 Gene

Function for VPS41 Gene

Molecular function for VPS41 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 in part as a core component of the putative HOPS endosomal tethering complexe is 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 (PubMed:23351085). Involved in homotypic vesicle fusions between late endosomes and in heterotypic fusions between late endosomes and lysosomes implicated in degradation of endocytosed cargo (PubMed:9159129, PubMed:23167963, PubMed:25445562, PubMed:25908847). Required for fusion of autophagosomes with lysosomes (PubMed:25783203). May link the HOPS complex to endosomal Rab7 via its association with RILP and to lysosomal membranes via its association with ARL8B, suggesting that these interactions may bring the compartments to close proximity for fusion (PubMed:25445562, PubMed:25908847). Involved in the direct trans-Golgi network to late endosomes transport of lysosomal membrane proteins independently of HOPS (PubMed:23322049). Involved in sorting to the regulated secretory pathway presumably implicating the AP-3 adaptor complex (By similarity). May play a role in HOPS-independent function in the regulated secretory pathway (PubMed:24210660).
genes like me logo Genes that share phenotypes with VPS41: view

Animal Models for VPS41 Gene

MGI Knock Outs for VPS41:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VPS41 Gene

Localization for VPS41 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS41 Gene

Endosome membrane. Late endosome. Lysosome. Golgi apparatus, trans-Golgi network. Early endosome. Cytoplasmic vesicle, clathrin-coated vesicle.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VPS41 Gene COMPARTMENTS Subcellular localization image for VPS41 gene
Compartment Confidence
cytosol 5
endosome 5
golgi apparatus 5
lysosome 5
vacuole 5
nucleus 3
cytoskeleton 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for VPS41 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005769 early endosome IEA --
GO:0016020 membrane IDA 11412045
GO:0030136 clathrin-coated vesicle IDA 21411634
GO:0030897 HOPS complex IDA 19109425
GO:0031902 late endosome membrane IDA 23167963
genes like me logo Genes that share ontologies with VPS41: view

Pathways & Interactions for VPS41 Gene

SuperPathways for VPS41 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS41 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006623 protein targeting to vacuole IBA --
GO:0006886 intracellular protein transport IEA --
GO:0035542 regulation of SNARE complex assembly IBA --
genes like me logo Genes that share ontologies with VPS41: view

No data available for Pathways by source and SIGNOR curated interactions for VPS41 Gene

Drugs & Compounds for VPS41 Gene

No Compound Related Data Available

Transcripts for VPS41 Gene

Unigene Clusters for VPS41 Gene

Vacuolar protein sorting 41 homolog (S. cerevisiae):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for VPS41 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^
SP1: - -
SP2: - - -
SP3: - - - -
SP4:
SP5: -
SP6:
SP7:

ExUns: 23 ^ 24a · 24b ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31a · 31b
SP1: - -
SP2: - -
SP3: - -
SP4:
SP5:
SP6:
SP7:

Relevant External Links for VPS41 Gene

GeneLoc Exon Structure for
VPS41
ECgene alternative splicing isoforms for
VPS41

Expression for VPS41 Gene

mRNA expression in normal human tissues for VPS41 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for VPS41 Gene

This gene is overexpressed in Bone (13.2), Peripheral blood mononuclear cells (7.8), Lymph node (7.6), and Monocytes (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for VPS41 Gene



SOURCE GeneReport for Unigene cluster for VPS41 Gene Hs.592184

genes like me logo Genes that share expression patterns with VPS41: view

Protein tissue co-expression partners for VPS41 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for VPS41 Gene

Orthologs for VPS41 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS41 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia VPS41 35
  • 92.7 (n)
  • 97.66 (a)
VPS41 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS41 35
  • 93.51 (n)
  • 97.82 (a)
VPS41 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vps41 35
  • 90.11 (n)
  • 96.37 (a)
Vps41 16
Vps41 36
  • 97 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia VPS41 35
  • 99.69 (n)
  • 100 (a)
VPS41 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps41 35
  • 90.05 (n)
  • 95.97 (a)
oppossum
(Monodelphis domestica)
Mammalia VPS41 36
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 86 (a)
OneToMany
-- 36
  • 90 (a)
OneToMany
chicken
(Gallus gallus)
Aves VPS41 35
  • 83.08 (n)
  • 92.16 (a)
VPS41 36
  • 92 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS41 36
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps41 35
  • 74.43 (n)
  • 80.8 (a)
zebrafish
(Danio rerio)
Actinopterygii vps41 35
  • 72.6 (n)
  • 82.2 (a)
wufa01f11 35
vps41 36
  • 82 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12328 35
fruit fly
(Drosophila melanogaster)
Insecta lt 37
  • 37 (a)
lt 35
  • 49.22 (n)
  • 39.72 (a)
lt 36
  • 36 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009174 35
  • 49.33 (n)
  • 41.12 (a)
worm
(Caenorhabditis elegans)
Secernentea F32A6.3 37
  • 27 (a)
vps-41 36
  • 26 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS41 36
  • 21 (a)
OneToOne
VPS41 38
thale cress
(Arabidopsis thaliana)
eudicotyledons VPS41 35
  • 48.65 (n)
  • 39.97 (a)
rice
(Oryza sativa)
Liliopsida Os04g0195000 35
  • 50.06 (n)
  • 40.64 (a)
Species with no ortholog for VPS41:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • wheat (Triticum aestivum)

Evolution for VPS41 Gene

ENSEMBL:
Gene Tree for VPS41 (if available)
TreeFam:
Gene Tree for VPS41 (if available)

Paralogs for VPS41 Gene

genes like me logo Genes that share paralogs with VPS41: view

No data available for Paralogs for VPS41 Gene

Variants for VPS41 Gene

Sequence variations from dbSNP and Humsavar for VPS41 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs35693565 - 38,817,831(+) TCCGG(G/T)CACAA nc-transcript-variant, reference, missense
rs11762417 - 38,745,601(+) TTGAC(A/G)GATCT nc-transcript-variant, reference, missense
rs1059508 - 38,726,283(-) GAACC(A/G)TGGAC nc-transcript-variant, reference, missense
rs37472 -- 38,817,151(-) AGAAA(A/G)TCTCT intron-variant
rs37473 -- 38,816,037(-) CTAAA(A/C)ACTTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VPS41 Gene

Variant ID Type Subtype PubMed ID
nsv887965 CNV Gain 21882294
nsv887966 CNV Loss 21882294
nsv830967 CNV Loss 17160897

Variation tolerance for VPS41 Gene

Residual Variation Intolerance Score: 10.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.76; 57.89% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VPS41 Gene

HapMap Linkage Disequilibrium report
VPS41

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS41 Gene

Disorders for VPS41 Gene

Relevant External Links for VPS41

Genetic Association Database (GAD)
VPS41
Human Genome Epidemiology (HuGE) Navigator
VPS41
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VPS41

No disorders were found for VPS41 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VPS41 Gene

Publications for VPS41 Gene

  1. Characterization of VPS41, a gene required for vacuolar trafficking and high-affinity iron transport in yeast. (PMID: 9159129) Radisky D.C. … Kaplan J. (Proc. Natl. Acad. Sci. U.S.A. 1997) 2 3 4 67
  2. Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome Fusion with Endosomes and Autophagosomes. (PMID: 25783203) Wartosch L. … Luzio J.P. (Traffic 2015) 3
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  4. RILP interacts with HOPS complex via VPS41 subunit to regulate endocytic trafficking. (PMID: 25445562) Lin X. … Wang T. (Sci. Rep. 2014) 3
  5. The HOPS proteins hVps41 and hVps39 are required for homotypic and heterotypic late endosome fusion. (PMID: 23167963) Pols M.S. … Klumperman J. (Traffic 2013) 3

Products for VPS41 Gene

Sources for VPS41 Gene

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