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Aliases for VPS41 Gene

Aliases for VPS41 Gene

  • VPS41, HOPS Complex Subunit 2 3 5
  • S53 3 4
  • Vacuolar Protein Sorting-Associated Protein 41 Homolog 3
  • 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. Diseases associated with VPS41 include Early-Onset Familial Alzheimer Disease. 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 complex 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

Enhancers for VPS41 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07F038846 0.2 ENCODE 12.9 +86.0 85959 0.2 PKNOX1 ATF1 JUN GATA3 CTBP1 NFE2 FOSL2 FOS MAFK CREM VPS41 LOC105375240 YAE1D1 GC07P038849 GC07M038790
GH07F038855 0.8 Ensembl 10.9 +76.7 76694 1.4 SRF JUND ATF1 ATF3 ELK1 SPI1 VPS41 GC07P038849
GH07F038908 0.4 ENCODE 10.5 +23.4 23405 1.6 HDGF ATF1 CREB3L1 ARID4B SIN3A GLI4 ZNF2 ETS1 YY1 GLIS2 RWDD4P2 VPS41 GC07P038849
GH07F038797 0.6 ENCODE 10.2 +135.3 135299 0.2 CTCF GATA3 ZNF654 SMC3 TRIM22 REST RAD21 VPS41 LOC105375240 YAE1D1 FAM183BP GC07M038790 GC07P038849
GH07F039465 0.8 ENCODE 9.9 -532.8 -532773 0.2 CTCF TEAD4 BACH1 ZNF384 RAD21 TEAD3 YY1 ZNF316 ZNF143 SMC3 VPS41 YAE1D1 LOC105375240 FAM183BP LOC105375238 POU6F2-AS1
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around VPS41 on UCSC Golden Path with GeneCards custom track

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

Post-translational modifications for VPS41 Gene

  • Ubiquitination at Lys 762
  • Modification sites at PhosphoSitePlus

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 complex 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).

Gene Ontology (GO) - Molecular Function for VPS41 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19109425
GO:0008017 microtubule binding IEA --
GO:0008270 zinc ion binding IEA --
GO:0042802 identical protein binding IPI 24210660
GO:0043621 protein self-association IEA --
genes like me logo Genes that share ontologies with VPS41: view
genes like me logo Genes that share phenotypes with VPS41: view

Animal Models for VPS41 Gene

MGI Knock Outs for VPS41:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , 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:0005622 intracellular IEA --
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane IDA 17897319
GO:0005768 endosome IEA --
GO:0005769 early endosome IEA --
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:0006810 transport IEA --
GO:0006886 intracellular protein transport IEA --
GO:0006914 autophagy IEA --
GO:0008333 endosome to lysosome transport IMP 25783203
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

Transcripts for VPS41 Gene

Unigene Clusters for VPS41 Gene

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

Inhibitory RNA Products

Flow Cytometry Products

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 from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for VPS41 Gene



Protein tissue co-expression partners for VPS41 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS41 Gene:

VPS41

SOURCE GeneReport for Unigene cluster for VPS41 Gene:

Hs.592184
genes like me logo Genes that share expression patterns with VPS41: view

Primer 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
chimpanzee
(Pan troglodytes)
Mammalia VPS41 34 35
  • 99.69 (n)
dog
(Canis familiaris)
Mammalia VPS41 34 35
  • 93.51 (n)
cow
(Bos Taurus)
Mammalia VPS41 34 35
  • 92.7 (n)
mouse
(Mus musculus)
Mammalia Vps41 34 16 35
  • 90.11 (n)
rat
(Rattus norvegicus)
Mammalia Vps41 34
  • 90.05 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 90 (a)
OneToMany
-- 35
  • 86 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia VPS41 35
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS41 34 35
  • 83.08 (n)
lizard
(Anolis carolinensis)
Reptilia VPS41 35
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps41 34
  • 74.43 (n)
zebrafish
(Danio rerio)
Actinopterygii vps41 34 35
  • 72.6 (n)
wufa01f11 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12328 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009174 34
  • 49.33 (n)
fruit fly
(Drosophila melanogaster)
Insecta lt 36 34 35
  • 49.22 (n)
worm
(Caenorhabditis elegans)
Secernentea F32A6.3 36
  • 27 (a)
vps-41 35
  • 26 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS41 35 37
  • 21 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons VPS41 34
  • 48.65 (n)
rice
(Oryza sativa)
Liliopsida Os04g0195000 34
  • 50.06 (n)
Species where no ortholog for VPS41 was found in the sources mined by GeneCards:
  • 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
rs1001476 -- 38,789,865(-) CAGGT(A/G)TGCTC nc-transcript-variant, reference, synonymous-codon
rs10085487 -- 38,830,780(+) CCACA(C/T)GAGCG intron-variant
rs10085898 -- 38,830,844(+) AATGT(C/T)AGAAG intron-variant
rs1012976 -- 38,769,390(+) AGCAA(A/G)CTAAG intron-variant, upstream-variant-2KB
rs1017028 -- 38,763,017(-) AAAAA(G/T)TTATT intron-variant

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

Variant ID Type Subtype PubMed ID
esv3612889 CNV gain 21293372
esv3612890 CNV gain 21293372
nsv1032637 CNV gain 25217958
nsv472463 CNV novel sequence insertion 20440878
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

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS41

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

Disorders for VPS41 Gene

MalaCards: The human disease database

(1) MalaCards diseases for VPS41 Gene - From: GeneCards

Disorder Aliases PubMed IDs
early-onset familial alzheimer disease
  • eofad
- elite association - COSMIC cancer census association via MalaCards
Search VPS41 in MalaCards View complete list of genes associated with diseases

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

No data available for 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 64
  2. Characterization of the Mammalian CORVET and HOPS Complexes and Their Modular Restructuring for Endosome Specificity. (PMID: 26463206) van der Kant R. … Neefjes J. (J. Biol. Chem. 2015) 2 3 64
  3. 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 4 64
  4. RILP interacts with HOPS complex via VPS41 subunit to regulate endocytic trafficking. (PMID: 25445562) Lin X. … Wang T. (Sci. Rep. 2014) 3 4 64
  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 4 64

Products for VPS41 Gene

Sources for VPS41 Gene

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