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 Arabidopsi... See more...

Aliases for VPS41 Gene

Aliases for VPS41 Gene

  • VPS41 Subunit Of HOPS Complex 2 3 5
  • Vacuolar Protein Sorting-Associated Protein 41 Homolog 3 4
  • VPS41, HOPS Complex Subunit 2 3
  • S53 3 4
  • Vacuolar Protein Sorting 41 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 41 (Yeast Homolog) 2
  • Vacuolar Protein Sorting 41 Homolog 3
  • Vacuolar Protein Sorting 41 (Yeast) 2
  • 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 Subunit Of HOPS Complex) is a Protein Coding gene. Diseases associated with VPS41 include Atypical Neurofibroma and Spherocytosis, Type 4. Gene Ontology (GO) annotations related to this gene include binding and GTPase binding.

UniProtKB/Swiss-Prot Summary 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).

Additional gene information for VPS41 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VPS41 Gene

Genomics for VPS41 Gene

GeneHancer (GH) Regulatory Elements for VPS41 Gene

Promoters and enhancers for VPS41 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
GH07J038908 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 510.6 +23.7 23689 2.2 ZBTB40 ZNF217 SIN3A TCF12 POLR2G USF1 GTF2E2 PHF8 SIX5 CTCF VPS41 FAM183BP HSALNG0057354 piR-55194-359
GH07J038932 Enhancer 0.7 ENCODE 500.7 -0.4 -362 0.2 CTCF REST RAD21 TRIM22 SMC3 FOXA2 ARNT BMI1 ELF1 FOXP1 VPS41 POU6F2
GH07J038934 Enhancer 0.2 Ensembl 500.7 -1.9 -1907 0.2 VPS41 POU6F2
GH07J038846 Enhancer 0.9 Ensembl ENCODE 13 +85.9 85894 0.6 ZNF217 FOS CTBP1 FOSL1 FOSL2 NEUROD1 JUND NFE2 GATA3 FOXA1 VPS41 ENSG00000227172 YAE1 piR-45099 piR-57133-544
GH07J038863 Enhancer 1.2 UCNEbase Ensembl ENCODE 8.2 +68.8 68795 2 RFX1 CUX1 CREB1 FOS JUND FOSL2 RXRA KDM1A SMARCA4 TFAP4 VPS41 piR-46501-090 piR-55194-359
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS41 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VPS41

Top Transcription factor binding sites by QIAGEN in the VPS41 gene promoter:
  • AML1a
  • FAC1
  • GATA-1
  • GATA-2
  • GATA-3
  • SREBP-1a
  • STAT1
  • STAT3
  • USF-1
  • USF1

Genomic Locations for VPS41 Gene

Genomic Locations for VPS41 Gene
chr7:38,722,974-38,932,394
(GRCh38/hg38)
Size:
209,421 bases
Orientation:
Minus strand
chr7:38,762,563-38,971,994
(GRCh37/hg19)
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 Parkinson's 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 Lys762
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS41 Gene

Domains & Families for VPS41 Gene

Gene Families for VPS41 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for VPS41 Gene

Suggested Antigen Peptide Sequences for VPS41 Gene

GenScript: Design optimal peptide antigens:
  • HVps41p (Q9H348_HUMAN)
  • S53 (VPS41_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P49754

UniProtKB/Swiss-Prot:

VPS41_HUMAN :
  • Belongs to the VPS41 family.
Family:
  • Belongs to the VPS41 family.
genes like me logo Genes that share domains with VPS41: view

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).

Phenotypes From GWAS Catalog for VPS41 Gene

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:0042802 identical protein binding IPI 24210660
GO:0043621 protein self-association IEA --
GO:0046872 metal ion binding 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:

Clone 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VPS41 gene
Compartment Confidence
endosome 5
cytosol 5
lysosome 5
golgi apparatus 4
cytoskeleton 3
nucleus 3
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for VPS41 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane IDA 23167963
GO:0005768 endosome IEA --
GO:0005769 early endosome IEA --
genes like me logo Genes that share ontologies with VPS41: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VPS41 Gene

Pathways & Interactions for VPS41 Gene

PathCards logo

SuperPathways for VPS41 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS41 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IEA --
GO:0006914 autophagy IEA --
GO:0008333 endosome to lysosome transport IMP 25783203
GO:0015031 protein transport IEA --
GO:0016192 vesicle-mediated transport IEA --
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

mRNA/cDNA for VPS41 Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone 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

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, MaxQB, and MOPED for VPS41 Gene



Protein tissue co-expression partners for VPS41 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VPS41

SOURCE GeneReport for Unigene cluster for VPS41 Gene:

Hs.592184

Evidence on tissue expression from TISSUES for VPS41 Gene

  • Nervous system(4.8)
  • Heart(4.3)
genes like me logo Genes that share expression patterns with VPS41: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 31 30
  • 99.69 (n)
OneToOne
dog
(Canis familiaris)
Mammalia VPS41 31 30
  • 93.51 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VPS41 31 30
  • 92.7 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Vps41 17 31 30
  • 90.11 (n)
rat
(Rattus norvegicus)
Mammalia Vps41 30
  • 90.05 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 90 (a)
OneToMany
-- 31
  • 86 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia VPS41 31
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS41 31 30
  • 83.08 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS41 31
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps41 30
  • 74.43 (n)
zebrafish
(Danio rerio)
Actinopterygii vps41 31 30
  • 72.6 (n)
OneToOne
wufa01f11 30
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12328 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009174 30
  • 49.33 (n)
fruit fly
(Drosophila melanogaster)
Insecta lt 31 32 30
  • 49.22 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F32A6.3 32
  • 27 (a)
vps-41 31
  • 26 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS41 33 31
  • 21 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons VPS41 30
  • 48.65 (n)
rice
(Oryza sativa)
Liliopsida Os04g0195000 30
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for VPS41: view image

Paralogs for VPS41 Gene

(1) SIMAP similar genes for VPS41 Gene using alignment to 12 proteins:

  • VPS41_HUMAN
  • C9J2U9_HUMAN
  • C9J3F8_HUMAN
  • C9JU58_HUMAN
  • C9JZ11_HUMAN
  • E9PF36_HUMAN
  • H7BXH3_HUMAN
  • H7BZX6_HUMAN
  • H7C0K2_HUMAN
  • Q75MS1_HUMAN
  • Q75MS2_HUMAN
  • Q75MX9_HUMAN
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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VPS41 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
707945 Benign: not provided 38,767,569(-) C/G SYNONYMOUS_VARIANT
rs1059508 - p.Arg843His
rs11762417 - p.Cys647Arg
rs35693565 - p.Thr146Pro

Additional dbSNP identifiers (rs#s) for VPS41 Gene

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)

Additional Variant Information for VPS41 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for VPS41 Gene

MalaCards: The human disease database

(4) MalaCards diseases for VPS41 Gene - From: DISEASES

Disorder Aliases PubMed IDs
atypical neurofibroma
spherocytosis, type 4
  • sph4
spherocytosis, type 3
  • hs3
hereditary spherocytosis
  • spherocytosis, type 1
- elite association - COSMIC cancer census association via MalaCards
Search VPS41 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VPS41

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 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 DC … Kaplan J (Proceedings of the National Academy of Sciences of the United States of America 1997) 2 3 4 54
  2. The small GTPase Arl8b regulates assembly of the mammalian HOPS complex on lysosomes. (PMID: 25908847) Khatter D … Sharma M (Journal of cell science 2015) 3 4 54
  3. 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 54
  4. 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 54
  5. RILP interacts with HOPS complex via VPS41 subunit to regulate endocytic trafficking. (PMID: 25445562) Lin X … Wang T (Scientific reports 2014) 3 4 54

Products for VPS41 Gene

Sources for VPS41 Gene