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Aliases for VPS45 Gene

Aliases for VPS45 Gene

  • Vacuolar Protein Sorting 45 Homolog 2 3 5
  • HlVps45 3 4
  • VPS45A 3 4
  • VPS45B 3 4
  • Vacuolar Protein Sorting 45 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting-Associated Protein 45 3
  • Vacuolar Protein Sorting 45A (Yeast Homolog) 2
  • Leucocyte Vacuolar Protein Sorting 45 3
  • Vacuolar Protein Sorting 45A (Yeast) 2
  • Vacuolar Protein Sorting 45A 3
  • H1VPS45 3
  • H-VPS45 4
  • VPS54A 3
  • VSP45A 3
  • VSP45 3
  • SCN5 3
  • H1 3

External Ids for VPS45 Gene

Previous HGNC Symbols for VPS45 Gene

  • VPS45B
  • VPS45A

Previous GeneCards Identifiers for VPS45 Gene

  • GC01P148306
  • GC01P150039
  • GC01P121419

Summaries for VPS45 Gene

Entrez Gene Summary for VPS45 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 is a member of the Sec1 domain family, and shows a high degree of sequence similarity to mouse, rat and yeast Vps45. The exact function of this gene is not known, but its high expression in peripheral blood mononuclear cells suggests a role in trafficking proteins, including inflammatory mediators. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2013]

GeneCards Summary for VPS45 Gene

VPS45 (Vacuolar Protein Sorting 45 Homolog) is a Protein Coding gene. Diseases associated with VPS45 include Neutropenia, Severe Congenital, 5, Autosomal Recessive and Neutropenia. Among its related pathways are Vesicle-mediated transport and Factors involved in megakaryocyte development and platelet production.

UniProtKB/Swiss-Prot for VPS45 Gene

  • May play a role in vesicle-mediated protein trafficking from the Golgi stack through the trans-Golgi network.

Gene Wiki entry for VPS45 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS45 Gene

Genomics for VPS45 Gene

Regulatory Elements for VPS45 Gene

Enhancers for VPS45 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
GH01F150185 1.5 FANTOM5 Ensembl ENCODE 11.2 +119.7 119677 2.5 HDGF ATF1 CBX3 THRB RAD21 RFX5 GTF3C2 ZNF121 ZNF766 POLR3A SF3B4 APH1A PLEKHO1 SETDB1 PRPF3 MTMR11 GOLPH3L UBE2D3P3 VPS45 BOLA1
GH01F150609 1.6 FANTOM5 ENCODE 10.2 +545.5 545494 7.4 PKNOX1 ARID4B SIN3A YY1 SLC30A9 ZNF143 FOS SP3 JUNB MXD4 HORMAD1 MCL1 CTSS ARNT GOLPH3L VPS72 CDC42SE1 LYSMD1 GABPB2 VPS45
GH01F149883 1.2 ENCODE 13.5 -180.6 -180591 5.9 CREB3L1 MLX ZFP64 FEZF1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 PRPF3 SF3B4 UBE2D3P3 CTSK SV2A GOLPH3L HIST2H2AB ADAMTSL4 VPS45 APH1A
GH01F150557 1.2 ENCODE 13.4 +502.0 502012 23.1 MLX CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC HORMAD1 SETDB1 GOLPH3L SF3B4 CTSK PRPF3 UBE2D3P3 CYCSP51 VPS45 GABPB2
GH01F150008 1.5 FANTOM5 ENCODE 10.4 -57.1 -57085 2.9 HDGF PKNOX1 ARNT CREB3L1 MLX WRNIP1 ZFP64 ARID4B SIN3A FEZF1 SETDB1 PRPF3 UBE2D3P3 CTSK HIST2H2AB MTMR11 SF3B4 GOLPH3L ADAMTSL4 SV2A
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VPS45 on UCSC Golden Path with GeneCards custom track

Promoters for VPS45 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000285678 307 2801 PKNOX1 ARNT CREB3L1 WRNIP1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1

Genomic Location for VPS45 Gene

Chromosome:
1
Start:
150,067,293 bp from pter
End:
150,145,327 bp from pter
Size:
78,035 bases
Orientation:
Plus strand

Genomic View for VPS45 Gene

Genes around VPS45 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS45 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS45 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS45 Gene

Proteins for VPS45 Gene

  • Protein details for VPS45 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NRW7-VPS45_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 45
    Protein Accession:
    Q9NRW7
    Secondary Accessions:
    • D3DUZ9
    • F5H8K1
    • Q15715
    • Q53FR8
    • Q5T4P6
    • Q9Y4Z6

    Protein attributes for VPS45 Gene

    Size:
    570 amino acids
    Molecular mass:
    65077 Da
    Quaternary structure:
    • Interacts with STX6 (By similarity). Interacts with ZFYVE20.

    Alternative splice isoforms for VPS45 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS45 Gene

Post-translational modifications for VPS45 Gene

  • Ubiquitination at Lys 371, Lys 378, Lys 450, and Lys 483
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS45 Gene

Domains & Families for VPS45 Gene

Protein Domains for VPS45 Gene

Graphical View of Domain Structure for InterPro Entry

Q9NRW7

UniProtKB/Swiss-Prot:

VPS45_HUMAN :
  • Belongs to the STXBP/unc-18/SEC1 family.
Family:
  • Belongs to the STXBP/unc-18/SEC1 family.
genes like me logo Genes that share domains with VPS45: view

No data available for Gene Families for VPS45 Gene

Function for VPS45 Gene

Molecular function for VPS45 Gene

UniProtKB/Swiss-Prot Function:
May play a role in vesicle-mediated protein trafficking from the Golgi stack through the trans-Golgi network.

Gene Ontology (GO) - Molecular Function for VPS45 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with VPS45: view
genes like me logo Genes that share phenotypes with VPS45: view

Human Phenotype Ontology for VPS45 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for VPS45 Gene

Localization for VPS45 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS45 Gene

Golgi apparatus membrane; Peripheral membrane protein. Endosome membrane; Peripheral membrane protein. Note=Associated with Golgi/endosomal vesicles and the trans-Golgi network. {ECO:0000250}.

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 VPS45 gene
Compartment Confidence
golgi apparatus 5
endosome 5
cytosol 3
cytoskeleton 2
nucleus 2
lysosome 1

Gene Ontology (GO) - Cellular Components for VPS45 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005575 cellular_component ND --
GO:0005768 endosome IEA --
GO:0005794 Golgi apparatus IEA,ISS --
GO:0010008 endosome membrane TAS --
genes like me logo Genes that share ontologies with VPS45: view

Pathways & Interactions for VPS45 Gene

genes like me logo Genes that share pathways with VPS45: view

Gene Ontology (GO) - Biological Process for VPS45 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006886 intracellular protein transport NAS 10404641
GO:0006904 vesicle docking involved in exocytosis IEA --
GO:0007596 blood coagulation TAS --
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with VPS45: view

No data available for SIGNOR curated interactions for VPS45 Gene

Transcripts for VPS45 Gene

Unigene Clusters for VPS45 Gene

Vacuolar protein sorting 45 homolog (S. cerevisiae):
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS45 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c · 2d ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12a ·
SP1: - - - - - -
SP2: - - - - - - - - -
SP3: - - - - -
SP4: - - - - - - - -
SP5: - - -
SP6: -
SP7:
SP8: - -
SP9:
SP10: - - - - -

ExUns: 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for VPS45 Gene

GeneLoc Exon Structure for
VPS45
ECgene alternative splicing isoforms for
VPS45

Expression for VPS45 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VPS45 Gene

Protein differential expression in normal tissues from HIPED for VPS45 Gene

This gene is overexpressed in Brain (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VPS45 Gene



Protein tissue co-expression partners for VPS45 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS45 Gene:

VPS45

SOURCE GeneReport for Unigene cluster for VPS45 Gene:

Hs.443750

mRNA Expression by UniProt/SwissProt for VPS45 Gene:

Q9NRW7-VPS45_HUMAN
Tissue specificity: Ubiquitous. Expression was highest in testis, heart and brain, intermediate in kidney, spleen, prostate, ovary, small intestine and thymus and low in lung, skeletal muscle, placenta, colon, pancreas, peripheral blood leukocytes and liver.
genes like me logo Genes that share expression patterns with VPS45: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for VPS45 Gene

Orthologs for VPS45 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS45 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS45 34 35
  • 99.77 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS45 35
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS45 34 35
  • 94.62 (n)
cow
(Bos Taurus)
Mammalia VPS45 34 35
  • 93.92 (n)
mouse
(Mus musculus)
Mammalia Vps45 34 16 35
  • 90.88 (n)
rat
(Rattus norvegicus)
Mammalia Vps45 34
  • 90.47 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VPS45 35
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS45 35
  • 90 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS45 35
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps45 34
  • 76.08 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.8703 34
zebrafish
(Danio rerio)
Actinopterygii vps45 34 35
  • 73.71 (n)
Dr.15874 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003980 34
  • 57.32 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vps45 34 35
  • 56.72 (n)
worm
(Caenorhabditis elegans)
Secernentea vps-45 34 35
  • 51.61 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS45 34 35 37
  • 49.87 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL053W 34
  • 48.05 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E18833g 34
  • 47.53 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons VPS45 34
  • 53.86 (n)
rice
(Oryza sativa)
Liliopsida Os02g0437800 34
  • 53.33 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU06192 34
  • 53.46 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vps45 34
  • 50.58 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.10162 34
Species where no ortholog for VPS45 was found in the sources mined by GeneCards:
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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)
  • wheat (Triticum aestivum)

Evolution for VPS45 Gene

ENSEMBL:
Gene Tree for VPS45 (if available)
TreeFam:
Gene Tree for VPS45 (if available)

Paralogs for VPS45 Gene

(2) SIMAP similar genes for VPS45 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with VPS45: view

No data available for Paralogs for VPS45 Gene

Variants for VPS45 Gene

Sequence variations from dbSNP and Humsavar for VPS45 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs782269909 Neutropenia, severe congenital 5, autosomal recessive (SCN5) [MIM:615285], Pathogenic 150,081,366(+) TCCAC(A/G)AACTA nc-transcript-variant, reference, missense
VAR_069865 Neutropenia, severe congenital 5, autosomal recessive (SCN5) [MIM:615285]
rs879255237 Pathogenic 150,077,763(+) CATCA(A/C)CCCAT nc-transcript-variant, reference, missense
rs192850081 Likely benign 150,076,223(+) ACTCA(C/T)GTGTT intron-variant
rs142968690 Uncertain significance 150,144,747(+) CAGCC(A/C/G)AAGCA nc-transcript-variant, reference, synonymous-codon, missense

Structural Variations from Database of Genomic Variants (DGV) for VPS45 Gene

Variant ID Type Subtype PubMed ID
esv2061124 CNV deletion 18987734
esv2605621 CNV deletion 19546169
esv3540589 CNV deletion 23714750
esv3578170 CNV loss 25503493
nsv831537 CNV loss 17160897

Variation tolerance for VPS45 Gene

Residual Variation Intolerance Score: 45.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.91; 59.40% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VPS45 Gene

Human Gene Mutation Database (HGMD)
VPS45
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS45

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS45 Gene

Disorders for VPS45 Gene

MalaCards: The human disease database

(3) MalaCards diseases for VPS45 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
neutropenia, severe congenital, 5, autosomal recessive
  • severe congenital neutropenia, autosomal recessive, 5
neutropenia
  • leukopenia
severe congenital neutropenia
  • kostmann disease
- elite association - COSMIC cancer census association via MalaCards
Search VPS45 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VPS45_HUMAN
  • Neutropenia, severe congenital 5, autosomal recessive (SCN5) [MIM:615285]: An autosomal recessive primary immunodeficiency disorder characterized primarily by neutropenia and neutrophil dysfunction, a lack of response to G-CSF, life-threatening infections, bone marrow fibrosis, and renal extramedullary hematopoiesis. {ECO:0000269 PubMed:23738510}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for VPS45

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VPS45
genes like me logo Genes that share disorders with VPS45: view

No data available for Genatlas for VPS45 Gene

Publications for VPS45 Gene

  1. Mammalian homologues of yeast vacuolar protein sorting (vps) genes implicated in Golgi-to-lysosome trafficking. (PMID: 8996080) Pevsner J. … Scheller R.H. (Gene 1996) 2 3 4 64
  2. A congenital neutrophil defect syndrome associated with mutations in VPS45. (PMID: 23738510) Vilboux T. … Somech R. (N. Engl. J. Med. 2013) 3 4 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Divalent Rab effectors regulate the sub-compartmental organization and sorting of early endosomes. (PMID: 11788822) de Renzis S. … Zerial M. (Nat. Cell Biol. 2002) 3 4 64

Products for VPS45 Gene

Sources for VPS45 Gene

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