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Aliases for VPS45 Gene

Aliases for VPS45 Gene

  • Vacuolar Protein Sorting 45 Homolog 2 3 5
  • 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
  • HlVps45 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 Severe Congenital Neutropenia. Among its related pathways are Delta508-CFTR traffic / Sorting endosome formation in CF and Response to elevated platelet cytosolic Ca2+.

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

Additional gene information for VPS45 Gene

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

Genomics for VPS45 Gene

GeneHancer (GH) Regulatory Elements for VPS45 Gene

Promoters and enhancers for VPS45 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
GH01J150065 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 -0.3 -316 3.8 ZFP64 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZC3H11A LOC105371427 VPS45 GC01M150063 OTUD7B PRPF3 SETDB1 ARNT SF3B4 UBE2D3P3 HIST2H2AB
GH01J149156 Promoter/Enhancer 2.3 FANTOM5 Ensembl ENCODE dbSUPER 32.2 -906.9 -906943 7.8 MLX ZFP64 DMAP1 YBX1 IRF4 YY1 ZNF143 ZNF548 NFYC PPARGC1A LOC647481 SF3B4 HIST2H2BD HIST2H2AB VPS45 LOC101927468 HIST2H2BC ENSG00000261716 PDE4DIP RNU1-59P
GH01J150626 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 13.8 +562.1 562092 4.9 HDGF PKNOX1 CLOCK SMAD1 FOXA2 ARNT ARID4B NEUROD1 SIN3A DMAP1 GC01P150630 ENSA SETDB1 PIP5K1A PRPF3 ARNT UBE2D3P3 PI4KB SF3B4 HORMAD1
GH01J150557 Promoter/Enhancer 2.6 EPDnew Ensembl ENCODE dbSUPER 13.4 +502.0 502025 23.1 CLOCK MLX DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC RN7SL600P MCL1 SETDB1 PIP5K1A PI4KB PRPF3 ARNT GOLPH3L HORMAD1 SF3B4
GH01J150232 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 13.8 +167.9 167857 4.8 CLOCK MLX DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 ANP32E GC01P150237 RNU2-17P SETDB1 PRPF3 PIP5K1A GABPB2 SF3B4 ARNT UBE2D3P3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS45 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VPS45 gene promoter:
  • IRF-1
  • STAT5A
  • Brachyury
  • Nkx3-1 v2
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v3
  • Nkx3-1 v4
  • Lhx3a

Genomic Locations for VPS45 Gene

Genomic Locations for VPS45 Gene
chr1:150,067,279-150,145,329
(GRCh38/hg38)
Size:
78,051 bases
Orientation:
Plus strand
chr1:150,039,342-150,117,505
(GRCh37/hg19)
Size:
78,164 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 posLast=483483, isoforms=2450, posLast=378378, and isoforms=2371
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS45 Gene

Domains & Families for VPS45 Gene

Gene Families for VPS45 Gene

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

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

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.

Phenotypes From GWAS Catalog for VPS45 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS45

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

Subcellular locations from the

Human Protein Atlas (HPA)

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 ISS --
GO:0010008 endosome membrane IEA,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:0006886 intracellular protein transport NAS 10404641
GO:0006904 vesicle docking involved in exocytosis IEA --
GO:0007596 blood coagulation TAS --
GO:0015031 protein transport IEA --
GO:0016192 vesicle-mediated transport IEA --
genes like me logo Genes that share ontologies with VPS45: view

No data available for SIGNOR curated interactions for VPS45 Gene

Drugs & Compounds for VPS45 Gene

No Compound Related Data Available

Transcripts for VPS45 Gene

Unigene Clusters for VPS45 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS45

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 CGAP 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, 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.

Evidence on tissue expression from TISSUES for VPS45 Gene

  • Nervous system(4.9)
  • Blood(4.2)
  • Intestine(4.2)
  • Liver(4.2)
  • Stomach(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS45 Gene

Germ Layers:
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • lymphatic
  • urinary
Regions:
Abdomen:
  • kidney
  • liver
  • spleen
General:
  • blood
  • bone marrow
  • coagulation system
  • red blood cell
  • white blood cell
genes like me logo Genes that share expression patterns with VPS45: view

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 33
  • 99.77 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VPS45 34
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS45 34 33
  • 94.62 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VPS45 34 33
  • 93.92 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Vps45 16 34 33
  • 90.88 (n)
rat
(Rattus norvegicus)
Mammalia Vps45 33
  • 90.47 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VPS45 34
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS45 34
  • 90 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS45 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps45 33
  • 76.08 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.8703 33
zebrafish
(Danio rerio)
Actinopterygii vps45 34 33
  • 73.71 (n)
OneToOne
Dr.15874 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003980 33
  • 57.32 (n)
fruit fly
(Drosophila melanogaster)
Insecta Vps45 34 33
  • 56.72 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea vps-45 34 33
  • 51.61 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS45 36 34 33
  • 49.87 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL053W 33
  • 48.05 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E18833g 33
  • 47.53 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons VPS45 33
  • 53.86 (n)
rice
(Oryza sativa)
Liliopsida Os02g0437800 33
  • 53.33 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU06192 33
  • 53.46 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vps45 33
  • 50.58 (n)
sea squirt
(Ciona savignyi)
Ascidiacea Cin.10162 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.10162 33
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)
Aminode:
Evolutionary constrained regions (ECRs) for VPS45: view image

Paralogs for VPS45 Gene

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

  • VPS45_HUMAN
  • F5GYC3_HUMAN
  • F5H8K1_HUMAN
  • Q5T4Q0_HUMAN
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 Variation AA Info Type
rs146660821 uncertain-significance, Severe congenital neutropenia 5, autosomal recessive 150,077,706(+) G/A/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs587716374 uncertain-significance, Severe congenital neutropenia 5, autosomal recessive 150,081,372(+) C/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs62622370 benign, Severe congenital neutropenia 5, autosomal recessive 150,072,183(+) T/G coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs74127419 benign, Severe congenital neutropenia 5, autosomal recessive 150,082,811(+) A/G coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs782269909 pathogenic, Severe congenital neutropenia 5, autosomal recessive, Neutropenia, severe congenital 5, autosomal recessive (SCN5) [MIM:615285] 150,081,366(+) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant

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)

Additional Variant Information for VPS45 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for VPS45 Gene

MalaCards: The human disease database

(4) MalaCards diseases for VPS45 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- 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.

Additional Disease Information for 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 RH (Gene 1996) 2 3 4 58
  2. A congenital neutrophil defect syndrome associated with mutations in VPS45. (PMID: 23738510) Vilboux T … Somech R (The New England journal of medicine 2013) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Divalent Rab effectors regulate the sub-compartmental organization and sorting of early endosomes. (PMID: 11788822) de Renzis S … Zerial M (Nature cell biology 2002) 3 4 58

Products for VPS45 Gene

Sources for VPS45 Gene

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