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    VPS45 vacuolar protein sorting 45 homolog [ Homo sapiens (human) ]

    Gene ID: 11311, updated on 3-Nov-2024

    Summary

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    Official Symbol
    VPS45provided by HGNC
    Official Full Name
    vacuolar protein sorting 45 homologprovided by HGNC
    Primary source
    HGNC:HGNC:14579
    See related
    Ensembl:ENSG00000136631 MIM:610035; AllianceGenome:HGNC:14579
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    H1; SCN5; VSP45; VPS45A; VPS45B; VPS54A; VSP45A; H1VPS45
    Summary
    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]
    Expression
    Ubiquitous expression in brain (RPKM 10.4), adrenal (RPKM 10.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VPS45 in Genome Data Viewer
    Location:
    1q21.2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (150067382..150145329)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (149191963..149270002)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (150039439..150117507)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:149908038-149908562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1667 Neighboring gene myotubularin related protein 11 Neighboring gene OTU deubiquitinase 7B Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:149981420-149982302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1292 Neighboring gene uncharacterized LOC124904413 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:149989091-149989750 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:149989751-149990408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1293 Neighboring gene ribosomal protein L6 pseudogene 31 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:150122046-150122546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:150131051-150131552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1297 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1671 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1673 Neighboring gene pleckstrin homology domain containing O1 Neighboring gene long intergenic non-protein coding RNA 2988 Neighboring gene Sharpr-MPRA regulatory region 9169

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Molecular cloning and characterization of a cDNA encoding the human leucocyte vacuolar protein sorting (h1Vps45). Rajasekariah P, et al. Int J Biochem Cell Biol, 1999 Jun. PMID 10404641
    2. Severe congenital neutropenia with neurological impairment due to a homozygous VPS45 p.E238K mutation: A case report suggesting a genotype-phenotype correlation. Meerschaut I, et al. Am J Med Genet A, 2015 Dec. PMID 26358756
    3. The Thr224Asn mutation in the VPS45 gene is associated with the congenital neutropenia and primary myelofibrosis of infancy. Stepensky P, et al. Blood, 2013 Jun 20. PMID 23599270
    4. Mammalian VPS45 orchestrates trafficking through the endosomal system. Frey L, et al. Blood, 2021 Apr 8. PMID 33512427
    5. A congenital neutrophil defect syndrome associated with mutations in VPS45. Vilboux T, et al. N Engl J Med, 2013 Jul 4. PMID 23738510, Free PMC Article

    See all (71) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Mammalian VPS45 orchestrates trafficking through the endosomal system.
      Title: Mammalian VPS45 orchestrates trafficking through the endosomal system.
    2. SPI1-induced upregulation of lncRNA SNHG6 promotes non-small cell lung cancer via miR-485-3p/VPS45 axis.
      Title: SPI1-induced upregulation of lncRNA SNHG6 promotes non-small cell lung cancer via miR-485-3p/VPS45 axis.
    3. The Rab-binding module of FERARI (factors for endosome recycling and Rab interactions) consists of Rab11FIP5 and rabenosyn-5, while the SNARE-interacting module comprises VPS45 and VIPAS39.
      Title: FERARI is required for Rab11-dependent endocytic recycling.
    4. A homozygous VPS45 p.E238K mutation is associated with severe congenital neutropenia with neurological impairment.
      Title: Severe congenital neutropenia with neurological impairment due to a homozygous VPS45 p.E238K mutation: A case report suggesting a genotype-phenotype correlation.
    5. we identified a Thr224Asn mutation in the VPS45 gene in infants from consanguineous families who suffered from life-threatening neutropenia.
      Title: The Thr224Asn mutation in the VPS45 gene is associated with the congenital neutropenia and primary myelofibrosis of infancy.
    6. Defective endosomal intracellular protein trafficking due to biallelic mutations in VPS45 underlies a new immunodeficiency syndrome involving impaired neutrophil function.
      Title: A congenital neutrophil defect syndrome associated with mutations in VPS45.
    7. Data implicate hVps45 and Rabenosyn-5 in post early endosome transport, and suggest that their interaction serves as a nexus to promote bidirectional transport along the endosome-to-recycling compartment and endosome-to-Golgi axes.
      Title: Common and distinct roles for the binding partners Rabenosyn-5 and Vps45 in the regulation of endocytic trafficking in mammalian cells.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Congenital neutropenia-myelofibrosis-nephromegaly syndrome
    MedGen: C3809031 OMIM: 615285 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study of serum uric acid in African Americans.
    EBI GWAS Catalog
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular protein transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in synaptic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein 45
    Names
    leucocyte vacuolar protein sorting 45
    vacuolar protein sorting 45A

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_033910.1 RefSeqGene

      Range
      5484..83037
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1170

    mRNA and Protein(s)

    1. NM_001279353.2 → NP_001266282.1  vacuolar protein sorting-associated protein 45 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and has multiple differences in the coding region, compared to variant 1. The resulting isoform (2) is shorter and has a shorter N-terminus, lacks an internal segment and has a longer and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC242988, AK298786, BC028382, BG176899
      Consensus CDS
      CCDS60244.1
      UniProtKB/TrEMBL
      B7Z5D4
      Related
      ENSP00000358124.5, ENST00000369128.9
      Conserved Domains (1) summary
      pfam00995
      Location:1 → 434
      Sec1; Sec1 family

    2. NM_001279354.2 → NP_001266283.1  vacuolar protein sorting-associated protein 45 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an alternate splice site in the 5' region, which results in a downstream translation start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC242988, AK295529, BC028382, DA374440
      Consensus CDS
      CCDS86017.1
      UniProtKB/TrEMBL
      A0A2R8YE10, B7Z360
      Conserved Domains (1) summary
      pfam00995
      Location:1 → 503
      Sec1; Sec1 family

    3. NM_007259.5 → NP_009190.2  vacuolar protein sorting-associated protein 45 isoform 1

      See identical proteins and their annotated locations for NP_009190.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AW243680, BC028382
      Consensus CDS
      CCDS944.1
      UniProtKB/Swiss-Prot
      D3DUZ9, F5H8K1, Q15715, Q53FR8, Q5T4P6, Q9NRW7, Q9Y4Z6
      UniProtKB/TrEMBL
      A0A8V8TM05
      Related
      ENSP00000495563.1, ENST00000644510.2
      Conserved Domains (1) summary
      pfam00995
      Location:23 → 539
      Sec1; Sec1 family

    RNA

    1. NR_103998.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two consecutive exons in the 5' region and has an additional exon in the central region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC242988, AK293555, BC012932, BC028382, DA374440
      Related
      ENST00000491789.2

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      150067382..150145329
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024452791.2 → XP_024308559.1  vacuolar protein sorting-associated protein 45 isoform X1

      UniProtKB/TrEMBL
      A0A2R8YE10, B7Z360
      Related
      ENSP00000495148.1, ENST00000643970.2
      Conserved Domains (1) summary
      pfam00995
      Location:1 → 503
      Sec1; Sec1 family

    RNA

    1. XR_007069452.1 RNA Sequence

    2. XR_921734.4 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      149191963..149270002
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334044.1 → XP_054190019.1  vacuolar protein sorting-associated protein 45 isoform X1

      UniProtKB/TrEMBL
      A0A2R8YE10

    RNA

    1. XR_008485883.1 RNA Sequence

    2. XR_008485884.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001279355.1: Suppressed sequence

      Description
      NM_001279355.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NRW7.1 GenPept UniProtKB/Swiss-Prot:Q9NRW7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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