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

Gene ID: 11311, updated on 14-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
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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.
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Phenotypes

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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
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EBI GWAS Catalog

Description
A genome-wide association study of serum uric acid in African Americans.
EBI GWAS Catalog
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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)

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 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
  
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

    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

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