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

Gene ID: 11311, updated on 7-Oct-2018

Summary

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; Vega:OTTHUMG00000012511
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

Genomic context

See VPS45 in Genome Data Viewer
Location:
1q21.2
Exon count:
18
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (150067279..150145327)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (150039350..150117505)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene OTU deubiquitinase 7B Neighboring gene uncharacterized LOC105371427 Neighboring gene ribosomal protein L6 pseudogene Neighboring gene uncharacterized LOC105371433 Neighboring gene pleckstrin homology domain containing O1

Genomic regions, transcripts, and products

Expression

  • Project title: 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Severe congenital neutropenia 5, autosomal recessive
MedGen: C3809031 OMIM: 615285 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Factors involved in megakaryocyte development and platelet production, organism-specific biosystem (from REACTOME)
    Factors involved in megakaryocyte development and platelet production, organism-specific biosystemMegakaryocytes (MKs) give rise to circulating platelets (thrombocytes) through terminal differentiation of MKs which release cytoplasmic fragments as circulating platelets. As MKs mature they underg...
  • Hemostasis, organism-specific biosystem (from REACTOME)
    Hemostasis, organism-specific biosystemHemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhe...
  • Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystem (from REACTOME)
    Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystemThe mammalian Golgi complex, a central hub of both anterograde and retrograde trafficking, is a ribbon of stacked cisterna with biochemically distinct compartments (reviewed in Glick and Nakano, 2009...
  • Intra-Golgi traffic, organism-specific biosystem (from REACTOME)
    Intra-Golgi traffic, organism-specific biosystemThe mammalian Golgi consists of at least three biochemically distinct cisternae, cis-, medial- and trans (reviewed in Szul and Sztul, 2011; Day et al, 2013). The structure and function of the Golgi a...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
molecular_function ND
No biological Data available
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
blood coagulation TAS
Traceable Author Statement
more info
 
intracellular protein transport NAS
Non-traceable Author Statement
more info
PubMed 
vesicle docking involved in exocytosis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
 
Golgi membrane TAS
Traceable Author Statement
more info
 
cellular_component ND
No biological Data available
more info
 
endosome membrane TAS
Traceable Author Statement
more info
 
integral component of membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptic vesicle IEA
Inferred from Electronic Annotation
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001279353.1NP_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)
    AK298786, BC028382, BG176899
    Consensus CDS
    CCDS60244.1
    UniProtKB/Swiss-Prot
    Q9NRW7
    UniProtKB/TrEMBL
    B7Z5D4
    Related
    ENSP00000358124.5, OTTHUMP00000277181, ENST00000369128.9, OTTHUMT00000478005
    Conserved Domains (1) summary
    pfam00995
    Location:1434
    Sec1; Sec1 family
  2. NM_001279354.1NP_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)
    AK295529, BC028382, DA374440
    Consensus CDS
    CCDS86017.1
    UniProtKB/Swiss-Prot
    Q9NRW7
    UniProtKB/TrEMBL
    B7Z360
    Related
    ENSP00000478403.1, ENST00000611412.4
    Conserved Domains (1) summary
    pfam00995
    Location:1503
    Sec1; Sec1 family
  3. NM_007259.5NP_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
    Q9NRW7
    Related
    ENSP00000358126.3, OTTHUMP00000014482, ENST00000369130.7
    Conserved Domains (1) summary
    pfam00995
    Location:23539
    Sec1; Sec1 family

RNA

  1. NR_103998.1 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)
    AK293555, BC012932, BC028382, DA374440
    Related
    ENST00000491789.2

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    150067279..150145327
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Related
    ENSP00000495148.1, ENST00000643970.1
    Conserved Domains (1) summary
    pfam00995
    Location:1503
    Sec1; Sec1 family

RNA

  1. XR_921734.3 RNA Sequence

    Related
    ENST00000642919.1
  2. XR_921733.3 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.
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