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    Npc1 NPC intracellular cholesterol transporter 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 266732, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Npc1provided by RGD
    Official Full Name
    NPC intracellular cholesterol transporter 1provided by RGD
    Primary source
    RGD:628693
    See related
    EnsemblRapid:ENSRNOG00000012016 AllianceGenome:RGD:628693
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Cdig2; SLC66A1
    Summary
    Predicted to enable cholesterol binding activity. Involved in negative regulation of epithelial cell apoptotic process and response to cadmium ion. Predicted to be located in several cellular components, including bounding membrane of organelle; membrane raft; and perinuclear region of cytoplasm. Predicted to be active in lysosome and plasma membrane. Human ortholog(s) of this gene implicated in Niemann-Pick disease type C1. Orthologous to human NPC1 (NPC intracellular cholesterol transporter 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Liver (RPKM 242.1), Lung (RPKM 117.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Npc1 in Genome Data Viewer
    Location:
    18p13
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 18 NC_086036.1 (3654237..3699853, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 18 NC_051353.1 (3379482..3425100, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (3616878..3662656, complement)

    Chromosome 18 - NC_086036.1Genomic Context describing neighboring genes Neighboring gene transmembrane protein 241 Neighboring gene uncharacterized LOC134482901 Neighboring gene RIO kinase 3 Neighboring gene regulator of MON1-CCZ1 Neighboring gene AKT interacting protein, pseudogene 1 Neighboring gene ankyrin repeat domain 29 Neighboring gene laminin subunit alpha 3 Neighboring gene uncharacterized LOC134482906

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. PCR-based subtraction analyses for upregulated gene transcription in cadmium-exposed rat lung type 2 epithelial cells. Hirano S, et al. Biochem Biophys Res Commun, 2003 Aug 15. PMID 12890491
    2. Defective endocytic trafficking of NPC1 and NPC2 underlying infantile Niemann-Pick type C disease. Blom TS, et al. Hum Mol Genet, 2003 Feb 1. PMID 12554680
    3. 3.3 Å structure of Niemann-Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport. Li X, et al. Proc Natl Acad Sci U S A, 2017 Aug 22. PMID 28784760, Free PMC Article
    4. Topological analysis of Niemann-Pick C1 protein reveals that the membrane orientation of the putative sterol-sensing domain is identical to those of 3-hydroxy-3-methylglutaryl-CoA reductase and sterol regulatory element binding protein cleavage-activating protein. Davies JP, et al. J Biol Chem, 2000 Aug 11. PMID 10821832
    5. Characterization of the Niemann-Pick C pathway in alveolar type II cells and lamellar bodies of the lung. Roszell BR, et al. Am J Physiol Lung Cell Mol Physiol, 2012 May 1. PMID 22367786, Free PMC Article

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Increased exosome secretion in neurons aging in vitro by NPC1-mediated endosomal cholesterol buildup.
      Title: Increased exosome secretion in neurons aging in vitro by NPC1-mediated endosomal cholesterol buildup.
    2. Here, we identify lamellar inclusions as the subcellular site of lipid accumulation in neurons, we uncover a vicious cycle of cholesterol synthesis and accretion, which may cause gradual neurodegeneration, and we reveal how beta-cyclodextrin, a potential therapeutic drug, reverts these changes. Our study provides new mechanistic insight in NPC disease and uncovers new targets for therapeutic approaches.
      Title: Reversal of Pathologic Lipid Accumulation in NPC1-Deficient Neurons by Drug-Promoted Release of LAMP1-Coated Lamellar Inclusions.
    3. NPC1 and NPC2 are associated with the lamellar bodies of type II pneumocyte cells and function to regulate cholesterol content within this organelle.
      Title: Characterization of the Niemann-Pick C pathway in alveolar type II cells and lamellar bodies of the lung.
    Submit: New GeneRIF Correction

    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 RGD

    Function Evidence Code Pubs
    enables cholesterol binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cholesterol binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cholesterol transfer activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cholesterol transfer activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables lipid transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within adult walking behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cellular response to low-density lipoprotein particle stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cellular response to steroid hormone stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cholesterol efflux ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cholesterol efflux ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cholesterol homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cholesterol homeostasis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cholesterol metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cholesterol storage ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cholesterol transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cholesterol transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cyclodextrin metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within endocytosis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within establishment of localization in cell ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in establishment of protein localization to membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in intestinal cholesterol absorption IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular cholesterol transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in intracellular lipid transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within liver development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of macroautophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in membrane raft organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of TORC1 signaling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of epithelial cell apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of macroautophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neurogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within programmed cell death ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein glycosylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to cadmium ion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within response to xenobiotic stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within sterol metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in sterol transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within sterol transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in symbiont entry into host cell ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in late endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosomal membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane raft ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear envelope ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    NPC intracellular cholesterol transporter 1
    Names
    Niemann-Pick disease, type C1
    solute carrier family 66 member 1

    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.

    mRNA and Protein(s)

    1. NM_153624.2 → NP_705888.2  NPC intracellular cholesterol transporter 1 precursor

      See identical proteins and their annotated locations for NP_705888.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000018
      UniProtKB/TrEMBL
      A0A8I6GB30, A6KNH0, G3V7K5
      Related
      ENSRNOP00000016167.4, ENSRNOT00000016167.9
      Conserved Domains (3) summary
      TIGR00917
      Location:26 → 1252
      2A060601; Niemann-Pick C type protein family
      pfam12349
      Location:650 → 803
      Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
      pfam16414
      Location:24 → 268
      NPC1_N; Niemann-Pick C1 N terminus

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086036.1 Reference GRCr8

      Range
      3654237..3699853 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039096607.2 → XP_038952535.1  NPC intracellular cholesterol transporter 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6GB30
      Conserved Domains (1) summary
      TIGR00917
      Location:26 → 1251
      2A060601; Niemann-Pick C type protein family
    Nucleotide Protein Strain
    Heading Accession and Version

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