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    NPC1 NPC intracellular cholesterol transporter 1 [ Homo sapiens (human) ]

    Gene ID: 4864, updated on 11-Apr-2024

    Summary

    Official Symbol
    NPC1provided by HGNC
    Official Full Name
    NPC intracellular cholesterol transporter 1provided by HGNC
    Primary source
    HGNC:HGNC:7897
    See related
    Ensembl:ENSG00000141458 MIM:607623; AllianceGenome:HGNC:7897
    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
    NPC; POGZ; SLC65A1
    Summary
    This gene encodes a large protein that resides in the limiting membrane of endosomes and lysosomes and mediates intracellular cholesterol trafficking via binding of cholesterol to its N-terminal domain. It is predicted to have a cytoplasmic C-terminus, 13 transmembrane domains, and 3 large loops in the lumen of the endosome - the last loop being at the N-terminus. This protein transports low-density lipoproteins to late endosomal/lysosomal compartments where they are hydrolized and released as free cholesterol. Defects in this gene cause Niemann-Pick type C disease, a rare autosomal recessive neurodegenerative disorder characterized by over accumulation of cholesterol and glycosphingolipids in late endosomal/lysosomal compartments.[provided by RefSeq, Aug 2009]
    Expression
    Ubiquitous expression in adrenal (RPKM 13.9), brain (RPKM 10.0) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NPC1 in Genome Data Viewer
    Location:
    18q11.2
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (23506184..23586506, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (23700273..23780767, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (21111406..21166470, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene Cdk5 and Abl enzyme substrate 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:20829775-20830276 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20839263-20839926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13152 Neighboring gene transmembrane protein 241 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20862678-20863368 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20864059-20864750 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20864751-20865440 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20869474-20870086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20870087-20870699 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20882361-20883251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:20887449-20887950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:20887951-20888450 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20910236-20910904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13153 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:20956411-20956910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13154 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:20963589-20963764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13155 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9356 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:21033050-21033550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13162 Neighboring gene NANOG hESC enhancer GRCh37_chr18:21085432-21085935 Neighboring gene RIO kinase 3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr18:21098843-21100042 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:21109032-21110231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13163 Neighboring gene regulator of MON1-CCZ1 Neighboring gene Sharpr-MPRA regulatory region 2631 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:21156116-21157315 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:21164994-21165541 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:21165542-21166088 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9358 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9359 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9360 Neighboring gene ankyrin repeat domain 29 Neighboring gene Sharpr-MPRA regulatory region 8852 Neighboring gene ribosomal protein S10 pseudogene 27

    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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Niemann-Pick disease, type C1
    MedGen: C3179455 OMIM: 257220 GeneReviews: Niemann-Pick Disease Type C
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study for early-onset and morbid adult obesity identifies three new risk loci in European populations.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag NPC2-deficient cells exhibit Gag accumulation in late endosomal/lysosomal (LE/L) compartments of these cells as well as decreased NPC1 expression after HIV infection PubMed
    gag Niemann-Pick type C-1 (NPC1)-deficient (NPCD) cells exhibit few HIV-1 budding events. HIV-1 Gag accumulates in late endosomal/lysosomal (LE/L) compartments in NPCD cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ98532

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cholesterol binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cholesterol binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables transmembrane signaling receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables virus receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in adult walking behavior IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within autophagy IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in bile acid metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to low-density lipoprotein particle stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to steroid hormone stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cholesterol efflux IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cholesterol homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cholesterol homeostasis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cholesterol homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cholesterol homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cholesterol metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cholesterol storage IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cholesterol transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cyclodextrin metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in establishment of protein localization to membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intestinal cholesterol absorption IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in intracellular cholesterol transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular lipid transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in liver development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lysosomal transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in macroautophagy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in membrane raft organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of TORC1 signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of epithelial cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of macroautophagy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neurogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in programmed cell death IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein glycosylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to cadmium ion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to xenobiotic stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in symbiont entry into host cell IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in extracellular region ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in late endosome membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in lysosomal membrane HDA PubMed 
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
     
    located_in lysosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in membrane HDA PubMed 
    located_in membrane raft IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nuclear envelope IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    NPC intracellular cholesterol transporter 1
    Names
    Niemann-Pick C1 protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_012795.2 RefSeqGene

      Range
      5000..60064
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000271.5NP_000262.2  NPC intracellular cholesterol transporter 1 precursor

      See identical proteins and their annotated locations for NP_000262.2

      Status: REVIEWED

      Source sequence(s)
      AB209048, AC010853, AF002020, BC063302, DR159421
      Consensus CDS
      CCDS11878.1
      UniProtKB/Swiss-Prot
      B4DET3, O15118, Q9P130
      UniProtKB/TrEMBL
      A0A193DRS0
      Related
      ENSP00000269228.4, ENST00000269228.10
      Conserved Domains (1) summary
      TIGR00917
      Location:251252
      2A060601; Niemann-Pick C type protein family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      23506184..23586506 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005258279.3XP_005258336.1  NPC intracellular cholesterol transporter 1 isoform X3

      UniProtKB/TrEMBL
      A0A193DRS0
      Conserved Domains (3) summary
      TIGR00917
      Location:251251
      2A060601; Niemann-Pick C type protein family
      pfam12349
      Location:649802
      Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
      pfam16414
      Location:23267
      NPC1_N; Niemann-Pick C1 N terminus
    2. XM_005258277.1XP_005258334.1  NPC intracellular cholesterol transporter 1 isoform X1

      UniProtKB/TrEMBL
      A0A193DRS0
      Conserved Domains (3) summary
      TIGR00917
      Location:251268
      2A060601; Niemann-Pick C type protein family
      pfam12349
      Location:666819
      Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
      pfam16414
      Location:23267
      NPC1_N; Niemann-Pick C1 N terminus
    3. XM_017025787.2XP_016881276.1  NPC intracellular cholesterol transporter 1 isoform X8

      UniProtKB/TrEMBL
      A0A193DRS0
    4. XM_006722479.4XP_006722542.1  NPC intracellular cholesterol transporter 1 isoform X5

      UniProtKB/TrEMBL
      A0A193DRS0
      Conserved Domains (3) summary
      TIGR00917
      Location:251269
      2A060601; Niemann-Pick C type protein family
      pfam12349
      Location:666819
      Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
      pfam16414
      Location:23267
      NPC1_N; Niemann-Pick C1 N terminus
    5. XM_047437539.1XP_047293495.1  NPC intracellular cholesterol transporter 1 isoform X9

    6. XM_017025786.2XP_016881275.1  NPC intracellular cholesterol transporter 1 isoform X7

      UniProtKB/TrEMBL
      A0A193DRS0
    7. XM_017025785.1XP_016881274.1  NPC intracellular cholesterol transporter 1 isoform X6

      UniProtKB/TrEMBL
      A0A193DRS0
    8. XM_017025784.1XP_016881273.1  NPC intracellular cholesterol transporter 1 isoform X4

      UniProtKB/TrEMBL
      A0A193DRS0
    9. XM_005258278.6XP_005258335.1  NPC intracellular cholesterol transporter 1 isoform X2

      UniProtKB/TrEMBL
      A0A193DRS0
      Conserved Domains (3) summary
      TIGR00917
      Location:251269
      2A060601; Niemann-Pick C type protein family
      pfam12349
      Location:666819
      Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
      pfam16414
      Location:23267
      NPC1_N; Niemann-Pick C1 N terminus

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      23700273..23780767 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054318666.1XP_054174641.1  NPC intracellular cholesterol transporter 1 isoform X3

    2. XM_054318664.1XP_054174639.1  NPC intracellular cholesterol transporter 1 isoform X1

    3. XM_054318671.1XP_054174646.1  NPC intracellular cholesterol transporter 1 isoform X8

    4. XM_054318668.1XP_054174643.1  NPC intracellular cholesterol transporter 1 isoform X5

    5. XM_054318672.1XP_054174647.1  NPC intracellular cholesterol transporter 1 isoform X9

    6. XM_054318670.1XP_054174645.1  NPC intracellular cholesterol transporter 1 isoform X7

    7. XM_054318669.1XP_054174644.1  NPC intracellular cholesterol transporter 1 isoform X6

    8. XM_054318667.1XP_054174642.1  NPC intracellular cholesterol transporter 1 isoform X4

    9. XM_054318665.1XP_054174640.1  NPC intracellular cholesterol transporter 1 isoform X2