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

Gene ID: 4864, updated on 18-Sep-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
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Genomic context

See NPC1 in Genome Data Viewer
Location:
18q11.2
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (23506184..23586506, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (23700273..23780767, complement)
RS_2024_09 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 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 lipid transporter activity IEA
Inferred from Electronic Annotation
more info
 
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 sterol transport IBA
Inferred from Biological aspect of Ancestor
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_2024_08

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

    UniProtKB/TrEMBL
    A0A193DRS0
  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

    UniProtKB/TrEMBL
    A0A0A8JCD0, A0A193DRS0
  2. XM_054318664.1XP_054174639.1  NPC intracellular cholesterol transporter 1 isoform X1

    UniProtKB/TrEMBL
    A0A0A8JCD0, A0A193DRS0
  3. XM_054318671.1XP_054174646.1  NPC intracellular cholesterol transporter 1 isoform X8

    UniProtKB/TrEMBL
    A0A0A8JCD0, A0A193DRS0
  4. XM_054318668.1XP_054174643.1  NPC intracellular cholesterol transporter 1 isoform X5

    UniProtKB/TrEMBL
    A0A0A8JCD0, A0A193DRS0
  5. XM_054318672.1XP_054174647.1  NPC intracellular cholesterol transporter 1 isoform X9

    UniProtKB/TrEMBL
    A0A0A8JCD0, A0A193DRS0
  6. XM_054318670.1XP_054174645.1  NPC intracellular cholesterol transporter 1 isoform X7

    UniProtKB/TrEMBL
    A0A0A8JCD0, A0A193DRS0
  7. XM_054318669.1XP_054174644.1  NPC intracellular cholesterol transporter 1 isoform X6

    UniProtKB/TrEMBL
    A0A0A8JCD0, A0A193DRS0
  8. XM_054318667.1XP_054174642.1  NPC intracellular cholesterol transporter 1 isoform X4

    UniProtKB/TrEMBL
    A0A0A8JCD0, A0A193DRS0
  9. XM_054318665.1XP_054174640.1  NPC intracellular cholesterol transporter 1 isoform X2

    UniProtKB/TrEMBL
    A0A0A8JCD0, A0A193DRS0