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NPC1 Gene

protein-coding   GIFtS: 64
GCID: GC18M021111

Niemann-Pick Disease, Type C1

  See NPC1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Niemann-Pick Disease, Type C11 2
NPC2 5
Niemann-Pick C1 Protein2

External Ids:    HGNC: 78971   Entrez Gene: 48642   Ensembl: ENSG000001414587   OMIM: 6076235   UniProtKB: O151183   

Export aliases for NPC1 gene to outside databases

Previous GC identifers: GC18M021004 GC18M020843 GC18M019363 GC18M019365 GC18M017967


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for NPC1 Gene:
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)

GeneCards Summary for NPC1 Gene:
NPC1 (Niemann-Pick disease, type C1) is a protein-coding gene. Diseases associated with NPC1 include niemann-pick disease type c, juvenile neurologic onset, and niemann-pick disease type c, late infantile neurologic onset. GO annotations related to this gene include cholesterol binding and receptor activity. An important paralog of this gene is PTCH1.

UniProtKB/Swiss-Prot: NPC1_HUMAN, O15118
Function: Intracellular cholesterol transporter which acts in concert with NPC2 and plays an important role in the
egress of cholesterol from the endosomal/lysosomal compartment. Both NPC1 and NPC2 function as the cellular 'tag
team duo' (TTD) to catalyze the mobilization of cholesterol within the multivesicular environment of the late
endosome (LE) to effect egress through the limiting bilayer of the LE. NPC2 binds unesterified cholesterol that
has been released from LDLs in the lumen of the late endosomes/lysosomes and transfers it to the
cholesterol-binding pocket of the N-terminal domain of NPC1. Cholesterol binds to NPC1 with the hydroxyl group
buried in the binding pocket and is exported from the limiting membrane of late endosomes/ lysosomes to the ER
and plasma membrane by an unknown mechanism. Binds oxysterol with higher affinity than cholesterol. May play a
role in vesicular trafficking in glia, a process that may be crucial for maintaining the structural and
functional integrity of nerve terminals

Gene Wiki entry for NPC1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the NPC1 gene promoter:
         CREB   ATF-2   deltaCREB   STAT3   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNPC1 promoter sequence
   Search Chromatin IP Primers for NPC1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NPC1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 18q11.2   Ensembl cytogenetic band:  18q11.2   HGNC cytogenetic band: 18q11.2

NPC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NPC1 gene location

GeneLoc information about chromosome 18         GeneLoc Exon Structure

GeneLoc location for GC18M021111:  view genomic region     (about GC identifiers)

Start:
21,086,148 bp from pter      End:
21,166,862 bp from pter
Size:
80,715 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: NPC1_HUMAN, O15118 (See protein sequence)
Recommended Name: Niemann-Pick C1 protein precursor  
Size: 1278 amino acids; 142167 Da
Subunit: Interacts with TMEM97. Interacts (via the second lumenal domain) with NPC2 in a cholestrol-dependent
manner (By similarity)
3 PDB 3D structures from and Proteopedia for NPC1:
3GKH (3D)        3GKI (3D)        3GKJ (3D)    
Secondary accessions: Q9P130

Explore the universe of human proteins at neXtProt for NPC1: NX_O15118

Explore proteomics data for NPC1 at MOPED

Post-translational modifications: 

  • Glycosylated1
  • Ubiquitination2 at Lys84, Lys585
  • Glycosylation2 at Asn70, Asn122, Asn135, Asn158, Asn185, Asn222, Asn452, Asn459, Asn478, Asn524,
                                 Asn961, Asn968, Asn1064, Asn1072
  • Modification sites at PhosphoSitePlus

  • See NPC1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_000262.2  
    ENSEMBL proteins: 
     ENSP00000468438   ENSP00000464755   ENSP00000467150   ENSP00000468321   ENSP00000269228  
     ENSP00000467636   ENSP00000408606  

    NPC1 Human Recombinant Protein Products:

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    Browse OriGene Protein Over-expression Lysates
    OriGene Custom MassSpec
    OriGene Custom Protein Services for NPC1
    GenScript Custom Purified and Recombinant Proteins Services for NPC1
    Novus Biologicals NPC1 Proteins
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for NPC1

     
    Search eBioscience for Proteins for NPC1 

    NPC1 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of NPC1
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    Novus Biologicals NPC1 Antibodies
    Abcam antibodies for NPC1
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    ThermoFisher Antibodies for NPC1
    LSBio Antibodies in human, mouse, rat for NPC1

    NPC1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for NPC1
    Cloud-Clone Corp. CLIAs for NPC1
    Search eBioscience for ELISAs for NPC1 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR004765 NP_C_type
     IPR003392 Patched
     IPR000731 SSD

    Graphical View of Domain Structure for InterPro Entry O15118

    ProtoNet protein and cluster: O15118

    1 Blocks protein domain: IPB003392 Patched family

    UniProtKB/Swiss-Prot: NPC1_HUMAN, O15118
    Domain: A cysteine-rich N-terminal domain and a C-terminal domain containing a di-leucine motif necessary for
    lysosomal targeting are critical for mobilization of cholesterol from lysosomes
    Similarity: Belongs to the patched family
    Similarity: Contains 1 SSD (sterol-sensing) domain


    Find genes that share domains with NPC1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NPC1_HUMAN, O15118
    Function: Intracellular cholesterol transporter which acts in concert with NPC2 and plays an important role in the
    egress of cholesterol from the endosomal/lysosomal compartment. Both NPC1 and NPC2 function as the cellular 'tag
    team duo' (TTD) to catalyze the mobilization of cholesterol within the multivesicular environment of the late
    endosome (LE) to effect egress through the limiting bilayer of the LE. NPC2 binds unesterified cholesterol that
    has been released from LDLs in the lumen of the late endosomes/lysosomes and transfers it to the
    cholesterol-binding pocket of the N-terminal domain of NPC1. Cholesterol binds to NPC1 with the hydroxyl group
    buried in the binding pocket and is exported from the limiting membrane of late endosomes/ lysosomes to the ER
    and plasma membrane by an unknown mechanism. Binds oxysterol with higher affinity than cholesterol. May play a
    role in vesicular trafficking in glia, a process that may be crucial for maintaining the structural and
    functional integrity of nerve terminals

         Genatlas biochemistry entry for NPC1:
    glycoprotein regulator of intracellular cholesterol trafficking,predominantly expressed in perisynaptic astrocytic
    glial processes,homolog to the mediators of cholesterol homeostasis and to the TM region of Drosophila patched

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004872receptor activity TAS9211849
    GO:0004888transmembrane signaling receptor activity TAS10521290
    GO:0005515protein binding IPI16757520
    GO:0008158hedgehog receptor activity IEA--
    GO:0015248sterol transporter activity TAS9927649
         
    Find genes that share ontologies with NPC1           About GenesLikeMe


    Phenotypes:
         15 MGI mutant phenotypes (inferred from 7 alleles(MGI details for Npc1):
     adipose tissue  behavior/neurological  cardiovascular system  cellular  endocrine/exocrine gland 
     growth/size/body  hematopoietic system  homeostasis/metabolism  immune system  liver/biliary system 
     mortality/aging  nervous system  reproductive system  respiratory system  vision/eye 

    Find genes that share phenotypes with NPC1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Npc1tm1.2Apl for NPC1

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NPC1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for NPC1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for NPC1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for NPC1

    miRNA
    Products:
        
    miRTarBase miRNAs that target NPC1:
    hsa-mir-33a-5p (MIRT004540), hsa-mir-335-5p (MIRT018683), hsa-let-7a-5p (MIRT052499)

    Block miRNA regulation of human, mouse, rat NPC1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate NPC1 (see all 24):
    hsa-miR-320a hsa-miR-520d-5p hsa-miR-137 hsa-miR-429 hsa-miR-25 hsa-miR-200b hsa-miR-33b hsa-miR-92b
    SwitchGear 3'UTR luciferase reporter plasmidNPC1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for NPC1
    Predesigned siRNA for gene silencing in human, mouse, rat NPC1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for NPC1

    Clone
    Products:
         
    OriGene clones in human, mouse for NPC1 (see all 7)
    OriGene ORF clones in mouse, rat for NPC1
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    GenScript: all cDNA clones in your preferred vector: NPC1 (NM_001812)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for NPC1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat NPC1
    Addgene plasmids for NPC1 

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for NPC1 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NPC1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    NPC1_HUMAN, O15118: Late endosome membrane; Multi-pass membrane protein. Lysosome membrane; Multi-pass membrane
    protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum5
    endosome5
    lysosome5
    nucleus5
    plasma membrane5
    vacuole5
    extracellular4
    golgi apparatus2
    cytosol1

    Gene Ontology (GO): Selected cellular component terms (see all 16):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region ISS--
    GO:0005635nuclear envelope IDA12554680
    GO:0005764lysosome ISS--
    GO:0005765lysosomal membrane IDA17897319
    GO:0005768endosome ----

    Find genes that share ontologies with NPC1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for NPC1 About    
    See pathways by source

    SuperPathContained pathways About
    1Cholesterol and Sphingolipids transport Distribution to the intracellular membrane compartments normal and CF
    Cholesterol and Sphingolipids transport Distribution to the intracellular membrane compartments normal and CF
    Cholesterol and Sphingolipids transport Generic schema normal and CF 0.00
    2Lysosome
    Lysosome


    Find genes that share SuperPaths with NPC1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    2 GeneGo (Thomson Reuters) Pathways for NPC1
        Cholesterol and Sphingolipids transport / Generic schema (normal and CF)
    Cholesterol and Sphingolipids transport / Distribution to the intracellular membrane compartments (normal and CF)


    1 Kegg Pathway  (Kegg details for NPC1):
        Lysosome

        Pathway & Disease-focused RT2 Profiler PCR Arrays including NPC1: 
              Hedgehog Signaling Pathway in human mouse rat
              Autophagy in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for NPC1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    Selected Interacting proteins for NPC1 (O151183 ENSP000002692284) via UniProtKB, MINT, STRING, and/or I2D (see all 46)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    OSBPL5Q9H0X93, ENSP000002636504I2D: score=1 STRING: ENSP00000263650
    UNC93B1Q9H1C43, ENSP000002274714I2D: score=1 STRING: ENSP00000227471
    UBCP0CG483, ENSP000003448184I2D: score=2 STRING: ENSP00000344818
    LRP6O755813, ENSP000002613494I2D: score=1 STRING: ENSP00000261349
    VPS4AQ9UN373, ENSP000002549504I2D: score=1 STRING: ENSP00000254950
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 17):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006486protein glycosylation IDA10821832
    GO:0006897endocytosis IEA--
    GO:0006914autophagy IGI19074461
    GO:0007041lysosomal transport ISS--
    GO:0007165signal transduction TAS10521290

    Find genes that share ontologies with NPC1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for NPC1

    Selected Novoseek inferred chemical compound relationships for NPC1 gene (see all 15)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    u18666a 91.5 14 10666334 (2), 12622792 (2), 11251074 (2), 19007772 (2) (see all 7)
    cholesterol 80.3 270 16757520 (7), 18272927 (5), 19884502 (5), 18060319 (5) (see all 99)
    sterol 76.7 48 15908696 (5), 12398991 (4), 15030792 (2), 17804599 (2) (see all 21)
    filipin 69.6 1 12606053 (1)
    lipid 58.3 40 19131362 (5), 11249924 (2), 15071184 (2), 16757520 (2) (see all 27)
    mannose 6-phosphate 49.9 3 12622792 (1), 10092649 (1), 10662671 (1)
    glycolipid 47.4 5 14989468 (1), 16606609 (1), 12955717 (1), 12398991 (1) (see all 5)
    ganglioside 46.9 3 9533562 (1), 14989468 (1), 12622792 (1)
    3-hydroxy-3-methylglutaryl-coa 38.3 1 15908696 (1)
    progesterone 21.5 10 10942596 (4), 10666334 (1), 12622792 (1), 16141411 (1) (see all 6)



    Find genes that share compounds with NPC1           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for NPC1 gene: 
    NM_000271.4  

    15 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000591107 ENST00000590723 ENST00000593280 ENST00000586150 ENST00000269228(uc010xaz.2 uc002kum.4 uc010xba.1)
    ENST00000588867 ENST00000591051 ENST00000587163 ENST00000591955 ENST00000591075
    ENST00000540608 ENST00000586718 ENST00000590301 ENST00000587223 ENST00000412552(uc010dlu.1)

    miRNA
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    Block miRNA regulation of human, mouse, rat NPC1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate NPC1 (see all 24):
    hsa-miR-320a hsa-miR-520d-5p hsa-miR-137 hsa-miR-429 hsa-miR-25 hsa-miR-200b hsa-miR-33b hsa-miR-92b
    SwitchGear 3'UTR luciferase reporter plasmidNPC1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat NPC1
    Clone
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    OriGene ORF clones in mouse, rat for NPC1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: NPC1 (NM_001812)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for NPC1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat NPC1
    Addgene plasmids for NPC1 
    Primer
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    OriGene qPCR primer pairs and template standards for NPC1
    OriGene qSTAR qPCR primer pairs in human, mouse for NPC1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat NPC1
      QuantiTect SYBR Green Assays in human, mouse, rat NPC1
      QuantiFast Probe-based Assays in human, mouse, rat NPC1

    Selected AceView cDNA sequences (see all 254):

    AA422019 BQ892954 BQ000143 AV708379 BX115657 AA470067 BF109596 CR600440 
    BM832227 BU542905 AA634249 CA446413 BI835794 CA749019 CD723034 AW369350 
    CB158050 AA953265 BQ430569 CA416741 CA438246 BU679425 AA631993 BM710173 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for NPC1 (see all 13)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b · 16c ^ 17 ^ 18a · 18b ^ 19a ·
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 19b · 19c ^ 20a · 20b ^ 21a · 21b ^ 22a · 22b ^ 23a · 23b · 23c ^ 24a · 24b ^ 25a · 25b ^ 26
    SP1:              -                                                                                 
    SP2:                                                                                                
    SP3:                                                                                                
    SP4:                                                                                                
    SP5:                                                                                                


    ECgene alternative splicing isoforms for NPC1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    NPC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAATGAGGGA
    NPC1 Expression
    About this image


    NPC1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Cerebellum
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
    NPC1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NPC1 Protein Expression
        Pathway & Disease-focused RT2 Profiler PCR Arrays including NPC1: 
              Hedgehog Signaling Pathway in human mouse rat
              Autophagy in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for NPC1 gene from Selected species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Npc11 , 5 Niemann Pick type C11, 5 83.6(n)1
    86.61(a)1
      18 (6.15 cM)5
    181451  NM_008720.21  NP_032746.21 
     121896935 
    chicken
    (Gallus gallus)
    Aves NPC11 Niemann-Pick disease, type C1 74.23(n)
    79.06(a)
      421076  XM_419162.4  XP_419162.3 
    lizard
    (Anolis carolinensis)
    Reptilia NPC16
    Niemann-Pick disease, type C1
    79(a)
    1 ↔ 1
    4(38225663-38260674)
    African clawed frog
    (Xenopus laevis)
    Amphibia BG731241.12   -- 73.76(n)    BG731241.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufc29a122 wufc29a12 78.01(n)   324441  CK030245.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta NPC13
    Npc1a1
    Niemann-Pick type C-1a1 43(a)
    (best of 2)3
    52.08(n)1
    47.25(a)1
      31B13
    343581  NM_001201840.11  NP_001188769.11 
    worm
    (Caenorhabditis elegans)
    Secernentea npc-13   -- 28(a)
    (best of 2)
        --
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes NCR1(YPL006W)4
    NCR11
    Vacuolar membrane protein that transits through the biosynthetic vacuolar protein sorting pathway, involved in sphingolipid metabolism; glycoprotein and functional orthologue of human Niemann Pick C1 (NPC1) protein less4
    NCR11
    45.61(n)1
    36.75(a)1
      16(544631-548143)4
    8561011, 4  NP_015319.11, 4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT4G383501 AT4G38350 48.11(n)
    40.65(a)
      829992  NM_001204024.1  NP_001190953.1 


    ENSEMBL Gene Tree for NPC1 (if available)
    TreeFam Gene Tree for NPC1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NPC1 gene
    PTCH12  SCAP2  NPC1L12  PTCH22  
    2 SIMAP similar genes for NPC1 using alignment to 7 protein entries:     NPC1_HUMAN (see all proteins):
    PTCH    NPC1L1

    Find genes that share paralogs with NPC1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for NPC1 (see all 1584)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 18 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2004440841,2,,4
    CNiemann-Pick disease C1 (NPC1)4 --21109374(+) CCGCGC/TGCTCC 2 H R mis10--------
    rs289421051,2,,4
    CNiemann-Pick disease C1 (NPC1)4 pathogenic121110373(-) GGTCAA/GCCTGG 2 N S mis10--------
    rs289421061,2,,4
    CNiemann-Pick disease C1 (NPC1)4 pathogenic121110577(-) CTTCTA/GCGAAC 2 Y C mis1 ese30--------
    rs289421081,2,,4
    CNiemann-Pick disease C1 (NPC1)4 pathogenic121113545(-) GCGTTC/TGCTGC 2 R C mis1 ese30--------
    rs340849841,2,,4
    C,FNiemann-Pick disease C1 (NPC1)4 --21114278(+) TGATAT/CTGTCC 2 /N /S mis15Minor allele frequency- C:0.01NA EU 5955
    rs289408971,2,,4
    CNiemann-Pick disease C1 (NPC1)4 pathogenic121114717(-) GGCGCA/CGCTGG 2 Q P mis1 ese30--------
    rs803582511,2,,4
    C,FNiemann-Pick disease C1 (NPC1)4 non-pathogenic121135295(-) CAGCAC/TCATGT 2 P S mis13Minor allele frequency- T:0.01NA EU 5905
    rs556800261,2,,4
    C,FNiemann-Pick disease C1 (NPC1)4 --21135339(+) TGGCAT/CTGTTC 2 /N /S mis12Minor allele frequency- C:0.00NA EU 5853
    VAR_0432764
    Niemann-Pick disease C1 (NPC1)4--see VAR_0432762 T K mis40--------
    VAR_0432064
    Niemann-Pick disease C1 (NPC1)4--see VAR_0432062 A S mis40--------

    HapMap Linkage Disequilibrium report for NPC1 (21086148 - 21166862 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for NPC1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv509688CNV Insertion20534489
    esv1106737CNV Insertion17803354
    esv34149CNV Loss18971310
    nsv909458CNV Gain21882294

    Human Gene Mutation Database (HGMD): NPC1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing NPC1
    DNA2.0 Custom Variant and Variant Library Synthesis for NPC1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607623   
    OMIM disorders: 257220  
    UniProtKB/Swiss-Prot: NPC1_HUMAN, O15118
  • Niemann-Pick disease C1 (NPC1) [MIM:257220]: A lysosomal storage disorder that affects the viscera and
    the central nervous system. It is due to defective intracellular processing and transport of low-density
    lipoprotein derived cholesterol. It causes accumulation of cholesterol in lysosomes, with delayed induction of
    cholesterol homeostatic reactions. Niemann-Pick disease type C1 has a highly variable clinical phenotype.
    Clinical features include variable hepatosplenomegaly and severe progressive neurological dysfunction such as
    ataxia, dystonia and dementia. The age of onset can vary from infancy to late adulthood. An allelic variant of
    Niemann-Pick disease type C1 is found in people with Nova Scotia ancestry. Patients with the Nova Scotian
    clinical variant are less severely affected. Note=The disease is caused by mutations affecting the gene
    represented in this entry

  • 14 diseases for NPC1:    
    About MalaCards
    niemann-pick disease type c, juvenile neurologic onset    niemann-pick disease type c, late infantile neurologic onset    niemann-pick disease type d    niemann-pick disease type c, severe perinatal form
    niemann-pick disease type c1    nasopharyngeal carcinoma 1    niemann-pick disease type c, severe early infantile neurologic onset    niemann-pick disease type c, adult neurologic onset
    acid sphingomyelinase deficiency    niemann-pick disease    pick's disease    sandhoff disease
    tangier disease    mucolipidosis ii

    2 diseases from the University of Copenhagen DISEASES database for NPC1:
    Niemann-Pick disease     Neurodegenerative disease

    Find genes that share disorders with NPC1           About GenesLikeMe

    Selected Novoseek inferred disease relationships for NPC1 gene (see all 19)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    niemann-picks disease type c 98 44 10480349 (2), 12955717 (2), 19718781 (2), 10942596 (2) (see all 38)
    niemann-pick diseases 81.5 9 16143556 (1), 18554276 (1), 9634529 (1), 18751914 (1) (see all 5)
    sphingolipidoses 79.7 1 18579730 (1)
    lipidosis 75.8 3 12606053 (1), 11249924 (1), 11525744 (1)
    neurodegeneration 63.8 9 15919659 (3), 11387550 (2), 15644330 (1), 10425213 (1)
    neurodegenerative diseases 58.7 13 17629950 (1), 17804599 (1), 18525117 (1), 20007703 (1) (see all 8)
    lysosomal storage diseases 57.3 1 15632139 (1)
    cataplexy 55.8 1 14629910 (1)
    sandhoff disease 53 1 15632139 (1)
    tangier disease 46.3 4 14747463 (3), 11533723 (1)

    GeneTests: NPC1
    GeneReviews: NPC1
    Genetic Association Database (GAD): NPC1
    Human Genome Epidemiology (HuGE) Navigator: NPC1 (22 documents)

    Export disorders for NPC1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for NPC1 gene, integrated from 10 sources (see all 258):
    (articles sorted by number of sources associating them with NPC1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Niemann-Pick type C disease: NPC1 mutations associated with severe and mild cellular cholesterol trafficking alterations. (PubMed id 11479732)1, 2, 4, 9 Ribeiro I....Millat G. (Hum. Genet. 2001)
    2. Six novel NPC1 mutations in Chinese patients with Niemann-Pick disease type C. (PubMed id 15774455)1, 2, 9 Yang C.-C....Lee M.-J. (J. Neurol. Neurosurg. Psych. 2005)
    3. Defective endocytic trafficking of NPC1 and NPC2 underlying infantile Niemann-Pick type C disease. (PubMed id 12554680)1, 2, 9 Blom T.S.... Ikonen E. (Hum. Mol. Genet. 2003)
    4. Niemann-Pick C1 disease: correlations between NPC1 mutations, levels of NPC1 protein, and phenotypes emphasize the functional significance of the putative sterol-sensing domain and of the cysteine-rich luminal loop. (PubMed id 11333381)1, 2, 9 Millat G.... Vanier M.T. (Am. J. Hum. Genet. 2001)
    5. Molecular analysis of NPC1 and NPC2 gene in 34 Niemann-Pick C Italian patients: identification and structural modeling of novel mutations. (PubMed id 19252935)1, 4, 9 Fancello T....Filocamo M. (Neurogenetics 2009)
    6. Niemann-Pick C variant detection by altered sphingolipid trafficking and correlation with mutations within a specific domain of NPC1. (PubMed id 11349231)1, 2, 9 Sun X.... Snow K. (Am. J. Hum. Genet. 2001)
    7. NPC1: complete genomic sequence, mutation analysis, and characterization of haplotypes. (PubMed id 11754101)1, 2, 9 Bauer P.... Rolfs A. (Hum. Mutat. 2002)
    8. 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. (PubMed id 10821832)1, 2, 9 Davies J.P. and Ioannou Y.A. (J. Biol. Chem. 2000)
    9. Structure of N-terminal domain of NPC1 reveals distinct subdomains for binding and transfer of cholesterol. (PubMed id 19563754)1, 2, 9 Kwon H.J....Infante R.E. (Cell 2009)
    10. NPC2 facilitates bidirectional transfer of cholesterol between NPC1 and lipid bilayers, a step in cholesterol egress from lysosomes. (PubMed id 18772377)1, 2, 9 Infante R.E....Goldstein J.L. (Proc. Natl. Acad. Sci. U.S.A. 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 4864 HGNC: 7897 AceView: NPC1 Ensembl:ENSG00000141458 euGenes: HUgn4864
    ECgene: NPC1 Kegg: 4864 H-InvDB: NPC1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for NPC1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for NPC1 Genetics and Cytogenetics in Oncology and Haematology
    Niemann-Pick type C disease gene variation databasehttp://npc.fzk.de
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=NPC1[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for NPC1 gene:
    Search GeneIP for patents involving NPC1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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