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    ABCA1 ATP binding cassette subfamily A member 1 [ Homo sapiens (human) ]

    Gene ID: 19, updated on 19-Jul-2016
    Official Symbol
    ABCA1provided by HGNC
    Official Full Name
    ATP binding cassette subfamily A member 1provided by HGNC
    Primary source
    HGNC:HGNC:29
    See related
    Ensembl:ENSG00000165029 HPRD:02501; MIM:600046; Vega:OTTHUMG00000020417
    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
    TGD; ABC1; CERP; ABC-1; HDLDT1
    Summary
    The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. With cholesterol as its substrate, this protein functions as a cholesteral efflux pump in the cellular lipid removal pathway. Mutations in this gene have been associated with Tangier's disease and familial high-density lipoprotein deficiency. [provided by RefSeq, Jul 2008]
    Orthologs
    Location:
    9q31.1
    Exon count:
    58
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 9 NC_000009.12 (104781002..104928246, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (107543283..107690527, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene nipsnap homolog 3A Neighboring gene nipsnap homolog 3B Neighboring gene uncharacterized LOC102724761 Neighboring gene uncharacterized LOC105376196 Neighboring gene uncharacterized LOC107987106 Neighboring gene uncharacterized LOC105376197 Neighboring gene RNA, 7SK small nuclear pseudogene 191

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Familial hypercholesterolemia
    MedGen: C0020445 OMIM: 143890 GeneReviews: Not available
    Compare labs
    Familial hypoalphalipoproteinemia
    MedGen: C1704429 OMIM: 604091 GeneReviews: Not available
    Compare labs
    Tangier disease
    MedGen: C0039292 OMIM: 205400 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population.
    NHGRI GWA Catalog
    Biological, clinical and population relevance of 95 loci for blood lipids.
    NHGRI GWA Catalog
    Common variants at 30 loci contribute to polygenic dyslipidemia.
    NHGRI GWA Catalog
    Common variants near ABCA1 and in PMM2 are associated with primary open-angle glaucoma.
    NHGRI GWA Catalog
    Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma.
    NHGRI GWA Catalog
    Discovery and refinement of loci associated with lipid levels.
    NHGRI GWA Catalog
    Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
    NHGRI GWA Catalog
    Genome-wide analysis of multi-ancestry cohorts identifies new loci influencing intraocular pressure and susceptibility to glaucoma.
    NHGRI GWA Catalog
    Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
    NHGRI GWA Catalog
    Genome-wide association study of chronic periodontitis in a general German population.
    NHGRI GWA Catalog
    Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.
    NHGRI GWA Catalog
    Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
    NHGRI GWA Catalog
    Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits.
    NHGRI GWA Catalog
    Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
    NHGRI GWA Catalog
    Integrated Genome-wide Association, Coexpression Network, and Expression Single Nucleotide Polymorphism Analysis Identifies Novel Pathway in Allergic Rhinitis.
    NHGRI GWA Catalog
    Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
    NHGRI GWA Catalog
    Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts.
    NHGRI GWA Catalog
    Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
    NHGRI GWA Catalog
    Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
    NHGRI GWA Catalog
    Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Knockdown of calnexin by siRNA mimics the effects of HIV-1 Nef on ABCA1 downregulation in cells PubMed
    nef HIV-1 Nef enhances interaction of calnexin with HIV-1 gp160 but inhibits physical interaction between calnexin and ABCA1 in cells PubMed
    nef A yeast 2-hybrid system does not reveal any interaction between HIV-1 Nef and the C-terminal cytoplasmic region (residues 1921-2261) of ABCA1, while a very weak interaction is detected in co-immunoprecipitation from cells expressing these polypeptides PubMed
    nef Inhibition of ABCA1 stimulates HIV-1 Nef-dependent formation of lipid rafts. HIV-1 infectivity negatively correlates with ABCA1 expression in host cell PubMed
    nef Physical interaction between HIV-1 Nef and ABCA1 depends on Nef myristoylation and involves residues 2225-2231 of ABCA1 PubMed
    nef HIV-1 Nef interacts with ABCA1 and induces downregulation and redistribution of ABCA1 to the plasma membrane PubMed
    matrix gag HIV-1 MA increases ABCA1 mRNA expression in HepG2 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ14958, MGC164864, MGC165011

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ATP binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    ATPase activity, coupled to transmembrane movement of substances IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    ATPase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    anion transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    apolipoprotein A-I binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    apolipoprotein A-I receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    apolipoprotein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    cholesterol binding IC
    Inferred by Curator
    more info
    PubMed 
    cholesterol transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    phospholipid binding IC
    Inferred by Curator
    more info
    PubMed 
    phospholipid transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    small GTPase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    syntaxin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    G-protein coupled receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    anion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    apolipoprotein A-I-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to cholesterol IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to lipopolysaccharide IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to retinoic acid IEA
    Inferred from Electronic Annotation
    more info
     
    cholesterol efflux IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cholesterol efflux IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cholesterol homeostasis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cholesterol metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endosomal transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    high-density lipoprotein particle assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    interleukin-1 beta secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    intracellular cholesterol transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    lipoprotein metabolic process TAS
    Traceable Author Statement
    more info
     
    lysosome organization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of cholesterol storage TAS
    Traceable Author Statement
    more info
    PubMed 
    negative regulation of macrophage derived foam cell differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    peptide secretion IEA
    Inferred from Electronic Annotation
    more info
     
    phagocytosis, engulfment IEA
    Inferred from Electronic Annotation
    more info
     
    phospholipid efflux IDA
    Inferred from Direct Assay
    more info
    PubMed 
    phospholipid efflux IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    phospholipid homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    phospholipid translocation IEA
    Inferred from Electronic Annotation
    more info
     
    platelet dense granule organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cAMP biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cholesterol efflux IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein lipidation IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of Cdc42 protein signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    response to drug IEA
    Inferred from Electronic Annotation
    more info
     
    response to laminar fluid shear stress IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to low-density lipoprotein particle IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to nutrient IEA
    Inferred from Electronic Annotation
    more info
     
    reverse cholesterol transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
     
    endocytic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    high-density lipoprotein particle IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    phagocytic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    ATP-binding cassette sub-family A member 1
    Names
    ATP-binding cassette transporter A1
    ATP-binding cassette, sub-family A (ABC1), member 1
    cholesterol efflux regulatory protein
    membrane-bound

    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_007981.1 RefSeqGene

      Range
      4910..152154
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005502.3NP_005493.2  ATP-binding cassette sub-family A member 1

      See identical proteins and their annotated locations for NP_005493.2

      Status: REVIEWED

      Source sequence(s)
      AB445477, AL359846, BC146856, BU753834, BX955241
      Consensus CDS
      CCDS6762.1
      UniProtKB/Swiss-Prot
      O95477
      UniProtKB/TrEMBL
      B2RUU2, B7XCW9
      Related
      ENSP00000363868, OTTHUMP00000021833, ENST00000374736, OTTHUMT00000053491
      Conserved Domains (3) summary
      TIGR01257
      Location:62236
      rim_protein; retinal-specific rim ABC transporter
      cd03263
      Location:8991119
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
      pfam13732
      Location:21262218
      DUF4162; Domain of unknown function (DUF4162)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p7 Primary Assembly

      Range
      104781002..104928246 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011518342.2XP_011516644.1  

      Conserved Domains (3) summary
      TIGR01257
      Location:82117
      rim_protein; retinal-specific rim ABC transporter
      cd03263
      Location:778998
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
      pfam13732
      Location:20072099
      DUF4162; Domain of unknown function (DUF4162)
    2. XM_005251773.2XP_005251830.1  

      Conserved Domains (3) summary
      TIGR01257
      Location:62238
      rim_protein; retinal-specific rim ABC transporter
      cd03263
      Location:8991119
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
      pfam13732
      Location:21282220
      DUF4162; Domain of unknown function (DUF4162)
    3. XM_011518339.2XP_011516641.1  

      See identical proteins and their annotated locations for XP_011516641.1

      Conserved Domains (3) summary
      TIGR01257
      Location:62263
      rim_protein; retinal-specific rim ABC transporter
      cd03263
      Location:9241144
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
      pfam13732
      Location:21532245
      DUF4162; Domain of unknown function (DUF4162)
    4. XM_011518341.2XP_011516643.1  

      Conserved Domains (3) summary
      TIGR01257
      Location:62261
      rim_protein; retinal-specific rim ABC transporter
      cd03263
      Location:9241144
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
      pfam13732
      Location:21512243
      DUF4162; Domain of unknown function (DUF4162)
    5. XM_005251776.2XP_005251833.1  

      Conserved Domains (3) summary
      TIGR01257
      Location:12178
      rim_protein; retinal-specific rim ABC transporter
      cd03263
      Location:8391059
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
      pfam13732
      Location:20682160
      DUF4162; Domain of unknown function (DUF4162)
    6. XM_017014380.1XP_016869869.1  

    7. XM_017014381.1XP_016869870.1  

    8. XM_011518340.2XP_011516642.1  

      See identical proteins and their annotated locations for XP_011516642.1

      Conserved Domains (3) summary
      TIGR01257
      Location:62263
      rim_protein; retinal-specific rim ABC transporter
      cd03263
      Location:9241144
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
      pfam13732
      Location:21532245
      DUF4162; Domain of unknown function (DUF4162)
    9. XM_017014378.1XP_016869867.1  

    10. XM_017014379.1XP_016869868.1  

    11. XM_017014382.1XP_016869871.1  

    12. XM_011518344.2XP_011516646.1  

      Conserved Domains (4) summary
      cd03263
      Location:9241144
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
      COG1125
      Location:9241229
      OpuBA; ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]
      pfam12698
      Location:665815
      ABC2_membrane_3; ABC-2 family transporter protein
      cl21472
      Location:657813
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...

    RNA

    1. XR_001746223.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018920.2 Alternate CHM1_1.1

      Range
      107690161..107837338 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)