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

    Gene ID: 19, updated on 2-Aug-2021

    Summary

    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 MIM:600046
    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; HPALP1; HDLCQTL13
    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 both alleles of this gene cause Tangier disease and familial high-density lipoprotein (HDL) deficiency. [provided by RefSeq, Sep 2019]
    Expression
    Ubiquitous expression in adrenal (RPKM 14.4), fat (RPKM 9.9) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See ABCA1 in Genome Data Viewer
    Location:
    9q31.1
    Exon count:
    50
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (104781006..104928155, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (107543287..107690436, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene nipsnap homolog 3A Neighboring gene nipsnap homolog 3B Neighboring gene Sharpr-MPRA regulatory region 1797 Neighboring gene uncharacterized LOC105376196 Neighboring gene cancer/testis associated transcript 70 Neighboring gene uncharacterized LOC105376197 Neighboring gene RN7SK pseudogene 191

    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
    A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population.
    GeneReviews: Not available
    Biological, clinical and population relevance of 95 loci for blood lipids.
    GeneReviews: Not available
    Common variants at 30 loci contribute to polygenic dyslipidemia.
    GeneReviews: Not available
    Common variants near ABCA1 and in PMM2 are associated with primary open-angle glaucoma.
    GeneReviews: Not available
    Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma.
    GeneReviews: Not available
    Discovery and refinement of loci associated with lipid levels.
    GeneReviews: Not available
    Familial hypoalphalipoproteinemia
    MedGen: C5231558 OMIM: 604091 GeneReviews: Not available
    Compare labs
    Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
    GeneReviews: Not available
    Genome-wide analysis of multi-ancestry cohorts identifies new loci influencing intraocular pressure and susceptibility to glaucoma.
    GeneReviews: Not available
    Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
    GeneReviews: Not available
    Genome-wide association study of chronic periodontitis in a general German population.
    GeneReviews: Not available
    Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.
    GeneReviews: Not available
    Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
    GeneReviews: Not available
    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.
    GeneReviews: Not available
    Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
    GeneReviews: Not available
    Integrated Genome-wide Association, Coexpression Network, and Expression Single Nucleotide Polymorphism Analysis Identifies Novel Pathway in Allergic Rhinitis.
    GeneReviews: Not available
    Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
    GeneReviews: Not available
    Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts.
    GeneReviews: Not available
    Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
    GeneReviews: Not available
    Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
    GeneReviews: Not available
    Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
    GeneReviews: Not available
    Tangier disease
    MedGen: C0039292 OMIM: 205400 GeneReviews: Tangier Disease
    Compare labs

    HIV-1 interactions

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ14958, MGC164864, MGC165011

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ABC-type transporter activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ATPase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ATPase-coupled transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables apolipoprotein A-I binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables apolipoprotein A-I receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables apolipoprotein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables cholesterol binding IC
    Inferred by Curator
    more info
    PubMed 
    enables cholesterol transfer activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables floppase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables high-density lipoprotein particle binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables lipid transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables phosphatidylcholine binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphatidylcholine floppase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables phosphatidylcholine floppase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphatidylserine floppase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables phosphatidylserine floppase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phospholipid transporter activity IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables signaling receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables small GTPase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sphingolipid floppase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables syntaxin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in G protein-coupled receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in adenylate cyclase-activating G protein-coupled receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in apolipoprotein A-I-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to cholesterol IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to cytokine stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to drug IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to lipopolysaccharide IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to low-density lipoprotein particle stimulus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in cellular response to retinoic acid IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cholesterol efflux IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cholesterol efflux IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in cholesterol efflux IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cholesterol homeostasis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cholesterol homeostasis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cholesterol metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in endosomal transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in export across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in high-density lipoprotein particle assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intermembrane lipid transfer IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intracellular cholesterol transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lipid transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in lysosome organization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cholesterol storage TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of macrophage derived foam cell differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in peptide secretion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in phagocytosis, engulfment IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in phospholipid efflux IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in phospholipid efflux IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in phospholipid efflux IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in phospholipid efflux IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in phospholipid homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in phospholipid translocation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in platelet dense granule organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cholesterol efflux IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of high-density lipoprotein particle assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein lipidation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in protein transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in regulation of Cdc42 protein signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of high-density lipoprotein particle assembly TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in response to laminar fluid shear stress IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to nutrient IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in reverse cholesterol transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in signal release IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in signal release ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in sphingolipid translocation IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in basolateral plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endocytic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in integral component of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in intracellular vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in phagocytic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    phospholipid-transporting ATPase ABCA1
    Names
    ATP-binding cassette sub-family A member 1
    ATP-binding cassette transporter A1
    ATP-binding cassette, sub-family A (ABC1), member 1
    cholesterol efflux regulatory protein
    membrane-bound
    NP_005493.2

    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_007981.1 RefSeqGene

      Range
      5001..152150
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_542

    mRNA and Protein(s)

    1. NM_005502.4NP_005493.2  phospholipid-transporting ATPase ABCA1

      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
      ENSP00000363868.3, ENST00000374736.8
      Conserved Domains (1) summary
      TIGR01257
      Location:62236
      rim_protein; retinal-specific rim ABC transporter

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

      Range
      104781006..104928155 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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