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

Gene ID: 19, updated on 12-Sep-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
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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 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 cellular response to xenobiotic stimulus 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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