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

Gene ID: 19, updated on 10-Dec-2019

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

Genomic context

See ABCA1 in Genome Data Viewer
Location:
9q31.1
Exon count:
58
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (104781006..104928232, 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 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
Familial hypoalphalipoproteinemia
MedGen: C1704429 OMIM: 604091 GeneReviews: Not available
Compare labs
Tangier disease
MedGen: C0039292 OMIM: 205400 GeneReviews: Tangier Disease
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

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 BioSystems

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
ATP binding IDA
Inferred from Direct Assay
more info
PubMed 
ATPase activity 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
PubMed 
ATPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
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 
high-density lipoprotein particle binding IEA
Inferred from Electronic Annotation
more info
 
intermembrane cholesterol transfer activity IDA
Inferred from Direct Assay
more info
PubMed 
lipid transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylcholine binding IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylcholine-translocating ATPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylcholine-translocating ATPase activity IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylserine-translocating ATPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylserine-translocating ATPase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling 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 
adenylate cyclase-activating G protein-coupled receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 low-density lipoprotein particle stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
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 homeostasis TAS
Traceable Author Statement
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 
high-density lipoprotein particle assembly TAS
Traceable Author Statement
more info
 
interleukin-1 beta secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
intracellular cholesterol transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
lipid transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
phagocytosis, engulfment IEA
Inferred from Electronic Annotation
more info
 
phospholipid efflux IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
platelet dense granule organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cholesterol efflux IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of high-density lipoprotein particle assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
protein lipidation IEA
Inferred from Electronic Annotation
more info
 
regulation of Cdc42 protein signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of high-density lipoprotein particle assembly TAS
Traceable Author Statement
more info
PubMed 
regulation of lipid metabolic process TAS
Traceable Author Statement
more info
 
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 nutrient IEA
Inferred from Electronic Annotation
more info
 
reverse cholesterol transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
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
 
endosome IDA
Inferred from Direct Assay
more info
PubMed 
external side of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
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
 

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
XP_005251830.1
XP_005251833.1
XP_011516641.1
XP_011516642.1
XP_011516643.1
XP_011516644.1
XP_011516646.1
XP_016869867.1
XP_016869868.1
XP_016869869.1
XP_016869870.1
XP_016869871.1

NCBI Reference Sequences (RefSeq)

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)

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 (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 Updated Annotation Release 109.

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..104928232 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518342.3XP_011516644.1  phospholipid-transporting ATPase ABCA1 isoform X6

    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_005251773.3XP_005251830.1  phospholipid-transporting ATPase ABCA1 isoform X3

    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_011518339.3XP_011516641.1  phospholipid-transporting ATPase ABCA1 isoform X1

    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_011518341.3XP_011516643.1  phospholipid-transporting ATPase ABCA1 isoform X2

    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_005251776.3XP_005251833.1  phospholipid-transporting ATPase ABCA1 isoform X5

    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_017014380.2XP_016869869.1  phospholipid-transporting ATPase ABCA1 isoform X1

    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)
  7. XM_017014381.2XP_016869870.1  phospholipid-transporting ATPase ABCA1 isoform X1

    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)
  8. XM_011518340.3XP_011516642.1  phospholipid-transporting ATPase ABCA1 isoform X1

    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_017014378.2XP_016869867.1  phospholipid-transporting ATPase ABCA1 isoform X1

    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)
  10. XM_017014379.2XP_016869868.1  phospholipid-transporting ATPase ABCA1 isoform X1

    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)
  11. XM_017014382.2XP_016869871.1  phospholipid-transporting ATPase ABCA1 isoform X4

  12. XM_011518344.2XP_011516646.1  phospholipid-transporting ATPase ABCA1 isoform X7

    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:665866
    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

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