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

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; AllianceGenome:HGNC:29
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: mouse all
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Genomic context

Location:: 9q31.1

Exon count:: 50

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (104781006..104928155, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (116955789..117102979, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (107543287..107690436, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ABCA1 variant rs9282541 is associated with metabolic syndrome in Maya children.
Title: ABCA1 variant rs9282541 is associated with metabolic syndrome in Maya children.
The ATPase activity of ABCA1 is increased by cholesterol in the presence of anionic lipids.
Title: The ATPase activity of ABCA1 is increased by cholesterol in the presence of anionic lipids.
Involvement of Expression of miR33-5p and ABCA1 in Human Peripheral Blood Mononuclear Cells in Coronary Artery Disease.
Title: Involvement of Expression of miR33-5p and ABCA1 in Human Peripheral Blood Mononuclear Cells in Coronary Artery Disease.
The ABCA1 gene polymorphisms rs1800977 and rs2230806 are differentially associated with the risk for myocardial infarction in Slovenian subjects with type 2 diabetes mellitus.
Title: The ABCA1 gene polymorphisms rs1800977 and rs2230806 are differentially associated with the risk for myocardial infarction in Slovenian subjects with type 2 diabetes mellitus.
Identification and Molecular Simulation of Genetic Variants in ABCA1 Gene Associated with Susceptibility to Dyslipidemia in Type 2 Diabetes.
Title: Identification and Molecular Simulation of Genetic Variants in ABCA1 Gene Associated with Susceptibility to Dyslipidemia in Type 2 Diabetes.
Decreased mRNA expression of NR1H3 and ABCA1 in pulmonary tuberculosis patients from population of Punjab, India.
Title: Decreased mRNA expression of NR1H3 and ABCA1 in pulmonary tuberculosis patients from population of Punjab, India.
Inflammatory corpuscle AIM2 facilitates macrophage foam cell formation by inhibiting cholesterol efflux protein ABCA1.
Title: Inflammatory corpuscle AIM2 facilitates macrophage foam cell formation by inhibiting cholesterol efflux protein ABCA1.
ALKBH5 facilitates the progression of skin cutaneous melanoma via mediating ABCA1 demethylation and modulating autophagy in an m[6]A-dependent manner.
Title: ALKBH5 facilitates the progression of skin cutaneous melanoma via mediating ABCA1 demethylation and modulating autophagy in an m(6)A-dependent manner.
Trimethylamine N-oxide promotes oxidative stress and lipid accumulation in macrophage foam cells via the Nrf2/ABCA1 pathway.
Title: Trimethylamine N-oxide promotes oxidative stress and lipid accumulation in macrophage foam cells via the Nrf2/ABCA1 pathway.
Functional characterization of missense variants affecting the extracellular domains of ABCA1 using a fluorescence-based assay.
Title: Functional characterization of missense variants affecting the extracellular domains of ABCA1 using a fluorescence-based assay.

Submit: New GeneRIF Correction See all GeneRIFs (676)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Hypoalphalipoproteinemia, primary, 1 MedGen: C5231558 OMIM: 604091 GeneReviews: Not available	not available
Tangier disease MedGen: C0039292 OMIM: 205400 GeneReviews: Tangier Disease	not available

EBI 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. EBI GWAS Catalog EBI GWAS CatalogPubMed
Biological, clinical and population relevance of 95 loci for blood lipids. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants at 30 loci contribute to polygenic dyslipidemia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants near ABCA1 and in PMM2 are associated with primary open-angle glaucoma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery and refinement of loci associated with lipid levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic variants influencing circulating lipid levels and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide analysis of multi-ancestry cohorts identifies new loci influencing intraocular pressure and susceptibility to glaucoma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies multiple loci influencing human serum metabolite levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of chronic periodontitis in a general German population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
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. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Integrated Genome-wide Association, Coexpression Network, and Expression Single Nucleotide Polymorphism Analysis Identifies Novel Pathway in Allergic Rhinitis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. EBI GWAS Catalog EBI GWAS CatalogPubMed
Newly identified loci that influence lipid concentrations and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH70166 (e-PCR)
- UniSTS:25346

PMC33205P1 (e-PCR)
- UniSTS:273156

G32950 (e-PCR)
- UniSTS:117528

STS-T64961 (e-PCR)
- UniSTS:69426

PMC207565P1 (e-PCR)
- UniSTS:271951

D9S53 (e-PCR), detects polymorphism
- UniSTS:50263

D9S1765 (e-PCR)
- UniSTS:154205

ABCA1_2173 (e-PCR)
- UniSTS:280414

RH81050 (e-PCR)
- UniSTS:87958

ABCA1 (e-PCR)
- UniSTS:509927

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 ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
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
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 phosphatidylcholine binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylcholine floppase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylcholine floppase activity	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylcholine floppase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables phosphatidylserine floppase activity	IBA Inferred from Biological aspect of Ancestor more info
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 intracellular cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lipoprotein biosynthetic process	IEA Inferred from Electronic Annotation more info
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
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 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 vitamin B3	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
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
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	IMP Inferred from Mutant Phenotype more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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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

EC 7.6.2.1

NCBI Reference Sequences (RefSeq)

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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.