ABCA1

ATP binding cassette subfamily A member 1 | TGD, ABC1, HDLDT1

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]

Member of: DE-4 DE-4.22 Developmental clusters: GC7

Biological processes 109 terms

ABC-type transporter activity (GO:0140359)ATP binding (GO:0005524)ATP binding (GO:0005524)ATP hydrolysis activity (GO:0016887)ATPase binding (GO:0051117)ATPase-coupled intramembrane lipid carrier activity (GO:0140326)ATPase-coupled intramembrane lipid carrier activity (GO:0140326)ATPase-coupled transmembrane transporter activity (GO:0042626)ATPase-coupled transmembrane transporter activity (GO:0042626)G protein-coupled receptor signaling pathway (GO:0007186)Golgi apparatus (GO:0005794)adenylate cyclase-activating G protein-coupled receptor signaling pathway (GO:0007189)apolipoprotein A-I binding (GO:0034186)apolipoprotein A-I receptor activity (GO:0034188)apolipoprotein A-I-mediated signaling pathway (GO:0038027)apolipoprotein binding (GO:0034185)basolateral plasma membrane (GO:0016323)cell surface (GO:0009986)cellular response to cholesterol (GO:0071397)cellular response to cytokine stimulus (GO:0071345)cellular response to lipopolysaccharide (GO:0071222)cellular response to low-density lipoprotein particle stimulus (GO:0071404)cellular response to retinoic acid (GO:0071300)cellular response to xenobiotic stimulus (GO:0071466)cholesterol binding (GO:0015485)cholesterol efflux (GO:0033344)cholesterol efflux (GO:0033344)cholesterol efflux (GO:0033344)cholesterol homeostasis (GO:0042632)cholesterol homeostasis (GO:0042632)cholesterol metabolic process (GO:0008203)cholesterol transfer activity (GO:0120020)cholesterol transfer activity (GO:0120020)cholesterol transport (GO:0030301)endocytic vesicle (GO:0030139)endoplasmic reticulum membrane (GO:0005789)endosomal transport (GO:0016197)endosome (GO:0005768)endosome (GO:0005768)export across plasma membrane (GO:0140115)export across plasma membrane (GO:0140115)external side of plasma membrane (GO:0009897)floppase activity (GO:0140328)high-density lipoprotein particle assembly (GO:0034380)high-density lipoprotein particle binding (GO:0008035)intracellular cholesterol transport (GO:0032367)intracellular membrane-bounded organelle (GO:0043231)intracellular vesicle (GO:0097708)lipoprotein biosynthetic process (GO:0042158)lysosome organization (GO:0007040)membrane (GO:0016020)membrane raft (GO:0045121)negative regulation of cholesterol storage (GO:0010887)negative regulation of macrophage derived foam cell differentiation (GO:0010745)organic hydroxy compound transport (GO:0015850)perinuclear region of cytoplasm (GO:0048471)phagocytic vesicle (GO:0045335)phosphatidylcholine binding (GO:0031210)phosphatidylcholine floppase activity (GO:0090554)phosphatidylcholine floppase activity (GO:0090554)phosphatidylcholine floppase activity (GO:0090554)phosphatidylcholine floppase activity (GO:0090554)phosphatidylserine floppase activity (GO:0090556)phosphatidylserine floppase activity (GO:0090556)phosphatidylserine floppase activity (GO:0090556)phospholipid efflux (GO:0033700)phospholipid efflux (GO:0033700)phospholipid efflux (GO:0033700)phospholipid efflux (GO:0033700)phospholipid homeostasis (GO:0055091)phospholipid transfer activity (GO:0120014)phospholipid transfer activity (GO:0120014)phospholipid translocation (GO:0045332)phospholipid translocation (GO:0045332)phospholipid transport (GO:0015914)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane (GO:0005886)platelet dense granule organization (GO:0060155)positive regulation of cholesterol efflux (GO:0010875)positive regulation of high-density lipoprotein particle assembly (GO:0090108)positive regulation of high-density lipoprotein particle assembly (GO:0090108)protein binding (GO:0005515)protein secretion (GO:0009306)protein secretion (GO:0009306)protein secretion (GO:0009306)protein transmembrane transport (GO:0071806)protein transmembrane transport (GO:0071806)regulation of Cdc42 protein signal transduction (GO:0032489)regulation of high-density lipoprotein particle assembly (GO:0090107)response to laminar fluid shear stress (GO:0034616)response to nutrient (GO:0007584)response to nutrient levels (GO:0031667)response to vitamin B3 (GO:0033552)response to xenobiotic stimulus (GO:0009410)reverse cholesterol transport (GO:0043691)reverse cholesterol transport (GO:0043691)signal release (GO:0023061)signal release (GO:0023061)signal release (GO:0023061)signaling receptor binding (GO:0005102)small GTPase binding (GO:0031267)sphingolipid floppase activity (GO:0046623)sphingolipid translocation (GO:0099039)syntaxin binding (GO:0019905)transmembrane protein transporter activity (GO:0008320)transmembrane protein transporter activity (GO:0008320)transmembrane transport (GO:0055085)

Expression (TPM)

TFs regulating ABCA1 0 TFs

Transcription factors with Perturb-seq knockdown data for ABCA1. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = ABCA1 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to ABCA1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of ABCA1, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr9:104,747,331–104,748,817	180.3 kb	Distal (>10kb) Multiome	758
chr9:104,763,613–104,764,841	163.9 kb	Distal (>10kb) Multiome	645
chr9:104,778,305–104,779,370	149.3 kb	Distal (>10kb) Multiome	109
chr9:104,868,780–104,869,418	59.0 kb	Distal (>10kb) Multiome	308
chr9:104,885,889–104,886,798	41.9 kb	Distal (>10kb) Multiome	467
chr9:104,926,377–104,928,757	1.5 kb	Proximal (<10kb) Multiome	898
chr9:104,934,663–104,934,869	6.5 kb	Proximal (<10kb)	13
chr9:104,961,289–104,961,961	33.3 kb	Distal (>10kb) Multiome	296
chr9:104,967,924–104,969,360	40.3 kb	Distal (>10kb) Multiome	657
chr9:104,990,922–104,992,163	63.6 kb	Distal (>10kb) Multiome	685
chr9:104,993,121–104,994,152	65.5 kb	Distal (>10kb) Multiome	314
chr9:105,104,550–105,105,176	176.6 kb	Distal (>10kb) Multiome	81
chr9:105,121,705–105,122,364	193.8 kb	Distal (>10kb) Multiome	74
chr9:105,138,128–105,139,010	210.4 kb	Distal (>10kb) Multiome	255
chr9:105,244,049–105,245,808	317.1 kb	Distal (>10kb) Multiome HiCAR	1131

Genome Browser

Genomic view of the ABCA1 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.