PharmGKB: The Pharmacogenomics Knowledge Base

Gene:
ABCA1
ATP-binding cassette, sub-family A (ABC1), member 1

Overview

Alternate Names: ATP binding cassette transporter 1; ATP-binding cassette 1; ATP-binding cassette transporter A1; ATP-binding cassette, sub-family A member 1; OTTHUMP00000021833; cholesterol efflux regulatory protein; high density lipoprotein deficiency, Tangier type, 1; membrane-bound
Alternate Symbols: ABC-1; ABC1; ABCA1; CERP; FLJ14958; HDLDT1; MGC164864; MGC165011; TGD; Tangier; Tangier disease
PharmGKB Accession Id: PA24373

Details

Cytogenetic Location: chr9 : q31.1
GP mRNA Boundary†: chr9 : 106583104 - 106730257
GP Gene Boundary†: chr9 : 106580104 - 106740257
Strand: minus
Product Name: ATP binding cassette transporter 1, ATP-binding cassette 1, ATP-binding cassette, sub-family A member 1, cholesterol efflux regulatory protein, high density lipoprotein deficiency, Tangier type, 1, membrane-bound
† The mRNA boundaries are calculated using the gene's default feature set from NCBI, mapped onto the UCSC Golden Path. PharmGKB sets gene boundaries by expanding the mRNA boundaries by no less than 10,000 bases upstream (5') and 3,000 bases downstream (3') to allow for potential regulatory regions.

Curated Annotations (Curated Annotation)

  1. rs2230806 at chr9:106660688 in ABCA1
    The ABCA1:Arg219Lys K allele frequency differs markedly between blacks and whites, and the variant-allele modulates the association between age and HDL cholesterol, as well as body fatness and triglycerides in a beneficial manner only in whites.
    Variant Name:
    ABCA1:Arg219Lys
    Evidence:
    PMID:12870173
    PMID:15044381

Non-Curated Annotations (Non-Curated Annotation)

  1. rs3905000 at chr9:106696891 in ABCA1
    GWAS results: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. (Initial Sample Size: 21,412 individuals; Replication Sample Size: NR); (Region: 9q31.1; Reported Gene(s): ABCA1; Risk Allele: rs3905000-G); (p-value= 0.0000000000009).This variant is associated with HDL cholesterol.
    Evidence:
    PMID:19060911
    http://www.genome.gov/gwastudies/
  2. rs1883025 at chr9:106704122 in ABCA1
    GWAS results: Common variants at 30 loci contribute to polygenic dyslipidemia. (Initial Sample Size: 19,840 individuals; Replication Sample Size: Up to 20,623 individuals); (Region: 9q31.1; Reported Gene(s): ABCA1; Risk Allele: rs1883025-T); (p-value= 0.000000001).This variant is associated with HDL cholesterol.
    Evidence:
    PMID:19060906
    http://www.genome.gov/gwastudies/
Variant names are different names that have been used in the literature and other resources to refer to the same variant. Non-curated variant information is accumulated solely by computational methods and has not been verified by the scientific staff at PharmGKB.

Non-Curated Information

A list of non-curated publications that mention this gene along with other genes is available.

Curated Information

The following drugs are in curated knowledge about this gene.

  Drug Class Relationship Evidence
Phenotype data available Genotype Data Available Literature annotations available Not annotated
hmg coa reductase inhibitors
  •   
  • PD
  •   
  •   
  •   
Pathways
  Drug Relationship Evidence
No phenotype data No genotype data Literature annotations available Not annotated
atorvastatin
  •   
  • PD
  •   
  •   
  • GN
Publications, Pathways
No phenotype data No genotype data Literature annotations available Not annotated
ezetimibe
  •   
  • PD
  •   
  •   
  •   
Pathways
No phenotype data No genotype data Literature annotations available Not annotated
fenofibrate
  •   
  •   
  •   
  • FA
  •   
Publications
No phenotype data No genotype data Literature annotations available Not annotated
fluvastatin
  •   
  • PD
  •   
  •   
  •   
Publications, Pathways
No phenotype data No genotype data Literature annotations available Not annotated
lovastatin
  •   
  • PD
  •   
  •   
  •   
Pathways
No phenotype data No genotype data Literature annotations available Not annotated
metoprolol
  •   
  • PD
  •   
  •   
  •   
Publications
No phenotype data No genotype data Literature annotations available Not annotated
pravastatin
  •   
  • PD
  •   
  •   
  •   
Pathways
No phenotype data No genotype data Literature annotations available Not annotated
rosuvastatin
  •   
  • PD
  •   
  •   
  •   
Pathways
Phenotype data available No genotype data Literature annotations available Not annotated
simvastatin
  •   
  • PD
  •   
  •   
  •   
Pathways

Non-Curated Information

A list of non-curated publications that mention this gene along with other drugs is available.

Curated Information

The following diseases are in curated knowledge about this gene.

  Disease Relationship Evidence
Phenotype data available Genotype Data Available Literature annotations available Not annotated
Cardiovascular Diseases
  •   
  • PD
  •   
  •   
  •   
Pathways
No phenotype data No genotype data Literature annotations available Not annotated
Carotid Stenosis
  •   
  • PD
  •   
  •   
  •   
Publications
Phenotype data available Genotype Data Available Literature annotations available Not annotated
Colonic Neoplasms
  • CO
  •   
  •   
  •   
  • GN
Publications
No phenotype data No genotype data Literature annotations available Not annotated
Hypercholesterolemia
  •   
  • PD
  •   
  •   
  •   
Pathways
No phenotype data No genotype data Literature annotations available Not annotated
Hyperlipidemias
  •   
  • PD
  •   
  •   
  •   
Pathways
No phenotype data No genotype data Literature annotations available Not annotated
Hyperlipoproteinemia Type II
  •   
  • PD
  •   
  •   
  •   
Pathways
No phenotype data No genotype data Literature annotations available Not annotated
Kidney Diseases
  •   
  •   
  •   
  •   
  • GN
Publications
No phenotype data No genotype data Literature annotations available Not annotated
Muscular Diseases
  •   
  • PD
  •   
  •   
  •   
Pathways
No phenotype data No genotype data Literature annotations available Not annotated
Myalgia unspecified
  •   
  • PD
  •   
  •   
  •   
Pathways
Phenotype data available Genotype Data Available Literature annotations available Not annotated
Myocardial Infarction
  •   
  • PD
  •   
  •   
  •   
Pathways
No phenotype data No genotype data Literature annotations available Not annotated
Myositis
  •   
  • PD
  •   
  •   
  •   
Pathways
No phenotype data No genotype data Literature annotations available Not annotated
Rhabdomyolysis
  •   
  • PD
  •   
  •   
  •   
Pathways

Non-Curated Information

A list of non-curated publications that mention this gene along with other diseases is available.

Downloads

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LinkOuts

Entrez Gene ID:
19
OMIM Accession:
143890
205400
600046
604091
UCSC Genome Browser ID:
NM_005502
Ref Seq NM Accession:
NM_005502
Ref Seq NP Accession:
AAD49849
AAD49851
AAD49852
AAD49853
AAD49854
AAF69513
AAF69516
AAF86276
AAF98175
AAI41817
AAI42694
AAI46857
AAK43526
BAB07875
BAB63210
BAD92076
BAH10664
CAA10005
CAC21428
CAH72442
CAH72443
CAH72444
CAH73579
EAW58992
EAW58993
EAW58994
NP_005493
O95477
Q59HC0
Q9H002
Q9NP93
Q9NS76
Ref Seq NT Accession:
AC_000052
AC_000141
NC_000009
NG_007981
NT_008470
NW_001839236
NW_924539
UniProtKB Accesssion:
ABCA1_HUMAN (O95477)
Ensembl ID:
ENSG00000165029
GenAtlas ID:
ABCA1
GeneCard ID:
ABCA1
SOURCE ID:
ABCA1
MutDB ID:
ABCA1
PromoLign ID:
ortho_3872
HuGE ID:
ABCA1
Comparative Toxicogenomics Acc ID:
19
ModBase:
Q9UN09

Common Searches

Non-Curated Publications

A list of non-curated publications that mention this gene is available.

The PharmGKB is financially supported by the NIH/ NIGMS and is managed at Stanford University (U01GM61374).
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