Gene Gene information from NCBI Gene database.
Entrez ID 19
Gene name ATP binding cassette subfamily A member 1
Gene symbol ABCA1
Synonyms (NCBI Gene)
ABC-1ABC1CERPHDLCQTL13HDLDT1HPALP1TGD
Chromosome 9
Chromosome location 9q31.1
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 s
SNPs SNP information provided by dbSNP.
27
SNP ID Visualize variation Clinical significance Consequence
rs2853574 G>A Pathogenic Missense variant, coding sequence variant, non coding transcript variant
rs2853578 T>A,C Pathogenic Missense variant, coding sequence variant, non coding transcript variant
rs9282541 G>A Conflicting-interpretations-of-pathogenicity, benign Missense variant, non coding transcript variant, coding sequence variant
rs28933692 C>A,T Pathogenic Missense variant, non coding transcript variant, coding sequence variant
rs28937313 T>C Pathogenic Missense variant, non coding transcript variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
696
miRTarBase ID miRNA Experiments Reference
MIRT003672 hsa-miR-33a-5p Luciferase reporter assay 20466885
MIRT003672 hsa-miR-33a-5p Luciferase reporter assay 20466885
MIRT003672 hsa-miR-33a-5p Luciferase reporter assay 20466885
MIRT003672 hsa-miR-33a-5p Luciferase reporter assay 20466882
MIRT003672 hsa-miR-33a-5p Luciferase reporter assay 20466882
Transcription factors Transcription factors information provided by TRRUST V2 database.
17
Transcription factor Regulation Reference
FOXA1 Repression 24807696
FOXA2 Repression 24807696
NFKB1 Repression 17135302
NR1H2 Activation 16141411
NR1H3 Activation 11264984;16141411;18580406;19201410
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
123
GO ID Ontology Definition Evidence Reference
GO:0000166 Function Nucleotide binding IEA
GO:0002790 Process Peptide secretion IEA
GO:0005102 Function Signaling receptor binding IPI 23931754
GO:0005515 Function Protein binding IPI 12084722, 14754908, 15469992, 16192269, 16443932, 23931754, 25170080, 30458687
GO:0005524 Function ATP binding IDA 11700048
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
600046 29 ENSG00000165029
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O95477
Protein name Phospholipid-transporting ATPase ABCA1 (EC 7.6.2.1) (ATP-binding cassette sub-family A member 1) (ATP-binding cassette transporter 1) (ABC-1) (ATP-binding cassette 1) (Cholesterol efflux regulatory protein)
Protein function Catalyzes the translocation of specific phospholipids from the cytoplasmic to the extracellular/lumenal leaflet of membrane coupled to the hydrolysis of ATP (PubMed:24097981, PubMed:35974019). Thereby, participates in phospholipid transfer to ap
PDB 5XJY , 7ROQ , 7TBW , 7TBY , 7TBZ , 7TC0 , 7TDT
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF12698 ABC2_membrane_3 594 841 Family
PF00005 ABC_tran 916 1061 ABC transporter Domain
PF12698 ABC2_membrane_3 1344 1869 Family
PF00005 ABC_tran 1929 2073 ABC transporter Domain
Tissue specificity TISSUE SPECIFICITY: Widely expressed, but most abundant in macrophages.
Sequence
MACWPQLRLLLWKNLTFRRRQTCQLLLEVAWPLFIFLILISVRLSYPPYEQHECHFPNKA
MPSAGTLPWVQGIICNANNPCFRYPTPGEAPGVVGNFNKSIVARLFSDARRLLLYSQKDT
SMKDMRKVLRTLQQIKKSSSNLKLQDFLVDNETFSGFLYHNLSLPKSTVDKMLRADVILH
KVFLQGYQLHLTSLCNGSKSEEMIQLGDQEVSELCGLPREKLAAAERVLRSNMDILKPIL
RTLNSTSPFPSKELAEATKTLLHSLGTLAQELFSMRSWSDMRQEVMFLTNVNSSSSSTQI
YQAVSRIVCGHPEGGGLKIKSLNWYEDNNYKALFGGNGTEEDAETFYDNSTTPYCNDLMK
NLESSPLSRIIWKALKPLLVGKILYTPDTPATRQVMAEVNKTFQELAVFHDLEGMWEELS
PKIWTFMENSQEMDLVRMLLDSRDNDHFWEQQLDGLDWTAQDIVAFLAKHPEDVQSSNGS
VYTWREAFNETNQAIRTISRFMECVNLNKLEPIATEVWLINKSMELLDERKFWAGIVFTG
ITPGSIELPHHVKYKIRMDIDNVERTNKIKDGYWDPGPRADPFEDMRYVWGGFAYLQDVV
EQAIIRVLTGTEKKTGVYMQQMPYPCYVDDIFLRVMSRSMPLFMTLAWIYSVAVIIKGIV
YEKEARLKETMRIMGLDNSILWFSWFISSLIPLLVSAGLLVVILKLGNLLPYSDPSVVFV
FLSVFAVVTILQCFLISTLFSRANLAAACGGIIYFTLYLPYVLCVAWQDYVGFTLKIFAS
LLSPVAFGFGCEYFALFEEQGIGVQWDNLFESPVEEDGFNLTTSVSMMLFDTFLYGVMTW
Y
IEAVFPGQYGIPRPWYFPCTKSYWFGEESDEKSHPGSNQKRISEICMEEEPTHLKLGVS
IQNLVKVYRDGMKVAVDGLALNFYEGQITSFLGHNGAGKTTTMSILTGLFPPTSGTAYIL
GKDIRSEMSTIRQNLGVCPQHNVLFDMLTVEEHIWFYARLKGLSEKHVKAEMEQMALDVG
LPSSKLKSKTSQLSGGMQRKLSVALAFVGGSKVVILDEPTA
GVDPYSRRGIWELLLKYRQ
GRTIILSTHHMDEADVLGDRIAIISHGKLCCVGSSLFLKNQLGTGYYLTLVKKDVESSLS
SCRNSSSTVSYLKKEDSVSQSSSDAGLGSDHESDTLTIDVSAISNLIRKHVSEARLVEDI
GHELTYVLPYEAAKEGAFVELFHEIDDRLSDLGISSYGISETTLEEIFLKVAEESGVDAE
TSDGTLPARRNRRAFGDKQSCLRPFTEDDAADPNDSDIDPESRETDLLSGMDGKGSYQVK
GWKLTQQQFVALLWKRLLIARRSRKGFFAQIVLPAVFVCIALVFSLIVPPFGKYPSLELQ
PWMYNEQYTFVSNDAPEDTGTLELLNALTKDPGFGTRCMEGNPIPDTPCQAGEEEWTTAP
VPQTIMDLFQNGNWTMQNPSPACQCSSDKIKKMLPVCPPGAGGLPPPQRKQNTADILQDL
TGRNISDYLVKTYVQIIAKSLKNKIWVNEFRYGGFSLGVSNTQALPPSQEVNDAIKQMKK
HLKLAKDSSADRFLNSLGRFMTGLDTKNNVKVWFNNKGWHAISSFLNVINNAILRANLQK
GENPSHYGITAFNHPLNLTKQQLSEVALMTTSVDVLVSICVIFAMSFVPASFVVFLIQER
VSKAKHLQFISGVKPVIYWLSNFVWDMCNYVVPATLVIIIFICFQQKSYVSSTNLPVLAL
LLLLYGWSITPLMYPASFVFKIPSTAYVVLTSVNLFIGINGSVATFVLELFTDNKLNNIN
DILKSVFLIFPHFCLGRGLIDMVKNQAMADALERFGENRFVSPLSWDLVGRNLFAMAVEG
VVFFLITVL
IQYRFFIRPRPVNAKLSPLNDEDEDVRRERQRILDGGGQNDILEIKELTKI
YRRKRKPAVDRICVGIPPGECFGLLGVNGAGKSSTFKMLTGDTTVTRGDAFLNKNSILSN
IHEVHQNMGYCPQFDAITELLTGREHVEFFALLRGVPEKEVGKVGEWAIRKLGLVKYGEK
YAGNYSGGNKRKLSTAMALIGGPPVVFLDEPTT
GMDPKARRFLWNCALSVVKEGRSVVLT
SHSMEECEALCTRMAIMVNGRFRCLGSVQHLKNRFGDGYTIVVRIAGSNPDLKPVQDFFG
LAFPGSVLKEKHRNMLQYQLPSSLSSLARIFSILSQSKKRLHIEDYSVSQTTLDQVFVNF
AKDQSDDDHLKDLSLHKNQTVVDVAVLTSFLQDEKVKESYV
Sequence length 2261
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
85
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
ABCA1-related disorder Likely pathogenic; Pathogenic rs137854494, rs146292819, rs2853574 RCV004532322
RCV000277325
RCV000778870
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
ABCA1-related dyslipidemia Pathogenic rs908256532 RCV003389311
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cardiovascular phenotype Likely pathogenic; Pathogenic rs375247413, rs1832453675, rs146292819, rs780321144, rs2538177209 RCV004990563
RCV005455823
RCV002348116
RCV004374980
RCV004521420
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Colorectal cancer Likely pathogenic rs375247413 RCV005925578
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign; Likely benign; Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ALZHEIMERS DISEASE Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 31795847
★☆☆☆☆
Found in Text Mining only
Age related macular degeneration Age-related macular degeneration BEFREE 15829498, 20385819, 21447678, 21613373, 21665990, 24223199, 24498989, 24608419, 24970616, 26608582, 27693409, 28943268, 28973423, 30185655, 30864945
★☆☆☆☆
Found in Text Mining only
Age related macular degeneration Age-related macular degeneration GWASDB_DG 21665990
★☆☆☆☆
Found in Text Mining only
Age related macular degeneration Age-related macular degeneration GWASCAT_DG 26691988
★☆☆☆☆
Found in Text Mining only
Alagille Syndrome Alagille syndrome Pubtator 15210845 Associate
★☆☆☆☆
Found in Text Mining only
Allergic rhinitis (disorder) Allergic rhinitis GWASCAT_DG 25085501
★☆☆☆☆
Found in Text Mining only
Alzheimer Disease Alzheimer disease Pubtator 17324514, 19606474, 20079340, 20571217, 23181436, 28943632, 29605487, 31167810, 34757660, 35361255, 36411364, 36889459, 37204126, 37598468 Associate
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Alzheimer disease, familial, type 3 Alzheimer disease BEFREE 28241068
★☆☆☆☆
Found in Text Mining only
Alzheimer Disease, Late Onset Alzheimer disease BEFREE 15288432, 16725228, 24081377, 29563219, 31641056
★☆☆☆☆
Found in Text Mining only
Alzheimer`s Disease Alzheimer disease GWASCAT_DG 30805717
★☆☆☆☆
Found in Text Mining only