Gene Gene information from NCBI Gene database. Download as csv Download as pdf
Entrez ID	20
Gene name	ATP binding cassette subfamily A member 2
Gene symbol	ABCA2
Synonyms (NCBI Gene)	ABC2IDPOGSA
Chromosome	9
Chromosome location	9q34.3
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

SNP ID	Visualize variation	Clinical significance	Consequence
rs1588511352	C>-	Pathogenic, uncertain-significance	Coding sequence variant, frameshift variant, non coding transcript variant
rs1588512383	TACTCGCGGCG>C	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1588524458	G>A	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs1588525874	->A	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant

58 Show/Hide all (58)

miRTarBase ID	miRNA	Experiments	Reference
MIRT437529	hsa-miR-19b-3p	Immunoprecipitaion	22382630
MIRT682989	hsa-miR-320a	HITS-CLIP	23706177
MIRT682988	hsa-miR-320b	HITS-CLIP	23706177
MIRT682987	hsa-miR-320c	HITS-CLIP	23706177
MIRT682986	hsa-miR-320d	HITS-CLIP	23706177
MIRT682985	hsa-miR-4429	HITS-CLIP	23706177
MIRT682984	hsa-miR-320e	HITS-CLIP	23706177
MIRT682983	hsa-miR-4768-3p	HITS-CLIP	23706177
MIRT682982	hsa-miR-7112-5p	HITS-CLIP	23706177
MIRT682981	hsa-miR-6089	HITS-CLIP	23706177
MIRT682980	hsa-miR-4722-5p	HITS-CLIP	23706177
MIRT682979	hsa-miR-6721-5p	HITS-CLIP	23706177
MIRT682978	hsa-miR-218-1-3p	HITS-CLIP	23706177
MIRT682977	hsa-miR-4644	HITS-CLIP	23706177
MIRT441311	hsa-miR-485-5p	HITS-CLIP	24374217
MIRT441311	hsa-miR-485-5p	HITS-CLIP	24374217
MIRT682989	hsa-miR-320a	HITS-CLIP	23706177
MIRT682988	hsa-miR-320b	HITS-CLIP	23706177
MIRT682987	hsa-miR-320c	HITS-CLIP	23706177
MIRT682986	hsa-miR-320d	HITS-CLIP	23706177
MIRT682985	hsa-miR-4429	HITS-CLIP	23706177
MIRT682984	hsa-miR-320e	HITS-CLIP	23706177
MIRT682983	hsa-miR-4768-3p	HITS-CLIP	23706177
MIRT682982	hsa-miR-7112-5p	HITS-CLIP	23706177
MIRT682981	hsa-miR-6089	HITS-CLIP	23706177
MIRT682980	hsa-miR-4722-5p	HITS-CLIP	23706177
MIRT682979	hsa-miR-6721-5p	HITS-CLIP	23706177
MIRT682978	hsa-miR-218-1-3p	HITS-CLIP	23706177
MIRT682977	hsa-miR-4644	HITS-CLIP	23706177
MIRT757890	hsa-miR-1207-5p	CLIP-seq
MIRT757891	hsa-miR-1275	CLIP-seq
MIRT757892	hsa-miR-1291	CLIP-seq
MIRT757893	hsa-miR-1307	CLIP-seq
MIRT757894	hsa-miR-205	CLIP-seq
MIRT757895	hsa-miR-3614-3p	CLIP-seq
MIRT757896	hsa-miR-3615	CLIP-seq
MIRT757897	hsa-miR-4267	CLIP-seq
MIRT757898	hsa-miR-4269	CLIP-seq
MIRT757899	hsa-miR-4304	CLIP-seq
MIRT757900	hsa-miR-4525	CLIP-seq
MIRT757901	hsa-miR-4638-5p	CLIP-seq
MIRT757902	hsa-miR-4652-5p	CLIP-seq
MIRT757903	hsa-miR-4665-5p	CLIP-seq
MIRT757904	hsa-miR-4711-5p	CLIP-seq
MIRT757905	hsa-miR-4723-5p	CLIP-seq
MIRT757906	hsa-miR-4736	CLIP-seq
MIRT757907	hsa-miR-4763-3p	CLIP-seq
MIRT757908	hsa-miR-625	CLIP-seq
MIRT757909	hsa-miR-637	CLIP-seq
MIRT757910	hsa-miR-4753-5p	CLIP-seq
MIRT2165022	hsa-miR-1207-3p	CLIP-seq
MIRT2165023	hsa-miR-124	CLIP-seq
MIRT2165024	hsa-miR-3136-3p	CLIP-seq
MIRT2165025	hsa-miR-330-3p	CLIP-seq
MIRT2165026	hsa-miR-3714	CLIP-seq
MIRT2165027	hsa-miR-3910	CLIP-seq
MIRT2165028	hsa-miR-4477b	CLIP-seq
MIRT2165029	hsa-miR-506	CLIP-seq

73 Show/Hide all (73)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000166	Function	Nucleotide binding	NAS	12363033
GO:0001573	Process	Ganglioside metabolic process	ISS
GO:0005319	Function	Lipid transporter activity	IBA
GO:0005524	Function	ATP binding	IDA	15999530
GO:0005524	Function	ATP binding	IEA
GO:0005524	Function	ATP binding	ISS
GO:0005764	Component	Lysosome	IDA	11309290
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IDA	15093135
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005765	Component	Lysosomal membrane	ISS
GO:0005765	Component	Lysosomal membrane	NAS	11309290
GO:0005768	Component	Endosome	IDA	11309290
GO:0005768	Component	Endosome	IEA
GO:0005815	Component	Microtubule organizing center	ISS
GO:0005886	Component	Plasma membrane	IDA	24201375
GO:0005886	Component	Plasma membrane	IDA	23137377
GO:0006629	Process	Lipid metabolic process	NAS	11178988
GO:0006684	Process	Sphingomyelin metabolic process	ISS
GO:0006687	Process	Glycosphingolipid metabolic process	ISS
GO:0006869	Process	Lipid transport	IBA
GO:0007626	Process	Locomotory behavior	ISS
GO:0009410	Process	Response to xenobiotic stimulus	TAS	12363033
GO:0010008	Component	Endosome membrane	IDA	15093135
GO:0010008	Component	Endosome membrane	IEA
GO:0010556	Process	Regulation of macromolecule biosynthetic process	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IDA	15999530
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	NAS	11309290, 12363033
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0019218	Process	Regulation of steroid metabolic process	IDA	24201375
GO:0031410	Component	Cytoplasmic vesicle	ISS
GO:0032289	Process	Central nervous system myelin formation	ISS
GO:0032289	Process	Central nervous system myelin formation	ISS
GO:0032383	Process	Regulation of intracellular cholesterol transport	IMP	15238223
GO:0032383	Process	Regulation of intracellular cholesterol transport	ISS
GO:0032384	Process	Negative regulation of intracellular cholesterol transport	IDA	21810484
GO:0032805	Process	Positive regulation of low-density lipoprotein particle receptor catabolic process	IDA	21810484
GO:0042626	Function	ATPase-coupled transmembrane transporter activity	IBA
GO:0042626	Function	ATPase-coupled transmembrane transporter activity	NAS	7766993
GO:0042632	Process	Cholesterol homeostasis	IEP	15238223
GO:0042986	Process	Positive regulation of amyloid precursor protein biosynthetic process	IDA	20704561
GO:0043190	Component	ATP-binding cassette (ABC) transporter complex	NAS	11178988
GO:0043231	Component	Intracellular membrane-bounded organelle	IBA
GO:0045540	Process	Regulation of cholesterol biosynthetic process	IDA	21810484
GO:0045939	Process	Negative regulation of steroid metabolic process	ISS	24201375
GO:0046512	Process	Sphingosine biosynthetic process	IDA	26510981
GO:0048545	Process	Response to steroid hormone	IEP	15238223
GO:0051247	Process	Positive regulation of protein metabolic process	IEA
GO:0055085	Process	Transmembrane transport	IEA
GO:0055085	Process	Transmembrane transport	NAS	7766993
GO:0060049	Process	Regulation of protein glycosylation	ISS	22086926
GO:0061135	Function	Endopeptidase regulator activity	IMP	22086926
GO:0070723	Process	Response to cholesterol	IEP	11178988
GO:0071072	Process	Negative regulation of phospholipid biosynthetic process	IDA	24201375
GO:0090155	Process	Negative regulation of sphingolipid biosynthetic process	IDA	24201375
GO:0090156	Process	Intracellular sphingolipid homeostasis	IDA	26510981
GO:0090370	Process	Negative regulation of cholesterol efflux	IDA	21810484
GO:0099038	Function	Ceramide floppase activity	IDA	24201375
GO:0099040	Process	Ceramide translocation	IDA	24201375
GO:0140328	Function	Floppase activity	IEA
GO:0140359	Function	ABC-type transporter activity	IEA
GO:0150104	Process	Transport across blood-brain barrier	NAS	26590417, 30280653
GO:1901873	Process	Regulation of post-translational protein modification	IMP	22086926
GO:1902004	Process	Positive regulation of amyloid-beta formation	IMP	22086926
GO:1902004	Process	Positive regulation of amyloid-beta formation	ISS	22086926
GO:1902993	Process	Positive regulation of amyloid precursor protein catabolic process	IGI	20704561
GO:1902993	Process	Positive regulation of amyloid precursor protein catabolic process	IMP	22086926
GO:1904375	Process	Regulation of protein localization to cell periphery	ISS	22086926
GO:1905601	Process	Negative regulation of receptor-mediated endocytosis involved in cholesterol transport	IDA	21810484
GO:2000008	Process	Regulation of protein localization to cell surface	ISS	22086926

MIM	HGNC	e!Ensembl
600047	32	ENSG00000107331

Q9BZC7

Protein name

ATP-binding cassette sub-family A member 2 (EC 7.6.2.-) (ATP-binding cassette transporter 2) (ATP-binding cassette 2)

Protein function

Probable lipid transporter that modulates cholesterol sequestration in the late endosome/lysosome by regulating the intracellular sphingolipid metabolism, in turn participates in cholesterol homeostasis (Probable) (PubMed:15238223, PubMed:218104

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF12698	ABC2_membrane_3	1692 → 2008		Family
PF12698	ABC2_membrane_3	684 → 912		Family
PF00005	ABC_tran	1007 → 1151	ABC transporter	Domain
PF00005	ABC_tran	2070 → 2214	ABC transporter	Domain

Tissue specificity

TISSUE SPECIFICITY: [Isoform 3]: Highly expressed in the brain,peripheral blood leukocytes and ovary, whereas lower levels of expression is observed in kidney and liver. {ECO:0000269|PubMed:11309290, ECO:0000269|PubMed:15093135}.; TISSUE SPECIFICITY: [Iso

Sequence

MGFLHQLQLLLWKNVTLKRRSPWVLAFEIFIPLVLFFILLGLRQKKPTISVKEAFYTAAP
LTSAGILPVMQSLCPDGQRDEFGFLQYANSTVTQLLERLDRVVEEGNLFDPARPSLGSEL
EALRQHLEALSAGPGTSGSHLDRSTVSSFSLDSVARNPQELWRFLTQNLSLPNSTAQALL
AARVDPPEVYHLLFGPSSALDSQSGLHKGQEPWSRLGGNPLFRMEELLLAPALLEQLTCT
PGSGELGRILTVPESQKGALQGYRDAVCSGQAAARARRFSGLSAELRNQLDVAKVSQQLG
LDAPNGSDSSPQAPPPRRLQALLGDLLDAQKVLQDVDVLSALALLLPQGACTGRTPGPPA
SGAGGAANGTGAGAVMGPNATAEEGAPSAAALATPDTLQGQCSAFVQLWAGLQPILCGNN
RTIEPEALRRGNMSSLGFTSKEQRNLGLLVHLMTSNPKILYAPAGSEVDRVILKANETFA
FVGNVTHYAQVWLNISAEIRSFLEQGRLQQHLRWLQQYVAELRLHPEALNLSLDELPPAL
RQDNFSLPSGMALLQQLDTIDNAACGWIQFMSKVSVDIFKGFPDEESIVNYTLNQAYQDN
VTVFASVIFQTRKDGSLPPHVHYKIRQNSSFTEKTNEIRRAYWRPGPNTGGRFYFLYGFV
WIQDMMERAIIDTFVGHDVVEPGSYVQMFPYPCYTRDDFLFVIEHMMPLCMVISWVYSVA
MTIQHIVAEKEHRLKEVMKTMGLNNAVHWVAWFITGFVQLSISVTALTAILKYGQVLMHS
HVVIIWLFLAVYAVATIMFCFLVSVLYSKAKLASACGGIIYFLSYVPYMYVAIREEVAHD
KITAFEKCIASLMSTTAFGLGSKYFALYEVAGVGIQWHTFSQSPVEGDDFNLLLAVTMLM
VDAVVYGILTWYIEAVHPGMYGLPRPWYFPLQKSYWLGSGRTEAWEWSWPWARTPRLSVM
EEDQACAMESRRFEETRGMEEEPTHLPLVVCVDKLTKVYKDDKKLALNKLSLNLYENQVV
SFLGHNGAGKTTTMSILTGLFPPTSGSATIYGHDIRTEMDEIRKNLGMCPQHNVLFDRLT
VEEHLWFYSRLKSMAQEEIRREMDKMIEDLELSNKRHSLVQTLSGGMKRKLSVAIAFVGG
SRAIILDEPTAGVDPYARRAIWDLILKYKPGRTILLSTHHMDEADLLGDRIAIISHGKLK
CCGSPLFLKGTYGDGYRLTLVKRPAEPGGPQEPGLASSPPGRAPLSSCSELQVSQFIRKH
VASCLLVSDTSTELSYILPSEAAKKGAFERLFQHLERSLDALHLSSFGLMDTTLEEVFLK
VSEEDQSLENSEADVKESRKDVLPGAEGPASGEGHAGNLARCSELTQSQASLQSASSVGS
ARGDEGAGYTDVYGDYRPLFDNPQDPDNVSLQEVEAEALSRVGQGSRKLDGGWLKVRQFH
GLLVKRFHCARRNSKALFSQILLPAFFVCVAMTVALSVPEIGDLPPLVLSPSQYHNYTQP
RGNFIPYANEERREYRLRLSPDASPQQLVSTFRLPSGVGATCVLKSPANGSLGPTLNLSS
GESRLLAARFFDSMCLESFTQGLPLSNFVPPPPSPAPSDSPASPDEDLQAWNVSLPPTAG
PEMWTSAPSLPRLVREPVRCTCSAQGTGFSCPSSVGGHPPQMRVVTGDILTDITGHNVSE
YLLFTSDRFRLHRYGAITFGNVLKSIPASFGTRAPPMVRKIAVRRAAQVFYNNKGYHSMP
TYLNSLNNAILRANLPKSKGNPAAYGITVTNHPMNKTSASLSLDYLLQGTDVVIAIFIIV
AMSFVPASFVVFLVAEKSTKAKHLQFVSGCNPIIYWLANYVWDMLNYLVPATCCVIILFV
FDLPAYTSPTNFPAVLSLFLLYGWSITPIMYPASFWFEVPSSAYVFLIVINLFIGITATV
ATFLLQLFEHDKDLKVVNSYLKSCFLIFPNYNLGHGLMEMAYNEYINEYYAKIGQFDKMK
SPFEWDIVTRGLVAMAVEGVVGFLLTIMCQYNFLRRPQRMPVSTKPVEDDVDVASERQRV
LRGDADNDMVKIENLTKVYKSRKIGRILAVDRLCLGVRPGECFGLLGVNGAGKTSTFKML
TGDESTTGGEAFVNGHSVLKELLQVQQSLGYCPQCDALFDELTAREHLQLYTRLRGISWK
DEARVVKWALEKLELTKYADKPAGTYSGGNKRKLSTAIALIGYPAFIFLDEPTTGMDPKA
RRFLWNLILDLIKTGRSVVLTSHSMEECEALCTRLAIMVNGRLRCLGSIQHLKNRFGDGY
MITVRTKSSQSVKDVVRFFNRNFPEAMLKERHHTKVQYQLKSEHISLAQVFSKMEQVSGV
LGIEDYSVSQTTLDNVFVNFAKKQSDNLEQQETEPPSALQSPLGCLLSLLRPRSAPTELR
ALVADEPEDLDTEDEGLISFEEERAQLSFNTDTLC

Sequence length

2435

Interactions

View interactions

KEGG Pathway	Reactome Pathway
ABC transporters	ABC transporters in lipid homeostasis
Lysosome

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)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Ataxia with Dysarthria	Pathogenic	rs1588511352	RCV000790425	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual developmental disorder with poor growth and with or without seizures or ataxia	Likely pathogenic; Pathogenic	rs2131443090, rs2538191594, rs2491538919, rs2491500575, rs2491492843, rs1588524458, rs1588525874, rs1588512383	RCV002071017 RCV003136702 RCV003314409 RCV003323265 RCV003330145 RCV001027878 RCV001027879 RCV001027880 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
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. Show/Hide Unknown Diseases (16)
ABCA2-related disorder	Likely benign; Uncertain significance; Benign; Conflicting classifications of pathogenicity	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	CTD	35663546	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE NON-SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet, Orphanet Disgenet, Orphanet	29302074	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Likely benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CUTANEOUS MASTOCYTOSIS	—	GWAS catalog	32752121	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MASTOCYTOSIS	—	GWAS catalog	32752121	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet, GenCC Disgenet, GenCC	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYSTEMIC MASTOCYTOSIS	—	GWAS catalog	32752121	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining Show/Hide Text Mining Associations (42)
Acoustic Neuroma	Acoustic Neuroma	BEFREE	15850583, 28394785		★★★★★ ★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Alzheimer disease	Pubtator	18336955, 29224028	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Alzheimer Disease, Early Onset	Alzheimer disease	BEFREE	15649702, 18336955, 18348684		★★★★★ ★☆☆☆☆ Found in Text Mining only
Arteriovenous Malformations, Cerebral	Cerebral arteriovenous malformation	BEFREE	31064679		★★★★★ ★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain Neoplasms	BEFREE	24305708		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	15182435	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	26820484		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiovascular Diseases	Cardiovascular Diseases	BEFREE	29223352		★★★★★ ★☆☆☆☆ Found in Text Mining only
Childhood Acute Lymphoblastic Leukemia	Lymphoblastic Leukemia	BEFREE	28744141, 31214760		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Colonic neoplasm	Pubtator	17541169	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

ABCA2 (ATP binding cassette subfamily A member 2)

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