Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs Other IDs Associated diseases
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

Show/Hide all (4)

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

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

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	684 → 912		Family
PF00005	ABC_tran	1007 → 1151	ABC transporter	Domain
PF12698	ABC2_membrane_3	1692 → 2008		Family
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

104

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Ataxia with Dysarthria	Pathogenic	rs1588511352	RCV000790425
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

Show/Hide Unknown Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
ABCA2-related disorder	Likely benign; Uncertain significance; Benign; Conflicting classifications of pathogenicity	rs149871834, rs1389978024, rs547600750, rs764315344, rs747266171, rs200952224, rs2131439130, rs202013393, rs149292740, rs546150662, rs111334624, rs1383480862, rs34039859, rs376809252, rs775254549 View all (29 more)	RCV003941022 RCV003404144 RCV003396847 RCV003414125 RCV003418862 RCV003954210 RCV003919234 RCV003954211 RCV003939270 RCV003909456 RCV003909501 RCV003929802 RCV003974539 RCV003906819 RCV003964551 RCV003979580 RCV003912183 RCV003977183 RCV003979395 RCV003959556 RCV003929434 RCV003941431 RCV003939588 RCV003951578 RCV003924503 RCV003971393 RCV003917329 RCV003931995 RCV003924670 RCV003942172 RCV003942248 RCV003954608 RCV003976996 RCV003971826 RCV003966791 RCV003981328 RCV003976304 RCV000626004 RCV000626005 RCV003926052 RCV003918468 RCV003936032 RCV003923238 RCV003978034
Cholangiocarcinoma	Likely benign	rs201649376	RCV005933203
Clear cell carcinoma of kidney	Benign	rs142807525	RCV005913395
Familial cancer of breast	Benign	rs142807525	RCV005913394
Gastric cancer	Likely benign	rs546150662	RCV005936871
Hepatocellular carcinoma	Benign	rs4880186	RCV005914941
Lung cancer	Benign	rs4880186	RCV005914942
Thyroid cancer, nonmedullary, 1	Benign	rs73564322	RCV005908633
Uterine corpus endometrial carcinoma	Benign	rs142807525	RCV005913396

Show/Hide Text Mining Associations (18)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alzheimer Disease	Associate	18336955, 29224028
Carcinoma Hepatocellular	Associate	15182435
Colonic Neoplasms	Associate	17541169
Focal Cortical Dysplasia	Associate	34301297
Focal cortical dysplasia of Taylor	Associate	34301297
Leukemia	Associate	39216403
Leukemia Myeloid	Associate	39216403
Lung Neoplasms	Associate	15150577
Lupus Erythematosus Systemic	Associate	19387463
Mastocytosis Cutaneous	Associate	32752121
Myasthenia Gravis	Associate	25246735
Neoplasm Residual	Stimulate	24145140
Neoplasms	Associate	15182435, 40641097
Neutropenia	Associate	32559325
Osteoporosis	Associate	36736467
Parkinson Disease	Associate	36736467
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	38039756
Tuberculosis Multidrug Resistant	Inhibit	24145140

ABCA2 (ATP binding cassette subfamily A member 2)