ABCA2 (ATP binding cassette subfamily A member 2)

Gene

• Entrez ID: 20
• Gene name: ATP binding cassette subfamily A member 2
• Gene symbol: ABCA2
• Synonyms: ABC2, IDPOGSA
• 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

SNPs

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

miRNA

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

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	NAS	12363033
GO:0001573	Process	Ganglioside metabolic process	ISS
GO:0005319	Function	Lipid transporter activity	IBA	21873635
GO:0005524	Function	ATP binding	IDA	15999530
GO:0005524	Function	ATP binding	ISS
GO:0005764	Component	Lysosome	IDA	11309290
GO:0005765	Component	Lysosomal membrane	ISS
GO:0005765	Component	Lysosomal membrane	NAS	11309290
GO:0005768	Component	Endosome	IDA	11309290
GO:0005815	Component	Microtubule organizing center	ISS
GO:0005886	Component	Plasma membrane	IDA	23137377, 24201375
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IDA	15238223
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	21873635
GO:0007626	Process	Locomotory behavior	ISS
GO:0010008	Component	Endosome membrane	IEA
GO:0010872	Process	Regulation of cholesterol esterification	IDA	24201375
GO:0010872	Process	Regulation of cholesterol esterification	IMP	15238223
GO:0016020	Component	Membrane	HDA	19946888
GO:0016021	Component	Integral component of membrane	IDA	15999530
GO:0016021	Component	Integral component of membrane	NAS	11309290, 12363033
GO:0016887	Function	ATPase activity	IDA	15999530
GO:0031410	Component	Cytoplasmic vesicle	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:0042493	Process	Response to drug	TAS	12363033
GO:0042626	Function	ATPase-coupled transmembrane transporter activity	IBA	21873635
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	21873635
GO:0045540	Process	Regulation of cholesterol biosynthetic process	IDA	21810484
GO:0046512	Process	Sphingosine biosynthetic process	IDA	26510981
GO:0048545	Process	Response to steroid hormone	IEP	15238223
GO:0052548	Process	Regulation of endopeptidase activity	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	Cellular 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:0150104	Process	Transport across blood-brain barrier	NAS	26590417, 30280653
GO:0150110	Process	Negative regulation of cholesterol esterification	IDA	21810484
GO:0150110	Process	Negative regulation of cholesterol esterification	ISS	24201375
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:1905598	Process	Negative regulation of low-density lipoprotein receptor activity	IDA	21810484
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

Other IDs

• MIM: 600047
• HGNC: 32
• e!Ensembl: ENSG00000107331

Protein

• UniProt ID: 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

• 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