ABCA12 (ATP binding cassette subfamily A member 12)

Gene

• Entrez ID: 26154
• Gene name: ATP binding cassette subfamily A member 12
• Gene symbol: ABCA12
• Synonyms: ARCI4A, ARCI4B, ICR2B, LI2
• Chromosome: 2
• Chromosome location: 2q35
• 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 subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White). This encoded protein is a member of the ABC1 subfamily, which is the only major ABC subfamily found exclusively in multicellular eukaryotes. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs11891778	G>A,C,T	Likely-pathogenic, likely-benign, pathogenic, benign	Missense variant, synonymous variant, coding sequence variant, non coding transcript variant, stop gained, genic upstream transcript variant
rs28940268	C>T	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs28940269	T>C	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs28940270	C>T	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs28940271	C>T	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs28940568	C>T	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs114863111	G>A,T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant, synonymous variant
rs142196906	T>A,C,G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Non coding transcript variant, coding sequence variant, missense variant
rs149243979	T>A,C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant, synonymous variant, non coding transcript variant
rs149399707	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Genic upstream transcript variant, missense variant, coding sequence variant, non coding transcript variant
rs201542666	G>A,C,T	Likely-pathogenic	Non coding transcript variant, synonymous variant, missense variant, coding sequence variant, genic upstream transcript variant
rs267606622	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs387906285	T>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs755391236	T>A,C	Pathogenic	Stop gained, missense variant, coding sequence variant, non coding transcript variant
rs756771290	T>C	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs757520757	G>A	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs758568142	C>A,T	Likely-pathogenic	Splice donor variant
rs761557390	A>C	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs762065937	C>G,T	Likely-pathogenic	Coding sequence variant, genic upstream transcript variant, missense variant, non coding transcript variant
rs763182554	A>C,G	Pathogenic	Splice donor variant
rs763481375	G>A,T	Pathogenic	Synonymous variant, coding sequence variant, stop gained, non coding transcript variant
rs767707248	G>A	Pathogenic	Genic upstream transcript variant, non coding transcript variant, coding sequence variant, stop gained
rs772046102	G>A,T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant, stop gained
rs886039296	G>A	Likely-pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs1064794286	A>-,AA	Likely-pathogenic	Frameshift variant, coding sequence variant, stop gained, non coding transcript variant
rs1131691611	C>T	Pathogenic	Splice acceptor variant
rs1187032187	C>A,T	Pathogenic	Missense variant, genic upstream transcript variant, stop gained, coding sequence variant, non coding transcript variant
rs1553522866	G>C	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1553523037	C>G	Pathogenic	Splice donor variant
rs1553523093	C>T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1553523630	A>G	Likely-pathogenic	Splice donor variant
rs1553526002	C>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1559120651	->T	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1559134341	A>G	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs1574955196	TC>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1574984736	->G	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1575019786	A>-	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant, genic upstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT017104	hsa-miR-335-5p	Microarray	18185580
MIRT661014	hsa-miR-1249-3p	HITS-CLIP	23824327
MIRT661015	hsa-miR-3679-3p	HITS-CLIP	23824327
MIRT661016	hsa-miR-642b-3p	HITS-CLIP	23824327
MIRT661017	hsa-miR-642a-3p	HITS-CLIP	23824327
MIRT661018	hsa-miR-6730-3p	HITS-CLIP	23824327
MIRT661019	hsa-miR-4287	HITS-CLIP	23824327
MIRT661020	hsa-miR-4685-3p	HITS-CLIP	23824327
MIRT661021	hsa-miR-6734-3p	HITS-CLIP	23824327
MIRT661022	hsa-miR-5088-3p	HITS-CLIP	23824327
MIRT661023	hsa-miR-6887-3p	HITS-CLIP	23824327
MIRT661024	hsa-miR-660-5p	HITS-CLIP	23824327
MIRT661025	hsa-miR-4482-5p	HITS-CLIP	23824327
MIRT661026	hsa-miR-3130-5p	HITS-CLIP	23824327
MIRT661027	hsa-miR-1912	HITS-CLIP	23824327
MIRT661028	hsa-miR-1295b-5p	HITS-CLIP	23824327
MIRT661029	hsa-miR-329-3p	HITS-CLIP	23824327
MIRT661030	hsa-miR-362-3p	HITS-CLIP	23824327

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005102	Function	Signaling receptor binding	IPI	23931754
GO:0005319	Function	Lipid transporter activity	IBA	21873635
GO:0005319	Function	Lipid transporter activity	IDA	16007253
GO:0005319	Function	Lipid transporter activity	TAS
GO:0005515	Function	Protein binding	IPI	23931754
GO:0005524	Function	ATP binding	NAS	12697999
GO:0005737	Component	Cytoplasm	IDA	23931754
GO:0005829	Component	Cytosol	IEA
GO:0005886	Component	Plasma membrane	IDA	23931754
GO:0005886	Component	Plasma membrane	TAS
GO:0006869	Process	Lipid transport	IBA	21873635
GO:0006869	Process	Lipid transport	IDA	16007253
GO:0006869	Process	Lipid transport	NAS	12915478
GO:0010875	Process	Positive regulation of cholesterol efflux	IDA	23931754
GO:0016021	Component	Integral component of membrane	NAS	12697999
GO:0016887	Function	ATPase activity	IEA
GO:0019725	Process	Cellular homeostasis	NAS	12697999
GO:0031424	Process	Keratinization	IEA
GO:0032940	Process	Secretion by cell	IMP	16007253
GO:0033700	Process	Phospholipid efflux	IMP	23931754
GO:0034040	Function	ATPase-coupled lipid transmembrane transporter activity	IC	16007253
GO:0034191	Function	Apolipoprotein A-I receptor binding	IBA	21873635
GO:0034191	Function	Apolipoprotein A-I receptor binding	IPI	23931754
GO:0035627	Process	Ceramide transport	IEA
GO:0042626	Function	ATPase-coupled transmembrane transporter activity	IBA	21873635
GO:0043129	Process	Surfactant homeostasis	IEA
GO:0043231	Component	Intracellular membrane-bounded organelle	IBA	21873635
GO:0045055	Process	Regulated exocytosis	IMP	16007253
GO:0048286	Process	Lung alveolus development	IEA
GO:0055085	Process	Transmembrane transport	TAS
GO:0055088	Process	Lipid homeostasis	IEA
GO:0061436	Process	Establishment of skin barrier	IEA
GO:0072659	Process	Protein localization to plasma membrane	IDA	23931754
GO:0072659	Process	Protein localization to plasma membrane	IMP	23931754
GO:0097209	Component	Epidermal lamellar body	IDA	16007253
GO:0098656	Process	Anion transmembrane transport	IEA
GO:2000010	Process	Positive regulation of protein localization to cell surface	IEA

Other IDs

• MIM: 607800
• HGNC: 14637
• e!Ensembl: ENSG00000144452

Protein

• UniProt ID: Q86UK0
• Protein name: Glucosylceramide transporter ABCA12 (EC 7.6.2.1) (ATP-binding cassette sub-family A member 12) (ATP-binding cassette transporter 12) (ATP-binding cassette 12)
• Protein function: Transports lipids such as glucosylceramides from the outer to the inner leaflet of lamellar granules (LGs) membrane, whereby the lipids are finally transported to the keratinocyte periphery via the trans-Golgi network and LGs and released to the apical surface of the granular keratinocytes to form lipid lamellae in the stratum corneum of the epidermis, which is essential for skin barrier function (PubMed:16007253, PubMed:20869849). In the mean time, participates in the transport of the lamellar granules-associated proteolytic enzymes, in turns regulates desquamation and keratinocyte differentiation (PubMed:19179616). Furthermore, is essential for the regulation of cellular cholesterol homeostasis by regulating ABCA1-dependent cholesterol efflux from macrophages through interaction with NR1H2 and ABCA1 (By similarity). Plays pleiotropic roles in regulating glucose stimulated insulin secretion from beta cells, regulating the morphology and fusion of insulin granules, lipid raft abundance and the actin cytoskeleton (By similarity). Also involved in lung surfactant biogenesis (By similarity).
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF12698	ABC2_membrane_3	896 → 1270		Family
  PF00005	ABC_tran	1361 → 1507	ABC transporter	Domain
  PF12698	ABC2_membrane_3	1744 → 2203		Family
  PF00005	ABC_tran	2273 → 2418	ABC transporter	Domain

• Sequence:

  MASLFHQLQILVWKNWLGVKRQPLWTLVLILWPVIIFIILAITRTKFPPTAKPTCYLAPR
  NLPSTGFFPFLQTLLCDTDSKCKDTPYGPQDLLRRKGIDDALFKDSEILRKSSNLDKDSS
  LSFQSTQVPERRHASLATVFPSPSSDLEIPGTYTFNGSQVLARILGLEKLLKQNSTSEDI
  RRELCDSYSGYIVDDAFSWTFLGRNVFNKFCLSNMTLLESSLQELNKQFSQLSSDPNNQK
  IVFQEIVRMLSFFSQVQEQKAVWQLLSSFPNVFQNDTSLSNLFDVLRKANSVLLVVQKVY
  PRFATNEGFRTLQKSVKHLLYTLDSPAQGDSDNITHVWNEDDGQTLSPSSLAAQLLILEN
  FEDALLNISANSPYIPYLACVRNVTDSLARGSPENLRLLQSTIRFKKSFLRNGSYEDYFP
  PVPEVLKSKLSQLRNLTELLCESETFSLIEKSCQLSDMSFGSLCEESEFDLQLLEAAELG
  TEIAASLLYHDNVISKKVRDLLTGDPSKINLNMDQFLEQALQMNYLENITQLIPIIEAML
  HVNNSADASEKPGQLLEMFKNVEELKEDLRRTTGMSNRTIDKLLAIPIPDNRAEIISQVF
  WLHSCDTNITTPKLEDAMKEFCNLSLSERSRQSYLIGLTLLHYLNIYNFTYKVFFPRKDQ
  KPVEKMMELFIRLKEILNQMASGTHPLLDKMRSLKQMHLPRSVPLTQAMYRSNRMNTPQG
  SFSTISQALCSQGITTEYLTAMLPSSQRPKGNHTKDFLTYKLTKEQIASKYGIPINSTPF
  CFSLYKDIINMPAGPVIWAFLKPMLLGRILYAPYNPVTKAIMEKSNVTLRQLAELREKSQ
  EWMDKSPLFMNSFHLLNQAIPMLQNTLRNPFVQVFVKFSVGLDAVELLKQIDELDILRLK
  LENNIDIIDQLNTLSSLTVNISSCVLYDRIQAAKTIDEMEREAKRLYKSNELFGSVIFKL
  PSNRSWHRGYDSGNVFLPPVIKYTIRMSLKTAQTTRSLRTKIWAPGPHNSPSHNQIYGRA
  FIYLQDSIERAIIELQTGRNSQEIAVQVQAIPYPCFMKDNFLTSVSYSLPIVLMVAWVVF
  IAAFVKKLVYEKDLRLHEYMKMMGVNSCSHFFAWLIESVGFLLVTIVILIIILKFGNILP
  KTNGFILFLYFSDYSFSVIAMSYLISVFFNNTNIAALIGSLIYIIAFFPFIVLVTVENEL
  SYVLKVFMSLLSPTAFSYASQYIARYEEQGIGLQWENMYTSPVQDDTTSFGWLCCLILAD
  SFIYFLIAWYVRNVFPGTYGMAAPWYFPILPSYWKERFGCAEVKPEKSNGLMFTNIMMQN
  TNPSASPEYMFSSNIEPEPKDLTVGVALHGVTKIYGSKVAVDNLNLNFYEGHITSLLGPN
  GAGKTTTISMLTGLFGASAGTIFVYGKDIKTDLHTVRKNMGVCMQHDVLFSYLTTKEHLL
  LYGSIKVPHWTKKQLHEEVKRTLKDTGLYSHRHKRVGTLSGGMKRKLSISIALIGGSRVV
  ILDEPSTGVDPCSRRSIWDVISKNKTARTIILSTHHLDEAEVLSDRIAFLEQGGLRCCGS
  PFYLKEAFGDGYHLTLTKKKSPNLNANAVCDTMAVTAMIQSHLPEAYLKEDIGGELVYVL
  PPFSTKVSGAYLSLLRALDNGMGDLNIGCYGISDTTVEEVFLNLTKESQKNSAMSLEHLT
  QKKIGNSNANGISTPDDLSVSSSNFTDRDDKILTRGERLDGFGLLLKKIMAILIKRFHHT
  RRNWKGLIAQVILPIVFVTTAMGLGTLRNSSNSYPEIQISPSLYGTSEQTAFYANYHPST
  EALVSAMWDFPGIDNMCLNTSDLQCLNKDSLEKWNTSGEPITNFGVCSCSENVQECPKFN
  YSPPHRRTYSSQVIYNLTGQRVENYLISTANEFVQKRYGGWSFGLPLTKDLRFDITGVPA
  NRTLAKVWYDPEGYHSLPAYLNSLNNFLLRVNMSKYDAARHGIIMYSHPYPGVQDQEQAT
  ISSLIDILVALSILMGYSVTTASFVTYVVREHQTKAKQLQHISGIGVTCYWVTNFIYDMV
  FYLVPVAFSIGIIAIFKLPAFYSENNLGAVSLLLLLFGYATFSWMYLLAGLFHETGMAFI
  TYVCVNLFFGINSIVSLSVVYFLSKEKPNDPTLELISETLKRIFLIFPQFCFGYGLIELS
  QQQSVLDFLKAYGVEYPNETFEMNKLGAMFVALVSQGTMFFSLRLLINESLIKKLRLFFR
  KFNSSHVRETIDEDEDVRAERLRVESGAAEFDLVQLYCLTKTYQLIHKKIIAVNNISIGI
  PAGECFGLLGVNGAGKTTIFKMLTGDIIPSSGNILIRNKTGSLGHVDSHSSLVGYCPQED
  ALDDLVTVEEHLYFYARVHGIPEKDIKETVHKLLRRLHLMPFKDRATSMCSYGTKRKLST
  ALALIGKPSILLLDEPSSGMDPKSKRHLWKIISEEVQNKCSVILTSHSMEECEALCTRLA
  IMVNGKFQCIGSLQHIKSRFGRGFTVKVHLKNNKVTMETLTKFMQLHFPKTYLKDQHLSM
  LEYHVPVTAGGVANIFDLLETNKTALNITNFLVSQTTLEEVFINFAKDQKSYETADTSSQ
  GSTISVDSQDDQMES

• Sequence length: 2595