Human Gene ABCA12 (ENST00000272895.12) from GENCODE V44
  Description: Homo sapiens ATP binding cassette subfamily A member 12 (ABCA12), transcript variant 3, non-coding RNA. (from RefSeq NR_103740)
RefSeq Summary (NM_173076): 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].
Gencode Transcript: ENST00000272895.12
Gencode Gene: ENSG00000144452.15
Transcript (Including UTRs)
   Position: hg38 chr2:214,931,542-215,138,626 Size: 207,085 Total Exon Count: 53 Strand: -
Coding Region
   Position: hg38 chr2:214,932,634-215,138,208 Size: 205,575 Coding Exon Count: 53 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:214,931,542-215,138,626)mRNA (may differ from genome)Protein (2595 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ABCAC_HUMAN
DESCRIPTION: RecName: Full=ATP-binding cassette sub-family A member 12; AltName: Full=ATP-binding cassette transporter 12; Short=ATP-binding cassette 12;
FUNCTION: Probable transporter involved in lipid homeostasis.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
TISSUE SPECIFICITY: Mainly expressed in the stomach, placenta, testis and fetal brain.
DOMAIN: Multifunctional polypeptide with two homologous halves, each containing an hydrophobic membrane-anchoring domain and an ATP binding cassette (ABC) domain (By similarity).
DISEASE: Note=ABCA12 mutations are a cause of different subtypes of autosomal recessive congenital ichthyosis (ARCI), including Harlequin ichthyosis (HI), lamellar ichthyosis (LI) and non- bullous congenital ichthyosiform erythroderma (NCIE). HI shows the most severe phenotype. NCIE and LI are clinically characterized by fine, whitish scales on a background of erythematous skin, and large, thick, dark scales over the entire body without serious background erythroderma, respectively.
DISEASE: Defects in ABCA12 are the cause of ichthyosis harlequin (HI) [MIM:242500]. A very severe skin disorder in which the neonate is born with a thick covering of armor-like scales. The skin dries out to form hard diamond-shaped plaques separated by fissures, resembling 'armor plating'. The normal facial features are severely affected, with distortion of the lips (eclabion), eyelids (ectropion), ears, and nostrils. Affected babies are often born prematurely and rarely survive the perinatal period.
DISEASE: Defects in ABCA12 are the cause of ichthyosis lamellar type 2 (LI2) [MIM:601277]. A non-bullous ichthyosis, a skin disorder characterized by abnormal cornification of the epidermis. It is one the most severe forms of ichthyoses apparent at birth and persisting throughout life. LI patients are born encased in a tight, shiny, translucent covering called collodion membrane. Over the first weeks of life, the collodion membrane is gradually replaced by generalized large, dark brown, plate-like scales with minimal to no erythroderma. Tautness of facial skin commonly results in ectropion, eclabium and scarring alopecia of the scalp. Common complications are severe heat intolerance and recurrent ear infections.
DISEASE: Defects in ABCA12 are a cause of erythroderma, ichthyosiform, congenital non-bullous (NCIE) [MIM:242100]. A non- bullous ichthyosis, a skin disorder characterized by abnormal cornification of the epidermis. Most affected individuals are born with a tight, shiny, translucent covering called collodion membrane. The collodion membrane subsequently evolves into generalized scaling and intense redness of the skin. Clinical features are milder than in lamellar ichthyoses and demonstrate a greater variability in the intensity of erythema, size and type of scales. In contrast to lamellar ichthyoses, scales are usually white, fine and powdery, and palms and soles are severely affected. Patients suffer from palmoplantar keratoderma, often with painful fissures, digital contractures, and loss of pulp volume.
SIMILARITY: Belongs to the ABC transporter superfamily. ABCA family.
SIMILARITY: Contains 2 ABC transporter domains.
SEQUENCE CAUTION: Sequence=AAN40735.1; Type=Erroneous initiation;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/ABCA12";
WEB RESOURCE: Name=ABCMdb; Note=Database for mutations in ABC proteins; URL="http://abcmutations.hegelab.org/proteinDetails?uniprot_id=Q86UK0";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: ABCA12
Diseases sorted by gene-association score: ichthyosis, congenital, autosomal recessive 4b* (1702), ichthyosis, congenital, autosomal recessive 4a* (1231), abca12-related autosomal recessive congenital ichthyosis* (200), autosomal recessive congenital ichthyosis* (194), congenital ichthyosiform erythroderma* (174), ichthyosis (30), ectropion (18), cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome (11), diabetes mellitus, insulin-dependent, 13 (11), ichthyosis vulgaris (11), skin disease (7), eyelid disease (6), ichthyosis, congenital, autosomal recessive 1 (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.39 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 31.81 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -108.80418-0.260 Picture PostScript Text
3' UTR -285.801092-0.262 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003593 - AAA+_ATPase
IPR026082 - ABC_A
IPR003439 - ABC_transporter-like
IPR017871 - ABC_transporter_CS

Pfam Domains:
PF00005 - ABC transporter

ModBase Predicted Comparative 3D Structure on Q86UK0
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005102 receptor binding
GO:0005215 transporter activity
GO:0005319 lipid transporter activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016887 ATPase activity
GO:0034040 lipid-transporting ATPase activity
GO:0034191 apolipoprotein A-I receptor binding
GO:0042626 ATPase activity, coupled to transmembrane movement of substances

Biological Process:
GO:0006869 lipid transport
GO:0010875 positive regulation of cholesterol efflux
GO:0019725 cellular homeostasis
GO:0030216 keratinocyte differentiation
GO:0031424 keratinization
GO:0032940 secretion by cell
GO:0033700 phospholipid efflux
GO:0035627 ceramide transport
GO:0043129 surfactant homeostasis
GO:0045055 regulated exocytosis
GO:0048286 lung alveolus development
GO:0055085 transmembrane transport
GO:0055088 lipid homeostasis
GO:0061436 establishment of skin barrier
GO:0072659 protein localization to plasma membrane
GO:2000010 positive regulation of protein localization to cell surface

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0097209 epidermal lamellar body


-  Descriptions from all associated GenBank mRNAs
  AY219711 - Homo sapiens ABCA12 transporter subfamily A mRNA, complete cds.
AK123578 - Homo sapiens cDNA FLJ41584 fis, clone CTONG2020445, highly similar to ATP-binding cassette sub-family A member 12.
BC144073 - Homo sapiens cDNA clone IMAGE:9052593, containing frame-shift errors.
AF418105 - Homo sapiens ATP-binding cassette transporter family A member 12 mRNA, complete cds.
AY033486 - Homo sapiens ATP-binding cassette transporter family A member 12 (ABCA12) mRNA, complete cds.
BC156327 - Synthetic construct Homo sapiens clone IMAGE:100061792, MGC:190103 ATP-binding cassette, sub-family A (ABC1), member 12 (ABCA12) mRNA, encodes complete protein.
AK096597 - Homo sapiens cDNA FLJ39278 fis, clone OCBBF2010863, weakly similar to ATP-BINDING CASSETTE, SUB-FAMILY A, MEMBER 1.
JD144813 - Sequence 125837 from Patent EP1572962.
JD083014 - Sequence 64038 from Patent EP1572962.
JD083108 - Sequence 64132 from Patent EP1572962.
JD181897 - Sequence 162921 from Patent EP1572962.
JD134947 - Sequence 115971 from Patent EP1572962.
JD507825 - Sequence 488849 from Patent EP1572962.
JD302039 - Sequence 283063 from Patent EP1572962.
AL080207 - Homo sapiens mRNA; cDNA DKFZp434G232 (from clone DKFZp434G232).
JD334302 - Sequence 315326 from Patent EP1572962.
JD363422 - Sequence 344446 from Patent EP1572962.
JD294574 - Sequence 275598 from Patent EP1572962.
JD444960 - Sequence 425984 from Patent EP1572962.
JD560025 - Sequence 541049 from Patent EP1572962.
JD301381 - Sequence 282405 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa02010 - ABC transporters

Reactome (by CSHL, EBI, and GO)

Protein Q86UK0 (Reactome details) participates in the following event(s):

R-HSA-5682285 ABCA12 transports lipids from cytosol to extracellular region
R-HSA-1369062 ABC transporters in lipid homeostasis
R-HSA-382556 ABC-family proteins mediated transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: ABC12, ABCAC_HUMAN, ENST00000272895.1, ENST00000272895.10, ENST00000272895.11, ENST00000272895.2, ENST00000272895.3, ENST00000272895.4, ENST00000272895.5, ENST00000272895.6, ENST00000272895.7, ENST00000272895.8, ENST00000272895.9, NR_103740, Q53QE2, Q53S55, Q86UK0, Q8IZW6, Q96JT3, Q9Y4M5, uc002vew.1, uc002vew.2, uc002vew.3, uc002vew.4
UCSC ID: ENST00000272895.12
RefSeq Accession: NM_173076
Protein: Q86UK0 (aka ABCAC_HUMAN or AB12_HUMAN)
CCDS: CCDS33372.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene ABCA12:
li-ar (Autosomal Recessive Congenital Ichthyosis)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.