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    ABCA12 ATP binding cassette subfamily A member 12 [ Homo sapiens (human) ]

    Gene ID: 26154, updated on 9-Dec-2024

    Summary

    Official Symbol
    ABCA12provided by HGNC
    Official Full Name
    ATP binding cassette subfamily A member 12provided by HGNC
    Primary source
    HGNC:HGNC:14637
    See related
    Ensembl:ENSG00000144452 MIM:607800; AllianceGenome:HGNC:14637
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LI2; ICR2B; ARCI4A; ARCI4B
    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]
    Expression
    Biased expression in skin (RPKM 10.7) and colon (RPKM 0.6) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See ABCA12 in Genome Data Viewer
    Location:
    2q35
    Exon count:
    55
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (214931542..215138626, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (215416237..215623360, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (215796266..216003349, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA host gene 31 Neighboring gene small nucleolar RNA, H/ACA box 70I Neighboring gene ribosomal protein L10 pseudogene 6 Neighboring gene NANOG hESC enhancer GRCh37_chr2:215769194-215769695 Neighboring gene uncharacterized LOC124906117 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:216028241-216028408 Neighboring gene uncharacterized LOC124907974 Neighboring gene MPRA-validated peak4041 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:216136088-216136636 Neighboring gene long intergenic non-protein coding RNA 2862

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ41584, DKFZp434G232

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ABC-type transporter activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATPase-coupled intramembrane lipid transporter activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATPase-coupled lipid transmembrane transporter activity IC
    Inferred by Curator
    more info
    PubMed 
    enables ATPase-coupled transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables apolipoprotein A-I receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables apolipoprotein A-I receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables lipid transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables lipid transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables lipid transporter activity TAS
    Traceable Author Statement
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cellular homeostasis NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in ceramide metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in ceramide metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in ceramide transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in ceramide transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ceramide transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cholesterol efflux IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in corneocyte desquamation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in corneocyte desquamation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in establishment of skin barrier ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in intracellular protein transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in keratinization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lipid homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lipid translocation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lipid transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in lipid transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lipid transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in lipid transport TAS
    Traceable Author Statement
    more info
     
    involved_in lung alveolus development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in phospholipid efflux IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cholesterol efflux IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of intracellular lipid transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of protein localization to cell surface IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein localization to plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein localization to plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulated exocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of insulin secretion involved in cellular response to glucose stimulus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of keratinocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of keratinocyte differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in secretion by cell IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT involved_in skin morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in surfactant homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in epidermal lamellar body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in epidermal lamellar body membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in transport vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    glucosylceramide transporter ABCA12
    Names
    ATP-binding cassette transporter 12
    ATP-binding cassette, sub-family A (ABC1), member 12
    NP_056472.2
    NP_775099.2
    XP_011509253.1
    XP_054197317.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_007074.2 RefSeqGene

      Range
      5000..212084
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015657.4NP_056472.2  glucosylceramide transporter ABCA12 isoform b

      See identical proteins and their annotated locations for NP_056472.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains a distinct 5' UTR and 5' coding region, compared to transcript variant 1. This results in a protein (isoform b) containing a shorter and distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AC072062, AF418105, AK096597, AK123578, AY033486, AY219711
      Consensus CDS
      CCDS33373.1
      UniProtKB/Swiss-Prot
      Q86UK0
      UniProtKB/TrEMBL
      B3KVV3
      Related
      ENSP00000374312.4, ENST00000389661.4
      Conserved Domains (4) summary
      cd03263
      Location:19362159
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
      COG1121
      Location:10281252
      ZnuC; ABC-type Mn2+/Zn2+ transport system, ATPase component [Inorganic ion transport and metabolism]
      COG1131
      Location:19412249
      CcmA; ABC-type multidrug transport system, ATPase component [Defense mechanisms]
      pfam12698
      Location:15951856
      ABC2_membrane_3; ABC-2 family transporter protein
    2. NM_173076.3NP_775099.2  glucosylceramide transporter ABCA12 isoform a

      See identical proteins and their annotated locations for NP_775099.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AC072062, AF418105, AK096597, AK123578, AY219711, BC144073
      Consensus CDS
      CCDS33372.1
      UniProtKB/Swiss-Prot
      Q53QE2, Q53S55, Q86UK0, Q8IZW6, Q96JT3, Q9Y4M5
      Related
      ENSP00000272895.7, ENST00000272895.12
      Conserved Domains (4) summary
      cd03263
      Location:22542477
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
      COG1121
      Location:13461570
      ZnuC; ABC-type Mn2+/Zn2+ transport system, ATPase component [Inorganic ion transport and metabolism]
      COG1131
      Location:22592567
      CcmA; ABC-type multidrug transport system, ATPase component [Defense mechanisms]
      pfam12698
      Location:19132174
      ABC2_membrane_3; ABC-2 family transporter protein

    RNA

    1. NR_103740.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has two additional internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC072062, AK096597, AK123578, AY219711, BC144073

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      214931542..215138626 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510951.3XP_011509253.1  glucosylceramide transporter ABCA12 isoform X1

      Conserved Domains (4) summary
      cd03263
      Location:22572480
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
      COG1121
      Location:13491573
      ZnuC; ABC-type Mn2+/Zn2+ transport system, ATPase component [Inorganic ion transport and metabolism]
      COG1131
      Location:22622570
      CcmA; ABC-type multidrug transport system, ATPase component [Defense mechanisms]
      pfam12698
      Location:19162177
      ABC2_membrane_3; ABC-2 family transporter protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      215416237..215623360 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341342.1XP_054197317.1  glucosylceramide transporter ABCA12 isoform X1