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    ABCA6 ATP binding cassette subfamily A member 6 [ Homo sapiens (human) ]

    Gene ID: 23460, updated on 27-Nov-2024

    Summary

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    Official Symbol
    ABCA6provided by HGNC
    Official Full Name
    ATP binding cassette subfamily A member 6provided by HGNC
    Primary source
    HGNC:HGNC:36
    See related
    Ensembl:ENSG00000154262 MIM:612504; AllianceGenome:HGNC:36
    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
    EST155051
    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. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This gene is clustered among 4 other ABC1 family members on 17q24 and may play a role in macrophage lipid homeostasis. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in liver (RPKM 14.4), urinary bladder (RPKM 9.9) and 19 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ABCA6 in Genome Data Viewer
    Location:
    17q24.2-q24.3
    Exon count:
    39
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (69078702..69141895, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (69955592..70018487, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (67074843..67138036, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATP binding cassette subfamily A member 9 Neighboring gene MPRA-validated peak2963 silencer Neighboring gene ABCA9 antisense RNA 1 Neighboring gene uncharacterized LOC124904051 Neighboring gene Sharpr-MPRA regulatory region 12590 Neighboring gene SEC24 homolog A pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12652 Neighboring gene microRNA 4524a Neighboring gene microRNA 4524b Neighboring gene Sharpr-MPRA regulatory region 12537 Neighboring gene MPRA-validated peak2964 silencer Neighboring gene ATP binding cassette subfamily A member 10 Neighboring gene MPRA-validated peak2965 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:67209122-67210042 Neighboring gene MPRA-validated peak2966 silencer Neighboring gene uncharacterized LOC100133319 Neighboring gene ATP binding cassette subfamily A member 5 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. ABCA6 affects the malignancy of Ewing sarcoma cells via cholesterol-guided inhibition of the IGF1R/AKT/MDM2 axis. Pasello M, et al. Cell Oncol (Dordr), 2022 Dec. PMID 36149602, Free PMC Article
    2. The Evolution of the Mammalian ABCA6-like Genes: Analysis of Phylogenetic, Expression, and Population Genetic Data Reveals Complex Evolutionary Histories. Breuss MW, et al. Genome Biol Evol, 2020 Nov 3. PMID 32877505, Free PMC Article
    3. Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels. van Leeuwen EM, et al. Nat Commun, 2015 Mar 9. PMID 25751400, Free PMC Article
    4. ABCA6, a novel a subclass ABC transporter. Kaminski WE, et al. Biochem Biophys Res Commun, 2001 Aug 3. PMID 11478798
    5. Hypercholesterolemia risk associated Abca6 does not regulate lipoprotein metabolism in mice or hamster. He B, et al. Biochim Biophys Acta Mol Cell Biol Lipids, 2021 Nov. PMID 34274505

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ABCA6 affects the malignancy of Ewing sarcoma cells via cholesterol-guided inhibition of the IGF1R/AKT/MDM2 axis.
      Title: ABCA6 affects the malignancy of Ewing sarcoma cells via cholesterol-guided inhibition of the IGF1R/AKT/MDM2 axis.
    2. Hypercholesterolemia risk associated Abca6 does not regulate lipoprotein metabolism in mice or hamster.
      Title: Hypercholesterolemia risk associated Abca6 does not regulate lipoprotein metabolism in mice or hamster.
    3. The Evolution of the Mammalian ABCA6-like Genes: Analysis of Phylogenetic, Expression, and Population Genetic Data Reveals Complex Evolutionary Histories.
      Title: The Evolution of the Mammalian ABCA6-like Genes: Analysis of Phylogenetic, Expression, and Population Genetic Data Reveals Complex Evolutionary Histories.
    4. A rare missense variant in ABCA6 (rs77542162, p.Cys1359Arg, frequency 0.034), found in a Dutch population, is predicted to be deleterious with respect to blood cholesterol levels.
      Title: Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels.
    5. Results suggest a possible role for multidrug resistance genes ABCA10 and ABCA6 in follicular lymphoma survival and add to the evidence that genetic variation in CD46 and IL8 may have prognostic implications follicular lymphoma.
      Title: A comprehensive evaluation of the role of genetic variation in follicular lymphoma survival.
    6. These data provide evidence for an essential role of FoxO proteins in the transcription of ABCA6 in human vascular endothelial cells.
      Title: FoxO regulates expression of ABCA6, an intracellular ATP-binding-cassette transporter responsive to cholesterol.
    7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    8. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Polymorphisms in innate immunity genes and lung cancer risk in Xuanwei, China.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic susceptibility to distinct bladder cancer subphenotypes.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ43498

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ABC-type transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATPase-coupled transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables lipid transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in lipid transport IBA
    Inferred from Biological aspect of Ancestor
    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 
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    ATP-binding cassette sub-family A member 6
    Names
    ABC transporter ABCA6
    ATP-binding cassette A6
    ATP-binding cassette, sub-family A (ABC1), member 6

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_080284.3 → NP_525023.2  ATP-binding cassette sub-family A member 6

      See identical proteins and their annotated locations for NP_525023.2

      Status: REVIEWED

      Source sequence(s)
      AC005495, AC005922
      Consensus CDS
      CCDS11683.1
      UniProtKB/Swiss-Prot
      Q6NSH9, Q8N139, Q8N856, Q8WWZ6
      UniProtKB/TrEMBL
      A4FVC6
      Related
      ENSP00000284425.1, ENST00000284425.7
      Conserved Domains (3) summary
      cd03263
      Location:1296 → 1501
      ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
      COG1131
      Location:1275 → 1592
      CcmA; ABC-type multidrug transport system, ATPase component [Defense mechanisms]
      pfam12698
      Location:34 → 375
      ABC2_membrane_3; ABC-2 family transporter protein

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      69078702..69141895 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      69955592..70018487 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_172346.1: Suppressed sequence

      Description
      NM_172346.1: This RefSeq was permanently suppressed because it is a nonsense-mediated decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N139.2 GenPept UniProtKB/Swiss-Prot:Q8N139

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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