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Aliases for ABCA6 Gene

Aliases for ABCA6 Gene

  • ATP Binding Cassette Subfamily A Member 6 2 3 5
  • ATP-Binding Cassette, Sub-Family A (ABC1), Member 6 2 3
  • ATP-Binding Cassette Sub-Family A Member 6 3
  • ATP-Binding Cassette A6 3
  • ABC Transporter ABCA6 3
  • EST155051 3

External Ids for ABCA6 Gene

Previous GeneCards Identifiers for ABCA6 Gene

  • GC17M066873
  • GC17M070035
  • GC17M067539
  • GC17M067671
  • GC17M064586
  • GC17M067074
  • GC17M062462

Summaries for ABCA6 Gene

Entrez Gene Summary for ABCA6 Gene

  • 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]

GeneCards Summary for ABCA6 Gene

ABCA6 (ATP Binding Cassette Subfamily A Member 6) is a Protein Coding gene. Among its related pathways are CDK-mediated phosphorylation and removal of Cdc6 and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. Gene Ontology (GO) annotations related to this gene include ATPase activity and ATPase activity, coupled to transmembrane movement of substances. An important paralog of this gene is ABCA8.

UniProtKB/Swiss-Prot for ABCA6 Gene

  • Probable transporter which may play a role in macrophage lipid homeostasis.

Additional gene information for ABCA6 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ABCA6 Gene

Genomics for ABCA6 Gene

GeneHancer (GH) Regulatory Elements for ABCA6 Gene

Promoters and enhancers for ABCA6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J069141 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 650.7 -0.6 -608 2.8 FOXA2 TAF1 NFRKB CEBPG BMI1 RAD21 RARA CHAMP1 YY1 FOXK2 ABCA6 ABCA10 ABCA5 GC17P069213
GH17J069115 Promoter/Enhancer 1.3 EPDnew ENCODE 662 +26.0 25972 1.4 HDGF SMAD1 STAT5A IRF4 RAD21 YY1 ZNF143 ATF7 ETV6 BCLAF1 ABCA6 ABCA10 ABCA9 ABCA5 GC17M069120 MIR4524A
GH17J069092 Enhancer 1.4 FANTOM5 Ensembl ENCODE 14.1 +48.2 48189 3.1 PKNOX1 FOXA2 ARNT IRF4 NCOA2 TCF12 POLR2B ZNF766 GATA2 E2F8 GC17M069097 ABCA6 ABCA9 ABCA10 SEC24AP1
GH17J068773 Enhancer 1.4 Ensembl ENCODE dbSUPER 11 +365.6 365571 5 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF143 FOS ABCA10 ABCA8 BPTF ABCA9 ABCA6 WIPI1 LINC01482 GC17P068795 LOC105371877
GH17J069175 Enhancer 1.1 Ensembl ENCODE 11.5 -33.9 -33910 1.8 FOXA2 FEZF1 ZNF766 ATF7 FOS ZNF518A ZNF592 KAT8 NFIL3 ATF4 ABCA10 ABCA6 GC17P069213
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ABCA6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ABCA6 gene promoter:
  • GATA-1
  • AML1a
  • Olf-1
  • HOXA9
  • HOXA9B
  • Meis-1
  • Meis-1b
  • AREB6
  • FOXD1
  • Sox9

Genomic Locations for ABCA6 Gene

Genomic Locations for ABCA6 Gene
chr17:69,078,089-69,141,992
(GRCh38/hg38)
Size:
63,904 bases
Orientation:
Minus strand
chr17:67,074,843-67,138,029
(GRCh37/hg19)
Size:
63,187 bases
Orientation:
Minus strand

Genomic View for ABCA6 Gene

Genes around ABCA6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ABCA6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ABCA6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ABCA6 Gene

Proteins for ABCA6 Gene

  • Protein details for ABCA6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N139-ABCA6_HUMAN
    Recommended name:
    ATP-binding cassette sub-family A member 6
    Protein Accession:
    Q8N139
    Secondary Accessions:
    • Q6NSH9
    • Q8N856
    • Q8WWZ6

    Protein attributes for ABCA6 Gene

    Size:
    1617 amino acids
    Molecular mass:
    184286 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAM77557.1; Type=Frameshift; Positions=998, 1000; Evidence={ECO:0000305}; Sequence=AAM77558.1; Type=Frameshift; Positions=998, 1000; Evidence={ECO:0000305}; Sequence=BAC04994.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for ABCA6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ABCA6 Gene

Post-translational modifications for ABCA6 Gene

  • Glycosylation at posLast=940940, Asn109, and Asn84
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for ABCA6 Gene

Domains & Families for ABCA6 Gene

Gene Families for ABCA6 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for ABCA6 Gene

Suggested Antigen Peptide Sequences for ABCA6 Gene

Graphical View of Domain Structure for InterPro Entry

Q8N139

UniProtKB/Swiss-Prot:

ABCA6_HUMAN :
  • Belongs to the ABC transporter superfamily. ABCA family.
Family:
  • Belongs to the ABC transporter superfamily. ABCA family.
genes like me logo Genes that share domains with ABCA6: view

Function for ABCA6 Gene

Molecular function for ABCA6 Gene

UniProtKB/Swiss-Prot Function:
Probable transporter which may play a role in macrophage lipid homeostasis.
UniProtKB/Swiss-Prot Induction:
Up-regulated during monocyte differentiation into macrophages. Down-regulated by cholesterol loading of macrophages.
GENATLAS Biochemistry:
ATP binding cassette superfamily A,member 6

Phenotypes From GWAS Catalog for ABCA6 Gene

Gene Ontology (GO) - Molecular Function for ABCA6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005524 ATP binding IEA --
GO:0016887 ATPase activity IEA --
GO:0042626 ATPase activity, coupled to transmembrane movement of substances IBA --
genes like me logo Genes that share ontologies with ABCA6: view
genes like me logo Genes that share phenotypes with ABCA6: view

Animal Models for ABCA6 Gene

MGI Knock Outs for ABCA6:
  • Abca6 Abca6<tm2b(KOMP)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for ABCA6

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ABCA6 Gene

Localization for ABCA6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ABCA6 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ABCA6 gene
Compartment Confidence
nucleus 4
plasma membrane 3

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ABCA6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0043231 intracellular membrane-bounded organelle IBA --
genes like me logo Genes that share ontologies with ABCA6: view

Pathways & Interactions for ABCA6 Gene

genes like me logo Genes that share pathways with ABCA6: view

Pathways by source for ABCA6 Gene

Interacting Proteins for ABCA6 Gene

Gene Ontology (GO) - Biological Process for ABCA6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006869 lipid transport IBA --
GO:0055085 transmembrane transport IEA --
genes like me logo Genes that share ontologies with ABCA6: view

No data available for SIGNOR curated interactions for ABCA6 Gene

Drugs & Compounds for ABCA6 Gene

No Compound Related Data Available

Transcripts for ABCA6 Gene

Unigene Clusters for ABCA6 Gene

ATP-binding cassette, sub-family A (ABC1), member 6:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ABCA6 Gene

No ASD Table

Relevant External Links for ABCA6 Gene

GeneLoc Exon Structure for
ABCA6
ECgene alternative splicing isoforms for
ABCA6

Expression for ABCA6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ABCA6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ABCA6 Gene

This gene is overexpressed in Liver (21.3), Adrenal (16.6), Gallbladder (15.0), and Fetal Liver (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ABCA6 Gene



NURSA nuclear receptor signaling pathways regulating expression of ABCA6 Gene:

ABCA6

SOURCE GeneReport for Unigene cluster for ABCA6 Gene:

Hs.709514

mRNA Expression by UniProt/SwissProt for ABCA6 Gene:

Q8N139-ABCA6_HUMAN
Tissue specificity: Widely expressed with higher expression in liver.

Evidence on tissue expression from TISSUES for ABCA6 Gene

  • Liver(4.5)
  • Lung(4.3)
  • Spleen(4.1)
  • Heart(2)
genes like me logo Genes that share expression patterns with ABCA6: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for ABCA6 Gene

Orthologs for ABCA6 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ABCA6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ABCA6 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia ABCA6 33
  • 82.5 (n)
cow
(Bos Taurus)
Mammalia ABCA6 34 33
  • 78.75 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Abca6 16 34 33
  • 76.48 (n)
rat
(Rattus norvegicus)
Mammalia Abca6 33
  • 75.4 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 60 (a)
ManyToMany
-- 34
  • 59 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 55 (a)
OneToMany
chicken
(Gallus gallus)
Aves -- 34
  • 47 (a)
ManyToMany
-- 34
  • 45 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 42 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii abch1 34
  • 17 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta CG31731 34
  • 20 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea abt-5 34
  • 19 (a)
ManyToMany
rice
(Oryza sativa)
Liliopsida Os.18695 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 28 (a)
OneToMany
Species where no ortholog for ABCA6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for ABCA6 Gene

ENSEMBL:
Gene Tree for ABCA6 (if available)
TreeFam:
Gene Tree for ABCA6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ABCA6: view image

Paralogs for ABCA6 Gene

Paralogs for ABCA6 Gene

(12) SIMAP similar genes for ABCA6 Gene using alignment to 2 proteins:

  • ABCA6_HUMAN
  • A4FVC6_HUMAN

Pseudogenes.org Pseudogenes for ABCA6 Gene

genes like me logo Genes that share paralogs with ABCA6: view

Variants for ABCA6 Gene

Sequence variations from dbSNP and Humsavar for ABCA6 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000121805 -- 69,062,869(-) T/C genic_downstream_transcript_variant, intron_variant
rs1000199865 -- 69,140,844(-) T/A genic_upstream_transcript_variant, intron_variant
rs1000283661 -- 69,101,723(-) A/C intron_variant
rs1000311054 -- 69,074,356(-) C/T genic_downstream_transcript_variant, intron_variant
rs1000312824 -- 69,087,779(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ABCA6 Gene

Variant ID Type Subtype PubMed ID
nsv954538 CNV deletion 24416366
nsv833526 CNV gain 17160897
nsv575930 CNV loss 21841781
nsv470598 CNV loss 18288195
nsv2128 CNV insertion 18451855
nsv1151781 CNV deletion 26484159
nsv1113886 CNV deletion 24896259
nsv1071799 CNV deletion 25765185
nsv1066998 CNV loss 25217958
esv3641122 CNV loss 21293372
esv3641121 CNV loss 21293372
esv3554709 CNV deletion 23714750
esv2716153 CNV deletion 23290073
esv2615334 CNV deletion 19546169
esv2556464 CNV deletion 19546169
esv2069389 CNV deletion 18987734
esv1450413 CNV deletion 17803354
dgv1502n106 CNV deletion 24896259

Variation tolerance for ABCA6 Gene

Residual Variation Intolerance Score: 90.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.24; 95.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ABCA6 Gene

Human Gene Mutation Database (HGMD)
ABCA6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ABCA6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ABCA6 Gene

Disorders for ABCA6 Gene

Additional Disease Information for ABCA6

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for ABCA6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ABCA6 Gene

Publications for ABCA6 Gene

  1. Genetic susceptibility to distinct bladder cancer subphenotypes. (PMID: 19692168) Guey LT … EPICURO/Spanish Bladder Cancer Study investigators (European urology 2010) 3 44 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. Polymorphisms in innate immunity genes and lung cancer risk in Xuanwei, China. (PMID: 19170196) Shen M … Lan Q (Environmental and molecular mutagenesis 2009) 3 44 58
  4. Association study between single-nucleotide polymorphisms in 199 drug-related genes and commonly measured quantitative traits of 752 healthy Japanese subjects. (PMID: 19343046) Saito A … Kamatani N (Journal of human genetics 2009) 3 44 58
  5. PTEN identified as important risk factor of chronic obstructive pulmonary disease. (PMID: 19625176) Hosgood HD … Lan Q (Respiratory medicine 2009) 3 44 58

Products for ABCA6 Gene

Sources for ABCA6 Gene

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