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ABCA4 Gene

protein-coding   GIFtS: 62
GCID: GC01M094458

ATP-Binding Cassette, Sub-Family A (ABC1), Member 4

(Previous names: ATP-binding cassette transporter, retinal-specific)
(Previous symbols: STGD1, ABCR, RP19, STGD)
  See ABCA4-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
ATP-Binding Cassette, Sub-Family A (ABC1), Member 41 2     FFM2 5
ABCR1 2 3 5     Stargardt Disease1
RP191 2 5     ABC102
STGD11 2 5     RMP2
STGD1 2     ATP Binding Cassette Transporter2
ATP-Binding Cassette Transporter, Retinal-Specific1 2     ATP-Binding Transporter, Retina-Specific2
Stargardt Disease Protein2 3     Photoreceptor Rim Protein2
ATP-Binding Cassette Sub-Family A Member 42 3     Retina-Specific ABC Transporter2
RIM ABC Transporter2 3     Retinal-Specific ATP-Binding Cassette Transporter2
RIM Protein2 3     RmP3
ARMD22 5     EC 3.6.38
CORD32 5     

External Ids:    HGNC: 341   Entrez Gene: 242   Ensembl: ENSG000001986917   OMIM: 6016915   UniProtKB: P783633   

Export aliases for ABCA4 gene to outside databases

Previous GC identifers: GC01M094859 GC01M093664 GC01M093808 GC01M093930 GC01M094170 GC01M094230 GC01M092582


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for ABCA4 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, White). This 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 protein is a retina-specific ABC transporter with N-retinylidene-PE as a
substrate. It is expressed exclusively in retina photoreceptor cells, indicating the gene product mediates
transport of an essental molecule across the photoreceptor cell membrane. Mutations in this gene are found in
patients diagnosed with Stargardt disease, a form of juvenile-onset macular degeneration. Mutations in this gene
are also associated with retinitis pigmentosa-19, cone-rod dystrophy type 3, early-onset severe retinal
dystrophy, fundus flavimaculatus, and macular degeneration age-related 2. (provided by RefSeq, Jul 2008)

GeneCards Summary for ABCA4 Gene:
ABCA4 (ATP-binding cassette, sub-family A (ABC1), member 4) is a protein-coding gene. Diseases associated with ABCA4 include retinitis pigmentosa 19, and fundus flavimaculatus. GO annotations related to this gene include phospholipid-translocating ATPase activity and transporter activity. An important paralog of this gene is ABCA1.

UniProtKB/Swiss-Prot: ABCA4_HUMAN, P78363
Function: In the visual cycle, acts as an inward-directed retinoid flipase, retinoid substrates imported by ABCA4
from the extracellular or intradiscal (rod) membrane surfaces to the cytoplasmic membrane surface are
all-trans-retinaldehyde (ATR) and N-retinyl-phosphatidyl-ethanolamine (NR-PE). Once transported to the
cytoplasmic surface, ATR is reduced to vitamin A by trans-retinol dehydrogenase (tRDH) and then transferred to
the retinal pigment epithelium (RPE) where it is converted to 11-cis-retinal. May play a role in photoresponse,
removing ATR/NR-PE from the extracellular photoreceptor surfaces during bleach recovery

Gene Wiki entry for ABCA4 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NC_018912.2  NT_032977.10  
Regulatory elements:
   Regulatory transcription factor binding sites in the ABCA4 gene promoter:
         STAT1   Lmo2   STAT1beta   NF-kappaB   Meis-1b   C/EBPalpha   STAT1alpha   HSF2   NF-kappaB1   En-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidABCA4 promoter sequence
   Search Chromatin IP Primers for ABCA4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ABCA4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p22   Ensembl cytogenetic band:  1p22.1   HGNC cytogenetic band: 1p22

ABCA4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ABCA4 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M094458:  view genomic region     (about GC identifiers)

Start:
94,458,393 bp from pter      End:
94,586,705 bp from pter
Size:
128,313 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: ABCA4_HUMAN, P78363 (See protein sequence)
Recommended Name: Retinal-specific ATP-binding cassette transporter  
Size: 2273 amino acids; 255944 Da
Sequence caution: Sequence=BAE06122.1; Type=Erroneous initiation;
Secondary accessions: O15112 O60438 O60915 Q0QD48 Q4LE31

Explore the universe of human proteins at neXtProt for ABCA4: NX_P78363

Explore proteomics data for ABCA4 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn98, Asn415, Asn444, Asn504, Asn1469, Asn1529, Asn1588, Asn1662
  • Modification sites at PhosphoSitePlus
  • 2 DME Specific Peptides for ABCA4 (P78363)
     LDEPTTG  NGAGKTT 


    See ABCA4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_000341.2  
    ENSEMBL proteins: 
     ENSP00000359245   ENSP00000439707   ENSP00000443203   ENSP00000437682  
    Reactome Protein details: P78363

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    Cloud-Clone Corp. Proteins for ABCA4

     
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    antibodies-online proteins for ABCA4 (2 products) 

     
    antibodies-online peptides for ABCA4

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    ABCA4 Assay Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ABCA: ATP binding cassette transporters / subfamily A

    IUPHAR Guide to PHARMACOLOGY protein family classification: ABCA4
    ABCA subfamily

    Selected InterPro protein domains (see all 6):
     IPR003439 ABC_transporter-like
     IPR027417 P-loop_NTPase
     IPR005951 Rim_ABC_transpt
     IPR003593 AAA+_ATPase
     IPR026082 ABC_A

    Graphical View of Domain Structure for InterPro Entry P78363

    ProtoNet protein and cluster: P78363

    UniProtKB/Swiss-Prot: ABCA4_HUMAN, P78363
    Similarity: Belongs to the ABC transporter superfamily. ABCA family
    Similarity: Contains 2 ABC transporter domains


    Find genes that share domains with ABCA4           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ABCA4_HUMAN, P78363
    Function: In the visual cycle, acts as an inward-directed retinoid flipase, retinoid substrates imported by ABCA4
    from the extracellular or intradiscal (rod) membrane surfaces to the cytoplasmic membrane surface are
    all-trans-retinaldehyde (ATR) and N-retinyl-phosphatidyl-ethanolamine (NR-PE). Once transported to the
    cytoplasmic surface, ATR is reduced to vitamin A by trans-retinol dehydrogenase (tRDH) and then transferred to
    the retinal pigment epithelium (RPE) where it is converted to 11-cis-retinal. May play a role in photoresponse,
    removing ATR/NR-PE from the extracellular photoreceptor surfaces during bleach recovery

         Genatlas biochemistry entry for ABCA4:
    ATP binding cassette superfamily,subfamily A,member 4,retinal specific,localized to the rim of rod phosphoreceptor
    outer segment discs (RMP protein) cell-specific ATP binding transporter gene

         Enzyme Number (IUBMB): EC 3.6.32

         Gene Ontology (GO): Selected molecular function terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding ----
    GO:0004012phospholipid-translocating ATPase activity IEA--
    GO:0005215transporter activity TAS9054934
    GO:0005524ATP binding IEA--
    GO:0005548phospholipid transporter activity ----
         
    Find genes that share ontologies with ABCA4           About GenesLikeMe


    Phenotypes:
         7 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Abca4):
     cardiovascular system  homeostasis/metabolism  integument  nervous system  no phenotypic analysis 
     pigmentation  vision/eye 

    Find genes that share phenotypes with ABCA4           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for ABCA4: Abca4tm1Kpal Abca4tm1Ght

       genOway: Develop your customized and physiologically relevant rodent model for ABCA4

    miRNA
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    miRTarBase miRNAs that target ABCA4:
    hsa-mir-335-5p (MIRT017969)

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    2 qRT-PCR Assays for microRNAs that regulate ABCA4:
    hsa-miR-194* hsa-miR-125a-3p
    SwitchGear 3'UTR luciferase reporter plasmidABCA4 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for ABCA4
    Predesigned siRNA for gene silencing in human, mouse, rat ABCA4

    Gene Editing
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    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat ABCA4

    Cell Line
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ABCA4


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    ABCA4_HUMAN, P78363: Membrane; Multi-pass membrane protein. Note=Localized to outer segment disk edges of rods
    and cones, with around one million copies/photoreceptor
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    lysosome1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005887integral component of plasma membrane IEA--
    GO:0016020membrane TAS9054934
    GO:0097381photoreceptor disc membrane TAS--

    Find genes that share ontologies with ABCA4           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for ABCA4 About   (see all 6)  
    See pathways by source

    SuperPathContained pathways About
    1ABC-family proteins mediated transport
    ABC-family proteins mediated transport0.69
    ABC transporters0.69
    2Diseases associated with visual transduction
    Visual phototransduction0.44
    Diseases associated with visual transduction0.43
    3Signaling by GPCR
    Signal Transduction0.58
    4Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
    Transmembrane transport of small molecules0.47
    5the visual cycle I (vertebrates)
    The canonical retinoid cycle in rods (twilight vision)0.44


    Find genes that share SuperPaths with ABCA4           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    2 Reactome Pathways for ABCA4
        ABC-family proteins mediated transport
    The canonical retinoid cycle in rods (twilight vision)


    1 Kegg Pathway  (Kegg details for ABCA4):
        ABC transporters

        Pathway & Disease-focused RT2 Profiler PCR Array including ABCA4: 
              Drug Transporters in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for ABCA4

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for ABCA4 (P783633 ENSP000003592454) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CNGB1Q140283, ENSP000002511024I2D: score=2 STRING: ENSP00000251102
    ABCG2ENSP000002376124STRING: ENSP00000237612
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001523retinoid metabolic process TAS--
    GO:0006649phospholipid transfer to membrane IEA--
    GO:0006810transport TAS9054934
    GO:0007601visual perception IEA--
    GO:0007603phototransduction, visible light TAS--

    Find genes that share ontologies with ABCA4           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for ABCA4

    10 Novoseek inferred chemical compound relationships for ABCA4 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    11-cis-retinol 71.2 1 15928609 (1)
    retinoid 48.5 13 15471866 (3), 14709597 (2), 15696369 (1), 19306869 (1)
    atp 31.4 21 15471866 (4), 10874631 (2), 12888572 (2), 11687513 (2) (see all 11)
    phosphatidylethanolamine 28.9 6 15471866 (2), 10412977 (1)
    vitamin a 21.8 4 15471866 (1), 19494204 (1), 15928609 (1), 18515570 (1)
    cholesterol 0 1 17029687 (1)
    gtp 0 1 15471866 (1)
    phospholipid 0 1 15044640 (1)
    lipid 0 2 17973979 (1), 12962493 (1)
    adp 0 3 12888572 (2), 15471866 (1)



    Find genes that share compounds with ABCA4           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for ABCA4 gene: 
    NM_000350.2  

    Unigene Cluster for ABCA4:

    ATP-binding cassette, sub-family A (ABC1), member 4
    Hs.416707  [show with all ESTs]
    Unigene Representative Sequence: NM_000350
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000370225(uc001dqh.3) ENST00000465352(uc001dqi.1) ENST00000484388
    ENST00000470771 ENST00000460514 ENST00000472033 ENST00000536513(uc009wdp.1)
    ENST00000535881 ENST00000535735(uc010otn.1)
    miRNA
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    hsa-miR-194* hsa-miR-125a-3p
    SwitchGear 3'UTR luciferase reporter plasmidABCA4 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat ABCA4

    Additional mRNA sequence: 

    AB210040.1 AF000148.1 AF001945.1 AK295818.1 AK296896.1 AK301733.1 AK301764.1 CR627391.1 
    DQ426859.1 U88667.1 

    12 DOTS entries:

    DT.314419  DT.97821623  DT.40115469  DT.314422  DT.121400333  DT.314421  DT.40255320  DT.121400340 
    DT.40270936  DT.97765193  DT.97843252  DT.40116675 

    Selected AceView cDNA sequences (see all 108):

    AL713451 CA398100 BM687039 AA970792 BU731300 AI932378 H85972 BU740200 
    AA905109 AI128615 BQ637957 CA394887 BQ639783 BU730994 BQ637768 BM673711 
    AI564136 CA390557 BM690592 BX092191 CA391240 AI827761 AA613174 CR627391 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    ABCA4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAAAAATAAA
    ABCA4 Expression
    About this image


    ABCA4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Eye (Sensory Organs)
             nGnG Amacrine Cells Inner Nuclear Layer
     
     Epithelial Cells
             Mature Choroid Plexus Cells Choroid Plexus
     
     Neural Ectoderm (Nervous System)
             Neural ectoderm cells
     
     Bone (Muscoskeletal System)
             Zeugopod Periosteum
     
     Neural Tube (Nervous System)
             Floor plate-like cells
    ABCA4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ABCA4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.416707

    UniProtKB/Swiss-Prot: ABCA4_HUMAN, P78363
    Tissue specificity: Retinal-specific. Seems to be exclusively found in the rims of rod photoreceptor cells

        Pathway & Disease-focused RT2 Profiler PCR Array including ABCA4: 
              Drug Transporters in human mouse rat

    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat ABCA4
    QuantiTect SYBR Green Assays in human, mouse, rat ABCA4
    QuantiFast Probe-based Assays in human, mouse, rat ABCA4
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ABCA4

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for ABCA4 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Abca41 , 5 ATP-binding cassette, sub-family A (ABC1), member 41, 5 86.47(n)1
    88.46(a)1
      3 (52.94 cM)5
    113041  NM_007378.11  NP_031404.11 
     1220444435 
    chicken
    (Gallus gallus)
    Aves ABCA41 ATP-binding cassette, sub-family A (ABC1), member 4 70.88(n)
    72.42(a)
      424490  XM_422330.4  XP_422330.3 
    lizard
    (Anolis carolinensis)
    Reptilia ABCA46
    ATP-binding cassette, sub-family A (ABC1), member ...
    71(a)
    1 ↔ 1
    4(88728876-88858884)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.175292 Xenopus laevis transcribed sequence with moderate similarity more 75.03(n)    CD328284.1 
    zebrafish
    (Danio rerio)
    Actinopterygii abca4b1 ATP-binding cassette, sub-family A (ABC1), member 4b 66.19(n)
    65.85(a)
      555506  XM_678031.6  XP_683123.5 


    ENSEMBL Gene Tree for ABCA4 (if available)
    TreeFam Gene Tree for ABCA4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ABCA4 gene
    ABCA12  ABCA102  ABCA132  ABCA32  ABCA82  ABCA122  ABCA72  ABCA22  
    ABCA92  ABCA62  ABCA52  
    15 SIMAP similar genes for ABCA4 using alignment to 4 protein entries:     ABCA4_HUMAN (see all proteins):
    DKFZp781N1972    DKFZp547P193    ABC1    DKFZp434E1030    ABCA2    ABCA1
    ABCA7    ABCA13    ABC2    ABCA12    NG-TRA    ABCA5
    ABCA9    ABCG2    ABCA3

    Find genes that share paralogs with ABCA4           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Polymorphic Variants from UniProtKB/Swiss-Prot
    ABCA4_HUMAN, P78363: The variant Ala-863 is present in the general population at a frequency of approximately 3% and 1%
    in Northern Europe and United States, respectively. It is a mild alteration probably leading to STGD phenotype
    only in combination with a more severe allele. The variant Glu-1961 is found with high frequency in healthy
    individuals of Somali ancestry


    Selected SNPs for ABCA4 (see all 4121)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs617485211,2,,4
    CStargardt disease 1 (STGD1)4 untested194486617(-) CCACAC/GTGGAC 2 L V mis11Minor allele frequency- G:0.00NA 4552
    rs626425641,2,,4
    C,FStargardt disease 1 (STGD1)4 untested194489816(-) ACGCCA/C/GCATGC 3 H P R mis12NA EU 5771
    rs22976691,2,,4
    C,F,HStargardt disease 1 (STGD1)4 --94489817(+) CATGCA/G/TGCGTG 3 S R C mis1 ese39NS EA NA 960
    rs412926771,2,,4
    C,FStargardt disease 1 (STGD1)4 pathogenic194490740(+) TGCAAC/GCTAGG 2 L V mis13Minor allele frequency- G:0.22NA EU 5877
    rs617506411,2,,4
    C,FStargardt disease 1 (STGD1)4 untested194494247(-) AGGACG/AAGAAC 2 /Q /R mis12Minor allele frequency- A:0.00NA EU 5873
    rs617514081,2,,4
    C,FStargardt disease 1 (STGD1)4 pathogenic194494257(-) AGCTGC/TTCACA 2 L F mis11Minor allele frequency- T:0.00NA 4550
    rs18005531,2,,4
    C,F,OStargardt disease 1 (STGD1)4 pathogenic194496999(-) TGTCGG/AAGTTC 2 /E /G mis14Minor allele frequency- A:0.00NA EU 5879
    rs18005521,2,,4
    C,FStargardt disease 1 (STGD1)4 untested194499569(-) CCAGCG/ACCACT 2 /H /R mis12Minor allele frequency- A:0.00NA EU 5869
    rs617505631,2,,4
    C,FStargardt disease 1 (STGD1)4 untested194508451(-) CCTTCG/ATCCCA 2 /I /V mis11Minor allele frequency- A:0.00NA 4546
    rs18005511,2,,4
    CMacular degeneration, age-related, 2 (ARMD2)4 untested194510637(-) TTGTTA/GGGTTT 2 R G mis10--------

    HapMap Linkage Disequilibrium report for ABCA4 (94458393 - 94586705 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for ABCA4:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv523430CNV Loss19592680
    dgv268n71CNV Loss21882294
    dgv269n71CNV Loss21882294
    nsv516137CNV Loss19592680
    nsv871679CNV Loss21882294
    dgv267n71CNV Gain21882294
    nsv871057CNV Gain21882294
    nsv871172CNV Gain21882294

    Human Gene Mutation Database (HGMD): ABCA4
    Locus Specific Mutation Databases (LSDB): ABCA4

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ABCA4
    DNA2.0 Custom Variant and Variant Library Synthesis for ABCA4

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 601691   
    OMIM disorders: 248200  601718  604116  153800  
    UniProtKB/Swiss-Prot: ABCA4_HUMAN, P78363
  • Stargardt disease 1 (STGD1) [MIM:248200]: A common hereditary macular degeneration. It is characterized
    by decreased central vision, atrophy of the macula and underlying retinal pigment epithelium, and frequent
    presence of prominent flecks in the posterior pole of the retina. Note=The disease is caused by mutations
    affecting the gene represented in this entry
  • Fundus flavimaculatus (FFM) [MIM:248200]: Autosomal recessive retinal disorder very similar to Stargardt
    disease. In contrast to Stargardt disease, FFM is characterized by later onset and slowly progressive course.
    Note=The disease is caused by mutations affecting the gene represented in this entry
  • Macular degeneration, age-related, 2 (ARMD2) [MIM:153800]: A form of age-related macular degeneration, a
    multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most
    patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid
    that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch
    membrane. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry
  • Cone-rod dystrophy 3 (CORD3) [MIM:604116]: An inherited retinal dystrophy characterized by retinal
    pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone
    photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central
    visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis
    pigmentosa. Note=The disease is caused by mutations affecting the gene represented in this entry
  • Retinitis pigmentosa 19 (RP19) [MIM:601718]: A retinal dystrophy belonging to the group of pigmentary
    retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination
    and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically
    have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose
    their far peripheral visual field and eventually central vision as well. RP19 is characterized by choroidal
    atrophy. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 19 diseases for ABCA4:    
    About MalaCards
    retinitis pigmentosa 19    fundus flavimaculatus    abca4-related retinitis pigmentosa    abca4-related stargardt disease 1
    age-related macular degeneration 2    scotoma    stargardt disease    cone-rod dystrophy 3
    stargardt macular degeneration    retinal dystrophy, early-onset, severe    cone-rod dystrophy    retinitis pigmentosa 3
    congenital toxoplasmosis    age related macular degeneration    macular holes    toxoplasmosis
    leber congenital amaurosis    cone-rod dystrophy 2    retinitis pigmentosa

    7 diseases from the University of Copenhagen DISEASES database for ABCA4:
    Retinal degeneration     Scotoma     Fundus dystrophy     Night blindness
    Blindness     Leber congenital amaurosis     Tangier disease

    Find genes that share disorders with ABCA4           About GenesLikeMe

    Selected Novoseek inferred disease relationships for ABCA4 gene (see all 15)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    stargardts disease 98.9 145 10612508 (4), 10746567 (3), 10711710 (3), 12224481 (3) (see all 76)
    stgd1 96.5 42 20029649 (4), 10711710 (4), 9973280 (3), 11379881 (3) (see all 16)
    cone-rod dystrophy 96.2 49 12224481 (4), 16681420 (3), 12796258 (3), 10958761 (2) (see all 30)
    fundus flavimaculatus 95.7 23 10206579 (2), 10509673 (2), 12192456 (2), 10396622 (1) (see all 16)
    retinitis pigmentosa 86.3 56 12224481 (3), 12353176 (3), 18285826 (3), 10874631 (2) (see all 30)
    retinal degeneration 74.7 11 16374319 (1), 15108289 (1), 16546111 (1), 9703434 (1) (see all 8)
    retinopathy 72.5 29 10396622 (2), 11384574 (2), 11017087 (2), 17653054 (1) (see all 19)
    blindness 64.9 4 10958763 (1), 14709597 (1), 14750597 (1)
    maculopathy 54.3 4 18024811 (2), 10958763 (1)
    maculopathy age-related 52.3 2 12824224 (1), 15696369 (1)

    Genetic Association Database (GAD): ABCA4
    Human Genome Epidemiology (HuGE) Navigator: ABCA4 (33 documents)

    Export disorders for ABCA4 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for ABCA4 gene, integrated from 10 sources (see all 228):
    (articles sorted by number of sources associating them with ABCA4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Late-onset Stargardt disease is associated with missense mutations that map outside known functional regions of ABCR (ABCA4). (PubMed id 11379881)1, 2, 4, 9 Yatsenko A.N.... Lupski J.R. (Hum. Genet. 2001)
    2. Molecular analysis of the ABCA4 gene for reliable detection of allelic variations in Spanish patients: identification of 21 novel variants. (PubMed id 19028736)1, 2, 4, 9 Aguirre-Lamban J.... Ayuso C. (Br. J. Ophthalmol. 2009)
    3. Variation of codons 1961 and 2177 of the Stargardt disease gene is not associated with age-related macular degeneration. (PubMed id 11346402)1, 2, 4, 9 Guymer R.H.... Stone E.M. (Arch. Ophthalmol. 2001)
    4. An analysis of allelic variation in the ABCA4 gene. (PubMed id 11328725)1, 2, 4, 9 Webster A.R.... Stone E.M. (Invest. Ophthalmol. Vis. Sci. 2001)
    5. Frequency of ABCA4 mutations in 278 Spanish controls: an insight into the prevalence of autosomal recessive Stargardt disease. (PubMed id 18977788)1, 2, 4, 9 Riveiro-Alvarez R.... Ayuso C. (Br. J. Ophthalmol. 2009)
    6. Mapping of the rod photoreceptor ABC transporter (ABCR) to 1p21-p22.1 and identification of novel mutations in Stargardt's disease. (PubMed id 9490294)1, 2, 3, 9 Nasonkin I....Weber B.H.F. (Hum. Genet. 1998)
    7. ABCA4 gene analysis in patients with autosomal recessive cone and cone rod dystrophies. (PubMed id 18285826)1, 4, 9 Kitiratschky V.B....Wissinger B. (Eur. J. Hum. Genet. 2008)
    8. Mutations in the ABCA4 (ABCR) gene are the major cause of autosomal recessive cone-rod dystrophy. (PubMed id 10958761)1, 2, 9 Maugeri A.... Cremers F.P.M. (Am. J. Hum. Genet. 2000)
    9. Association of a homozygous nonsense mutation in the ABCA4 (ABCR) gene with cone-rod dystrophy phenotype in an Italian family. (PubMed id 15017103)1, 4, 9 Simonelli F....Allikmets R. (Ophthalmic Res. 2004)
    10. Biochemical defects in ABCR protein variants associated with human retinopathies. (PubMed id 11017087)1, 2, 9 Sun H.... Nathans J. (Nat. Genet. 2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 24 HGNC: 34 AceView: ABCA4 Ensembl:ENSG00000198691 euGenes: HUgn24
    ECgene: ABCA4 Kegg: 24 H-InvDB: ABCA4

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for ABCA4 Pharmacogenomics, SNPs, Pathways
    Mutations of the ABCA4 genehttp://www.retina-international.org/files/sci-news/abcrmut.htm
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=ABCA4[genesymbol]
    ABCMdbhttp://abcmutations.hegelab.org/proteinDetails?uniprot_id=P78363

    (Patent information from GeneIP,
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    Patent Information for ABCA4 gene:
    Search GeneIP for patents involving ABCA4

    GeneCards and IP:
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