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BEST1 Gene

protein-coding   GIFtS: 58
GCID: GC11P061717

Bestrophin 1

(Previous name: vitelliform macular dystrophy 2)
(Previous symbol: VMD2)
  See 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
Bestrophin 11 2     RP502 5
VMD21 2 3 5     Vitelliform Macular Dystrophy 21
Best Disease1 2     BEST2
Vitelliform Macular Dystrophy Protein 22 3     BMD2
TU15B2 3     Best1V1Delta22
ARB2 5     bestrophin-12

External Ids:    HGNC: 127031   Entrez Gene: 74392   Ensembl: ENSG000001679957   OMIM: 6078545   UniProtKB: O760903   

Export aliases for BEST1 gene to outside databases

Previous GC identifers: GC11P061475 GC11P058045


(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 BEST1 Gene:
This gene encodes a member of the bestrophin gene family. This small gene family is characterized by proteins with
a highly conserved N-terminus with four to six transmembrane domains. Bestrophins may form chloride ion channels
or may regulate voltage-gated L-type calcium-ion channels. Bestrophins are generally believed to form
calcium-activated chloride-ion channels in epithelial cells but they have also been shown to be highly permeable
to bicarbonate ion transport in retinal tissue. Mutations in this gene are responsible for juvenile-onset
vitelliform macular dystrophy (VMD2), also known as Best macular dystrophy, in addition to adult-onset
vitelliform macular dystrophy (AVMD) and other retinopathies. Alternative splicing results in multiple variants
encoding distinct isoforms.(provided by RefSeq, Nov 2008)

GeneCards Summary for BEST1 Gene:
BEST1 (bestrophin 1) is a protein-coding gene. Diseases associated with BEST1 include vitreoretinochoroidopathy, and best1-related retinitis pigmentosa. GO annotations related to this gene include chloride channel activity. An important paralog of this gene is BEST2.

UniProtKB/Swiss-Prot: BEST1_HUMAN, O76090
Function: Forms calcium-sensitive chloride channels. Highly permeable to bicarbonate

Gene Wiki entry for BEST1 (Bestrophin 1) 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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Regulatory elements:
   Regulatory transcription factor binding sites in the BEST1 gene promoter:
         NRSF form 1   LCR-F1   NRSF form 2   CBF-C   CBF-A   CBF-B   CP1A   CP1C   NF-Y   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidBEST1 promoter sequence
   Search Chromatin IP Primers for BEST1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BEST1


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

Entrez Gene cytogenetic band: 11q13   Ensembl cytogenetic band:  11q12.3   HGNC cytogenetic band: 11q12

BEST1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BEST1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P061717:  view genomic region     (about GC identifiers)

Start:
61,717,293 bp from pter      End:
61,732,987 bp from pter
Size:
15,695 bases      Orientation:
plus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: BEST1_HUMAN, O76090 (See protein sequence)
Recommended Name: Bestrophin-1  
Size: 585 amino acids; 67684 Da
Subunit: Tetramer or pentamers. May interact with PPP2CB and PPP2R1B (By similarity)
Sequence caution: Sequence=BAH12234.1; Type=Erroneous initiation; Sequence=BAH13472.1; Type=Erroneous initiation;
Secondary accessions: A8K0W6 B7Z3J8 B7Z736 O75904 Q53YQ9 Q8IUR9 Q8IZ80
Alternative splicing: 3 isoforms:  O76090-1   O76090-3   O76090-4   

Explore the universe of human proteins at neXtProt for BEST1: NX_O76090

Explore proteomics data for BEST1 at MOPED

Post-translational modifications: 

  • Phosphorylated by PP2A (By similarity)1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See BEST1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001132915.1  NP_004174.1  

    ENSEMBL proteins: 
     ENSP00000367282   ENSP00000431189   ENSP00000432681   ENSP00000399709   ENSP00000433195  
     ENSP00000408390   ENSP00000367281   ENSP00000301774  
    Reactome Protein details: O76090

    BEST1 Human Recombinant Protein Products:

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    Novus Biologicals BEST1 Proteins
    Novus Biologicals BEST1 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
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    Cloud-Clone Corp. Proteins for BEST1

    BEST1 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of BEST1
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    Search for Antibodies for BEST1 at Abcam
    Cloud-Clone Corp. Antibodies for BEST1
    ThermoFisher Antibodies for BEST1
    LSBio Antibodies in human, mouse, rat for BEST1

    BEST1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for BEST1
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for BEST1
    Cloud-Clone Corp. CLIAs for BEST1


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    BEST: Ion channels / Chloride channels : Calcium activated : Bestrophins

    2 InterPro protein domains:
     IPR000615 Bestrophin
     IPR021134 Bestrophin/UPF0187

    Graphical View of Domain Structure for InterPro Entry O76090

    ProtoNet protein and cluster: O76090

    1 Blocks protein domain: IPB000615 Putative membrane protein

    UniProtKB/Swiss-Prot: BEST1_HUMAN, O76090
    Similarity: Belongs to the bestrophin family


    BEST1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: BEST1_HUMAN, O76090
    Function: Forms calcium-sensitive chloride channels. Highly permeable to bicarbonate

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005254contributes to chloride channel activity IDA17003041
         
    BEST1 for ontologies           About GeneDecksing


    Phenotypes:
         5 GenomeRNAi human phenotypes for BEST1:
     Decreased POU5F1-GFP protein e  Decreased cilium length after   Increased G2M DNA content  Increased circadian rhythm amp 
     Increased number of mitotic ce 

         2 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Best1):
     pigmentation  vision/eye 

    BEST1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Best1tm1Lmar for BEST1

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for BEST1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for BEST1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for BEST1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for BEST1

    miRNA
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    Block miRNA regulation of human, mouse, rat BEST1 using miScript Target Protectors
    2 qRT-PCR Assays for microRNAs that regulate BEST1:
    hsa-miR-542-3p hsa-miR-4302
    SwitchGear 3'UTR luciferase reporter plasmidBEST1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for BEST1
    Predesigned siRNA for gene silencing in human, mouse, rat BEST1

    Gene Editing
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    Clone
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    OriGene clones in human, mouse for BEST1 (see all 12)
    OriGene ORF clones in mouse, rat for BEST1
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    GenScript: all cDNA clones in your preferred vector (see all 2): BEST1 (NM_004183)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for BEST1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat BEST1

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for BEST1
    Browse ESI BIO Cell Lines and PureStem Progenitors for BEST1 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BEST1


    (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
    BEST1_HUMAN, O76090: Cell membrane; Multi-pass membrane protein. Basolateral cell membrane
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    cytosol4
    cytoskeleton1
    endoplasmic reticulum1
    extracellular1
    nucleus1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005829cytosol TAS17003041
    GO:0005886plasma membrane TAS--
    GO:0016020membrane TAS10737974
    GO:0016021integral component of membrane TAS10737974
    GO:0016323basolateral plasma membrane IDA11050159

    BEST1 for ontologies           About GeneDecksing


    (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 BEST1 About    
    See pathways by source

    SuperPathContained pathways About
    1Ion channel transport
    Ion channel transport0.58
    Stimuli-sensing channels0.58
    2Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
    Transmembrane transport of small molecules0.47

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for BEST1
        Stimuli-sensing channels



    BEST1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including BEST1: 
              Neuronal Ion Channels in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for BEST1

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

    2 Interacting proteins for BEST1 (O760903 ENSP000003017744) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PPP2R5AQ151723, ENSP000002614614I2D: score=1 STRING: ENSP00000261461
    PPP2CAP677753, ENSP000004184474I2D: score=1 STRING: ENSP00000418447
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006821chloride transport IDA17003041
    GO:0007601visual perception TAS9662395
    GO:0030321transepithelial chloride transport IDA17003041
    GO:0034220ion transmembrane transport TAS--
    GO:0050908detection of light stimulus involved in visual perception IEA--

    BEST1 for ontologies           About GeneDecksing



    (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 BEST1

    3 HMDB Compounds for BEST1    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    ChlorineCl2 (see all 13)16887-00-6--
    Hydrogen carbonateBicarbonate (see all 19)71-52-3--

    4 Novoseek inferred chemical compound relationships for BEST1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    chloride 66 18 12565808 (1), 19635817 (1), 20238019 (1), 15627199 (1) (see all 15)
    phenylalanine 17 1 15218265 (1)
    calcium 15.5 11 12939260 (4), 19262692 (3), 11904445 (1), 18945938 (1) (see all 5)
    vegf 0 2 15389527 (1), 16971894 (1)



    BEST1 for compounds           About GeneDecksing



    (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,
    Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for BEST1 gene (2 alternative transcripts): 
    NM_001139443.1  NM_004183.3  

    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000378043(uc010rlq.1 uc001nss.3 uc009ynt.3 uc010rlt.2)
    ENST00000534553 ENST00000529265(uc010rlp.2) ENST00000533521 ENST00000524877(uc001nsq.3 uc010rlu.1)
    ENST00000524926 ENST00000449131(uc001nsr.2 uc010rlv.2) ENST00000526988
    ENST00000435278 ENST00000378042(uc010rlr.1 uc001nst.3) ENST00000301774(uc010rls.1)

    miRNA
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    Block miRNA regulation of human, mouse, rat BEST1 using miScript Target Protectors
    2 qRT-PCR Assays for microRNAs that regulate BEST1:
    hsa-miR-542-3p hsa-miR-4302
    SwitchGear 3'UTR luciferase reporter plasmidBEST1 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for BEST1
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): BEST1 (NM_004183)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for BEST1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat BEST1
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for BEST1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat BEST1
      QuantiTect SYBR Green Assays in human, mouse, rat BEST1
      QuantiFast Probe-based Assays in human, mouse, rat BEST1

    Selected AceView cDNA sequences (see all 86):

    AF057170 CA395098 BM707649 BQ185946 BQ184248 AY515704 CD518675 BM707813 
    CA389968 AF057169 AF073501 BC015220 BC041664 BU733312 NM_004183 CA397980 
    BU731149 BM694530 BM562042 AA307119 CA391418 AA991578 AA318352 BE410951 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for BEST1 (see all 6)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c ^ 11
    SP1:                                                                          -                                   -         
    SP2:                                                                                                              -         
    SP3:                    -     -                                               -     -     -                       -         
    SP4:                    -     -                                               -                                             
    SP5:                          -     -     -     -     -     -     -     -     -     -                                       


    ECgene alternative splicing isoforms for BEST1

    (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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    BEST1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCCTACAACA
    BEST1 Expression
    About this image


    BEST1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Eye (Sensory Organs)    fully expand to see all 9 entries
             Mature Retinal Pigmented Epithelium Cells Retinal Pigmented Epithelium
             Retinal pigmented epithelium cells
     
     NULL (Sensory Organs)    fully expand to see all 6 entries
             Retinal pigmented epithelium cells
     
     Epithelial Cells
             Mature Retinal Pigmented Epithelium Cells Retinal Pigmented Epithelium
     
     Blood (Hematopoietic System)
             Granulocytes Peripheral Blood
    BEST1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    BEST1 Protein Expression

    UniProtKB/Swiss-Prot: BEST1_HUMAN, O76090
    Tissue specificity: Predominantly expressed in the basolateral membrane of the retinal pigment epithelium

        Pathway & Disease-focused RT2 Profiler PCR Array including BEST1: 
              Neuronal Ion Channels in human mouse rat

    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat BEST1
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    QuantiFast Probe-based Assays in human, mouse, rat BEST1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BEST1

    (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 animals.

    Orthologs for BEST1 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Best11 , 5 bestrophin 11, 5 76.89(n)1
    70.26(a)1
      19 (6.24 cM)5
    241151  NM_011913.21  NP_036043.21 
     99851745 
    chicken
    (Gallus gallus)
    Aves BEST11 bestrophin 1 66.72(n)
    61.87(a)
      423124  XM_004941488.1  XP_004941545.1 
    lizard
    (Anolis carolinensis)
    Reptilia BEST16
    bestrophin 1
    53(a)
    1 ↔ 1
    GL343235.1(2236871-2272751)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia best11 bestrophin 1 65.54(n)
    65.04(a)
      100302038  NM_001161751.1  NP_001155223.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5606081 bestrophin-1-like 64.19(n)
    62.71(a)
      560608  XM_684006.6  XP_689098.3 
    fruit fly
    (Drosophila melanogaster)
    Insecta Best46
    Best36
    (see all 4)
    Bestrophin 3
    (see all 4)
    29(a)
    29(a)
    (see all 4)
    many ↔ many
    many ↔ many
    (see all 4)
    3L(15292058-15294042)
    3L(15294015-15295885)
    worm
    (Caenorhabditis elegans)
    Secernentea best-236
    best-136
    (see all 27)
    Protein BEST-13 (best-13) mRNA, complete cds
    (see all 27)
    32(a)
    30(a)
    (see all 27)
    many ↔ many
    many ↔ many
    (see all 27)
    II(7904638-7907589) WBGene00014989
    IV(9903912-9905910) WBGene00009323


    ENSEMBL Gene Tree for BEST1 (if available)
    TreeFam Gene Tree for BEST1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for BEST1 gene
    BEST22  BEST42  BEST32  
    4 SIMAP similar genes for BEST1 using alignment to 5 protein entries:     BEST1_HUMAN (see all proteins):
    BEST2    NARF    BEST3    BEST4

    BEST1 for paralogs           About GeneDecksing



    (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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    Selected SNPs for BEST1 (see all 700)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs289402751,2,,4
    CVitelliform macular dystrophy 2 (VMD2)4 pathogenic161639814(+) CTTACA/CCAAGC 3 T P mis1 int1 ese30--------
    rs289402761,2,,4
    CVitelliform macular dystrophy 2 (VMD2)4 pathogenic161639823(+) GCCAAA/GTGGCT 3 M V mis1 int10--------
    rs289402781,2,,4
    CAdult-onset vitelliform macular dystrophy (AVMD)4 pathogenic161639938(+) CATCCA/GCTTTA 3 H R mis1 int10--------
    rs289402741,2,,4
    CVitelliform macular dystrophy 2 (VMD2)4 pathogenic161643713(+) GCTTCC/TACGTG 4 H Y mis1 ese30--------
    rs289402731,2,,4
    CVitelliform macular dystrophy 2 (VMD2)4 pathogenic161643739(+) CGCTGC/GTGGAA 4 C W mis1 ese30--------
    rs1219182841,2,,4
    CVitelliform macular dystrophy 2 (VMD2)4 pathogenic161643882(+) CCTGCA/GCAGCG 4 H R mis10--------
    rs2002774761,2,,4
    CVitelliform macular dystrophy 2 (VMD2)4 untested161644936(+) GAAGGC/TGTGGC 4 A V mis10--------
    rs746536911,2,,4
    C,FVitelliform macular dystrophy 2 (VMD2)4 untested161644971(+) TCCTGC/ATCCAG 4 /I /L mis12Minor allele frequency- A:0.02WA NA 4670
    rs289414691,2,,4
    CVitelliform macular dystrophy 2 (VMD2)4 pathogenic161645419(+) ATGCCA/TACGAC 4 N Y mis1 ese30--------
    rs289405701,2,,4
    CVitelliform macular dystrophy 2 (VMD2)4 pathogenic161646149(+) TGTGGC/TGGTGT 4 A V mis1 ese30--------

    HapMap Linkage Disequilibrium report for BEST1 (61717293 - 61732987 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for BEST1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv897617CNV Loss21882294

    Human Gene Mutation Database (HGMD): BEST1
    Locus Specific Mutation Databases (LSDB): BEST1

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing BEST1
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607854   
    OMIM disorders: 153700  608161  611809  193220  613194  
    UniProtKB/Swiss-Prot: BEST1_HUMAN, O76090
  • Vitelliform macular dystrophy 2 (VMD2) [MIM:153700]: VMD2 is an autosomal dominant form of macular
    degeneration that usually begins in childhood or adolescence. VMD2 is characterized by typical 'egg-yolk' macular
    lesions due to abnormal accumulation of lipofuscin within and beneath the retinal pigment epithelium cells.
    Progression of the disease leads to destruction of the retinal pigment epithelium and vision loss. Note=The
    disease is caused by mutations affecting the gene represented in this entry
  • Retinitis pigmentosa 50 (RP50) [MIM:613194]: 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. Note=The disease is caused by mutations
    affecting the gene represented in this entry
  • Adult-onset vitelliform macular dystrophy (AVMD) [MIM:608161]: A rare autosomal dominant disorder with
    incomplete penetrance and highly variable expression. Patients usually become symptomatic in the fourth or fifth
    decade of life with a protracted disease of decreased visual acuity. Note=The disease is caused by mutations
    affecting the gene represented in this entry
  • Bestrophinopathy, autosomal recessive (ARB) [MIM:611809]: A retinopathy characterized by loss of central
    vision, an absent electro-oculogram light rise, and electroretinogram anomalies. Note=The disease is caused by
    mutations affecting the gene represented in this entry
  • Vitreoretinochoroidopathy, autosomal dominant (ADVIRC) [MIM:193220]: A disorder characterized by
    vitreoretinochoroidal dystrophy. The clinical presentation is variable. VRCP may be associated with cataract,
    nanophthalmos, microcornea, shallow anterior chamber, and glaucoma. Note=The disease is caused by mutations
    affecting the gene represented in this entry

  • Selected diseases for BEST1 (see all 35):    
    About MalaCards
    vitreoretinochoroidopathy    best1-related retinitis pigmentosa    best vitelliform macular dystrophy    retinitis pigmentosa-50
    retinitis pigmentosa, concentric    bestrophinopathy    macular dystrophy, concentric annular    vitelliform macular dystrophy
    adult-onset vitelliform macular dystrophy    microcornea, rod-cone dystrophy, cataract, and posterior staphyloma    neurogenic bowel    macular dystrophy
    cone dystrophy    leber congenital amaurosis    retinoschisis    pigmentary retinopathy
    rhyns syndrome    fundus dystrophy    age related macular degeneration    retinal disease

    3 diseases from the University of Copenhagen DISEASES database for BEST1:
    Vitelliform macular dystrophy     Bestrophinopathy     Fundus dystrophy

    BEST1 for disorders           About GeneDecksing

    7 Novoseek inferred disease relationships for BEST1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    macular dystrophy, vitelliform 98.7 69 10682987 (3), 16754206 (3), 11449320 (2), 10854112 (2) (see all 41)
    vitreoretinochoroidopathy 95.2 5 15452077 (1), 15627199 (1), 18309337 (1), 16707793 (1)
    drusen 67.2 4 19421767 (4)
    maculopathy 60.5 6 19421767 (3), 17646752 (2), 10737974 (1)
    retinopathy 57.8 9 10682987 (1), 12565808 (1), 10854112 (1), 15627199 (1) (see all 9)
    retinal degeneration 51.2 5 16707793 (1), 16940553 (1), 18955594 (1), 17968025 (1)
    cystic fibrosis 42.7 5 20100480 (1), 17361457 (1), 16314923 (1), 19237432 (1) (see all 5)

    GeneTests: BEST1
    GeneReviews: BEST1
    Genetic Association Database (GAD): BEST1
    Human Genome Epidemiology (HuGE) Navigator: BEST1 (2 documents)

    Export disorders for BEST1 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 BEST1 gene, integrated from 10 sources (see all 175):
    (articles sorted by number of sources associating them with BEST1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Missense mutations in a retinal pigment epithelium protein, bestrophin-1, cause retinitis pigmentosa. (PubMed id 19853238)1, 2, 9 Davidson A.E....Manson F.D. (Am. J. Hum. Genet. 2009)
    2. Mutations of VMD2 splicing regulators cause nanophthalmos and autosomal dominant vitreoretinochoroidopathy (ADVIRC). (PubMed id 15452077)1, 2, 9 Yardley J.... Black G.C.M. (Invest. Ophthalmol. Vis. Sci. 2004)
    3. A novel spontaneous missense mutation in VMD2 gene is a cause of a Best macular dystrophy sporadic case. (PubMed id 10682987)1, 2, 9 Palomba G....Pirastu M. (Am. J. Ophthalmol. 2000)
    4. Bestrophin Cl- channels are highly permeable to HCO3-. (PubMed id 18400985)1, 2, 9 Qu Z. and Hartzell H.C. (Am. J. Physiol. 2008)
    5. Best's vitelliform macular dystrophy caused by a new mutation (Val89Ala) in the VMD2 gene. (PubMed id 11449320)1, 2, 9 Eksandh L.... Andreasson S. (Ophthalmic Genet. 2001)
    6. Allelic variation in the VMD2 gene in best disease and age-related macular degeneration. (PubMed id 10798642)1, 2, 9 Lotery A.J....Stone E.M. (Invest. Ophthalmol. Vis. Sci. 2000)
    7. Mutation analysis of the VMD2 gene in Thai families with Best macular dystrophy. (PubMed id 18766995)1, 2, 9 Atchaneeyasakul L.O.... Limwongse C. (Ophthalmic Genet. 2008)
    8. Identification of a novel VMD2 mutation in Japanese patients with Best disease. (PubMed id 12187431)1, 2, 9 Yanagi Y.... Mori M. (Ophthalmic Genet. 2002)
    9. Bestrophin-1 enables Ca2+-activated Cl- conductance in epithelia. (PubMed id 17003041)1, 3, 9 Barro Soria R....Kunzelmann K. (J. Biol. Chem. 2009)
    10. Structure-function analysis of the bestrophin family of anion channels. (PubMed id 12907679)1, 2, 9 Tsunenari T....Nathans J. (J. Biol. Chem. 2003)

    (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)
    About This Section

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    Entrez Gene: 7439 HGNC: 12703 AceView: VMD2 Ensembl:ENSG00000167995 euGenes: HUgn7439
    ECgene: BEST1 H-InvDB: BEST1

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for BEST1 Pharmacogenomics, SNPs, Pathways
    VMD2 mutation databasehttp://www-huge.uni-regensburg.de/VMD2_database/index.php?select_db=VMD2
    Mutations of the VMD2 genehttp://www.retina-international.org/sci-news/databases/mutation-database/best1-mutation/
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=BEST1[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for BEST1 gene:
    Search GeneIP for patents involving BEST1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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