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Aliases for BEST1 Gene

Aliases for BEST1 Gene

  • Bestrophin 1 2 3
  • VMD2 3 4 6
  • Vitelliform Macular Dystrophy Protein 2 3 4
  • Best Disease 2 3
  • TU15B 3 4
  • RP50 3 6
  • ARB 3 6
  • Vitelliform Macular Dystrophy 2 2
  • Best1V1Delta2 3
  • Bestrophin-1 3
  • BEST 3
  • BMD 3

External Ids for BEST1 Gene

Previous Symbols for BEST1 Gene

  • VMD2

Summaries for BEST1 Gene

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 retinitis pigmentosa-50 and vitreoretinochoroidopathy. Among its related pathways are Ion channel transport and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. GO annotations related to this gene include chloride channel activity. An important paralog of this gene is BEST2.

UniProtKB/Swiss-Prot for BEST1 Gene

  • Forms calcium-sensitive chloride channels. Highly permeable to bicarbonate.

Gene Wiki entry for BEST1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BEST1 Gene

Genomics for BEST1 Gene

Genomic Location for BEST1 Gene

Start:
61,949,821 bp from pter
End:
61,965,515 bp from pter
Size:
15,695 bases
Orientation:
Plus strand

Genomic View for BEST1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for BEST1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BEST1 Gene

Regulatory Elements for BEST1 Gene

Proteins for BEST1 Gene

  • Protein details for BEST1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O76090-BEST1_HUMAN
    Recommended name:
    Bestrophin-1
    Protein Accession:
    O76090
    Secondary Accessions:
    • A8K0W6
    • B7Z3J8
    • B7Z736
    • O75904
    • Q53YQ9
    • Q8IUR9
    • Q8IZ80

    Protein attributes for BEST1 Gene

    Size:
    585 amino acids
    Molecular mass:
    67684 Da
    Quaternary structure:
    • Tetramer or pentamers. May interact with PPP2CB and PPP2R1B (By similarity).
    SequenceCaution:
    • Sequence=BAH12234.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAH13472.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for BEST1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for BEST1 Gene

Proteomics data for BEST1 Gene at MOPED

Post-translational modifications for BEST1 Gene

Other Protein References for BEST1 Gene

No data available for DME Specific Peptides for BEST1 Gene

Domains for BEST1 Gene

Gene Families for BEST1 Gene

HGNC:
  • BEST :Ion channels / Chloride channels : Calcium activated : Bestrophins

Protein Domains for BEST1 Gene

UniProtKB/Swiss-Prot:

BEST1_HUMAN
Family:
  • Belongs to the bestrophin family.:
    • O76090
genes like me logo Genes that share domains with BEST1: view

Function for BEST1 Gene

Molecular function for BEST1 Gene

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

Gene Ontology (GO) - Molecular Function for BEST1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005254 contributes_to chloride channel activity IDA 17003041
genes like me logo Genes that share ontologies with BEST1: view
genes like me logo Genes that share phenotypes with BEST1: view

Animal Models for BEST1 Gene

MGI Knock Outs for BEST1:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for BEST1 Gene

Localization for BEST1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BEST1 Gene

Cell membrane; Multi-pass membrane protein. Basolateral cell membrane.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for BEST1 Gene COMPARTMENTS Subcellular localization image for BEST1 gene
Compartment Confidence
plasma membrane 5
cytosol 4
cytoskeleton 1
endoplasmic reticulum 1
extracellular 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for BEST1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS 17003041
GO:0005886 plasma membrane TAS --
GO:0016020 membrane TAS 10737974
GO:0016021 integral component of membrane TAS 10737974
GO:0016323 basolateral plasma membrane IDA 11050159
genes like me logo Genes that share ontologies with BEST1: view

Pathways for BEST1 Gene

genes like me logo Genes that share pathways with BEST1: view

Pathways by source for BEST1 Gene

Gene Ontology (GO) - Biological Process for BEST1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006821 chloride transport IDA 17003041
GO:0007601 visual perception TAS 9662395
GO:0030321 transepithelial chloride transport IDA 17003041
GO:0034220 ion transmembrane transport TAS --
GO:0050908 detection of light stimulus involved in visual perception IEA --
genes like me logo Genes that share ontologies with BEST1: view

Compounds for BEST1 Gene

(3) HMDB Compounds for BEST1 Gene

Compound Synonyms Cas Number PubMed IDs
Calcium
  • Ca
7440-70-2
Chlorine
  • Cl2
16887-00-6
Hydrogen carbonate
  • Bicarbonate
71-52-3

(4) Novoseek inferred chemical compound relationships for BEST1 Gene

Compound -log(P) Hits PubMed IDs
chloride 66 15
phenylalanine 17 1
calcium 15.5 10
vegf 0 2
genes like me logo Genes that share compounds with BEST1: view

Transcripts for BEST1 Gene

Unigene Clusters for BEST1 Gene

Bestrophin 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for BEST1 Gene

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: - - - - - - - - - -
SP6:

Relevant External Links for BEST1 Gene

GeneLoc Exon Structure for
BEST1
ECgene alternative splicing isoforms for
BEST1

Expression for BEST1 Gene

mRNA expression in normal human tissues for BEST1 Gene

mRNA differential expression in normal tissues according to GTEx for BEST1 Gene

This gene is overexpressed in Whole Blood (6.4), Brain - Spinal cord (cervical c-1) (4.6), and Nerve - Tibial (4.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for BEST1 Gene

SOURCE GeneReport for Unigene cluster for BEST1 Gene Hs.712676

mRNA Expression by UniProt/SwissProt for BEST1 Gene

O76090-BEST1_HUMAN
Tissue specificity: Predominantly expressed in the basolateral membrane of the retinal pigment epithelium
genes like me logo Genes that share expressions with BEST1: view

Orthologs for BEST1 Gene

This gene was present in the common ancestor of animals.

Orthologs for BEST1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia BEST1 36
  • 99.72 (n)
  • 100 (a)
BEST1 37
  • 89 (a)
OneToOne
cow
(Bos Taurus)
Mammalia BEST1 36
  • 84.71 (n)
  • 81.27 (a)
BEST1 37
  • 72 (a)
OneToOne
dog
(Canis familiaris)
Mammalia BEST1 36
  • 86.31 (n)
  • 81.28 (a)
VMD2 37
  • 71 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Best1 36
  • 76.89 (n)
  • 70.26 (a)
Best1 16
Best1 37
  • 59 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia BEST1 37
  • 57 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia BEST1 37
  • 58 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Best1 36
  • 77.26 (n)
  • 69.72 (a)
chicken
(Gallus gallus)
Aves BEST1 36
  • 66.72 (n)
  • 61.87 (a)
BEST1 37
  • 41 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia BEST1 37
  • 53 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia best1 36
  • 65.54 (n)
  • 65.04 (a)
zebrafish
(Danio rerio)
Actinopterygii best1 37
  • 38 (a)
OneToOne
LOC560608 36
  • 64.19 (n)
  • 62.71 (a)
fruit fly
(Drosophila melanogaster)
Insecta Best1 37
  • 25 (a)
ManyToMany
Best2 37
  • 23 (a)
ManyToMany
Best3 37
  • 29 (a)
ManyToMany
Best4 37
  • 29 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea best-1 37
  • 25 (a)
ManyToMany
best-10 37
  • 24 (a)
ManyToMany
best-11 37
  • 23 (a)
ManyToMany
best-12 37
  • 22 (a)
ManyToMany
best-13 37
  • 30 (a)
ManyToMany
best-14 37
  • 29 (a)
ManyToMany
best-15 37
  • 24 (a)
ManyToMany
best-16 37
  • 21 (a)
ManyToMany
best-17 37
  • 23 (a)
ManyToMany
best-18 37
  • 25 (a)
ManyToMany
best-19 37
  • 23 (a)
ManyToMany
best-2 37
  • 28 (a)
ManyToMany
best-20 37
  • 23 (a)
ManyToMany
best-21 37
  • 28 (a)
ManyToMany
best-22 37
  • 24 (a)
ManyToMany
best-23 37
  • 32 (a)
ManyToMany
best-24 37
  • 20 (a)
ManyToMany
best-25 37
  • 20 (a)
ManyToMany
best-26 37
  • 23 (a)
ManyToMany
best-3 37
  • 26 (a)
ManyToMany
best-4 37
  • 25 (a)
ManyToMany
best-5 37
  • 24 (a)
ManyToMany
best-6 37
  • 25 (a)
ManyToMany
best-7 37
  • 24 (a)
ManyToMany
best-8 37
  • 22 (a)
ManyToMany
best-9 37
  • 30 (a)
ManyToMany
C09B9.85 37
  • 17 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 48 (a)
OneToMany
Species with no ortholog for BEST1:
  • 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 (Oryza sativa)
  • 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)
  • wheat (Triticum aestivum)

Evolution for BEST1 Gene

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

Paralogs for BEST1 Gene

Paralogs for BEST1 Gene

Selected SIMAP similar genes for BEST1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with BEST1: view

Variants for BEST1 Gene

Sequence variations from dbSNP and Humsavar for BEST1 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs149698 -- 61,962,564(+) CAGAC(A/G)CCCCT synonymous-codon, reference, utr-variant-3-prime, nc-transcript-variant
rs168990 -- 61,956,387(+) TGGCT(C/G)TCGCC intron-variant
rs168991 -- 61,953,405(-) agaca(A/G)gatca intron-variant, upstream-variant-2KB
rs174481 -- 61,948,923(+) AAATA(C/G)CTAAT upstream-variant-2KB
rs183176 -- 61,954,793(-) ATGCA(G/T)CCAAG intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for BEST1 Gene

Variant ID Type Subtype PubMed ID
nsv897617 CNV Loss 21882294

Relevant External Links for BEST1 Gene

HapMap Linkage Disequilibrium report
BEST1
Human Gene Mutation Database (HGMD)
BEST1
Locus Specific Mutation Databases (LSDB)
BEST1

Disorders for BEST1 Gene

(5) OMIM Diseases for BEST1 Gene (607854)

UniProtKB/Swiss-Prot

BEST1_HUMAN
  • Macular dystrophy, vitelliform, 2 (VMD2) [MIM:153700]: 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. {ECO:0000269 PubMed:10331951, ECO:0000269 PubMed:10394929, ECO:0000269 PubMed:10453731, ECO:0000269 PubMed:10682987, ECO:0000269 PubMed:10798642, ECO:0000269 PubMed:11241846, ECO:0000269 PubMed:11449320, ECO:0000269 PubMed:12187431, ECO:0000269 PubMed:12324875, ECO:0000269 PubMed:13129869, ECO:0000269 PubMed:14517959, ECO:0000269 PubMed:15176385, ECO:0000269 PubMed:18766995, ECO:0000269 PubMed:19357557, ECO:0000269 PubMed:9662395, ECO:0000269 PubMed:9700209}. 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. {ECO:0000269 PubMed:19853238}. 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. {ECO:0000269 PubMed:18179881}. 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. {ECO:0000269 PubMed:15452077}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) University of Copenhagen DISEASES for BEST1 Gene

(7) Novoseek inferred disease relationships for BEST1 Gene

Disease -log(P) Hits PubMed IDs
macular dystrophy, vitelliform 98.7 55
vitreoretinochoroidopathy 95.2 4
drusen 67.2 4
maculopathy 60.5 6
retinopathy 57.8 9

Relevant External Links for BEST1

GeneTests
BEST1
GeneReviews
BEST1
Genetic Association Database (GAD)
BEST1
Human Genome Epidemiology (HuGE) Navigator
BEST1
genes like me logo Genes that share disorders with BEST1: view

Publications for BEST1 Gene

  1. Identification of the gene responsible for Best macular dystrophy. (PMID: 9662395) Petrukhin K. … Wadelius C. (Nat. Genet. 1998) 3 4 23
  2. Mutations in a novel gene, VMD2, encoding a protein of unknown properties cause juvenile-onset vitelliform macular dystrophy (Best's disease). (PMID: 9700209) Marquardt A. … Weber B.H.F. (Hum. Mol. Genet. 1998) 3 4 23
  3. Evaluation of the Best disease gene in patients with age-related macular degeneration and other maculopathies. (PMID: 10453731) Allikmets R. … Petrukhin K. (Hum. Genet. 1999) 3 4 23
  4. A novel spontaneous missense mutation in VMD2 gene is a cause of a Best macular dystrophy sporadic case. (PMID: 10682987) Palomba G. … Pirastu M. (Am. J. Ophthalmol. 2000) 3 4 23
  5. Allelic variation in the VMD2 gene in best disease and age-related macular degeneration. (PMID: 10798642) Lotery A.J. … Stone E.M. (Invest. Ophthalmol. Vis. Sci. 2000) 3 4 23

Products for BEST1 Gene

Sources for BEST1 Gene

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