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Aliases for BEST1 Gene

Aliases for BEST1 Gene

  • Bestrophin 1 2 3 5
  • Vitelliform Macular Dystrophy Protein 2 3 4
  • Best Disease 2 3
  • TU15B 3 4
  • VMD2 3 4
  • Vitelliform Macular Dystrophy 2 2
  • Best1V1Delta2 3
  • Bestrophin-1 3
  • BEST 3
  • RP50 3
  • ARB 3
  • BMD 3

External Ids for BEST1 Gene

Previous HGNC Symbols for BEST1 Gene

  • VMD2

Previous GeneCards Identifiers for BEST1 Gene

  • GC11P061475
  • GC11P061717
  • GC11P058045

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 Vitreoretinochoroidopathy and Bestrophinopathy, Autosomal Recessive. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Ion channel transport. GO annotations related to this gene include chloride channel activity. An important paralog of this gene is BEST3.

UniProtKB/Swiss-Prot for BEST1 Gene

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

Gene Wiki entry for BEST1 Gene

Additional gene information for BEST1 Gene

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

Genomics for BEST1 Gene

Regulatory Elements for BEST1 Gene

Enhancers for BEST1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11H061960 1.8 FANTOM5 ENCODE dbSUPER 22.6 +22.2 22209 16.4 MLX ZFP64 DMAP1 YBX1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D UBXN1 LOC105369332 WDR74 INTS5 MTA2 CPSF7 TMEM138 NXF1 EML3 STX5
GH11H062024 2.1 FANTOM5 Ensembl ENCODE dbSUPER 11.3 +78.9 78850 2.9 PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 YY1 ZNF766 CBX5 FTH1 BEST1 DAGLA FEN1 TTC9C RPS2P37 GC11P062053
GH11H061980 1.4 Ensembl ENCODE dbSUPER 16.6 +34.8 34845 2.2 ELF3 FOXA2 ARID4B DMAP1 RAD21 RARA YY1 ZNF121 CREM SP5 BEST1 UBXN1 GC11M061991 PIR56238
GH11H062551 2.1 FANTOM5 Ensembl ENCODE dbSUPER 10.6 +610.5 610462 12.9 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 YBX1 ZNF207 EML3 TUT1 MTA2 TAF6L NXF1 LOC105369332 WDR74 STX5 INTS5 TTC9C
GH11H061826 2 FANTOM5 Ensembl ENCODE dbSUPER 10.4 -114.3 -114346 12.6 HDGF PKNOX1 ARNT ARID4B SIN3A YY1 ZNF766 ZNF143 SP3 SP5 FADS2 MTA2 FADS1 TMEM138 EML3 STX5 CPSF7 NXF1 GANAB TMEM179B
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around BEST1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for BEST1 Gene

Genomic Locations for BEST1 Gene
18,801 bases
Plus strand

Genomic View for BEST1 Gene

Genes around BEST1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BEST1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BEST1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BEST1 Gene

Proteins for BEST1 Gene

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

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A8K0W6
    • B7Z3J8
    • B7Z736
    • O75904
    • Q53YQ9
    • Q8IUR9
    • Q8IZ80

    Protein attributes for BEST1 Gene

    585 amino acids
    Molecular mass:
    67684 Da
    Quaternary structure:
    • Homooligomer (tetramer or pentamer) (PubMed:26200502). May interact with PPP2CB and PPP2R1B (By similarity).
    • Sequence=BAH12234.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAH13472.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for BEST1 Gene


neXtProt entry for BEST1 Gene

Post-translational modifications for BEST1 Gene

No data available for DME Specific Peptides for BEST1 Gene

Domains & Families for BEST1 Gene

Gene Families for BEST1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for BEST1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the bestrophin family.
  • Belongs to the bestrophin family.
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.

Phenotypes From GWAS Catalog for BEST1 Gene

Gene Ontology (GO) - Molecular Function for BEST1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005229 intracellular calcium activated chloride channel activity TAS --
GO:0005254 contributes_to chloride channel activity IDA,IEA 17003041
GO:0015106 bicarbonate transmembrane transporter activity TAS --
GO:0042802 identical protein binding IPI 19372599
genes like me logo Genes that share ontologies with BEST1: view
genes like me logo Genes that share phenotypes with BEST1: view

Human Phenotype Ontology for BEST1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for BEST1 Gene

MGI Knock Outs for BEST1:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets 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

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 BEST1 gene
Compartment Confidence
plasma membrane 5
cytosol 5
cytoskeleton 2
extracellular 1
peroxisome 1
endoplasmic reticulum 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,IEA --
GO:0016020 membrane TAS 10737974
GO:0016021 integral component of membrane TAS 10737974
GO:0016323 basolateral plasma membrane IDA,IEA 11050159
genes like me logo Genes that share ontologies with BEST1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for BEST1 Gene

Pathways & Interactions 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:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006821 chloride transport IEA,IDA 17003041
GO:0007601 visual perception IEA,TAS 9662395
GO:0015701 bicarbonate transport IEA --
genes like me logo Genes that share ontologies with BEST1: view

No data available for SIGNOR curated interactions for BEST1 Gene

Drugs & Compounds for BEST1 Gene

(2) Drugs for BEST1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0

(4) Additional Compounds for BEST1 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Chloride ion
  • Bertholite
  • Chloor
  • Chlor
  • Chlore
  • Chloride
Hydrogen carbonate
  • Bicarbonate
  • Bicarbonate (HCO3-)
  • Bicarbonate anion
  • Bicarbonate ion
  • Bicarbonate ion (HCO31-)
genes like me logo Genes that share compounds with BEST1: view

Transcripts for BEST1 Gene

Unigene Clusters for BEST1 Gene

Bestrophin 1:
Representative Sequences:

Clone Products

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: - - - - - - - - - -

Relevant External Links for BEST1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for BEST1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BEST1 Gene

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

This gene is overexpressed in Whole Blood (x6.4), Brain - Spinal cord (cervical c-1) (x4.6), and Nerve - Tibial (x4.1).

Protein differential expression in normal tissues from HIPED for BEST1 Gene

This gene is overexpressed in Breast (66.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for BEST1 Gene

Protein tissue co-expression partners for BEST1 Gene

NURSA nuclear receptor signaling pathways regulating expression of BEST1 Gene:


SOURCE GeneReport for Unigene cluster for BEST1 Gene:


mRNA Expression by UniProt/SwissProt for BEST1 Gene:

Tissue specificity: Predominantly expressed in the basolateral membrane of the retinal pigment epithelium.

Evidence on tissue expression from TISSUES for BEST1 Gene

  • Nervous system(4.8)
  • Eye(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for BEST1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • outer ear
  • skull
  • penis
  • testicle
  • blood
  • blood vessel
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns 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
(Pan troglodytes)
Mammalia BEST1 33 34
  • 99.72 (n)
(Canis familiaris)
Mammalia BEST1 33
  • 86.31 (n)
VMD2 34
  • 71 (a)
(Bos Taurus)
Mammalia BEST1 33 34
  • 84.71 (n)
(Rattus norvegicus)
Mammalia Best1 33
  • 77.26 (n)
(Mus musculus)
Mammalia Best1 33 16 34
  • 76.89 (n)
(Ornithorhynchus anatinus)
Mammalia BEST1 34
  • 58 (a)
(Monodelphis domestica)
Mammalia BEST1 34
  • 57 (a)
(Gallus gallus)
Aves BEST1 33 34
  • 66.72 (n)
(Anolis carolinensis)
Reptilia BEST1 34
  • 53 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia best1 33
  • 65.54 (n)
(Danio rerio)
Actinopterygii LOC560608 33
  • 64.19 (n)
best1 34
  • 38 (a)
fruit fly
(Drosophila melanogaster)
Insecta Best3 34
  • 29 (a)
Best4 34
  • 29 (a)
Best1 34
  • 25 (a)
Best2 34
  • 23 (a)
(Caenorhabditis elegans)
Secernentea best-23 34
  • 32 (a)
best-13 34
  • 30 (a)
best-9 34
  • 30 (a)
best-14 34
  • 29 (a)
best-2 34
  • 28 (a)
best-21 34
  • 28 (a)
best-3 34
  • 26 (a)
best-1 34
  • 25 (a)
best-18 34
  • 25 (a)
best-4 34
  • 25 (a)
best-6 34
  • 25 (a)
best-10 34
  • 24 (a)
best-15 34
  • 24 (a)
best-22 34
  • 24 (a)
best-5 34
  • 24 (a)
best-7 34
  • 24 (a)
best-11 34
  • 23 (a)
best-17 34
  • 23 (a)
best-19 34
  • 23 (a)
best-20 34
  • 23 (a)
best-26 34
  • 23 (a)
best-12 34
  • 22 (a)
best-8 34
  • 22 (a)
best-16 34
  • 21 (a)
best-24 34
  • 20 (a)
best-25 34
  • 20 (a)
C09B9.85 34
  • 17 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 48 (a)
Species where no ortholog for BEST1 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 (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

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

Paralogs for BEST1 Gene

Paralogs for BEST1 Gene

(4) 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
rs121918284 Pathogenic, Bestrophinopathy, autosomal recessive (ARB) [MIM:611809], Macular dystrophy, vitelliform, 2 (VMD2) [MIM:153700] 61,955,892(+) CCTGC(A/G)CAGCG nc-transcript-variant, reference, missense
rs121918287 Pathogenic, Bestrophinopathy, autosomal recessive (ARB) [MIM:611809] 61,959,892(+) ACCAG(A/G)TGTCC intron-variant, nc-transcript-variant, reference, synonymous-codon, missense
rs121918288 Pathogenic, Bestrophinopathy, autosomal recessive (ARB) [MIM:611809], Macular dystrophy, vitelliform, 2 (VMD2) [MIM:153700] 61,951,928(+) CCTGC(C/T)CTGCT intron-variant, nc-transcript-variant, reference, missense
rs121918289 Pathogenic, Vitreoretinochoroidopathy, autosomal dominant (ADVIRC) [MIM:193220] 61,955,726(+) TCTAC(A/G)TGACG nc-transcript-variant, reference, missense, utr-variant-5-prime
rs121918290 Pathogenic, Vitreoretinochoroidopathy, autosomal dominant (ADVIRC) [MIM:193220] 61,958,146(+) CCCAG(A/G/T)TGGTG intron-variant, nc-transcript-variant, upstream-variant-2KB, reference, missense

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

Variant ID Type Subtype PubMed ID
nsv975936 CNV duplication 23825009
esv3892020 CNV loss 25118596

Variation tolerance for BEST1 Gene

Residual Variation Intolerance Score: 72.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.64; 72.72% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for BEST1 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for BEST1 Gene

Disorders for BEST1 Gene

MalaCards: The human disease database

(20) MalaCards diseases for BEST1 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
  • microcornea, rod-cone dystrophy, cataract, and posterior staphyloma
bestrophinopathy, autosomal recessive
  • bestrophinopathy
macular dystrophy, vitelliform, 2
  • best vitelliform macular dystrophy
retinitis pigmentosa-50
  • retinitis pigmentosa, concentric
best vitelliform macular dystrophy
  • vitelliform macular dystrophy
- elite association - COSMIC cancer census association via MalaCards
Search BEST1 in MalaCards View complete list of genes associated with diseases


  • 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, ECO:0000269 PubMed:19853238, ECO:0000269 PubMed:21330666, ECO:0000269 PubMed:26200502, ECO:0000269 PubMed:26720466}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 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:18400985, ECO:0000269 PubMed:18766995, ECO:0000269 PubMed:19357557, ECO:0000269 PubMed:21330666, 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.
  • 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.

Relevant External Links for BEST1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with BEST1: view

No data available for Genatlas for BEST1 Gene

Publications for BEST1 Gene

  1. Bestrophin-1 enables Ca2+-activated Cl- conductance in epithelia. (PMID: 17003041) Barro Soria R … Kunzelmann K (The Journal of biological chemistry 2009) 2 3 22 60
  2. Missense mutations in a retinal pigment epithelium protein, bestrophin-1, cause retinitis pigmentosa. (PMID: 19853238) Davidson AE … Manson FD (American journal of human genetics 2009) 3 4 22 60
  3. Biallelic mutation of BEST1 causes a distinct retinopathy in humans. (PMID: 18179881) Burgess R … Black GC (American journal of human genetics 2008) 3 4 22 60
  4. Bestrophin Cl- channels are highly permeable to HCO3-. (PMID: 18400985) Qu Z … Hartzell HC (American journal of physiology. Cell physiology 2008) 3 4 22 60
  5. Mutation analysis of the VMD2 gene in thai families with best macular dystrophy. (PMID: 18766995) Atchaneeyasakul LO … Limwongse C (Ophthalmic genetics 2008) 3 4 22 60

Products for BEST1 Gene

Sources for BEST1 Gene

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