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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 Macular Dystrophy, Vitelliform, 2 and Vitreoretinochoroidopathy. 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. Gene Ontology (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

GeneHancer (GH) Regulatory Elements for BEST1 Gene

Promoters and enhancers for BEST1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J061949 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 650.7 +3.4 3402 2 PKNOX1 SMAD1 ATF1 BRCA1 POLR2B ZNF766 GLIS2 ZNF548 FOS ATF7 BEST1 CPSF7 NXF1 SNHG1 GANAB TMEM138 EML3 MTA2 CSKMT UBXN1
GH11J061947 Enhancer 1.3 Ensembl ENCODE dbSUPER 650.7 +1.3 1265 0.9 HDGF PKNOX1 ARID4B SIN3A FEZF1 ZNF2 ZNF48 ARID2 ZNF207 ZNF143 BEST1 RAB3IL1 GC11M061964
GH11J061946 Promoter/Enhancer 0.7 EPDnew dbSUPER 650.7 -0.4 -383 0.1 BEST1 RAB3IL1
GH11J061952 Promoter/Enhancer 0.7 EPDnew dbSUPER 650.4 +5.5 5519 0.1 BEST1 GC11M061964
GH11J061948 Enhancer 0.6 dbSUPER 650.7 +1.9 1912 0.3 MEIS2 PKNOX1 CEBPA CEBPB ZMYM3 NFE2 CEBPG ZBTB40 BEST1 GC11M061964
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BEST1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BEST1 gene promoter:
  • NRSF form 2
  • NRSF form 1
  • LCR-F1
  • CBF(2)
  • CBF-A
  • CBF-B
  • CBF-C
  • CP1A
  • CP1C
  • NF-Y

Genomic Locations for BEST1 Gene

Genomic Locations for BEST1 Gene
18,801 bases
Plus strand
15,695 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 IEA,IDA 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:0006811 ion transport IEA --
GO:0006821 chloride transport IDA,IEA 17003041
GO:0007601 visual perception TAS,IEA 9662395
GO:0015701 bicarbonate transport IEA --
GO:0030321 transepithelial chloride transport IDA 17003041
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 Approved Nutra 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Chloride ion
  • Chloride(1-)
  • Chlorine anion
  • CL(-)
  • Bertholite
  • Chloor
Hydrogen carbonate
  • [co(OH)2]
  • Dihydrogen carbonate
  • H2CO3
  • Koehlensaeure
  • Carbonate
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 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 34 33
  • 99.72 (n)
(Canis familiaris)
Mammalia BEST1 33
  • 86.31 (n)
VMD2 34
  • 71 (a)
(Bos Taurus)
Mammalia BEST1 34 33
  • 84.71 (n)
(Rattus norvegicus)
Mammalia Best1 33
  • 77.26 (n)
(Mus musculus)
Mammalia Best1 16 34 33
  • 76.89 (n)
(Ornithorhynchus anatinus)
Mammalia BEST1 34
  • 58 (a)
(Monodelphis domestica)
Mammalia BEST1 34
  • 57 (a)
(Gallus gallus)
Aves BEST1 34 33
  • 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 Best4 34
  • 29 (a)
Best3 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-21 34
  • 28 (a)
best-2 34
  • 28 (a)
best-3 34
  • 26 (a)
best-6 34
  • 25 (a)
best-4 34
  • 25 (a)
best-1 34
  • 25 (a)
best-18 34
  • 25 (a)
best-22 34
  • 24 (a)
best-5 34
  • 24 (a)
best-10 34
  • 24 (a)
best-15 34
  • 24 (a)
best-7 34
  • 24 (a)
best-26 34
  • 23 (a)
best-11 34
  • 23 (a)
best-19 34
  • 23 (a)
best-20 34
  • 23 (a)
best-17 34
  • 23 (a)
best-8 34
  • 22 (a)
best-12 34
  • 22 (a)
best-16 34
  • 21 (a)
best-25 34
  • 20 (a)
best-24 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)
Evolutionary constrained regions (ECRs) for BEST1: view image

Paralogs for BEST1 Gene

Paralogs for BEST1 Gene

(4) SIMAP similar genes for BEST1 Gene using alignment to 5 proteins:

  • B7Z1N8_HUMAN
  • B7Z375_HUMAN
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 Variation AA Info Type
rs1036086403 uncertain-significance, Retinitis Pigmentosa, Recessive, Vitelliform macular dystrophy type 2, Vitreoretinochoroidopathy 61,962,611(+) C/T 3_prime_UTR_variant, coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1109748 not-provided, benign, not provided, not specified, Vitelliform macular dystrophy type 2, Retinitis Pigmentosa, Recessive, Vitreoretinochoroidopathy 61,955,173(+) C/A 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, non_coding_transcript_variant, synonymous_variant
rs111326315 benign, likely-benign, not specified, Vitelliform macular dystrophy type 2, Iron Overload, Vitreoretinochoroidopathy, Retinitis Pigmentosa, Recessive 61,962,628(+) G/A 3_prime_UTR_variant, coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs112199774 likely-benign, Vitelliform macular dystrophy type 2, Retinitis Pigmentosa, Recessive, Iron Overload, Vitreoretinochoroidopathy 61,962,297(+) C/T 3_prime_UTR_variant, coding_sequence_variant, non_coding_transcript_variant, stop_gained, synonymous_variant
rs117165769 likely-benign, Vitelliform macular dystrophy type 2, Retinitis Pigmentosa, Recessive, Vitreoretinochoroidopathy 61,950,091(+) T/A 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, non_coding_transcript_variant

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

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

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)

Additional Variant Information for BEST1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for BEST1 Gene

MalaCards: The human disease database

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

- elite association - COSMIC cancer census association via MalaCards
Search BEST1 in MalaCards View complete list of genes associated with diseases


  • 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.
  • 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.
  • 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.

Additional Disease Information for BEST1

Genetic Association Database
Human Genome Epidemiology 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. 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 58
  2. 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 58
  3. Bestrophin Cl- channels are highly permeable to HCO3-. (PMID: 18400985) Qu Z … Hartzell HC (American journal of physiology. Cell physiology 2008) 3 4 22 58
  4. 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 58
  5. 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 58

Products for BEST1 Gene

Sources for BEST1 Gene

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