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Aliases for BEST3 Gene

Aliases for BEST3 Gene

  • Bestrophin 3 2 3 5
  • Vitelliform Macular Dystrophy 2-Like Protein 3 3 4
  • Vitelliform Macular Dystrophy 2-Like 3 2 3
  • VMD2L3 3 4
  • Bestrophin-3 3

External Ids for BEST3 Gene

Previous HGNC Symbols for BEST3 Gene

  • VMD2L3

Previous GeneCards Identifiers for BEST3 Gene

  • GC12M068326
  • GC12M070037
  • GC12M067096

Summaries for BEST3 Gene

Entrez Gene Summary for BEST3 Gene

  • BEST3 belongs to the bestrophin family of anion channels, which includes BEST1 (MIM 607854), the gene mutant in vitelliform macular dystrophy (VMD; MIM 153700), and 2 other BEST1-like genes, BEST2 (MIM 607335) and BEST4 (MIM 607336). Bestrophins are transmembrane (TM) proteins that share a homology region containing a high content of aromatic residues, including an invariant arg-phe-pro (RFP) motif. The bestrophin genes share a conserved gene structure, with almost identical sizes of the 8 RFP-TM domain-encoding exons and highly conserved exon-intron boundaries. Each of the 4 bestrophin genes has a unique 3-prime end of variable length (Stohr et al., 2002 [PubMed 12032738]; Tsunenari et al., 2003 [PubMed 12907679]).[supplied by OMIM, Mar 2008]

GeneCards Summary for BEST3 Gene

BEST3 (Bestrophin 3) is a Protein Coding gene. Diseases associated with BEST3 include Vitelliform Macular Dystrophy. 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 BEST2.

UniProtKB/Swiss-Prot for BEST3 Gene

  • Forms calcium-sensitive chloride channels. Permeable to bicarbonate.

Additional gene information for BEST3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BEST3 Gene

Genomics for BEST3 Gene

GeneHancer (GH) Regulatory Elements for BEST3 Gene

Promoters and enhancers for BEST3 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
GH12J069685 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 671.6 +11.2 11215 5.5 ELF3 PKNOX1 SIN3A ZNF2 ZNF335 GLIS2 ELK1 RCOR1 FOS DEK BEST3 RAB3IP LOC101928002 LYZ MDM2 ENSG00000279551
GH12J069698 Promoter/Enhancer 1 EPDnew ENCODE 672.1 +0.3 325 1.7 SMARCE1 SP1 SMAD5 POLR2A ATF7 ATF2 BEST3 RAB3IP ENSG00000279551
GH12J069655 Enhancer 1.1 Ensembl ENCODE 30.1 +42.5 42545 3.9 HDAC1 PKNOX1 ATF1 TAF9B TCF12 GATA2 ATF7 CREM CEBPB ZNF592 BEST3 RAB3IP LRRC10 LOC101928002 ENSG00000279551 LOC105369823
GH12J069648 Enhancer 0.6 ENCODE 10.1 +50.7 50711 1.3 CTCF JUN CEBPB EP300 ATF2 JUND STAT3 FOS ATF7 ZNF558 BEST3 RAB3IP ENSG00000279551 LOC105369823
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BEST3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BEST3 gene promoter:
  • USF-1
  • Lmo2
  • USF1
  • aMEF-2
  • MEF-2A

Genomic Locations for BEST3 Gene

Genomic Locations for BEST3 Gene
56,117 bases
Minus strand
56,117 bases
Minus strand

Genomic View for BEST3 Gene

Genes around BEST3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BEST3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BEST3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BEST3 Gene

Proteins for BEST3 Gene

  • Protein details for BEST3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B5MDI8
    • F8VVZ2
    • Q53YQ7
    • Q8N356
    • Q8NFT9
    • Q9BR80

    Protein attributes for BEST3 Gene

    668 amino acids
    Molecular mass:
    76107 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for BEST3 Gene


neXtProt entry for BEST3 Gene

Post-translational modifications for BEST3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for BEST3 Gene

Domains & Families for BEST3 Gene

Gene Families for BEST3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for BEST3 Gene

Suggested Antigen Peptide Sequences for BEST3 Gene

GenScript: Design optimal peptide antigens:

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 BEST3: view

Function for BEST3 Gene

Molecular function for BEST3 Gene

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

Phenotypes From GWAS Catalog for BEST3 Gene

Gene Ontology (GO) - Molecular Function for BEST3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005254 chloride channel activity IEA --
genes like me logo Genes that share ontologies with BEST3: view
genes like me logo Genes that share phenotypes with BEST3: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for BEST3 Gene

Localization for BEST3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BEST3 Gene

Cell membrane; Multi-pass membrane protein.

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 BEST3 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for BEST3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0034707 chloride channel complex IEA --
genes like me logo Genes that share ontologies with BEST3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for BEST3 Gene

Pathways & Interactions for BEST3 Gene

genes like me logo Genes that share pathways with BEST3: view

Pathways by source for BEST3 Gene

Gene Ontology (GO) - Biological Process for BEST3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006821 chloride transport IEA --
GO:0008150 biological_process ND --
GO:0015698 inorganic anion transport IEA --
GO:0043271 negative regulation of ion transport IEA --
genes like me logo Genes that share ontologies with BEST3: view

No data available for SIGNOR curated interactions for BEST3 Gene

Drugs & Compounds for BEST3 Gene

(1) Drugs for BEST3 Gene - From: HMDB

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

(2) Additional Compounds for BEST3 Gene - From: HMDB

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 BEST3: view

Transcripts for BEST3 Gene

Unigene Clusters for BEST3 Gene

Bestrophin 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for BEST3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b
SP1: - - - - - -
SP2: - - - -
SP3: - - - -
SP4: - - - - - - - -
SP5: - - - -
SP6: - - - - -
SP7: - - -
SP8: - -
SP9: - - - -

Relevant External Links for BEST3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for BEST3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BEST3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for BEST3 Gene

This gene is overexpressed in Muscle - Skeletal (x33.3).

Protein differential expression in normal tissues from HIPED for BEST3 Gene

This gene is overexpressed in Prostate (40.1) and Peripheral blood mononuclear cells (28.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for BEST3 Gene

Protein tissue co-expression partners for BEST3 Gene

NURSA nuclear receptor signaling pathways regulating expression of BEST3 Gene:


SOURCE GeneReport for Unigene cluster for BEST3 Gene:


mRNA Expression by UniProt/SwissProt for BEST3 Gene:

Tissue specificity: Present in skeletal muscle and weakly in brain, spinal cord, bone marrow and retina.

Evidence on tissue expression from TISSUES for BEST3 Gene

  • Muscle(2.2)
genes like me logo Genes that share expression patterns with BEST3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for BEST3 Gene

Orthologs for BEST3 Gene

This gene was present in the common ancestor of animals.

Orthologs for BEST3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia BEST3 34 33
  • 99.6 (n)
(Bos Taurus)
Mammalia BEST3 34 33
  • 86.07 (n)
(Rattus norvegicus)
Mammalia Best3 33
  • 84.2 (n)
(Mus musculus)
Mammalia Best3 16 34 33
  • 83.87 (n)
(Canis familiaris)
Mammalia BEST3 34 33
  • 80.52 (n)
(Monodelphis domestica)
Mammalia BEST3 34
  • 76 (a)
(Ornithorhynchus anatinus)
Mammalia BEST3 34
  • 74 (a)
(Gallus gallus)
Aves BEST3 34 33
  • 66.67 (n)
(Anolis carolinensis)
Reptilia BEST3 34
  • 61 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia best3 33
  • 64.03 (n)
fruit fly
(Drosophila melanogaster)
Insecta Best3 34 33
  • 52.37 (n)
Best4 34
  • 35 (a)
Best2 34
  • 27 (a)
Best1 34
  • 27 (a)
(Caenorhabditis elegans)
Secernentea best-23 34
  • 36 (a)
best-14 34
  • 35 (a)
best-2 34
  • 35 (a)
best-21 34
  • 34 (a)
best-9 34
  • 33 (a)
best-5 34
  • 32 (a)
best-1 34
  • 32 (a)
best-6 34
  • 31 (a)
best-3 34
  • 31 (a)
best-13 34
  • 31 (a)
best-4 34
  • 31 (a)
best-18 34
  • 30 (a)
best-10 34
  • 30 (a)
best-8 34
  • 30 (a)
best-15 34
  • 30 (a)
best-16 34
  • 29 (a)
best-7 34
  • 29 (a)
best-22 34
  • 29 (a)
best-20 34
  • 28 (a)
best-19 34
  • 28 (a)
best-26 34
  • 27 (a)
best-17 34
  • 27 (a)
best-12 34
  • 26 (a)
best-24 34
  • 25 (a)
best-11 34
  • 25 (a)
best-25 34
  • 23 (a)
C09B9.85 34
  • 21 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 55 (a)
Species where no ortholog for BEST3 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)
  • zebrafish (Danio rerio)

Evolution for BEST3 Gene

Gene Tree for BEST3 (if available)
Gene Tree for BEST3 (if available)
Evolutionary constrained regions (ECRs) for BEST3: view image

Paralogs for BEST3 Gene

Paralogs for BEST3 Gene

(3) SIMAP similar genes for BEST3 Gene using alignment to 6 proteins:

  • F8VR37_HUMAN
genes like me logo Genes that share paralogs with BEST3: view

Variants for BEST3 Gene

Sequence variations from dbSNP and Humsavar for BEST3 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000048747 -- 69,691,777(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000130620 -- 69,663,448(-) A/G genic_downstream_transcript_variant, intron_variant
rs1000155971 -- 69,699,818(-) A/T upstream_transcript_variant
rs1000160421 -- 69,666,610(-) T/C genic_downstream_transcript_variant, intron_variant
rs1000219217 -- 69,673,421(-) G/A genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for BEST3 Gene

Variant ID Type Subtype PubMed ID
esv2667241 CNV deletion 23128226
esv2746019 CNV deletion 23290073
nsv507651 OTHER sequence alteration 20534489

Variation tolerance for BEST3 Gene

Residual Variation Intolerance Score: 54.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.25; 76.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BEST3 Gene

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 BEST3 Gene

Disorders for BEST3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for BEST3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
vitelliform macular dystrophy
  • best macular dystrophy
- elite association - COSMIC cancer census association via MalaCards
Search BEST3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for BEST3

genes like me logo Genes that share disorders with BEST3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for BEST3 Gene

Publications for BEST3 Gene

  1. Three novel human VMD2-like genes are members of the evolutionary highly conserved RFP-TM family. (PMID: 12032738) Stöhr H … Weber BH (European journal of human genetics : EJHG 2002) 2 3 4 58
  2. Activation of bestrophin Cl- channels is regulated by C-terminal domains. (PMID: 17442670) Qu ZQ … Hartzell C (The Journal of biological chemistry 2007) 3 22 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Structure-function analysis of the bestrophin family of anion channels. (PMID: 12907679) Tsunenari T … Nathans J (The Journal of biological chemistry 2003) 3 4 58

Products for BEST3 Gene

Sources for BEST3 Gene

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