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Aliases for BEST2 Gene

Aliases for BEST2 Gene

  • Bestrophin 2 2 3 5
  • Vitelliform Macular Dystrophy 2-Like Protein 1 3 4
  • Vitelliform Macular Dystrophy 2-Like 1 2 3
  • Bestrophin-2 3 4
  • VMD2L1 3 4
  • VMD2-Like Gene 1 3

External Ids for BEST2 Gene

Previous HGNC Symbols for BEST2 Gene

  • VMD2L1

Previous GeneCards Identifiers for BEST2 Gene

  • GC19P012725
  • GC19P012864
  • GC19P012436

Summaries for BEST2 Gene

Entrez Gene Summary for BEST2 Gene

  • This gene is a member of the bestrophin gene family of anion channels. Bestrophin genes share a similar gene structure with highly conserved exon-intron boundaries, but with distinct 3' ends. Bestrophins are transmembrane proteins that contain a homologous region rich in aromatic residues, including an invariant arg-phe-pro motif. Mutation in one of the family members (bestrophin 1) is associated with vitelliform macular dystrophy. The bestrophin 2 gene is mainly expressed in the retinal pigment epithelium and colon. [provided by RefSeq, Jul 2008]

GeneCards Summary for BEST2 Gene

BEST2 (Bestrophin 2) is a Protein Coding gene. Diseases associated with BEST2 include Vitelliform Macular Dystrophy and Bestrophinopathy. 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. Gene Ontology (GO) annotations related to this gene include chloride channel activity. An important paralog of this gene is BEST4.

UniProtKB/Swiss-Prot for BEST2 Gene

Gene Wiki entry for BEST2 Gene

Additional gene information for BEST2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BEST2 Gene

Genomics for BEST2 Gene

GeneHancer (GH) Regulatory Elements for BEST2 Gene

Promoters and enhancers for BEST2 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
GH19J012751 Promoter/Enhancer 1 Ensembl ENCODE 600.7 +0.3 325 0.8 KLF9 SCRT2 SCRT1 WT1 ZNF143 POLR2A KLF1 BEST2 GC19M012838 GC19M012808
GH19J012749 Enhancer 0.7 ENCODE 600.7 -1.5 -1470 1.5 ZNF121 PRDM10 ZIC2 ZEB2 ZNF639 ZNF629 PATZ1 ZXDB OSR2 ZFHX2 BEST2 GET3
GH19J012753 Promoter 0.5 EPDnew 600.7 +1.0 952 0.1 BEST2 ENSG00000269560 GC19M012808 GC19M012838
GH19J012805 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 11.9 +55.2 55191 1.9 SP1 ELF3 ZFX SIX5 ZNF148 NKRF MLLT1 CEBPG POLR2A ZNF384 RNASEH2A ZNF136 ZNF763 ZNF20 ZNF442 TRMT1 ZNF625 ZNF490 ZNF439 ZNF788P
GH19J012825 Promoter/Enhancer 1.4 Ensembl ENCODE 12 +74.1 74146 1.4 ZFX ELF3 ZNF148 AHR NCOA6 TRIM24 PPARG SP5 KLF14 EGR1 GC19M012832 LOC105372281 ENSG00000267424 PRDX2 BEST2 GCDH RTBDN HOOK2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BEST2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BEST2 gene promoter:
  • AP-2gamma
  • GCNF
  • GCNF-1
  • ITF-2
  • Pax-5
  • Pax-6
  • Sp1
  • Tal-1beta

Genomic Locations for BEST2 Gene

Genomic Locations for BEST2 Gene
6,783 bases
Plus strand
6,757 bases
Plus strand

Genomic View for BEST2 Gene

Genes around BEST2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BEST2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BEST2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BEST2 Gene

Proteins for BEST2 Gene

  • Protein details for BEST2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q53YQ8
    • Q9NXP0

    Protein attributes for BEST2 Gene

    509 amino acids
    Molecular mass:
    57139 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA90970.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

neXtProt entry for BEST2 Gene

Post-translational modifications for BEST2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for BEST2 Gene

No data available for DME Specific Peptides for BEST2 Gene

Domains & Families for BEST2 Gene

Gene Families for BEST2 Gene

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

Protein Domains for BEST2 Gene

Suggested Antigen Peptide Sequences for BEST2 Gene

GenScript: Design optimal peptide antigens:
  • Vitelliform macular dystrophy 2-like protein 1 (BEST2_HUMAN)

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 BEST2: view

Function for BEST2 Gene

Molecular function for BEST2 Gene

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

Phenotypes From GWAS Catalog for BEST2 Gene

Gene Ontology (GO) - Molecular Function for BEST2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005254 contributes_to chloride channel activity ISS --
genes like me logo Genes that share ontologies with BEST2: view
genes like me logo Genes that share phenotypes with BEST2: view

Animal Models for BEST2 Gene

MGI Knock Outs for BEST2:
  • Best2 Best2<tm1Dgen>
  • Best2 Best2<tm1b(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for BEST2 - Now 50% OFF >
  • * BEST2 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * BEST2 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for BEST2 Gene

Localization for BEST2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BEST2 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 BEST2 gene
Compartment Confidence
plasma membrane 5
extracellular 1
mitochondrion 1
cytosol 1
lysosome 0

Gene Ontology (GO) - Cellular Components for BEST2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005929 cilium ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0034707 chloride channel complex ISS,IBA --
genes like me logo Genes that share ontologies with BEST2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for BEST2 Gene

Pathways & Interactions for BEST2 Gene

genes like me logo Genes that share pathways with BEST2: view

Pathways by source for BEST2 Gene

1 KEGG pathway for BEST2 Gene

Interacting Proteins for BEST2 Gene

Gene Ontology (GO) - Biological Process for BEST2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006821 chloride transport IEA --
GO:0007608 sensory perception of smell ISS --
GO:0008150 biological_process ND --
GO:0051899 membrane depolarization ISS --
genes like me logo Genes that share ontologies with BEST2: view

No data available for SIGNOR curated interactions for BEST2 Gene

Drugs & Compounds for BEST2 Gene

(2) Drugs for BEST2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7611
Chloride ion Experimental Pharma 0

(1) Additional Compounds for BEST2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Carbonic acid
  • [co(OH)2]
  • Dihydrogen carbonate
  • H2CO3
  • Koehlensaeure
  • Carbonate
71-52-3, 463-79-6
genes like me logo Genes that share compounds with BEST2: view

Transcripts for BEST2 Gene

mRNA/cDNA for BEST2 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(8) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Unigene Clusters for BEST2 Gene

Bestrophin 2:
Representative Sequences:

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for BEST2 - Now 50% OFF >
  • * BEST2 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * BEST2 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

Alternative Splicing Database (ASD) splice patterns (SP) for BEST2 Gene

No ASD Table

Relevant External Links for BEST2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for BEST2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for BEST2 Gene

mRNA differential expression in normal tissues according to GTEx for BEST2 Gene

This gene is overexpressed in Colon - Transverse (x30.6), Skin - Sun Exposed (Lower leg) (x7.5), Skin - Not Sun Exposed (Suprapubic) (x6.9), and Small Intestine - Terminal Ileum (x4.4).

Protein differential expression in normal tissues from HIPED for BEST2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (52.5) and Colon (14.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for BEST2 Gene

Protein tissue co-expression partners for BEST2 Gene

NURSA nuclear receptor signaling pathways regulating expression of BEST2 Gene:


SOURCE GeneReport for Unigene cluster for BEST2 Gene:


mRNA Expression by UniProt/SwissProt for BEST2 Gene:

Tissue specificity: Mainly confined to the retinal pigment epithelium and colon.

Evidence on tissue expression from TISSUES for BEST2 Gene

  • Intestine(4.2)
genes like me logo Genes that share expression patterns with BEST2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for BEST2 Gene

Orthologs for BEST2 Gene

This gene was present in the common ancestor of animals.

Orthologs for BEST2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia BEST2 35 34
  • 99.48 (n)
(Canis familiaris)
Mammalia BEST2 35 34
  • 87.62 (n)
(Bos Taurus)
Mammalia BEST2 35 34
  • 85.53 (n)
(Mus musculus)
Mammalia Best2 17 35 34
  • 83.04 (n)
(Rattus norvegicus)
Mammalia Best2 34
  • 82.38 (n)
(Monodelphis domestica)
Mammalia BEST2 35
  • 72 (a)
(Anolis carolinensis)
Reptilia BEST2 35
  • 63 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia best2 34
  • 69.82 (n)
MGC75942 34
African clawed frog
(Xenopus laevis)
Amphibia MGC53680 34
(Danio rerio)
Actinopterygii best2 35 34
  • 69.41 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011745 34
  • 60.7 (n)
fruit fly
(Drosophila melanogaster)
Insecta Best1 35 34
  • 57.93 (n)
Best4 35
  • 36 (a)
Best3 35
  • 34 (a)
Best2 35
  • 25 (a)
(Caenorhabditis elegans)
Secernentea best-23 35 34
  • 45.29 (n)
best-14 35
  • 35 (a)
best-21 35
  • 33 (a)
best-18 35
  • 32 (a)
best-6 35
  • 32 (a)
best-9 35
  • 32 (a)
best-2 35
  • 32 (a)
best-1 35
  • 31 (a)
best-13 35
  • 30 (a)
best-10 35
  • 29 (a)
best-3 35
  • 28 (a)
best-16 35
  • 28 (a)
best-15 35
  • 28 (a)
best-4 35
  • 28 (a)
best-5 35
  • 28 (a)
best-22 35
  • 28 (a)
best-17 35
  • 28 (a)
best-8 35
  • 27 (a)
best-7 35
  • 27 (a)
best-19 35
  • 27 (a)
best-20 35
  • 27 (a)
best-26 35
  • 27 (a)
best-11 35
  • 26 (a)
best-24 35
  • 25 (a)
best-12 35
  • 25 (a)
best-25 35
  • 22 (a)
C09B9.85 35
  • 21 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 55 (a)
Species where no ortholog for BEST2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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 BEST2 Gene

Gene Tree for BEST2 (if available)
Gene Tree for BEST2 (if available)
Evolutionary constrained regions (ECRs) for BEST2: view image

Paralogs for BEST2 Gene

Paralogs for BEST2 Gene

(3) SIMAP similar genes for BEST2 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with BEST2: view

Variants for BEST2 Gene

Sequence variations from dbSNP and Humsavar for BEST2 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000625487 -- 12,749,850(+) C/A upstream_transcript_variant
rs1000699938 -- 12,754,406(+) G/A intron_variant
rs1000804567 -- 12,755,250(+) C/A/T intron_variant
rs1001243055 -- 12,752,078(+) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1002123241 -- 12,753,707(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for BEST2 Gene

Variant ID Type Subtype PubMed ID
dgv138n111 CNV deletion 26073780
nsv1160586 CNV duplication 26073780
nsv953977 CNV deletion 24416366

Variation tolerance for BEST2 Gene

Residual Variation Intolerance Score: 21.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.73; 66.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BEST2 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 BEST2 Gene

Disorders for BEST2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for BEST2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
vitelliform macular dystrophy
  • best macular dystrophy
  • bestrophinopathy, autosomal recessive
- elite association - COSMIC cancer census association via MalaCards
Search BEST2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for BEST2

genes like me logo Genes that share disorders with BEST2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for BEST2 Gene

Publications for BEST2 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. Bestrophin 2 is expressed in human non-pigmented ciliary epithelium but not retinal pigment epithelium. (PMID: 20157619) Zhang Y … Marmorstein AD (Molecular vision 2010) 3 23 58
  3. Bestrophin-2 is a candidate calcium-activated chloride channel involved in olfactory transduction. (PMID: 16912113) Pifferi S … Zucchelli S (Proceedings of the National Academy of Sciences of the United States of America 2006) 2 3 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 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 BEST2 Gene

Sources for BEST2 Gene

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