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    BEST1 bestrophin 1 [ Homo sapiens (human) ]

    Gene ID: 7439, updated on 4-Jan-2025

    Summary

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    Official Symbol
    BEST1provided by HGNC
    Official Full Name
    bestrophin 1provided by HGNC
    Primary source
    HGNC:HGNC:12703
    See related
    Ensembl:ENSG00000167995 MIM:607854; AllianceGenome:HGNC:12703
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ARB; BMD; BEST; RP50; VMD2; TU15B; Best1V1Delta2
    Summary
    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]
    Expression
    Broad expression in brain (RPKM 5.3), appendix (RPKM 3.0) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See BEST1 in Genome Data Viewer
    Location:
    11q12.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (61949821..61965515)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (61938644..61954340)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (61717293..61732987)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61646639-61647348 Neighboring gene fatty acid desaturase 3 Neighboring gene microRNA 6746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61655245-61655746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61657348-61658037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61658038-61658726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61666908-61667879 Neighboring gene RAB3A interacting protein like 1 Neighboring gene Sharpr-MPRA regulatory region 8487 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:61705992-61706140 Neighboring gene RNA, U6 small nuclear 1243, pseudogene Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:61709325-61709979 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:61711149-61711650 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:61713521-61713684 Neighboring gene uncharacterized LOC107984334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3409 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4808 Neighboring gene NFE2L2 motif-containing MPRA enhancer 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4809 Neighboring gene uncharacterized LOC399900 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:61745853-61746069 Neighboring gene ferritin heavy chain 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61768209-61768961 Neighboring gene ribosomal protein S2 pseudogene 37

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. OCT findings in young asymptomatic subjects carrying familial BEST1 gene mutations. Chacon-Camacho OF, et al. Ophthalmic Genet, 2011 Mar. PMID 21077756
    2. A homozygous frameshift mutation in BEST1 causes the classical form of Best disease in an autosomal recessive mode. Bitner H, et al. Invest Ophthalmol Vis Sci, 2011 Jul 18. PMID 21467170
    3. The spectrum of subclinical Best vitelliform macular dystrophy in subjects with mutations in BEST1 gene. Querques G, et al. Invest Ophthalmol Vis Sci, 2011 Jun 28. PMID 21436265
    4. Functional characterization of bestrophin-1 missense mutations associated with autosomal recessive bestrophinopathy. Davidson AE, et al. Invest Ophthalmol Vis Sci, 2011 Jun 1. PMID 21330666
    5. Autosomal recessive best vitelliform macular dystrophy: report of a family and management of early-onset neovascular complications. Iannaccone A, et al. Arch Ophthalmol, 2011 Feb. PMID 21320969

    See all (195) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. GAD65 tunes the functions of Best1 as a GABA receptor and a neurotransmitter conducting channel.
      Title: GAD65 tunes the functions of Best1 as a GABA receptor and a neurotransmitter conducting channel.
    2. The Retinal Phenotype Associated with the p.Pro101Thr BEST1 Variant.
      Title: The Retinal Phenotype Associated with the p.Pro101Thr BEST1 Variant.
    3. Typical best vitelliform dystrophy secondary to biallelic variants in BEST1.
      Title: Typical best vitelliform dystrophy secondary to biallelic variants in BEST1.
    4. Comprehensive Genetic Analysis Unraveled the Missing Heritability and a Founder Variant of BEST1 in a Chinese Cohort With Autosomal Recessive Bestrophinopathy.
      Title: Comprehensive Genetic Analysis Unraveled the Missing Heritability and a Founder Variant of BEST1 in a Chinese Cohort With Autosomal Recessive Bestrophinopathy.
    5. A novel compound heterozygous BEST1 gene mutation in two siblings causing autosomal recessive bestrophinopathy.
      Title: A novel compound heterozygous BEST1 gene mutation in two siblings causing autosomal recessive bestrophinopathy.
    6. Photoreceptor function and structure in retinal degenerations caused by biallelic BEST1 mutations.
      Title: Photoreceptor function and structure in retinal degenerations caused by biallelic BEST1 mutations.
    7. BEST1 novel mutation causes Bestrophinopathies in six families with distinct phenotypic diversity.
      Title: BEST1 novel mutation causes Bestrophinopathies in six families with distinct phenotypic diversity.
    8. Genetic and clinical features of BEST1-associated retinopathy based on 59 Chinese families and database comparisons.
      Title: Genetic and clinical features of BEST1-associated retinopathy based on 59 Chinese families and database comparisons.
    9. Impaired Bestrophin Channel Activity in an iPSC-RPE Model of Best Vitelliform Macular Dystrophy (BVMD) from an Early Onset Patient Carrying the P77S Dominant Mutation.
      Title: Impaired Bestrophin Channel Activity in an iPSC-RPE Model of Best Vitelliform Macular Dystrophy (BVMD) from an Early Onset Patient Carrying the P77S Dominant Mutation.
    10. Self-organization and surface properties of hBest1 in models of biological membranes.
      Title: Self-organization and surface properties of hBest1 in models of biological membranes.
    Submit: New GeneRIF Correction See all GeneRIFs (155)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
    EBI GWAS Catalog
    Genome-wide association study of circulating estradiol, testosterone, and sex hormone-binding globulin in postmenopausal women.
    EBI GWAS Catalog
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables bicarbonate channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables bicarbonate transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    contributes_to chloride channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chloride channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chloride channel activity TAS
    Traceable Author Statement
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables intracellularly calcium-gated chloride channel activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables intracellularly calcium-gated chloride channel activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables ligand-gated channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in bicarbonate transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chloride transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within chloride transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in detection of light stimulus involved in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in gamma-aminobutyric acid secretion, neurotransmission ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in glutamate secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in monoatomic ion transmembrane transport TAS
    Traceable Author Statement
    more info
    		  
    involved_in protein complex oligomerization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of calcium ion transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of synaptic plasticity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in transepithelial chloride transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in visual perception TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in basal plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in basolateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of chloride channel complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in membrane microdomain ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    bestrophin-1
    Names
    Best disease
    vitelliform macular dystrophy protein 2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_009033.1 RefSeqGene

      Range
      5468..19578
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001139443.2 → NP_001132915.1  bestrophin-1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) encodes the longest isoform (2).
      Source sequence(s)
      AF057169, AP003733, BC015220, BC041664
      Consensus CDS
      CCDS44623.1
      UniProtKB/TrEMBL
      J7LCD9
      Related
      ENSP00000399709.2, ENST00000449131.6
      Conserved Domains (1) summary
      pfam01062
      Location:16 → 255
      Bestrophin; Bestrophin, RFP-TM, chloride channel

    2. NM_001300786.2 → NP_001287715.1  bestrophin-1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon and differs in the 3' UTR and coding sequence compared to variant 2. The resulting isoform (3) lacks an alternate internal segment and has a shorter and distinct C-terminus compared to isoform 2.
      Source sequence(s)
      AP003733, BC015220
      UniProtKB/TrEMBL
      A0A0S2Z4M4, J7LCD9
      Conserved Domains (1) summary
      pfam01062
      Location:16 → 231
      Bestrophin; Bestrophin, RFP-TM, chloride channel

    3. NM_001300787.2 → NP_001287716.1  bestrophin-1 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 3' UTR and coding sequence compared to variant 2. The resulting isoform (4) has a shorter and distinct C-terminus compared to isoform 2.
      Source sequence(s)
      AK295998, AP003733, BC015220
      UniProtKB/TrEMBL
      A0A0S2Z579, J7LCD9
      Conserved Domains (1) summary
      pfam01062
      Location:16 → 256
      Bestrophin; RFP-TM, chloride channel

    4. NM_001363591.2 → NP_001350520.1  bestrophin-1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AP003733
      UniProtKB/TrEMBL
      J7LCD9
      Conserved Domains (1) summary
      pfam01062
      Location:3 → 210
      Bestrophin; RFP-TM, chloride channel

    5. NM_001363592.1 → NP_001350521.1  bestrophin-1 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AK289681, AP003733
      Consensus CDS
      CCDS86208.1
      UniProtKB/TrEMBL
      A0A0C4DGE9, B7Z336
      Related
      ENSP00000432681.1, ENST00000524926.5
      Conserved Domains (1) summary
      pfam01062
      Location:9 → 291
      Bestrophin; Bestrophin, RFP-TM, chloride channel

    6. NM_001363593.2 → NP_001350522.1  bestrophin-1 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AP003733
      UniProtKB/TrEMBL
      B7Z5C9

    7. NM_004183.4 → NP_004174.1  bestrophin-1 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence and in the 3' UTR and coding sequence compared to variant 2. The resulting isoform (1) is longer at the N-terminus and has a shorter and distinct C-terminus compared to isoform 2.
      Source sequence(s)
      AF057169, BC015220
      Consensus CDS
      CCDS31580.1
      UniProtKB/Swiss-Prot
      A8K0W6, B7Z3J8, B7Z736, O75904, O76090, Q53YQ9, Q8IUR9, Q8IZ80
      UniProtKB/TrEMBL
      J7LCD9
      Related
      ENSP00000367282.4, ENST00000378043.9
      Conserved Domains (1) summary
      pfam01062
      Location:9 → 315
      Bestrophin; Bestrophin, RFP-TM, chloride channel

    RNA

    1. NR_134580.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains an alternate exon, uses an alternate internal splice junction, and differs in the 3' end compared to variant 2. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF057170, AP003733, BC015220

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      61949821..61965515
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005274210.5 → XP_005274267.1  bestrophin-1 isoform X1

      Conserved Domains (1) summary
      pfam01062
      Location:9 → 315
      Bestrophin; Bestrophin, RFP-TM, chloride channel

    2. XM_005274221.5 → XP_005274278.1  bestrophin-1 isoform X3

      UniProtKB/TrEMBL
      B7Z375, E9PDT5
      Conserved Domains (1) summary
      pfam01062
      Location:9 → 238
      Bestrophin; Bestrophin, RFP-TM, chloride channel

    3. XM_047427523.1 → XP_047283479.1  bestrophin-1 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      61938644..61954340
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369819.1 → XP_054225794.1  bestrophin-1 isoform X1

    2. XM_054369821.1 → XP_054225796.1  bestrophin-1 isoform X3

      UniProtKB/TrEMBL
      B7Z375, E9PDT5

    3. XM_054369820.1 → XP_054225795.1  bestrophin-1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O76090.1 GenPept UniProtKB/Swiss-Prot:O76090

    Gene LinkOut

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