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BEST1 bestrophin 1 [ Homo sapiens (human) ]

Gene ID: 7439, updated on 13-Apr-2024

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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (61949821..61965515)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (61938644..61954340)
105.20220307 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: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A novel compound heterozygous BEST1 gene mutation in two siblings causing autosomal recessive bestrophinopathy. Haque OI, et al. BMC Ophthalmol, 2022 Dec 16. PMID 36527004, Free PMC Article
  2. Photoreceptor function and structure in retinal degenerations caused by biallelic BEST1 mutations. Cideciyan AV, et al. Vision Res, 2023 Feb. PMID 36450205, Free PMC Article
  3. BEST1 novel mutation causes Bestrophinopathies in six families with distinct phenotypic diversity. Yang S, et al. Mol Genet Genomic Med, 2023 Jan. PMID 36378562, Free PMC Article
  4. Genetic and clinical features of BEST1-associated retinopathy based on 59 Chinese families and database comparisons. Wang Y, et al. Exp Eye Res, 2022 Oct. PMID 35973442
  5. 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. Navinés-Ferrer A, et al. Int J Mol Sci, 2022 Jul 4. PMID 35806438, Free PMC Article

See all (190) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The Retinal Phenotype Associated with the p.Pro101Thr BEST1 Variant.
    Title: The Retinal Phenotype Associated with the p.Pro101Thr BEST1 Variant.
  2. Typical best vitelliform dystrophy secondary to biallelic variants in BEST1.
    Title: Typical best vitelliform dystrophy secondary to biallelic variants in BEST1.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Clinical reassessments and whole-exome sequencing uncover novel BEST1 mutation associated with bestrophinopathy phenotype.
    Title: Clinical reassessments and whole-exome sequencing uncover novel BEST1 mutation associated with bestrophinopathy phenotype.
Submit: New GeneRIF Correction See all GeneRIFs (154)

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)

Genotypes

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 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 intracellularly calcium-gated chloride channel activity TAS
Traceable Author Statement
more info
  
enables ligand-gated channel activity ISS
Inferred from Sequence or Structural Similarity
more info
  
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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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

    See identical proteins and their annotated locations for NP_001132915.1

    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

    See identical proteins and their annotated locations for NP_001287715.1

    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

    See identical proteins and their annotated locations for NP_001287716.1

    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

    See identical proteins and their annotated locations for NP_004174.1

    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_2023_10

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

    See identical proteins and their annotated locations for XP_005274267.1

    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

    See identical proteins and their annotated locations for XP_005274278.1

    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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