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BEST1 bestrophin 1 [ Homo sapiens (human) ]

Gene ID: 7439, updated on 9-Oct-2022

Summary

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

See BEST1 in Genome Data Viewer
Location:
11q12.3
Exon count:
13
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (61949821..61965515)
110 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 RAB3A interacting protein like 1 Neighboring gene Sharpr-MPRA regulatory region 8487 Neighboring gene RNA, U6 small nuclear 1243, pseudogene Neighboring gene uncharacterized LOC107984334 Neighboring gene NFE2L2 motif-containing MPRA enhancer 20 Neighboring gene uncharacterized LOC399900 Neighboring gene ferritin heavy chain 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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 plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001139443.2NP_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/Swiss-Prot
    O76090
    Related
    ENSP00000399709.2, ENST00000449131.6
    Conserved Domains (1) summary
    pfam01062
    Location:16255
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  2. NM_001300786.2NP_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/Swiss-Prot
    O76090
    UniProtKB/TrEMBL
    A0A0S2Z4M4
    Conserved Domains (1) summary
    pfam01062
    Location:16231
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  3. NM_001300787.2NP_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/Swiss-Prot
    O76090
    UniProtKB/TrEMBL
    A0A0S2Z579
    Conserved Domains (1) summary
    pfam01062
    Location:16256
    Bestrophin; RFP-TM, chloride channel
  4. NM_001363591.2NP_001350520.1  bestrophin-1 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AP003733
    Conserved Domains (1) summary
    pfam01062
    Location:3210
    Bestrophin; RFP-TM, chloride channel
  5. NM_001363592.1NP_001350521.1  bestrophin-1 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AK289681, AP003733
    Consensus CDS
    CCDS86208.1
    UniProtKB/TrEMBL
    A0A0C4DGE9
    Related
    ENSP00000432681.1, ENST00000524926.5
    Conserved Domains (1) summary
    pfam01062
    Location:9291
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  6. NM_001363593.2NP_001350522.1  bestrophin-1 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AP003733
  7. NM_004183.4NP_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
    O76090, Q8IZ80
    Related
    ENSP00000367282.4, ENST00000378043.9
    Conserved Domains (1) summary
    pfam01062
    Location:9315
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_005274210.5XP_005274267.1  bestrophin-1 isoform X1

    See identical proteins and their annotated locations for XP_005274267.1

    Conserved Domains (1) summary
    pfam01062
    Location:9315
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  2. XM_005274221.5XP_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:9238
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  3. XM_047427523.1XP_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)