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BEST1 bestrophin 1 [ Homo sapiens (human) ]

Gene ID: 7439, updated on 23-Nov-2021

Summary

Official Symbol
BEST1provided by HGNC
Official Full Name
bestrophin 1provided by HGNC
Primary source
HGNC:HGNC:12703
See related
Ensembl:ENSG00000167995 MIM:607854
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:
14
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (61946722..61965515)
105.20201022 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

Associated conditions

Description Tests
Bestrophinopathy, autosomal recessive
MedGen: C3888198 OMIM: 611809 GeneReviews: Bestrophinopathies
Compare labs
Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
GeneReviews: Not available
Genome-wide association study of circulating estradiol, testosterone, and sex hormone-binding globulin in postmenopausal women.
GeneReviews: Not available
Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
GeneReviews: Not available
Retinitis pigmentosa 50 Compare labs
Vitelliform macular dystrophy type 2
MedGen: C2745945 OMIM: 153700 GeneReviews: Bestrophinopathies
Compare labs
Vitreoretinochoroidopathy
MedGen: C3888099 OMIM: 193220 GeneReviews: Bestrophinopathies
Compare labs

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 integral component of membrane 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)

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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_001139443.2NP_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
    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
    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 Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    61946722..61965515
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545229.3XP_011543531.1  bestrophin-1 isoform X1

    See identical proteins and their annotated locations for XP_011543531.1

    Conserved Domains (1) summary
    pfam01062
    Location:9315
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  2. XM_011545230.3XP_011543532.1  bestrophin-1 isoform X2

    Conserved Domains (1) summary
    pfam01062
    Location:20284
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  3. XM_005274210.4XP_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
  4. XM_005274219.4XP_005274276.1  bestrophin-1 isoform X9

    Conserved Domains (1) summary
    pfam01062
    Location:9289
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  5. XM_005274221.4XP_005274278.1  bestrophin-1 isoform X10

    See identical proteins and their annotated locations for XP_005274278.1

    UniProtKB/TrEMBL
    B7Z375
    Conserved Domains (1) summary
    pfam01062
    Location:9238
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  6. XM_005274216.4XP_005274273.1  bestrophin-1 isoform X7

    Conserved Domains (1) summary
    pfam01062
    Location:16231
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  7. XM_005274215.4XP_005274272.1  bestrophin-1 isoform X4

    See identical proteins and their annotated locations for XP_005274272.1

    UniProtKB/Swiss-Prot
    O76090
    Conserved Domains (1) summary
    pfam01062
    Location:3210
    Bestrophin; RFP-TM, chloride channel
  8. XM_017018230.2XP_016873719.1  bestrophin-1 isoform X8

    UniProtKB/TrEMBL
    B7Z1N8
    Related
    ENSP00000433195.1, ENST00000526988.1
    Conserved Domains (1) summary
    pfam01062
    Location:3185
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  9. XM_011545233.3XP_011543535.1  bestrophin-1 isoform X6

    Conserved Domains (1) summary
    cl01544
    Location:734
    Bestrophin; Bestrophin, RFP-TM, chloride channel

RNA

  1. XR_001747953.2 RNA Sequence

  2. XR_001747954.2 RNA Sequence

  3. XR_001747952.2 RNA Sequence

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