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BEST3 bestrophin 3 [ Homo sapiens (human) ]

Gene ID: 144453, updated on 1-Aug-2020

Summary

Official Symbol
BEST3provided by HGNC
Official Full Name
bestrophin 3provided by HGNC
Primary source
HGNC:HGNC:17105
See related
Ensembl:ENSG00000127325 MIM:607337
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
VMD2L3
Summary
BEST3 belongs to the bestrophin family of anion channels, which includes BEST1 (MIM 607854), the gene mutant in vitelliform macular dystrophy (VMD; MIM 153700), and 2 other BEST1-like genes, BEST2 (MIM 607335) and BEST4 (MIM 607336). Bestrophins are transmembrane (TM) proteins that share a homology region containing a high content of aromatic residues, including an invariant arg-phe-pro (RFP) motif. The bestrophin genes share a conserved gene structure, with almost identical sizes of the 8 RFP-TM domain-encoding exons and highly conserved exon-intron boundaries. Each of the 4 bestrophin genes has a unique 3-prime end of variable length (Stohr et al., 2002 [PubMed 12032738]; Tsunenari et al., 2003 [PubMed 12907679]).[supplied by OMIM, Mar 2008]
Expression
Biased expression in brain (RPKM 1.2), testis (RPKM 0.5) and 4 other tissues See more
Orthologs

Genomic context

See BEST3 in Genome Data Viewer
Location:
12q15
Exon count:
14
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (69643508..69699416, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (70037334..70093196, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369823 Neighboring gene chaperonin containing TCP1 subunit 2 Neighboring gene leucine rich repeat containing 10 Neighboring gene uncharacterized LOC101928002 Neighboring gene RAB3A interacting protein Neighboring gene myelin regulatory factor like

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

NHGRI GWAS Catalog

Description
Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC13168, MGC40411

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chloride channel activity IEA
Inferred from Electronic Annotation
more info
 
molecular_function ND
No biological Data available
more info
 
Process Evidence Code Pubs
biological_process ND
No biological Data available
more info
 
chloride transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
negative regulation of ion transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
chloride channel complex IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
bestrophin-3
Names
vitelliform macular dystrophy 2-like 3
vitelliform macular dystrophy 2-like protein 3

NCBI Reference Sequences (RefSeq)

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.

mRNA and Protein(s)

  1. NM_001282613.1NP_001269542.1  bestrophin-3 isoform 3

    See identical proteins and their annotated locations for NP_001269542.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    BC028087, BC151138, DA767581
    Consensus CDS
    CCDS61192.1
    UniProtKB/Swiss-Prot
    Q8N1M1
    Related
    ENSP00000449548.1, ENST00000553096.5
    Conserved Domains (1) summary
    pfam01062
    Location:1209
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  2. NM_001282614.1NP_001269543.1  bestrophin-3 isoform 4

    See identical proteins and their annotated locations for NP_001269543.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an alternate 3' terminal exon and it thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (4) has a distinct and shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AF440758, AY515706, BX374313, DA767581
    Consensus CDS
    CCDS61193.1
    UniProtKB/Swiss-Prot
    Q8N1M1
    Related
    ENSP00000329064.4, ENST00000331471.8
    Conserved Domains (1) summary
    pfam01062
    Location:8315
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  3. NM_001282615.2NP_001269544.1  bestrophin-3 isoform 5

    See identical proteins and their annotated locations for NP_001269544.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks a portion of the 5' UTR and 5' coding region, uses a downstream in-frame start codon, and lacks several 3' exons but includes an alternate 3' terminal exon, compared to variant 1. The encoded isoform (5) is shorter at the N-terminus, has a distinct C-terminus and is significantly shorter than isoform 1. Both variants 5 and 6 encode isoform 5.
    Source sequence(s)
    AC025263, BC006440
    Consensus CDS
    CCDS73496.1
    UniProtKB/Swiss-Prot
    Q8N1M1
    Related
    ENSP00000266661.4, ENST00000266661.8
    Conserved Domains (1) summary
    cl01544
    Location:167
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  4. NM_001282616.2NP_001269545.1  bestrophin-3 isoform 5

    See identical proteins and their annotated locations for NP_001269545.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks a portion of the 5' UTR and 5' coding region, uses a downstream in-frame start codon, and lacks several 3' exons but includes an alternate 3' terminal exon, compared to variant 1. The encoded isoform (5) is shorter at the N-terminus, has a distinct C-terminus and is significantly shorter than isoform 1. Both variants 5 and 6 encode isoform 5.
    Source sequence(s)
    AC025263, BC006440, BP225850
    Consensus CDS
    CCDS73496.1
    UniProtKB/Swiss-Prot
    Q8N1M1
    Related
    ENSP00000449377.1, ENST00000551160.5
    Conserved Domains (1) summary
    cl01544
    Location:167
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  5. NM_032735.3NP_116124.2  bestrophin-3 isoform 1

    See identical proteins and their annotated locations for NP_116124.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC025263, AK096459, BC028087
    Consensus CDS
    CCDS8992.2
    UniProtKB/Swiss-Prot
    Q8N1M1
    Related
    ENSP00000332413.5, ENST00000330891.10
    Conserved Domains (1) summary
    pfam01062
    Location:8315
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  6. NM_152439.3NP_689652.2  bestrophin-3 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream in-frame start codon, and lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AK096459, BC028087, BF739974
    Consensus CDS
    CCDS41810.1
    UniProtKB/Swiss-Prot
    Q8N1M1
    Related
    ENSP00000433213.1, ENST00000488961.5
    Conserved Domains (1) summary
    cl01544
    Location:5102
    Bestrophin; Bestrophin, RFP-TM, chloride channel

RNA

  1. NR_104220.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) consists of two exons that variant 1 lacks, but it shares its 5' exon with variant 2 and its 3' exon with variants 5 and 6. This variant is represented as non-coding because it lacks an in-frame ORF that is likely to be translated.
    Source sequence(s)
    AC025263, BC006440, BC028087, BF739974

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    69643508..69699416 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011537963.1XP_011536265.1  bestrophin-3 isoform X3

    See identical proteins and their annotated locations for XP_011536265.1

    Conserved Domains (1) summary
    pfam01062
    Location:18153
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  2. XM_011537961.1XP_011536263.1  bestrophin-3 isoform X2

    See identical proteins and their annotated locations for XP_011536263.1

    UniProtKB/Swiss-Prot
    Q8N1M1
    Conserved Domains (1) summary
    pfam01062
    Location:1209
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  3. XM_011537962.2XP_011536264.1  bestrophin-3 isoform X3

    See identical proteins and their annotated locations for XP_011536264.1

    Conserved Domains (1) summary
    pfam01062
    Location:18153
    Bestrophin; Bestrophin, RFP-TM, chloride channel
  4. XM_011537965.2XP_011536267.1  bestrophin-3 isoform X4

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