BEST4 bestrophin 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: BEST4provided by HGNC
Official Full Name: bestrophin 4provided by HGNC
Primary source: HGNC:HGNC:17106
See related: Ensembl:ENSG00000142959 MIM:607336; AllianceGenome:HGNC:17106
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: VMD2L2
Summary: This gene is a member of the bestrophin gene family of anion channels. Bestrophin genes share a similar gene structure with highly conserved exon-intron boundaries, but with distinct 3' ends. Bestrophins are transmembrane proteins that contain a homologous region rich in aromatic residues, including an invariant arg-phe-pro motif. Mutation in one of the family members (bestrophin 1) is associated with vitelliform macular dystrophy. The bestrophin 4 gene is predominantly expressed in the colon. [provided by RefSeq, Jul 2008]
Expression: Biased expression in colon (RPKM 7.6), duodenum (RPKM 2.6) and 2 other tissues See more
Orthologs: all
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Genomic context

Location:: 1p34.1

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (44781840..44792828, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (44652829..44664929, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (45249257..45253842, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

BEST2 and BEST4 could be added to the lineage-specific genes of humans intestinal epithelial cells
Title: Lineage-specific expression of bestrophin-2 and bestrophin-4 in human intestinal epithelial cells.
Results provide evidence that the bestrophins are expressed in pancreatic duct cells and, more specifically, that hBest1 plays a role in the calcium activated chloride channels found in these cells.
Title: Bestrophin expression and function in the human pancreatic duct cell line, CFPAC-1.
identified three novel VMD2-related human genes demonstrating a high degree of conservation in their respective RFP-TM domains
Title: Three novel human VMD2-like genes are members of the evolutionary highly conserved RFP-TM family.
Human Best4 chloride channels on excised membrane patches can be activated by free calcium (Ca2+) on the cytoplasmic side.
Title: Ca2+-activated Cl- current from human bestrophin-4 in excised membrane patches.

Submit: New GeneRIF Correction

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

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

NoName (e-PCR)
- UniSTS:485577

NoName (e-PCR)
- UniSTS:481489

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables bicarbonate channel activity	IDA Inferred from Direct Assay more info	PubMed
enables chloride channel activity	IDA Inferred from Direct Assay more info	PubMed
enables intracellularly calcium-gated chloride channel activity	IDA Inferred from Direct Assay more info	PubMed
enables molecular_function	ND No biological Data available more info

Process	Evidence Code	Pubs
involved_in bicarbonate transport	IEA Inferred from Electronic Annotation more info
involved_in biological_process	ND No biological Data available more info
involved_in chloride transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of chloride channel complex	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: bestrophin-4

Names: vitelliform macular dystrophy 2-like 2; vitelliform macular dystrophy 2-like 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.

mRNA and Protein(s)

NM_153274.3 → NP_695006.1 bestrophin-4

See identical proteins and their annotated locations for NP_695006.1

Status: REVIEWED

Source sequence(s)

AF440757, AL592166, BC101823, BM142321

Consensus CDS

CCDS514.1

UniProtKB/Swiss-Prot

Q5JR93, Q8NFU0

Related

ENSP00000361281.3, ENST00000372207.4

Conserved Domains (1) summary

pfam01062
Location:8 → 331

Bestrophin; RFP-TM, chloride channel

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

44781840..44792828 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017001023.2 → XP_016856512.1 bestrophin-4 isoform X1

UniProtKB/Swiss-Prot

Q5JR93, Q8NFU0

Conserved Domains (1) summary

pfam01062
Location:8 → 331

Bestrophin; RFP-TM, chloride channel
XM_024446367.1 → XP_024302135.1 bestrophin-4 isoform X1

UniProtKB/Swiss-Prot

Q5JR93, Q8NFU0

Conserved Domains (1) summary

pfam01062
Location:8 → 331

Bestrophin; RFP-TM, chloride channel
XM_047417823.1 → XP_047273779.1 bestrophin-4 isoform X1

UniProtKB/Swiss-Prot

Q5JR93, Q8NFU0
XM_047417821.1 → XP_047273777.1 bestrophin-4 isoform X1

UniProtKB/Swiss-Prot

Q5JR93, Q8NFU0
XM_047417826.1 → XP_047273782.1 bestrophin-4 isoform X2