Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	7439
Gene name Gene Name - the full gene name approved by the HGNC.	Bestrophin 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	BEST1
Synonyms (NCBI Gene) Gene synonyms aliases	ARB, BEST, BMD, Best1V1Delta2, RP50, TU15B, VMD2
Chromosome Chromosome number	11
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	11q12.3
Summary Summary of gene provided in NCBI Entrez Gene.	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-gat

Show/Hide all(22)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28940275	A>C	Pathogenic, not-provided	Missense variant, coding sequence variant, non coding transcript variant, genic upstream transcript variant, intron variant
rs28940276	G>A	Pathogenic, not-provided	Missense variant, coding sequence variant, non coding transcript variant, genic upstream transcript variant, intron variant
rs28940278	G>A	Not-provided, pathogenic-likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant, genic upstream transcript variant, intron variant
rs121918285	C>G,T	Not-provided, pathogenic	Synonymous variant, coding sequence variant, genic upstream transcript variant, intron variant, stop gained, non coding transcript variant
rs121918288	T>C	Not-provided, pathogenic	Coding sequence variant, genic upstream transcript variant, intron variant, missense variant, non coding transcript variant
rs281865205	T>C,G	Likely-pathogenic, not-provided	Intron variant, non coding transcript variant, missense variant, coding sequence variant, genic upstream transcript variant
rs281865207	C>T	Pathogenic, not-provided	Intron variant, non coding transcript variant, missense variant, coding sequence variant, genic upstream transcript variant
rs281865209	G>A,C	Likely-pathogenic, not-provided	Intron variant, non coding transcript variant, missense variant, coding sequence variant, genic upstream transcript variant
rs281865215	G>A	Pathogenic, not-provided	Intron variant, non coding transcript variant, missense variant, coding sequence variant, genic upstream transcript variant
rs281865218	A>G	Uncertain-significance, likely-pathogenic	Intron variant, non coding transcript variant, missense variant, coding sequence variant, genic upstream transcript variant
rs281865528	CA>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, 3 prime UTR variant
rs752125512	T>-	Likely-pathogenic	Frameshift variant, 3 prime UTR variant, coding sequence variant, non coding transcript variant
rs752521456	TG>-	Likely-pathogenic	Frameshift variant, 3 prime UTR variant, coding sequence variant, non coding transcript variant
rs766357080	->G	Pathogenic	3 prime UTR variant, coding sequence variant, non coding transcript variant, frameshift variant
rs766379510	G>A,C	Pathogenic	Intron variant, genic upstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs771898125	C>T	Likely-pathogenic	Intron variant, genic upstream transcript variant, non coding transcript variant, synonymous variant, coding sequence variant
rs886041141	C>G,T	Uncertain-significance, likely-pathogenic	Missense variant, genic upstream transcript variant, non coding transcript variant, coding sequence variant, intron variant
rs886041142	G>A	Likely-pathogenic	Missense variant, genic upstream transcript variant, non coding transcript variant, coding sequence variant, intron variant
rs1554964287	C>G	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant, 3 prime UTR variant
rs1555096248	G>T	Pathogenic	Splice donor variant, intron variant, genic upstream transcript variant
rs1565382549	A>G	Likely-pathogenic	Coding sequence variant, missense variant, intron variant, non coding transcript variant, genic upstream transcript variant
rs1591266379	C>G	Pathogenic	Non coding transcript variant, genic upstream transcript variant, coding sequence variant, missense variant, intron variant

Show/Hide all(35)

miRTarBase ID	miRNA	Experiments
MIRT1942624	hsa-miR-4277	CLIP-seq
MIRT1942625	hsa-miR-4292	CLIP-seq
MIRT1942626	hsa-miR-4690-3p	CLIP-seq
MIRT1942627	hsa-miR-486-3p	CLIP-seq
MIRT1942628	hsa-miR-515-5p	CLIP-seq
MIRT2181412	hsa-miR-4302	CLIP-seq
MIRT1942624	hsa-miR-4277	CLIP-seq
MIRT1942625	hsa-miR-4292	CLIP-seq
MIRT1942626	hsa-miR-4690-3p	CLIP-seq
MIRT1942627	hsa-miR-486-3p	CLIP-seq
MIRT1942628	hsa-miR-515-5p	CLIP-seq
MIRT2484663	hsa-miR-1178	CLIP-seq
MIRT2484664	hsa-miR-3157-5p	CLIP-seq
MIRT2484665	hsa-miR-382	CLIP-seq
MIRT2484666	hsa-miR-3973	CLIP-seq
MIRT2484667	hsa-miR-4259	CLIP-seq
MIRT2484668	hsa-miR-4260	CLIP-seq
MIRT2484669	hsa-miR-4640-5p	CLIP-seq
MIRT2484670	hsa-miR-4691-3p	CLIP-seq
MIRT2484671	hsa-miR-4715-3p	CLIP-seq
MIRT2484672	hsa-miR-4726-5p	CLIP-seq
MIRT2484673	hsa-miR-520g	CLIP-seq
MIRT2484674	hsa-miR-520h	CLIP-seq
MIRT2484675	hsa-miR-548a-5p	CLIP-seq
MIRT2484676	hsa-miR-548ab	CLIP-seq
MIRT2484677	hsa-miR-548ak	CLIP-seq
MIRT2484678	hsa-miR-548b-5p	CLIP-seq
MIRT2484679	hsa-miR-548c-5p	CLIP-seq
MIRT2484680	hsa-miR-548d-5p	CLIP-seq
MIRT2484681	hsa-miR-548h	CLIP-seq
MIRT2484682	hsa-miR-548i	CLIP-seq
MIRT2484683	hsa-miR-548j	CLIP-seq
MIRT2484684	hsa-miR-548w	CLIP-seq
MIRT2484685	hsa-miR-548y	CLIP-seq
MIRT2484686	hsa-miR-559	CLIP-seq

Transcription factors

Show/Hide all(7)

Transcription factor	Regulation	Reference
CRX	Activation	18849347
MITF	Activation	14982938
MITF	Unknown	20530484
OTX1	Activation	18849347
OTX2	Activation	18849347
OTX2	Unknown	20530484
SOX9	Activation	20530484

Show/Hide all(47)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005229	Function	Intracellularly calcium-gated chloride channel activity	IDA	11904445, 12907679, 18400985, 26720466, 35789156
GO:0005229	Function	Intracellularly calcium-gated chloride channel activity	IMP	18179881, 19853238, 21330666, 26200502
GO:0005254	Function	Chloride channel activity	IDA	17003041
GO:0005254	Function	Chloride channel activity	IDA	17003041
GO:0005254	Function	Chloride channel activity	IEA
GO:0005254	Function	Chloride channel activity	TAS
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005829	Component	Cytosol	TAS	17003041
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	26200502
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006821	Process	Chloride transport	IDA	17003041
GO:0006821	Process	Chloride transport	IEA
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	TAS	9662395
GO:0009925	Component	Basal plasma membrane	IDA	31791063
GO:0014047	Process	Glutamate secretion	IEA
GO:0014047	Process	Glutamate secretion	ISS
GO:0015106	Function	Bicarbonate transmembrane transporter activity	TAS
GO:0015267	Function	Channel activity	IEA
GO:0015701	Process	Bicarbonate transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	10737974
GO:0016323	Component	Basolateral plasma membrane	IDA	11050159, 19853238, 21330666, 26200502
GO:0016323	Component	Basolateral plasma membrane	IEA
GO:0022834	Function	Ligand-gated channel activity	IEA
GO:0022834	Function	Ligand-gated channel activity	ISS
GO:0030321	Process	Transepithelial chloride transport	IDA	17003041
GO:0034220	Process	Monoatomic ion transmembrane transport	IEA
GO:0034220	Process	Monoatomic ion transmembrane transport	TAS
GO:0034707	Component	Chloride channel complex	IDA	17003041
GO:0034707	Component	Chloride channel complex	IEA
GO:0042802	Function	Identical protein binding	IPI	19372599
GO:0048167	Process	Regulation of synaptic plasticity	IEA
GO:0048167	Process	Regulation of synaptic plasticity	ISS
GO:0050908	Process	Detection of light stimulus involved in visual perception	IEA
GO:0051259	Process	Protein complex oligomerization	IDA	26200502
GO:0051924	Process	Regulation of calcium ion transport	IEA
GO:0061534	Process	Gamma-aminobutyric acid secretion, neurotransmission	IEA
GO:0061534	Process	Gamma-aminobutyric acid secretion, neurotransmission	ISS
GO:0098793	Component	Presynapse	IEA
GO:0098857	Component	Membrane microdomain	IEA
GO:0098857	Component	Membrane microdomain	ISS
GO:0160133	Function	Bicarbonate channel activity	IDA	18400985
GO:1902476	Process	Chloride transmembrane transport	IBA

MIM	HGNC	e!Ensembl
607854	12703	ENSG00000167995

Protein

UniProt ID

O76090

Protein name

Bestrophin-1 (TU15B) (Vitelliform macular dystrophy protein 2)

Protein function

Ligand-gated anion channel that allows the movement of anions across cell membranes when activated by calcium (Ca2+) (PubMed:11904445, PubMed:12907679, PubMed:18179881, PubMed:18400985, PubMed:19853238, PubMed:21330666, PubMed:26200502, PubMed:2

PDB

8D1I , 8D1J , 8D1K , 8D1L , 8D1M , 8D1O , 9CTQ , 9CTR , 9CTS , 9CTT , 9DYL , 9DYM

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01062	Bestrophin	8 → 316	Bestrophin, RFP-TM, chloride channel	Family

Tissue specificity

TISSUE SPECIFICITY: Predominantly expressed in the basolateral membrane of the retinal pigment epithelium.

Sequence

MTITYTSQVANARLGSFSRLLLCWRGSIYKLLYGEFLIFLLCYYIIRFIYRLALTEEQQL
MFEKLTLYCDSYIQLIPISFVLGFYVTLVVTRWWNQYENLPWPDRLMSLVSGFVEGKDEQ
GRLLRRTLIRYANLGNVLILRSVSTAVYKRFPSAQHLVQAGFMTPAEHKQLEKLSLPHNM
FWVPWVWFANLSMKAWLGGRIRDPILLQSLLNEMNTLRTQCGHLYAYDWISIPLVYTQVV
TVAVYSFFLTCLVGRQFLNPAKAYPGHELDLVVPVFTFLQFFFYVGWLKVAEQLINPFGE
DDDDFETNWIVDRNLQVSLLAVDEMHQDLPRMEPDMYWNKPEPQPPYTAASAQFRRASFM
GSTFNISLNKEEMEFQPNQEDEEDAHAGIIGRFLGLQSHDHHPPRANSRTKLLWPKRESL
LHEGLPKNHKAAKQNVRGQEDNKAWKLKAVDAFKSAPLYQRPGYYSAPQTPLSPTPMFFP
LEPSAPSKLHSVTGIDTKDKSLKTVSSGAKKSFELLSESDGALMEHPEVSQVRRKTVEFN
LTDMPEIPENHLKEPLEQSPTNIHTTLKDHMDPYWALENRDEAHS

Sequence length

585

Interactions

View interactions

	Reactome
			Stimuli-sensing channels

Show/Hide Causal Diseases (7)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Bestrophinopathy	autosomal recessive bestrophinopathy	rs199529046, rs121918286, rs62637337, rs753614067, rs121918287, rs752521456, rs121918288, rs281865225, rs1565392261, rs1431752515, rs281865528, rs372989281, rs1555096248, rs281865215, rs886041142 View all (6 more)	N/A
retinal dystrophy	Retinal dystrophy	rs28941468, rs281865253, rs281865204, rs28940570, rs281865262, rs775283269, rs281865247, rs1941898895, rs281865221, rs1554963058, rs281865265, rs137853905, rs121918286, rs886039311, rs28940275 View all (63 more)	N/A
Retinitis Pigmentosa	retinitis pigmentosa	rs372989281, rs1555099048	N/A
Stargardt Disease	stargardt disease	rs1591303900, rs1591266591, rs121918284	N/A
Vitelliform Macular Dystrophy	Vitelliform macular dystrophy 2	rs1591280478, rs1591284563, rs886039311, rs1225032182, rs1591280714, rs121918285, rs1555100476, rs281865255, rs199529046, rs28940275, rs1591283793, rs28941469, rs1554963095, rs281865221, rs281865212 View all (35 more)	N/A
Vitreoretinochoroidopathy	autosomal dominant vitreoretinochoroidopathy	rs28940570, rs267606676, rs121918289, rs267606679	N/A
Macular dystrophy	Isolated macular dystrophy, macular dystrophy	rs886041141, rs368383940, rs1225032182, rs281865255, rs281865239, rs1565387045	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Cone-rod dystrophy	Cone-rod dystrophy 6	N/A	N/A	ClinVar
Rod-cone dystrophy	rod-cone dystrophy	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (55)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Atherosclerosis	Associate	31875420
Axenfeld Rieger syndrome	Associate	28056057, 32646389
Behcet Syndrome	Associate	32111077
Best Vitelliform Macular Dystrophy Multifocal	Associate	21293734
Bestrophinopathy	Associate	21738390, 25489231, 27163236, 28831140, 29976937, 30781664, 31766397, 31836750, 32111077, 32421148, 34061021, 34327816, 36378562, 37747403
Blindness	Associate	29063836
Cataract	Associate	37076855
Cataract microcornea syndrome	Associate	37076855
Choroidal Neovascularization	Associate	30498755
Choroiditis	Associate	33302512
Cone Rod Dystrophies	Associate	29555955, 35656873
Crohn Disease	Associate	35260635
Cysts	Associate	30781664
Epilepsy	Associate	39674551
Eye Abnormalities	Associate	21072067
Genetic Diseases Inborn	Associate	32421148
Glaucoma	Associate	28056057
Glaucoma Angle Closure	Associate	21921978, 24859690, 28056057, 30593719, 32646389, 35768830, 40414863
Heredodegenerative Disorders Nervous System	Associate	25878489
Hyperlipidemias	Associate	30781664, 37041514
Hypertensive Retinopathy	Associate	18179881, 18985398, 19029375, 19635817, 27287821, 36264634
Hypomagnesemia 5 Renal with Ocular Involvement	Associate	28677725
Macular Degeneration	Associate	16885924, 20057903, 32707085, 37041716, 39596324
Macular Dystrophy Retinal 2	Associate	33988224
Macular Edema	Associate	37246744
Microphthalmos	Associate	37076855
Multiple Pterygium Syndrome Autosomal Dominant	Associate	19853238, 31766397
Neoplasms	Associate	31455904, 37088729
Neoplasms Cystic Mucinous and Serous	Associate	40724865
Nerve Degeneration	Associate	39674551
Neurodegenerative Diseases	Associate	21072067, 31263784
Paralysis Hyperkalemic Periodic	Associate	19372599
Patterned dystrophy of retinal pigment epithelium	Associate	32882766
Plaque Atherosclerotic	Associate	31875420
Refsum Disease Infantile	Associate	27391102
Retinal Degeneration	Associate	27193166
Retinal Detachment	Associate	37761846
Retinal Diseases	Associate	29063836, 30199040, 30628889, 31836750, 32423767, 34061021, 38160664, 40724865
Retinal Dystrophies	Associate	18985398, 19853238, 22162627, 27391102, 32646389, 34996991, 39596324
Retinal Vein Occlusion	Associate	35768830
Retinitis	Associate	28056057, 40724865
Retinitis Pigmentosa	Associate	19853238, 35656873
Retinitis Pigmentosa Concentric	Associate	31766397
Retinoschisis	Associate	32646389
Squamous Cell Carcinoma of Head and Neck	Associate	37088729
Stargardt Disease	Associate	28050124, 33988224, 36264634
Sveinsson Chorioretinal Atrophy	Associate	23617333
Usher Syndromes	Associate	35656873
Uveitis	Associate	40414863
Vision Disorders	Associate	21293734, 29063836
Vitamin D Deficiency	Associate	29976937
Vitelliform Macular Dystrophy	Associate	16865191, 16885924, 17287362, 18179881, 19372599, 19597114, 19635817, 19853238, 20057903, 21109774, 21293734, 21738390, 21921978, 22084158, 22162627 View all (40 more)
Vitreoretinochoroidopathy	Associate	16707793, 18179881, 21072067, 32111077
Vitreoretinopathy Proliferative	Associate	28777835
White Dot Syndromes	Associate	31766397

BEST1 (bestrophin 1)