BEST3

bestrophin 3, the group of Bestrophins

Basic information

Region (hg38): 12:69643359-69699476

Previous symbols: [ "VMD2L3" ]

Links

ENSG00000127325 ∙ NCBI:144453 ∙ OMIM:607337 ∙ HGNC:17105 ∙ Uniprot:Q8N1M1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BEST3 gene.

• Inborn genetic diseases (25 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEST3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			23		1	24
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	25	2	2

Variants in BEST3

This is a list of pathogenic ClinVar variants found in the BEST3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-69643740-G-A			Benign (Jan 18, 2019)
12-69654914-G-A		not specified	Uncertain significance (Mar 06, 2023)
12-69654944-A-G		not specified	Uncertain significance (Feb 07, 2023)
12-69654950-T-C		not specified	Uncertain significance (Aug 02, 2023)
12-69655019-A-G		not specified	Uncertain significance (Jun 16, 2023)
12-69655050-C-T		not specified	Uncertain significance (Sep 15, 2021)
12-69655062-A-C		not specified	Uncertain significance (Feb 27, 2024)
12-69655148-C-T		not specified	Uncertain significance (May 23, 2023)
12-69655270-G-A			Likely benign (Nov 01, 2022)
12-69655278-T-C		not specified	Likely benign (Jan 23, 2024)
12-69655290-G-C		not specified	Uncertain significance (Oct 17, 2023)
12-69655310-T-G		not specified	Uncertain significance (Dec 01, 2022)
12-69655315-C-A			Likely benign (Nov 01, 2022)
12-69655403-A-G		not specified	Uncertain significance (Oct 26, 2022)
12-69655413-G-A		not specified	Uncertain significance (Jun 27, 2022)
12-69655587-G-C		not specified	Uncertain significance (Dec 02, 2022)
12-69655707-C-T		not specified	Uncertain significance (Feb 28, 2023)
12-69655725-G-A		not specified	Uncertain significance (Jan 16, 2024)
12-69655784-T-C		not specified	Uncertain significance (May 03, 2023)
12-69655784-T-G		not specified	Uncertain significance (Jul 06, 2021)
12-69655789-G-T		not specified	Uncertain significance (Oct 06, 2021)
12-69671476-G-C			Uncertain significance (Nov 09, 2023)
12-69671497-C-T		not specified	Uncertain significance (Jun 11, 2021)
12-69671510-C-T		not specified	Uncertain significance (Feb 11, 2022)
12-69672889-A-G		not specified	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEST3	protein_coding	protein_coding	ENST00000330891	9	56117

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.01e-19	0.00178	125509	0	239	125748	0.000951

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.556	337	367	0.918	0.0000193	4375
Missense in Polyphen		91	104.92	0.86734		1256
Synonymous	-0.0233	142	142	1.00	0.00000809	1302
Loss of Function	-0.209	28	26.8	1.04	0.00000138	305

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00134	0.00132
Ashkenazi Jewish	0.00646	0.00647
East Asian	0.000613	0.000598
Finnish	0.00102	0.00102
European (Non-Finnish)	0.000550	0.000440
Middle Eastern	0.000613	0.000598
South Asian	0.00159	0.00134
Other	0.00166	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Forms calcium-sensitive chloride channels. Permeable to bicarbonate. {ECO:0000269|PubMed:12907679}.
• Pathway: Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.227
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.57

Haploinsufficiency Scores

• pHI: 0.148
• hipred: N
• hipred_score: 0.197
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.482

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Best3

Gene ontology

• Biological process: biological_process;negative regulation of ion transport;chloride transmembrane transport
• Cellular component: plasma membrane;chloride channel complex
• Molecular function: molecular_function;chloride channel activity