BEST4

bestrophin 4, the group of Bestrophins

Basic information

Region (hg38): 1:44781836-44788170

Previous symbols: [ "VMD2L2" ]

Links

ENSG00000142959 ∙ NCBI:266675 ∙ OMIM:607336 ∙ HGNC:17106 ∙ Uniprot:Q8NFU0 ∙ 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 BEST4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEST4 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					1	1
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	1

Variants in BEST4

This is a list of pathogenic ClinVar variants found in the BEST4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-44784241-G-A		not specified	Uncertain significance (Apr 01, 2024)
1-44784314-G-C		not specified	Uncertain significance (Feb 10, 2022)
1-44784391-C-T		not specified	Uncertain significance (Nov 13, 2024)
1-44784419-G-T		not specified	Uncertain significance (May 25, 2022)
1-44784458-G-T		not specified	Uncertain significance (Jan 06, 2023)
1-44784473-C-T		not specified	Uncertain significance (Mar 27, 2023)
1-44784652-G-C		not specified	Uncertain significance (Dec 12, 2024)
1-44784674-G-T		not specified	Uncertain significance (Aug 02, 2023)
1-44784695-G-A		not specified	Uncertain significance (Jul 14, 2021)
1-44784915-C-T		not specified	Uncertain significance (Oct 26, 2021)
1-44785129-G-T		not specified	Uncertain significance (Aug 14, 2024)
1-44785170-G-T		not specified	Uncertain significance (Mar 29, 2024)
1-44785227-C-T		not specified	Uncertain significance (Apr 09, 2024)
1-44785295-A-G		not specified	Uncertain significance (Jul 30, 2024)
1-44785610-C-G		not specified	Uncertain significance (Apr 15, 2024)
1-44785674-C-A		not specified	Uncertain significance (Apr 20, 2024)
1-44786467-G-C		not specified	Uncertain significance (May 16, 2024)
1-44786475-C-T		not specified	Uncertain significance (Feb 01, 2023)
1-44786516-A-G		not specified	Uncertain significance (Oct 01, 2024)
1-44786519-G-A		not specified	Uncertain significance (Nov 18, 2022)
1-44786562-G-C		not specified	Uncertain significance (Apr 11, 2023)
1-44786580-G-C		not specified	Uncertain significance (Jul 12, 2022)
1-44786595-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-44786609-G-A		not specified	Uncertain significance (Aug 28, 2024)
1-44787454-G-C			Benign (Sep 19, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEST4	protein_coding	protein_coding	ENST00000372207	9	4121

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000470	0.963	125686	0	60	125746	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	159	248	0.641	0.0000136	2998
Missense in Polyphen		64	115.89	0.55226		1363
Synonymous	1.77	83	106	0.781	0.00000599	980
Loss of Function	1.94	12	21.8	0.551	0.00000101	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.00100
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.000110	0.000109
South Asian	0.0000981	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Forms calcium-sensitive chloride channels. Permeable to bicarbonate. {ECO:0000269|PubMed:12907679, ECO:0000269|PubMed:18400985}.
• Pathway: Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.335
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.420
• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.450

Gene Damage Prediction

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

Gene ontology

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