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.

• not_specified (37 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000153274.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			37			37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	0	1

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