BEST2

bestrophin 2, the group of Bestrophins

Basic information

Region (hg38): 19:12751702-12758458

Previous symbols: [ "VMD2L1" ]

Links

ENSG00000039987 ∙ NCBI:54831 ∙ OMIM:607335 ∙ HGNC:17107 ∙ Uniprot:Q8NFU1 ∙ 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 BEST2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEST2 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						0
missense			35	3		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	3	0

Variants in BEST2

This is a list of pathogenic ClinVar variants found in the BEST2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12752599-G-A		not specified	Uncertain significance (Jun 07, 2024)
19-12752602-A-G		not specified	Uncertain significance (Feb 06, 2024)
19-12752617-G-T		not specified	Uncertain significance (Aug 12, 2024)
19-12752625-C-A		not specified	Uncertain significance (Jun 28, 2022)
19-12752635-G-A		not specified	Uncertain significance (Oct 10, 2023)
19-12752666-G-A		not specified	Uncertain significance (Dec 16, 2022)
19-12752693-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-12753273-G-A		not specified	Uncertain significance (May 05, 2023)
19-12753322-A-G		not specified	Uncertain significance (Feb 20, 2025)
19-12754593-T-C		not specified	Uncertain significance (Jan 23, 2024)
19-12754616-C-G		not specified	Uncertain significance (Oct 07, 2024)
19-12754672-T-A		not specified	Uncertain significance (May 07, 2024)
19-12754678-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-12754686-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
19-12754713-G-C		not specified	Uncertain significance (Oct 21, 2024)
19-12754731-G-A		not specified	Uncertain significance (Dec 23, 2024)
19-12754951-G-A		not specified	Uncertain significance (Aug 10, 2023)
19-12755395-G-A		not specified	Uncertain significance (Sep 16, 2021)
19-12755440-C-A		not specified	Uncertain significance (Feb 19, 2025)
19-12755618-G-A		not specified	Uncertain significance (Aug 27, 2024)
19-12755663-C-T		not specified	Uncertain significance (Jun 22, 2023)
19-12755679-C-T		not specified	Uncertain significance (Jul 09, 2024)
19-12755702-G-A		not specified	Likely benign (Oct 08, 2024)
19-12755753-G-A		not specified	Uncertain significance (Dec 20, 2021)
19-12755870-A-G		not specified	Uncertain significance (Aug 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEST2	protein_coding	protein_coding	ENST00000549706	9	6757

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.52e-13	0.0516	125296	0	47	125343	0.000188

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	252	324	0.777	0.0000208	3235
Missense in Polyphen		100	137.92	0.72507		1372
Synonymous	-0.0296	140	140	1.00	0.00000940	1027
Loss of Function	0.416	21	23.2	0.907	0.00000134	227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000180
Ashkenazi Jewish	0.00	0.00
East Asian	0.000389	0.000382
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.000389	0.000382
South Asian	0.000197	0.000196
Other	0.000330	0.000328

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Forms calcium-sensitive chloride channels. Permeable to bicarbonate. {ECO:0000269|PubMed:11904445, ECO:0000269|PubMed:12907679, ECO:0000269|PubMed:18400985}.
• Pathway: Salivary secretion - Homo sapiens (human);Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.348
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.478
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.421

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Best2
• Phenotype: homeostasis/metabolism phenotype; vision/eye phenotype

Gene ontology

• Biological process: sensory perception of smell;biological_process;membrane depolarization;chloride transmembrane transport
• Cellular component: plasma membrane;cilium;chloride channel complex
• Molecular function: molecular_function;chloride channel activity