OR52B4

olfactory receptor family 52 subfamily B member 4, the group of Olfactory receptors, family 52

Basic information

Region (hg38): 11:4367263-4368386

Links

ENSG00000221996 ∙ NCBI:143496 ∙ ∙ HGNC:15209 ∙ Uniprot:Q8NGK2 ∙ 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 OR52B4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52B4 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			23	2		25
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	1

Variants in OR52B4

This is a list of pathogenic ClinVar variants found in the OR52B4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-4367400-T-C		not specified	Uncertain significance (Jun 28, 2023)
11-4367404-T-G		not specified	Uncertain significance (Jul 09, 2021)
11-4367446-G-C		not specified	Uncertain significance (Mar 29, 2023)
11-4367449-T-C		not specified	Uncertain significance (Dec 27, 2023)
11-4367451-C-T		not specified	Uncertain significance (Mar 15, 2024)
11-4367476-T-A		not specified	Uncertain significance (Jun 16, 2024)
11-4367486-A-C		not specified	Uncertain significance (Apr 06, 2024)
11-4367493-C-T		not specified	Likely benign (Jan 18, 2022)
11-4367517-G-C		not specified	Uncertain significance (Jan 24, 2024)
11-4367562-G-A		not specified	Uncertain significance (Jan 10, 2023)
11-4367580-G-C		not specified	Uncertain significance (Sep 16, 2021)
11-4367596-C-T		not specified	Uncertain significance (Aug 30, 2021)
11-4367635-T-C		not specified	Likely benign (Jul 21, 2021)
11-4367673-G-A		not specified	Uncertain significance (Jan 10, 2022)
11-4367692-A-T		not specified	Uncertain significance (May 05, 2023)
11-4367749-G-C		not specified	Uncertain significance (Sep 16, 2021)
11-4367767-G-C		not specified	Uncertain significance (Dec 08, 2023)
11-4367815-T-G		not specified	Uncertain significance (Apr 26, 2023)
11-4367853-A-C		not specified	Uncertain significance (Dec 07, 2021)
11-4367945-C-G		not specified	Uncertain significance (Aug 08, 2023)
11-4367952-C-T		not specified	Uncertain significance (May 31, 2023)
11-4368007-C-A		not specified	Uncertain significance (Dec 11, 2023)
11-4368019-C-T		not specified	Uncertain significance (Nov 16, 2021)
11-4368028-G-A		not specified	Uncertain significance (Feb 15, 2023)
11-4368033-C-A		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52B4	protein_coding	protein_coding	ENST00000408920	1	1124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.26e-7	0.0724	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.992	210	173	1.21	0.00000838	2075
Missense in Polyphen		45	43.49	1.0347		601
Synonymous	-2.27	88	64.8	1.36	0.00000316	634
Loss of Function	-1.14	8	5.19	1.54	2.85e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Odorant receptor. {ECO:0000305}.
• Pathway: Olfactory transduction - Homo sapiens (human);Olfactory receptor activity (Consensus)

Intolerance Scores

• loftool: 0.647
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.398

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0000357

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr547

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;cognition;detection of chemical stimulus involved in sensory perception of smell
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: G protein-coupled receptor activity;olfactory receptor activity