OR5B2

olfactory receptor family 5 subfamily B member 2, the group of Olfactory receptors, family 5

Basic information

Region (hg38): 11:58421237-58428121

Links

ENSG00000172365 ∙ NCBI:390190 ∙ ∙ HGNC:8323 ∙ Uniprot:Q96R09 ∙ 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 OR5B2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5B2 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			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in OR5B2

This is a list of pathogenic ClinVar variants found in the OR5B2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-58422337-G-C		not specified	Uncertain significance (Apr 07, 2023)
11-58422462-T-A		not specified	Uncertain significance (Apr 07, 2022)
11-58422502-T-C		not specified	Uncertain significance (Feb 21, 2024)
11-58422513-T-A		not specified	Uncertain significance (Sep 12, 2023)
11-58422540-G-A		not specified	Uncertain significance (Apr 28, 2023)
11-58422633-A-G		not specified	Uncertain significance (Feb 15, 2023)
11-58422678-A-G		not specified	Likely benign (Nov 08, 2022)
11-58422693-T-A		not specified	Uncertain significance (Dec 07, 2021)
11-58422745-G-A		not specified	Uncertain significance (Oct 13, 2023)
11-58422777-A-C		not specified	Uncertain significance (May 22, 2023)
11-58422789-A-C		not specified	Uncertain significance (Aug 08, 2022)
11-58422789-A-G		not specified	Likely benign (Aug 13, 2021)
11-58422825-G-A		not specified	Uncertain significance (Dec 20, 2023)
11-58422868-T-C		not specified	Uncertain significance (Aug 08, 2023)
11-58422984-T-C		not specified	Uncertain significance (Dec 15, 2023)
11-58423125-A-C		not specified	Uncertain significance (Mar 19, 2024)
11-58423174-T-C		not specified	Uncertain significance (Jun 16, 2024)
11-58423188-A-G		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR5B2	protein_coding	protein_coding	ENST00000302581	1	1049

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0721	0.756	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.628	184	162	1.14	0.00000736	2033
Missense in Polyphen		27	28.969	0.93204		441
Synonymous	-0.689	71	64.0	1.11	0.00000303	622
Loss of Function	0.957	2	4.09	0.489	1.65e-7	75

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;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0944

Intolerance Scores

• loftool: 0.760
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.17

Haploinsufficiency Scores

• pHI: 0.0835
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0148

Gene Damage Prediction

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

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;sensory perception of smell;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;odorant binding