OR5B3

olfactory receptor family 5 subfamily B member 3, the group of Olfactory receptors, family 5

Basic information

Region (hg38): 11:58402464-58406874

Previous symbols: [ "OR5B13" ]

Links

ENSG00000172769 ∙ NCBI:441608 ∙ ∙ HGNC:8324 ∙ Uniprot:Q8NH48 ∙ 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 OR5B3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5B3 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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	0

Variants in OR5B3

This is a list of pathogenic ClinVar variants found in the OR5B3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-58402489-T-A		not specified	Uncertain significance (Dec 12, 2023)
11-58402518-C-T		not specified	Uncertain significance (Mar 20, 2024)
11-58402576-C-T		not specified	Uncertain significance (May 16, 2022)
11-58402631-G-C		not specified	Uncertain significance (Feb 11, 2022)
11-58402652-A-G		not specified	Uncertain significance (Aug 02, 2023)
11-58402681-G-T		not specified	Likely benign (Dec 17, 2021)
11-58402785-G-A		not specified	Uncertain significance (Aug 03, 2022)
11-58402826-A-G		not specified	Uncertain significance (Dec 11, 2023)
11-58402904-G-T		not specified	Uncertain significance (Oct 10, 2023)
11-58402920-G-A		not specified	Uncertain significance (Apr 01, 2024)
11-58403040-C-T		not specified	Uncertain significance (Jun 24, 2022)
11-58403075-A-G		not specified	Uncertain significance (Oct 26, 2022)
11-58403142-T-C		not specified	Uncertain significance (Dec 01, 2022)
11-58403215-A-G			Likely benign (Jan 01, 2023)
11-58403223-T-C		not specified	Uncertain significance (Sep 22, 2023)
11-58403270-A-G		not specified	Uncertain significance (Mar 11, 2022)
11-58403312-T-C		not specified	Uncertain significance (Apr 25, 2022)
11-58403327-G-A		not specified	Likely benign (Aug 15, 2023)
11-58403390-A-G		not specified	Uncertain significance (Dec 12, 2023)
11-58403394-C-T		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR5B3	protein_coding	protein_coding	ENST00000309403	1	946

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000470	0.252	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.337	178	166	1.07	0.00000769	2062
Missense in Polyphen		36	32.816	1.097		504
Synonymous	-1.83	79	60.9	1.30	0.00000286	630
Loss of Function	-0.394	6	5.05	1.19	2.09e-7	80

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: 0.0789

Intolerance Scores

• loftool: 0.768
• rvis_EVS: 2.15
• rvis_percentile_EVS: 97.99

Haploinsufficiency Scores

• pHI: 0.0704
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00390

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Olfr1469

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