OR5T3

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

Basic information

Region (hg38): 11:56252254-56253222

Links

ENSG00000172489 ∙ NCBI:390154 ∙ ∙ HGNC:15297 ∙ Uniprot:Q8NGG3 ∙ 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 OR5T3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5T3 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in OR5T3

This is a list of pathogenic ClinVar variants found in the OR5T3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-56252270-C-T		not specified	Uncertain significance (May 23, 2023)
11-56252306-A-C		not specified	Uncertain significance (Apr 12, 2024)
11-56252309-C-A		not specified	Uncertain significance (Oct 29, 2021)
11-56252318-C-T		not specified	Uncertain significance (Mar 02, 2023)
11-56252357-T-G		not specified	Uncertain significance (Jun 22, 2023)
11-56252393-A-G		not specified	Uncertain significance (Dec 16, 2023)
11-56252410-G-A		not specified	Uncertain significance (Mar 27, 2023)
11-56252461-C-T		not specified	Uncertain significance (Mar 24, 2023)
11-56252522-C-T		not specified	Uncertain significance (May 23, 2024)
11-56252557-A-G		not specified	Uncertain significance (Dec 14, 2023)
11-56252592-G-A		not specified	Uncertain significance (May 13, 2024)
11-56252623-T-C		not specified	Uncertain significance (Feb 03, 2022)
11-56252652-T-A		not specified	Uncertain significance (Jun 17, 2024)
11-56252701-C-T		not specified	Uncertain significance (Aug 17, 2021)
11-56252707-G-T		not specified	Uncertain significance (Dec 09, 2023)
11-56252743-G-A		not specified	Uncertain significance (Oct 29, 2021)
11-56252764-C-T		not specified	Uncertain significance (Dec 07, 2024)
11-56252770-G-A		not specified	Uncertain significance (Apr 27, 2023)
11-56252828-A-G		not specified	Uncertain significance (Dec 03, 2024)
11-56252882-T-C		not specified	Uncertain significance (Apr 08, 2024)
11-56252885-T-G		not specified	Uncertain significance (Feb 06, 2024)
11-56252939-C-T		not specified	Uncertain significance (Aug 02, 2021)
11-56252966-T-C		not specified	Uncertain significance (Apr 07, 2023)
11-56252999-C-T		not specified	Likely benign (Jul 06, 2021)
11-56253043-C-G		not specified	Uncertain significance (Jan 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR5T3	protein_coding	protein_coding	ENST00000303059	1	1023

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000420	0.426	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.06	207	168	1.23	0.00000760	2218
Missense in Polyphen		29	29.9	0.96991		474
Synonymous	0.615	57	63.2	0.902	0.00000295	683
Loss of Function	0.0351	5	5.09	0.983	2.12e-7	92

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: 0.0839

Intolerance Scores

• loftool: 0.896
• rvis_EVS: 1.04
• rvis_percentile_EVS: 91.26

Haploinsufficiency Scores

• pHI: 0.0968
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00966

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1093

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;chemical synaptic transmission;detection of chemical stimulus involved in sensory perception of smell;G protein-coupled serotonin receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;dendrite
• Molecular function: G protein-coupled receptor activity;olfactory receptor activity;G protein-coupled serotonin receptor activity;neurotransmitter receptor activity