OR5T2

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

Basic information

Region (hg38): 11:56231282-56234255

Links

ENSG00000181718 ∙ NCBI:219464 ∙ ∙ HGNC:15296 ∙ Uniprot:Q8NGG2 ∙ 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 OR5T2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5T2 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			37	5		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5			5
Total	0	0	42	5	0

Variants in OR5T2

This is a list of pathogenic ClinVar variants found in the OR5T2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-56232119-T-G		not specified	Uncertain significance (Aug 19, 2024)
11-56232135-T-A		not specified	Uncertain significance (Sep 15, 2021)
11-56232154-A-C		not specified	Uncertain significance (Aug 28, 2023)
11-56232188-T-C		not specified	Uncertain significance (Feb 15, 2023)
11-56232197-C-A		not specified	Uncertain significance (Jan 09, 2025)
11-56232198-T-C		not specified	Uncertain significance (Mar 01, 2023)
11-56232207-C-T		not specified	Likely benign (Sep 27, 2021)
11-56232211-A-T		not specified	Uncertain significance (Sep 15, 2021)
11-56232242-A-T		not specified	Uncertain significance (May 17, 2023)
11-56232251-A-G		not specified	Uncertain significance (Jun 21, 2023)
11-56232253-C-T		not specified	Uncertain significance (Jul 06, 2024)
11-56232321-T-C		not specified	Uncertain significance (May 23, 2023)
11-56232324-A-G		not specified	Uncertain significance (Feb 16, 2023)
11-56232342-C-T		not specified	Uncertain significance (May 18, 2023)
11-56232377-G-A		not specified	Uncertain significance (Jun 18, 2024)
11-56232437-A-G		not specified	Uncertain significance (Mar 03, 2022)
11-56232449-T-C		not specified	Uncertain significance (Sep 27, 2024)
11-56232452-A-G		not specified	Uncertain significance (Sep 22, 2023)
11-56232513-C-G		not specified	Uncertain significance (Nov 06, 2023)
11-56232548-A-T		not specified	Uncertain significance (Jun 22, 2023)
11-56232558-C-A		not specified	Likely benign (Apr 24, 2023)
11-56232560-C-T		not specified	Uncertain significance (Sep 06, 2022)
11-56232596-A-G		not specified	Uncertain significance (May 23, 2023)
11-56232597-T-C		not specified	Likely benign (Aug 11, 2024)
11-56232629-G-A		not specified	Uncertain significance (Jul 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR5T2	protein_coding	protein_coding	ENST00000313264	1	1248

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000378	0.407	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.08	264	185	1.43	0.00000844	2344
Missense in Polyphen		54	36.695	1.4716		568
Synonymous	-0.569	76	69.9	1.09	0.00000338	709
Loss of Function	-0.0278	5	4.93	1.01	1.99e-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)

Intolerance Scores

• loftool: 0.807
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.84

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.112
• ghis: 0.394

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0137

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1086

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