OR2T3

olfactory receptor family 2 subfamily T member 3, the group of Olfactory receptors, family 2

Basic information

Region (hg38): 1:248473351-248474307

Links

ENSG00000196539 ∙ NCBI:343173 ∙ ∙ HGNC:14727 ∙ Uniprot:Q8NH03 ∙ 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 OR2T3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2T3 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			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	0	0

Variants in OR2T3

This is a list of pathogenic ClinVar variants found in the OR2T3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-248473357-T-C		not specified	Uncertain significance (Dec 26, 2023)
1-248473360-G-C		not specified	Uncertain significance (Jan 04, 2022)
1-248473409-C-T		not specified	Uncertain significance (Mar 07, 2024)
1-248473425-G-C		not specified	Uncertain significance (Mar 24, 2023)
1-248473429-A-C		not specified	Uncertain significance (Apr 27, 2023)
1-248473448-A-C		not specified	Uncertain significance (Oct 26, 2022)
1-248473456-A-T		not specified	Uncertain significance (Aug 02, 2021)
1-248473459-T-G		not specified	Uncertain significance (Jan 19, 2022)
1-248473460-T-A		not specified	Uncertain significance (May 01, 2024)
1-248473472-T-C		not specified	Uncertain significance (May 31, 2023)
1-248473498-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-248473502-T-A		not specified	Uncertain significance (May 26, 2024)
1-248473564-G-A		not specified	Uncertain significance (Apr 25, 2023)
1-248473571-T-C		not specified	Uncertain significance (Mar 24, 2023)
1-248473580-T-C		not specified	Uncertain significance (Mar 19, 2024)
1-248473637-C-T		not specified	Uncertain significance (Jun 23, 2023)
1-248473649-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-248473655-G-A		not specified	Uncertain significance (Oct 29, 2021)
1-248473679-T-C		not specified	Uncertain significance (Jan 19, 2024)
1-248473699-G-T		not specified	Likely benign (May 09, 2024)
1-248473718-T-C		not specified	Uncertain significance (Jun 01, 2023)
1-248473826-T-C		not specified	Uncertain significance (Jan 26, 2022)
1-248473849-A-G		not specified	Uncertain significance (Dec 03, 2021)
1-248473907-C-A		not specified	Uncertain significance (Oct 18, 2021)
1-248473915-C-A		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2T3	protein_coding	protein_coding	ENST00000359594	1	1008

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.766	185	158	1.17	0.00000786	2011
Missense in Polyphen		45	43.501	1.0345		607
Synonymous	-0.279	69	66.1	1.04	0.00000358	626
Loss of Function

LoF frequencies by population

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

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: 0.948
• rvis_EVS: 1.15
• rvis_percentile_EVS: 92.52

Haploinsufficiency Scores

• pHI: 0.0878
• hipred: N
• hipred_score: 0.238

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.102

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;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