OR2T1

olfactory receptor family 2 subfamily T member 1, the group of Olfactory receptors, family 2

Basic information

Region (hg38): 1:248403047-248408020

Links

ENSG00000175143 ∙ NCBI:26696 ∙ ∙ HGNC:8277 ∙ Uniprot:O43869 ∙ 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 OR2T1 gene.

• Inborn genetic diseases (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2T1 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			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			2			2
Total	0	0	16	0	0

Variants in OR2T1

This is a list of pathogenic ClinVar variants found in the OR2T1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-248406056-C-A		not specified	Uncertain significance (Aug 30, 2022)
1-248406115-A-T		not specified	Uncertain significance (Jun 05, 2023)
1-248406130-G-A		Malignant tumor of prostate	Uncertain significance (-)
1-248406137-C-A		not specified	Uncertain significance (Aug 16, 2022)
1-248406149-T-C		not specified	Uncertain significance (Oct 03, 2023)
1-248406209-A-G		not specified	Uncertain significance (Sep 22, 2023)
1-248406212-C-T		not specified	Uncertain significance (Aug 21, 2023)
1-248406229-G-C		not specified	Uncertain significance (Dec 20, 2023)
1-248406256-G-A		not specified	Uncertain significance (Sep 15, 2021)
1-248406304-C-T		not specified	Uncertain significance (May 01, 2022)
1-248406311-A-G		not specified	Uncertain significance (Aug 13, 2021)
1-248406321-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-248406340-C-T		not specified	Uncertain significance (Sep 09, 2021)
1-248406385-A-T		not specified	Uncertain significance (Jun 22, 2021)
1-248406649-T-C		not specified	Uncertain significance (Nov 09, 2021)
1-248406680-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-248406784-G-C		not specified	Uncertain significance (Aug 16, 2022)
1-248406811-A-G		not specified	Uncertain significance (Jul 12, 2022)
1-248406922-A-G		not specified	Uncertain significance (Oct 12, 2022)
1-248406923-T-G		not specified	Uncertain significance (Apr 07, 2023)
1-248406976-T-C		not specified	Uncertain significance (Jul 13, 2022)
1-248407066-T-C		not specified	Uncertain significance (Dec 28, 2023)
1-248407082-G-T		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2T1	protein_coding	protein_coding	ENST00000366474	1	1110

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.19e-10	0.0192	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.707	225	197	1.14	0.00000970	2402
Missense in Polyphen		66	64.883	1.0172		916
Synonymous	-2.60	103	74.4	1.38	0.00000351	758
Loss of Function	-1.17	12	8.34	1.44	4.03e-7	110

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;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0739

Intolerance Scores

• loftool: 0.852
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.25

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr31

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